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<li><a class="reference internal" href="#">pymatgen.analysis namespace</a><ul>
<li><a class="reference internal" href="#subpackages">Subpackages</a></li>
<li><a class="reference internal" href="#submodules">Submodules</a></li>
<li><a class="reference internal" href="#module-pymatgen.analysis.adsorption">pymatgen.analysis.adsorption module</a><ul>
<li><a class="reference internal" href="#pymatgen.analysis.adsorption.AdsorbateSiteFinder"><code class="docutils literal notranslate"><span class="pre">AdsorbateSiteFinder</span></code></a><ul>
<li><a class="reference internal" href="#pymatgen.analysis.adsorption.AdsorbateSiteFinder.add_adsorbate"><code class="docutils literal notranslate"><span class="pre">AdsorbateSiteFinder.add_adsorbate()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.adsorption.AdsorbateSiteFinder.adsorb_both_surfaces"><code class="docutils literal notranslate"><span class="pre">AdsorbateSiteFinder.adsorb_both_surfaces()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.adsorption.AdsorbateSiteFinder.assign_selective_dynamics"><code class="docutils literal notranslate"><span class="pre">AdsorbateSiteFinder.assign_selective_dynamics()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.adsorption.AdsorbateSiteFinder.assign_site_properties"><code class="docutils literal notranslate"><span class="pre">AdsorbateSiteFinder.assign_site_properties()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.adsorption.AdsorbateSiteFinder.ensemble_center"><code class="docutils literal notranslate"><span class="pre">AdsorbateSiteFinder.ensemble_center()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.adsorption.AdsorbateSiteFinder.find_adsorption_sites"><code class="docutils literal notranslate"><span class="pre">AdsorbateSiteFinder.find_adsorption_sites()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.adsorption.AdsorbateSiteFinder.find_surface_sites_by_height"><code class="docutils literal notranslate"><span class="pre">AdsorbateSiteFinder.find_surface_sites_by_height()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.adsorption.AdsorbateSiteFinder.from_bulk_and_miller"><code class="docutils literal notranslate"><span class="pre">AdsorbateSiteFinder.from_bulk_and_miller()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.adsorption.AdsorbateSiteFinder.generate_adsorption_structures"><code class="docutils literal notranslate"><span class="pre">AdsorbateSiteFinder.generate_adsorption_structures()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.adsorption.AdsorbateSiteFinder.generate_substitution_structures"><code class="docutils literal notranslate"><span class="pre">AdsorbateSiteFinder.generate_substitution_structures()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.adsorption.AdsorbateSiteFinder.get_extended_surface_mesh"><code class="docutils literal notranslate"><span class="pre">AdsorbateSiteFinder.get_extended_surface_mesh()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.adsorption.AdsorbateSiteFinder.near_reduce"><code class="docutils literal notranslate"><span class="pre">AdsorbateSiteFinder.near_reduce()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.adsorption.AdsorbateSiteFinder.subsurface_sites"><code class="docutils literal notranslate"><span class="pre">AdsorbateSiteFinder.subsurface_sites()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.adsorption.AdsorbateSiteFinder.surface_sites"><code class="docutils literal notranslate"><span class="pre">AdsorbateSiteFinder.surface_sites</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.adsorption.AdsorbateSiteFinder.symm_reduce"><code class="docutils literal notranslate"><span class="pre">AdsorbateSiteFinder.symm_reduce()</span></code></a></li>
</ul>
</li>
<li><a class="reference internal" href="#pymatgen.analysis.adsorption.get_mi_vec"><code class="docutils literal notranslate"><span class="pre">get_mi_vec()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.adsorption.get_rot"><code class="docutils literal notranslate"><span class="pre">get_rot()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.adsorption.plot_slab"><code class="docutils literal notranslate"><span class="pre">plot_slab()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.adsorption.put_coord_inside"><code class="docutils literal notranslate"><span class="pre">put_coord_inside()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.adsorption.reorient_z"><code class="docutils literal notranslate"><span class="pre">reorient_z()</span></code></a></li>
</ul>
</li>
<li><a class="reference internal" href="#module-pymatgen.analysis.bond_dissociation">pymatgen.analysis.bond_dissociation module</a><ul>
<li><a class="reference internal" href="#pymatgen.analysis.bond_dissociation.BondDissociationEnergies"><code class="docutils literal notranslate"><span class="pre">BondDissociationEnergies</span></code></a><ul>
<li><a class="reference internal" href="#pymatgen.analysis.bond_dissociation.BondDissociationEnergies.build_new_entry"><code class="docutils literal notranslate"><span class="pre">BondDissociationEnergies.build_new_entry()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.bond_dissociation.BondDissociationEnergies.filter_fragment_entries"><code class="docutils literal notranslate"><span class="pre">BondDissociationEnergies.filter_fragment_entries()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.bond_dissociation.BondDissociationEnergies.fragment_and_process"><code class="docutils literal notranslate"><span class="pre">BondDissociationEnergies.fragment_and_process()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.bond_dissociation.BondDissociationEnergies.search_fragment_entries"><code class="docutils literal notranslate"><span class="pre">BondDissociationEnergies.search_fragment_entries()</span></code></a></li>
</ul>
</li>
</ul>
</li>
<li><a class="reference internal" href="#module-pymatgen.analysis.bond_valence">pymatgen.analysis.bond_valence module</a><ul>
<li><a class="reference internal" href="#pymatgen.analysis.bond_valence.BVAnalyzer"><code class="docutils literal notranslate"><span class="pre">BVAnalyzer</span></code></a><ul>
<li><a class="reference internal" href="#pymatgen.analysis.bond_valence.BVAnalyzer.CHARGE_NEUTRALITY_TOLERANCE"><code class="docutils literal notranslate"><span class="pre">BVAnalyzer.CHARGE_NEUTRALITY_TOLERANCE</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.bond_valence.BVAnalyzer.get_oxi_state_decorated_structure"><code class="docutils literal notranslate"><span class="pre">BVAnalyzer.get_oxi_state_decorated_structure()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.bond_valence.BVAnalyzer.get_valences"><code class="docutils literal notranslate"><span class="pre">BVAnalyzer.get_valences()</span></code></a></li>
</ul>
</li>
<li><a class="reference internal" href="#pymatgen.analysis.bond_valence.add_oxidation_state_by_site_fraction"><code class="docutils literal notranslate"><span class="pre">add_oxidation_state_by_site_fraction()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.bond_valence.calculate_bv_sum"><code class="docutils literal notranslate"><span class="pre">calculate_bv_sum()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.bond_valence.calculate_bv_sum_unordered"><code class="docutils literal notranslate"><span class="pre">calculate_bv_sum_unordered()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.bond_valence.get_z_ordered_elmap"><code class="docutils literal notranslate"><span class="pre">get_z_ordered_elmap()</span></code></a></li>
</ul>
</li>
<li><a class="reference internal" href="#module-pymatgen.analysis.chempot_diagram">pymatgen.analysis.chempot_diagram module</a><ul>
<li><a class="reference internal" href="#pymatgen.analysis.chempot_diagram.ChemicalPotentialDiagram"><code class="docutils literal notranslate"><span class="pre">ChemicalPotentialDiagram</span></code></a><ul>
<li><a class="reference internal" href="#pymatgen.analysis.chempot_diagram.ChemicalPotentialDiagram.border_hyperplanes"><code class="docutils literal notranslate"><span class="pre">ChemicalPotentialDiagram.border_hyperplanes</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.chempot_diagram.ChemicalPotentialDiagram.chemical_system"><code class="docutils literal notranslate"><span class="pre">ChemicalPotentialDiagram.chemical_system</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.chempot_diagram.ChemicalPotentialDiagram.domains"><code class="docutils literal notranslate"><span class="pre">ChemicalPotentialDiagram.domains</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.chempot_diagram.ChemicalPotentialDiagram.el_refs"><code class="docutils literal notranslate"><span class="pre">ChemicalPotentialDiagram.el_refs</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.chempot_diagram.ChemicalPotentialDiagram.entry_dict"><code class="docutils literal notranslate"><span class="pre">ChemicalPotentialDiagram.entry_dict</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.chempot_diagram.ChemicalPotentialDiagram.get_plot"><code class="docutils literal notranslate"><span class="pre">ChemicalPotentialDiagram.get_plot()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.chempot_diagram.ChemicalPotentialDiagram.hyperplane_entries"><code class="docutils literal notranslate"><span class="pre">ChemicalPotentialDiagram.hyperplane_entries</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.chempot_diagram.ChemicalPotentialDiagram.hyperplanes"><code class="docutils literal notranslate"><span class="pre">ChemicalPotentialDiagram.hyperplanes</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.chempot_diagram.ChemicalPotentialDiagram.lims"><code class="docutils literal notranslate"><span class="pre">ChemicalPotentialDiagram.lims</span></code></a></li>
</ul>
</li>
<li><a class="reference internal" href="#pymatgen.analysis.chempot_diagram.get_2d_orthonormal_vector"><code class="docutils literal notranslate"><span class="pre">get_2d_orthonormal_vector()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.chempot_diagram.get_centroid_2d"><code class="docutils literal notranslate"><span class="pre">get_centroid_2d()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.chempot_diagram.simple_pca"><code class="docutils literal notranslate"><span class="pre">simple_pca()</span></code></a></li>
</ul>
</li>
<li><a class="reference internal" href="#module-pymatgen.analysis.cost">pymatgen.analysis.cost module</a><ul>
<li><a class="reference internal" href="#pymatgen.analysis.cost.CostAnalyzer"><code class="docutils literal notranslate"><span class="pre">CostAnalyzer</span></code></a><ul>
<li><a class="reference internal" href="#pymatgen.analysis.cost.CostAnalyzer.get_cost_per_kg"><code class="docutils literal notranslate"><span class="pre">CostAnalyzer.get_cost_per_kg()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.cost.CostAnalyzer.get_cost_per_mol"><code class="docutils literal notranslate"><span class="pre">CostAnalyzer.get_cost_per_mol()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.cost.CostAnalyzer.get_lowest_decomposition"><code class="docutils literal notranslate"><span class="pre">CostAnalyzer.get_lowest_decomposition()</span></code></a></li>
</ul>
</li>
<li><a class="reference internal" href="#pymatgen.analysis.cost.CostDB"><code class="docutils literal notranslate"><span class="pre">CostDB</span></code></a><ul>
<li><a class="reference internal" href="#pymatgen.analysis.cost.CostDB.get_entries"><code class="docutils literal notranslate"><span class="pre">CostDB.get_entries()</span></code></a></li>
</ul>
</li>
<li><a class="reference internal" href="#pymatgen.analysis.cost.CostDBCSV"><code class="docutils literal notranslate"><span class="pre">CostDBCSV</span></code></a><ul>
<li><a class="reference internal" href="#pymatgen.analysis.cost.CostDBCSV.get_entries"><code class="docutils literal notranslate"><span class="pre">CostDBCSV.get_entries()</span></code></a></li>
</ul>
</li>
<li><a class="reference internal" href="#pymatgen.analysis.cost.CostEntry"><code class="docutils literal notranslate"><span class="pre">CostEntry</span></code></a></li>
</ul>
</li>
<li><a class="reference internal" href="#module-pymatgen.analysis.dimensionality">pymatgen.analysis.dimensionality module</a><ul>
<li><a class="reference internal" href="#pymatgen.analysis.dimensionality.calculate_dimensionality_of_site"><code class="docutils literal notranslate"><span class="pre">calculate_dimensionality_of_site()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.dimensionality.find_clusters"><code class="docutils literal notranslate"><span class="pre">find_clusters()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.dimensionality.find_connected_atoms"><code class="docutils literal notranslate"><span class="pre">find_connected_atoms()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.dimensionality.get_dimensionality_cheon"><code class="docutils literal notranslate"><span class="pre">get_dimensionality_cheon()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.dimensionality.get_dimensionality_gorai"><code class="docutils literal notranslate"><span class="pre">get_dimensionality_gorai()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.dimensionality.get_dimensionality_larsen"><code class="docutils literal notranslate"><span class="pre">get_dimensionality_larsen()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.dimensionality.get_structure_components"><code class="docutils literal notranslate"><span class="pre">get_structure_components()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.dimensionality.zero_d_graph_to_molecule_graph"><code class="docutils literal notranslate"><span class="pre">zero_d_graph_to_molecule_graph()</span></code></a></li>
</ul>
</li>
<li><a class="reference internal" href="#module-pymatgen.analysis.disorder">pymatgen.analysis.disorder module</a><ul>
<li><a class="reference internal" href="#pymatgen.analysis.disorder.get_warren_cowley_parameters"><code class="docutils literal notranslate"><span class="pre">get_warren_cowley_parameters()</span></code></a></li>
</ul>
</li>
<li><a class="reference internal" href="#module-pymatgen.analysis.energy_models">pymatgen.analysis.energy_models module</a><ul>
<li><a class="reference internal" href="#pymatgen.analysis.energy_models.EnergyModel"><code class="docutils literal notranslate"><span class="pre">EnergyModel</span></code></a><ul>
<li><a class="reference internal" href="#pymatgen.analysis.energy_models.EnergyModel.from_dict"><code class="docutils literal notranslate"><span class="pre">EnergyModel.from_dict()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.energy_models.EnergyModel.get_energy"><code class="docutils literal notranslate"><span class="pre">EnergyModel.get_energy()</span></code></a></li>
</ul>
</li>
<li><a class="reference internal" href="#pymatgen.analysis.energy_models.EwaldElectrostaticModel"><code class="docutils literal notranslate"><span class="pre">EwaldElectrostaticModel</span></code></a><ul>
<li><a class="reference internal" href="#pymatgen.analysis.energy_models.EwaldElectrostaticModel.as_dict"><code class="docutils literal notranslate"><span class="pre">EwaldElectrostaticModel.as_dict()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.energy_models.EwaldElectrostaticModel.get_energy"><code class="docutils literal notranslate"><span class="pre">EwaldElectrostaticModel.get_energy()</span></code></a></li>
</ul>
</li>
<li><a class="reference internal" href="#pymatgen.analysis.energy_models.IsingModel"><code class="docutils literal notranslate"><span class="pre">IsingModel</span></code></a><ul>
<li><a class="reference internal" href="#pymatgen.analysis.energy_models.IsingModel.as_dict"><code class="docutils literal notranslate"><span class="pre">IsingModel.as_dict()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.energy_models.IsingModel.get_energy"><code class="docutils literal notranslate"><span class="pre">IsingModel.get_energy()</span></code></a></li>
</ul>
</li>
<li><a class="reference internal" href="#pymatgen.analysis.energy_models.NsitesModel"><code class="docutils literal notranslate"><span class="pre">NsitesModel</span></code></a><ul>
<li><a class="reference internal" href="#pymatgen.analysis.energy_models.NsitesModel.as_dict"><code class="docutils literal notranslate"><span class="pre">NsitesModel.as_dict()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.energy_models.NsitesModel.get_energy"><code class="docutils literal notranslate"><span class="pre">NsitesModel.get_energy()</span></code></a></li>
</ul>
</li>
<li><a class="reference internal" href="#pymatgen.analysis.energy_models.SymmetryModel"><code class="docutils literal notranslate"><span class="pre">SymmetryModel</span></code></a><ul>
<li><a class="reference internal" href="#pymatgen.analysis.energy_models.SymmetryModel.as_dict"><code class="docutils literal notranslate"><span class="pre">SymmetryModel.as_dict()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.energy_models.SymmetryModel.get_energy"><code class="docutils literal notranslate"><span class="pre">SymmetryModel.get_energy()</span></code></a></li>
</ul>
</li>
</ul>
</li>
<li><a class="reference internal" href="#module-pymatgen.analysis.eos">pymatgen.analysis.eos module</a><ul>
<li><a class="reference internal" href="#pymatgen.analysis.eos.Birch"><code class="docutils literal notranslate"><span class="pre">Birch</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.eos.BirchMurnaghan"><code class="docutils literal notranslate"><span class="pre">BirchMurnaghan</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.eos.DeltaFactor"><code class="docutils literal notranslate"><span class="pre">DeltaFactor</span></code></a><ul>
<li><a class="reference internal" href="#pymatgen.analysis.eos.DeltaFactor.fit"><code class="docutils literal notranslate"><span class="pre">DeltaFactor.fit()</span></code></a></li>
</ul>
</li>
<li><a class="reference internal" href="#pymatgen.analysis.eos.EOS"><code class="docutils literal notranslate"><span class="pre">EOS</span></code></a><ul>
<li><a class="reference internal" href="#pymatgen.analysis.eos.EOS.MODELS"><code class="docutils literal notranslate"><span class="pre">EOS.MODELS</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.eos.EOS.fit"><code class="docutils literal notranslate"><span class="pre">EOS.fit()</span></code></a></li>
</ul>
</li>
<li><a class="reference internal" href="#pymatgen.analysis.eos.EOSBase"><code class="docutils literal notranslate"><span class="pre">EOSBase</span></code></a><ul>
<li><a class="reference internal" href="#pymatgen.analysis.eos.EOSBase.b0"><code class="docutils literal notranslate"><span class="pre">EOSBase.b0</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.eos.EOSBase.b0_GPa"><code class="docutils literal notranslate"><span class="pre">EOSBase.b0_GPa</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.eos.EOSBase.b1"><code class="docutils literal notranslate"><span class="pre">EOSBase.b1</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.eos.EOSBase.e0"><code class="docutils literal notranslate"><span class="pre">EOSBase.e0</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.eos.EOSBase.fit"><code class="docutils literal notranslate"><span class="pre">EOSBase.fit()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.eos.EOSBase.func"><code class="docutils literal notranslate"><span class="pre">EOSBase.func()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.eos.EOSBase.plot"><code class="docutils literal notranslate"><span class="pre">EOSBase.plot()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.eos.EOSBase.plot_ax"><code class="docutils literal notranslate"><span class="pre">EOSBase.plot_ax()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.eos.EOSBase.results"><code class="docutils literal notranslate"><span class="pre">EOSBase.results</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.eos.EOSBase.v0"><code class="docutils literal notranslate"><span class="pre">EOSBase.v0</span></code></a></li>
</ul>
</li>
<li><a class="reference internal" href="#pymatgen.analysis.eos.EOSError"><code class="docutils literal notranslate"><span class="pre">EOSError</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.eos.Murnaghan"><code class="docutils literal notranslate"><span class="pre">Murnaghan</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.eos.NumericalEOS"><code class="docutils literal notranslate"><span class="pre">NumericalEOS</span></code></a><ul>
<li><a class="reference internal" href="#pymatgen.analysis.eos.NumericalEOS.fit"><code class="docutils literal notranslate"><span class="pre">NumericalEOS.fit()</span></code></a></li>
</ul>
</li>
<li><a class="reference internal" href="#pymatgen.analysis.eos.PolynomialEOS"><code class="docutils literal notranslate"><span class="pre">PolynomialEOS</span></code></a><ul>
<li><a class="reference internal" href="#pymatgen.analysis.eos.PolynomialEOS.fit"><code class="docutils literal notranslate"><span class="pre">PolynomialEOS.fit()</span></code></a></li>
</ul>
</li>
<li><a class="reference internal" href="#pymatgen.analysis.eos.PourierTarantola"><code class="docutils literal notranslate"><span class="pre">PourierTarantola</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.eos.Vinet"><code class="docutils literal notranslate"><span class="pre">Vinet</span></code></a></li>
</ul>
</li>
<li><a class="reference internal" href="#module-pymatgen.analysis.ewald">pymatgen.analysis.ewald module</a><ul>
<li><a class="reference internal" href="#pymatgen.analysis.ewald.EwaldMinimizer"><code class="docutils literal notranslate"><span class="pre">EwaldMinimizer</span></code></a><ul>
<li><a class="reference internal" href="#pymatgen.analysis.ewald.EwaldMinimizer.ALGO_BEST_FIRST"><code class="docutils literal notranslate"><span class="pre">EwaldMinimizer.ALGO_BEST_FIRST</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.ewald.EwaldMinimizer.ALGO_COMPLETE"><code class="docutils literal notranslate"><span class="pre">EwaldMinimizer.ALGO_COMPLETE</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.ewald.EwaldMinimizer.ALGO_FAST"><code class="docutils literal notranslate"><span class="pre">EwaldMinimizer.ALGO_FAST</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.ewald.EwaldMinimizer.ALGO_TIME_LIMIT"><code class="docutils literal notranslate"><span class="pre">EwaldMinimizer.ALGO_TIME_LIMIT</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.ewald.EwaldMinimizer.add_m_list"><code class="docutils literal notranslate"><span class="pre">EwaldMinimizer.add_m_list()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.ewald.EwaldMinimizer.best_case"><code class="docutils literal notranslate"><span class="pre">EwaldMinimizer.best_case()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.ewald.EwaldMinimizer.best_m_list"><code class="docutils literal notranslate"><span class="pre">EwaldMinimizer.best_m_list</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.ewald.EwaldMinimizer.get_next_index"><code class="docutils literal notranslate"><span class="pre">EwaldMinimizer.get_next_index()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.ewald.EwaldMinimizer.minimize_matrix"><code class="docutils literal notranslate"><span class="pre">EwaldMinimizer.minimize_matrix()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.ewald.EwaldMinimizer.minimized_sum"><code class="docutils literal notranslate"><span class="pre">EwaldMinimizer.minimized_sum</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.ewald.EwaldMinimizer.output_lists"><code class="docutils literal notranslate"><span class="pre">EwaldMinimizer.output_lists</span></code></a></li>
</ul>
</li>
<li><a class="reference internal" href="#pymatgen.analysis.ewald.EwaldSummation"><code class="docutils literal notranslate"><span class="pre">EwaldSummation</span></code></a><ul>
<li><a class="reference internal" href="#pymatgen.analysis.ewald.EwaldSummation.CONV_FACT"><code class="docutils literal notranslate"><span class="pre">EwaldSummation.CONV_FACT</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.ewald.EwaldSummation.as_dict"><code class="docutils literal notranslate"><span class="pre">EwaldSummation.as_dict()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.ewald.EwaldSummation.compute_partial_energy"><code class="docutils literal notranslate"><span class="pre">EwaldSummation.compute_partial_energy()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.ewald.EwaldSummation.compute_sub_structure"><code class="docutils literal notranslate"><span class="pre">EwaldSummation.compute_sub_structure()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.ewald.EwaldSummation.eta"><code class="docutils literal notranslate"><span class="pre">EwaldSummation.eta</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.ewald.EwaldSummation.forces"><code class="docutils literal notranslate"><span class="pre">EwaldSummation.forces</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.ewald.EwaldSummation.from_dict"><code class="docutils literal notranslate"><span class="pre">EwaldSummation.from_dict()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.ewald.EwaldSummation.get_site_energy"><code class="docutils literal notranslate"><span class="pre">EwaldSummation.get_site_energy()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.ewald.EwaldSummation.point_energy"><code class="docutils literal notranslate"><span class="pre">EwaldSummation.point_energy</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.ewald.EwaldSummation.point_energy_matrix"><code class="docutils literal notranslate"><span class="pre">EwaldSummation.point_energy_matrix</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.ewald.EwaldSummation.real_space_energy"><code class="docutils literal notranslate"><span class="pre">EwaldSummation.real_space_energy</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.ewald.EwaldSummation.real_space_energy_matrix"><code class="docutils literal notranslate"><span class="pre">EwaldSummation.real_space_energy_matrix</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.ewald.EwaldSummation.reciprocal_space_energy"><code class="docutils literal notranslate"><span class="pre">EwaldSummation.reciprocal_space_energy</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.ewald.EwaldSummation.reciprocal_space_energy_matrix"><code class="docutils literal notranslate"><span class="pre">EwaldSummation.reciprocal_space_energy_matrix</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.ewald.EwaldSummation.total_energy"><code class="docutils literal notranslate"><span class="pre">EwaldSummation.total_energy</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.ewald.EwaldSummation.total_energy_matrix"><code class="docutils literal notranslate"><span class="pre">EwaldSummation.total_energy_matrix</span></code></a></li>
</ul>
</li>
<li><a class="reference internal" href="#pymatgen.analysis.ewald.compute_average_oxidation_state"><code class="docutils literal notranslate"><span class="pre">compute_average_oxidation_state()</span></code></a></li>
</ul>
</li>
<li><a class="reference internal" href="#module-pymatgen.analysis.excitation">pymatgen.analysis.excitation module</a><ul>
<li><a class="reference internal" href="#pymatgen.analysis.excitation.ExcitationSpectrum"><code class="docutils literal notranslate"><span class="pre">ExcitationSpectrum</span></code></a><ul>
<li><a class="reference internal" href="#pymatgen.analysis.excitation.ExcitationSpectrum.x"><code class="docutils literal notranslate"><span class="pre">ExcitationSpectrum.x</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.excitation.ExcitationSpectrum.y"><code class="docutils literal notranslate"><span class="pre">ExcitationSpectrum.y</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.excitation.ExcitationSpectrum.XLABEL"><code class="docutils literal notranslate"><span class="pre">ExcitationSpectrum.XLABEL</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.excitation.ExcitationSpectrum.YLABEL"><code class="docutils literal notranslate"><span class="pre">ExcitationSpectrum.YLABEL</span></code></a></li>
</ul>
</li>
</ul>
</li>
<li><a class="reference internal" href="#module-pymatgen.analysis.fragmenter">pymatgen.analysis.fragmenter module</a><ul>
<li><a class="reference internal" href="#pymatgen.analysis.fragmenter.Fragmenter"><code class="docutils literal notranslate"><span class="pre">Fragmenter</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.fragmenter.open_ring"><code class="docutils literal notranslate"><span class="pre">open_ring()</span></code></a></li>
</ul>
</li>
<li><a class="reference internal" href="#module-pymatgen.analysis.functional_groups">pymatgen.analysis.functional_groups module</a><ul>
<li><a class="reference internal" href="#pymatgen.analysis.functional_groups.FunctionalGroupExtractor"><code class="docutils literal notranslate"><span class="pre">FunctionalGroupExtractor</span></code></a><ul>
<li><a class="reference internal" href="#pymatgen.analysis.functional_groups.FunctionalGroupExtractor.categorize_functional_groups"><code class="docutils literal notranslate"><span class="pre">FunctionalGroupExtractor.categorize_functional_groups()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.functional_groups.FunctionalGroupExtractor.get_all_functional_groups"><code class="docutils literal notranslate"><span class="pre">FunctionalGroupExtractor.get_all_functional_groups()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.functional_groups.FunctionalGroupExtractor.get_basic_functional_groups"><code class="docutils literal notranslate"><span class="pre">FunctionalGroupExtractor.get_basic_functional_groups()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.functional_groups.FunctionalGroupExtractor.get_heteroatoms"><code class="docutils literal notranslate"><span class="pre">FunctionalGroupExtractor.get_heteroatoms()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.functional_groups.FunctionalGroupExtractor.get_special_carbon"><code class="docutils literal notranslate"><span class="pre">FunctionalGroupExtractor.get_special_carbon()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.functional_groups.FunctionalGroupExtractor.link_marked_atoms"><code class="docutils literal notranslate"><span class="pre">FunctionalGroupExtractor.link_marked_atoms()</span></code></a></li>
</ul>
</li>
</ul>
</li>
<li><a class="reference internal" href="#module-pymatgen.analysis.graphs">pymatgen.analysis.graphs module</a><ul>
<li><a class="reference internal" href="#pymatgen.analysis.graphs.ConnectedSite"><code class="docutils literal notranslate"><span class="pre">ConnectedSite</span></code></a><ul>
<li><a class="reference internal" href="#pymatgen.analysis.graphs.ConnectedSite.dist"><code class="docutils literal notranslate"><span class="pre">ConnectedSite.dist</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.graphs.ConnectedSite.index"><code class="docutils literal notranslate"><span class="pre">ConnectedSite.index</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.graphs.ConnectedSite.jimage"><code class="docutils literal notranslate"><span class="pre">ConnectedSite.jimage</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.graphs.ConnectedSite.site"><code class="docutils literal notranslate"><span class="pre">ConnectedSite.site</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.graphs.ConnectedSite.weight"><code class="docutils literal notranslate"><span class="pre">ConnectedSite.weight</span></code></a></li>
</ul>
</li>
<li><a class="reference internal" href="#pymatgen.analysis.graphs.MolGraphSplitError"><code class="docutils literal notranslate"><span class="pre">MolGraphSplitError</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.graphs.MoleculeGraph"><code class="docutils literal notranslate"><span class="pre">MoleculeGraph</span></code></a><ul>
<li><a class="reference internal" href="#pymatgen.analysis.graphs.MoleculeGraph.add_edge"><code class="docutils literal notranslate"><span class="pre">MoleculeGraph.add_edge()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.graphs.MoleculeGraph.alter_edge"><code class="docutils literal notranslate"><span class="pre">MoleculeGraph.alter_edge()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.graphs.MoleculeGraph.as_dict"><code class="docutils literal notranslate"><span class="pre">MoleculeGraph.as_dict()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.graphs.MoleculeGraph.break_edge"><code class="docutils literal notranslate"><span class="pre">MoleculeGraph.break_edge()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.graphs.MoleculeGraph.build_unique_fragments"><code class="docutils literal notranslate"><span class="pre">MoleculeGraph.build_unique_fragments()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.graphs.MoleculeGraph.diff"><code class="docutils literal notranslate"><span class="pre">MoleculeGraph.diff()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.graphs.MoleculeGraph.draw_graph_to_file"><code class="docutils literal notranslate"><span class="pre">MoleculeGraph.draw_graph_to_file()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.graphs.MoleculeGraph.edge_weight_name"><code class="docutils literal notranslate"><span class="pre">MoleculeGraph.edge_weight_name</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.graphs.MoleculeGraph.edge_weight_unit"><code class="docutils literal notranslate"><span class="pre">MoleculeGraph.edge_weight_unit</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.graphs.MoleculeGraph.find_rings"><code class="docutils literal notranslate"><span class="pre">MoleculeGraph.find_rings()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.graphs.MoleculeGraph.from_dict"><code class="docutils literal notranslate"><span class="pre">MoleculeGraph.from_dict()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.graphs.MoleculeGraph.from_edges"><code class="docutils literal notranslate"><span class="pre">MoleculeGraph.from_edges()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.graphs.MoleculeGraph.from_empty_graph"><code class="docutils literal notranslate"><span class="pre">MoleculeGraph.from_empty_graph()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.graphs.MoleculeGraph.from_local_env_strategy"><code class="docutils literal notranslate"><span class="pre">MoleculeGraph.from_local_env_strategy()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.graphs.MoleculeGraph.get_connected_sites"><code class="docutils literal notranslate"><span class="pre">MoleculeGraph.get_connected_sites()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.graphs.MoleculeGraph.get_coordination_of_site"><code class="docutils literal notranslate"><span class="pre">MoleculeGraph.get_coordination_of_site()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.graphs.MoleculeGraph.get_disconnected_fragments"><code class="docutils literal notranslate"><span class="pre">MoleculeGraph.get_disconnected_fragments()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.graphs.MoleculeGraph.insert_node"><code class="docutils literal notranslate"><span class="pre">MoleculeGraph.insert_node()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.graphs.MoleculeGraph.isomorphic_to"><code class="docutils literal notranslate"><span class="pre">MoleculeGraph.isomorphic_to()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.graphs.MoleculeGraph.name"><code class="docutils literal notranslate"><span class="pre">MoleculeGraph.name</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.graphs.MoleculeGraph.remove_nodes"><code class="docutils literal notranslate"><span class="pre">MoleculeGraph.remove_nodes()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.graphs.MoleculeGraph.replace_group"><code class="docutils literal notranslate"><span class="pre">MoleculeGraph.replace_group()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.graphs.MoleculeGraph.set_node_attributes"><code class="docutils literal notranslate"><span class="pre">MoleculeGraph.set_node_attributes()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.graphs.MoleculeGraph.sort"><code class="docutils literal notranslate"><span class="pre">MoleculeGraph.sort()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.graphs.MoleculeGraph.split_molecule_subgraphs"><code class="docutils literal notranslate"><span class="pre">MoleculeGraph.split_molecule_subgraphs()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.graphs.MoleculeGraph.substitute_group"><code class="docutils literal notranslate"><span class="pre">MoleculeGraph.substitute_group()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.graphs.MoleculeGraph.with_edges"><code class="docutils literal notranslate"><span class="pre">MoleculeGraph.with_edges()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.graphs.MoleculeGraph.with_empty_graph"><code class="docutils literal notranslate"><span class="pre">MoleculeGraph.with_empty_graph()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.graphs.MoleculeGraph.with_local_env_strategy"><code class="docutils literal notranslate"><span class="pre">MoleculeGraph.with_local_env_strategy()</span></code></a></li>
</ul>
</li>
<li><a class="reference internal" href="#pymatgen.analysis.graphs.StructureGraph"><code class="docutils literal notranslate"><span class="pre">StructureGraph</span></code></a><ul>
<li><a class="reference internal" href="#pymatgen.analysis.graphs.StructureGraph.add_edge"><code class="docutils literal notranslate"><span class="pre">StructureGraph.add_edge()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.graphs.StructureGraph.alter_edge"><code class="docutils literal notranslate"><span class="pre">StructureGraph.alter_edge()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.graphs.StructureGraph.as_dict"><code class="docutils literal notranslate"><span class="pre">StructureGraph.as_dict()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.graphs.StructureGraph.break_edge"><code class="docutils literal notranslate"><span class="pre">StructureGraph.break_edge()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.graphs.StructureGraph.diff"><code class="docutils literal notranslate"><span class="pre">StructureGraph.diff()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.graphs.StructureGraph.draw_graph_to_file"><code class="docutils literal notranslate"><span class="pre">StructureGraph.draw_graph_to_file()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.graphs.StructureGraph.edge_weight_name"><code class="docutils literal notranslate"><span class="pre">StructureGraph.edge_weight_name</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.graphs.StructureGraph.edge_weight_unit"><code class="docutils literal notranslate"><span class="pre">StructureGraph.edge_weight_unit</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.graphs.StructureGraph.from_dict"><code class="docutils literal notranslate"><span class="pre">StructureGraph.from_dict()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.graphs.StructureGraph.from_edges"><code class="docutils literal notranslate"><span class="pre">StructureGraph.from_edges()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.graphs.StructureGraph.from_empty_graph"><code class="docutils literal notranslate"><span class="pre">StructureGraph.from_empty_graph()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.graphs.StructureGraph.from_local_env_strategy"><code class="docutils literal notranslate"><span class="pre">StructureGraph.from_local_env_strategy()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.graphs.StructureGraph.get_connected_sites"><code class="docutils literal notranslate"><span class="pre">StructureGraph.get_connected_sites()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.graphs.StructureGraph.get_coordination_of_site"><code class="docutils literal notranslate"><span class="pre">StructureGraph.get_coordination_of_site()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.graphs.StructureGraph.get_subgraphs_as_molecules"><code class="docutils literal notranslate"><span class="pre">StructureGraph.get_subgraphs_as_molecules()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.graphs.StructureGraph.insert_node"><code class="docutils literal notranslate"><span class="pre">StructureGraph.insert_node()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.graphs.StructureGraph.name"><code class="docutils literal notranslate"><span class="pre">StructureGraph.name</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.graphs.StructureGraph.remove_nodes"><code class="docutils literal notranslate"><span class="pre">StructureGraph.remove_nodes()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.graphs.StructureGraph.set_node_attributes"><code class="docutils literal notranslate"><span class="pre">StructureGraph.set_node_attributes()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.graphs.StructureGraph.sort"><code class="docutils literal notranslate"><span class="pre">StructureGraph.sort()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.graphs.StructureGraph.substitute_group"><code class="docutils literal notranslate"><span class="pre">StructureGraph.substitute_group()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.graphs.StructureGraph.types_and_weights_of_connections"><code class="docutils literal notranslate"><span class="pre">StructureGraph.types_and_weights_of_connections</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.graphs.StructureGraph.types_of_coordination_environments"><code class="docutils literal notranslate"><span class="pre">StructureGraph.types_of_coordination_environments()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.graphs.StructureGraph.weight_statistics"><code class="docutils literal notranslate"><span class="pre">StructureGraph.weight_statistics</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.graphs.StructureGraph.with_edges"><code class="docutils literal notranslate"><span class="pre">StructureGraph.with_edges()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.graphs.StructureGraph.with_empty_graph"><code class="docutils literal notranslate"><span class="pre">StructureGraph.with_empty_graph()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.graphs.StructureGraph.with_local_env_strategy"><code class="docutils literal notranslate"><span class="pre">StructureGraph.with_local_env_strategy()</span></code></a></li>
</ul>
</li>
</ul>
</li>
<li><a class="reference internal" href="#module-pymatgen.analysis.hhi">pymatgen.analysis.hhi module</a></li>
<li><a class="reference internal" href="#module-pymatgen.analysis.interface_reactions">pymatgen.analysis.interface_reactions module</a><ul>
<li><a class="reference internal" href="#pymatgen.analysis.interface_reactions.GrandPotentialInterfacialReactivity"><code class="docutils literal notranslate"><span class="pre">GrandPotentialInterfacialReactivity</span></code></a><ul>
<li><a class="reference internal" href="#pymatgen.analysis.interface_reactions.GrandPotentialInterfacialReactivity.get_no_mixing_energy"><code class="docutils literal notranslate"><span class="pre">GrandPotentialInterfacialReactivity.get_no_mixing_energy()</span></code></a></li>
</ul>
</li>
<li><a class="reference internal" href="#pymatgen.analysis.interface_reactions.InterfacialReactivity"><code class="docutils literal notranslate"><span class="pre">InterfacialReactivity</span></code></a><ul>
<li><a class="reference internal" href="#pymatgen.analysis.interface_reactions.InterfacialReactivity.EV_TO_KJ_PER_MOL"><code class="docutils literal notranslate"><span class="pre">InterfacialReactivity.EV_TO_KJ_PER_MOL</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.interface_reactions.InterfacialReactivity.get_chempot_correction"><code class="docutils literal notranslate"><span class="pre">InterfacialReactivity.get_chempot_correction()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.interface_reactions.InterfacialReactivity.get_critical_original_kink_ratio"><code class="docutils literal notranslate"><span class="pre">InterfacialReactivity.get_critical_original_kink_ratio()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.interface_reactions.InterfacialReactivity.get_dataframe"><code class="docutils literal notranslate"><span class="pre">InterfacialReactivity.get_dataframe()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.interface_reactions.InterfacialReactivity.get_kinks"><code class="docutils literal notranslate"><span class="pre">InterfacialReactivity.get_kinks()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.interface_reactions.InterfacialReactivity.labels"><code class="docutils literal notranslate"><span class="pre">InterfacialReactivity.labels</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.interface_reactions.InterfacialReactivity.minimum"><code class="docutils literal notranslate"><span class="pre">InterfacialReactivity.minimum</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.interface_reactions.InterfacialReactivity.plot"><code class="docutils literal notranslate"><span class="pre">InterfacialReactivity.plot()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.interface_reactions.InterfacialReactivity.products"><code class="docutils literal notranslate"><span class="pre">InterfacialReactivity.products</span></code></a></li>
</ul>
</li>
</ul>
</li>
<li><a class="reference internal" href="#module-pymatgen.analysis.local_env">pymatgen.analysis.local_env module</a><ul>
<li><a class="reference internal" href="#pymatgen.analysis.local_env.BrunnerNNReal"><code class="docutils literal notranslate"><span class="pre">BrunnerNNReal</span></code></a><ul>
<li><a class="reference internal" href="#pymatgen.analysis.local_env.BrunnerNNReal.get_nn_info"><code class="docutils literal notranslate"><span class="pre">BrunnerNNReal.get_nn_info()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.local_env.BrunnerNNReal.molecules_allowed"><code class="docutils literal notranslate"><span class="pre">BrunnerNNReal.molecules_allowed</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.local_env.BrunnerNNReal.structures_allowed"><code class="docutils literal notranslate"><span class="pre">BrunnerNNReal.structures_allowed</span></code></a></li>
</ul>
</li>
<li><a class="reference internal" href="#pymatgen.analysis.local_env.BrunnerNNReciprocal"><code class="docutils literal notranslate"><span class="pre">BrunnerNNReciprocal</span></code></a><ul>
<li><a class="reference internal" href="#pymatgen.analysis.local_env.BrunnerNNReciprocal.get_nn_info"><code class="docutils literal notranslate"><span class="pre">BrunnerNNReciprocal.get_nn_info()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.local_env.BrunnerNNReciprocal.molecules_allowed"><code class="docutils literal notranslate"><span class="pre">BrunnerNNReciprocal.molecules_allowed</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.local_env.BrunnerNNReciprocal.structures_allowed"><code class="docutils literal notranslate"><span class="pre">BrunnerNNReciprocal.structures_allowed</span></code></a></li>
</ul>
</li>
<li><a class="reference internal" href="#pymatgen.analysis.local_env.BrunnerNNRelative"><code class="docutils literal notranslate"><span class="pre">BrunnerNNRelative</span></code></a><ul>
<li><a class="reference internal" href="#pymatgen.analysis.local_env.BrunnerNNRelative.get_nn_info"><code class="docutils literal notranslate"><span class="pre">BrunnerNNRelative.get_nn_info()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.local_env.BrunnerNNRelative.molecules_allowed"><code class="docutils literal notranslate"><span class="pre">BrunnerNNRelative.molecules_allowed</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.local_env.BrunnerNNRelative.structures_allowed"><code class="docutils literal notranslate"><span class="pre">BrunnerNNRelative.structures_allowed</span></code></a></li>
</ul>
</li>
<li><a class="reference internal" href="#pymatgen.analysis.local_env.BrunnerNN_real"><code class="docutils literal notranslate"><span class="pre">BrunnerNN_real</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.local_env.BrunnerNN_reciprocal"><code class="docutils literal notranslate"><span class="pre">BrunnerNN_reciprocal</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.local_env.BrunnerNN_relative"><code class="docutils literal notranslate"><span class="pre">BrunnerNN_relative</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.local_env.CovalentBondNN"><code class="docutils literal notranslate"><span class="pre">CovalentBondNN</span></code></a><ul>
<li><a class="reference internal" href="#pymatgen.analysis.local_env.CovalentBondNN.extend_structure_molecules"><code class="docutils literal notranslate"><span class="pre">CovalentBondNN.extend_structure_molecules</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.local_env.CovalentBondNN.get_bonded_structure"><code class="docutils literal notranslate"><span class="pre">CovalentBondNN.get_bonded_structure()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.local_env.CovalentBondNN.get_nn_info"><code class="docutils literal notranslate"><span class="pre">CovalentBondNN.get_nn_info()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.local_env.CovalentBondNN.get_nn_shell_info"><code class="docutils literal notranslate"><span class="pre">CovalentBondNN.get_nn_shell_info()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.local_env.CovalentBondNN.molecules_allowed"><code class="docutils literal notranslate"><span class="pre">CovalentBondNN.molecules_allowed</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.local_env.CovalentBondNN.structures_allowed"><code class="docutils literal notranslate"><span class="pre">CovalentBondNN.structures_allowed</span></code></a></li>
</ul>
</li>
<li><a class="reference internal" href="#pymatgen.analysis.local_env.Critic2NN"><code class="docutils literal notranslate"><span class="pre">Critic2NN</span></code></a><ul>
<li><a class="reference internal" href="#pymatgen.analysis.local_env.Critic2NN.extend_structure_molecules"><code class="docutils literal notranslate"><span class="pre">Critic2NN.extend_structure_molecules</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.local_env.Critic2NN.get_bonded_structure"><code class="docutils literal notranslate"><span class="pre">Critic2NN.get_bonded_structure()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.local_env.Critic2NN.get_nn_info"><code class="docutils literal notranslate"><span class="pre">Critic2NN.get_nn_info()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.local_env.Critic2NN.molecules_allowed"><code class="docutils literal notranslate"><span class="pre">Critic2NN.molecules_allowed</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.local_env.Critic2NN.structures_allowed"><code class="docutils literal notranslate"><span class="pre">Critic2NN.structures_allowed</span></code></a></li>
</ul>
</li>
<li><a class="reference internal" href="#pymatgen.analysis.local_env.CrystalNN"><code class="docutils literal notranslate"><span class="pre">CrystalNN</span></code></a><ul>
<li><a class="reference internal" href="#pymatgen.analysis.local_env.CrystalNN.NNData"><code class="docutils literal notranslate"><span class="pre">CrystalNN.NNData</span></code></a><ul>
<li><a class="reference internal" href="#pymatgen.analysis.local_env.CrystalNN.NNData.all_nninfo"><code class="docutils literal notranslate"><span class="pre">CrystalNN.NNData.all_nninfo</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.local_env.CrystalNN.NNData.cn_nninfo"><code class="docutils literal notranslate"><span class="pre">CrystalNN.NNData.cn_nninfo</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.local_env.CrystalNN.NNData.cn_weights"><code class="docutils literal notranslate"><span class="pre">CrystalNN.NNData.cn_weights</span></code></a></li>
</ul>
</li>
<li><a class="reference internal" href="#pymatgen.analysis.local_env.CrystalNN.get_cn"><code class="docutils literal notranslate"><span class="pre">CrystalNN.get_cn()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.local_env.CrystalNN.get_cn_dict"><code class="docutils literal notranslate"><span class="pre">CrystalNN.get_cn_dict()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.local_env.CrystalNN.get_nn_data"><code class="docutils literal notranslate"><span class="pre">CrystalNN.get_nn_data()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.local_env.CrystalNN.get_nn_info"><code class="docutils literal notranslate"><span class="pre">CrystalNN.get_nn_info()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.local_env.CrystalNN.molecules_allowed"><code class="docutils literal notranslate"><span class="pre">CrystalNN.molecules_allowed</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.local_env.CrystalNN.structures_allowed"><code class="docutils literal notranslate"><span class="pre">CrystalNN.structures_allowed</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.local_env.CrystalNN.transform_to_length"><code class="docutils literal notranslate"><span class="pre">CrystalNN.transform_to_length()</span></code></a></li>
</ul>
</li>
<li><a class="reference internal" href="#pymatgen.analysis.local_env.CutOffDictNN"><code class="docutils literal notranslate"><span class="pre">CutOffDictNN</span></code></a><ul>
<li><a class="reference internal" href="#pymatgen.analysis.local_env.CutOffDictNN.extend_structure_molecules"><code class="docutils literal notranslate"><span class="pre">CutOffDictNN.extend_structure_molecules</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.local_env.CutOffDictNN.from_preset"><code class="docutils literal notranslate"><span class="pre">CutOffDictNN.from_preset()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.local_env.CutOffDictNN.get_nn_info"><code class="docutils literal notranslate"><span class="pre">CutOffDictNN.get_nn_info()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.local_env.CutOffDictNN.molecules_allowed"><code class="docutils literal notranslate"><span class="pre">CutOffDictNN.molecules_allowed</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.local_env.CutOffDictNN.structures_allowed"><code class="docutils literal notranslate"><span class="pre">CutOffDictNN.structures_allowed</span></code></a></li>
</ul>
</li>
<li><a class="reference internal" href="#pymatgen.analysis.local_env.EconNN"><code class="docutils literal notranslate"><span class="pre">EconNN</span></code></a><ul>
<li><a class="reference internal" href="#pymatgen.analysis.local_env.EconNN.extend_structure_molecules"><code class="docutils literal notranslate"><span class="pre">EconNN.extend_structure_molecules</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.local_env.EconNN.get_nn_info"><code class="docutils literal notranslate"><span class="pre">EconNN.get_nn_info()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.local_env.EconNN.molecules_allowed"><code class="docutils literal notranslate"><span class="pre">EconNN.molecules_allowed</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.local_env.EconNN.structures_allowed"><code class="docutils literal notranslate"><span class="pre">EconNN.structures_allowed</span></code></a></li>
</ul>
</li>
<li><a class="reference internal" href="#pymatgen.analysis.local_env.IsayevNN"><code class="docutils literal notranslate"><span class="pre">IsayevNN</span></code></a><ul>
<li><a class="reference internal" href="#pymatgen.analysis.local_env.IsayevNN.get_all_nn_info"><code class="docutils literal notranslate"><span class="pre">IsayevNN.get_all_nn_info()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.local_env.IsayevNN.get_nn_info"><code class="docutils literal notranslate"><span class="pre">IsayevNN.get_nn_info()</span></code></a></li>
</ul>
</li>
<li><a class="reference internal" href="#pymatgen.analysis.local_env.JmolNN"><code class="docutils literal notranslate"><span class="pre">JmolNN</span></code></a><ul>
<li><a class="reference internal" href="#pymatgen.analysis.local_env.JmolNN.extend_structure_molecules"><code class="docutils literal notranslate"><span class="pre">JmolNN.extend_structure_molecules</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.local_env.JmolNN.get_max_bond_distance"><code class="docutils literal notranslate"><span class="pre">JmolNN.get_max_bond_distance()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.local_env.JmolNN.get_nn_info"><code class="docutils literal notranslate"><span class="pre">JmolNN.get_nn_info()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.local_env.JmolNN.molecules_allowed"><code class="docutils literal notranslate"><span class="pre">JmolNN.molecules_allowed</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.local_env.JmolNN.structures_allowed"><code class="docutils literal notranslate"><span class="pre">JmolNN.structures_allowed</span></code></a></li>
</ul>
</li>
<li><a class="reference internal" href="#pymatgen.analysis.local_env.LocalStructOrderParams"><code class="docutils literal notranslate"><span class="pre">LocalStructOrderParams</span></code></a><ul>
<li><a class="reference internal" href="#pymatgen.analysis.local_env.LocalStructOrderParams.compute_trigonometric_terms"><code class="docutils literal notranslate"><span class="pre">LocalStructOrderParams.compute_trigonometric_terms()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.local_env.LocalStructOrderParams.get_order_parameters"><code class="docutils literal notranslate"><span class="pre">LocalStructOrderParams.get_order_parameters()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.local_env.LocalStructOrderParams.get_parameters"><code class="docutils literal notranslate"><span class="pre">LocalStructOrderParams.get_parameters()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.local_env.LocalStructOrderParams.get_q2"><code class="docutils literal notranslate"><span class="pre">LocalStructOrderParams.get_q2()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.local_env.LocalStructOrderParams.get_q4"><code class="docutils literal notranslate"><span class="pre">LocalStructOrderParams.get_q4()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.local_env.LocalStructOrderParams.get_q6"><code class="docutils literal notranslate"><span class="pre">LocalStructOrderParams.get_q6()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.local_env.LocalStructOrderParams.get_type"><code class="docutils literal notranslate"><span class="pre">LocalStructOrderParams.get_type()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.local_env.LocalStructOrderParams.last_nneigh"><code class="docutils literal notranslate"><span class="pre">LocalStructOrderParams.last_nneigh</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.local_env.LocalStructOrderParams.num_ops"><code class="docutils literal notranslate"><span class="pre">LocalStructOrderParams.num_ops</span></code></a></li>
</ul>
</li>
<li><a class="reference internal" href="#pymatgen.analysis.local_env.MinimumDistanceNN"><code class="docutils literal notranslate"><span class="pre">MinimumDistanceNN</span></code></a><ul>
<li><a class="reference internal" href="#pymatgen.analysis.local_env.MinimumDistanceNN.extend_structure_molecules"><code class="docutils literal notranslate"><span class="pre">MinimumDistanceNN.extend_structure_molecules</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.local_env.MinimumDistanceNN.get_nn_info"><code class="docutils literal notranslate"><span class="pre">MinimumDistanceNN.get_nn_info()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.local_env.MinimumDistanceNN.molecules_allowed"><code class="docutils literal notranslate"><span class="pre">MinimumDistanceNN.molecules_allowed</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.local_env.MinimumDistanceNN.structures_allowed"><code class="docutils literal notranslate"><span class="pre">MinimumDistanceNN.structures_allowed</span></code></a></li>
</ul>
</li>
<li><a class="reference internal" href="#pymatgen.analysis.local_env.MinimumOKeeffeNN"><code class="docutils literal notranslate"><span class="pre">MinimumOKeeffeNN</span></code></a><ul>
<li><a class="reference internal" href="#pymatgen.analysis.local_env.MinimumOKeeffeNN.extend_structure_molecules"><code class="docutils literal notranslate"><span class="pre">MinimumOKeeffeNN.extend_structure_molecules</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.local_env.MinimumOKeeffeNN.get_nn_info"><code class="docutils literal notranslate"><span class="pre">MinimumOKeeffeNN.get_nn_info()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.local_env.MinimumOKeeffeNN.molecules_allowed"><code class="docutils literal notranslate"><span class="pre">MinimumOKeeffeNN.molecules_allowed</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.local_env.MinimumOKeeffeNN.structures_allowed"><code class="docutils literal notranslate"><span class="pre">MinimumOKeeffeNN.structures_allowed</span></code></a></li>
</ul>
</li>
<li><a class="reference internal" href="#pymatgen.analysis.local_env.MinimumVIRENN"><code class="docutils literal notranslate"><span class="pre">MinimumVIRENN</span></code></a><ul>
<li><a class="reference internal" href="#pymatgen.analysis.local_env.MinimumVIRENN.get_nn_info"><code class="docutils literal notranslate"><span class="pre">MinimumVIRENN.get_nn_info()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.local_env.MinimumVIRENN.molecules_allowed"><code class="docutils literal notranslate"><span class="pre">MinimumVIRENN.molecules_allowed</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.local_env.MinimumVIRENN.structures_allowed"><code class="docutils literal notranslate"><span class="pre">MinimumVIRENN.structures_allowed</span></code></a></li>
</ul>
</li>
<li><a class="reference internal" href="#pymatgen.analysis.local_env.NearNeighbors"><code class="docutils literal notranslate"><span class="pre">NearNeighbors</span></code></a><ul>
<li><a class="reference internal" href="#pymatgen.analysis.local_env.NearNeighbors.extend_structure_molecules"><code class="docutils literal notranslate"><span class="pre">NearNeighbors.extend_structure_molecules</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.local_env.NearNeighbors.get_all_nn_info"><code class="docutils literal notranslate"><span class="pre">NearNeighbors.get_all_nn_info()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.local_env.NearNeighbors.get_bonded_structure"><code class="docutils literal notranslate"><span class="pre">NearNeighbors.get_bonded_structure()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.local_env.NearNeighbors.get_cn"><code class="docutils literal notranslate"><span class="pre">NearNeighbors.get_cn()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.local_env.NearNeighbors.get_cn_dict"><code class="docutils literal notranslate"><span class="pre">NearNeighbors.get_cn_dict()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.local_env.NearNeighbors.get_local_order_parameters"><code class="docutils literal notranslate"><span class="pre">NearNeighbors.get_local_order_parameters()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.local_env.NearNeighbors.get_nn"><code class="docutils literal notranslate"><span class="pre">NearNeighbors.get_nn()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.local_env.NearNeighbors.get_nn_images"><code class="docutils literal notranslate"><span class="pre">NearNeighbors.get_nn_images()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.local_env.NearNeighbors.get_nn_info"><code class="docutils literal notranslate"><span class="pre">NearNeighbors.get_nn_info()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.local_env.NearNeighbors.get_nn_shell_info"><code class="docutils literal notranslate"><span class="pre">NearNeighbors.get_nn_shell_info()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.local_env.NearNeighbors.get_weights_of_nn_sites"><code class="docutils literal notranslate"><span class="pre">NearNeighbors.get_weights_of_nn_sites()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.local_env.NearNeighbors.molecules_allowed"><code class="docutils literal notranslate"><span class="pre">NearNeighbors.molecules_allowed</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.local_env.NearNeighbors.structures_allowed"><code class="docutils literal notranslate"><span class="pre">NearNeighbors.structures_allowed</span></code></a></li>
</ul>
</li>
<li><a class="reference internal" href="#pymatgen.analysis.local_env.OpenBabelNN"><code class="docutils literal notranslate"><span class="pre">OpenBabelNN</span></code></a><ul>
<li><a class="reference internal" href="#pymatgen.analysis.local_env.OpenBabelNN.extend_structure_molecules"><code class="docutils literal notranslate"><span class="pre">OpenBabelNN.extend_structure_molecules</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.local_env.OpenBabelNN.get_bonded_structure"><code class="docutils literal notranslate"><span class="pre">OpenBabelNN.get_bonded_structure()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.local_env.OpenBabelNN.get_nn_info"><code class="docutils literal notranslate"><span class="pre">OpenBabelNN.get_nn_info()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.local_env.OpenBabelNN.get_nn_shell_info"><code class="docutils literal notranslate"><span class="pre">OpenBabelNN.get_nn_shell_info()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.local_env.OpenBabelNN.molecules_allowed"><code class="docutils literal notranslate"><span class="pre">OpenBabelNN.molecules_allowed</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.local_env.OpenBabelNN.structures_allowed"><code class="docutils literal notranslate"><span class="pre">OpenBabelNN.structures_allowed</span></code></a></li>
</ul>
</li>
<li><a class="reference internal" href="#pymatgen.analysis.local_env.ValenceIonicRadiusEvaluator"><code class="docutils literal notranslate"><span class="pre">ValenceIonicRadiusEvaluator</span></code></a><ul>
<li><a class="reference internal" href="#pymatgen.analysis.local_env.ValenceIonicRadiusEvaluator.radii"><code class="docutils literal notranslate"><span class="pre">ValenceIonicRadiusEvaluator.radii</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.local_env.ValenceIonicRadiusEvaluator.structure"><code class="docutils literal notranslate"><span class="pre">ValenceIonicRadiusEvaluator.structure</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.local_env.ValenceIonicRadiusEvaluator.valences"><code class="docutils literal notranslate"><span class="pre">ValenceIonicRadiusEvaluator.valences</span></code></a></li>
</ul>
</li>
<li><a class="reference internal" href="#pymatgen.analysis.local_env.VoronoiNN"><code class="docutils literal notranslate"><span class="pre">VoronoiNN</span></code></a><ul>
<li><a class="reference internal" href="#pymatgen.analysis.local_env.VoronoiNN.get_all_nn_info"><code class="docutils literal notranslate"><span class="pre">VoronoiNN.get_all_nn_info()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.local_env.VoronoiNN.get_all_voronoi_polyhedra"><code class="docutils literal notranslate"><span class="pre">VoronoiNN.get_all_voronoi_polyhedra()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.local_env.VoronoiNN.get_nn_info"><code class="docutils literal notranslate"><span class="pre">VoronoiNN.get_nn_info()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.local_env.VoronoiNN.get_voronoi_polyhedra"><code class="docutils literal notranslate"><span class="pre">VoronoiNN.get_voronoi_polyhedra()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.local_env.VoronoiNN.molecules_allowed"><code class="docutils literal notranslate"><span class="pre">VoronoiNN.molecules_allowed</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.local_env.VoronoiNN.structures_allowed"><code class="docutils literal notranslate"><span class="pre">VoronoiNN.structures_allowed</span></code></a></li>
</ul>
</li>
<li><a class="reference internal" href="#pymatgen.analysis.local_env.get_neighbors_of_site_with_index"><code class="docutils literal notranslate"><span class="pre">get_neighbors_of_site_with_index()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.local_env.get_okeeffe_distance_prediction"><code class="docutils literal notranslate"><span class="pre">get_okeeffe_distance_prediction()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.local_env.get_okeeffe_params"><code class="docutils literal notranslate"><span class="pre">get_okeeffe_params()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.local_env.gramschmidt"><code class="docutils literal notranslate"><span class="pre">gramschmidt()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.local_env.metal_edge_extender"><code class="docutils literal notranslate"><span class="pre">metal_edge_extender()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.local_env.oxygen_edge_extender"><code class="docutils literal notranslate"><span class="pre">oxygen_edge_extender()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.local_env.site_is_of_motif_type"><code class="docutils literal notranslate"><span class="pre">site_is_of_motif_type()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.local_env.solid_angle"><code class="docutils literal notranslate"><span class="pre">solid_angle()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.local_env.vol_tetra"><code class="docutils literal notranslate"><span class="pre">vol_tetra()</span></code></a></li>
</ul>
</li>
<li><a class="reference internal" href="#module-pymatgen.analysis.molecule_matcher">pymatgen.analysis.molecule_matcher module</a><ul>
<li><a class="reference internal" href="#pymatgen.analysis.molecule_matcher.AbstractMolAtomMapper"><code class="docutils literal notranslate"><span class="pre">AbstractMolAtomMapper</span></code></a><ul>
<li><a class="reference internal" href="#pymatgen.analysis.molecule_matcher.AbstractMolAtomMapper.from_dict"><code class="docutils literal notranslate"><span class="pre">AbstractMolAtomMapper.from_dict()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.molecule_matcher.AbstractMolAtomMapper.get_molecule_hash"><code class="docutils literal notranslate"><span class="pre">AbstractMolAtomMapper.get_molecule_hash()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.molecule_matcher.AbstractMolAtomMapper.uniform_labels"><code class="docutils literal notranslate"><span class="pre">AbstractMolAtomMapper.uniform_labels()</span></code></a></li>
</ul>
</li>
<li><a class="reference internal" href="#pymatgen.analysis.molecule_matcher.BruteForceOrderMatcher"><code class="docutils literal notranslate"><span class="pre">BruteForceOrderMatcher</span></code></a><ul>
<li><a class="reference internal" href="#pymatgen.analysis.molecule_matcher.BruteForceOrderMatcher.fit"><code class="docutils literal notranslate"><span class="pre">BruteForceOrderMatcher.fit()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.molecule_matcher.BruteForceOrderMatcher.match"><code class="docutils literal notranslate"><span class="pre">BruteForceOrderMatcher.match()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.molecule_matcher.BruteForceOrderMatcher.permutations"><code class="docutils literal notranslate"><span class="pre">BruteForceOrderMatcher.permutations()</span></code></a></li>
</ul>
</li>
<li><a class="reference internal" href="#pymatgen.analysis.molecule_matcher.GeneticOrderMatcher"><code class="docutils literal notranslate"><span class="pre">GeneticOrderMatcher</span></code></a><ul>
<li><a class="reference internal" href="#pymatgen.analysis.molecule_matcher.GeneticOrderMatcher.fit"><code class="docutils literal notranslate"><span class="pre">GeneticOrderMatcher.fit()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.molecule_matcher.GeneticOrderMatcher.match"><code class="docutils literal notranslate"><span class="pre">GeneticOrderMatcher.match()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.molecule_matcher.GeneticOrderMatcher.permutations"><code class="docutils literal notranslate"><span class="pre">GeneticOrderMatcher.permutations()</span></code></a></li>
</ul>
</li>
<li><a class="reference internal" href="#pymatgen.analysis.molecule_matcher.HungarianOrderMatcher"><code class="docutils literal notranslate"><span class="pre">HungarianOrderMatcher</span></code></a><ul>
<li><a class="reference internal" href="#pymatgen.analysis.molecule_matcher.HungarianOrderMatcher.fit"><code class="docutils literal notranslate"><span class="pre">HungarianOrderMatcher.fit()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.molecule_matcher.HungarianOrderMatcher.get_principal_axis"><code class="docutils literal notranslate"><span class="pre">HungarianOrderMatcher.get_principal_axis()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.molecule_matcher.HungarianOrderMatcher.match"><code class="docutils literal notranslate"><span class="pre">HungarianOrderMatcher.match()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.molecule_matcher.HungarianOrderMatcher.permutations"><code class="docutils literal notranslate"><span class="pre">HungarianOrderMatcher.permutations()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.molecule_matcher.HungarianOrderMatcher.rotation_matrix_vectors"><code class="docutils literal notranslate"><span class="pre">HungarianOrderMatcher.rotation_matrix_vectors()</span></code></a></li>
</ul>
</li>
<li><a class="reference internal" href="#pymatgen.analysis.molecule_matcher.InchiMolAtomMapper"><code class="docutils literal notranslate"><span class="pre">InchiMolAtomMapper</span></code></a><ul>
<li><a class="reference internal" href="#pymatgen.analysis.molecule_matcher.InchiMolAtomMapper.as_dict"><code class="docutils literal notranslate"><span class="pre">InchiMolAtomMapper.as_dict()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.molecule_matcher.InchiMolAtomMapper.from_dict"><code class="docutils literal notranslate"><span class="pre">InchiMolAtomMapper.from_dict()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.molecule_matcher.InchiMolAtomMapper.get_molecule_hash"><code class="docutils literal notranslate"><span class="pre">InchiMolAtomMapper.get_molecule_hash()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.molecule_matcher.InchiMolAtomMapper.uniform_labels"><code class="docutils literal notranslate"><span class="pre">InchiMolAtomMapper.uniform_labels()</span></code></a></li>
</ul>
</li>
<li><a class="reference internal" href="#pymatgen.analysis.molecule_matcher.IsomorphismMolAtomMapper"><code class="docutils literal notranslate"><span class="pre">IsomorphismMolAtomMapper</span></code></a><ul>
<li><a class="reference internal" href="#pymatgen.analysis.molecule_matcher.IsomorphismMolAtomMapper.as_dict"><code class="docutils literal notranslate"><span class="pre">IsomorphismMolAtomMapper.as_dict()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.molecule_matcher.IsomorphismMolAtomMapper.from_dict"><code class="docutils literal notranslate"><span class="pre">IsomorphismMolAtomMapper.from_dict()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.molecule_matcher.IsomorphismMolAtomMapper.get_molecule_hash"><code class="docutils literal notranslate"><span class="pre">IsomorphismMolAtomMapper.get_molecule_hash()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.molecule_matcher.IsomorphismMolAtomMapper.uniform_labels"><code class="docutils literal notranslate"><span class="pre">IsomorphismMolAtomMapper.uniform_labels()</span></code></a></li>
</ul>
</li>
<li><a class="reference internal" href="#pymatgen.analysis.molecule_matcher.KabschMatcher"><code class="docutils literal notranslate"><span class="pre">KabschMatcher</span></code></a><ul>
<li><a class="reference internal" href="#pymatgen.analysis.molecule_matcher.KabschMatcher.fit"><code class="docutils literal notranslate"><span class="pre">KabschMatcher.fit()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.molecule_matcher.KabschMatcher.kabsch"><code class="docutils literal notranslate"><span class="pre">KabschMatcher.kabsch()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.molecule_matcher.KabschMatcher.match"><code class="docutils literal notranslate"><span class="pre">KabschMatcher.match()</span></code></a></li>
</ul>
</li>
<li><a class="reference internal" href="#pymatgen.analysis.molecule_matcher.MoleculeMatcher"><code class="docutils literal notranslate"><span class="pre">MoleculeMatcher</span></code></a><ul>
<li><a class="reference internal" href="#pymatgen.analysis.molecule_matcher.MoleculeMatcher.as_dict"><code class="docutils literal notranslate"><span class="pre">MoleculeMatcher.as_dict()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.molecule_matcher.MoleculeMatcher.fit"><code class="docutils literal notranslate"><span class="pre">MoleculeMatcher.fit()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.molecule_matcher.MoleculeMatcher.from_dict"><code class="docutils literal notranslate"><span class="pre">MoleculeMatcher.from_dict()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.molecule_matcher.MoleculeMatcher.get_rmsd"><code class="docutils literal notranslate"><span class="pre">MoleculeMatcher.get_rmsd()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.molecule_matcher.MoleculeMatcher.group_molecules"><code class="docutils literal notranslate"><span class="pre">MoleculeMatcher.group_molecules()</span></code></a></li>
</ul>
</li>
</ul>
</li>
<li><a class="reference internal" href="#module-pymatgen.analysis.molecule_structure_comparator">pymatgen.analysis.molecule_structure_comparator module</a><ul>
<li><a class="reference internal" href="#pymatgen.analysis.molecule_structure_comparator.CovalentRadius"><code class="docutils literal notranslate"><span class="pre">CovalentRadius</span></code></a><ul>
<li><a class="reference internal" href="#pymatgen.analysis.molecule_structure_comparator.CovalentRadius.radius"><code class="docutils literal notranslate"><span class="pre">CovalentRadius.radius</span></code></a></li>
</ul>
</li>
<li><a class="reference internal" href="#pymatgen.analysis.molecule_structure_comparator.MoleculeStructureComparator"><code class="docutils literal notranslate"><span class="pre">MoleculeStructureComparator</span></code></a><ul>
<li><a class="reference internal" href="#pymatgen.analysis.molecule_structure_comparator.MoleculeStructureComparator.are_equal"><code class="docutils literal notranslate"><span class="pre">MoleculeStructureComparator.are_equal()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.molecule_structure_comparator.MoleculeStructureComparator.as_dict"><code class="docutils literal notranslate"><span class="pre">MoleculeStructureComparator.as_dict()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.molecule_structure_comparator.MoleculeStructureComparator.from_dict"><code class="docutils literal notranslate"><span class="pre">MoleculeStructureComparator.from_dict()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.molecule_structure_comparator.MoleculeStructureComparator.get_13_bonds"><code class="docutils literal notranslate"><span class="pre">MoleculeStructureComparator.get_13_bonds()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.molecule_structure_comparator.MoleculeStructureComparator.halogen_list"><code class="docutils literal notranslate"><span class="pre">MoleculeStructureComparator.halogen_list</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.molecule_structure_comparator.MoleculeStructureComparator.ionic_element_list"><code class="docutils literal notranslate"><span class="pre">MoleculeStructureComparator.ionic_element_list</span></code></a></li>
</ul>
</li>
</ul>
</li>
<li><a class="reference internal" href="#module-pymatgen.analysis.nmr">pymatgen.analysis.nmr module</a><ul>
<li><a class="reference internal" href="#pymatgen.analysis.nmr.ChemicalShielding"><code class="docutils literal notranslate"><span class="pre">ChemicalShielding</span></code></a><ul>
<li><a class="reference internal" href="#pymatgen.analysis.nmr.ChemicalShielding.HaeberlenNotation"><code class="docutils literal notranslate"><span class="pre">ChemicalShielding.HaeberlenNotation</span></code></a><ul>
<li><a class="reference internal" href="#pymatgen.analysis.nmr.ChemicalShielding.HaeberlenNotation.delta_sigma_iso"><code class="docutils literal notranslate"><span class="pre">ChemicalShielding.HaeberlenNotation.delta_sigma_iso</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.nmr.ChemicalShielding.HaeberlenNotation.eta"><code class="docutils literal notranslate"><span class="pre">ChemicalShielding.HaeberlenNotation.eta</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.nmr.ChemicalShielding.HaeberlenNotation.sigma_iso"><code class="docutils literal notranslate"><span class="pre">ChemicalShielding.HaeberlenNotation.sigma_iso</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.nmr.ChemicalShielding.HaeberlenNotation.zeta"><code class="docutils literal notranslate"><span class="pre">ChemicalShielding.HaeberlenNotation.zeta</span></code></a></li>
</ul>
</li>
<li><a class="reference internal" href="#pymatgen.analysis.nmr.ChemicalShielding.MarylandNotation"><code class="docutils literal notranslate"><span class="pre">ChemicalShielding.MarylandNotation</span></code></a><ul>
<li><a class="reference internal" href="#pymatgen.analysis.nmr.ChemicalShielding.MarylandNotation.kappa"><code class="docutils literal notranslate"><span class="pre">ChemicalShielding.MarylandNotation.kappa</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.nmr.ChemicalShielding.MarylandNotation.omega"><code class="docutils literal notranslate"><span class="pre">ChemicalShielding.MarylandNotation.omega</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.nmr.ChemicalShielding.MarylandNotation.sigma_iso"><code class="docutils literal notranslate"><span class="pre">ChemicalShielding.MarylandNotation.sigma_iso</span></code></a></li>
</ul>
</li>
<li><a class="reference internal" href="#pymatgen.analysis.nmr.ChemicalShielding.MehringNotation"><code class="docutils literal notranslate"><span class="pre">ChemicalShielding.MehringNotation</span></code></a><ul>
<li><a class="reference internal" href="#pymatgen.analysis.nmr.ChemicalShielding.MehringNotation.sigma_11"><code class="docutils literal notranslate"><span class="pre">ChemicalShielding.MehringNotation.sigma_11</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.nmr.ChemicalShielding.MehringNotation.sigma_22"><code class="docutils literal notranslate"><span class="pre">ChemicalShielding.MehringNotation.sigma_22</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.nmr.ChemicalShielding.MehringNotation.sigma_33"><code class="docutils literal notranslate"><span class="pre">ChemicalShielding.MehringNotation.sigma_33</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.nmr.ChemicalShielding.MehringNotation.sigma_iso"><code class="docutils literal notranslate"><span class="pre">ChemicalShielding.MehringNotation.sigma_iso</span></code></a></li>
</ul>
</li>
<li><a class="reference internal" href="#pymatgen.analysis.nmr.ChemicalShielding.from_maryland_notation"><code class="docutils literal notranslate"><span class="pre">ChemicalShielding.from_maryland_notation()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.nmr.ChemicalShielding.haeberlen_values"><code class="docutils literal notranslate"><span class="pre">ChemicalShielding.haeberlen_values</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.nmr.ChemicalShielding.maryland_values"><code class="docutils literal notranslate"><span class="pre">ChemicalShielding.maryland_values</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.nmr.ChemicalShielding.mehring_values"><code class="docutils literal notranslate"><span class="pre">ChemicalShielding.mehring_values</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.nmr.ChemicalShielding.principal_axis_system"><code class="docutils literal notranslate"><span class="pre">ChemicalShielding.principal_axis_system</span></code></a></li>
</ul>
</li>
<li><a class="reference internal" href="#pymatgen.analysis.nmr.ElectricFieldGradient"><code class="docutils literal notranslate"><span class="pre">ElectricFieldGradient</span></code></a><ul>
<li><a class="reference internal" href="#pymatgen.analysis.nmr.ElectricFieldGradient.V_xx"><code class="docutils literal notranslate"><span class="pre">ElectricFieldGradient.V_xx</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.nmr.ElectricFieldGradient.V_yy"><code class="docutils literal notranslate"><span class="pre">ElectricFieldGradient.V_yy</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.nmr.ElectricFieldGradient.V_zz"><code class="docutils literal notranslate"><span class="pre">ElectricFieldGradient.V_zz</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.nmr.ElectricFieldGradient.asymmetry"><code class="docutils literal notranslate"><span class="pre">ElectricFieldGradient.asymmetry</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.nmr.ElectricFieldGradient.coupling_constant"><code class="docutils literal notranslate"><span class="pre">ElectricFieldGradient.coupling_constant()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.nmr.ElectricFieldGradient.principal_axis_system"><code class="docutils literal notranslate"><span class="pre">ElectricFieldGradient.principal_axis_system</span></code></a></li>
</ul>
</li>
</ul>
</li>
<li><a class="reference internal" href="#module-pymatgen.analysis.phase_diagram">pymatgen.analysis.phase_diagram module</a><ul>
<li><a class="reference internal" href="#pymatgen.analysis.phase_diagram.CompoundPhaseDiagram"><code class="docutils literal notranslate"><span class="pre">CompoundPhaseDiagram</span></code></a><ul>
<li><a class="reference internal" href="#pymatgen.analysis.phase_diagram.CompoundPhaseDiagram.amount_tol"><code class="docutils literal notranslate"><span class="pre">CompoundPhaseDiagram.amount_tol</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.phase_diagram.CompoundPhaseDiagram.as_dict"><code class="docutils literal notranslate"><span class="pre">CompoundPhaseDiagram.as_dict()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.phase_diagram.CompoundPhaseDiagram.from_dict"><code class="docutils literal notranslate"><span class="pre">CompoundPhaseDiagram.from_dict()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.phase_diagram.CompoundPhaseDiagram.num2str"><code class="docutils literal notranslate"><span class="pre">CompoundPhaseDiagram.num2str()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.phase_diagram.CompoundPhaseDiagram.transform_entries"><code class="docutils literal notranslate"><span class="pre">CompoundPhaseDiagram.transform_entries()</span></code></a></li>
</ul>
</li>
<li><a class="reference internal" href="#pymatgen.analysis.phase_diagram.GrandPotPDEntry"><code class="docutils literal notranslate"><span class="pre">GrandPotPDEntry</span></code></a><ul>
<li><a class="reference internal" href="#pymatgen.analysis.phase_diagram.GrandPotPDEntry.as_dict"><code class="docutils literal notranslate"><span class="pre">GrandPotPDEntry.as_dict()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.phase_diagram.GrandPotPDEntry.chemical_energy"><code class="docutils literal notranslate"><span class="pre">GrandPotPDEntry.chemical_energy</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.phase_diagram.GrandPotPDEntry.composition"><code class="docutils literal notranslate"><span class="pre">GrandPotPDEntry.composition</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.phase_diagram.GrandPotPDEntry.energy"><code class="docutils literal notranslate"><span class="pre">GrandPotPDEntry.energy</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.phase_diagram.GrandPotPDEntry.from_dict"><code class="docutils literal notranslate"><span class="pre">GrandPotPDEntry.from_dict()</span></code></a></li>
</ul>
</li>
<li><a class="reference internal" href="#pymatgen.analysis.phase_diagram.GrandPotentialPhaseDiagram"><code class="docutils literal notranslate"><span class="pre">GrandPotentialPhaseDiagram</span></code></a><ul>
<li><a class="reference internal" href="#pymatgen.analysis.phase_diagram.GrandPotentialPhaseDiagram.as_dict"><code class="docutils literal notranslate"><span class="pre">GrandPotentialPhaseDiagram.as_dict()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.phase_diagram.GrandPotentialPhaseDiagram.from_dict"><code class="docutils literal notranslate"><span class="pre">GrandPotentialPhaseDiagram.from_dict()</span></code></a></li>
</ul>
</li>
<li><a class="reference internal" href="#pymatgen.analysis.phase_diagram.PDEntry"><code class="docutils literal notranslate"><span class="pre">PDEntry</span></code></a><ul>
<li><a class="reference internal" href="#pymatgen.analysis.phase_diagram.PDEntry.composition"><code class="docutils literal notranslate"><span class="pre">PDEntry.composition</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.phase_diagram.PDEntry.energy"><code class="docutils literal notranslate"><span class="pre">PDEntry.energy</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.phase_diagram.PDEntry.name"><code class="docutils literal notranslate"><span class="pre">PDEntry.name</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.phase_diagram.PDEntry.attribute"><code class="docutils literal notranslate"><span class="pre">PDEntry.attribute</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.phase_diagram.PDEntry.as_dict"><code class="docutils literal notranslate"><span class="pre">PDEntry.as_dict()</span></code></a></li>
<li><a class="reference internal" href="#id0"><code class="docutils literal notranslate"><span class="pre">PDEntry.energy</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.phase_diagram.PDEntry.from_dict"><code class="docutils literal notranslate"><span class="pre">PDEntry.from_dict()</span></code></a></li>
</ul>
</li>
<li><a class="reference internal" href="#pymatgen.analysis.phase_diagram.PDPlotter"><code class="docutils literal notranslate"><span class="pre">PDPlotter</span></code></a><ul>
<li><a class="reference internal" href="#pymatgen.analysis.phase_diagram.PDPlotter.get_chempot_range_map_plot"><code class="docutils literal notranslate"><span class="pre">PDPlotter.get_chempot_range_map_plot()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.phase_diagram.PDPlotter.get_contour_pd_plot"><code class="docutils literal notranslate"><span class="pre">PDPlotter.get_contour_pd_plot()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.phase_diagram.PDPlotter.get_plot"><code class="docutils literal notranslate"><span class="pre">PDPlotter.get_plot()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.phase_diagram.PDPlotter.pd_plot_data"><code class="docutils literal notranslate"><span class="pre">PDPlotter.pd_plot_data</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.phase_diagram.PDPlotter.plot_chempot_range_map"><code class="docutils literal notranslate"><span class="pre">PDPlotter.plot_chempot_range_map()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.phase_diagram.PDPlotter.plot_element_profile"><code class="docutils literal notranslate"><span class="pre">PDPlotter.plot_element_profile()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.phase_diagram.PDPlotter.show"><code class="docutils literal notranslate"><span class="pre">PDPlotter.show()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.phase_diagram.PDPlotter.write_image"><code class="docutils literal notranslate"><span class="pre">PDPlotter.write_image()</span></code></a></li>
</ul>
</li>
<li><a class="reference internal" href="#pymatgen.analysis.phase_diagram.PatchedPhaseDiagram"><code class="docutils literal notranslate"><span class="pre">PatchedPhaseDiagram</span></code></a><ul>
<li><a class="reference internal" href="#pymatgen.analysis.phase_diagram.PatchedPhaseDiagram.all_entries"><code class="docutils literal notranslate"><span class="pre">PatchedPhaseDiagram.all_entries</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.phase_diagram.PatchedPhaseDiagram.min_entries"><code class="docutils literal notranslate"><span class="pre">PatchedPhaseDiagram.min_entries</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.phase_diagram.PatchedPhaseDiagram.el_refs"><code class="docutils literal notranslate"><span class="pre">PatchedPhaseDiagram.el_refs</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.phase_diagram.PatchedPhaseDiagram.elements"><code class="docutils literal notranslate"><span class="pre">PatchedPhaseDiagram.elements</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.phase_diagram.PatchedPhaseDiagram.as_dict"><code class="docutils literal notranslate"><span class="pre">PatchedPhaseDiagram.as_dict()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.phase_diagram.PatchedPhaseDiagram.from_dict"><code class="docutils literal notranslate"><span class="pre">PatchedPhaseDiagram.from_dict()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.phase_diagram.PatchedPhaseDiagram.get_all_chempots"><code class="docutils literal notranslate"><span class="pre">PatchedPhaseDiagram.get_all_chempots()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.phase_diagram.PatchedPhaseDiagram.get_chempot_range_map"><code class="docutils literal notranslate"><span class="pre">PatchedPhaseDiagram.get_chempot_range_map()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.phase_diagram.PatchedPhaseDiagram.get_chempot_range_stability_phase"><code class="docutils literal notranslate"><span class="pre">PatchedPhaseDiagram.get_chempot_range_stability_phase()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.phase_diagram.PatchedPhaseDiagram.get_composition_chempots"><code class="docutils literal notranslate"><span class="pre">PatchedPhaseDiagram.get_composition_chempots()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.phase_diagram.PatchedPhaseDiagram.get_critical_compositions"><code class="docutils literal notranslate"><span class="pre">PatchedPhaseDiagram.get_critical_compositions()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.phase_diagram.PatchedPhaseDiagram.get_decomp_and_e_above_hull"><code class="docutils literal notranslate"><span class="pre">PatchedPhaseDiagram.get_decomp_and_e_above_hull()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.phase_diagram.PatchedPhaseDiagram.get_decomposition"><code class="docutils literal notranslate"><span class="pre">PatchedPhaseDiagram.get_decomposition()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.phase_diagram.PatchedPhaseDiagram.get_element_profile"><code class="docutils literal notranslate"><span class="pre">PatchedPhaseDiagram.get_element_profile()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.phase_diagram.PatchedPhaseDiagram.get_equilibrium_reaction_energy"><code class="docutils literal notranslate"><span class="pre">PatchedPhaseDiagram.get_equilibrium_reaction_energy()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.phase_diagram.PatchedPhaseDiagram.get_pd_for_entry"><code class="docutils literal notranslate"><span class="pre">PatchedPhaseDiagram.get_pd_for_entry()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.phase_diagram.PatchedPhaseDiagram.get_transition_chempots"><code class="docutils literal notranslate"><span class="pre">PatchedPhaseDiagram.get_transition_chempots()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.phase_diagram.PatchedPhaseDiagram.getmu_vertices_stability_phase"><code class="docutils literal notranslate"><span class="pre">PatchedPhaseDiagram.getmu_vertices_stability_phase()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.phase_diagram.PatchedPhaseDiagram.remove_redundant_spaces"><code class="docutils literal notranslate"><span class="pre">PatchedPhaseDiagram.remove_redundant_spaces()</span></code></a></li>
</ul>
</li>
<li><a class="reference internal" href="#pymatgen.analysis.phase_diagram.PhaseDiagram"><code class="docutils literal notranslate"><span class="pre">PhaseDiagram</span></code></a><ul>
<li><a class="reference internal" href="#pymatgen.analysis.phase_diagram.PhaseDiagram.dim"><code class="docutils literal notranslate"><span class="pre">PhaseDiagram.dim</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.phase_diagram.PhaseDiagram.elements"><code class="docutils literal notranslate"><span class="pre">PhaseDiagram.elements</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.phase_diagram.PhaseDiagram.el_refs"><code class="docutils literal notranslate"><span class="pre">PhaseDiagram.el_refs</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.phase_diagram.PhaseDiagram.all_entries"><code class="docutils literal notranslate"><span class="pre">PhaseDiagram.all_entries</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.phase_diagram.PhaseDiagram.qhull_entries"><code class="docutils literal notranslate"><span class="pre">PhaseDiagram.qhull_entries</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.phase_diagram.PhaseDiagram.qhull_data"><code class="docutils literal notranslate"><span class="pre">PhaseDiagram.qhull_data</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.phase_diagram.PhaseDiagram.facets"><code class="docutils literal notranslate"><span class="pre">PhaseDiagram.facets</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.phase_diagram.PhaseDiagram.simplices"><code class="docutils literal notranslate"><span class="pre">PhaseDiagram.simplices</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.phase_diagram.PhaseDiagram.all_entries_hulldata"><code class="docutils literal notranslate"><span class="pre">PhaseDiagram.all_entries_hulldata</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.phase_diagram.PhaseDiagram.as_dict"><code class="docutils literal notranslate"><span class="pre">PhaseDiagram.as_dict()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.phase_diagram.PhaseDiagram.formation_energy_tol"><code class="docutils literal notranslate"><span class="pre">PhaseDiagram.formation_energy_tol</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.phase_diagram.PhaseDiagram.from_dict"><code class="docutils literal notranslate"><span class="pre">PhaseDiagram.from_dict()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.phase_diagram.PhaseDiagram.get_all_chempots"><code class="docutils literal notranslate"><span class="pre">PhaseDiagram.get_all_chempots()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.phase_diagram.PhaseDiagram.get_chempot_range_map"><code class="docutils literal notranslate"><span class="pre">PhaseDiagram.get_chempot_range_map()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.phase_diagram.PhaseDiagram.get_chempot_range_stability_phase"><code class="docutils literal notranslate"><span class="pre">PhaseDiagram.get_chempot_range_stability_phase()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.phase_diagram.PhaseDiagram.get_composition_chempots"><code class="docutils literal notranslate"><span class="pre">PhaseDiagram.get_composition_chempots()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.phase_diagram.PhaseDiagram.get_critical_compositions"><code class="docutils literal notranslate"><span class="pre">PhaseDiagram.get_critical_compositions()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.phase_diagram.PhaseDiagram.get_decomp_and_e_above_hull"><code class="docutils literal notranslate"><span class="pre">PhaseDiagram.get_decomp_and_e_above_hull()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.phase_diagram.PhaseDiagram.get_decomp_and_hull_energy_per_atom"><code class="docutils literal notranslate"><span class="pre">PhaseDiagram.get_decomp_and_hull_energy_per_atom()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.phase_diagram.PhaseDiagram.get_decomp_and_phase_separation_energy"><code class="docutils literal notranslate"><span class="pre">PhaseDiagram.get_decomp_and_phase_separation_energy()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.phase_diagram.PhaseDiagram.get_decomposition"><code class="docutils literal notranslate"><span class="pre">PhaseDiagram.get_decomposition()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.phase_diagram.PhaseDiagram.get_e_above_hull"><code class="docutils literal notranslate"><span class="pre">PhaseDiagram.get_e_above_hull()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.phase_diagram.PhaseDiagram.get_element_profile"><code class="docutils literal notranslate"><span class="pre">PhaseDiagram.get_element_profile()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.phase_diagram.PhaseDiagram.get_equilibrium_reaction_energy"><code class="docutils literal notranslate"><span class="pre">PhaseDiagram.get_equilibrium_reaction_energy()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.phase_diagram.PhaseDiagram.get_form_energy"><code class="docutils literal notranslate"><span class="pre">PhaseDiagram.get_form_energy()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.phase_diagram.PhaseDiagram.get_form_energy_per_atom"><code class="docutils literal notranslate"><span class="pre">PhaseDiagram.get_form_energy_per_atom()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.phase_diagram.PhaseDiagram.get_hull_energy"><code class="docutils literal notranslate"><span class="pre">PhaseDiagram.get_hull_energy()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.phase_diagram.PhaseDiagram.get_hull_energy_per_atom"><code class="docutils literal notranslate"><span class="pre">PhaseDiagram.get_hull_energy_per_atom()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.phase_diagram.PhaseDiagram.get_phase_separation_energy"><code class="docutils literal notranslate"><span class="pre">PhaseDiagram.get_phase_separation_energy()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.phase_diagram.PhaseDiagram.get_plot"><code class="docutils literal notranslate"><span class="pre">PhaseDiagram.get_plot()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.phase_diagram.PhaseDiagram.get_reference_energy"><code class="docutils literal notranslate"><span class="pre">PhaseDiagram.get_reference_energy()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.phase_diagram.PhaseDiagram.get_reference_energy_per_atom"><code class="docutils literal notranslate"><span class="pre">PhaseDiagram.get_reference_energy_per_atom()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.phase_diagram.PhaseDiagram.get_transition_chempots"><code class="docutils literal notranslate"><span class="pre">PhaseDiagram.get_transition_chempots()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.phase_diagram.PhaseDiagram.getmu_vertices_stability_phase"><code class="docutils literal notranslate"><span class="pre">PhaseDiagram.getmu_vertices_stability_phase()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.phase_diagram.PhaseDiagram.numerical_tol"><code class="docutils literal notranslate"><span class="pre">PhaseDiagram.numerical_tol</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.phase_diagram.PhaseDiagram.pd_coords"><code class="docutils literal notranslate"><span class="pre">PhaseDiagram.pd_coords()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.phase_diagram.PhaseDiagram.stable_entries"><code class="docutils literal notranslate"><span class="pre">PhaseDiagram.stable_entries</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.phase_diagram.PhaseDiagram.unstable_entries"><code class="docutils literal notranslate"><span class="pre">PhaseDiagram.unstable_entries</span></code></a></li>
</ul>
</li>
<li><a class="reference internal" href="#pymatgen.analysis.phase_diagram.PhaseDiagramError"><code class="docutils literal notranslate"><span class="pre">PhaseDiagramError</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.phase_diagram.ReactionDiagram"><code class="docutils literal notranslate"><span class="pre">ReactionDiagram</span></code></a><ul>
<li><a class="reference internal" href="#pymatgen.analysis.phase_diagram.ReactionDiagram.get_compound_pd"><code class="docutils literal notranslate"><span class="pre">ReactionDiagram.get_compound_pd()</span></code></a></li>
</ul>
</li>
<li><a class="reference internal" href="#pymatgen.analysis.phase_diagram.TransformedPDEntry"><code class="docutils literal notranslate"><span class="pre">TransformedPDEntry</span></code></a><ul>
<li><a class="reference internal" href="#pymatgen.analysis.phase_diagram.TransformedPDEntry.amount_tol"><code class="docutils literal notranslate"><span class="pre">TransformedPDEntry.amount_tol</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.phase_diagram.TransformedPDEntry.as_dict"><code class="docutils literal notranslate"><span class="pre">TransformedPDEntry.as_dict()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.phase_diagram.TransformedPDEntry.composition"><code class="docutils literal notranslate"><span class="pre">TransformedPDEntry.composition</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.phase_diagram.TransformedPDEntry.from_dict"><code class="docutils literal notranslate"><span class="pre">TransformedPDEntry.from_dict()</span></code></a></li>
</ul>
</li>
<li><a class="reference internal" href="#pymatgen.analysis.phase_diagram.TransformedPDEntryError"><code class="docutils literal notranslate"><span class="pre">TransformedPDEntryError</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.phase_diagram.get_facets"><code class="docutils literal notranslate"><span class="pre">get_facets()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.phase_diagram.order_phase_diagram"><code class="docutils literal notranslate"><span class="pre">order_phase_diagram()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.phase_diagram.tet_coord"><code class="docutils literal notranslate"><span class="pre">tet_coord()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.phase_diagram.triangular_coord"><code class="docutils literal notranslate"><span class="pre">triangular_coord()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.phase_diagram.uniquelines"><code class="docutils literal notranslate"><span class="pre">uniquelines()</span></code></a></li>
</ul>
</li>
<li><a class="reference internal" href="#module-pymatgen.analysis.piezo">pymatgen.analysis.piezo module</a><ul>
<li><a class="reference internal" href="#pymatgen.analysis.piezo.PiezoTensor"><code class="docutils literal notranslate"><span class="pre">PiezoTensor</span></code></a><ul>
<li><a class="reference internal" href="#pymatgen.analysis.piezo.PiezoTensor.from_vasp_voigt"><code class="docutils literal notranslate"><span class="pre">PiezoTensor.from_vasp_voigt()</span></code></a></li>
</ul>
</li>
</ul>
</li>
<li><a class="reference internal" href="#module-pymatgen.analysis.piezo_sensitivity">pymatgen.analysis.piezo_sensitivity module</a><ul>
<li><a class="reference internal" href="#pymatgen.analysis.piezo_sensitivity.BornEffectiveCharge"><code class="docutils literal notranslate"><span class="pre">BornEffectiveCharge</span></code></a><ul>
<li><a class="reference internal" href="#pymatgen.analysis.piezo_sensitivity.BornEffectiveCharge.get_BEC_operations"><code class="docutils literal notranslate"><span class="pre">BornEffectiveCharge.get_BEC_operations()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.piezo_sensitivity.BornEffectiveCharge.get_rand_BEC"><code class="docutils literal notranslate"><span class="pre">BornEffectiveCharge.get_rand_BEC()</span></code></a></li>
</ul>
</li>
<li><a class="reference internal" href="#pymatgen.analysis.piezo_sensitivity.ForceConstantMatrix"><code class="docutils literal notranslate"><span class="pre">ForceConstantMatrix</span></code></a><ul>
<li><a class="reference internal" href="#pymatgen.analysis.piezo_sensitivity.ForceConstantMatrix.get_FCM_operations"><code class="docutils literal notranslate"><span class="pre">ForceConstantMatrix.get_FCM_operations()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.piezo_sensitivity.ForceConstantMatrix.get_asum_FCM"><code class="docutils literal notranslate"><span class="pre">ForceConstantMatrix.get_asum_FCM()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.piezo_sensitivity.ForceConstantMatrix.get_rand_FCM"><code class="docutils literal notranslate"><span class="pre">ForceConstantMatrix.get_rand_FCM()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.piezo_sensitivity.ForceConstantMatrix.get_stable_FCM"><code class="docutils literal notranslate"><span class="pre">ForceConstantMatrix.get_stable_FCM()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.piezo_sensitivity.ForceConstantMatrix.get_symmetrized_FCM"><code class="docutils literal notranslate"><span class="pre">ForceConstantMatrix.get_symmetrized_FCM()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.piezo_sensitivity.ForceConstantMatrix.get_unstable_FCM"><code class="docutils literal notranslate"><span class="pre">ForceConstantMatrix.get_unstable_FCM()</span></code></a></li>
</ul>
</li>
<li><a class="reference internal" href="#pymatgen.analysis.piezo_sensitivity.InternalStrainTensor"><code class="docutils literal notranslate"><span class="pre">InternalStrainTensor</span></code></a><ul>
<li><a class="reference internal" href="#pymatgen.analysis.piezo_sensitivity.InternalStrainTensor.get_IST_operations"><code class="docutils literal notranslate"><span class="pre">InternalStrainTensor.get_IST_operations()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.piezo_sensitivity.InternalStrainTensor.get_rand_IST"><code class="docutils literal notranslate"><span class="pre">InternalStrainTensor.get_rand_IST()</span></code></a></li>
</ul>
</li>
<li><a class="reference internal" href="#pymatgen.analysis.piezo_sensitivity.get_piezo"><code class="docutils literal notranslate"><span class="pre">get_piezo()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.piezo_sensitivity.rand_piezo"><code class="docutils literal notranslate"><span class="pre">rand_piezo()</span></code></a></li>
</ul>
</li>
<li><a class="reference internal" href="#module-pymatgen.analysis.pourbaix_diagram">pymatgen.analysis.pourbaix_diagram module</a><ul>
<li><a class="reference internal" href="#pymatgen.analysis.pourbaix_diagram.IonEntry"><code class="docutils literal notranslate"><span class="pre">IonEntry</span></code></a><ul>
<li><a class="reference internal" href="#pymatgen.analysis.pourbaix_diagram.IonEntry.name"><code class="docutils literal notranslate"><span class="pre">IonEntry.name</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.pourbaix_diagram.IonEntry.as_dict"><code class="docutils literal notranslate"><span class="pre">IonEntry.as_dict()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.pourbaix_diagram.IonEntry.from_dict"><code class="docutils literal notranslate"><span class="pre">IonEntry.from_dict()</span></code></a></li>
</ul>
</li>
<li><a class="reference internal" href="#pymatgen.analysis.pourbaix_diagram.MultiEntry"><code class="docutils literal notranslate"><span class="pre">MultiEntry</span></code></a><ul>
<li><a class="reference internal" href="#pymatgen.analysis.pourbaix_diagram.MultiEntry.as_dict"><code class="docutils literal notranslate"><span class="pre">MultiEntry.as_dict()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.pourbaix_diagram.MultiEntry.from_dict"><code class="docutils literal notranslate"><span class="pre">MultiEntry.from_dict()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.pourbaix_diagram.MultiEntry.name"><code class="docutils literal notranslate"><span class="pre">MultiEntry.name</span></code></a></li>
</ul>
</li>
<li><a class="reference internal" href="#pymatgen.analysis.pourbaix_diagram.PourbaixDiagram"><code class="docutils literal notranslate"><span class="pre">PourbaixDiagram</span></code></a><ul>
<li><a class="reference internal" href="#pymatgen.analysis.pourbaix_diagram.PourbaixDiagram.all_entries"><code class="docutils literal notranslate"><span class="pre">PourbaixDiagram.all_entries</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.pourbaix_diagram.PourbaixDiagram.as_dict"><code class="docutils literal notranslate"><span class="pre">PourbaixDiagram.as_dict()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.pourbaix_diagram.PourbaixDiagram.elements_ho"><code class="docutils literal notranslate"><span class="pre">PourbaixDiagram.elements_ho</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.pourbaix_diagram.PourbaixDiagram.find_stable_entry"><code class="docutils literal notranslate"><span class="pre">PourbaixDiagram.find_stable_entry()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.pourbaix_diagram.PourbaixDiagram.from_dict"><code class="docutils literal notranslate"><span class="pre">PourbaixDiagram.from_dict()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.pourbaix_diagram.PourbaixDiagram.get_decomposition_energy"><code class="docutils literal notranslate"><span class="pre">PourbaixDiagram.get_decomposition_energy()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.pourbaix_diagram.PourbaixDiagram.get_hull_energy"><code class="docutils literal notranslate"><span class="pre">PourbaixDiagram.get_hull_energy()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.pourbaix_diagram.PourbaixDiagram.get_pourbaix_domains"><code class="docutils literal notranslate"><span class="pre">PourbaixDiagram.get_pourbaix_domains()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.pourbaix_diagram.PourbaixDiagram.get_stable_entry"><code class="docutils literal notranslate"><span class="pre">PourbaixDiagram.get_stable_entry()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.pourbaix_diagram.PourbaixDiagram.process_multientry"><code class="docutils literal notranslate"><span class="pre">PourbaixDiagram.process_multientry()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.pourbaix_diagram.PourbaixDiagram.stable_entries"><code class="docutils literal notranslate"><span class="pre">PourbaixDiagram.stable_entries</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.pourbaix_diagram.PourbaixDiagram.unprocessed_entries"><code class="docutils literal notranslate"><span class="pre">PourbaixDiagram.unprocessed_entries</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.pourbaix_diagram.PourbaixDiagram.unstable_entries"><code class="docutils literal notranslate"><span class="pre">PourbaixDiagram.unstable_entries</span></code></a></li>
</ul>
</li>
<li><a class="reference internal" href="#pymatgen.analysis.pourbaix_diagram.PourbaixEntry"><code class="docutils literal notranslate"><span class="pre">PourbaixEntry</span></code></a><ul>
<li><a class="reference internal" href="#pymatgen.analysis.pourbaix_diagram.PourbaixEntry.as_dict"><code class="docutils literal notranslate"><span class="pre">PourbaixEntry.as_dict()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.pourbaix_diagram.PourbaixEntry.composition"><code class="docutils literal notranslate"><span class="pre">PourbaixEntry.composition</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.pourbaix_diagram.PourbaixEntry.conc_term"><code class="docutils literal notranslate"><span class="pre">PourbaixEntry.conc_term</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.pourbaix_diagram.PourbaixEntry.elements"><code class="docutils literal notranslate"><span class="pre">PourbaixEntry.elements</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.pourbaix_diagram.PourbaixEntry.energy"><code class="docutils literal notranslate"><span class="pre">PourbaixEntry.energy</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.pourbaix_diagram.PourbaixEntry.energy_at_conditions"><code class="docutils literal notranslate"><span class="pre">PourbaixEntry.energy_at_conditions()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.pourbaix_diagram.PourbaixEntry.energy_per_atom"><code class="docutils literal notranslate"><span class="pre">PourbaixEntry.energy_per_atom</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.pourbaix_diagram.PourbaixEntry.from_dict"><code class="docutils literal notranslate"><span class="pre">PourbaixEntry.from_dict()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.pourbaix_diagram.PourbaixEntry.get_element_fraction"><code class="docutils literal notranslate"><span class="pre">PourbaixEntry.get_element_fraction()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.pourbaix_diagram.PourbaixEntry.nH2O"><code class="docutils literal notranslate"><span class="pre">PourbaixEntry.nH2O</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.pourbaix_diagram.PourbaixEntry.nPhi"><code class="docutils literal notranslate"><span class="pre">PourbaixEntry.nPhi</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.pourbaix_diagram.PourbaixEntry.name"><code class="docutils literal notranslate"><span class="pre">PourbaixEntry.name</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.pourbaix_diagram.PourbaixEntry.normalization_factor"><code class="docutils literal notranslate"><span class="pre">PourbaixEntry.normalization_factor</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.pourbaix_diagram.PourbaixEntry.normalized_energy"><code class="docutils literal notranslate"><span class="pre">PourbaixEntry.normalized_energy</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.pourbaix_diagram.PourbaixEntry.normalized_energy_at_conditions"><code class="docutils literal notranslate"><span class="pre">PourbaixEntry.normalized_energy_at_conditions()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.pourbaix_diagram.PourbaixEntry.npH"><code class="docutils literal notranslate"><span class="pre">PourbaixEntry.npH</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.pourbaix_diagram.PourbaixEntry.num_atoms"><code class="docutils literal notranslate"><span class="pre">PourbaixEntry.num_atoms</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.pourbaix_diagram.PourbaixEntry.to_pretty_string"><code class="docutils literal notranslate"><span class="pre">PourbaixEntry.to_pretty_string()</span></code></a></li>
</ul>
</li>
<li><a class="reference internal" href="#pymatgen.analysis.pourbaix_diagram.PourbaixPlotter"><code class="docutils literal notranslate"><span class="pre">PourbaixPlotter</span></code></a><ul>
<li><a class="reference internal" href="#pymatgen.analysis.pourbaix_diagram.PourbaixPlotter.domain_vertices"><code class="docutils literal notranslate"><span class="pre">PourbaixPlotter.domain_vertices()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.pourbaix_diagram.PourbaixPlotter.get_pourbaix_plot"><code class="docutils literal notranslate"><span class="pre">PourbaixPlotter.get_pourbaix_plot()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.pourbaix_diagram.PourbaixPlotter.plot_entry_stability"><code class="docutils literal notranslate"><span class="pre">PourbaixPlotter.plot_entry_stability()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.pourbaix_diagram.PourbaixPlotter.show"><code class="docutils literal notranslate"><span class="pre">PourbaixPlotter.show()</span></code></a></li>
</ul>
</li>
<li><a class="reference internal" href="#pymatgen.analysis.pourbaix_diagram.ion_or_solid_comp_object"><code class="docutils literal notranslate"><span class="pre">ion_or_solid_comp_object()</span></code></a></li>
</ul>
</li>
<li><a class="reference internal" href="#module-pymatgen.analysis.prototypes">pymatgen.analysis.prototypes module</a><ul>
<li><a class="reference internal" href="#pymatgen.analysis.prototypes.AflowPrototypeMatcher"><code class="docutils literal notranslate"><span class="pre">AflowPrototypeMatcher</span></code></a><ul>
<li><a class="reference internal" href="#pymatgen.analysis.prototypes.AflowPrototypeMatcher.get_prototypes"><code class="docutils literal notranslate"><span class="pre">AflowPrototypeMatcher.get_prototypes()</span></code></a></li>
</ul>
</li>
</ul>
</li>
<li><a class="reference internal" href="#module-pymatgen.analysis.quasiharmonic">pymatgen.analysis.quasiharmonic module</a><ul>
<li><a class="reference internal" href="#pymatgen.analysis.quasiharmonic.QuasiHarmonicDebyeApprox"><code class="docutils literal notranslate"><span class="pre">QuasiHarmonicDebyeApprox</span></code></a><ul>
<li><a class="reference internal" href="#pymatgen.analysis.quasiharmonic.QuasiHarmonicDebyeApprox.debye_integral"><code class="docutils literal notranslate"><span class="pre">QuasiHarmonicDebyeApprox.debye_integral()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.quasiharmonic.QuasiHarmonicDebyeApprox.debye_temperature"><code class="docutils literal notranslate"><span class="pre">QuasiHarmonicDebyeApprox.debye_temperature()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.quasiharmonic.QuasiHarmonicDebyeApprox.get_summary_dict"><code class="docutils literal notranslate"><span class="pre">QuasiHarmonicDebyeApprox.get_summary_dict()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.quasiharmonic.QuasiHarmonicDebyeApprox.gruneisen_parameter"><code class="docutils literal notranslate"><span class="pre">QuasiHarmonicDebyeApprox.gruneisen_parameter()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.quasiharmonic.QuasiHarmonicDebyeApprox.optimize_gibbs_free_energy"><code class="docutils literal notranslate"><span class="pre">QuasiHarmonicDebyeApprox.optimize_gibbs_free_energy()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.quasiharmonic.QuasiHarmonicDebyeApprox.optimizer"><code class="docutils literal notranslate"><span class="pre">QuasiHarmonicDebyeApprox.optimizer()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.quasiharmonic.QuasiHarmonicDebyeApprox.thermal_conductivity"><code class="docutils literal notranslate"><span class="pre">QuasiHarmonicDebyeApprox.thermal_conductivity()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.quasiharmonic.QuasiHarmonicDebyeApprox.vibrational_free_energy"><code class="docutils literal notranslate"><span class="pre">QuasiHarmonicDebyeApprox.vibrational_free_energy()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.quasiharmonic.QuasiHarmonicDebyeApprox.vibrational_internal_energy"><code class="docutils literal notranslate"><span class="pre">QuasiHarmonicDebyeApprox.vibrational_internal_energy()</span></code></a></li>
</ul>
</li>
<li><a class="reference internal" href="#pymatgen.analysis.quasiharmonic.QuasiharmonicDebyeApprox"><code class="docutils literal notranslate"><span class="pre">QuasiharmonicDebyeApprox</span></code></a></li>
</ul>
</li>
<li><a class="reference internal" href="#module-pymatgen.analysis.quasirrho">pymatgen.analysis.quasirrho module</a><ul>
<li><a class="reference internal" href="#pymatgen.analysis.quasirrho.QuasiRRHO"><code class="docutils literal notranslate"><span class="pre">QuasiRRHO</span></code></a><ul>
<li><a class="reference internal" href="#pymatgen.analysis.quasirrho.QuasiRRHO.temp"><code class="docutils literal notranslate"><span class="pre">QuasiRRHO.temp</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.quasirrho.QuasiRRHO.press"><code class="docutils literal notranslate"><span class="pre">QuasiRRHO.press</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.quasirrho.QuasiRRHO.v0"><code class="docutils literal notranslate"><span class="pre">QuasiRRHO.v0</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.quasirrho.QuasiRRHO.entropy_quasiRRHO"><code class="docutils literal notranslate"><span class="pre">QuasiRRHO.entropy_quasiRRHO</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.quasirrho.QuasiRRHO.entropy_ho"><code class="docutils literal notranslate"><span class="pre">QuasiRRHO.entropy_ho</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.quasirrho.QuasiRRHO.h_corrected"><code class="docutils literal notranslate"><span class="pre">QuasiRRHO.h_corrected</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.quasirrho.QuasiRRHO.free_energy_quasiRRHO"><code class="docutils literal notranslate"><span class="pre">QuasiRRHO.free_energy_quasiRRHO</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.quasirrho.QuasiRRHO.free_energy_ho"><code class="docutils literal notranslate"><span class="pre">QuasiRRHO.free_energy_ho</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.quasirrho.QuasiRRHO.from_gaussian_output"><code class="docutils literal notranslate"><span class="pre">QuasiRRHO.from_gaussian_output()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.quasirrho.QuasiRRHO.from_qc_output"><code class="docutils literal notranslate"><span class="pre">QuasiRRHO.from_qc_output()</span></code></a></li>
</ul>
</li>
<li><a class="reference internal" href="#pymatgen.analysis.quasirrho.get_avg_mom_inertia"><code class="docutils literal notranslate"><span class="pre">get_avg_mom_inertia()</span></code></a></li>
</ul>
</li>
<li><a class="reference internal" href="#module-pymatgen.analysis.reaction_calculator">pymatgen.analysis.reaction_calculator module</a><ul>
<li><a class="reference internal" href="#pymatgen.analysis.reaction_calculator.BalancedReaction"><code class="docutils literal notranslate"><span class="pre">BalancedReaction</span></code></a><ul>
<li><a class="reference internal" href="#pymatgen.analysis.reaction_calculator.BalancedReaction.TOLERANCE"><code class="docutils literal notranslate"><span class="pre">BalancedReaction.TOLERANCE</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.reaction_calculator.BalancedReaction.all_comp"><code class="docutils literal notranslate"><span class="pre">BalancedReaction.all_comp</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.reaction_calculator.BalancedReaction.as_dict"><code class="docutils literal notranslate"><span class="pre">BalancedReaction.as_dict()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.reaction_calculator.BalancedReaction.as_entry"><code class="docutils literal notranslate"><span class="pre">BalancedReaction.as_entry()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.reaction_calculator.BalancedReaction.calculate_energy"><code class="docutils literal notranslate"><span class="pre">BalancedReaction.calculate_energy()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.reaction_calculator.BalancedReaction.coeffs"><code class="docutils literal notranslate"><span class="pre">BalancedReaction.coeffs</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.reaction_calculator.BalancedReaction.elements"><code class="docutils literal notranslate"><span class="pre">BalancedReaction.elements</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.reaction_calculator.BalancedReaction.from_dict"><code class="docutils literal notranslate"><span class="pre">BalancedReaction.from_dict()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.reaction_calculator.BalancedReaction.from_str"><code class="docutils literal notranslate"><span class="pre">BalancedReaction.from_str()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.reaction_calculator.BalancedReaction.get_coeff"><code class="docutils literal notranslate"><span class="pre">BalancedReaction.get_coeff()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.reaction_calculator.BalancedReaction.get_el_amount"><code class="docutils literal notranslate"><span class="pre">BalancedReaction.get_el_amount()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.reaction_calculator.BalancedReaction.normalize_to"><code class="docutils literal notranslate"><span class="pre">BalancedReaction.normalize_to()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.reaction_calculator.BalancedReaction.normalize_to_element"><code class="docutils literal notranslate"><span class="pre">BalancedReaction.normalize_to_element()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.reaction_calculator.BalancedReaction.normalized_repr"><code class="docutils literal notranslate"><span class="pre">BalancedReaction.normalized_repr</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.reaction_calculator.BalancedReaction.normalized_repr_and_factor"><code class="docutils literal notranslate"><span class="pre">BalancedReaction.normalized_repr_and_factor()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.reaction_calculator.BalancedReaction.products"><code class="docutils literal notranslate"><span class="pre">BalancedReaction.products</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.reaction_calculator.BalancedReaction.reactants"><code class="docutils literal notranslate"><span class="pre">BalancedReaction.reactants</span></code></a></li>
</ul>
</li>
<li><a class="reference internal" href="#pymatgen.analysis.reaction_calculator.ComputedReaction"><code class="docutils literal notranslate"><span class="pre">ComputedReaction</span></code></a><ul>
<li><a class="reference internal" href="#pymatgen.analysis.reaction_calculator.ComputedReaction.all_entries"><code class="docutils literal notranslate"><span class="pre">ComputedReaction.all_entries</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.reaction_calculator.ComputedReaction.as_dict"><code class="docutils literal notranslate"><span class="pre">ComputedReaction.as_dict()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.reaction_calculator.ComputedReaction.calculated_reaction_energy"><code class="docutils literal notranslate"><span class="pre">ComputedReaction.calculated_reaction_energy</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.reaction_calculator.ComputedReaction.calculated_reaction_energy_uncertainty"><code class="docutils literal notranslate"><span class="pre">ComputedReaction.calculated_reaction_energy_uncertainty</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.reaction_calculator.ComputedReaction.from_dict"><code class="docutils literal notranslate"><span class="pre">ComputedReaction.from_dict()</span></code></a></li>
</ul>
</li>
<li><a class="reference internal" href="#pymatgen.analysis.reaction_calculator.Reaction"><code class="docutils literal notranslate"><span class="pre">Reaction</span></code></a><ul>
<li><a class="reference internal" href="#pymatgen.analysis.reaction_calculator.Reaction.as_dict"><code class="docutils literal notranslate"><span class="pre">Reaction.as_dict()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.reaction_calculator.Reaction.copy"><code class="docutils literal notranslate"><span class="pre">Reaction.copy()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.reaction_calculator.Reaction.from_dict"><code class="docutils literal notranslate"><span class="pre">Reaction.from_dict()</span></code></a></li>
</ul>
</li>
<li><a class="reference internal" href="#pymatgen.analysis.reaction_calculator.ReactionError"><code class="docutils literal notranslate"><span class="pre">ReactionError</span></code></a></li>
</ul>
</li>
<li><a class="reference internal" href="#module-pymatgen.analysis.structure_analyzer">pymatgen.analysis.structure_analyzer module</a><ul>
<li><a class="reference internal" href="#pymatgen.analysis.structure_analyzer.OxideType"><code class="docutils literal notranslate"><span class="pre">OxideType</span></code></a><ul>
<li><a class="reference internal" href="#pymatgen.analysis.structure_analyzer.OxideType.parse_oxide"><code class="docutils literal notranslate"><span class="pre">OxideType.parse_oxide()</span></code></a></li>
</ul>
</li>
<li><a class="reference internal" href="#pymatgen.analysis.structure_analyzer.RelaxationAnalyzer"><code class="docutils literal notranslate"><span class="pre">RelaxationAnalyzer</span></code></a><ul>
<li><a class="reference internal" href="#pymatgen.analysis.structure_analyzer.RelaxationAnalyzer.get_percentage_bond_dist_changes"><code class="docutils literal notranslate"><span class="pre">RelaxationAnalyzer.get_percentage_bond_dist_changes()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.structure_analyzer.RelaxationAnalyzer.get_percentage_lattice_parameter_changes"><code class="docutils literal notranslate"><span class="pre">RelaxationAnalyzer.get_percentage_lattice_parameter_changes()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.structure_analyzer.RelaxationAnalyzer.get_percentage_volume_change"><code class="docutils literal notranslate"><span class="pre">RelaxationAnalyzer.get_percentage_volume_change()</span></code></a></li>
</ul>
</li>
<li><a class="reference internal" href="#pymatgen.analysis.structure_analyzer.VoronoiAnalyzer"><code class="docutils literal notranslate"><span class="pre">VoronoiAnalyzer</span></code></a><ul>
<li><a class="reference internal" href="#pymatgen.analysis.structure_analyzer.VoronoiAnalyzer.analyze"><code class="docutils literal notranslate"><span class="pre">VoronoiAnalyzer.analyze()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.structure_analyzer.VoronoiAnalyzer.analyze_structures"><code class="docutils literal notranslate"><span class="pre">VoronoiAnalyzer.analyze_structures()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.structure_analyzer.VoronoiAnalyzer.plot_vor_analysis"><code class="docutils literal notranslate"><span class="pre">VoronoiAnalyzer.plot_vor_analysis()</span></code></a></li>
</ul>
</li>
<li><a class="reference internal" href="#pymatgen.analysis.structure_analyzer.VoronoiConnectivity"><code class="docutils literal notranslate"><span class="pre">VoronoiConnectivity</span></code></a><ul>
<li><a class="reference internal" href="#pymatgen.analysis.structure_analyzer.VoronoiConnectivity.connectivity_array"><code class="docutils literal notranslate"><span class="pre">VoronoiConnectivity.connectivity_array</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.structure_analyzer.VoronoiConnectivity.get_connections"><code class="docutils literal notranslate"><span class="pre">VoronoiConnectivity.get_connections()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.structure_analyzer.VoronoiConnectivity.get_sitej"><code class="docutils literal notranslate"><span class="pre">VoronoiConnectivity.get_sitej()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.structure_analyzer.VoronoiConnectivity.max_connectivity"><code class="docutils literal notranslate"><span class="pre">VoronoiConnectivity.max_connectivity</span></code></a></li>
</ul>
</li>
<li><a class="reference internal" href="#pymatgen.analysis.structure_analyzer.average_coordination_number"><code class="docutils literal notranslate"><span class="pre">average_coordination_number()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.structure_analyzer.contains_peroxide"><code class="docutils literal notranslate"><span class="pre">contains_peroxide()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.structure_analyzer.get_max_bond_lengths"><code class="docutils literal notranslate"><span class="pre">get_max_bond_lengths()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.structure_analyzer.oxide_type"><code class="docutils literal notranslate"><span class="pre">oxide_type()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.structure_analyzer.solid_angle"><code class="docutils literal notranslate"><span class="pre">solid_angle()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.structure_analyzer.sulfide_type"><code class="docutils literal notranslate"><span class="pre">sulfide_type()</span></code></a></li>
</ul>
</li>
<li><a class="reference internal" href="#module-pymatgen.analysis.structure_matcher">pymatgen.analysis.structure_matcher module</a><ul>
<li><a class="reference internal" href="#pymatgen.analysis.structure_matcher.AbstractComparator"><code class="docutils literal notranslate"><span class="pre">AbstractComparator</span></code></a><ul>
<li><a class="reference internal" href="#pymatgen.analysis.structure_matcher.AbstractComparator.are_equal"><code class="docutils literal notranslate"><span class="pre">AbstractComparator.are_equal()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.structure_matcher.AbstractComparator.as_dict"><code class="docutils literal notranslate"><span class="pre">AbstractComparator.as_dict()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.structure_matcher.AbstractComparator.from_dict"><code class="docutils literal notranslate"><span class="pre">AbstractComparator.from_dict()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.structure_matcher.AbstractComparator.get_hash"><code class="docutils literal notranslate"><span class="pre">AbstractComparator.get_hash()</span></code></a></li>
</ul>
</li>
<li><a class="reference internal" href="#pymatgen.analysis.structure_matcher.ElementComparator"><code class="docutils literal notranslate"><span class="pre">ElementComparator</span></code></a><ul>
<li><a class="reference internal" href="#pymatgen.analysis.structure_matcher.ElementComparator.are_equal"><code class="docutils literal notranslate"><span class="pre">ElementComparator.are_equal()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.structure_matcher.ElementComparator.get_hash"><code class="docutils literal notranslate"><span class="pre">ElementComparator.get_hash()</span></code></a></li>
</ul>
</li>
<li><a class="reference internal" href="#pymatgen.analysis.structure_matcher.FrameworkComparator"><code class="docutils literal notranslate"><span class="pre">FrameworkComparator</span></code></a><ul>
<li><a class="reference internal" href="#pymatgen.analysis.structure_matcher.FrameworkComparator.are_equal"><code class="docutils literal notranslate"><span class="pre">FrameworkComparator.are_equal()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.structure_matcher.FrameworkComparator.get_hash"><code class="docutils literal notranslate"><span class="pre">FrameworkComparator.get_hash()</span></code></a></li>
</ul>
</li>
<li><a class="reference internal" href="#pymatgen.analysis.structure_matcher.OccupancyComparator"><code class="docutils literal notranslate"><span class="pre">OccupancyComparator</span></code></a><ul>
<li><a class="reference internal" href="#pymatgen.analysis.structure_matcher.OccupancyComparator.are_equal"><code class="docutils literal notranslate"><span class="pre">OccupancyComparator.are_equal()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.structure_matcher.OccupancyComparator.get_hash"><code class="docutils literal notranslate"><span class="pre">OccupancyComparator.get_hash()</span></code></a></li>
</ul>
</li>
<li><a class="reference internal" href="#pymatgen.analysis.structure_matcher.OrderDisorderElementComparator"><code class="docutils literal notranslate"><span class="pre">OrderDisorderElementComparator</span></code></a><ul>
<li><a class="reference internal" href="#pymatgen.analysis.structure_matcher.OrderDisorderElementComparator.are_equal"><code class="docutils literal notranslate"><span class="pre">OrderDisorderElementComparator.are_equal()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.structure_matcher.OrderDisorderElementComparator.get_hash"><code class="docutils literal notranslate"><span class="pre">OrderDisorderElementComparator.get_hash()</span></code></a></li>
</ul>
</li>
<li><a class="reference internal" href="#pymatgen.analysis.structure_matcher.SiteOrderedIStructure"><code class="docutils literal notranslate"><span class="pre">SiteOrderedIStructure</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.structure_matcher.SpeciesComparator"><code class="docutils literal notranslate"><span class="pre">SpeciesComparator</span></code></a><ul>
<li><a class="reference internal" href="#pymatgen.analysis.structure_matcher.SpeciesComparator.are_equal"><code class="docutils literal notranslate"><span class="pre">SpeciesComparator.are_equal()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.structure_matcher.SpeciesComparator.get_hash"><code class="docutils literal notranslate"><span class="pre">SpeciesComparator.get_hash()</span></code></a></li>
</ul>
</li>
<li><a class="reference internal" href="#pymatgen.analysis.structure_matcher.SpinComparator"><code class="docutils literal notranslate"><span class="pre">SpinComparator</span></code></a><ul>
<li><a class="reference internal" href="#pymatgen.analysis.structure_matcher.SpinComparator.are_equal"><code class="docutils literal notranslate"><span class="pre">SpinComparator.are_equal()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.structure_matcher.SpinComparator.get_hash"><code class="docutils literal notranslate"><span class="pre">SpinComparator.get_hash()</span></code></a></li>
</ul>
</li>
<li><a class="reference internal" href="#pymatgen.analysis.structure_matcher.StructureMatcher"><code class="docutils literal notranslate"><span class="pre">StructureMatcher</span></code></a><ul>
<li><a class="reference internal" href="#pymatgen.analysis.structure_matcher.StructureMatcher.as_dict"><code class="docutils literal notranslate"><span class="pre">StructureMatcher.as_dict()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.structure_matcher.StructureMatcher.fit"><code class="docutils literal notranslate"><span class="pre">StructureMatcher.fit()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.structure_matcher.StructureMatcher.fit_anonymous"><code class="docutils literal notranslate"><span class="pre">StructureMatcher.fit_anonymous()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.structure_matcher.StructureMatcher.from_dict"><code class="docutils literal notranslate"><span class="pre">StructureMatcher.from_dict()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.structure_matcher.StructureMatcher.get_all_anonymous_mappings"><code class="docutils literal notranslate"><span class="pre">StructureMatcher.get_all_anonymous_mappings()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.structure_matcher.StructureMatcher.get_best_electronegativity_anonymous_mapping"><code class="docutils literal notranslate"><span class="pre">StructureMatcher.get_best_electronegativity_anonymous_mapping()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.structure_matcher.StructureMatcher.get_mapping"><code class="docutils literal notranslate"><span class="pre">StructureMatcher.get_mapping()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.structure_matcher.StructureMatcher.get_rms_anonymous"><code class="docutils literal notranslate"><span class="pre">StructureMatcher.get_rms_anonymous()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.structure_matcher.StructureMatcher.get_rms_dist"><code class="docutils literal notranslate"><span class="pre">StructureMatcher.get_rms_dist()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.structure_matcher.StructureMatcher.get_s2_like_s1"><code class="docutils literal notranslate"><span class="pre">StructureMatcher.get_s2_like_s1()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.structure_matcher.StructureMatcher.get_supercell_matrix"><code class="docutils literal notranslate"><span class="pre">StructureMatcher.get_supercell_matrix()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.structure_matcher.StructureMatcher.get_transformation"><code class="docutils literal notranslate"><span class="pre">StructureMatcher.get_transformation()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.structure_matcher.StructureMatcher.group_structures"><code class="docutils literal notranslate"><span class="pre">StructureMatcher.group_structures()</span></code></a></li>
</ul>
</li>
</ul>
</li>
<li><a class="reference internal" href="#module-pymatgen.analysis.surface_analysis">pymatgen.analysis.surface_analysis module</a><ul>
<li><a class="reference internal" href="#pymatgen.analysis.surface_analysis.NanoscaleStability"><code class="docutils literal notranslate"><span class="pre">NanoscaleStability</span></code></a><ul>
<li><a class="reference internal" href="#pymatgen.analysis.surface_analysis.NanoscaleStability.se_analyzers"><code class="docutils literal notranslate"><span class="pre">NanoscaleStability.se_analyzers</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.surface_analysis.NanoscaleStability.symprec"><code class="docutils literal notranslate"><span class="pre">NanoscaleStability.symprec</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.surface_analysis.NanoscaleStability.bulk_gform"><code class="docutils literal notranslate"><span class="pre">NanoscaleStability.bulk_gform()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.surface_analysis.NanoscaleStability.plot_all_stability_map"><code class="docutils literal notranslate"><span class="pre">NanoscaleStability.plot_all_stability_map()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.surface_analysis.NanoscaleStability.plot_one_stability_map"><code class="docutils literal notranslate"><span class="pre">NanoscaleStability.plot_one_stability_map()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.surface_analysis.NanoscaleStability.scaled_wulff"><code class="docutils literal notranslate"><span class="pre">NanoscaleStability.scaled_wulff()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.surface_analysis.NanoscaleStability.solve_equilibrium_point"><code class="docutils literal notranslate"><span class="pre">NanoscaleStability.solve_equilibrium_point()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.surface_analysis.NanoscaleStability.wulff_gform_and_r"><code class="docutils literal notranslate"><span class="pre">NanoscaleStability.wulff_gform_and_r()</span></code></a></li>
</ul>
</li>
<li><a class="reference internal" href="#pymatgen.analysis.surface_analysis.SlabEntry"><code class="docutils literal notranslate"><span class="pre">SlabEntry</span></code></a><ul>
<li><a class="reference internal" href="#pymatgen.analysis.surface_analysis.SlabEntry.miller_index"><code class="docutils literal notranslate"><span class="pre">SlabEntry.miller_index</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.surface_analysis.SlabEntry.label"><code class="docutils literal notranslate"><span class="pre">SlabEntry.label</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.surface_analysis.SlabEntry.adsorbates"><code class="docutils literal notranslate"><span class="pre">SlabEntry.adsorbates</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.surface_analysis.SlabEntry.clean_entry"><code class="docutils literal notranslate"><span class="pre">SlabEntry.clean_entry</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.surface_analysis.SlabEntry.ads_entries_dict"><code class="docutils literal notranslate"><span class="pre">SlabEntry.ads_entries_dict</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.surface_analysis.SlabEntry.Nads_in_slab"><code class="docutils literal notranslate"><span class="pre">SlabEntry.Nads_in_slab</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.surface_analysis.SlabEntry.Nsurfs_ads_in_slab"><code class="docutils literal notranslate"><span class="pre">SlabEntry.Nsurfs_ads_in_slab</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.surface_analysis.SlabEntry.as_dict"><code class="docutils literal notranslate"><span class="pre">SlabEntry.as_dict()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.surface_analysis.SlabEntry.cleaned_up_slab"><code class="docutils literal notranslate"><span class="pre">SlabEntry.cleaned_up_slab</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.surface_analysis.SlabEntry.create_slab_label"><code class="docutils literal notranslate"><span class="pre">SlabEntry.create_slab_label</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.surface_analysis.SlabEntry.from_computed_structure_entry"><code class="docutils literal notranslate"><span class="pre">SlabEntry.from_computed_structure_entry()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.surface_analysis.SlabEntry.from_dict"><code class="docutils literal notranslate"><span class="pre">SlabEntry.from_dict()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.surface_analysis.SlabEntry.get_monolayer"><code class="docutils literal notranslate"><span class="pre">SlabEntry.get_monolayer</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.surface_analysis.SlabEntry.get_unit_primitive_area"><code class="docutils literal notranslate"><span class="pre">SlabEntry.get_unit_primitive_area</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.surface_analysis.SlabEntry.gibbs_binding_energy"><code class="docutils literal notranslate"><span class="pre">SlabEntry.gibbs_binding_energy()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.surface_analysis.SlabEntry.surface_area"><code class="docutils literal notranslate"><span class="pre">SlabEntry.surface_area</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.surface_analysis.SlabEntry.surface_energy"><code class="docutils literal notranslate"><span class="pre">SlabEntry.surface_energy()</span></code></a></li>
</ul>
</li>
<li><a class="reference internal" href="#pymatgen.analysis.surface_analysis.SurfaceEnergyPlotter"><code class="docutils literal notranslate"><span class="pre">SurfaceEnergyPlotter</span></code></a><ul>
<li><a class="reference internal" href="#pymatgen.analysis.surface_analysis.SurfaceEnergyPlotter.all_slab_entries"><code class="docutils literal notranslate"><span class="pre">SurfaceEnergyPlotter.all_slab_entries</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.surface_analysis.SurfaceEnergyPlotter.color_dict"><code class="docutils literal notranslate"><span class="pre">SurfaceEnergyPlotter.color_dict</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.surface_analysis.SurfaceEnergyPlotter.ucell_entry"><code class="docutils literal notranslate"><span class="pre">SurfaceEnergyPlotter.ucell_entry</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.surface_analysis.SurfaceEnergyPlotter.ref_entries"><code class="docutils literal notranslate"><span class="pre">SurfaceEnergyPlotter.ref_entries</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.surface_analysis.SurfaceEnergyPlotter.facet_color_dict"><code class="docutils literal notranslate"><span class="pre">SurfaceEnergyPlotter.facet_color_dict</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.surface_analysis.SurfaceEnergyPlotter.BE_vs_clean_SE"><code class="docutils literal notranslate"><span class="pre">SurfaceEnergyPlotter.BE_vs_clean_SE()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.surface_analysis.SurfaceEnergyPlotter.area_frac_vs_chempot_plot"><code class="docutils literal notranslate"><span class="pre">SurfaceEnergyPlotter.area_frac_vs_chempot_plot()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.surface_analysis.SurfaceEnergyPlotter.chempot_plot_addons"><code class="docutils literal notranslate"><span class="pre">SurfaceEnergyPlotter.chempot_plot_addons()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.surface_analysis.SurfaceEnergyPlotter.chempot_vs_gamma"><code class="docutils literal notranslate"><span class="pre">SurfaceEnergyPlotter.chempot_vs_gamma()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.surface_analysis.SurfaceEnergyPlotter.chempot_vs_gamma_plot_one"><code class="docutils literal notranslate"><span class="pre">SurfaceEnergyPlotter.chempot_vs_gamma_plot_one()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.surface_analysis.SurfaceEnergyPlotter.color_palette_dict"><code class="docutils literal notranslate"><span class="pre">SurfaceEnergyPlotter.color_palette_dict()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.surface_analysis.SurfaceEnergyPlotter.get_stable_entry_at_u"><code class="docutils literal notranslate"><span class="pre">SurfaceEnergyPlotter.get_stable_entry_at_u()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.surface_analysis.SurfaceEnergyPlotter.get_surface_equilibrium"><code class="docutils literal notranslate"><span class="pre">SurfaceEnergyPlotter.get_surface_equilibrium()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.surface_analysis.SurfaceEnergyPlotter.monolayer_vs_BE"><code class="docutils literal notranslate"><span class="pre">SurfaceEnergyPlotter.monolayer_vs_BE()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.surface_analysis.SurfaceEnergyPlotter.set_all_variables"><code class="docutils literal notranslate"><span class="pre">SurfaceEnergyPlotter.set_all_variables()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.surface_analysis.SurfaceEnergyPlotter.stable_u_range_dict"><code class="docutils literal notranslate"><span class="pre">SurfaceEnergyPlotter.stable_u_range_dict()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.surface_analysis.SurfaceEnergyPlotter.surface_chempot_range_map"><code class="docutils literal notranslate"><span class="pre">SurfaceEnergyPlotter.surface_chempot_range_map()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.surface_analysis.SurfaceEnergyPlotter.wulff_from_chempot"><code class="docutils literal notranslate"><span class="pre">SurfaceEnergyPlotter.wulff_from_chempot()</span></code></a></li>
</ul>
</li>
<li><a class="reference internal" href="#pymatgen.analysis.surface_analysis.WorkFunctionAnalyzer"><code class="docutils literal notranslate"><span class="pre">WorkFunctionAnalyzer</span></code></a><ul>
<li><a class="reference internal" href="#pymatgen.analysis.surface_analysis.WorkFunctionAnalyzer.efermi"><code class="docutils literal notranslate"><span class="pre">WorkFunctionAnalyzer.efermi</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.surface_analysis.WorkFunctionAnalyzer.locpot_along_c"><code class="docutils literal notranslate"><span class="pre">WorkFunctionAnalyzer.locpot_along_c</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.surface_analysis.WorkFunctionAnalyzer.vacuum_locpot"><code class="docutils literal notranslate"><span class="pre">WorkFunctionAnalyzer.vacuum_locpot</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.surface_analysis.WorkFunctionAnalyzer.work_function"><code class="docutils literal notranslate"><span class="pre">WorkFunctionAnalyzer.work_function</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.surface_analysis.WorkFunctionAnalyzer.slab"><code class="docutils literal notranslate"><span class="pre">WorkFunctionAnalyzer.slab</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.surface_analysis.WorkFunctionAnalyzer.along_c"><code class="docutils literal notranslate"><span class="pre">WorkFunctionAnalyzer.along_c</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.surface_analysis.WorkFunctionAnalyzer.ave_locpot"><code class="docutils literal notranslate"><span class="pre">WorkFunctionAnalyzer.ave_locpot</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.surface_analysis.WorkFunctionAnalyzer.sorted_sites"><code class="docutils literal notranslate"><span class="pre">WorkFunctionAnalyzer.sorted_sites</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.surface_analysis.WorkFunctionAnalyzer.ave_bulk_p"><code class="docutils literal notranslate"><span class="pre">WorkFunctionAnalyzer.ave_bulk_p</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.surface_analysis.WorkFunctionAnalyzer.from_files"><code class="docutils literal notranslate"><span class="pre">WorkFunctionAnalyzer.from_files()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.surface_analysis.WorkFunctionAnalyzer.get_labels"><code class="docutils literal notranslate"><span class="pre">WorkFunctionAnalyzer.get_labels()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.surface_analysis.WorkFunctionAnalyzer.get_locpot_along_slab_plot"><code class="docutils literal notranslate"><span class="pre">WorkFunctionAnalyzer.get_locpot_along_slab_plot()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.surface_analysis.WorkFunctionAnalyzer.is_converged"><code class="docutils literal notranslate"><span class="pre">WorkFunctionAnalyzer.is_converged()</span></code></a></li>
</ul>
</li>
<li><a class="reference internal" href="#pymatgen.analysis.surface_analysis.entry_dict_from_list"><code class="docutils literal notranslate"><span class="pre">entry_dict_from_list()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.surface_analysis.sub_chempots"><code class="docutils literal notranslate"><span class="pre">sub_chempots()</span></code></a></li>
</ul>
</li>
<li><a class="reference internal" href="#module-pymatgen.analysis.thermochemistry">pymatgen.analysis.thermochemistry module</a><ul>
<li><a class="reference internal" href="#pymatgen.analysis.thermochemistry.ThermoData"><code class="docutils literal notranslate"><span class="pre">ThermoData</span></code></a><ul>
<li><a class="reference internal" href="#pymatgen.analysis.thermochemistry.ThermoData.as_dict"><code class="docutils literal notranslate"><span class="pre">ThermoData.as_dict()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.thermochemistry.ThermoData.from_dict"><code class="docutils literal notranslate"><span class="pre">ThermoData.from_dict()</span></code></a></li>
</ul>
</li>
</ul>
</li>
<li><a class="reference internal" href="#module-pymatgen.analysis.transition_state">pymatgen.analysis.transition_state module</a><ul>
<li><a class="reference internal" href="#pymatgen.analysis.transition_state.NEBAnalysis"><code class="docutils literal notranslate"><span class="pre">NEBAnalysis</span></code></a><ul>
<li><a class="reference internal" href="#pymatgen.analysis.transition_state.NEBAnalysis.as_dict"><code class="docutils literal notranslate"><span class="pre">NEBAnalysis.as_dict()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.transition_state.NEBAnalysis.from_dir"><code class="docutils literal notranslate"><span class="pre">NEBAnalysis.from_dir()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.transition_state.NEBAnalysis.from_outcars"><code class="docutils literal notranslate"><span class="pre">NEBAnalysis.from_outcars()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.transition_state.NEBAnalysis.get_extrema"><code class="docutils literal notranslate"><span class="pre">NEBAnalysis.get_extrema()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.transition_state.NEBAnalysis.get_plot"><code class="docutils literal notranslate"><span class="pre">NEBAnalysis.get_plot()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.transition_state.NEBAnalysis.setup_spline"><code class="docutils literal notranslate"><span class="pre">NEBAnalysis.setup_spline()</span></code></a></li>
</ul>
</li>
<li><a class="reference internal" href="#pymatgen.analysis.transition_state.combine_neb_plots"><code class="docutils literal notranslate"><span class="pre">combine_neb_plots()</span></code></a></li>
</ul>
</li>
<li><a class="reference internal" href="#module-pymatgen.analysis.wulff">pymatgen.analysis.wulff module</a><ul>
<li><a class="reference internal" href="#pymatgen.analysis.wulff.WulffFacet"><code class="docutils literal notranslate"><span class="pre">WulffFacet</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.wulff.WulffShape"><code class="docutils literal notranslate"><span class="pre">WulffShape</span></code></a><ul>
<li><a class="reference internal" href="#pymatgen.analysis.wulff.WulffShape.debug"><code class="docutils literal notranslate"><span class="pre">WulffShape.debug</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.wulff.WulffShape.alpha"><code class="docutils literal notranslate"><span class="pre">WulffShape.alpha</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.wulff.WulffShape.color_set"><code class="docutils literal notranslate"><span class="pre">WulffShape.color_set</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.wulff.WulffShape.grid_off"><code class="docutils literal notranslate"><span class="pre">WulffShape.grid_off</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.wulff.WulffShape.axis_off"><code class="docutils literal notranslate"><span class="pre">WulffShape.axis_off</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.wulff.WulffShape.show_area"><code class="docutils literal notranslate"><span class="pre">WulffShape.show_area</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.wulff.WulffShape.off_color"><code class="docutils literal notranslate"><span class="pre">WulffShape.off_color</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.wulff.WulffShape.structure"><code class="docutils literal notranslate"><span class="pre">WulffShape.structure</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.wulff.WulffShape.miller_list"><code class="docutils literal notranslate"><span class="pre">WulffShape.miller_list</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.wulff.WulffShape.hkl_list"><code class="docutils literal notranslate"><span class="pre">WulffShape.hkl_list</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.wulff.WulffShape.e_surf_list"><code class="docutils literal notranslate"><span class="pre">WulffShape.e_surf_list</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.wulff.WulffShape.lattice"><code class="docutils literal notranslate"><span class="pre">WulffShape.lattice</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.wulff.WulffShape.facets"><code class="docutils literal notranslate"><span class="pre">WulffShape.facets</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.wulff.WulffShape.dual_cv_simp"><code class="docutils literal notranslate"><span class="pre">WulffShape.dual_cv_simp</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.wulff.WulffShape.wulff_pt_list"><code class="docutils literal notranslate"><span class="pre">WulffShape.wulff_pt_list</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.wulff.WulffShape.wulff_cv_simp"><code class="docutils literal notranslate"><span class="pre">WulffShape.wulff_cv_simp</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.wulff.WulffShape.on_wulff"><code class="docutils literal notranslate"><span class="pre">WulffShape.on_wulff</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.wulff.WulffShape.color_area"><code class="docutils literal notranslate"><span class="pre">WulffShape.color_area</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.wulff.WulffShape.miller_area"><code class="docutils literal notranslate"><span class="pre">WulffShape.miller_area</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.wulff.WulffShape.anisotropy"><code class="docutils literal notranslate"><span class="pre">WulffShape.anisotropy</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.wulff.WulffShape.area_fraction_dict"><code class="docutils literal notranslate"><span class="pre">WulffShape.area_fraction_dict</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.wulff.WulffShape.effective_radius"><code class="docutils literal notranslate"><span class="pre">WulffShape.effective_radius</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.wulff.WulffShape.get_line_in_facet"><code class="docutils literal notranslate"><span class="pre">WulffShape.get_line_in_facet()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.wulff.WulffShape.get_plot"><code class="docutils literal notranslate"><span class="pre">WulffShape.get_plot()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.wulff.WulffShape.get_plotly"><code class="docutils literal notranslate"><span class="pre">WulffShape.get_plotly()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.wulff.WulffShape.miller_area_dict"><code class="docutils literal notranslate"><span class="pre">WulffShape.miller_area_dict</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.wulff.WulffShape.miller_energy_dict"><code class="docutils literal notranslate"><span class="pre">WulffShape.miller_energy_dict</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.wulff.WulffShape.shape_factor"><code class="docutils literal notranslate"><span class="pre">WulffShape.shape_factor</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.wulff.WulffShape.show"><code class="docutils literal notranslate"><span class="pre">WulffShape.show()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.wulff.WulffShape.surface_area"><code class="docutils literal notranslate"><span class="pre">WulffShape.surface_area</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.wulff.WulffShape.tot_corner_sites"><code class="docutils literal notranslate"><span class="pre">WulffShape.tot_corner_sites</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.wulff.WulffShape.tot_edges"><code class="docutils literal notranslate"><span class="pre">WulffShape.tot_edges</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.wulff.WulffShape.total_surface_energy"><code class="docutils literal notranslate"><span class="pre">WulffShape.total_surface_energy</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.wulff.WulffShape.volume"><code class="docutils literal notranslate"><span class="pre">WulffShape.volume</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.wulff.WulffShape.weighted_surface_energy"><code class="docutils literal notranslate"><span class="pre">WulffShape.weighted_surface_energy</span></code></a></li>
</ul>
</li>
<li><a class="reference internal" href="#pymatgen.analysis.wulff.get_tri_area"><code class="docutils literal notranslate"><span class="pre">get_tri_area()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.wulff.hkl_tuple_to_str"><code class="docutils literal notranslate"><span class="pre">hkl_tuple_to_str()</span></code></a></li>
</ul>
</li>
<li><a class="reference internal" href="#module-pymatgen.analysis.xps">pymatgen.analysis.xps module</a><ul>
<li><a class="reference internal" href="#pymatgen.analysis.xps.XPS"><code class="docutils literal notranslate"><span class="pre">XPS</span></code></a><ul>
<li><a class="reference internal" href="#pymatgen.analysis.xps.XPS.XLABEL"><code class="docutils literal notranslate"><span class="pre">XPS.XLABEL</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.xps.XPS.YLABEL"><code class="docutils literal notranslate"><span class="pre">XPS.YLABEL</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.xps.XPS.from_dos"><code class="docutils literal notranslate"><span class="pre">XPS.from_dos()</span></code></a></li>
</ul>
</li>
</ul>
</li>
</ul>
</li>
</ul>
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<section id="module-pymatgen.analysis">
<span id="pymatgen-analysis-namespace"></span><h1>pymatgen.analysis namespace<a class="headerlink" href="#module-pymatgen.analysis" title="Link to this heading"></a></h1>
<section id="subpackages">
<h2>Subpackages<a class="headerlink" href="#subpackages" title="Link to this heading"></a></h2>
<div class="toctree-wrapper compound">
<ul>
<li class="toctree-l1"><a class="reference internal" href="pymatgen.analysis.chemenv.html">pymatgen.analysis.chemenv package</a><ul>
<li class="toctree-l2"><a class="reference internal" href="pymatgen.analysis.chemenv.html#subpackages">Subpackages</a><ul>
<li class="toctree-l3"><a class="reference internal" href="pymatgen.analysis.chemenv.connectivity.html">pymatgen.analysis.chemenv.connectivity package</a><ul>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.chemenv.connectivity.html#submodules">Submodules</a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.chemenv.connectivity.html#module-pymatgen.analysis.chemenv.connectivity.connected_components">pymatgen.analysis.chemenv.connectivity.connected_components module</a><ul>
<li class="toctree-l5"><a class="reference internal" href="pymatgen.analysis.chemenv.connectivity.html#pymatgen.analysis.chemenv.connectivity.connected_components.ConnectedComponent"><code class="docutils literal notranslate"><span class="pre">ConnectedComponent</span></code></a><ul>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.connectivity.html#pymatgen.analysis.chemenv.connectivity.connected_components.ConnectedComponent.as_dict"><code class="docutils literal notranslate"><span class="pre">ConnectedComponent.as_dict()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.connectivity.html#pymatgen.analysis.chemenv.connectivity.connected_components.ConnectedComponent.compute_periodicity"><code class="docutils literal notranslate"><span class="pre">ConnectedComponent.compute_periodicity()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.connectivity.html#pymatgen.analysis.chemenv.connectivity.connected_components.ConnectedComponent.compute_periodicity_all_simple_paths_algorithm"><code class="docutils literal notranslate"><span class="pre">ConnectedComponent.compute_periodicity_all_simple_paths_algorithm()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.connectivity.html#pymatgen.analysis.chemenv.connectivity.connected_components.ConnectedComponent.compute_periodicity_cycle_basis"><code class="docutils literal notranslate"><span class="pre">ConnectedComponent.compute_periodicity_cycle_basis()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.connectivity.html#pymatgen.analysis.chemenv.connectivity.connected_components.ConnectedComponent.coordination_sequence"><code class="docutils literal notranslate"><span class="pre">ConnectedComponent.coordination_sequence()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.connectivity.html#pymatgen.analysis.chemenv.connectivity.connected_components.ConnectedComponent.description"><code class="docutils literal notranslate"><span class="pre">ConnectedComponent.description()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.connectivity.html#pymatgen.analysis.chemenv.connectivity.connected_components.ConnectedComponent.elastic_centered_graph"><code class="docutils literal notranslate"><span class="pre">ConnectedComponent.elastic_centered_graph()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.connectivity.html#pymatgen.analysis.chemenv.connectivity.connected_components.ConnectedComponent.from_dict"><code class="docutils literal notranslate"><span class="pre">ConnectedComponent.from_dict()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.connectivity.html#pymatgen.analysis.chemenv.connectivity.connected_components.ConnectedComponent.from_graph"><code class="docutils literal notranslate"><span class="pre">ConnectedComponent.from_graph()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.connectivity.html#pymatgen.analysis.chemenv.connectivity.connected_components.ConnectedComponent.graph"><code class="docutils literal notranslate"><span class="pre">ConnectedComponent.graph</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.connectivity.html#pymatgen.analysis.chemenv.connectivity.connected_components.ConnectedComponent.is_0d"><code class="docutils literal notranslate"><span class="pre">ConnectedComponent.is_0d</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.connectivity.html#pymatgen.analysis.chemenv.connectivity.connected_components.ConnectedComponent.is_1d"><code class="docutils literal notranslate"><span class="pre">ConnectedComponent.is_1d</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.connectivity.html#pymatgen.analysis.chemenv.connectivity.connected_components.ConnectedComponent.is_2d"><code class="docutils literal notranslate"><span class="pre">ConnectedComponent.is_2d</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.connectivity.html#pymatgen.analysis.chemenv.connectivity.connected_components.ConnectedComponent.is_3d"><code class="docutils literal notranslate"><span class="pre">ConnectedComponent.is_3d</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.connectivity.html#pymatgen.analysis.chemenv.connectivity.connected_components.ConnectedComponent.is_periodic"><code class="docutils literal notranslate"><span class="pre">ConnectedComponent.is_periodic</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.connectivity.html#pymatgen.analysis.chemenv.connectivity.connected_components.ConnectedComponent.make_supergraph"><code class="docutils literal notranslate"><span class="pre">ConnectedComponent.make_supergraph()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.connectivity.html#pymatgen.analysis.chemenv.connectivity.connected_components.ConnectedComponent.periodicity"><code class="docutils literal notranslate"><span class="pre">ConnectedComponent.periodicity</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.connectivity.html#pymatgen.analysis.chemenv.connectivity.connected_components.ConnectedComponent.periodicity_vectors"><code class="docutils literal notranslate"><span class="pre">ConnectedComponent.periodicity_vectors</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.connectivity.html#pymatgen.analysis.chemenv.connectivity.connected_components.ConnectedComponent.show_graph"><code class="docutils literal notranslate"><span class="pre">ConnectedComponent.show_graph()</span></code></a></li>
</ul>
</li>
<li class="toctree-l5"><a class="reference internal" href="pymatgen.analysis.chemenv.connectivity.html#pymatgen.analysis.chemenv.connectivity.connected_components.draw_network"><code class="docutils literal notranslate"><span class="pre">draw_network()</span></code></a></li>
<li class="toctree-l5"><a class="reference internal" href="pymatgen.analysis.chemenv.connectivity.html#pymatgen.analysis.chemenv.connectivity.connected_components.make_supergraph"><code class="docutils literal notranslate"><span class="pre">make_supergraph()</span></code></a></li>
</ul>
</li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.chemenv.connectivity.html#module-pymatgen.analysis.chemenv.connectivity.connectivity_finder">pymatgen.analysis.chemenv.connectivity.connectivity_finder module</a><ul>
<li class="toctree-l5"><a class="reference internal" href="pymatgen.analysis.chemenv.connectivity.html#pymatgen.analysis.chemenv.connectivity.connectivity_finder.ConnectivityFinder"><code class="docutils literal notranslate"><span class="pre">ConnectivityFinder</span></code></a><ul>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.connectivity.html#pymatgen.analysis.chemenv.connectivity.connectivity_finder.ConnectivityFinder.get_structure_connectivity"><code class="docutils literal notranslate"><span class="pre">ConnectivityFinder.get_structure_connectivity()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.connectivity.html#pymatgen.analysis.chemenv.connectivity.connectivity_finder.ConnectivityFinder.setup_parameters"><code class="docutils literal notranslate"><span class="pre">ConnectivityFinder.setup_parameters()</span></code></a></li>
</ul>
</li>
</ul>
</li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.chemenv.connectivity.html#module-pymatgen.analysis.chemenv.connectivity.environment_nodes">pymatgen.analysis.chemenv.connectivity.environment_nodes module</a><ul>
<li class="toctree-l5"><a class="reference internal" href="pymatgen.analysis.chemenv.connectivity.html#pymatgen.analysis.chemenv.connectivity.environment_nodes.AbstractEnvironmentNode"><code class="docutils literal notranslate"><span class="pre">AbstractEnvironmentNode</span></code></a><ul>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.connectivity.html#pymatgen.analysis.chemenv.connectivity.environment_nodes.AbstractEnvironmentNode.ATOM"><code class="docutils literal notranslate"><span class="pre">AbstractEnvironmentNode.ATOM</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.connectivity.html#pymatgen.analysis.chemenv.connectivity.environment_nodes.AbstractEnvironmentNode.CE_NNBCES_NBCES_LIGANDS"><code class="docutils literal notranslate"><span class="pre">AbstractEnvironmentNode.CE_NNBCES_NBCES_LIGANDS</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.connectivity.html#pymatgen.analysis.chemenv.connectivity.environment_nodes.AbstractEnvironmentNode.COORDINATION_ENVIRONMENT"><code class="docutils literal notranslate"><span class="pre">AbstractEnvironmentNode.COORDINATION_ENVIRONMENT</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.connectivity.html#pymatgen.analysis.chemenv.connectivity.environment_nodes.AbstractEnvironmentNode.DEFAULT_EXTENSIONS"><code class="docutils literal notranslate"><span class="pre">AbstractEnvironmentNode.DEFAULT_EXTENSIONS</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.connectivity.html#pymatgen.analysis.chemenv.connectivity.environment_nodes.AbstractEnvironmentNode.LIGANDS_ARRANGEMENT"><code class="docutils literal notranslate"><span class="pre">AbstractEnvironmentNode.LIGANDS_ARRANGEMENT</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.connectivity.html#pymatgen.analysis.chemenv.connectivity.environment_nodes.AbstractEnvironmentNode.NEIGHBORING_CES"><code class="docutils literal notranslate"><span class="pre">AbstractEnvironmentNode.NEIGHBORING_CES</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.connectivity.html#pymatgen.analysis.chemenv.connectivity.environment_nodes.AbstractEnvironmentNode.NEIGHBORING_COORDINATION_ENVIRONMENTS"><code class="docutils literal notranslate"><span class="pre">AbstractEnvironmentNode.NEIGHBORING_COORDINATION_ENVIRONMENTS</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.connectivity.html#pymatgen.analysis.chemenv.connectivity.environment_nodes.AbstractEnvironmentNode.NEIGHBORS_LIGANDS_ARRANGEMENT"><code class="docutils literal notranslate"><span class="pre">AbstractEnvironmentNode.NEIGHBORS_LIGANDS_ARRANGEMENT</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.connectivity.html#pymatgen.analysis.chemenv.connectivity.environment_nodes.AbstractEnvironmentNode.NUMBER_OF_LIGANDS_FOR_EACH_NEIGHBORING_CE"><code class="docutils literal notranslate"><span class="pre">AbstractEnvironmentNode.NUMBER_OF_LIGANDS_FOR_EACH_NEIGHBORING_CE</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.connectivity.html#pymatgen.analysis.chemenv.connectivity.environment_nodes.AbstractEnvironmentNode.NUMBER_OF_LIGANDS_FOR_EACH_NEIGHBORING_COORDINATION_ENVIRONMENT"><code class="docutils literal notranslate"><span class="pre">AbstractEnvironmentNode.NUMBER_OF_LIGANDS_FOR_EACH_NEIGHBORING_COORDINATION_ENVIRONMENT</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.connectivity.html#pymatgen.analysis.chemenv.connectivity.environment_nodes.AbstractEnvironmentNode.NUMBER_OF_NEIGHBORING_CES"><code class="docutils literal notranslate"><span class="pre">AbstractEnvironmentNode.NUMBER_OF_NEIGHBORING_CES</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.connectivity.html#pymatgen.analysis.chemenv.connectivity.environment_nodes.AbstractEnvironmentNode.NUMBER_OF_NEIGHBORING_COORDINATION_ENVIRONMENTS"><code class="docutils literal notranslate"><span class="pre">AbstractEnvironmentNode.NUMBER_OF_NEIGHBORING_COORDINATION_ENVIRONMENTS</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.connectivity.html#pymatgen.analysis.chemenv.connectivity.environment_nodes.AbstractEnvironmentNode.atom_symbol"><code class="docutils literal notranslate"><span class="pre">AbstractEnvironmentNode.atom_symbol</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.connectivity.html#pymatgen.analysis.chemenv.connectivity.environment_nodes.AbstractEnvironmentNode.ce"><code class="docutils literal notranslate"><span class="pre">AbstractEnvironmentNode.ce</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.connectivity.html#pymatgen.analysis.chemenv.connectivity.environment_nodes.AbstractEnvironmentNode.ce_symbol"><code class="docutils literal notranslate"><span class="pre">AbstractEnvironmentNode.ce_symbol</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.connectivity.html#pymatgen.analysis.chemenv.connectivity.environment_nodes.AbstractEnvironmentNode.coordination_environment"><code class="docutils literal notranslate"><span class="pre">AbstractEnvironmentNode.coordination_environment</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.connectivity.html#pymatgen.analysis.chemenv.connectivity.environment_nodes.AbstractEnvironmentNode.everything_equal"><code class="docutils literal notranslate"><span class="pre">AbstractEnvironmentNode.everything_equal()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.connectivity.html#pymatgen.analysis.chemenv.connectivity.environment_nodes.AbstractEnvironmentNode.isite"><code class="docutils literal notranslate"><span class="pre">AbstractEnvironmentNode.isite</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.connectivity.html#pymatgen.analysis.chemenv.connectivity.environment_nodes.AbstractEnvironmentNode.mp_symbol"><code class="docutils literal notranslate"><span class="pre">AbstractEnvironmentNode.mp_symbol</span></code></a></li>
</ul>
</li>
<li class="toctree-l5"><a class="reference internal" href="pymatgen.analysis.chemenv.connectivity.html#pymatgen.analysis.chemenv.connectivity.environment_nodes.EnvironmentNode"><code class="docutils literal notranslate"><span class="pre">EnvironmentNode</span></code></a><ul>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.connectivity.html#pymatgen.analysis.chemenv.connectivity.environment_nodes.EnvironmentNode.coordination_environment"><code class="docutils literal notranslate"><span class="pre">EnvironmentNode.coordination_environment</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.connectivity.html#pymatgen.analysis.chemenv.connectivity.environment_nodes.EnvironmentNode.everything_equal"><code class="docutils literal notranslate"><span class="pre">EnvironmentNode.everything_equal()</span></code></a></li>
</ul>
</li>
<li class="toctree-l5"><a class="reference internal" href="pymatgen.analysis.chemenv.connectivity.html#pymatgen.analysis.chemenv.connectivity.environment_nodes.get_environment_node"><code class="docutils literal notranslate"><span class="pre">get_environment_node()</span></code></a></li>
</ul>
</li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.chemenv.connectivity.html#module-pymatgen.analysis.chemenv.connectivity.structure_connectivity">pymatgen.analysis.chemenv.connectivity.structure_connectivity module</a><ul>
<li class="toctree-l5"><a class="reference internal" href="pymatgen.analysis.chemenv.connectivity.html#pymatgen.analysis.chemenv.connectivity.structure_connectivity.StructureConnectivity"><code class="docutils literal notranslate"><span class="pre">StructureConnectivity</span></code></a><ul>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.connectivity.html#pymatgen.analysis.chemenv.connectivity.structure_connectivity.StructureConnectivity.add_bonds"><code class="docutils literal notranslate"><span class="pre">StructureConnectivity.add_bonds()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.connectivity.html#pymatgen.analysis.chemenv.connectivity.structure_connectivity.StructureConnectivity.add_sites"><code class="docutils literal notranslate"><span class="pre">StructureConnectivity.add_sites()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.connectivity.html#pymatgen.analysis.chemenv.connectivity.structure_connectivity.StructureConnectivity.as_dict"><code class="docutils literal notranslate"><span class="pre">StructureConnectivity.as_dict()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.connectivity.html#pymatgen.analysis.chemenv.connectivity.structure_connectivity.StructureConnectivity.environment_subgraph"><code class="docutils literal notranslate"><span class="pre">StructureConnectivity.environment_subgraph()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.connectivity.html#pymatgen.analysis.chemenv.connectivity.structure_connectivity.StructureConnectivity.from_dict"><code class="docutils literal notranslate"><span class="pre">StructureConnectivity.from_dict()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.connectivity.html#pymatgen.analysis.chemenv.connectivity.structure_connectivity.StructureConnectivity.get_connected_components"><code class="docutils literal notranslate"><span class="pre">StructureConnectivity.get_connected_components()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.connectivity.html#pymatgen.analysis.chemenv.connectivity.structure_connectivity.StructureConnectivity.print_links"><code class="docutils literal notranslate"><span class="pre">StructureConnectivity.print_links()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.connectivity.html#pymatgen.analysis.chemenv.connectivity.structure_connectivity.StructureConnectivity.setup_atom_environment_subgraph"><code class="docutils literal notranslate"><span class="pre">StructureConnectivity.setup_atom_environment_subgraph()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.connectivity.html#pymatgen.analysis.chemenv.connectivity.structure_connectivity.StructureConnectivity.setup_atom_environments_subgraph"><code class="docutils literal notranslate"><span class="pre">StructureConnectivity.setup_atom_environments_subgraph()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.connectivity.html#pymatgen.analysis.chemenv.connectivity.structure_connectivity.StructureConnectivity.setup_connectivity_description"><code class="docutils literal notranslate"><span class="pre">StructureConnectivity.setup_connectivity_description()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.connectivity.html#pymatgen.analysis.chemenv.connectivity.structure_connectivity.StructureConnectivity.setup_environment_subgraph"><code class="docutils literal notranslate"><span class="pre">StructureConnectivity.setup_environment_subgraph()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.connectivity.html#pymatgen.analysis.chemenv.connectivity.structure_connectivity.StructureConnectivity.setup_environments_subgraph"><code class="docutils literal notranslate"><span class="pre">StructureConnectivity.setup_environments_subgraph()</span></code></a></li>
</ul>
</li>
<li class="toctree-l5"><a class="reference internal" href="pymatgen.analysis.chemenv.connectivity.html#pymatgen.analysis.chemenv.connectivity.structure_connectivity.get_delta_image"><code class="docutils literal notranslate"><span class="pre">get_delta_image()</span></code></a></li>
</ul>
</li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html">pymatgen.analysis.chemenv.coordination_environments package</a><ul>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#subpackages">Subpackages</a><ul>
<li class="toctree-l5"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.coordination_geometries_files.html">pymatgen.analysis.chemenv.coordination_environments.coordination_geometries_files package</a></li>
</ul>
</li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#submodules">Submodules</a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#module-pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies">pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies module</a><ul>
<li class="toctree-l5"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.AbstractChemenvStrategy"><code class="docutils literal notranslate"><span class="pre">AbstractChemenvStrategy</span></code></a><ul>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.AbstractChemenvStrategy.AC"><code class="docutils literal notranslate"><span class="pre">AbstractChemenvStrategy.AC</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.AbstractChemenvStrategy.DEFAULT_SYMMETRY_MEASURE_TYPE"><code class="docutils literal notranslate"><span class="pre">AbstractChemenvStrategy.DEFAULT_SYMMETRY_MEASURE_TYPE</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.AbstractChemenvStrategy.STRATEGY_DESCRIPTION"><code class="docutils literal notranslate"><span class="pre">AbstractChemenvStrategy.STRATEGY_DESCRIPTION</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.AbstractChemenvStrategy.STRATEGY_INFO_FIELDS"><code class="docutils literal notranslate"><span class="pre">AbstractChemenvStrategy.STRATEGY_INFO_FIELDS</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.AbstractChemenvStrategy.STRATEGY_OPTIONS"><code class="docutils literal notranslate"><span class="pre">AbstractChemenvStrategy.STRATEGY_OPTIONS</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.AbstractChemenvStrategy.as_dict"><code class="docutils literal notranslate"><span class="pre">AbstractChemenvStrategy.as_dict()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.AbstractChemenvStrategy.equivalent_site_index_and_transform"><code class="docutils literal notranslate"><span class="pre">AbstractChemenvStrategy.equivalent_site_index_and_transform()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.AbstractChemenvStrategy.from_dict"><code class="docutils literal notranslate"><span class="pre">AbstractChemenvStrategy.from_dict()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.AbstractChemenvStrategy.get_site_ce_fractions_and_neighbors"><code class="docutils literal notranslate"><span class="pre">AbstractChemenvStrategy.get_site_ce_fractions_and_neighbors()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.AbstractChemenvStrategy.get_site_coordination_environment"><code class="docutils literal notranslate"><span class="pre">AbstractChemenvStrategy.get_site_coordination_environment()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.AbstractChemenvStrategy.get_site_coordination_environments"><code class="docutils literal notranslate"><span class="pre">AbstractChemenvStrategy.get_site_coordination_environments()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.AbstractChemenvStrategy.get_site_coordination_environments_fractions"><code class="docutils literal notranslate"><span class="pre">AbstractChemenvStrategy.get_site_coordination_environments_fractions()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.AbstractChemenvStrategy.get_site_neighbors"><code class="docutils literal notranslate"><span class="pre">AbstractChemenvStrategy.get_site_neighbors()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.AbstractChemenvStrategy.prepare_symmetries"><code class="docutils literal notranslate"><span class="pre">AbstractChemenvStrategy.prepare_symmetries()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.AbstractChemenvStrategy.set_option"><code class="docutils literal notranslate"><span class="pre">AbstractChemenvStrategy.set_option()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.AbstractChemenvStrategy.set_structure_environments"><code class="docutils literal notranslate"><span class="pre">AbstractChemenvStrategy.set_structure_environments()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.AbstractChemenvStrategy.setup_options"><code class="docutils literal notranslate"><span class="pre">AbstractChemenvStrategy.setup_options()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.AbstractChemenvStrategy.symmetry_measure_type"><code class="docutils literal notranslate"><span class="pre">AbstractChemenvStrategy.symmetry_measure_type</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.AbstractChemenvStrategy.uniquely_determines_coordination_environments"><code class="docutils literal notranslate"><span class="pre">AbstractChemenvStrategy.uniquely_determines_coordination_environments</span></code></a></li>
</ul>
</li>
<li class="toctree-l5"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.AdditionalConditionInt"><code class="docutils literal notranslate"><span class="pre">AdditionalConditionInt</span></code></a><ul>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.AdditionalConditionInt.allowed_values"><code class="docutils literal notranslate"><span class="pre">AdditionalConditionInt.allowed_values</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.AdditionalConditionInt.as_dict"><code class="docutils literal notranslate"><span class="pre">AdditionalConditionInt.as_dict()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.AdditionalConditionInt.description"><code class="docutils literal notranslate"><span class="pre">AdditionalConditionInt.description</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.AdditionalConditionInt.from_dict"><code class="docutils literal notranslate"><span class="pre">AdditionalConditionInt.from_dict()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.AdditionalConditionInt.integer"><code class="docutils literal notranslate"><span class="pre">AdditionalConditionInt.integer</span></code></a></li>
</ul>
</li>
<li class="toctree-l5"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.AngleCutoffFloat"><code class="docutils literal notranslate"><span class="pre">AngleCutoffFloat</span></code></a><ul>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.AngleCutoffFloat.allowed_values"><code class="docutils literal notranslate"><span class="pre">AngleCutoffFloat.allowed_values</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.AngleCutoffFloat.as_dict"><code class="docutils literal notranslate"><span class="pre">AngleCutoffFloat.as_dict()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.AngleCutoffFloat.from_dict"><code class="docutils literal notranslate"><span class="pre">AngleCutoffFloat.from_dict()</span></code></a></li>
</ul>
</li>
<li class="toctree-l5"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.AngleNbSetWeight"><code class="docutils literal notranslate"><span class="pre">AngleNbSetWeight</span></code></a><ul>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.AngleNbSetWeight.SHORT_NAME"><code class="docutils literal notranslate"><span class="pre">AngleNbSetWeight.SHORT_NAME</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.AngleNbSetWeight.angle_sum"><code class="docutils literal notranslate"><span class="pre">AngleNbSetWeight.angle_sum()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.AngleNbSetWeight.angle_sumn"><code class="docutils literal notranslate"><span class="pre">AngleNbSetWeight.angle_sumn()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.AngleNbSetWeight.as_dict"><code class="docutils literal notranslate"><span class="pre">AngleNbSetWeight.as_dict()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.AngleNbSetWeight.from_dict"><code class="docutils literal notranslate"><span class="pre">AngleNbSetWeight.from_dict()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.AngleNbSetWeight.weight"><code class="docutils literal notranslate"><span class="pre">AngleNbSetWeight.weight()</span></code></a></li>
</ul>
</li>
<li class="toctree-l5"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.AnglePlateauNbSetWeight"><code class="docutils literal notranslate"><span class="pre">AnglePlateauNbSetWeight</span></code></a><ul>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.AnglePlateauNbSetWeight.SHORT_NAME"><code class="docutils literal notranslate"><span class="pre">AnglePlateauNbSetWeight.SHORT_NAME</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.AnglePlateauNbSetWeight.as_dict"><code class="docutils literal notranslate"><span class="pre">AnglePlateauNbSetWeight.as_dict()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.AnglePlateauNbSetWeight.from_dict"><code class="docutils literal notranslate"><span class="pre">AnglePlateauNbSetWeight.from_dict()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.AnglePlateauNbSetWeight.weight"><code class="docutils literal notranslate"><span class="pre">AnglePlateauNbSetWeight.weight()</span></code></a></li>
</ul>
</li>
<li class="toctree-l5"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.CNBiasNbSetWeight"><code class="docutils literal notranslate"><span class="pre">CNBiasNbSetWeight</span></code></a><ul>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.CNBiasNbSetWeight.SHORT_NAME"><code class="docutils literal notranslate"><span class="pre">CNBiasNbSetWeight.SHORT_NAME</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.CNBiasNbSetWeight.as_dict"><code class="docutils literal notranslate"><span class="pre">CNBiasNbSetWeight.as_dict()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.CNBiasNbSetWeight.explicit"><code class="docutils literal notranslate"><span class="pre">CNBiasNbSetWeight.explicit()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.CNBiasNbSetWeight.from_description"><code class="docutils literal notranslate"><span class="pre">CNBiasNbSetWeight.from_description()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.CNBiasNbSetWeight.from_dict"><code class="docutils literal notranslate"><span class="pre">CNBiasNbSetWeight.from_dict()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.CNBiasNbSetWeight.geometrically_equidistant"><code class="docutils literal notranslate"><span class="pre">CNBiasNbSetWeight.geometrically_equidistant()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.CNBiasNbSetWeight.linearly_equidistant"><code class="docutils literal notranslate"><span class="pre">CNBiasNbSetWeight.linearly_equidistant()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.CNBiasNbSetWeight.weight"><code class="docutils literal notranslate"><span class="pre">CNBiasNbSetWeight.weight()</span></code></a></li>
</ul>
</li>
<li class="toctree-l5"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.CSMFloat"><code class="docutils literal notranslate"><span class="pre">CSMFloat</span></code></a><ul>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.CSMFloat.allowed_values"><code class="docutils literal notranslate"><span class="pre">CSMFloat.allowed_values</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.CSMFloat.as_dict"><code class="docutils literal notranslate"><span class="pre">CSMFloat.as_dict()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.CSMFloat.from_dict"><code class="docutils literal notranslate"><span class="pre">CSMFloat.from_dict()</span></code></a></li>
</ul>
</li>
<li class="toctree-l5"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.DeltaCSMNbSetWeight"><code class="docutils literal notranslate"><span class="pre">DeltaCSMNbSetWeight</span></code></a><ul>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.DeltaCSMNbSetWeight.DEFAULT_EFFECTIVE_CSM_ESTIMATOR"><code class="docutils literal notranslate"><span class="pre">DeltaCSMNbSetWeight.DEFAULT_EFFECTIVE_CSM_ESTIMATOR</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.DeltaCSMNbSetWeight.DEFAULT_SYMMETRY_MEASURE_TYPE"><code class="docutils literal notranslate"><span class="pre">DeltaCSMNbSetWeight.DEFAULT_SYMMETRY_MEASURE_TYPE</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.DeltaCSMNbSetWeight.DEFAULT_WEIGHT_ESTIMATOR"><code class="docutils literal notranslate"><span class="pre">DeltaCSMNbSetWeight.DEFAULT_WEIGHT_ESTIMATOR</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.DeltaCSMNbSetWeight.SHORT_NAME"><code class="docutils literal notranslate"><span class="pre">DeltaCSMNbSetWeight.SHORT_NAME</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.DeltaCSMNbSetWeight.as_dict"><code class="docutils literal notranslate"><span class="pre">DeltaCSMNbSetWeight.as_dict()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.DeltaCSMNbSetWeight.delta_cn_specifics"><code class="docutils literal notranslate"><span class="pre">DeltaCSMNbSetWeight.delta_cn_specifics()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.DeltaCSMNbSetWeight.from_dict"><code class="docutils literal notranslate"><span class="pre">DeltaCSMNbSetWeight.from_dict()</span></code></a></li>
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<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.DistanceAngleAreaNbSetWeight.weight"><code class="docutils literal notranslate"><span class="pre">DistanceAngleAreaNbSetWeight.weight()</span></code></a></li>
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<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.SimpleAbundanceChemenvStrategy.as_dict"><code class="docutils literal notranslate"><span class="pre">SimpleAbundanceChemenvStrategy.as_dict()</span></code></a></li>
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<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.SimpleAbundanceChemenvStrategy.get_site_coordination_environment"><code class="docutils literal notranslate"><span class="pre">SimpleAbundanceChemenvStrategy.get_site_coordination_environment()</span></code></a></li>
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<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.SimpleAbundanceChemenvStrategy.get_site_neighbors"><code class="docutils literal notranslate"><span class="pre">SimpleAbundanceChemenvStrategy.get_site_neighbors()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.SimpleAbundanceChemenvStrategy.uniquely_determines_coordination_environments"><code class="docutils literal notranslate"><span class="pre">SimpleAbundanceChemenvStrategy.uniquely_determines_coordination_environments</span></code></a></li>
</ul>
</li>
<li class="toctree-l5"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.SimplestChemenvStrategy"><code class="docutils literal notranslate"><span class="pre">SimplestChemenvStrategy</span></code></a><ul>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.SimplestChemenvStrategy.DEFAULT_ADDITIONAL_CONDITION"><code class="docutils literal notranslate"><span class="pre">SimplestChemenvStrategy.DEFAULT_ADDITIONAL_CONDITION</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.SimplestChemenvStrategy.DEFAULT_ANGLE_CUTOFF"><code class="docutils literal notranslate"><span class="pre">SimplestChemenvStrategy.DEFAULT_ANGLE_CUTOFF</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.SimplestChemenvStrategy.DEFAULT_CONTINUOUS_SYMMETRY_MEASURE_CUTOFF"><code class="docutils literal notranslate"><span class="pre">SimplestChemenvStrategy.DEFAULT_CONTINUOUS_SYMMETRY_MEASURE_CUTOFF</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.SimplestChemenvStrategy.DEFAULT_DISTANCE_CUTOFF"><code class="docutils literal notranslate"><span class="pre">SimplestChemenvStrategy.DEFAULT_DISTANCE_CUTOFF</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.SimplestChemenvStrategy.STRATEGY_DESCRIPTION"><code class="docutils literal notranslate"><span class="pre">SimplestChemenvStrategy.STRATEGY_DESCRIPTION</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.SimplestChemenvStrategy.STRATEGY_OPTIONS"><code class="docutils literal notranslate"><span class="pre">SimplestChemenvStrategy.STRATEGY_OPTIONS</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.SimplestChemenvStrategy.add_strategy_visualization_to_subplot"><code class="docutils literal notranslate"><span class="pre">SimplestChemenvStrategy.add_strategy_visualization_to_subplot()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.SimplestChemenvStrategy.additional_condition"><code class="docutils literal notranslate"><span class="pre">SimplestChemenvStrategy.additional_condition</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.SimplestChemenvStrategy.angle_cutoff"><code class="docutils literal notranslate"><span class="pre">SimplestChemenvStrategy.angle_cutoff</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.SimplestChemenvStrategy.as_dict"><code class="docutils literal notranslate"><span class="pre">SimplestChemenvStrategy.as_dict()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.SimplestChemenvStrategy.continuous_symmetry_measure_cutoff"><code class="docutils literal notranslate"><span class="pre">SimplestChemenvStrategy.continuous_symmetry_measure_cutoff</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.SimplestChemenvStrategy.distance_cutoff"><code class="docutils literal notranslate"><span class="pre">SimplestChemenvStrategy.distance_cutoff</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.SimplestChemenvStrategy.from_dict"><code class="docutils literal notranslate"><span class="pre">SimplestChemenvStrategy.from_dict()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.SimplestChemenvStrategy.get_site_coordination_environment"><code class="docutils literal notranslate"><span class="pre">SimplestChemenvStrategy.get_site_coordination_environment()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.SimplestChemenvStrategy.get_site_coordination_environments"><code class="docutils literal notranslate"><span class="pre">SimplestChemenvStrategy.get_site_coordination_environments()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.SimplestChemenvStrategy.get_site_coordination_environments_fractions"><code class="docutils literal notranslate"><span class="pre">SimplestChemenvStrategy.get_site_coordination_environments_fractions()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.SimplestChemenvStrategy.get_site_neighbors"><code class="docutils literal notranslate"><span class="pre">SimplestChemenvStrategy.get_site_neighbors()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.SimplestChemenvStrategy.uniquely_determines_coordination_environments"><code class="docutils literal notranslate"><span class="pre">SimplestChemenvStrategy.uniquely_determines_coordination_environments</span></code></a></li>
</ul>
</li>
<li class="toctree-l5"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.StrategyOption"><code class="docutils literal notranslate"><span class="pre">StrategyOption</span></code></a><ul>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.StrategyOption.allowed_values"><code class="docutils literal notranslate"><span class="pre">StrategyOption.allowed_values</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.StrategyOption.as_dict"><code class="docutils literal notranslate"><span class="pre">StrategyOption.as_dict()</span></code></a></li>
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<li class="toctree-l5"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.TargetedPenaltiedAbundanceChemenvStrategy"><code class="docutils literal notranslate"><span class="pre">TargetedPenaltiedAbundanceChemenvStrategy</span></code></a><ul>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.TargetedPenaltiedAbundanceChemenvStrategy.DEFAULT_TARGET_ENVIRONMENTS"><code class="docutils literal notranslate"><span class="pre">TargetedPenaltiedAbundanceChemenvStrategy.DEFAULT_TARGET_ENVIRONMENTS</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.TargetedPenaltiedAbundanceChemenvStrategy.as_dict"><code class="docutils literal notranslate"><span class="pre">TargetedPenaltiedAbundanceChemenvStrategy.as_dict()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.TargetedPenaltiedAbundanceChemenvStrategy.from_dict"><code class="docutils literal notranslate"><span class="pre">TargetedPenaltiedAbundanceChemenvStrategy.from_dict()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.TargetedPenaltiedAbundanceChemenvStrategy.get_site_coordination_environment"><code class="docutils literal notranslate"><span class="pre">TargetedPenaltiedAbundanceChemenvStrategy.get_site_coordination_environment()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.TargetedPenaltiedAbundanceChemenvStrategy.uniquely_determines_coordination_environments"><code class="docutils literal notranslate"><span class="pre">TargetedPenaltiedAbundanceChemenvStrategy.uniquely_determines_coordination_environments</span></code></a></li>
</ul>
</li>
<li class="toctree-l5"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.WeightedNbSetChemenvStrategy"><code class="docutils literal notranslate"><span class="pre">WeightedNbSetChemenvStrategy</span></code></a><ul>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.WeightedNbSetChemenvStrategy.DEFAULT_CE_ESTIMATOR"><code class="docutils literal notranslate"><span class="pre">WeightedNbSetChemenvStrategy.DEFAULT_CE_ESTIMATOR</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.WeightedNbSetChemenvStrategy.STRATEGY_DESCRIPTION"><code class="docutils literal notranslate"><span class="pre">WeightedNbSetChemenvStrategy.STRATEGY_DESCRIPTION</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.WeightedNbSetChemenvStrategy.as_dict"><code class="docutils literal notranslate"><span class="pre">WeightedNbSetChemenvStrategy.as_dict()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.WeightedNbSetChemenvStrategy.from_dict"><code class="docutils literal notranslate"><span class="pre">WeightedNbSetChemenvStrategy.from_dict()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.WeightedNbSetChemenvStrategy.get_site_coordination_environment"><code class="docutils literal notranslate"><span class="pre">WeightedNbSetChemenvStrategy.get_site_coordination_environment()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.WeightedNbSetChemenvStrategy.get_site_coordination_environments"><code class="docutils literal notranslate"><span class="pre">WeightedNbSetChemenvStrategy.get_site_coordination_environments()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.WeightedNbSetChemenvStrategy.get_site_coordination_environments_fractions"><code class="docutils literal notranslate"><span class="pre">WeightedNbSetChemenvStrategy.get_site_coordination_environments_fractions()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.WeightedNbSetChemenvStrategy.get_site_neighbors"><code class="docutils literal notranslate"><span class="pre">WeightedNbSetChemenvStrategy.get_site_neighbors()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.WeightedNbSetChemenvStrategy.uniquely_determines_coordination_environments"><code class="docutils literal notranslate"><span class="pre">WeightedNbSetChemenvStrategy.uniquely_determines_coordination_environments</span></code></a></li>
</ul>
</li>
<li class="toctree-l5"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.get_effective_csm"><code class="docutils literal notranslate"><span class="pre">get_effective_csm()</span></code></a></li>
<li class="toctree-l5"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies.set_info"><code class="docutils literal notranslate"><span class="pre">set_info()</span></code></a></li>
</ul>
</li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#module-pymatgen.analysis.chemenv.coordination_environments.coordination_geometries">pymatgen.analysis.chemenv.coordination_environments.coordination_geometries module</a><ul>
<li class="toctree-l5"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.coordination_geometries.AbstractChemenvAlgorithm"><code class="docutils literal notranslate"><span class="pre">AbstractChemenvAlgorithm</span></code></a><ul>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.coordination_geometries.AbstractChemenvAlgorithm.algorithm_type"><code class="docutils literal notranslate"><span class="pre">AbstractChemenvAlgorithm.algorithm_type</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.coordination_geometries.AbstractChemenvAlgorithm.as_dict"><code class="docutils literal notranslate"><span class="pre">AbstractChemenvAlgorithm.as_dict()</span></code></a></li>
</ul>
</li>
<li class="toctree-l5"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.coordination_geometries.AllCoordinationGeometries"><code class="docutils literal notranslate"><span class="pre">AllCoordinationGeometries</span></code></a><ul>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.coordination_geometries.AllCoordinationGeometries.get_geometries"><code class="docutils literal notranslate"><span class="pre">AllCoordinationGeometries.get_geometries()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.coordination_geometries.AllCoordinationGeometries.get_geometry_from_IUCr_symbol"><code class="docutils literal notranslate"><span class="pre">AllCoordinationGeometries.get_geometry_from_IUCr_symbol()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.coordination_geometries.AllCoordinationGeometries.get_geometry_from_IUPAC_symbol"><code class="docutils literal notranslate"><span class="pre">AllCoordinationGeometries.get_geometry_from_IUPAC_symbol()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.coordination_geometries.AllCoordinationGeometries.get_geometry_from_mp_symbol"><code class="docutils literal notranslate"><span class="pre">AllCoordinationGeometries.get_geometry_from_mp_symbol()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.coordination_geometries.AllCoordinationGeometries.get_geometry_from_name"><code class="docutils literal notranslate"><span class="pre">AllCoordinationGeometries.get_geometry_from_name()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.coordination_geometries.AllCoordinationGeometries.get_implemented_geometries"><code class="docutils literal notranslate"><span class="pre">AllCoordinationGeometries.get_implemented_geometries()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.coordination_geometries.AllCoordinationGeometries.get_not_implemented_geometries"><code class="docutils literal notranslate"><span class="pre">AllCoordinationGeometries.get_not_implemented_geometries()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.coordination_geometries.AllCoordinationGeometries.get_symbol_cn_mapping"><code class="docutils literal notranslate"><span class="pre">AllCoordinationGeometries.get_symbol_cn_mapping()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.coordination_geometries.AllCoordinationGeometries.get_symbol_name_mapping"><code class="docutils literal notranslate"><span class="pre">AllCoordinationGeometries.get_symbol_name_mapping()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.coordination_geometries.AllCoordinationGeometries.is_a_valid_coordination_geometry"><code class="docutils literal notranslate"><span class="pre">AllCoordinationGeometries.is_a_valid_coordination_geometry()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.coordination_geometries.AllCoordinationGeometries.pretty_print"><code class="docutils literal notranslate"><span class="pre">AllCoordinationGeometries.pretty_print()</span></code></a></li>
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<li class="toctree-l5"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.coordination_geometries.CoordinationGeometry"><code class="docutils literal notranslate"><span class="pre">CoordinationGeometry</span></code></a><ul>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.coordination_geometries.CoordinationGeometry.CSM_SKIP_SEPARATION_PLANE_ALGO"><code class="docutils literal notranslate"><span class="pre">CoordinationGeometry.CSM_SKIP_SEPARATION_PLANE_ALGO</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.coordination_geometries.CoordinationGeometry.IUCr_symbol"><code class="docutils literal notranslate"><span class="pre">CoordinationGeometry.IUCr_symbol</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.coordination_geometries.CoordinationGeometry.IUCr_symbol_str"><code class="docutils literal notranslate"><span class="pre">CoordinationGeometry.IUCr_symbol_str</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.coordination_geometries.CoordinationGeometry.IUPAC_symbol"><code class="docutils literal notranslate"><span class="pre">CoordinationGeometry.IUPAC_symbol</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.coordination_geometries.CoordinationGeometry.IUPAC_symbol_str"><code class="docutils literal notranslate"><span class="pre">CoordinationGeometry.IUPAC_symbol_str</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.coordination_geometries.CoordinationGeometry.NeighborsSetsHints"><code class="docutils literal notranslate"><span class="pre">CoordinationGeometry.NeighborsSetsHints</span></code></a><ul>
<li class="toctree-l7"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.coordination_geometries.CoordinationGeometry.NeighborsSetsHints.ALLOWED_HINTS_TYPES"><code class="docutils literal notranslate"><span class="pre">CoordinationGeometry.NeighborsSetsHints.ALLOWED_HINTS_TYPES</span></code></a></li>
<li class="toctree-l7"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.coordination_geometries.CoordinationGeometry.NeighborsSetsHints.as_dict"><code class="docutils literal notranslate"><span class="pre">CoordinationGeometry.NeighborsSetsHints.as_dict()</span></code></a></li>
<li class="toctree-l7"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.coordination_geometries.CoordinationGeometry.NeighborsSetsHints.double_cap_hints"><code class="docutils literal notranslate"><span class="pre">CoordinationGeometry.NeighborsSetsHints.double_cap_hints()</span></code></a></li>
<li class="toctree-l7"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.coordination_geometries.CoordinationGeometry.NeighborsSetsHints.from_dict"><code class="docutils literal notranslate"><span class="pre">CoordinationGeometry.NeighborsSetsHints.from_dict()</span></code></a></li>
<li class="toctree-l7"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.coordination_geometries.CoordinationGeometry.NeighborsSetsHints.hints"><code class="docutils literal notranslate"><span class="pre">CoordinationGeometry.NeighborsSetsHints.hints()</span></code></a></li>
<li class="toctree-l7"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.coordination_geometries.CoordinationGeometry.NeighborsSetsHints.single_cap_hints"><code class="docutils literal notranslate"><span class="pre">CoordinationGeometry.NeighborsSetsHints.single_cap_hints()</span></code></a></li>
<li class="toctree-l7"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.coordination_geometries.CoordinationGeometry.NeighborsSetsHints.triple_cap_hints"><code class="docutils literal notranslate"><span class="pre">CoordinationGeometry.NeighborsSetsHints.triple_cap_hints()</span></code></a></li>
</ul>
</li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.coordination_geometries.CoordinationGeometry.algorithms"><code class="docutils literal notranslate"><span class="pre">CoordinationGeometry.algorithms</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.coordination_geometries.CoordinationGeometry.as_dict"><code class="docutils literal notranslate"><span class="pre">CoordinationGeometry.as_dict()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.coordination_geometries.CoordinationGeometry.ce_symbol"><code class="docutils literal notranslate"><span class="pre">CoordinationGeometry.ce_symbol</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.coordination_geometries.CoordinationGeometry.coordination_number"><code class="docutils literal notranslate"><span class="pre">CoordinationGeometry.coordination_number</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.coordination_geometries.CoordinationGeometry.distfactor_max"><code class="docutils literal notranslate"><span class="pre">CoordinationGeometry.distfactor_max</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.coordination_geometries.CoordinationGeometry.edges"><code class="docutils literal notranslate"><span class="pre">CoordinationGeometry.edges()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.coordination_geometries.CoordinationGeometry.faces"><code class="docutils literal notranslate"><span class="pre">CoordinationGeometry.faces()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.coordination_geometries.CoordinationGeometry.from_dict"><code class="docutils literal notranslate"><span class="pre">CoordinationGeometry.from_dict()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.coordination_geometries.CoordinationGeometry.get_central_site"><code class="docutils literal notranslate"><span class="pre">CoordinationGeometry.get_central_site()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.coordination_geometries.CoordinationGeometry.get_coordination_number"><code class="docutils literal notranslate"><span class="pre">CoordinationGeometry.get_coordination_number()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.coordination_geometries.CoordinationGeometry.get_name"><code class="docutils literal notranslate"><span class="pre">CoordinationGeometry.get_name()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.coordination_geometries.CoordinationGeometry.get_pmeshes"><code class="docutils literal notranslate"><span class="pre">CoordinationGeometry.get_pmeshes()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.coordination_geometries.CoordinationGeometry.is_implemented"><code class="docutils literal notranslate"><span class="pre">CoordinationGeometry.is_implemented()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.coordination_geometries.CoordinationGeometry.mp_symbol"><code class="docutils literal notranslate"><span class="pre">CoordinationGeometry.mp_symbol</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.coordination_geometries.CoordinationGeometry.number_of_permutations"><code class="docutils literal notranslate"><span class="pre">CoordinationGeometry.number_of_permutations</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.coordination_geometries.CoordinationGeometry.pauling_stability_ratio"><code class="docutils literal notranslate"><span class="pre">CoordinationGeometry.pauling_stability_ratio</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.coordination_geometries.CoordinationGeometry.ref_permutation"><code class="docutils literal notranslate"><span class="pre">CoordinationGeometry.ref_permutation()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.coordination_geometries.CoordinationGeometry.solid_angles"><code class="docutils literal notranslate"><span class="pre">CoordinationGeometry.solid_angles()</span></code></a></li>
</ul>
</li>
<li class="toctree-l5"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.coordination_geometries.ExplicitPermutationsAlgorithm"><code class="docutils literal notranslate"><span class="pre">ExplicitPermutationsAlgorithm</span></code></a><ul>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.coordination_geometries.ExplicitPermutationsAlgorithm.as_dict"><code class="docutils literal notranslate"><span class="pre">ExplicitPermutationsAlgorithm.as_dict()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.coordination_geometries.ExplicitPermutationsAlgorithm.from_dict"><code class="docutils literal notranslate"><span class="pre">ExplicitPermutationsAlgorithm.from_dict()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.coordination_geometries.ExplicitPermutationsAlgorithm.permutations"><code class="docutils literal notranslate"><span class="pre">ExplicitPermutationsAlgorithm.permutations</span></code></a></li>
</ul>
</li>
<li class="toctree-l5"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.coordination_geometries.SeparationPlane"><code class="docutils literal notranslate"><span class="pre">SeparationPlane</span></code></a><ul>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.coordination_geometries.SeparationPlane.argsorted_ref_separation_perm"><code class="docutils literal notranslate"><span class="pre">SeparationPlane.argsorted_ref_separation_perm</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.coordination_geometries.SeparationPlane.as_dict"><code class="docutils literal notranslate"><span class="pre">SeparationPlane.as_dict()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.coordination_geometries.SeparationPlane.from_dict"><code class="docutils literal notranslate"><span class="pre">SeparationPlane.from_dict()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.coordination_geometries.SeparationPlane.permutations"><code class="docutils literal notranslate"><span class="pre">SeparationPlane.permutations</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.coordination_geometries.SeparationPlane.ref_separation_perm"><code class="docutils literal notranslate"><span class="pre">SeparationPlane.ref_separation_perm</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.coordination_geometries.SeparationPlane.safe_separation_permutations"><code class="docutils literal notranslate"><span class="pre">SeparationPlane.safe_separation_permutations()</span></code></a></li>
</ul>
</li>
</ul>
</li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#module-pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder">pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder module</a><ul>
<li class="toctree-l5"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder.AbstractGeometry"><code class="docutils literal notranslate"><span class="pre">AbstractGeometry</span></code></a><ul>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder.AbstractGeometry.cn"><code class="docutils literal notranslate"><span class="pre">AbstractGeometry.cn</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder.AbstractGeometry.coordination_number"><code class="docutils literal notranslate"><span class="pre">AbstractGeometry.coordination_number</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder.AbstractGeometry.from_cg"><code class="docutils literal notranslate"><span class="pre">AbstractGeometry.from_cg()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder.AbstractGeometry.points_wcs_csc"><code class="docutils literal notranslate"><span class="pre">AbstractGeometry.points_wcs_csc()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder.AbstractGeometry.points_wcs_ctwcc"><code class="docutils literal notranslate"><span class="pre">AbstractGeometry.points_wcs_ctwcc()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder.AbstractGeometry.points_wcs_ctwocc"><code class="docutils literal notranslate"><span class="pre">AbstractGeometry.points_wcs_ctwocc()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder.AbstractGeometry.points_wocs_csc"><code class="docutils literal notranslate"><span class="pre">AbstractGeometry.points_wocs_csc()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder.AbstractGeometry.points_wocs_ctwcc"><code class="docutils literal notranslate"><span class="pre">AbstractGeometry.points_wocs_ctwcc()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder.AbstractGeometry.points_wocs_ctwocc"><code class="docutils literal notranslate"><span class="pre">AbstractGeometry.points_wocs_ctwocc()</span></code></a></li>
</ul>
</li>
<li class="toctree-l5"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder.LocalGeometryFinder"><code class="docutils literal notranslate"><span class="pre">LocalGeometryFinder</span></code></a><ul>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder.LocalGeometryFinder.BVA_DISTANCE_SCALE_FACTORS"><code class="docutils literal notranslate"><span class="pre">LocalGeometryFinder.BVA_DISTANCE_SCALE_FACTORS</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder.LocalGeometryFinder.DEFAULT_BVA_DISTANCE_SCALE_FACTOR"><code class="docutils literal notranslate"><span class="pre">LocalGeometryFinder.DEFAULT_BVA_DISTANCE_SCALE_FACTOR</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder.LocalGeometryFinder.DEFAULT_SPG_ANALYZER_OPTIONS"><code class="docutils literal notranslate"><span class="pre">LocalGeometryFinder.DEFAULT_SPG_ANALYZER_OPTIONS</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder.LocalGeometryFinder.DEFAULT_STRATEGY"><code class="docutils literal notranslate"><span class="pre">LocalGeometryFinder.DEFAULT_STRATEGY</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder.LocalGeometryFinder.PRESETS"><code class="docutils literal notranslate"><span class="pre">LocalGeometryFinder.PRESETS</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder.LocalGeometryFinder.STRUCTURE_REFINEMENT_NONE"><code class="docutils literal notranslate"><span class="pre">LocalGeometryFinder.STRUCTURE_REFINEMENT_NONE</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder.LocalGeometryFinder.STRUCTURE_REFINEMENT_REFINED"><code class="docutils literal notranslate"><span class="pre">LocalGeometryFinder.STRUCTURE_REFINEMENT_REFINED</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder.LocalGeometryFinder.STRUCTURE_REFINEMENT_SYMMETRIZED"><code class="docutils literal notranslate"><span class="pre">LocalGeometryFinder.STRUCTURE_REFINEMENT_SYMMETRIZED</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder.LocalGeometryFinder.compute_coordination_environments"><code class="docutils literal notranslate"><span class="pre">LocalGeometryFinder.compute_coordination_environments()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder.LocalGeometryFinder.compute_structure_environments"><code class="docutils literal notranslate"><span class="pre">LocalGeometryFinder.compute_structure_environments()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder.LocalGeometryFinder.coordination_geometry_symmetry_measures"><code class="docutils literal notranslate"><span class="pre">LocalGeometryFinder.coordination_geometry_symmetry_measures()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder.LocalGeometryFinder.coordination_geometry_symmetry_measures_fallback_random"><code class="docutils literal notranslate"><span class="pre">LocalGeometryFinder.coordination_geometry_symmetry_measures_fallback_random()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder.LocalGeometryFinder.coordination_geometry_symmetry_measures_separation_plane"><code class="docutils literal notranslate"><span class="pre">LocalGeometryFinder.coordination_geometry_symmetry_measures_separation_plane()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder.LocalGeometryFinder.coordination_geometry_symmetry_measures_separation_plane_optim"><code class="docutils literal notranslate"><span class="pre">LocalGeometryFinder.coordination_geometry_symmetry_measures_separation_plane_optim()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder.LocalGeometryFinder.coordination_geometry_symmetry_measures_sepplane_optim"><code class="docutils literal notranslate"><span class="pre">LocalGeometryFinder.coordination_geometry_symmetry_measures_sepplane_optim()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder.LocalGeometryFinder.coordination_geometry_symmetry_measures_standard"><code class="docutils literal notranslate"><span class="pre">LocalGeometryFinder.coordination_geometry_symmetry_measures_standard()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder.LocalGeometryFinder.get_coordination_symmetry_measures"><code class="docutils literal notranslate"><span class="pre">LocalGeometryFinder.get_coordination_symmetry_measures()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder.LocalGeometryFinder.get_coordination_symmetry_measures_optim"><code class="docutils literal notranslate"><span class="pre">LocalGeometryFinder.get_coordination_symmetry_measures_optim()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder.LocalGeometryFinder.get_structure"><code class="docutils literal notranslate"><span class="pre">LocalGeometryFinder.get_structure()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder.LocalGeometryFinder.set_structure"><code class="docutils literal notranslate"><span class="pre">LocalGeometryFinder.set_structure()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder.LocalGeometryFinder.setup_explicit_indices_local_geometry"><code class="docutils literal notranslate"><span class="pre">LocalGeometryFinder.setup_explicit_indices_local_geometry()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder.LocalGeometryFinder.setup_local_geometry"><code class="docutils literal notranslate"><span class="pre">LocalGeometryFinder.setup_local_geometry()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder.LocalGeometryFinder.setup_ordered_indices_local_geometry"><code class="docutils literal notranslate"><span class="pre">LocalGeometryFinder.setup_ordered_indices_local_geometry()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder.LocalGeometryFinder.setup_parameter"><code class="docutils literal notranslate"><span class="pre">LocalGeometryFinder.setup_parameter()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder.LocalGeometryFinder.setup_parameters"><code class="docutils literal notranslate"><span class="pre">LocalGeometryFinder.setup_parameters()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder.LocalGeometryFinder.setup_random_indices_local_geometry"><code class="docutils literal notranslate"><span class="pre">LocalGeometryFinder.setup_random_indices_local_geometry()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder.LocalGeometryFinder.setup_random_structure"><code class="docutils literal notranslate"><span class="pre">LocalGeometryFinder.setup_random_structure()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder.LocalGeometryFinder.setup_structure"><code class="docutils literal notranslate"><span class="pre">LocalGeometryFinder.setup_structure()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder.LocalGeometryFinder.setup_test_perfect_environment"><code class="docutils literal notranslate"><span class="pre">LocalGeometryFinder.setup_test_perfect_environment()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder.LocalGeometryFinder.update_nb_set_environments"><code class="docutils literal notranslate"><span class="pre">LocalGeometryFinder.update_nb_set_environments()</span></code></a></li>
</ul>
</li>
<li class="toctree-l5"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder.find_rotation"><code class="docutils literal notranslate"><span class="pre">find_rotation()</span></code></a></li>
<li class="toctree-l5"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder.find_scaling_factor"><code class="docutils literal notranslate"><span class="pre">find_scaling_factor()</span></code></a></li>
<li class="toctree-l5"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder.symmetry_measure"><code class="docutils literal notranslate"><span class="pre">symmetry_measure()</span></code></a></li>
</ul>
</li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#module-pymatgen.analysis.chemenv.coordination_environments.structure_environments">pymatgen.analysis.chemenv.coordination_environments.structure_environments module</a><ul>
<li class="toctree-l5"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.structure_environments.ChemicalEnvironments"><code class="docutils literal notranslate"><span class="pre">ChemicalEnvironments</span></code></a><ul>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.structure_environments.ChemicalEnvironments.add_coord_geom"><code class="docutils literal notranslate"><span class="pre">ChemicalEnvironments.add_coord_geom()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.structure_environments.ChemicalEnvironments.as_dict"><code class="docutils literal notranslate"><span class="pre">ChemicalEnvironments.as_dict()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.structure_environments.ChemicalEnvironments.from_dict"><code class="docutils literal notranslate"><span class="pre">ChemicalEnvironments.from_dict()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.structure_environments.ChemicalEnvironments.is_close_to"><code class="docutils literal notranslate"><span class="pre">ChemicalEnvironments.is_close_to()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.structure_environments.ChemicalEnvironments.minimum_geometries"><code class="docutils literal notranslate"><span class="pre">ChemicalEnvironments.minimum_geometries()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.structure_environments.ChemicalEnvironments.minimum_geometry"><code class="docutils literal notranslate"><span class="pre">ChemicalEnvironments.minimum_geometry()</span></code></a></li>
</ul>
</li>
<li class="toctree-l5"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.structure_environments.LightStructureEnvironments"><code class="docutils literal notranslate"><span class="pre">LightStructureEnvironments</span></code></a><ul>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.structure_environments.LightStructureEnvironments.DEFAULT_STATISTICS_FIELDS"><code class="docutils literal notranslate"><span class="pre">LightStructureEnvironments.DEFAULT_STATISTICS_FIELDS</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.structure_environments.LightStructureEnvironments.DELTA_MAX_OXIDATION_STATE"><code class="docutils literal notranslate"><span class="pre">LightStructureEnvironments.DELTA_MAX_OXIDATION_STATE</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.structure_environments.LightStructureEnvironments.NeighborsSet"><code class="docutils literal notranslate"><span class="pre">LightStructureEnvironments.NeighborsSet</span></code></a><ul>
<li class="toctree-l7"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.structure_environments.LightStructureEnvironments.NeighborsSet.as_dict"><code class="docutils literal notranslate"><span class="pre">LightStructureEnvironments.NeighborsSet.as_dict()</span></code></a></li>
<li class="toctree-l7"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.structure_environments.LightStructureEnvironments.NeighborsSet.from_dict"><code class="docutils literal notranslate"><span class="pre">LightStructureEnvironments.NeighborsSet.from_dict()</span></code></a></li>
<li class="toctree-l7"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.structure_environments.LightStructureEnvironments.NeighborsSet.neighb_coords"><code class="docutils literal notranslate"><span class="pre">LightStructureEnvironments.NeighborsSet.neighb_coords</span></code></a></li>
<li class="toctree-l7"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.structure_environments.LightStructureEnvironments.NeighborsSet.neighb_indices_and_images"><code class="docutils literal notranslate"><span class="pre">LightStructureEnvironments.NeighborsSet.neighb_indices_and_images</span></code></a></li>
<li class="toctree-l7"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.structure_environments.LightStructureEnvironments.NeighborsSet.neighb_sites"><code class="docutils literal notranslate"><span class="pre">LightStructureEnvironments.NeighborsSet.neighb_sites</span></code></a></li>
<li class="toctree-l7"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.structure_environments.LightStructureEnvironments.NeighborsSet.neighb_sites_and_indices"><code class="docutils literal notranslate"><span class="pre">LightStructureEnvironments.NeighborsSet.neighb_sites_and_indices</span></code></a></li>
</ul>
</li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.structure_environments.LightStructureEnvironments.as_dict"><code class="docutils literal notranslate"><span class="pre">LightStructureEnvironments.as_dict()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.structure_environments.LightStructureEnvironments.clear_environments"><code class="docutils literal notranslate"><span class="pre">LightStructureEnvironments.clear_environments()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.structure_environments.LightStructureEnvironments.contains_only_one_anion"><code class="docutils literal notranslate"><span class="pre">LightStructureEnvironments.contains_only_one_anion()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.structure_environments.LightStructureEnvironments.contains_only_one_anion_atom"><code class="docutils literal notranslate"><span class="pre">LightStructureEnvironments.contains_only_one_anion_atom()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.structure_environments.LightStructureEnvironments.environments_identified"><code class="docutils literal notranslate"><span class="pre">LightStructureEnvironments.environments_identified()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.structure_environments.LightStructureEnvironments.from_dict"><code class="docutils literal notranslate"><span class="pre">LightStructureEnvironments.from_dict()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.structure_environments.LightStructureEnvironments.from_structure_environments"><code class="docutils literal notranslate"><span class="pre">LightStructureEnvironments.from_structure_environments()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.structure_environments.LightStructureEnvironments.get_site_info_for_specie_allces"><code class="docutils literal notranslate"><span class="pre">LightStructureEnvironments.get_site_info_for_specie_allces()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.structure_environments.LightStructureEnvironments.get_site_info_for_specie_ce"><code class="docutils literal notranslate"><span class="pre">LightStructureEnvironments.get_site_info_for_specie_ce()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.structure_environments.LightStructureEnvironments.get_statistics"><code class="docutils literal notranslate"><span class="pre">LightStructureEnvironments.get_statistics()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.structure_environments.LightStructureEnvironments.setup_statistic_lists"><code class="docutils literal notranslate"><span class="pre">LightStructureEnvironments.setup_statistic_lists()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.structure_environments.LightStructureEnvironments.site_contains_environment"><code class="docutils literal notranslate"><span class="pre">LightStructureEnvironments.site_contains_environment()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.structure_environments.LightStructureEnvironments.site_has_clear_environment"><code class="docutils literal notranslate"><span class="pre">LightStructureEnvironments.site_has_clear_environment()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.structure_environments.LightStructureEnvironments.structure_contains_atom_environment"><code class="docutils literal notranslate"><span class="pre">LightStructureEnvironments.structure_contains_atom_environment()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.structure_environments.LightStructureEnvironments.structure_has_clear_environments"><code class="docutils literal notranslate"><span class="pre">LightStructureEnvironments.structure_has_clear_environments()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.structure_environments.LightStructureEnvironments.uniquely_determines_coordination_environments"><code class="docutils literal notranslate"><span class="pre">LightStructureEnvironments.uniquely_determines_coordination_environments</span></code></a></li>
</ul>
</li>
<li class="toctree-l5"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.structure_environments.StructureEnvironments"><code class="docutils literal notranslate"><span class="pre">StructureEnvironments</span></code></a><ul>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.structure_environments.StructureEnvironments.AC"><code class="docutils literal notranslate"><span class="pre">StructureEnvironments.AC</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.structure_environments.StructureEnvironments.NeighborsSet"><code class="docutils literal notranslate"><span class="pre">StructureEnvironments.NeighborsSet</span></code></a><ul>
<li class="toctree-l7"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.structure_environments.StructureEnvironments.NeighborsSet.add_source"><code class="docutils literal notranslate"><span class="pre">StructureEnvironments.NeighborsSet.add_source()</span></code></a></li>
<li class="toctree-l7"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.structure_environments.StructureEnvironments.NeighborsSet.angle_plateau"><code class="docutils literal notranslate"><span class="pre">StructureEnvironments.NeighborsSet.angle_plateau()</span></code></a></li>
<li class="toctree-l7"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.structure_environments.StructureEnvironments.NeighborsSet.angles"><code class="docutils literal notranslate"><span class="pre">StructureEnvironments.NeighborsSet.angles</span></code></a></li>
<li class="toctree-l7"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.structure_environments.StructureEnvironments.NeighborsSet.as_dict"><code class="docutils literal notranslate"><span class="pre">StructureEnvironments.NeighborsSet.as_dict()</span></code></a></li>
<li class="toctree-l7"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.structure_environments.StructureEnvironments.NeighborsSet.coords"><code class="docutils literal notranslate"><span class="pre">StructureEnvironments.NeighborsSet.coords</span></code></a></li>
<li class="toctree-l7"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.structure_environments.StructureEnvironments.NeighborsSet.distance_plateau"><code class="docutils literal notranslate"><span class="pre">StructureEnvironments.NeighborsSet.distance_plateau()</span></code></a></li>
<li class="toctree-l7"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.structure_environments.StructureEnvironments.NeighborsSet.distances"><code class="docutils literal notranslate"><span class="pre">StructureEnvironments.NeighborsSet.distances</span></code></a></li>
<li class="toctree-l7"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.structure_environments.StructureEnvironments.NeighborsSet.from_dict"><code class="docutils literal notranslate"><span class="pre">StructureEnvironments.NeighborsSet.from_dict()</span></code></a></li>
<li class="toctree-l7"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.structure_environments.StructureEnvironments.NeighborsSet.get_neighb_voronoi_indices"><code class="docutils literal notranslate"><span class="pre">StructureEnvironments.NeighborsSet.get_neighb_voronoi_indices()</span></code></a></li>
<li class="toctree-l7"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.structure_environments.StructureEnvironments.NeighborsSet.info"><code class="docutils literal notranslate"><span class="pre">StructureEnvironments.NeighborsSet.info</span></code></a></li>
<li class="toctree-l7"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.structure_environments.StructureEnvironments.NeighborsSet.neighb_coords"><code class="docutils literal notranslate"><span class="pre">StructureEnvironments.NeighborsSet.neighb_coords</span></code></a></li>
<li class="toctree-l7"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.structure_environments.StructureEnvironments.NeighborsSet.neighb_coordsOpt"><code class="docutils literal notranslate"><span class="pre">StructureEnvironments.NeighborsSet.neighb_coordsOpt</span></code></a></li>
<li class="toctree-l7"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.structure_environments.StructureEnvironments.NeighborsSet.neighb_sites"><code class="docutils literal notranslate"><span class="pre">StructureEnvironments.NeighborsSet.neighb_sites</span></code></a></li>
<li class="toctree-l7"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.structure_environments.StructureEnvironments.NeighborsSet.neighb_sites_and_indices"><code class="docutils literal notranslate"><span class="pre">StructureEnvironments.NeighborsSet.neighb_sites_and_indices</span></code></a></li>
<li class="toctree-l7"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.structure_environments.StructureEnvironments.NeighborsSet.normalized_angles"><code class="docutils literal notranslate"><span class="pre">StructureEnvironments.NeighborsSet.normalized_angles</span></code></a></li>
<li class="toctree-l7"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.structure_environments.StructureEnvironments.NeighborsSet.normalized_distances"><code class="docutils literal notranslate"><span class="pre">StructureEnvironments.NeighborsSet.normalized_distances</span></code></a></li>
<li class="toctree-l7"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.structure_environments.StructureEnvironments.NeighborsSet.source"><code class="docutils literal notranslate"><span class="pre">StructureEnvironments.NeighborsSet.source</span></code></a></li>
<li class="toctree-l7"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.structure_environments.StructureEnvironments.NeighborsSet.voronoi_grid_surface_points"><code class="docutils literal notranslate"><span class="pre">StructureEnvironments.NeighborsSet.voronoi_grid_surface_points()</span></code></a></li>
</ul>
</li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.structure_environments.StructureEnvironments.add_neighbors_set"><code class="docutils literal notranslate"><span class="pre">StructureEnvironments.add_neighbors_set()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.structure_environments.StructureEnvironments.as_dict"><code class="docutils literal notranslate"><span class="pre">StructureEnvironments.as_dict()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.structure_environments.StructureEnvironments.differences_wrt"><code class="docutils literal notranslate"><span class="pre">StructureEnvironments.differences_wrt()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.structure_environments.StructureEnvironments.from_dict"><code class="docutils literal notranslate"><span class="pre">StructureEnvironments.from_dict()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.structure_environments.StructureEnvironments.get_coordination_environments"><code class="docutils literal notranslate"><span class="pre">StructureEnvironments.get_coordination_environments()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.structure_environments.StructureEnvironments.get_csm"><code class="docutils literal notranslate"><span class="pre">StructureEnvironments.get_csm()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.structure_environments.StructureEnvironments.get_csm_and_maps"><code class="docutils literal notranslate"><span class="pre">StructureEnvironments.get_csm_and_maps()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.structure_environments.StructureEnvironments.get_csms"><code class="docutils literal notranslate"><span class="pre">StructureEnvironments.get_csms()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.structure_environments.StructureEnvironments.get_environments_figure"><code class="docutils literal notranslate"><span class="pre">StructureEnvironments.get_environments_figure()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.structure_environments.StructureEnvironments.init_neighbors_sets"><code class="docutils literal notranslate"><span class="pre">StructureEnvironments.init_neighbors_sets()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.structure_environments.StructureEnvironments.plot_csm_and_maps"><code class="docutils literal notranslate"><span class="pre">StructureEnvironments.plot_csm_and_maps()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.structure_environments.StructureEnvironments.plot_environments"><code class="docutils literal notranslate"><span class="pre">StructureEnvironments.plot_environments()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.structure_environments.StructureEnvironments.save_environments_figure"><code class="docutils literal notranslate"><span class="pre">StructureEnvironments.save_environments_figure()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.structure_environments.StructureEnvironments.update_coordination_environments"><code class="docutils literal notranslate"><span class="pre">StructureEnvironments.update_coordination_environments()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.structure_environments.StructureEnvironments.update_site_info"><code class="docutils literal notranslate"><span class="pre">StructureEnvironments.update_site_info()</span></code></a></li>
</ul>
</li>
</ul>
</li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#module-pymatgen.analysis.chemenv.coordination_environments.voronoi">pymatgen.analysis.chemenv.coordination_environments.voronoi module</a><ul>
<li class="toctree-l5"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.voronoi.DetailedVoronoiContainer"><code class="docutils literal notranslate"><span class="pre">DetailedVoronoiContainer</span></code></a><ul>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.voronoi.DetailedVoronoiContainer.AC"><code class="docutils literal notranslate"><span class="pre">DetailedVoronoiContainer.AC</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.voronoi.DetailedVoronoiContainer.as_dict"><code class="docutils literal notranslate"><span class="pre">DetailedVoronoiContainer.as_dict()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.voronoi.DetailedVoronoiContainer.default_normalized_angle_tolerance"><code class="docutils literal notranslate"><span class="pre">DetailedVoronoiContainer.default_normalized_angle_tolerance</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.voronoi.DetailedVoronoiContainer.default_normalized_distance_tolerance"><code class="docutils literal notranslate"><span class="pre">DetailedVoronoiContainer.default_normalized_distance_tolerance</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.voronoi.DetailedVoronoiContainer.default_voronoi_cutoff"><code class="docutils literal notranslate"><span class="pre">DetailedVoronoiContainer.default_voronoi_cutoff</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.voronoi.DetailedVoronoiContainer.from_dict"><code class="docutils literal notranslate"><span class="pre">DetailedVoronoiContainer.from_dict()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.voronoi.DetailedVoronoiContainer.get_rdf_figure"><code class="docutils literal notranslate"><span class="pre">DetailedVoronoiContainer.get_rdf_figure()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.voronoi.DetailedVoronoiContainer.get_sadf_figure"><code class="docutils literal notranslate"><span class="pre">DetailedVoronoiContainer.get_sadf_figure()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.voronoi.DetailedVoronoiContainer.is_close_to"><code class="docutils literal notranslate"><span class="pre">DetailedVoronoiContainer.is_close_to()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.voronoi.DetailedVoronoiContainer.maps_and_surfaces"><code class="docutils literal notranslate"><span class="pre">DetailedVoronoiContainer.maps_and_surfaces()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.voronoi.DetailedVoronoiContainer.maps_and_surfaces_bounded"><code class="docutils literal notranslate"><span class="pre">DetailedVoronoiContainer.maps_and_surfaces_bounded()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.voronoi.DetailedVoronoiContainer.neighbors"><code class="docutils literal notranslate"><span class="pre">DetailedVoronoiContainer.neighbors()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.voronoi.DetailedVoronoiContainer.neighbors_surfaces"><code class="docutils literal notranslate"><span class="pre">DetailedVoronoiContainer.neighbors_surfaces()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.voronoi.DetailedVoronoiContainer.neighbors_surfaces_bounded"><code class="docutils literal notranslate"><span class="pre">DetailedVoronoiContainer.neighbors_surfaces_bounded()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.voronoi.DetailedVoronoiContainer.setup_neighbors_distances_and_angles"><code class="docutils literal notranslate"><span class="pre">DetailedVoronoiContainer.setup_neighbors_distances_and_angles()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.voronoi.DetailedVoronoiContainer.setup_voronoi_list"><code class="docutils literal notranslate"><span class="pre">DetailedVoronoiContainer.setup_voronoi_list()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.voronoi.DetailedVoronoiContainer.to_bson_voronoi_list2"><code class="docutils literal notranslate"><span class="pre">DetailedVoronoiContainer.to_bson_voronoi_list2()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.voronoi.DetailedVoronoiContainer.voronoi_parameters_bounds_and_limits"><code class="docutils literal notranslate"><span class="pre">DetailedVoronoiContainer.voronoi_parameters_bounds_and_limits()</span></code></a></li>
</ul>
</li>
<li class="toctree-l5"><a class="reference internal" href="pymatgen.analysis.chemenv.coordination_environments.html#pymatgen.analysis.chemenv.coordination_environments.voronoi.from_bson_voronoi_list2"><code class="docutils literal notranslate"><span class="pre">from_bson_voronoi_list2()</span></code></a></li>
</ul>
</li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="pymatgen.analysis.chemenv.utils.html">pymatgen.analysis.chemenv.utils package</a><ul>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.chemenv.utils.html#submodules">Submodules</a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.chemenv.utils.html#module-pymatgen.analysis.chemenv.utils.chemenv_config">pymatgen.analysis.chemenv.utils.chemenv_config module</a><ul>
<li class="toctree-l5"><a class="reference internal" href="pymatgen.analysis.chemenv.utils.html#pymatgen.analysis.chemenv.utils.chemenv_config.ChemEnvConfig"><code class="docutils literal notranslate"><span class="pre">ChemEnvConfig</span></code></a><ul>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.utils.html#pymatgen.analysis.chemenv.utils.chemenv_config.ChemEnvConfig.DEFAULT_PACKAGE_OPTIONS"><code class="docutils literal notranslate"><span class="pre">ChemEnvConfig.DEFAULT_PACKAGE_OPTIONS</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.utils.html#pymatgen.analysis.chemenv.utils.chemenv_config.ChemEnvConfig.auto_load"><code class="docutils literal notranslate"><span class="pre">ChemEnvConfig.auto_load()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.utils.html#pymatgen.analysis.chemenv.utils.chemenv_config.ChemEnvConfig.has_materials_project_access"><code class="docutils literal notranslate"><span class="pre">ChemEnvConfig.has_materials_project_access</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.utils.html#pymatgen.analysis.chemenv.utils.chemenv_config.ChemEnvConfig.package_options_description"><code class="docutils literal notranslate"><span class="pre">ChemEnvConfig.package_options_description()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.utils.html#pymatgen.analysis.chemenv.utils.chemenv_config.ChemEnvConfig.save"><code class="docutils literal notranslate"><span class="pre">ChemEnvConfig.save()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.utils.html#pymatgen.analysis.chemenv.utils.chemenv_config.ChemEnvConfig.setup"><code class="docutils literal notranslate"><span class="pre">ChemEnvConfig.setup()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.utils.html#pymatgen.analysis.chemenv.utils.chemenv_config.ChemEnvConfig.setup_package_options"><code class="docutils literal notranslate"><span class="pre">ChemEnvConfig.setup_package_options()</span></code></a></li>
</ul>
</li>
</ul>
</li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.chemenv.utils.html#module-pymatgen.analysis.chemenv.utils.chemenv_errors">pymatgen.analysis.chemenv.utils.chemenv_errors module</a><ul>
<li class="toctree-l5"><a class="reference internal" href="pymatgen.analysis.chemenv.utils.html#pymatgen.analysis.chemenv.utils.chemenv_errors.AbstractChemenvError"><code class="docutils literal notranslate"><span class="pre">AbstractChemenvError</span></code></a></li>
<li class="toctree-l5"><a class="reference internal" href="pymatgen.analysis.chemenv.utils.html#pymatgen.analysis.chemenv.utils.chemenv_errors.ChemenvError"><code class="docutils literal notranslate"><span class="pre">ChemenvError</span></code></a></li>
<li class="toctree-l5"><a class="reference internal" href="pymatgen.analysis.chemenv.utils.html#pymatgen.analysis.chemenv.utils.chemenv_errors.EquivalentSiteSearchError"><code class="docutils literal notranslate"><span class="pre">EquivalentSiteSearchError</span></code></a></li>
<li class="toctree-l5"><a class="reference internal" href="pymatgen.analysis.chemenv.utils.html#pymatgen.analysis.chemenv.utils.chemenv_errors.NeighborsNotComputedChemenvError"><code class="docutils literal notranslate"><span class="pre">NeighborsNotComputedChemenvError</span></code></a></li>
<li class="toctree-l5"><a class="reference internal" href="pymatgen.analysis.chemenv.utils.html#pymatgen.analysis.chemenv.utils.chemenv_errors.SolidAngleError"><code class="docutils literal notranslate"><span class="pre">SolidAngleError</span></code></a></li>
</ul>
</li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.chemenv.utils.html#module-pymatgen.analysis.chemenv.utils.coordination_geometry_utils">pymatgen.analysis.chemenv.utils.coordination_geometry_utils module</a><ul>
<li class="toctree-l5"><a class="reference internal" href="pymatgen.analysis.chemenv.utils.html#pymatgen.analysis.chemenv.utils.coordination_geometry_utils.Plane"><code class="docutils literal notranslate"><span class="pre">Plane</span></code></a><ul>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.utils.html#pymatgen.analysis.chemenv.utils.coordination_geometry_utils.Plane.TEST_2D_POINTS"><code class="docutils literal notranslate"><span class="pre">Plane.TEST_2D_POINTS</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.utils.html#pymatgen.analysis.chemenv.utils.coordination_geometry_utils.Plane.a"><code class="docutils literal notranslate"><span class="pre">Plane.a</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.utils.html#pymatgen.analysis.chemenv.utils.coordination_geometry_utils.Plane.abcd"><code class="docutils literal notranslate"><span class="pre">Plane.abcd</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.utils.html#pymatgen.analysis.chemenv.utils.coordination_geometry_utils.Plane.b"><code class="docutils literal notranslate"><span class="pre">Plane.b</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.utils.html#pymatgen.analysis.chemenv.utils.coordination_geometry_utils.Plane.c"><code class="docutils literal notranslate"><span class="pre">Plane.c</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.utils.html#pymatgen.analysis.chemenv.utils.coordination_geometry_utils.Plane.coefficients"><code class="docutils literal notranslate"><span class="pre">Plane.coefficients</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.utils.html#pymatgen.analysis.chemenv.utils.coordination_geometry_utils.Plane.crosses_origin"><code class="docutils literal notranslate"><span class="pre">Plane.crosses_origin</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.utils.html#pymatgen.analysis.chemenv.utils.coordination_geometry_utils.Plane.d"><code class="docutils literal notranslate"><span class="pre">Plane.d</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.utils.html#pymatgen.analysis.chemenv.utils.coordination_geometry_utils.Plane.distance_to_origin"><code class="docutils literal notranslate"><span class="pre">Plane.distance_to_origin</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.utils.html#pymatgen.analysis.chemenv.utils.coordination_geometry_utils.Plane.distance_to_point"><code class="docutils literal notranslate"><span class="pre">Plane.distance_to_point()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.utils.html#pymatgen.analysis.chemenv.utils.coordination_geometry_utils.Plane.distances"><code class="docutils literal notranslate"><span class="pre">Plane.distances()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.utils.html#pymatgen.analysis.chemenv.utils.coordination_geometry_utils.Plane.distances_indices_groups"><code class="docutils literal notranslate"><span class="pre">Plane.distances_indices_groups()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.utils.html#pymatgen.analysis.chemenv.utils.coordination_geometry_utils.Plane.distances_indices_sorted"><code class="docutils literal notranslate"><span class="pre">Plane.distances_indices_sorted()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.utils.html#pymatgen.analysis.chemenv.utils.coordination_geometry_utils.Plane.fit_error"><code class="docutils literal notranslate"><span class="pre">Plane.fit_error()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.utils.html#pymatgen.analysis.chemenv.utils.coordination_geometry_utils.Plane.fit_least_square_distance_error"><code class="docutils literal notranslate"><span class="pre">Plane.fit_least_square_distance_error()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.utils.html#pymatgen.analysis.chemenv.utils.coordination_geometry_utils.Plane.fit_maximum_distance_error"><code class="docutils literal notranslate"><span class="pre">Plane.fit_maximum_distance_error()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.utils.html#pymatgen.analysis.chemenv.utils.coordination_geometry_utils.Plane.from_2points_and_origin"><code class="docutils literal notranslate"><span class="pre">Plane.from_2points_and_origin()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.utils.html#pymatgen.analysis.chemenv.utils.coordination_geometry_utils.Plane.from_3points"><code class="docutils literal notranslate"><span class="pre">Plane.from_3points()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.utils.html#pymatgen.analysis.chemenv.utils.coordination_geometry_utils.Plane.from_coefficients"><code class="docutils literal notranslate"><span class="pre">Plane.from_coefficients()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.utils.html#pymatgen.analysis.chemenv.utils.coordination_geometry_utils.Plane.from_npoints"><code class="docutils literal notranslate"><span class="pre">Plane.from_npoints()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.utils.html#pymatgen.analysis.chemenv.utils.coordination_geometry_utils.Plane.from_npoints_least_square_distance"><code class="docutils literal notranslate"><span class="pre">Plane.from_npoints_least_square_distance()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.utils.html#pymatgen.analysis.chemenv.utils.coordination_geometry_utils.Plane.from_npoints_maximum_distance"><code class="docutils literal notranslate"><span class="pre">Plane.from_npoints_maximum_distance()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.utils.html#pymatgen.analysis.chemenv.utils.coordination_geometry_utils.Plane.indices_separate"><code class="docutils literal notranslate"><span class="pre">Plane.indices_separate()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.utils.html#pymatgen.analysis.chemenv.utils.coordination_geometry_utils.Plane.init_3points"><code class="docutils literal notranslate"><span class="pre">Plane.init_3points()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.utils.html#pymatgen.analysis.chemenv.utils.coordination_geometry_utils.Plane.is_in_list"><code class="docutils literal notranslate"><span class="pre">Plane.is_in_list()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.utils.html#pymatgen.analysis.chemenv.utils.coordination_geometry_utils.Plane.is_in_plane"><code class="docutils literal notranslate"><span class="pre">Plane.is_in_plane()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.utils.html#pymatgen.analysis.chemenv.utils.coordination_geometry_utils.Plane.is_same_plane_as"><code class="docutils literal notranslate"><span class="pre">Plane.is_same_plane_as()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.utils.html#pymatgen.analysis.chemenv.utils.coordination_geometry_utils.Plane.orthonormal_vectors"><code class="docutils literal notranslate"><span class="pre">Plane.orthonormal_vectors()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.utils.html#pymatgen.analysis.chemenv.utils.coordination_geometry_utils.Plane.perpendicular_bisector"><code class="docutils literal notranslate"><span class="pre">Plane.perpendicular_bisector()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.utils.html#pymatgen.analysis.chemenv.utils.coordination_geometry_utils.Plane.project_and_to2dim"><code class="docutils literal notranslate"><span class="pre">Plane.project_and_to2dim()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.utils.html#pymatgen.analysis.chemenv.utils.coordination_geometry_utils.Plane.project_and_to2dim_ordered_indices"><code class="docutils literal notranslate"><span class="pre">Plane.project_and_to2dim_ordered_indices()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.utils.html#pymatgen.analysis.chemenv.utils.coordination_geometry_utils.Plane.projectionpoints"><code class="docutils literal notranslate"><span class="pre">Plane.projectionpoints()</span></code></a></li>
</ul>
</li>
<li class="toctree-l5"><a class="reference internal" href="pymatgen.analysis.chemenv.utils.html#pymatgen.analysis.chemenv.utils.coordination_geometry_utils.anticlockwise_sort"><code class="docutils literal notranslate"><span class="pre">anticlockwise_sort()</span></code></a></li>
<li class="toctree-l5"><a class="reference internal" href="pymatgen.analysis.chemenv.utils.html#pymatgen.analysis.chemenv.utils.coordination_geometry_utils.anticlockwise_sort_indices"><code class="docutils literal notranslate"><span class="pre">anticlockwise_sort_indices()</span></code></a></li>
<li class="toctree-l5"><a class="reference internal" href="pymatgen.analysis.chemenv.utils.html#pymatgen.analysis.chemenv.utils.coordination_geometry_utils.changebasis"><code class="docutils literal notranslate"><span class="pre">changebasis()</span></code></a></li>
<li class="toctree-l5"><a class="reference internal" href="pymatgen.analysis.chemenv.utils.html#pymatgen.analysis.chemenv.utils.coordination_geometry_utils.collinear"><code class="docutils literal notranslate"><span class="pre">collinear()</span></code></a></li>
<li class="toctree-l5"><a class="reference internal" href="pymatgen.analysis.chemenv.utils.html#pymatgen.analysis.chemenv.utils.coordination_geometry_utils.diamond_functions"><code class="docutils literal notranslate"><span class="pre">diamond_functions()</span></code></a></li>
<li class="toctree-l5"><a class="reference internal" href="pymatgen.analysis.chemenv.utils.html#pymatgen.analysis.chemenv.utils.coordination_geometry_utils.function_comparison"><code class="docutils literal notranslate"><span class="pre">function_comparison()</span></code></a></li>
<li class="toctree-l5"><a class="reference internal" href="pymatgen.analysis.chemenv.utils.html#pymatgen.analysis.chemenv.utils.coordination_geometry_utils.get_lower_and_upper_f"><code class="docutils literal notranslate"><span class="pre">get_lower_and_upper_f()</span></code></a></li>
<li class="toctree-l5"><a class="reference internal" href="pymatgen.analysis.chemenv.utils.html#pymatgen.analysis.chemenv.utils.coordination_geometry_utils.is_anion_cation_bond"><code class="docutils literal notranslate"><span class="pre">is_anion_cation_bond()</span></code></a></li>
<li class="toctree-l5"><a class="reference internal" href="pymatgen.analysis.chemenv.utils.html#pymatgen.analysis.chemenv.utils.coordination_geometry_utils.matrixTimesVector"><code class="docutils literal notranslate"><span class="pre">matrixTimesVector()</span></code></a></li>
<li class="toctree-l5"><a class="reference internal" href="pymatgen.analysis.chemenv.utils.html#pymatgen.analysis.chemenv.utils.coordination_geometry_utils.quarter_ellipsis_functions"><code class="docutils literal notranslate"><span class="pre">quarter_ellipsis_functions()</span></code></a></li>
<li class="toctree-l5"><a class="reference internal" href="pymatgen.analysis.chemenv.utils.html#pymatgen.analysis.chemenv.utils.coordination_geometry_utils.rectangle_surface_intersection"><code class="docutils literal notranslate"><span class="pre">rectangle_surface_intersection()</span></code></a></li>
<li class="toctree-l5"><a class="reference internal" href="pymatgen.analysis.chemenv.utils.html#pymatgen.analysis.chemenv.utils.coordination_geometry_utils.rotateCoords"><code class="docutils literal notranslate"><span class="pre">rotateCoords()</span></code></a></li>
<li class="toctree-l5"><a class="reference internal" href="pymatgen.analysis.chemenv.utils.html#pymatgen.analysis.chemenv.utils.coordination_geometry_utils.rotateCoordsOpt"><code class="docutils literal notranslate"><span class="pre">rotateCoordsOpt()</span></code></a></li>
<li class="toctree-l5"><a class="reference internal" href="pymatgen.analysis.chemenv.utils.html#pymatgen.analysis.chemenv.utils.coordination_geometry_utils.separation_in_list"><code class="docutils literal notranslate"><span class="pre">separation_in_list()</span></code></a></li>
<li class="toctree-l5"><a class="reference internal" href="pymatgen.analysis.chemenv.utils.html#pymatgen.analysis.chemenv.utils.coordination_geometry_utils.solid_angle"><code class="docutils literal notranslate"><span class="pre">solid_angle()</span></code></a></li>
<li class="toctree-l5"><a class="reference internal" href="pymatgen.analysis.chemenv.utils.html#pymatgen.analysis.chemenv.utils.coordination_geometry_utils.sort_separation"><code class="docutils literal notranslate"><span class="pre">sort_separation()</span></code></a></li>
<li class="toctree-l5"><a class="reference internal" href="pymatgen.analysis.chemenv.utils.html#pymatgen.analysis.chemenv.utils.coordination_geometry_utils.sort_separation_tuple"><code class="docutils literal notranslate"><span class="pre">sort_separation_tuple()</span></code></a></li>
<li class="toctree-l5"><a class="reference internal" href="pymatgen.analysis.chemenv.utils.html#pymatgen.analysis.chemenv.utils.coordination_geometry_utils.spline_functions"><code class="docutils literal notranslate"><span class="pre">spline_functions()</span></code></a></li>
<li class="toctree-l5"><a class="reference internal" href="pymatgen.analysis.chemenv.utils.html#pymatgen.analysis.chemenv.utils.coordination_geometry_utils.vectorsToMatrix"><code class="docutils literal notranslate"><span class="pre">vectorsToMatrix()</span></code></a></li>
</ul>
</li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.chemenv.utils.html#module-pymatgen.analysis.chemenv.utils.defs_utils">pymatgen.analysis.chemenv.utils.defs_utils module</a><ul>
<li class="toctree-l5"><a class="reference internal" href="pymatgen.analysis.chemenv.utils.html#pymatgen.analysis.chemenv.utils.defs_utils.AdditionalConditions"><code class="docutils literal notranslate"><span class="pre">AdditionalConditions</span></code></a><ul>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.utils.html#pymatgen.analysis.chemenv.utils.defs_utils.AdditionalConditions.ALL"><code class="docutils literal notranslate"><span class="pre">AdditionalConditions.ALL</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.utils.html#pymatgen.analysis.chemenv.utils.defs_utils.AdditionalConditions.CONDITION_DESCRIPTION"><code class="docutils literal notranslate"><span class="pre">AdditionalConditions.CONDITION_DESCRIPTION</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.utils.html#pymatgen.analysis.chemenv.utils.defs_utils.AdditionalConditions.NONE"><code class="docutils literal notranslate"><span class="pre">AdditionalConditions.NONE</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.utils.html#pymatgen.analysis.chemenv.utils.defs_utils.AdditionalConditions.NO_AC"><code class="docutils literal notranslate"><span class="pre">AdditionalConditions.NO_AC</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.utils.html#pymatgen.analysis.chemenv.utils.defs_utils.AdditionalConditions.NO_ADDITIONAL_CONDITION"><code class="docutils literal notranslate"><span class="pre">AdditionalConditions.NO_ADDITIONAL_CONDITION</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.utils.html#pymatgen.analysis.chemenv.utils.defs_utils.AdditionalConditions.NO_E2SEB"><code class="docutils literal notranslate"><span class="pre">AdditionalConditions.NO_E2SEB</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.utils.html#pymatgen.analysis.chemenv.utils.defs_utils.AdditionalConditions.NO_ELEMENT_TO_SAME_ELEMENT_BONDS"><code class="docutils literal notranslate"><span class="pre">AdditionalConditions.NO_ELEMENT_TO_SAME_ELEMENT_BONDS</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.utils.html#pymatgen.analysis.chemenv.utils.defs_utils.AdditionalConditions.ONLY_ACB"><code class="docutils literal notranslate"><span class="pre">AdditionalConditions.ONLY_ACB</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.utils.html#pymatgen.analysis.chemenv.utils.defs_utils.AdditionalConditions.ONLY_ACB_AND_NO_E2SEB"><code class="docutils literal notranslate"><span class="pre">AdditionalConditions.ONLY_ACB_AND_NO_E2SEB</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.utils.html#pymatgen.analysis.chemenv.utils.defs_utils.AdditionalConditions.ONLY_ANION_CATION_BONDS"><code class="docutils literal notranslate"><span class="pre">AdditionalConditions.ONLY_ANION_CATION_BONDS</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.utils.html#pymatgen.analysis.chemenv.utils.defs_utils.AdditionalConditions.ONLY_ANION_CATION_BONDS_AND_NO_ELEMENT_TO_SAME_ELEMENT_BONDS"><code class="docutils literal notranslate"><span class="pre">AdditionalConditions.ONLY_ANION_CATION_BONDS_AND_NO_ELEMENT_TO_SAME_ELEMENT_BONDS</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.utils.html#pymatgen.analysis.chemenv.utils.defs_utils.AdditionalConditions.ONLY_E2OB"><code class="docutils literal notranslate"><span class="pre">AdditionalConditions.ONLY_E2OB</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.utils.html#pymatgen.analysis.chemenv.utils.defs_utils.AdditionalConditions.ONLY_ELEMENT_TO_OXYGEN_BONDS"><code class="docutils literal notranslate"><span class="pre">AdditionalConditions.ONLY_ELEMENT_TO_OXYGEN_BONDS</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.utils.html#pymatgen.analysis.chemenv.utils.defs_utils.AdditionalConditions.check_condition"><code class="docutils literal notranslate"><span class="pre">AdditionalConditions.check_condition()</span></code></a></li>
</ul>
</li>
</ul>
</li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.chemenv.utils.html#module-pymatgen.analysis.chemenv.utils.func_utils">pymatgen.analysis.chemenv.utils.func_utils module</a><ul>
<li class="toctree-l5"><a class="reference internal" href="pymatgen.analysis.chemenv.utils.html#pymatgen.analysis.chemenv.utils.func_utils.AbstractRatioFunction"><code class="docutils literal notranslate"><span class="pre">AbstractRatioFunction</span></code></a><ul>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.utils.html#pymatgen.analysis.chemenv.utils.func_utils.AbstractRatioFunction.ALLOWED_FUNCTIONS"><code class="docutils literal notranslate"><span class="pre">AbstractRatioFunction.ALLOWED_FUNCTIONS</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.utils.html#pymatgen.analysis.chemenv.utils.func_utils.AbstractRatioFunction.evaluate"><code class="docutils literal notranslate"><span class="pre">AbstractRatioFunction.evaluate()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.utils.html#pymatgen.analysis.chemenv.utils.func_utils.AbstractRatioFunction.from_dict"><code class="docutils literal notranslate"><span class="pre">AbstractRatioFunction.from_dict()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.utils.html#pymatgen.analysis.chemenv.utils.func_utils.AbstractRatioFunction.setup_parameters"><code class="docutils literal notranslate"><span class="pre">AbstractRatioFunction.setup_parameters()</span></code></a></li>
</ul>
</li>
<li class="toctree-l5"><a class="reference internal" href="pymatgen.analysis.chemenv.utils.html#pymatgen.analysis.chemenv.utils.func_utils.CSMFiniteRatioFunction"><code class="docutils literal notranslate"><span class="pre">CSMFiniteRatioFunction</span></code></a><ul>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.utils.html#pymatgen.analysis.chemenv.utils.func_utils.CSMFiniteRatioFunction.ALLOWED_FUNCTIONS"><code class="docutils literal notranslate"><span class="pre">CSMFiniteRatioFunction.ALLOWED_FUNCTIONS</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.utils.html#pymatgen.analysis.chemenv.utils.func_utils.CSMFiniteRatioFunction.fractions"><code class="docutils literal notranslate"><span class="pre">CSMFiniteRatioFunction.fractions()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.utils.html#pymatgen.analysis.chemenv.utils.func_utils.CSMFiniteRatioFunction.mean_estimator"><code class="docutils literal notranslate"><span class="pre">CSMFiniteRatioFunction.mean_estimator()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.utils.html#pymatgen.analysis.chemenv.utils.func_utils.CSMFiniteRatioFunction.power2_decreasing_exp"><code class="docutils literal notranslate"><span class="pre">CSMFiniteRatioFunction.power2_decreasing_exp()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.utils.html#pymatgen.analysis.chemenv.utils.func_utils.CSMFiniteRatioFunction.ratios"><code class="docutils literal notranslate"><span class="pre">CSMFiniteRatioFunction.ratios()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.utils.html#pymatgen.analysis.chemenv.utils.func_utils.CSMFiniteRatioFunction.smootherstep"><code class="docutils literal notranslate"><span class="pre">CSMFiniteRatioFunction.smootherstep()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.utils.html#pymatgen.analysis.chemenv.utils.func_utils.CSMFiniteRatioFunction.smoothstep"><code class="docutils literal notranslate"><span class="pre">CSMFiniteRatioFunction.smoothstep()</span></code></a></li>
</ul>
</li>
<li class="toctree-l5"><a class="reference internal" href="pymatgen.analysis.chemenv.utils.html#pymatgen.analysis.chemenv.utils.func_utils.CSMInfiniteRatioFunction"><code class="docutils literal notranslate"><span class="pre">CSMInfiniteRatioFunction</span></code></a><ul>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.utils.html#pymatgen.analysis.chemenv.utils.func_utils.CSMInfiniteRatioFunction.ALLOWED_FUNCTIONS"><code class="docutils literal notranslate"><span class="pre">CSMInfiniteRatioFunction.ALLOWED_FUNCTIONS</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.utils.html#pymatgen.analysis.chemenv.utils.func_utils.CSMInfiniteRatioFunction.fractions"><code class="docutils literal notranslate"><span class="pre">CSMInfiniteRatioFunction.fractions()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.utils.html#pymatgen.analysis.chemenv.utils.func_utils.CSMInfiniteRatioFunction.mean_estimator"><code class="docutils literal notranslate"><span class="pre">CSMInfiniteRatioFunction.mean_estimator()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.utils.html#pymatgen.analysis.chemenv.utils.func_utils.CSMInfiniteRatioFunction.power2_inverse_decreasing"><code class="docutils literal notranslate"><span class="pre">CSMInfiniteRatioFunction.power2_inverse_decreasing()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.utils.html#pymatgen.analysis.chemenv.utils.func_utils.CSMInfiniteRatioFunction.power2_inverse_power2_decreasing"><code class="docutils literal notranslate"><span class="pre">CSMInfiniteRatioFunction.power2_inverse_power2_decreasing()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.utils.html#pymatgen.analysis.chemenv.utils.func_utils.CSMInfiniteRatioFunction.ratios"><code class="docutils literal notranslate"><span class="pre">CSMInfiniteRatioFunction.ratios()</span></code></a></li>
</ul>
</li>
<li class="toctree-l5"><a class="reference internal" href="pymatgen.analysis.chemenv.utils.html#pymatgen.analysis.chemenv.utils.func_utils.DeltaCSMRatioFunction"><code class="docutils literal notranslate"><span class="pre">DeltaCSMRatioFunction</span></code></a><ul>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.utils.html#pymatgen.analysis.chemenv.utils.func_utils.DeltaCSMRatioFunction.ALLOWED_FUNCTIONS"><code class="docutils literal notranslate"><span class="pre">DeltaCSMRatioFunction.ALLOWED_FUNCTIONS</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.utils.html#pymatgen.analysis.chemenv.utils.func_utils.DeltaCSMRatioFunction.smootherstep"><code class="docutils literal notranslate"><span class="pre">DeltaCSMRatioFunction.smootherstep()</span></code></a></li>
</ul>
</li>
<li class="toctree-l5"><a class="reference internal" href="pymatgen.analysis.chemenv.utils.html#pymatgen.analysis.chemenv.utils.func_utils.RatioFunction"><code class="docutils literal notranslate"><span class="pre">RatioFunction</span></code></a><ul>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.utils.html#pymatgen.analysis.chemenv.utils.func_utils.RatioFunction.ALLOWED_FUNCTIONS"><code class="docutils literal notranslate"><span class="pre">RatioFunction.ALLOWED_FUNCTIONS</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.utils.html#pymatgen.analysis.chemenv.utils.func_utils.RatioFunction.inverse_smootherstep"><code class="docutils literal notranslate"><span class="pre">RatioFunction.inverse_smootherstep()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.utils.html#pymatgen.analysis.chemenv.utils.func_utils.RatioFunction.inverse_smoothstep"><code class="docutils literal notranslate"><span class="pre">RatioFunction.inverse_smoothstep()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.utils.html#pymatgen.analysis.chemenv.utils.func_utils.RatioFunction.power2_decreasing_exp"><code class="docutils literal notranslate"><span class="pre">RatioFunction.power2_decreasing_exp()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.utils.html#pymatgen.analysis.chemenv.utils.func_utils.RatioFunction.power2_inverse_decreasing"><code class="docutils literal notranslate"><span class="pre">RatioFunction.power2_inverse_decreasing()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.utils.html#pymatgen.analysis.chemenv.utils.func_utils.RatioFunction.power2_inverse_power2_decreasing"><code class="docutils literal notranslate"><span class="pre">RatioFunction.power2_inverse_power2_decreasing()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.utils.html#pymatgen.analysis.chemenv.utils.func_utils.RatioFunction.smootherstep"><code class="docutils literal notranslate"><span class="pre">RatioFunction.smootherstep()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.utils.html#pymatgen.analysis.chemenv.utils.func_utils.RatioFunction.smoothstep"><code class="docutils literal notranslate"><span class="pre">RatioFunction.smoothstep()</span></code></a></li>
</ul>
</li>
</ul>
</li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.chemenv.utils.html#module-pymatgen.analysis.chemenv.utils.graph_utils">pymatgen.analysis.chemenv.utils.graph_utils module</a><ul>
<li class="toctree-l5"><a class="reference internal" href="pymatgen.analysis.chemenv.utils.html#pymatgen.analysis.chemenv.utils.graph_utils.MultiGraphCycle"><code class="docutils literal notranslate"><span class="pre">MultiGraphCycle</span></code></a><ul>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.utils.html#pymatgen.analysis.chemenv.utils.graph_utils.MultiGraphCycle.order"><code class="docutils literal notranslate"><span class="pre">MultiGraphCycle.order()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.utils.html#pymatgen.analysis.chemenv.utils.graph_utils.MultiGraphCycle.validate"><code class="docutils literal notranslate"><span class="pre">MultiGraphCycle.validate()</span></code></a></li>
</ul>
</li>
<li class="toctree-l5"><a class="reference internal" href="pymatgen.analysis.chemenv.utils.html#pymatgen.analysis.chemenv.utils.graph_utils.SimpleGraphCycle"><code class="docutils literal notranslate"><span class="pre">SimpleGraphCycle</span></code></a><ul>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.utils.html#pymatgen.analysis.chemenv.utils.graph_utils.SimpleGraphCycle.as_dict"><code class="docutils literal notranslate"><span class="pre">SimpleGraphCycle.as_dict()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.utils.html#pymatgen.analysis.chemenv.utils.graph_utils.SimpleGraphCycle.from_dict"><code class="docutils literal notranslate"><span class="pre">SimpleGraphCycle.from_dict()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.utils.html#pymatgen.analysis.chemenv.utils.graph_utils.SimpleGraphCycle.from_edges"><code class="docutils literal notranslate"><span class="pre">SimpleGraphCycle.from_edges()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.utils.html#pymatgen.analysis.chemenv.utils.graph_utils.SimpleGraphCycle.order"><code class="docutils literal notranslate"><span class="pre">SimpleGraphCycle.order()</span></code></a></li>
<li class="toctree-l6"><a class="reference internal" href="pymatgen.analysis.chemenv.utils.html#pymatgen.analysis.chemenv.utils.graph_utils.SimpleGraphCycle.validate"><code class="docutils literal notranslate"><span class="pre">SimpleGraphCycle.validate()</span></code></a></li>
</ul>
</li>
<li class="toctree-l5"><a class="reference internal" href="pymatgen.analysis.chemenv.utils.html#pymatgen.analysis.chemenv.utils.graph_utils.get_all_elementary_cycles"><code class="docutils literal notranslate"><span class="pre">get_all_elementary_cycles()</span></code></a></li>
<li class="toctree-l5"><a class="reference internal" href="pymatgen.analysis.chemenv.utils.html#pymatgen.analysis.chemenv.utils.graph_utils.get_all_simple_paths_edges"><code class="docutils literal notranslate"><span class="pre">get_all_simple_paths_edges()</span></code></a></li>
<li class="toctree-l5"><a class="reference internal" href="pymatgen.analysis.chemenv.utils.html#pymatgen.analysis.chemenv.utils.graph_utils.get_delta"><code class="docutils literal notranslate"><span class="pre">get_delta()</span></code></a></li>
</ul>
</li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.chemenv.utils.html#module-pymatgen.analysis.chemenv.utils.math_utils">pymatgen.analysis.chemenv.utils.math_utils module</a><ul>
<li class="toctree-l5"><a class="reference internal" href="pymatgen.analysis.chemenv.utils.html#pymatgen.analysis.chemenv.utils.math_utils.cosinus_step"><code class="docutils literal notranslate"><span class="pre">cosinus_step()</span></code></a></li>
<li class="toctree-l5"><a class="reference internal" href="pymatgen.analysis.chemenv.utils.html#pymatgen.analysis.chemenv.utils.math_utils.divisors"><code class="docutils literal notranslate"><span class="pre">divisors()</span></code></a></li>
<li class="toctree-l5"><a class="reference internal" href="pymatgen.analysis.chemenv.utils.html#pymatgen.analysis.chemenv.utils.math_utils.get_center_of_arc"><code class="docutils literal notranslate"><span class="pre">get_center_of_arc()</span></code></a></li>
<li class="toctree-l5"><a class="reference internal" href="pymatgen.analysis.chemenv.utils.html#pymatgen.analysis.chemenv.utils.math_utils.get_linearly_independent_vectors"><code class="docutils literal notranslate"><span class="pre">get_linearly_independent_vectors()</span></code></a></li>
<li class="toctree-l5"><a class="reference internal" href="pymatgen.analysis.chemenv.utils.html#pymatgen.analysis.chemenv.utils.math_utils.normal_cdf_step"><code class="docutils literal notranslate"><span class="pre">normal_cdf_step()</span></code></a></li>
<li class="toctree-l5"><a class="reference internal" href="pymatgen.analysis.chemenv.utils.html#pymatgen.analysis.chemenv.utils.math_utils.power2_decreasing_exp"><code class="docutils literal notranslate"><span class="pre">power2_decreasing_exp()</span></code></a></li>
<li class="toctree-l5"><a class="reference internal" href="pymatgen.analysis.chemenv.utils.html#pymatgen.analysis.chemenv.utils.math_utils.power2_inverse_decreasing"><code class="docutils literal notranslate"><span class="pre">power2_inverse_decreasing()</span></code></a></li>
<li class="toctree-l5"><a class="reference internal" href="pymatgen.analysis.chemenv.utils.html#pymatgen.analysis.chemenv.utils.math_utils.power2_inverse_power2_decreasing"><code class="docutils literal notranslate"><span class="pre">power2_inverse_power2_decreasing()</span></code></a></li>
<li class="toctree-l5"><a class="reference internal" href="pymatgen.analysis.chemenv.utils.html#pymatgen.analysis.chemenv.utils.math_utils.power2_inverse_powern_decreasing"><code class="docutils literal notranslate"><span class="pre">power2_inverse_powern_decreasing()</span></code></a></li>
<li class="toctree-l5"><a class="reference internal" href="pymatgen.analysis.chemenv.utils.html#pymatgen.analysis.chemenv.utils.math_utils.power2_tangent_decreasing"><code class="docutils literal notranslate"><span class="pre">power2_tangent_decreasing()</span></code></a></li>
<li class="toctree-l5"><a class="reference internal" href="pymatgen.analysis.chemenv.utils.html#pymatgen.analysis.chemenv.utils.math_utils.power3_step"><code class="docutils literal notranslate"><span class="pre">power3_step()</span></code></a></li>
<li class="toctree-l5"><a class="reference internal" href="pymatgen.analysis.chemenv.utils.html#pymatgen.analysis.chemenv.utils.math_utils.powern_decreasing"><code class="docutils literal notranslate"><span class="pre">powern_decreasing()</span></code></a></li>
<li class="toctree-l5"><a class="reference internal" href="pymatgen.analysis.chemenv.utils.html#pymatgen.analysis.chemenv.utils.math_utils.powern_parts_step"><code class="docutils literal notranslate"><span class="pre">powern_parts_step()</span></code></a></li>
<li class="toctree-l5"><a class="reference internal" href="pymatgen.analysis.chemenv.utils.html#pymatgen.analysis.chemenv.utils.math_utils.prime_factors"><code class="docutils literal notranslate"><span class="pre">prime_factors()</span></code></a></li>
<li class="toctree-l5"><a class="reference internal" href="pymatgen.analysis.chemenv.utils.html#pymatgen.analysis.chemenv.utils.math_utils.scale_and_clamp"><code class="docutils literal notranslate"><span class="pre">scale_and_clamp()</span></code></a></li>
<li class="toctree-l5"><a class="reference internal" href="pymatgen.analysis.chemenv.utils.html#pymatgen.analysis.chemenv.utils.math_utils.smootherstep"><code class="docutils literal notranslate"><span class="pre">smootherstep()</span></code></a></li>
<li class="toctree-l5"><a class="reference internal" href="pymatgen.analysis.chemenv.utils.html#pymatgen.analysis.chemenv.utils.math_utils.smoothstep"><code class="docutils literal notranslate"><span class="pre">smoothstep()</span></code></a></li>
</ul>
</li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.chemenv.utils.html#module-pymatgen.analysis.chemenv.utils.scripts_utils">pymatgen.analysis.chemenv.utils.scripts_utils module</a><ul>
<li class="toctree-l5"><a class="reference internal" href="pymatgen.analysis.chemenv.utils.html#pymatgen.analysis.chemenv.utils.scripts_utils.compute_environments"><code class="docutils literal notranslate"><span class="pre">compute_environments()</span></code></a></li>
<li class="toctree-l5"><a class="reference internal" href="pymatgen.analysis.chemenv.utils.html#pymatgen.analysis.chemenv.utils.scripts_utils.draw_cg"><code class="docutils literal notranslate"><span class="pre">draw_cg()</span></code></a></li>
<li class="toctree-l5"><a class="reference internal" href="pymatgen.analysis.chemenv.utils.html#pymatgen.analysis.chemenv.utils.scripts_utils.visualize"><code class="docutils literal notranslate"><span class="pre">visualize()</span></code></a></li>
</ul>
</li>
</ul>
</li>
</ul>
</li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="pymatgen.analysis.diffraction.html">pymatgen.analysis.diffraction package</a><ul>
<li class="toctree-l2"><a class="reference internal" href="pymatgen.analysis.diffraction.html#submodules">Submodules</a></li>
<li class="toctree-l2"><a class="reference internal" href="pymatgen.analysis.diffraction.html#module-pymatgen.analysis.diffraction.core">pymatgen.analysis.diffraction.core module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="pymatgen.analysis.diffraction.html#pymatgen.analysis.diffraction.core.AbstractDiffractionPatternCalculator"><code class="docutils literal notranslate"><span class="pre">AbstractDiffractionPatternCalculator</span></code></a><ul>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.diffraction.html#pymatgen.analysis.diffraction.core.AbstractDiffractionPatternCalculator.SCALED_INTENSITY_TOL"><code class="docutils literal notranslate"><span class="pre">AbstractDiffractionPatternCalculator.SCALED_INTENSITY_TOL</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.diffraction.html#pymatgen.analysis.diffraction.core.AbstractDiffractionPatternCalculator.TWO_THETA_TOL"><code class="docutils literal notranslate"><span class="pre">AbstractDiffractionPatternCalculator.TWO_THETA_TOL</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.diffraction.html#pymatgen.analysis.diffraction.core.AbstractDiffractionPatternCalculator.get_pattern"><code class="docutils literal notranslate"><span class="pre">AbstractDiffractionPatternCalculator.get_pattern()</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.diffraction.html#pymatgen.analysis.diffraction.core.AbstractDiffractionPatternCalculator.get_plot"><code class="docutils literal notranslate"><span class="pre">AbstractDiffractionPatternCalculator.get_plot()</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.diffraction.html#pymatgen.analysis.diffraction.core.AbstractDiffractionPatternCalculator.plot_structures"><code class="docutils literal notranslate"><span class="pre">AbstractDiffractionPatternCalculator.plot_structures()</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.diffraction.html#pymatgen.analysis.diffraction.core.AbstractDiffractionPatternCalculator.show_plot"><code class="docutils literal notranslate"><span class="pre">AbstractDiffractionPatternCalculator.show_plot()</span></code></a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="pymatgen.analysis.diffraction.html#pymatgen.analysis.diffraction.core.DiffractionPattern"><code class="docutils literal notranslate"><span class="pre">DiffractionPattern</span></code></a><ul>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.diffraction.html#pymatgen.analysis.diffraction.core.DiffractionPattern.XLABEL"><code class="docutils literal notranslate"><span class="pre">DiffractionPattern.XLABEL</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.diffraction.html#pymatgen.analysis.diffraction.core.DiffractionPattern.YLABEL"><code class="docutils literal notranslate"><span class="pre">DiffractionPattern.YLABEL</span></code></a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="pymatgen.analysis.diffraction.html#pymatgen.analysis.diffraction.core.get_unique_families"><code class="docutils literal notranslate"><span class="pre">get_unique_families()</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="pymatgen.analysis.diffraction.html#module-pymatgen.analysis.diffraction.neutron">pymatgen.analysis.diffraction.neutron module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="pymatgen.analysis.diffraction.html#pymatgen.analysis.diffraction.neutron.NDCalculator"><code class="docutils literal notranslate"><span class="pre">NDCalculator</span></code></a><ul>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.diffraction.html#pymatgen.analysis.diffraction.neutron.NDCalculator.get_pattern"><code class="docutils literal notranslate"><span class="pre">NDCalculator.get_pattern()</span></code></a></li>
</ul>
</li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="pymatgen.analysis.diffraction.html#module-pymatgen.analysis.diffraction.tem">pymatgen.analysis.diffraction.tem module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="pymatgen.analysis.diffraction.html#pymatgen.analysis.diffraction.tem.TEMCalculator"><code class="docutils literal notranslate"><span class="pre">TEMCalculator</span></code></a><ul>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.diffraction.html#pymatgen.analysis.diffraction.tem.TEMCalculator.bragg_angles"><code class="docutils literal notranslate"><span class="pre">TEMCalculator.bragg_angles()</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.diffraction.html#pymatgen.analysis.diffraction.tem.TEMCalculator.cell_intensity"><code class="docutils literal notranslate"><span class="pre">TEMCalculator.cell_intensity()</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.diffraction.html#pymatgen.analysis.diffraction.tem.TEMCalculator.cell_scattering_factors"><code class="docutils literal notranslate"><span class="pre">TEMCalculator.cell_scattering_factors()</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.diffraction.html#pymatgen.analysis.diffraction.tem.TEMCalculator.electron_scattering_factors"><code class="docutils literal notranslate"><span class="pre">TEMCalculator.electron_scattering_factors()</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.diffraction.html#pymatgen.analysis.diffraction.tem.TEMCalculator.generate_points"><code class="docutils literal notranslate"><span class="pre">TEMCalculator.generate_points()</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.diffraction.html#pymatgen.analysis.diffraction.tem.TEMCalculator.get_first_point"><code class="docutils literal notranslate"><span class="pre">TEMCalculator.get_first_point()</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.diffraction.html#pymatgen.analysis.diffraction.tem.TEMCalculator.get_interplanar_angle"><code class="docutils literal notranslate"><span class="pre">TEMCalculator.get_interplanar_angle()</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.diffraction.html#pymatgen.analysis.diffraction.tem.TEMCalculator.get_interplanar_spacings"><code class="docutils literal notranslate"><span class="pre">TEMCalculator.get_interplanar_spacings()</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.diffraction.html#pymatgen.analysis.diffraction.tem.TEMCalculator.get_pattern"><code class="docutils literal notranslate"><span class="pre">TEMCalculator.get_pattern()</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.diffraction.html#pymatgen.analysis.diffraction.tem.TEMCalculator.get_plot_2d"><code class="docutils literal notranslate"><span class="pre">TEMCalculator.get_plot_2d()</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.diffraction.html#pymatgen.analysis.diffraction.tem.TEMCalculator.get_plot_2d_concise"><code class="docutils literal notranslate"><span class="pre">TEMCalculator.get_plot_2d_concise()</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.diffraction.html#pymatgen.analysis.diffraction.tem.TEMCalculator.get_plot_coeffs"><code class="docutils literal notranslate"><span class="pre">TEMCalculator.get_plot_coeffs()</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.diffraction.html#pymatgen.analysis.diffraction.tem.TEMCalculator.get_positions"><code class="docutils literal notranslate"><span class="pre">TEMCalculator.get_positions()</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.diffraction.html#pymatgen.analysis.diffraction.tem.TEMCalculator.get_s2"><code class="docutils literal notranslate"><span class="pre">TEMCalculator.get_s2()</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.diffraction.html#pymatgen.analysis.diffraction.tem.TEMCalculator.is_parallel"><code class="docutils literal notranslate"><span class="pre">TEMCalculator.is_parallel()</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.diffraction.html#pymatgen.analysis.diffraction.tem.TEMCalculator.normalized_cell_intensity"><code class="docutils literal notranslate"><span class="pre">TEMCalculator.normalized_cell_intensity()</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.diffraction.html#pymatgen.analysis.diffraction.tem.TEMCalculator.tem_dots"><code class="docutils literal notranslate"><span class="pre">TEMCalculator.tem_dots()</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.diffraction.html#pymatgen.analysis.diffraction.tem.TEMCalculator.wavelength_rel"><code class="docutils literal notranslate"><span class="pre">TEMCalculator.wavelength_rel()</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.diffraction.html#pymatgen.analysis.diffraction.tem.TEMCalculator.x_ray_factors"><code class="docutils literal notranslate"><span class="pre">TEMCalculator.x_ray_factors()</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.diffraction.html#pymatgen.analysis.diffraction.tem.TEMCalculator.zone_axis_filter"><code class="docutils literal notranslate"><span class="pre">TEMCalculator.zone_axis_filter()</span></code></a></li>
</ul>
</li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="pymatgen.analysis.diffraction.html#module-pymatgen.analysis.diffraction.xrd">pymatgen.analysis.diffraction.xrd module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="pymatgen.analysis.diffraction.html#pymatgen.analysis.diffraction.xrd.XRDCalculator"><code class="docutils literal notranslate"><span class="pre">XRDCalculator</span></code></a><ul>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.diffraction.html#pymatgen.analysis.diffraction.xrd.XRDCalculator.AVAILABLE_RADIATION"><code class="docutils literal notranslate"><span class="pre">XRDCalculator.AVAILABLE_RADIATION</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.diffraction.html#pymatgen.analysis.diffraction.xrd.XRDCalculator.get_pattern"><code class="docutils literal notranslate"><span class="pre">XRDCalculator.get_pattern()</span></code></a></li>
</ul>
</li>
</ul>
</li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="pymatgen.analysis.elasticity.html">pymatgen.analysis.elasticity package</a><ul>
<li class="toctree-l2"><a class="reference internal" href="pymatgen.analysis.elasticity.html#submodules">Submodules</a></li>
<li class="toctree-l2"><a class="reference internal" href="pymatgen.analysis.elasticity.html#module-pymatgen.analysis.elasticity.elastic">pymatgen.analysis.elasticity.elastic module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="pymatgen.analysis.elasticity.html#pymatgen.analysis.elasticity.elastic.ComplianceTensor"><code class="docutils literal notranslate"><span class="pre">ComplianceTensor</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="pymatgen.analysis.elasticity.html#pymatgen.analysis.elasticity.elastic.ElasticTensor"><code class="docutils literal notranslate"><span class="pre">ElasticTensor</span></code></a><ul>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.elasticity.html#pymatgen.analysis.elasticity.elastic.ElasticTensor.agne_diffusive_thermalcond"><code class="docutils literal notranslate"><span class="pre">ElasticTensor.agne_diffusive_thermalcond()</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.elasticity.html#pymatgen.analysis.elasticity.elastic.ElasticTensor.cahill_thermalcond"><code class="docutils literal notranslate"><span class="pre">ElasticTensor.cahill_thermalcond()</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.elasticity.html#pymatgen.analysis.elasticity.elastic.ElasticTensor.clarke_thermalcond"><code class="docutils literal notranslate"><span class="pre">ElasticTensor.clarke_thermalcond()</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.elasticity.html#pymatgen.analysis.elasticity.elastic.ElasticTensor.compliance_tensor"><code class="docutils literal notranslate"><span class="pre">ElasticTensor.compliance_tensor</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.elasticity.html#pymatgen.analysis.elasticity.elastic.ElasticTensor.debye_temperature"><code class="docutils literal notranslate"><span class="pre">ElasticTensor.debye_temperature()</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.elasticity.html#pymatgen.analysis.elasticity.elastic.ElasticTensor.directional_elastic_mod"><code class="docutils literal notranslate"><span class="pre">ElasticTensor.directional_elastic_mod()</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.elasticity.html#pymatgen.analysis.elasticity.elastic.ElasticTensor.directional_poisson_ratio"><code class="docutils literal notranslate"><span class="pre">ElasticTensor.directional_poisson_ratio()</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.elasticity.html#pymatgen.analysis.elasticity.elastic.ElasticTensor.from_independent_strains"><code class="docutils literal notranslate"><span class="pre">ElasticTensor.from_independent_strains()</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.elasticity.html#pymatgen.analysis.elasticity.elastic.ElasticTensor.from_pseudoinverse"><code class="docutils literal notranslate"><span class="pre">ElasticTensor.from_pseudoinverse()</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.elasticity.html#pymatgen.analysis.elasticity.elastic.ElasticTensor.g_reuss"><code class="docutils literal notranslate"><span class="pre">ElasticTensor.g_reuss</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.elasticity.html#pymatgen.analysis.elasticity.elastic.ElasticTensor.g_voigt"><code class="docutils literal notranslate"><span class="pre">ElasticTensor.g_voigt</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.elasticity.html#pymatgen.analysis.elasticity.elastic.ElasticTensor.g_vrh"><code class="docutils literal notranslate"><span class="pre">ElasticTensor.g_vrh</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.elasticity.html#pymatgen.analysis.elasticity.elastic.ElasticTensor.get_structure_property_dict"><code class="docutils literal notranslate"><span class="pre">ElasticTensor.get_structure_property_dict()</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.elasticity.html#pymatgen.analysis.elasticity.elastic.ElasticTensor.green_kristoffel"><code class="docutils literal notranslate"><span class="pre">ElasticTensor.green_kristoffel()</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.elasticity.html#pymatgen.analysis.elasticity.elastic.ElasticTensor.homogeneous_poisson"><code class="docutils literal notranslate"><span class="pre">ElasticTensor.homogeneous_poisson</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.elasticity.html#pymatgen.analysis.elasticity.elastic.ElasticTensor.k_reuss"><code class="docutils literal notranslate"><span class="pre">ElasticTensor.k_reuss</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.elasticity.html#pymatgen.analysis.elasticity.elastic.ElasticTensor.k_voigt"><code class="docutils literal notranslate"><span class="pre">ElasticTensor.k_voigt</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.elasticity.html#pymatgen.analysis.elasticity.elastic.ElasticTensor.k_vrh"><code class="docutils literal notranslate"><span class="pre">ElasticTensor.k_vrh</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.elasticity.html#pymatgen.analysis.elasticity.elastic.ElasticTensor.long_v"><code class="docutils literal notranslate"><span class="pre">ElasticTensor.long_v()</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.elasticity.html#pymatgen.analysis.elasticity.elastic.ElasticTensor.property_dict"><code class="docutils literal notranslate"><span class="pre">ElasticTensor.property_dict</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.elasticity.html#pymatgen.analysis.elasticity.elastic.ElasticTensor.snyder_ac"><code class="docutils literal notranslate"><span class="pre">ElasticTensor.snyder_ac()</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.elasticity.html#pymatgen.analysis.elasticity.elastic.ElasticTensor.snyder_opt"><code class="docutils literal notranslate"><span class="pre">ElasticTensor.snyder_opt()</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.elasticity.html#pymatgen.analysis.elasticity.elastic.ElasticTensor.snyder_total"><code class="docutils literal notranslate"><span class="pre">ElasticTensor.snyder_total()</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.elasticity.html#pymatgen.analysis.elasticity.elastic.ElasticTensor.trans_v"><code class="docutils literal notranslate"><span class="pre">ElasticTensor.trans_v()</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.elasticity.html#pymatgen.analysis.elasticity.elastic.ElasticTensor.universal_anisotropy"><code class="docutils literal notranslate"><span class="pre">ElasticTensor.universal_anisotropy</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.elasticity.html#pymatgen.analysis.elasticity.elastic.ElasticTensor.y_mod"><code class="docutils literal notranslate"><span class="pre">ElasticTensor.y_mod</span></code></a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="pymatgen.analysis.elasticity.html#pymatgen.analysis.elasticity.elastic.ElasticTensorExpansion"><code class="docutils literal notranslate"><span class="pre">ElasticTensorExpansion</span></code></a><ul>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.elasticity.html#pymatgen.analysis.elasticity.elastic.ElasticTensorExpansion.calculate_stress"><code class="docutils literal notranslate"><span class="pre">ElasticTensorExpansion.calculate_stress()</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.elasticity.html#pymatgen.analysis.elasticity.elastic.ElasticTensorExpansion.energy_density"><code class="docutils literal notranslate"><span class="pre">ElasticTensorExpansion.energy_density()</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.elasticity.html#pymatgen.analysis.elasticity.elastic.ElasticTensorExpansion.from_diff_fit"><code class="docutils literal notranslate"><span class="pre">ElasticTensorExpansion.from_diff_fit()</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.elasticity.html#pymatgen.analysis.elasticity.elastic.ElasticTensorExpansion.get_compliance_expansion"><code class="docutils literal notranslate"><span class="pre">ElasticTensorExpansion.get_compliance_expansion()</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.elasticity.html#pymatgen.analysis.elasticity.elastic.ElasticTensorExpansion.get_effective_ecs"><code class="docutils literal notranslate"><span class="pre">ElasticTensorExpansion.get_effective_ecs()</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.elasticity.html#pymatgen.analysis.elasticity.elastic.ElasticTensorExpansion.get_ggt"><code class="docutils literal notranslate"><span class="pre">ElasticTensorExpansion.get_ggt()</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.elasticity.html#pymatgen.analysis.elasticity.elastic.ElasticTensorExpansion.get_gruneisen_parameter"><code class="docutils literal notranslate"><span class="pre">ElasticTensorExpansion.get_gruneisen_parameter()</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.elasticity.html#pymatgen.analysis.elasticity.elastic.ElasticTensorExpansion.get_heat_capacity"><code class="docutils literal notranslate"><span class="pre">ElasticTensorExpansion.get_heat_capacity()</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.elasticity.html#pymatgen.analysis.elasticity.elastic.ElasticTensorExpansion.get_stability_criteria"><code class="docutils literal notranslate"><span class="pre">ElasticTensorExpansion.get_stability_criteria()</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.elasticity.html#pymatgen.analysis.elasticity.elastic.ElasticTensorExpansion.get_strain_from_stress"><code class="docutils literal notranslate"><span class="pre">ElasticTensorExpansion.get_strain_from_stress()</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.elasticity.html#pymatgen.analysis.elasticity.elastic.ElasticTensorExpansion.get_symmetric_wallace_tensor"><code class="docutils literal notranslate"><span class="pre">ElasticTensorExpansion.get_symmetric_wallace_tensor()</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.elasticity.html#pymatgen.analysis.elasticity.elastic.ElasticTensorExpansion.get_tgt"><code class="docutils literal notranslate"><span class="pre">ElasticTensorExpansion.get_tgt()</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.elasticity.html#pymatgen.analysis.elasticity.elastic.ElasticTensorExpansion.get_wallace_tensor"><code class="docutils literal notranslate"><span class="pre">ElasticTensorExpansion.get_wallace_tensor()</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.elasticity.html#pymatgen.analysis.elasticity.elastic.ElasticTensorExpansion.get_yield_stress"><code class="docutils literal notranslate"><span class="pre">ElasticTensorExpansion.get_yield_stress()</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.elasticity.html#pymatgen.analysis.elasticity.elastic.ElasticTensorExpansion.omega"><code class="docutils literal notranslate"><span class="pre">ElasticTensorExpansion.omega()</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.elasticity.html#pymatgen.analysis.elasticity.elastic.ElasticTensorExpansion.order"><code class="docutils literal notranslate"><span class="pre">ElasticTensorExpansion.order</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.elasticity.html#pymatgen.analysis.elasticity.elastic.ElasticTensorExpansion.thermal_expansion_coeff"><code class="docutils literal notranslate"><span class="pre">ElasticTensorExpansion.thermal_expansion_coeff()</span></code></a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="pymatgen.analysis.elasticity.html#pymatgen.analysis.elasticity.elastic.NthOrderElasticTensor"><code class="docutils literal notranslate"><span class="pre">NthOrderElasticTensor</span></code></a><ul>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.elasticity.html#pymatgen.analysis.elasticity.elastic.NthOrderElasticTensor.GPa_to_eV_A3"><code class="docutils literal notranslate"><span class="pre">NthOrderElasticTensor.GPa_to_eV_A3</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.elasticity.html#pymatgen.analysis.elasticity.elastic.NthOrderElasticTensor.calculate_stress"><code class="docutils literal notranslate"><span class="pre">NthOrderElasticTensor.calculate_stress()</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.elasticity.html#pymatgen.analysis.elasticity.elastic.NthOrderElasticTensor.energy_density"><code class="docutils literal notranslate"><span class="pre">NthOrderElasticTensor.energy_density()</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.elasticity.html#pymatgen.analysis.elasticity.elastic.NthOrderElasticTensor.from_diff_fit"><code class="docutils literal notranslate"><span class="pre">NthOrderElasticTensor.from_diff_fit()</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.elasticity.html#pymatgen.analysis.elasticity.elastic.NthOrderElasticTensor.order"><code class="docutils literal notranslate"><span class="pre">NthOrderElasticTensor.order</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.elasticity.html#pymatgen.analysis.elasticity.elastic.NthOrderElasticTensor.symbol"><code class="docutils literal notranslate"><span class="pre">NthOrderElasticTensor.symbol</span></code></a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="pymatgen.analysis.elasticity.html#pymatgen.analysis.elasticity.elastic.diff_fit"><code class="docutils literal notranslate"><span class="pre">diff_fit()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="pymatgen.analysis.elasticity.html#pymatgen.analysis.elasticity.elastic.find_eq_stress"><code class="docutils literal notranslate"><span class="pre">find_eq_stress()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="pymatgen.analysis.elasticity.html#pymatgen.analysis.elasticity.elastic.generate_pseudo"><code class="docutils literal notranslate"><span class="pre">generate_pseudo()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="pymatgen.analysis.elasticity.html#pymatgen.analysis.elasticity.elastic.get_diff_coeff"><code class="docutils literal notranslate"><span class="pre">get_diff_coeff()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="pymatgen.analysis.elasticity.html#pymatgen.analysis.elasticity.elastic.get_strain_state_dict"><code class="docutils literal notranslate"><span class="pre">get_strain_state_dict()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="pymatgen.analysis.elasticity.html#pymatgen.analysis.elasticity.elastic.get_symbol_list"><code class="docutils literal notranslate"><span class="pre">get_symbol_list()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="pymatgen.analysis.elasticity.html#pymatgen.analysis.elasticity.elastic.raise_if_unphysical"><code class="docutils literal notranslate"><span class="pre">raise_if_unphysical()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="pymatgen.analysis.elasticity.html#pymatgen.analysis.elasticity.elastic.subs"><code class="docutils literal notranslate"><span class="pre">subs()</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="pymatgen.analysis.elasticity.html#module-pymatgen.analysis.elasticity.strain">pymatgen.analysis.elasticity.strain module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="pymatgen.analysis.elasticity.html#pymatgen.analysis.elasticity.strain.Deformation"><code class="docutils literal notranslate"><span class="pre">Deformation</span></code></a><ul>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.elasticity.html#pymatgen.analysis.elasticity.strain.Deformation.apply_to_structure"><code class="docutils literal notranslate"><span class="pre">Deformation.apply_to_structure()</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.elasticity.html#pymatgen.analysis.elasticity.strain.Deformation.from_index_amount"><code class="docutils literal notranslate"><span class="pre">Deformation.from_index_amount()</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.elasticity.html#pymatgen.analysis.elasticity.strain.Deformation.get_perturbed_indices"><code class="docutils literal notranslate"><span class="pre">Deformation.get_perturbed_indices()</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.elasticity.html#pymatgen.analysis.elasticity.strain.Deformation.green_lagrange_strain"><code class="docutils literal notranslate"><span class="pre">Deformation.green_lagrange_strain</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.elasticity.html#pymatgen.analysis.elasticity.strain.Deformation.is_independent"><code class="docutils literal notranslate"><span class="pre">Deformation.is_independent()</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.elasticity.html#pymatgen.analysis.elasticity.strain.Deformation.symbol"><code class="docutils literal notranslate"><span class="pre">Deformation.symbol</span></code></a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="pymatgen.analysis.elasticity.html#pymatgen.analysis.elasticity.strain.DeformedStructureSet"><code class="docutils literal notranslate"><span class="pre">DeformedStructureSet</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="pymatgen.analysis.elasticity.html#pymatgen.analysis.elasticity.strain.Strain"><code class="docutils literal notranslate"><span class="pre">Strain</span></code></a><ul>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.elasticity.html#pymatgen.analysis.elasticity.strain.Strain.from_deformation"><code class="docutils literal notranslate"><span class="pre">Strain.from_deformation()</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.elasticity.html#pymatgen.analysis.elasticity.strain.Strain.from_index_amount"><code class="docutils literal notranslate"><span class="pre">Strain.from_index_amount()</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.elasticity.html#pymatgen.analysis.elasticity.strain.Strain.get_deformation_matrix"><code class="docutils literal notranslate"><span class="pre">Strain.get_deformation_matrix()</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.elasticity.html#pymatgen.analysis.elasticity.strain.Strain.symbol"><code class="docutils literal notranslate"><span class="pre">Strain.symbol</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.elasticity.html#pymatgen.analysis.elasticity.strain.Strain.von_mises_strain"><code class="docutils literal notranslate"><span class="pre">Strain.von_mises_strain</span></code></a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="pymatgen.analysis.elasticity.html#pymatgen.analysis.elasticity.strain.convert_strain_to_deformation"><code class="docutils literal notranslate"><span class="pre">convert_strain_to_deformation()</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="pymatgen.analysis.elasticity.html#module-pymatgen.analysis.elasticity.stress">pymatgen.analysis.elasticity.stress module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="pymatgen.analysis.elasticity.html#pymatgen.analysis.elasticity.stress.Stress"><code class="docutils literal notranslate"><span class="pre">Stress</span></code></a><ul>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.elasticity.html#pymatgen.analysis.elasticity.stress.Stress.dev_principal_invariants"><code class="docutils literal notranslate"><span class="pre">Stress.dev_principal_invariants</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.elasticity.html#pymatgen.analysis.elasticity.stress.Stress.deviator_stress"><code class="docutils literal notranslate"><span class="pre">Stress.deviator_stress</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.elasticity.html#pymatgen.analysis.elasticity.stress.Stress.mean_stress"><code class="docutils literal notranslate"><span class="pre">Stress.mean_stress</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.elasticity.html#pymatgen.analysis.elasticity.stress.Stress.piola_kirchoff_1"><code class="docutils literal notranslate"><span class="pre">Stress.piola_kirchoff_1()</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.elasticity.html#pymatgen.analysis.elasticity.stress.Stress.piola_kirchoff_2"><code class="docutils literal notranslate"><span class="pre">Stress.piola_kirchoff_2()</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.elasticity.html#pymatgen.analysis.elasticity.stress.Stress.symbol"><code class="docutils literal notranslate"><span class="pre">Stress.symbol</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.elasticity.html#pymatgen.analysis.elasticity.stress.Stress.von_mises"><code class="docutils literal notranslate"><span class="pre">Stress.von_mises</span></code></a></li>
</ul>
</li>
</ul>
</li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="pymatgen.analysis.ferroelectricity.html">pymatgen.analysis.ferroelectricity package</a><ul>
<li class="toctree-l2"><a class="reference internal" href="pymatgen.analysis.ferroelectricity.html#submodules">Submodules</a></li>
<li class="toctree-l2"><a class="reference internal" href="pymatgen.analysis.ferroelectricity.html#module-pymatgen.analysis.ferroelectricity.polarization">pymatgen.analysis.ferroelectricity.polarization module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="pymatgen.analysis.ferroelectricity.html#pymatgen.analysis.ferroelectricity.polarization.EnergyTrend"><code class="docutils literal notranslate"><span class="pre">EnergyTrend</span></code></a><ul>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.ferroelectricity.html#pymatgen.analysis.ferroelectricity.polarization.EnergyTrend.endpoints_minima"><code class="docutils literal notranslate"><span class="pre">EnergyTrend.endpoints_minima()</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.ferroelectricity.html#pymatgen.analysis.ferroelectricity.polarization.EnergyTrend.max_spline_jump"><code class="docutils literal notranslate"><span class="pre">EnergyTrend.max_spline_jump()</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.ferroelectricity.html#pymatgen.analysis.ferroelectricity.polarization.EnergyTrend.smoothness"><code class="docutils literal notranslate"><span class="pre">EnergyTrend.smoothness()</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.ferroelectricity.html#pymatgen.analysis.ferroelectricity.polarization.EnergyTrend.spline"><code class="docutils literal notranslate"><span class="pre">EnergyTrend.spline()</span></code></a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="pymatgen.analysis.ferroelectricity.html#pymatgen.analysis.ferroelectricity.polarization.Polarization"><code class="docutils literal notranslate"><span class="pre">Polarization</span></code></a><ul>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.ferroelectricity.html#pymatgen.analysis.ferroelectricity.polarization.Polarization.from_outcars_and_structures"><code class="docutils literal notranslate"><span class="pre">Polarization.from_outcars_and_structures()</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.ferroelectricity.html#pymatgen.analysis.ferroelectricity.polarization.Polarization.get_lattice_quanta"><code class="docutils literal notranslate"><span class="pre">Polarization.get_lattice_quanta()</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.ferroelectricity.html#pymatgen.analysis.ferroelectricity.polarization.Polarization.get_pelecs_and_pions"><code class="docutils literal notranslate"><span class="pre">Polarization.get_pelecs_and_pions()</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.ferroelectricity.html#pymatgen.analysis.ferroelectricity.polarization.Polarization.get_polarization_change"><code class="docutils literal notranslate"><span class="pre">Polarization.get_polarization_change()</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.ferroelectricity.html#pymatgen.analysis.ferroelectricity.polarization.Polarization.get_polarization_change_norm"><code class="docutils literal notranslate"><span class="pre">Polarization.get_polarization_change_norm()</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.ferroelectricity.html#pymatgen.analysis.ferroelectricity.polarization.Polarization.get_same_branch_polarization_data"><code class="docutils literal notranslate"><span class="pre">Polarization.get_same_branch_polarization_data()</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.ferroelectricity.html#pymatgen.analysis.ferroelectricity.polarization.Polarization.max_spline_jumps"><code class="docutils literal notranslate"><span class="pre">Polarization.max_spline_jumps()</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.ferroelectricity.html#pymatgen.analysis.ferroelectricity.polarization.Polarization.same_branch_splines"><code class="docutils literal notranslate"><span class="pre">Polarization.same_branch_splines()</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.ferroelectricity.html#pymatgen.analysis.ferroelectricity.polarization.Polarization.smoothness"><code class="docutils literal notranslate"><span class="pre">Polarization.smoothness()</span></code></a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="pymatgen.analysis.ferroelectricity.html#pymatgen.analysis.ferroelectricity.polarization.calc_ionic"><code class="docutils literal notranslate"><span class="pre">calc_ionic()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="pymatgen.analysis.ferroelectricity.html#pymatgen.analysis.ferroelectricity.polarization.get_nearest_site"><code class="docutils literal notranslate"><span class="pre">get_nearest_site()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="pymatgen.analysis.ferroelectricity.html#pymatgen.analysis.ferroelectricity.polarization.get_total_ionic_dipole"><code class="docutils literal notranslate"><span class="pre">get_total_ionic_dipole()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="pymatgen.analysis.ferroelectricity.html#pymatgen.analysis.ferroelectricity.polarization.zval_dict_from_potcar"><code class="docutils literal notranslate"><span class="pre">zval_dict_from_potcar()</span></code></a></li>
</ul>
</li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="pymatgen.analysis.gb.html">pymatgen.analysis.gb package</a><ul>
<li class="toctree-l2"><a class="reference internal" href="pymatgen.analysis.gb.html#submodules">Submodules</a></li>
<li class="toctree-l2"><a class="reference internal" href="pymatgen.analysis.gb.html#module-pymatgen.analysis.gb.grain">pymatgen.analysis.gb.grain module</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="pymatgen.analysis.interfaces.html">pymatgen.analysis.interfaces package</a><ul>
<li class="toctree-l2"><a class="reference internal" href="pymatgen.analysis.interfaces.html#submodules">Submodules</a></li>
<li class="toctree-l2"><a class="reference internal" href="pymatgen.analysis.interfaces.html#module-pymatgen.analysis.interfaces.coherent_interfaces">pymatgen.analysis.interfaces.coherent_interfaces module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="pymatgen.analysis.interfaces.html#pymatgen.analysis.interfaces.coherent_interfaces.CoherentInterfaceBuilder"><code class="docutils literal notranslate"><span class="pre">CoherentInterfaceBuilder</span></code></a><ul>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.interfaces.html#pymatgen.analysis.interfaces.coherent_interfaces.CoherentInterfaceBuilder.get_interfaces"><code class="docutils literal notranslate"><span class="pre">CoherentInterfaceBuilder.get_interfaces()</span></code></a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="pymatgen.analysis.interfaces.html#pymatgen.analysis.interfaces.coherent_interfaces.from_2d_to_3d"><code class="docutils literal notranslate"><span class="pre">from_2d_to_3d()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="pymatgen.analysis.interfaces.html#pymatgen.analysis.interfaces.coherent_interfaces.get_2d_transform"><code class="docutils literal notranslate"><span class="pre">get_2d_transform()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="pymatgen.analysis.interfaces.html#pymatgen.analysis.interfaces.coherent_interfaces.get_rot_3d_for_2d"><code class="docutils literal notranslate"><span class="pre">get_rot_3d_for_2d()</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="pymatgen.analysis.interfaces.html#module-pymatgen.analysis.interfaces.substrate_analyzer">pymatgen.analysis.interfaces.substrate_analyzer module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="pymatgen.analysis.interfaces.html#pymatgen.analysis.interfaces.substrate_analyzer.SubstrateAnalyzer"><code class="docutils literal notranslate"><span class="pre">SubstrateAnalyzer</span></code></a><ul>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.interfaces.html#pymatgen.analysis.interfaces.substrate_analyzer.SubstrateAnalyzer.calculate"><code class="docutils literal notranslate"><span class="pre">SubstrateAnalyzer.calculate()</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.interfaces.html#pymatgen.analysis.interfaces.substrate_analyzer.SubstrateAnalyzer.generate_surface_vectors"><code class="docutils literal notranslate"><span class="pre">SubstrateAnalyzer.generate_surface_vectors()</span></code></a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="pymatgen.analysis.interfaces.html#pymatgen.analysis.interfaces.substrate_analyzer.SubstrateMatch"><code class="docutils literal notranslate"><span class="pre">SubstrateMatch</span></code></a><ul>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.interfaces.html#pymatgen.analysis.interfaces.substrate_analyzer.SubstrateMatch.elastic_energy"><code class="docutils literal notranslate"><span class="pre">SubstrateMatch.elastic_energy</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.interfaces.html#pymatgen.analysis.interfaces.substrate_analyzer.SubstrateMatch.film_miller"><code class="docutils literal notranslate"><span class="pre">SubstrateMatch.film_miller</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.interfaces.html#pymatgen.analysis.interfaces.substrate_analyzer.SubstrateMatch.from_zsl"><code class="docutils literal notranslate"><span class="pre">SubstrateMatch.from_zsl()</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.interfaces.html#pymatgen.analysis.interfaces.substrate_analyzer.SubstrateMatch.ground_state_energy"><code class="docutils literal notranslate"><span class="pre">SubstrateMatch.ground_state_energy</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.interfaces.html#pymatgen.analysis.interfaces.substrate_analyzer.SubstrateMatch.strain"><code class="docutils literal notranslate"><span class="pre">SubstrateMatch.strain</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.interfaces.html#pymatgen.analysis.interfaces.substrate_analyzer.SubstrateMatch.substrate_miller"><code class="docutils literal notranslate"><span class="pre">SubstrateMatch.substrate_miller</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.interfaces.html#pymatgen.analysis.interfaces.substrate_analyzer.SubstrateMatch.total_energy"><code class="docutils literal notranslate"><span class="pre">SubstrateMatch.total_energy</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.interfaces.html#pymatgen.analysis.interfaces.substrate_analyzer.SubstrateMatch.von_mises_strain"><code class="docutils literal notranslate"><span class="pre">SubstrateMatch.von_mises_strain</span></code></a></li>
</ul>
</li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="pymatgen.analysis.interfaces.html#module-pymatgen.analysis.interfaces.zsl">pymatgen.analysis.interfaces.zsl module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="pymatgen.analysis.interfaces.html#pymatgen.analysis.interfaces.zsl.ZSLGenerator"><code class="docutils literal notranslate"><span class="pre">ZSLGenerator</span></code></a><ul>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.interfaces.html#pymatgen.analysis.interfaces.zsl.ZSLGenerator.generate_sl_transformation_sets"><code class="docutils literal notranslate"><span class="pre">ZSLGenerator.generate_sl_transformation_sets()</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.interfaces.html#pymatgen.analysis.interfaces.zsl.ZSLGenerator.get_equiv_transformations"><code class="docutils literal notranslate"><span class="pre">ZSLGenerator.get_equiv_transformations()</span></code></a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="pymatgen.analysis.interfaces.html#pymatgen.analysis.interfaces.zsl.ZSLMatch"><code class="docutils literal notranslate"><span class="pre">ZSLMatch</span></code></a><ul>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.interfaces.html#pymatgen.analysis.interfaces.zsl.ZSLMatch.film_sl_vectors"><code class="docutils literal notranslate"><span class="pre">ZSLMatch.film_sl_vectors</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.interfaces.html#pymatgen.analysis.interfaces.zsl.ZSLMatch.film_transformation"><code class="docutils literal notranslate"><span class="pre">ZSLMatch.film_transformation</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.interfaces.html#pymatgen.analysis.interfaces.zsl.ZSLMatch.film_vectors"><code class="docutils literal notranslate"><span class="pre">ZSLMatch.film_vectors</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.interfaces.html#pymatgen.analysis.interfaces.zsl.ZSLMatch.match_area"><code class="docutils literal notranslate"><span class="pre">ZSLMatch.match_area</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.interfaces.html#pymatgen.analysis.interfaces.zsl.ZSLMatch.match_transformation"><code class="docutils literal notranslate"><span class="pre">ZSLMatch.match_transformation</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.interfaces.html#pymatgen.analysis.interfaces.zsl.ZSLMatch.substrate_sl_vectors"><code class="docutils literal notranslate"><span class="pre">ZSLMatch.substrate_sl_vectors</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.interfaces.html#pymatgen.analysis.interfaces.zsl.ZSLMatch.substrate_transformation"><code class="docutils literal notranslate"><span class="pre">ZSLMatch.substrate_transformation</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.interfaces.html#pymatgen.analysis.interfaces.zsl.ZSLMatch.substrate_vectors"><code class="docutils literal notranslate"><span class="pre">ZSLMatch.substrate_vectors</span></code></a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="pymatgen.analysis.interfaces.html#pymatgen.analysis.interfaces.zsl.fast_norm"><code class="docutils literal notranslate"><span class="pre">fast_norm()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="pymatgen.analysis.interfaces.html#pymatgen.analysis.interfaces.zsl.gen_sl_transform_matrices"><code class="docutils literal notranslate"><span class="pre">gen_sl_transform_matrices()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="pymatgen.analysis.interfaces.html#pymatgen.analysis.interfaces.zsl.get_factors"><code class="docutils literal notranslate"><span class="pre">get_factors()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="pymatgen.analysis.interfaces.html#pymatgen.analysis.interfaces.zsl.is_same_vectors"><code class="docutils literal notranslate"><span class="pre">is_same_vectors()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="pymatgen.analysis.interfaces.html#pymatgen.analysis.interfaces.zsl.reduce_vectors"><code class="docutils literal notranslate"><span class="pre">reduce_vectors()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="pymatgen.analysis.interfaces.html#pymatgen.analysis.interfaces.zsl.rel_angle"><code class="docutils literal notranslate"><span class="pre">rel_angle()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="pymatgen.analysis.interfaces.html#pymatgen.analysis.interfaces.zsl.rel_strain"><code class="docutils literal notranslate"><span class="pre">rel_strain()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="pymatgen.analysis.interfaces.html#pymatgen.analysis.interfaces.zsl.vec_angle"><code class="docutils literal notranslate"><span class="pre">vec_angle()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="pymatgen.analysis.interfaces.html#pymatgen.analysis.interfaces.zsl.vec_area"><code class="docutils literal notranslate"><span class="pre">vec_area()</span></code></a></li>
</ul>
</li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="pymatgen.analysis.magnetism.html">pymatgen.analysis.magnetism package</a><ul>
<li class="toctree-l2"><a class="reference internal" href="pymatgen.analysis.magnetism.html#submodules">Submodules</a></li>
<li class="toctree-l2"><a class="reference internal" href="pymatgen.analysis.magnetism.html#module-pymatgen.analysis.magnetism.analyzer">pymatgen.analysis.magnetism.analyzer module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="pymatgen.analysis.magnetism.html#pymatgen.analysis.magnetism.analyzer.CollinearMagneticStructureAnalyzer"><code class="docutils literal notranslate"><span class="pre">CollinearMagneticStructureAnalyzer</span></code></a><ul>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.magnetism.html#pymatgen.analysis.magnetism.analyzer.CollinearMagneticStructureAnalyzer.get_exchange_group_info"><code class="docutils literal notranslate"><span class="pre">CollinearMagneticStructureAnalyzer.get_exchange_group_info()</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.magnetism.html#pymatgen.analysis.magnetism.analyzer.CollinearMagneticStructureAnalyzer.get_ferromagnetic_structure"><code class="docutils literal notranslate"><span class="pre">CollinearMagneticStructureAnalyzer.get_ferromagnetic_structure()</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.magnetism.html#pymatgen.analysis.magnetism.analyzer.CollinearMagneticStructureAnalyzer.get_nonmagnetic_structure"><code class="docutils literal notranslate"><span class="pre">CollinearMagneticStructureAnalyzer.get_nonmagnetic_structure()</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.magnetism.html#pymatgen.analysis.magnetism.analyzer.CollinearMagneticStructureAnalyzer.get_structure_with_only_magnetic_atoms"><code class="docutils literal notranslate"><span class="pre">CollinearMagneticStructureAnalyzer.get_structure_with_only_magnetic_atoms()</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.magnetism.html#pymatgen.analysis.magnetism.analyzer.CollinearMagneticStructureAnalyzer.get_structure_with_spin"><code class="docutils literal notranslate"><span class="pre">CollinearMagneticStructureAnalyzer.get_structure_with_spin()</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.magnetism.html#pymatgen.analysis.magnetism.analyzer.CollinearMagneticStructureAnalyzer.is_magnetic"><code class="docutils literal notranslate"><span class="pre">CollinearMagneticStructureAnalyzer.is_magnetic</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.magnetism.html#pymatgen.analysis.magnetism.analyzer.CollinearMagneticStructureAnalyzer.magmoms"><code class="docutils literal notranslate"><span class="pre">CollinearMagneticStructureAnalyzer.magmoms</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.magnetism.html#pymatgen.analysis.magnetism.analyzer.CollinearMagneticStructureAnalyzer.magnetic_species_and_magmoms"><code class="docutils literal notranslate"><span class="pre">CollinearMagneticStructureAnalyzer.magnetic_species_and_magmoms</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.magnetism.html#pymatgen.analysis.magnetism.analyzer.CollinearMagneticStructureAnalyzer.matches_ordering"><code class="docutils literal notranslate"><span class="pre">CollinearMagneticStructureAnalyzer.matches_ordering()</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.magnetism.html#pymatgen.analysis.magnetism.analyzer.CollinearMagneticStructureAnalyzer.number_of_magnetic_sites"><code class="docutils literal notranslate"><span class="pre">CollinearMagneticStructureAnalyzer.number_of_magnetic_sites</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.magnetism.html#pymatgen.analysis.magnetism.analyzer.CollinearMagneticStructureAnalyzer.number_of_unique_magnetic_sites"><code class="docutils literal notranslate"><span class="pre">CollinearMagneticStructureAnalyzer.number_of_unique_magnetic_sites()</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.magnetism.html#pymatgen.analysis.magnetism.analyzer.CollinearMagneticStructureAnalyzer.ordering"><code class="docutils literal notranslate"><span class="pre">CollinearMagneticStructureAnalyzer.ordering</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.magnetism.html#pymatgen.analysis.magnetism.analyzer.CollinearMagneticStructureAnalyzer.types_of_magnetic_specie"><code class="docutils literal notranslate"><span class="pre">CollinearMagneticStructureAnalyzer.types_of_magnetic_specie</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.magnetism.html#pymatgen.analysis.magnetism.analyzer.CollinearMagneticStructureAnalyzer.types_of_magnetic_species"><code class="docutils literal notranslate"><span class="pre">CollinearMagneticStructureAnalyzer.types_of_magnetic_species</span></code></a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="pymatgen.analysis.magnetism.html#pymatgen.analysis.magnetism.analyzer.MagneticDeformation"><code class="docutils literal notranslate"><span class="pre">MagneticDeformation</span></code></a><ul>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.magnetism.html#pymatgen.analysis.magnetism.analyzer.MagneticDeformation.deformation"><code class="docutils literal notranslate"><span class="pre">MagneticDeformation.deformation</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.magnetism.html#pymatgen.analysis.magnetism.analyzer.MagneticDeformation.type"><code class="docutils literal notranslate"><span class="pre">MagneticDeformation.type</span></code></a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="pymatgen.analysis.magnetism.html#pymatgen.analysis.magnetism.analyzer.MagneticStructureEnumerator"><code class="docutils literal notranslate"><span class="pre">MagneticStructureEnumerator</span></code></a><ul>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.magnetism.html#pymatgen.analysis.magnetism.analyzer.MagneticStructureEnumerator.available_strategies"><code class="docutils literal notranslate"><span class="pre">MagneticStructureEnumerator.available_strategies</span></code></a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="pymatgen.analysis.magnetism.html#pymatgen.analysis.magnetism.analyzer.Ordering"><code class="docutils literal notranslate"><span class="pre">Ordering</span></code></a><ul>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.magnetism.html#pymatgen.analysis.magnetism.analyzer.Ordering.AFM"><code class="docutils literal notranslate"><span class="pre">Ordering.AFM</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.magnetism.html#pymatgen.analysis.magnetism.analyzer.Ordering.FM"><code class="docutils literal notranslate"><span class="pre">Ordering.FM</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.magnetism.html#pymatgen.analysis.magnetism.analyzer.Ordering.FiM"><code class="docutils literal notranslate"><span class="pre">Ordering.FiM</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.magnetism.html#pymatgen.analysis.magnetism.analyzer.Ordering.NM"><code class="docutils literal notranslate"><span class="pre">Ordering.NM</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.magnetism.html#pymatgen.analysis.magnetism.analyzer.Ordering.Unknown"><code class="docutils literal notranslate"><span class="pre">Ordering.Unknown</span></code></a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="pymatgen.analysis.magnetism.html#pymatgen.analysis.magnetism.analyzer.OverwriteMagmomMode"><code class="docutils literal notranslate"><span class="pre">OverwriteMagmomMode</span></code></a><ul>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.magnetism.html#pymatgen.analysis.magnetism.analyzer.OverwriteMagmomMode.none"><code class="docutils literal notranslate"><span class="pre">OverwriteMagmomMode.none</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.magnetism.html#pymatgen.analysis.magnetism.analyzer.OverwriteMagmomMode.normalize"><code class="docutils literal notranslate"><span class="pre">OverwriteMagmomMode.normalize</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.magnetism.html#pymatgen.analysis.magnetism.analyzer.OverwriteMagmomMode.replace_all"><code class="docutils literal notranslate"><span class="pre">OverwriteMagmomMode.replace_all</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.magnetism.html#pymatgen.analysis.magnetism.analyzer.OverwriteMagmomMode.replace_all_if_undefined"><code class="docutils literal notranslate"><span class="pre">OverwriteMagmomMode.replace_all_if_undefined</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.magnetism.html#pymatgen.analysis.magnetism.analyzer.OverwriteMagmomMode.respect_sign"><code class="docutils literal notranslate"><span class="pre">OverwriteMagmomMode.respect_sign</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.magnetism.html#pymatgen.analysis.magnetism.analyzer.OverwriteMagmomMode.respect_zeros"><code class="docutils literal notranslate"><span class="pre">OverwriteMagmomMode.respect_zeros</span></code></a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="pymatgen.analysis.magnetism.html#pymatgen.analysis.magnetism.analyzer.magnetic_deformation"><code class="docutils literal notranslate"><span class="pre">magnetic_deformation()</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="pymatgen.analysis.magnetism.html#module-pymatgen.analysis.magnetism.heisenberg">pymatgen.analysis.magnetism.heisenberg module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="pymatgen.analysis.magnetism.html#pymatgen.analysis.magnetism.heisenberg.HeisenbergMapper"><code class="docutils literal notranslate"><span class="pre">HeisenbergMapper</span></code></a><ul>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.magnetism.html#pymatgen.analysis.magnetism.heisenberg.HeisenbergMapper.strategy"><code class="docutils literal notranslate"><span class="pre">HeisenbergMapper.strategy</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.magnetism.html#pymatgen.analysis.magnetism.heisenberg.HeisenbergMapper.sgraphs"><code class="docutils literal notranslate"><span class="pre">HeisenbergMapper.sgraphs</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.magnetism.html#pymatgen.analysis.magnetism.heisenberg.HeisenbergMapper.unique_site_ids"><code class="docutils literal notranslate"><span class="pre">HeisenbergMapper.unique_site_ids</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.magnetism.html#pymatgen.analysis.magnetism.heisenberg.HeisenbergMapper.wyckoff_ids"><code class="docutils literal notranslate"><span class="pre">HeisenbergMapper.wyckoff_ids</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.magnetism.html#pymatgen.analysis.magnetism.heisenberg.HeisenbergMapper.nn_interactions"><code class="docutils literal notranslate"><span class="pre">HeisenbergMapper.nn_interactions</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.magnetism.html#pymatgen.analysis.magnetism.heisenberg.HeisenbergMapper.dists"><code class="docutils literal notranslate"><span class="pre">HeisenbergMapper.dists</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.magnetism.html#pymatgen.analysis.magnetism.heisenberg.HeisenbergMapper.ex_mat"><code class="docutils literal notranslate"><span class="pre">HeisenbergMapper.ex_mat</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.magnetism.html#pymatgen.analysis.magnetism.heisenberg.HeisenbergMapper.ex_params"><code class="docutils literal notranslate"><span class="pre">HeisenbergMapper.ex_params</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.magnetism.html#pymatgen.analysis.magnetism.heisenberg.HeisenbergMapper.estimate_exchange"><code class="docutils literal notranslate"><span class="pre">HeisenbergMapper.estimate_exchange()</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.magnetism.html#pymatgen.analysis.magnetism.heisenberg.HeisenbergMapper.get_exchange"><code class="docutils literal notranslate"><span class="pre">HeisenbergMapper.get_exchange()</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.magnetism.html#pymatgen.analysis.magnetism.heisenberg.HeisenbergMapper.get_heisenberg_model"><code class="docutils literal notranslate"><span class="pre">HeisenbergMapper.get_heisenberg_model()</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.magnetism.html#pymatgen.analysis.magnetism.heisenberg.HeisenbergMapper.get_interaction_graph"><code class="docutils literal notranslate"><span class="pre">HeisenbergMapper.get_interaction_graph()</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.magnetism.html#pymatgen.analysis.magnetism.heisenberg.HeisenbergMapper.get_low_energy_orderings"><code class="docutils literal notranslate"><span class="pre">HeisenbergMapper.get_low_energy_orderings()</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.magnetism.html#pymatgen.analysis.magnetism.heisenberg.HeisenbergMapper.get_mft_temperature"><code class="docutils literal notranslate"><span class="pre">HeisenbergMapper.get_mft_temperature()</span></code></a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="pymatgen.analysis.magnetism.html#pymatgen.analysis.magnetism.heisenberg.HeisenbergModel"><code class="docutils literal notranslate"><span class="pre">HeisenbergModel</span></code></a><ul>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.magnetism.html#pymatgen.analysis.magnetism.heisenberg.HeisenbergModel.as_dict"><code class="docutils literal notranslate"><span class="pre">HeisenbergModel.as_dict()</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.magnetism.html#pymatgen.analysis.magnetism.heisenberg.HeisenbergModel.from_dict"><code class="docutils literal notranslate"><span class="pre">HeisenbergModel.from_dict()</span></code></a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="pymatgen.analysis.magnetism.html#pymatgen.analysis.magnetism.heisenberg.HeisenbergScreener"><code class="docutils literal notranslate"><span class="pre">HeisenbergScreener</span></code></a><ul>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.magnetism.html#pymatgen.analysis.magnetism.heisenberg.HeisenbergScreener.screened_structures"><code class="docutils literal notranslate"><span class="pre">HeisenbergScreener.screened_structures</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.magnetism.html#pymatgen.analysis.magnetism.heisenberg.HeisenbergScreener.screened_energies"><code class="docutils literal notranslate"><span class="pre">HeisenbergScreener.screened_energies</span></code></a></li>
</ul>
</li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="pymatgen.analysis.magnetism.html#module-pymatgen.analysis.magnetism.jahnteller">pymatgen.analysis.magnetism.jahnteller module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="pymatgen.analysis.magnetism.html#pymatgen.analysis.magnetism.jahnteller.JahnTellerAnalyzer"><code class="docutils literal notranslate"><span class="pre">JahnTellerAnalyzer</span></code></a><ul>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.magnetism.html#pymatgen.analysis.magnetism.jahnteller.JahnTellerAnalyzer.get_analysis"><code class="docutils literal notranslate"><span class="pre">JahnTellerAnalyzer.get_analysis()</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.magnetism.html#pymatgen.analysis.magnetism.jahnteller.JahnTellerAnalyzer.get_analysis_and_structure"><code class="docutils literal notranslate"><span class="pre">JahnTellerAnalyzer.get_analysis_and_structure()</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.magnetism.html#pymatgen.analysis.magnetism.jahnteller.JahnTellerAnalyzer.get_magnitude_of_effect_from_species"><code class="docutils literal notranslate"><span class="pre">JahnTellerAnalyzer.get_magnitude_of_effect_from_species()</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.magnetism.html#pymatgen.analysis.magnetism.jahnteller.JahnTellerAnalyzer.get_magnitude_of_effect_from_spin_config"><code class="docutils literal notranslate"><span class="pre">JahnTellerAnalyzer.get_magnitude_of_effect_from_spin_config()</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.magnetism.html#pymatgen.analysis.magnetism.jahnteller.JahnTellerAnalyzer.is_jahn_teller_active"><code class="docutils literal notranslate"><span class="pre">JahnTellerAnalyzer.is_jahn_teller_active()</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.magnetism.html#pymatgen.analysis.magnetism.jahnteller.JahnTellerAnalyzer.mu_so"><code class="docutils literal notranslate"><span class="pre">JahnTellerAnalyzer.mu_so()</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.magnetism.html#pymatgen.analysis.magnetism.jahnteller.JahnTellerAnalyzer.tag_structure"><code class="docutils literal notranslate"><span class="pre">JahnTellerAnalyzer.tag_structure()</span></code></a></li>
</ul>
</li>
</ul>
</li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="pymatgen.analysis.solar.html">pymatgen.analysis.solar package</a><ul>
<li class="toctree-l2"><a class="reference internal" href="pymatgen.analysis.solar.html#submodules">Submodules</a></li>
<li class="toctree-l2"><a class="reference internal" href="pymatgen.analysis.solar.html#module-pymatgen.analysis.solar.slme">pymatgen.analysis.solar.slme module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="pymatgen.analysis.solar.html#pymatgen.analysis.solar.slme.absorption_coefficient"><code class="docutils literal notranslate"><span class="pre">absorption_coefficient()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="pymatgen.analysis.solar.html#pymatgen.analysis.solar.slme.get_dir_indir_gap"><code class="docutils literal notranslate"><span class="pre">get_dir_indir_gap()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="pymatgen.analysis.solar.html#pymatgen.analysis.solar.slme.optics"><code class="docutils literal notranslate"><span class="pre">optics()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="pymatgen.analysis.solar.html#pymatgen.analysis.solar.slme.parse_dielectric_data"><code class="docutils literal notranslate"><span class="pre">parse_dielectric_data()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="pymatgen.analysis.solar.html#pymatgen.analysis.solar.slme.slme"><code class="docutils literal notranslate"><span class="pre">slme()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="pymatgen.analysis.solar.html#pymatgen.analysis.solar.slme.to_matrix"><code class="docutils literal notranslate"><span class="pre">to_matrix()</span></code></a></li>
</ul>
</li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="pymatgen.analysis.structure_prediction.html">pymatgen.analysis.structure_prediction package</a><ul>
<li class="toctree-l2"><a class="reference internal" href="pymatgen.analysis.structure_prediction.html#submodules">Submodules</a></li>
<li class="toctree-l2"><a class="reference internal" href="pymatgen.analysis.structure_prediction.html#module-pymatgen.analysis.structure_prediction.dopant_predictor">pymatgen.analysis.structure_prediction.dopant_predictor module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="pymatgen.analysis.structure_prediction.html#pymatgen.analysis.structure_prediction.dopant_predictor.get_dopants_from_shannon_radii"><code class="docutils literal notranslate"><span class="pre">get_dopants_from_shannon_radii()</span></code></a></li>
<li class="toctree-l3"><a class="reference internal" href="pymatgen.analysis.structure_prediction.html#pymatgen.analysis.structure_prediction.dopant_predictor.get_dopants_from_substitution_probabilities"><code class="docutils literal notranslate"><span class="pre">get_dopants_from_substitution_probabilities()</span></code></a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="pymatgen.analysis.structure_prediction.html#module-pymatgen.analysis.structure_prediction.substitution_probability">pymatgen.analysis.structure_prediction.substitution_probability module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="pymatgen.analysis.structure_prediction.html#pymatgen.analysis.structure_prediction.substitution_probability.SubstitutionPredictor"><code class="docutils literal notranslate"><span class="pre">SubstitutionPredictor</span></code></a><ul>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.structure_prediction.html#pymatgen.analysis.structure_prediction.substitution_probability.SubstitutionPredictor.composition_prediction"><code class="docutils literal notranslate"><span class="pre">SubstitutionPredictor.composition_prediction()</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.structure_prediction.html#pymatgen.analysis.structure_prediction.substitution_probability.SubstitutionPredictor.list_prediction"><code class="docutils literal notranslate"><span class="pre">SubstitutionPredictor.list_prediction()</span></code></a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="pymatgen.analysis.structure_prediction.html#pymatgen.analysis.structure_prediction.substitution_probability.SubstitutionProbability"><code class="docutils literal notranslate"><span class="pre">SubstitutionProbability</span></code></a><ul>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.structure_prediction.html#pymatgen.analysis.structure_prediction.substitution_probability.SubstitutionProbability.as_dict"><code class="docutils literal notranslate"><span class="pre">SubstitutionProbability.as_dict()</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.structure_prediction.html#pymatgen.analysis.structure_prediction.substitution_probability.SubstitutionProbability.cond_prob"><code class="docutils literal notranslate"><span class="pre">SubstitutionProbability.cond_prob()</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.structure_prediction.html#pymatgen.analysis.structure_prediction.substitution_probability.SubstitutionProbability.cond_prob_list"><code class="docutils literal notranslate"><span class="pre">SubstitutionProbability.cond_prob_list()</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.structure_prediction.html#pymatgen.analysis.structure_prediction.substitution_probability.SubstitutionProbability.from_dict"><code class="docutils literal notranslate"><span class="pre">SubstitutionProbability.from_dict()</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.structure_prediction.html#pymatgen.analysis.structure_prediction.substitution_probability.SubstitutionProbability.get_lambda"><code class="docutils literal notranslate"><span class="pre">SubstitutionProbability.get_lambda()</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.structure_prediction.html#pymatgen.analysis.structure_prediction.substitution_probability.SubstitutionProbability.get_px"><code class="docutils literal notranslate"><span class="pre">SubstitutionProbability.get_px()</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.structure_prediction.html#pymatgen.analysis.structure_prediction.substitution_probability.SubstitutionProbability.pair_corr"><code class="docutils literal notranslate"><span class="pre">SubstitutionProbability.pair_corr()</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.structure_prediction.html#pymatgen.analysis.structure_prediction.substitution_probability.SubstitutionProbability.prob"><code class="docutils literal notranslate"><span class="pre">SubstitutionProbability.prob()</span></code></a></li>
</ul>
</li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="pymatgen.analysis.structure_prediction.html#module-pymatgen.analysis.structure_prediction.substitutor">pymatgen.analysis.structure_prediction.substitutor module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="pymatgen.analysis.structure_prediction.html#pymatgen.analysis.structure_prediction.substitutor.Substitutor"><code class="docutils literal notranslate"><span class="pre">Substitutor</span></code></a><ul>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.structure_prediction.html#pymatgen.analysis.structure_prediction.substitutor.Substitutor.as_dict"><code class="docutils literal notranslate"><span class="pre">Substitutor.as_dict()</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.structure_prediction.html#pymatgen.analysis.structure_prediction.substitutor.Substitutor.charge_balanced_tol"><code class="docutils literal notranslate"><span class="pre">Substitutor.charge_balanced_tol</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.structure_prediction.html#pymatgen.analysis.structure_prediction.substitutor.Substitutor.from_dict"><code class="docutils literal notranslate"><span class="pre">Substitutor.from_dict()</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.structure_prediction.html#pymatgen.analysis.structure_prediction.substitutor.Substitutor.get_allowed_species"><code class="docutils literal notranslate"><span class="pre">Substitutor.get_allowed_species()</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.structure_prediction.html#pymatgen.analysis.structure_prediction.substitutor.Substitutor.pred_from_comp"><code class="docutils literal notranslate"><span class="pre">Substitutor.pred_from_comp()</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.structure_prediction.html#pymatgen.analysis.structure_prediction.substitutor.Substitutor.pred_from_list"><code class="docutils literal notranslate"><span class="pre">Substitutor.pred_from_list()</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.structure_prediction.html#pymatgen.analysis.structure_prediction.substitutor.Substitutor.pred_from_structures"><code class="docutils literal notranslate"><span class="pre">Substitutor.pred_from_structures()</span></code></a></li>
</ul>
</li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="pymatgen.analysis.structure_prediction.html#module-pymatgen.analysis.structure_prediction.volume_predictor">pymatgen.analysis.structure_prediction.volume_predictor module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="pymatgen.analysis.structure_prediction.html#pymatgen.analysis.structure_prediction.volume_predictor.DLSVolumePredictor"><code class="docutils literal notranslate"><span class="pre">DLSVolumePredictor</span></code></a><ul>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.structure_prediction.html#pymatgen.analysis.structure_prediction.volume_predictor.DLSVolumePredictor.get_predicted_structure"><code class="docutils literal notranslate"><span class="pre">DLSVolumePredictor.get_predicted_structure()</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.structure_prediction.html#pymatgen.analysis.structure_prediction.volume_predictor.DLSVolumePredictor.predict"><code class="docutils literal notranslate"><span class="pre">DLSVolumePredictor.predict()</span></code></a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="pymatgen.analysis.structure_prediction.html#pymatgen.analysis.structure_prediction.volume_predictor.RLSVolumePredictor"><code class="docutils literal notranslate"><span class="pre">RLSVolumePredictor</span></code></a><ul>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.structure_prediction.html#pymatgen.analysis.structure_prediction.volume_predictor.RLSVolumePredictor.get_predicted_structure"><code class="docutils literal notranslate"><span class="pre">RLSVolumePredictor.get_predicted_structure()</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.structure_prediction.html#pymatgen.analysis.structure_prediction.volume_predictor.RLSVolumePredictor.predict"><code class="docutils literal notranslate"><span class="pre">RLSVolumePredictor.predict()</span></code></a></li>
</ul>
</li>
</ul>
</li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="pymatgen.analysis.topological.html">pymatgen.analysis.topological package</a><ul>
<li class="toctree-l2"><a class="reference internal" href="pymatgen.analysis.topological.html#submodules">Submodules</a></li>
<li class="toctree-l2"><a class="reference internal" href="pymatgen.analysis.topological.html#module-pymatgen.analysis.topological.spillage">pymatgen.analysis.topological.spillage module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="pymatgen.analysis.topological.html#pymatgen.analysis.topological.spillage.SOCSpillage"><code class="docutils literal notranslate"><span class="pre">SOCSpillage</span></code></a><ul>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.topological.html#pymatgen.analysis.topological.spillage.SOCSpillage.isclose"><code class="docutils literal notranslate"><span class="pre">SOCSpillage.isclose()</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.topological.html#pymatgen.analysis.topological.spillage.SOCSpillage.orth"><code class="docutils literal notranslate"><span class="pre">SOCSpillage.orth()</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.topological.html#pymatgen.analysis.topological.spillage.SOCSpillage.overlap_so_spinpol"><code class="docutils literal notranslate"><span class="pre">SOCSpillage.overlap_so_spinpol()</span></code></a></li>
</ul>
</li>
</ul>
</li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="pymatgen.analysis.xas.html">pymatgen.analysis.xas package</a><ul>
<li class="toctree-l2"><a class="reference internal" href="pymatgen.analysis.xas.html#submodules">Submodules</a></li>
<li class="toctree-l2"><a class="reference internal" href="pymatgen.analysis.xas.html#module-pymatgen.analysis.xas.spectrum">pymatgen.analysis.xas.spectrum module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="pymatgen.analysis.xas.html#pymatgen.analysis.xas.spectrum.XAS"><code class="docutils literal notranslate"><span class="pre">XAS</span></code></a><ul>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.xas.html#pymatgen.analysis.xas.spectrum.XAS.x"><code class="docutils literal notranslate"><span class="pre">XAS.x</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.xas.html#pymatgen.analysis.xas.spectrum.XAS.y"><code class="docutils literal notranslate"><span class="pre">XAS.y</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.xas.html#pymatgen.analysis.xas.spectrum.XAS.absorbing_element"><code class="docutils literal notranslate"><span class="pre">XAS.absorbing_element</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.xas.html#pymatgen.analysis.xas.spectrum.XAS.edge"><code class="docutils literal notranslate"><span class="pre">XAS.edge</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.xas.html#pymatgen.analysis.xas.spectrum.XAS.spectrum_type"><code class="docutils literal notranslate"><span class="pre">XAS.spectrum_type</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.xas.html#pymatgen.analysis.xas.spectrum.XAS.absorbing_index"><code class="docutils literal notranslate"><span class="pre">XAS.absorbing_index</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.xas.html#pymatgen.analysis.xas.spectrum.XAS.zero_negative_intensity"><code class="docutils literal notranslate"><span class="pre">XAS.zero_negative_intensity</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.xas.html#pymatgen.analysis.xas.spectrum.XAS.XLABEL"><code class="docutils literal notranslate"><span class="pre">XAS.XLABEL</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.xas.html#pymatgen.analysis.xas.spectrum.XAS.YLABEL"><code class="docutils literal notranslate"><span class="pre">XAS.YLABEL</span></code></a></li>
<li class="toctree-l4"><a class="reference internal" href="pymatgen.analysis.xas.html#pymatgen.analysis.xas.spectrum.XAS.stitch"><code class="docutils literal notranslate"><span class="pre">XAS.stitch()</span></code></a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="pymatgen.analysis.xas.html#pymatgen.analysis.xas.spectrum.site_weighted_spectrum"><code class="docutils literal notranslate"><span class="pre">site_weighted_spectrum()</span></code></a></li>
</ul>
</li>
</ul>
</li>
</ul>
</div>
</section>
<section id="submodules">
<h2>Submodules<a class="headerlink" href="#submodules" title="Link to this heading"></a></h2>
</section>
<section id="module-pymatgen.analysis.adsorption">
<span id="pymatgen-analysis-adsorption-module"></span><h2>pymatgen.analysis.adsorption module<a class="headerlink" href="#module-pymatgen.analysis.adsorption" title="Link to this heading"></a></h2>
<p>This module provides classes used to enumerate surface sites and to find
adsorption sites on slabs.</p>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.analysis.adsorption.AdsorbateSiteFinder">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">AdsorbateSiteFinder</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">slab</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="pymatgen.core.html#pymatgen.core.surface.Slab" title="pymatgen.core.surface.Slab"><span class="pre">Slab</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">selective_dynamics</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">height</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">float</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">0.9</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">mi_vec</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">ArrayLike</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/adsorption.py#L41-L597"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.adsorption.AdsorbateSiteFinder" title="Link to this definition"></a></dt>
<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></p>
<p>This class finds adsorbate sites on slabs and generates adsorbate
structures according to user-defined criteria.</p>
<dl class="simple">
<dt>The algorithm for finding sites is essentially as follows:</dt><dd><ol class="arabic simple">
<li><dl class="simple">
<dt>Determine “surface sites” by finding those within</dt><dd><p>a height threshold along the miller index of the
highest site</p>
</dd>
</dl>
</li>
<li><dl class="simple">
<dt>Create a network of surface sites using the Delaunay</dt><dd><p>triangulation of the surface sites</p>
</dd>
</dl>
</li>
<li><dl class="simple">
<dt>Assign on-top, bridge, and hollow adsorption sites</dt><dd><p>at the nodes, edges, and face centers of the Del.
Triangulation</p>
</dd>
</dl>
</li>
<li><dl class="simple">
<dt>Generate structures from a molecule positioned at</dt><dd><p>these sites</p>
</dd>
</dl>
</li>
</ol>
</dd>
</dl>
<p>Create an AdsorbateSiteFinder object.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>slab</strong> (<a class="reference internal" href="pymatgen.core.html#pymatgen.core.surface.Slab" title="pymatgen.core.surface.Slab"><em>Slab</em></a>) – slab object for which to find adsorbate sites</p></li>
<li><p><strong>selective_dynamics</strong> (<em>bool</em>) – flag for whether to assign
non-surface sites as fixed for selective dynamics</p></li>
<li><p><strong>height</strong> (<em>float</em>) – height criteria for selection of surface sites</p></li>
<li><p><strong>mi_vec</strong> (<em>3-D array-like</em>) – vector corresponding to the vector
concurrent with the miller index, this enables use with
slabs that have been reoriented, but the miller vector
must be supplied manually</p></li>
</ul>
</dd>
</dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.adsorption.AdsorbateSiteFinder.add_adsorbate">
<span class="sig-name descname"><span class="pre">add_adsorbate</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">molecule</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Molecule" title="pymatgen.core.structure.Molecule"><span class="pre">Molecule</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">ads_coord</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">repeat</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">translate</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">reorient</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/adsorption.py#L367-L409"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.adsorption.AdsorbateSiteFinder.add_adsorbate" title="Link to this definition"></a></dt>
<dd><p>Add an adsorbate at a particular coordinate. Adsorbate represented
by a Molecule object and is translated to (0, 0, 0) if translate is
True, or positioned relative to the input adsorbate coordinate if
translate is False.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>molecule</strong> (<a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Molecule" title="pymatgen.core.structure.Molecule"><em>Molecule</em></a>) – molecule object representing the adsorbate</p></li>
<li><p><strong>ads_coord</strong> (<em>array</em>) – coordinate of adsorbate position</p></li>
<li><p><strong>repeat</strong> (<em>3-tuple</em><em> or </em><em>list</em>) – input for making a supercell of slab
prior to placing the adsorbate</p></li>
<li><p><strong>translate</strong> (<em>bool</em>) – flag on whether to translate the molecule so
that its CoM is at the origin prior to adding it to the surface</p></li>
<li><p><strong>reorient</strong> (<em>bool</em>) – flag on whether to reorient the molecule to
have its z-axis concurrent with miller index</p></li>
</ul>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.adsorption.AdsorbateSiteFinder.adsorb_both_surfaces">
<span class="sig-name descname"><span class="pre">adsorb_both_surfaces</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">molecule</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">repeat</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">min_lw</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">5.0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">translate</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">reorient</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">find_args</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/adsorption.py#L472-L533"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.adsorption.AdsorbateSiteFinder.adsorb_both_surfaces" title="Link to this definition"></a></dt>
<dd><p>Generate all adsorption structures for a given
molecular adsorbate on both surfaces of a slab. This is useful for
calculating surface energy where both surfaces need to be equivalent or
if we want to calculate nonpolar systems.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>molecule</strong> (<a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Molecule" title="pymatgen.core.structure.Molecule"><em>Molecule</em></a>) – molecule corresponding to adsorbate</p></li>
<li><p><strong>repeat</strong> (<em>3-tuple</em><em> or </em><em>list</em>) – repeat argument for supercell generation</p></li>
<li><p><strong>min_lw</strong> (<em>float</em>) – minimum length and width of the slab, only used
if repeat is None</p></li>
<li><p><strong>reorient</strong> (<em>bool</em>) – flag on whether or not to reorient adsorbate
along the miller index</p></li>
<li><p><strong>find_args</strong> (<em>dict</em>) – dictionary of arguments to be passed to the
call to self.find_adsorption_sites, e.g. {“distance”:2.0}</p></li>
</ul>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.adsorption.AdsorbateSiteFinder.assign_selective_dynamics">
<em class="property"><span class="pre">classmethod</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">assign_selective_dynamics</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">slab</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/adsorption.py#L411-L426"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.adsorption.AdsorbateSiteFinder.assign_selective_dynamics" title="Link to this definition"></a></dt>
<dd><p>Helper function to assign selective dynamics site_properties based
on surface, subsurface site properties.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>slab</strong> (<a class="reference internal" href="pymatgen.core.html#pymatgen.core.surface.Slab" title="pymatgen.core.surface.Slab"><em>Slab</em></a>) – slab for which to assign selective dynamics</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.adsorption.AdsorbateSiteFinder.assign_site_properties">
<span class="sig-name descname"><span class="pre">assign_site_properties</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">slab</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="pymatgen.core.html#pymatgen.core.surface.Slab" title="pymatgen.core.surface.Slab"><span class="pre">Slab</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">height</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0.9</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/adsorption.py#L200-L207"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.adsorption.AdsorbateSiteFinder.assign_site_properties" title="Link to this definition"></a></dt>
<dd><p>Assign site properties.</p>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.adsorption.AdsorbateSiteFinder.ensemble_center">
<em class="property"><span class="pre">classmethod</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">ensemble_center</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">site_list</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">indices</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">cartesian</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/adsorption.py#L350-L365"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.adsorption.AdsorbateSiteFinder.ensemble_center" title="Link to this definition"></a></dt>
<dd><p>Find the center of an ensemble of sites selected from a list of
sites. Helper method for the find_adsorption_sites algorithm.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>site_list</strong> (<em>list</em><em>[</em><a class="reference internal" href="pymatgen.core.html#pymatgen.core.sites.Site" title="pymatgen.core.sites.Site"><em>Site</em></a><em>]</em>) – sites from which to select</p></li>
<li><p><strong>indices</strong> (<em>list</em><em>[</em><em>int</em><em>]</em>) – indices of sites from which to select
sites from site list</p></li>
<li><p><strong>cartesian</strong> (<em>bool</em>) – whether to get average fractional or
Cartesian coordinate</p></li>
</ul>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.adsorption.AdsorbateSiteFinder.find_adsorption_sites">
<span class="sig-name descname"><span class="pre">find_adsorption_sites</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">distance</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">2.0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">put_inside</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">symm_reduce</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0.01</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">near_reduce</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0.01</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">positions</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">('ontop',</span> <span class="pre">'bridge',</span> <span class="pre">'hollow')</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">no_obtuse_hollow</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/adsorption.py#L229-L309"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.adsorption.AdsorbateSiteFinder.find_adsorption_sites" title="Link to this definition"></a></dt>
<dd><p>Find surface sites according to the above algorithm. Returns a list
of corresponding Cartesian coordinates.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>distance</strong> (<em>float</em>) – distance from the coordinating ensemble
of atoms along the miller index for the site (i.e.
the distance from the slab itself)</p></li>
<li><p><strong>put_inside</strong> (<em>bool</em>) – whether to put the site inside the cell</p></li>
<li><p><strong>symm_reduce</strong> (<em>float</em>) – symm reduction threshold</p></li>
<li><p><strong>near_reduce</strong> (<em>float</em>) – near reduction threshold</p></li>
<li><p><strong>positions</strong> (<em>list</em>) – <p>which positions to include in the site finding
“ontop”: sites on top of surface sites
“bridge”: sites at edges between surface sites in Delaunay</p>
<blockquote>
<div><p>triangulation of surface sites in the miller plane</p>
</div></blockquote>
<p>”hollow”: sites at centers of Delaunay triangulation faces
“subsurface”: subsurface positions projected into miller plane</p>
</p></li>
<li><p><strong>no_obtuse_hollow</strong> (<em>bool</em>) – flag to indicate whether to include
obtuse triangular ensembles in hollow sites</p></li>
</ul>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.adsorption.AdsorbateSiteFinder.find_surface_sites_by_height">
<span class="sig-name descname"><span class="pre">find_surface_sites_by_height</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">slab</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="pymatgen.core.html#pymatgen.core.surface.Slab" title="pymatgen.core.surface.Slab"><span class="pre">Slab</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">height</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0.9</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">xy_tol</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0.05</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/adsorption.py#L162-L198"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.adsorption.AdsorbateSiteFinder.find_surface_sites_by_height" title="Link to this definition"></a></dt>
<dd><p>Find surface sites by determining which sites are
within a threshold value in height from the topmost site in a list of
sites.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>slab</strong> (<a class="reference internal" href="pymatgen.core.html#pymatgen.core.surface.Slab" title="pymatgen.core.surface.Slab"><em>Slab</em></a>) – slab for which to find surface sites</p></li>
<li><p><strong>height</strong> (<em>float</em>) – threshold in angstroms of distance from topmost
site in slab along the slab c-vector to include in surface
site determination</p></li>
<li><p><strong>xy_tol</strong> (<em>float</em>) – if supplied, will remove any sites which are
within a certain distance in the miller plane.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>list of sites selected to be within a threshold of the highest</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.adsorption.AdsorbateSiteFinder.from_bulk_and_miller">
<em class="property"><span class="pre">classmethod</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">from_bulk_and_miller</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">structure</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">miller_index</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">min_slab_size</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">8.0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">min_vacuum_size</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">10.0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">max_normal_search</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">center_slab</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">selective_dynamics</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">undercoord_threshold</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0.09</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">Self</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/adsorption.py#L86-L160"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.adsorption.AdsorbateSiteFinder.from_bulk_and_miller" title="Link to this definition"></a></dt>
<dd><p>Construct the adsorbate site finder from a bulk
structure and a miller index, which allows the surface sites to be
determined from the difference in bulk and slab coordination, as
opposed to the height threshold.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>structure</strong> (<a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><em>Structure</em></a>) – structure from which slab
input to the ASF is constructed</p></li>
<li><p><strong>miller_index</strong> (<em>3-tuple</em><em> or </em><em>list</em>) – miller index to be used</p></li>
<li><p><strong>min_slab_size</strong> (<em>float</em>) – min slab size for slab generation</p></li>
<li><p><strong>min_vacuum_size</strong> (<em>float</em>) – min vacuum size for slab generation</p></li>
<li><p><strong>max_normal_search</strong> (<em>int</em>) – max normal search for slab generation</p></li>
<li><p><strong>center_slab</strong> (<em>bool</em>) – whether to center slab in slab generation</p></li>
<li><p><strong>dynamics</strong> (<em>selective</em>) – whether to assign surface sites
to selective dynamics</p></li>
<li><p><strong>undercoord_threshold</strong> (<em>float</em>) – threshold of “undercoordation”
to use for the assignment of surface sites. Default is
0.1, for which surface sites will be designated if they
are 10% less coordinated than their bulk counterpart</p></li>
</ul>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.adsorption.AdsorbateSiteFinder.generate_adsorption_structures">
<span class="sig-name descname"><span class="pre">generate_adsorption_structures</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">molecule</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">repeat</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">min_lw</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">5.0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">translate</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">reorient</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">find_args</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/adsorption.py#L428-L470"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.adsorption.AdsorbateSiteFinder.generate_adsorption_structures" title="Link to this definition"></a></dt>
<dd><p>Generate all adsorption structures for a given
molecular adsorbate. Can take repeat argument or minimum length/width
of precursor slab as an input.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>molecule</strong> (<a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Molecule" title="pymatgen.core.structure.Molecule"><em>Molecule</em></a>) – molecule corresponding to adsorbate</p></li>
<li><p><strong>repeat</strong> (<em>3-tuple</em><em> or </em><em>list</em>) – repeat argument for supercell generation</p></li>
<li><p><strong>min_lw</strong> (<em>float</em>) – minimum length and width of the slab, only used
if repeat is None</p></li>
<li><p><strong>translate</strong> (<em>bool</em>) – flag on whether to translate the molecule so
that its CoM is at the origin prior to adding it to the surface</p></li>
<li><p><strong>reorient</strong> (<em>bool</em>) – flag on whether or not to reorient adsorbate
along the miller index</p></li>
<li><p><strong>find_args</strong> (<em>dict</em>) – dictionary of arguments to be passed to the
call to self.find_adsorption_sites, e.g. {“distance”:2.0}</p></li>
</ul>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.adsorption.AdsorbateSiteFinder.generate_substitution_structures">
<span class="sig-name descname"><span class="pre">generate_substitution_structures</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">atom</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">target_species</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">sub_both_sides</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">range_tol</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0.01</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">dist_from_surf</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/adsorption.py#L535-L597"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.adsorption.AdsorbateSiteFinder.generate_substitution_structures" title="Link to this definition"></a></dt>
<dd><p>Perform substitution-type doping on the surface and
returns all possible configurations where one dopant is substituted per
surface. Can substitute one surface or both.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>atom</strong> (<em>str</em>) – atom corresponding to substitutional dopant</p></li>
<li><p><strong>sub_both_sides</strong> (<em>bool</em>) – If true, substitute an equivalent
site on the other surface</p></li>
<li><p><strong>target_species</strong> (<em>list</em>) – Specific species to substitute</p></li>
<li><p><strong>range_tol</strong> (<em>float</em>) – Find viable substitution sites at a specific
distance from the surface +- this tolerance</p></li>
<li><p><strong>dist_from_surf</strong> (<em>float</em>) – Distance from the surface to find viable
substitution sites, defaults to 0 to substitute at the surface</p></li>
</ul>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.adsorption.AdsorbateSiteFinder.get_extended_surface_mesh">
<span class="sig-name descname"><span class="pre">get_extended_surface_mesh</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">repeat</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">(5,</span> <span class="pre">5,</span> <span class="pre">1)</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/adsorption.py#L209-L218"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.adsorption.AdsorbateSiteFinder.get_extended_surface_mesh" title="Link to this definition"></a></dt>
<dd><p>Get an extended surface mesh for to use for adsorption site finding
by constructing supercell of surface sites.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>repeat</strong> (<em>3-tuple</em>) – repeat for getting extended surface mesh</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.adsorption.AdsorbateSiteFinder.near_reduce">
<span class="sig-name descname"><span class="pre">near_reduce</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">coords_set</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">threshold</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0.0001</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/adsorption.py#L336-L348"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.adsorption.AdsorbateSiteFinder.near_reduce" title="Link to this definition"></a></dt>
<dd><p>Prune coordinate set for coordinates that are within threshold.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>coords_set</strong> (<em>Nx3 array-like</em>) – list or array of coordinates</p></li>
<li><p><strong>threshold</strong> (<em>float</em>) – threshold value for distance</p></li>
</ul>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.adsorption.AdsorbateSiteFinder.subsurface_sites">
<span class="sig-name descname"><span class="pre">subsurface_sites</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/adsorption.py#L225-L227"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.adsorption.AdsorbateSiteFinder.subsurface_sites" title="Link to this definition"></a></dt>
<dd><p>Convenience method to return list of subsurface sites.</p>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.analysis.adsorption.AdsorbateSiteFinder.surface_sites">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">surface_sites</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/adsorption.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.adsorption.AdsorbateSiteFinder.surface_sites" title="Link to this definition"></a></dt>
<dd><p>Convenience method to return a list of surface sites.</p>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.adsorption.AdsorbateSiteFinder.symm_reduce">
<span class="sig-name descname"><span class="pre">symm_reduce</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">coords_set</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">threshold</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1e-06</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/adsorption.py#L311-L334"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.adsorption.AdsorbateSiteFinder.symm_reduce" title="Link to this definition"></a></dt>
<dd><p>Reduce the set of adsorbate sites by finding removing symmetrically
equivalent duplicates.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>coords_set</strong> – coordinate set in Cartesian coordinates</p></li>
<li><p><strong>threshold</strong> – tolerance for distance equivalence, used
as input to in_coord_list_pbc for dupl. checking</p></li>
</ul>
</dd>
</dl>
</dd></dl>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="pymatgen.analysis.adsorption.get_mi_vec">
<span class="sig-name descname"><span class="pre">get_mi_vec</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">slab</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/adsorption.py#L600-L605"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.adsorption.get_mi_vec" title="Link to this definition"></a></dt>
<dd><p>Convenience function which returns the unit vector aligned with the
miller index.</p>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="pymatgen.analysis.adsorption.get_rot">
<span class="sig-name descname"><span class="pre">get_rot</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">slab</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="pymatgen.core.html#pymatgen.core.surface.Slab" title="pymatgen.core.surface.Slab"><span class="pre">Slab</span></a></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><a class="reference internal" href="pymatgen.core.html#pymatgen.core.operations.SymmOp" title="pymatgen.core.operations.SymmOp"><span class="pre">SymmOp</span></a></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/adsorption.py#L608-L617"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.adsorption.get_rot" title="Link to this definition"></a></dt>
<dd><p>Get the transformation to rotate the z axis into the miller index.</p>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="pymatgen.analysis.adsorption.plot_slab">
<span class="sig-name descname"><span class="pre">plot_slab</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">slab</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="pymatgen.core.html#pymatgen.core.surface.Slab" title="pymatgen.core.surface.Slab"><span class="pre">Slab</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">ax</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">plt.Axes</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">scale</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0.8</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">repeat</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">5</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">window</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1.5</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">draw_unit_cell</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">decay</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0.2</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">adsorption_sites</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">inverse</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/adsorption.py#L641-L746"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.adsorption.plot_slab" title="Link to this definition"></a></dt>
<dd><p>Help visualize the slab in a 2-D plot, for convenient viewing of output of AdsorbateSiteFinder.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>slab</strong> (<em>slab</em>) – Slab object to be visualized</p></li>
<li><p><strong>ax</strong> (<em>axes</em>) – matplotlib axes with which to visualize</p></li>
<li><p><strong>scale</strong> (<em>float</em>) – radius scaling for sites</p></li>
<li><p><strong>repeat</strong> (<em>int</em>) – number of repeating unit cells to visualize</p></li>
<li><p><strong>window</strong> (<em>float</em>) – window for setting the axes limits, is essentially
a fraction of the unit cell limits</p></li>
<li><p><strong>draw_unit_cell</strong> (<em>bool</em>) – flag indicating whether or not to draw cell</p></li>
<li><p><strong>decay</strong> (<em>float</em>) – how the alpha-value decays along the z-axis</p></li>
<li><p><strong>inverse</strong> (<em>bool</em>) – invert z axis to plot opposite surface</p></li>
</ul>
</dd>
</dl>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="pymatgen.analysis.adsorption.put_coord_inside">
<span class="sig-name descname"><span class="pre">put_coord_inside</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">lattice</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">cart_coordinate</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/adsorption.py#L620-L623"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.adsorption.put_coord_inside" title="Link to this definition"></a></dt>
<dd><p>Convert a Cartesian coordinate such that it is inside the unit cell.</p>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="pymatgen.analysis.adsorption.reorient_z">
<span class="sig-name descname"><span class="pre">reorient_z</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">structure</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/adsorption.py#L626-L633"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.adsorption.reorient_z" title="Link to this definition"></a></dt>
<dd><p>Reorient a structure such that the z axis is concurrent with the normal
to the A-B plane.</p>
</dd></dl>
</section>
<section id="module-pymatgen.analysis.bond_dissociation">
<span id="pymatgen-analysis-bond-dissociation-module"></span><h2>pymatgen.analysis.bond_dissociation module<a class="headerlink" href="#module-pymatgen.analysis.bond_dissociation" title="Link to this heading"></a></h2>
<p>Module for BondDissociationEnergies.</p>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.analysis.bond_dissociation.BondDissociationEnergies">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">BondDissociationEnergies</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">molecule_entry</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">int</span><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="n"><span class="pre">fragment_entries</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">int</span><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="n"><span class="pre">allow_additional_charge_separation</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">multibreak</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/bond_dissociation.py#L26-L379"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.bond_dissociation.BondDissociationEnergies" title="Link to this definition"></a></dt>
<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">MSONable</span></code></p>
<p>Standard constructor for bond dissociation energies. All bonds in the principle molecule are
looped through and their dissociation energies are calculated given the energies of the resulting
fragments, or, in the case of a ring bond, from the energy of the molecule obtained from breaking
the bond and opening the ring. This class should only be called after the energies of the optimized
principle molecule and all relevant optimized fragments have been determined, either from quantum
chemistry or elsewhere. It was written to provide the analysis after running an <cite>atomate</cite> fragmentation
workflow.</p>
<p>The provided entries must have the following keys: formula_pretty, initial_molecule,
final_molecule. If a PCM is present, all entries should also have a pcm_dielectric key.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>molecule_entry</strong> (<em>dict</em>) – Entry for the principle molecule. Should have the keys mentioned above.</p></li>
<li><p><strong>fragment_entries</strong> (<em>list</em><em>[</em><em>dict</em><em>]</em>) – Fragment entries. Each should have the keys mentioned above.</p></li>
<li><p><strong>allow_additional_charge_separation</strong> (<em>bool</em>) – If True, consider larger than normal charge separation
among fragments. Defaults to False. See the definition of self.expected_charges below for more
specific information.</p></li>
<li><p><strong>multibreak</strong> (<em>bool</em>) – If True, additionally attempt to break pairs of bonds. Defaults to False.</p></li>
</ul>
</dd>
</dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.bond_dissociation.BondDissociationEnergies.build_new_entry">
<span class="sig-name descname"><span class="pre">build_new_entry</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">frags</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">list</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">bonds</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">list</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">list</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/bond_dissociation.py#L337-L379"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.bond_dissociation.BondDissociationEnergies.build_new_entry" title="Link to this definition"></a></dt>
<dd><p>Build a new entry for bond dissociation that will be returned to the user.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>frags</strong> (<em>list</em>) – Fragments involved in the bond dissociation.</p></li>
<li><p><strong>bonds</strong> (<em>list</em>) – Bonds broken in the dissociation process.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>Formatted bond dissociation entries.</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>list</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.bond_dissociation.BondDissociationEnergies.filter_fragment_entries">
<span class="sig-name descname"><span class="pre">filter_fragment_entries</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">fragment_entries</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">list</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">None</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/bond_dissociation.py#L276-L335"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.bond_dissociation.BondDissociationEnergies.filter_fragment_entries" title="Link to this definition"></a></dt>
<dd><p>Filter the fragment entries.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>fragment_entries</strong> (<em>List</em>) – Fragment entries to be filtered.</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.bond_dissociation.BondDissociationEnergies.fragment_and_process">
<span class="sig-name descname"><span class="pre">fragment_and_process</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">bonds</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/bond_dissociation.py#L121-L253"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.bond_dissociation.BondDissociationEnergies.fragment_and_process" title="Link to this definition"></a></dt>
<dd><p>Fragment and process bonds.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>bonds</strong> (<em>list</em>) – bonds to process.</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.bond_dissociation.BondDissociationEnergies.search_fragment_entries">
<span class="sig-name descname"><span class="pre">search_fragment_entries</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">frag</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">list</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/bond_dissociation.py#L255-L274"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.bond_dissociation.BondDissociationEnergies.search_fragment_entries" title="Link to this definition"></a></dt>
<dd><p>Search all fragment entries for those isomorphic to the given fragment.
We distinguish between entries where both initial and final MoleculeGraphs are isomorphic to the
given fragment (entries) vs those where only the initial MoleculeGraph is isomorphic to the given
fragment (initial_entries) vs those where only the final MoleculeGraph is isomorphic (final_entries).</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>frag</strong> – Fragment</p>
</dd>
</dl>
</dd></dl>
</dd></dl>
</section>
<section id="module-pymatgen.analysis.bond_valence">
<span id="pymatgen-analysis-bond-valence-module"></span><h2>pymatgen.analysis.bond_valence module<a class="headerlink" href="#module-pymatgen.analysis.bond_valence" title="Link to this heading"></a></h2>
<p>This module implements classes to perform bond valence analyses.</p>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.analysis.bond_valence.BVAnalyzer">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">BVAnalyzer</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">symm_tol</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0.1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">max_radius</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">4</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">max_permutations</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">100000</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">distance_scale_factor</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1.015</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">charge_neutrality_tolerance</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1e-05</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">forbidden_species</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/bond_valence.py#L100-L449"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.bond_valence.BVAnalyzer" title="Link to this definition"></a></dt>
<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></p>
<p>This class implements a maximum a posteriori (MAP) estimation method to
determine oxidation states in a structure. The algorithm is as follows:
1) The bond valence sum of all symmetrically distinct sites in a structure
is calculated using the element-based parameters in M. O’Keefe, & N. Brese,
JACS, 1991, 113(9), 3226-3229. doi:10.1021/ja00009a002.
2) The posterior probabilities of all oxidation states is then calculated
using: P(oxi_state/BV) = K * P(BV/oxi_state) * P(oxi_state), where K is
a constant factor for each element. P(BV/oxi_state) is calculated as a
Gaussian with mean and std deviation determined from an analysis of
the ICSD. The posterior P(oxi_state) is determined from a frequency
analysis of the ICSD.
3) The oxidation states are then ranked in order of decreasing probability
and the oxidation state combination that result in a charge neutral cell
is selected.</p>
<p>Initialize the BV analyzer, with useful defaults.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>symm_tol</strong> – Symmetry tolerance used to determine which sites are
symmetrically equivalent. Set to 0 to turn off symmetry.</p></li>
<li><p><strong>max_radius</strong> – Maximum radius in Angstrom used to find nearest neighbors.</p></li>
<li><p><strong>max_permutations</strong> – The maximum number of permutations of oxidation states to test.</p></li>
<li><p><strong>distance_scale_factor</strong> – A scale factor to be applied. This is useful for scaling
distances, esp in the case of calculation-relaxed structures
which may tend to under (GGA) or over bind (LDA). The default
of 1.015 works for GGA. For experimental structure, set this to
1.</p></li>
<li><p><strong>charge_neutrality_tolerance</strong> – Tolerance on the charge neutrality when unordered structures
are at stake.</p></li>
<li><p><strong>forbidden_species</strong> – List of species that are forbidden (example : [“O-”] cannot be
used) It is used when e.g. someone knows that some oxidation
state cannot occur for some atom in a structure or list of
structures.</p></li>
</ul>
</dd>
</dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.analysis.bond_valence.BVAnalyzer.CHARGE_NEUTRALITY_TOLERANCE">
<span class="sig-name descname"><span class="pre">CHARGE_NEUTRALITY_TOLERANCE</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">1e-05</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/bond_valence.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.bond_valence.BVAnalyzer.CHARGE_NEUTRALITY_TOLERANCE" title="Link to this definition"></a></dt>
<dd></dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.bond_valence.BVAnalyzer.get_oxi_state_decorated_structure">
<span class="sig-name descname"><span class="pre">get_oxi_state_decorated_structure</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">structure</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><span class="pre">Structure</span></a></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><span class="pre">Structure</span></a></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/bond_valence.py#L429-L449"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.bond_valence.BVAnalyzer.get_oxi_state_decorated_structure" title="Link to this definition"></a></dt>
<dd><p>Get an oxidation state decorated structure. This currently works only
for ordered structures only.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>structure</strong> – Structure to analyze</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>modified with oxidation state decorations.</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p><a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure">Structure</a></p>
</dd>
<dt class="field-even">Raises<span class="colon">:</span></dt>
<dd class="field-even"><p><strong>ValueError if the valences cannot be determined.</strong> – </p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.bond_valence.BVAnalyzer.get_valences">
<span class="sig-name descname"><span class="pre">get_valences</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">structure</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><span class="pre">Structure</span></a></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/bond_valence.py#L205-L427"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.bond_valence.BVAnalyzer.get_valences" title="Link to this definition"></a></dt>
<dd><p>Get a list of valences for each site in the structure.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>structure</strong> – Structure to analyze</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>A list of valences for each site in the structure (for an ordered structure),
e.g. [1, 1, -2] or a list of lists with the valences for each fractional
element of each site in the structure (for an unordered structure), e.g. [[2,
4], [3], [-2], [-2], [-2]]</p>
</dd>
<dt class="field-odd">Raises<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>A ValueError if the valences cannot be determined.</strong> – </p>
</dd>
</dl>
</dd></dl>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="pymatgen.analysis.bond_valence.add_oxidation_state_by_site_fraction">
<span class="sig-name descname"><span class="pre">add_oxidation_state_by_site_fraction</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">structure</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><span class="pre">Structure</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">oxidation_states</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">int</span><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">]</span></span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><span class="pre">Structure</span></a></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/bond_valence.py#L468-L486"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.bond_valence.add_oxidation_state_by_site_fraction" title="Link to this definition"></a></dt>
<dd><p>Add oxidation states to a structure by fractional site.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>oxidation_states</strong> (<em>list</em><em>[</em><em>list</em><em>[</em><em>int</em><em>]</em><em>]</em>) – List of list of oxidation states for each
site fraction for each site.
e.g. [[2, 4], [3], [-2], [-2], [-2]]</p>
</dd>
</dl>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="pymatgen.analysis.bond_valence.calculate_bv_sum">
<span class="sig-name descname"><span class="pre">calculate_bv_sum</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">site</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">nn_list</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">scale_factor</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1.0</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/bond_valence.py#L38-L61"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.bond_valence.calculate_bv_sum" title="Link to this definition"></a></dt>
<dd><p>Calculate the BV sum of a site.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>site</strong> (<a class="reference internal" href="pymatgen.core.html#pymatgen.core.sites.PeriodicSite" title="pymatgen.core.sites.PeriodicSite"><em>PeriodicSite</em></a>) – The central site to calculate the bond valence</p></li>
<li><p><strong>nn_list</strong> (<em>[</em><a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Neighbor" title="pymatgen.core.structure.Neighbor"><em>Neighbor</em></a><em>]</em>) – A list of namedtuple Neighbors having “distance”
and “site” attributes</p></li>
<li><p><strong>scale_factor</strong> (<em>float</em>) – A scale factor to be applied. This is useful for
scaling distance, esp in the case of calculation-relaxed structures
which may tend to under (GGA) or over bind (LDA).</p></li>
</ul>
</dd>
</dl>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="pymatgen.analysis.bond_valence.calculate_bv_sum_unordered">
<span class="sig-name descname"><span class="pre">calculate_bv_sum_unordered</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">site</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">nn_list</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">scale_factor</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/bond_valence.py#L64-L97"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.bond_valence.calculate_bv_sum_unordered" title="Link to this definition"></a></dt>
<dd><p>Calculate the BV sum of a site for unordered structures.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>site</strong> (<a class="reference internal" href="pymatgen.core.html#pymatgen.core.sites.PeriodicSite" title="pymatgen.core.sites.PeriodicSite"><em>PeriodicSite</em></a>) – The central site to calculate the bond valence</p></li>
<li><p><strong>nn_list</strong> (<em>[</em><a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Neighbor" title="pymatgen.core.structure.Neighbor"><em>Neighbor</em></a><em>]</em>) – A list of namedtuple Neighbors having “distance”
and “site” attributes</p></li>
<li><p><strong>scale_factor</strong> (<em>float</em>) – A scale factor to be applied. This is useful for
scaling distance, esp in the case of calculation-relaxed structures
which may tend to under (GGA) or over bind (LDA).</p></li>
</ul>
</dd>
</dl>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="pymatgen.analysis.bond_valence.get_z_ordered_elmap">
<span class="sig-name descname"><span class="pre">get_z_ordered_elmap</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">comp</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/bond_valence.py#L452-L465"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.bond_valence.get_z_ordered_elmap" title="Link to this definition"></a></dt>
<dd><p>Arbitrary ordered element map on the elements/species of a composition of a
given site in an unordered structure. Returns a list of tuples (
element_or_specie: occupation) in the arbitrary order.</p>
<p>The arbitrary order is based on the Z of the element and the smallest
fractional occupations first.
Example : {“Ni3+”: 0.2, “Ni4+”: 0.2, “Cr3+”: 0.15, “Zn2+”: 0.34,
“Cr4+”: 0.11} will yield the species in the following order :
Cr4+, Cr3+, Ni3+, Ni4+, Zn2+ … or
Cr4+, Cr3+, Ni4+, Ni3+, Zn2+</p>
</dd></dl>
</section>
<section id="module-pymatgen.analysis.chempot_diagram">
<span id="pymatgen-analysis-chempot-diagram-module"></span><h2>pymatgen.analysis.chempot_diagram module<a class="headerlink" href="#module-pymatgen.analysis.chempot_diagram" title="Link to this heading"></a></h2>
<p>This module implements the construction and plotting of chemical potential diagrams
from a list of entries within a chemical system containing 2 or more elements. The
chemical potential diagram is the mathematical dual to the traditional compositional
phase diagram.</p>
<p>For more information, please cite/reference the paper below:</p>
<blockquote>
<div><p>Todd, P. K., McDermott, M. J., Rom, C. L., Corrao, A. A., Denney, J. J., Dwaraknath,
S. S., Khalifah, P. G., Persson, K. A., & Neilson, J. R. (2021). Selectivity in
Yttrium Manganese Oxide Synthesis via Local Chemical Potentials in Hyperdimensional
Phase Space. Journal of the American Chemical Society, 143(37), 15185-15194.
<a class="reference external" href="https://doi.org/10.1021/jacs.1c06229">https://doi.org/10.1021/jacs.1c06229</a></p>
</div></blockquote>
<p>Please also consider referencing the original 1999 paper by H. Yokokawa,
who outlined many of its possible uses:</p>
<blockquote>
<div><p>Yokokawa, H. “Generalized chemical potential diagram and its applications to
chemical reactions at interfaces between dissimilar materials.” JPE 20,
258 (1999). <a class="reference external" href="https://doi.org/10.1361/105497199770335794">https://doi.org/10.1361/105497199770335794</a></p>
</div></blockquote>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.analysis.chempot_diagram.ChemicalPotentialDiagram">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">ChemicalPotentialDiagram</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entries</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">list</span><span class="p"><span class="pre">[</span></span><a class="reference internal" href="#pymatgen.analysis.phase_diagram.PDEntry" title="pymatgen.analysis.phase_diagram.PDEntry"><span class="pre">PDEntry</span></a><span class="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="n"><span class="pre">limits</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><a class="reference internal" href="pymatgen.core.html#pymatgen.core.periodic_table.Element" title="pymatgen.core.periodic_table.Element"><span class="pre">Element</span></a><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">tuple</span><span class="p"><span class="pre">[</span></span><span class="pre">float</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">float</span><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">default_min_limit</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">float</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">-50.0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">formal_chempots</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/chempot_diagram.py#L51-L643"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.chempot_diagram.ChemicalPotentialDiagram" title="Link to this definition"></a></dt>
<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">MSONable</span></code></p>
<p>The chemical potential diagram is the mathematical dual to the compositional
phase diagram. To create the diagram, convex minimization is
performed in energy (E) vs. chemical potential (μ) space by taking the lower convex
envelope of hyperplanes. Accordingly, “points” on the compositional phase diagram
become N-dimensional convex polytopes (domains) in chemical potential space.</p>
<p>For more information on this specific implementation of the algorithm,
please cite/reference the paper below:</p>
<blockquote>
<div><p>Todd, P. K., McDermott, M. J., Rom, C. L., Corrao, A. A., Denney, J. J., Dwaraknath,
S. S., Khalifah, P. G., Persson, K. A., & Neilson, J. R. (2021). Selectivity in
Yttrium Manganese Oxide Synthesis via Local Chemical Potentials in Hyperdimensional
Phase Space. Journal of the American Chemical Society, 143(37), 15185-15194.
<a class="reference external" href="https://doi.org/10.1021/jacs.1c06229">https://doi.org/10.1021/jacs.1c06229</a></p>
</div></blockquote>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>entries</strong> (<em>list</em><em>[</em><a class="reference internal" href="#pymatgen.analysis.phase_diagram.PDEntry" title="pymatgen.analysis.phase_diagram.PDEntry"><em>PDEntry</em></a><em>]</em>) – PDEntry-like objects containing a composition and
energy. Must contain elemental references and be suitable for typical
phase diagram construction. Entries must be within a chemical system
of with 2+ elements.</p></li>
<li><p><strong>limits</strong> (<em>dict</em><em>[</em><a class="reference internal" href="pymatgen.core.html#pymatgen.core.periodic_table.Element" title="pymatgen.core.periodic_table.Element"><em>Element</em></a><em>, </em><em>float</em><em>] </em><em>| </em><em>None</em>) – Bounds of elemental chemical potentials (min, max),
which are used to construct the border hyperplanes used in the HalfSpaceIntersection
algorithm; these constrain the space over which the domains are calculated and also
determine the size of the plotted diagram. Any elemental limits not specified are
covered in the default_min_limit argument. e.g. {Element(“Li”): [-12.0, 0.0], …}</p></li>
<li><p><strong>default_min_limit</strong> (<em>float</em>) – Default minimum chemical potential limit (i.e.,
lower bound) for unspecified elements within the “limits” argument.</p></li>
<li><p><strong>formal_chempots</strong> (<em>bool</em>) – Whether to plot the formal (‘reference’) chemical potentials
(i.e. μ_X - μ_X^0) or the absolute DFT reference energies (i.e. μ_X(DFT)).
Default is True (i.e. plot formal chemical potentials).</p></li>
</ul>
</dd>
</dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.analysis.chempot_diagram.ChemicalPotentialDiagram.border_hyperplanes">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">border_hyperplanes</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">ndarray</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/chempot_diagram.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.chempot_diagram.ChemicalPotentialDiagram.border_hyperplanes" title="Link to this definition"></a></dt>
<dd><p>Bordering hyperplanes.</p>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.analysis.chempot_diagram.ChemicalPotentialDiagram.chemical_system">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">chemical_system</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">str</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/chempot_diagram.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.chempot_diagram.ChemicalPotentialDiagram.chemical_system" title="Link to this definition"></a></dt>
<dd><p>The chemical system (A-B-C-…) of diagram object.</p>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.analysis.chempot_diagram.ChemicalPotentialDiagram.domains">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">domains</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">ndarray</span><span class="p"><span class="pre">]</span></span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/chempot_diagram.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.chempot_diagram.ChemicalPotentialDiagram.domains" title="Link to this definition"></a></dt>
<dd><p>Mapping of formulas to array of domain boundary points.</p>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.analysis.chempot_diagram.ChemicalPotentialDiagram.el_refs">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">el_refs</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><a class="reference internal" href="pymatgen.core.html#pymatgen.core.periodic_table.Element" title="pymatgen.core.periodic_table.Element"><span class="pre">Element</span></a><span class="p"><span class="pre">,</span></span><span class="w"> </span><a class="reference internal" href="#pymatgen.analysis.phase_diagram.PDEntry" title="pymatgen.analysis.phase_diagram.PDEntry"><span class="pre">PDEntry</span></a><span class="p"><span class="pre">]</span></span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/chempot_diagram.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.chempot_diagram.ChemicalPotentialDiagram.el_refs" title="Link to this definition"></a></dt>
<dd><p>A dictionary of elements and reference entries.</p>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.analysis.chempot_diagram.ChemicalPotentialDiagram.entry_dict">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">entry_dict</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><a class="reference internal" href="pymatgen.entries.html#pymatgen.entries.computed_entries.ComputedEntry" title="pymatgen.entries.computed_entries.ComputedEntry"><span class="pre">ComputedEntry</span></a><span class="p"><span class="pre">]</span></span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/chempot_diagram.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.chempot_diagram.ChemicalPotentialDiagram.entry_dict" title="Link to this definition"></a></dt>
<dd><p>Mapping between reduced formula and ComputedEntry.</p>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.chempot_diagram.ChemicalPotentialDiagram.get_plot">
<span class="sig-name descname"><span class="pre">get_plot</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">elements</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">list</span><span class="p"><span class="pre">[</span></span><a class="reference internal" href="pymatgen.core.html#pymatgen.core.periodic_table.Element" title="pymatgen.core.periodic_table.Element"><span class="pre">Element</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">label_stable</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">formulas_to_draw</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">draw_formula_meshes</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">draw_formula_lines</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">formula_colors</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">['rgb(27,158,119)',</span> <span class="pre">'rgb(217,95,2)',</span> <span class="pre">'rgb(117,112,179)',</span> <span class="pre">'rgb(231,41,138)',</span> <span class="pre">'rgb(102,166,30)',</span> <span class="pre">'rgb(230,171,2)',</span> <span class="pre">'rgb(166,118,29)',</span> <span class="pre">'rgb(102,102,102)']</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">element_padding</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">float</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">1.0</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">Figure</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/chempot_diagram.py#L129-L206"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.chempot_diagram.ChemicalPotentialDiagram.get_plot" title="Link to this definition"></a></dt>
<dd><p>Plot the 2-dimensional or 3-dimensional chemical potential diagram using an
interactive Plotly interface.</p>
<p>Elemental axes can be specified; if none provided, will automatically default
to first 2-3 elements within the “elements” attribute.</p>
<p>In 3D, this method also allows for plotting of lower-dimensional “slices” of
hyperdimensional polytopes (e.g., the LiMnO2 domain within a Y-Mn-O diagram).
This allows for visualization of some of the phase boundaries that can only
be seen fully in high dimensional space; see the “formulas_to_draw” argument.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>elements</strong> – list of elements to use as axes in the diagram. If None,
automatically defaults to the first 2 or elements within the
object’s “elements” attribute.</p></li>
<li><p><strong>label_stable</strong> – whether to label stable phases by their reduced
formulas. Defaults to True.</p></li>
<li><p><strong>formulas_to_draw</strong> – for 3-dimensional diagrams, an optional list of
formulas to plot on the diagram; if these are from a different
chemical system a 3-d polyhedron “slice” will be plotted. Defaults to None.</p></li>
<li><p><strong>draw_formula_meshes</strong> – whether to draw a colored mesh for the
optionally specified formulas_to_draw. Defaults to True.</p></li>
<li><p><strong>draw_formula_lines</strong> – whether to draw bounding lines for the
optionally specified formulas_to_draw. Defaults to True.</p></li>
<li><p><strong>formula_colors</strong> – a list of colors to use in the plotting of the optionally
specified formulas_to-draw. Defaults to the Plotly Dark2 color scheme.</p></li>
<li><p><strong>element_padding</strong> – if provided, automatically adjusts chemical potential axis
limits of the plot such that elemental domains have the specified padding
(in eV/atom), helping provide visual clarity. Defaults to 1.0.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>plotly.graph_objects.Figure</p>
</dd>
</dl>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.analysis.chempot_diagram.ChemicalPotentialDiagram.hyperplane_entries">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">hyperplane_entries</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">list</span><span class="p"><span class="pre">[</span></span><a class="reference internal" href="#pymatgen.analysis.phase_diagram.PDEntry" title="pymatgen.analysis.phase_diagram.PDEntry"><span class="pre">PDEntry</span></a><span class="p"><span class="pre">]</span></span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/chempot_diagram.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.chempot_diagram.ChemicalPotentialDiagram.hyperplane_entries" title="Link to this definition"></a></dt>
<dd><p>List of entries corresponding to hyperplanes.</p>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.analysis.chempot_diagram.ChemicalPotentialDiagram.hyperplanes">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">hyperplanes</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">ndarray</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/chempot_diagram.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.chempot_diagram.ChemicalPotentialDiagram.hyperplanes" title="Link to this definition"></a></dt>
<dd><p>Array of hyperplane data.</p>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.analysis.chempot_diagram.ChemicalPotentialDiagram.lims">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">lims</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">ndarray</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/chempot_diagram.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.chempot_diagram.ChemicalPotentialDiagram.lims" title="Link to this definition"></a></dt>
<dd><p>Array of limits used in constructing hyperplanes.</p>
</dd></dl>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="pymatgen.analysis.chempot_diagram.get_2d_orthonormal_vector">
<span class="sig-name descname"><span class="pre">get_2d_orthonormal_vector</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">line_pts</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">ndarray</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">ndarray</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/chempot_diagram.py#L701-L721"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.chempot_diagram.get_2d_orthonormal_vector" title="Link to this definition"></a></dt>
<dd><p>Calculates a vector that is orthonormal to a line given by a set of points. Used
for determining the location of an annotation on a 2-d chemical potential diagram.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>line_pts</strong> – a 2x2 array in the form of [[x0, y0], [x1, y1]] giving the
coordinates of a line</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>A length-2 vector that is orthonormal to the line.</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>np.ndarray</p>
</dd>
</dl>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="pymatgen.analysis.chempot_diagram.get_centroid_2d">
<span class="sig-name descname"><span class="pre">get_centroid_2d</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">vertices</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">ndarray</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">ndarray</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/chempot_diagram.py#L669-L698"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.chempot_diagram.get_centroid_2d" title="Link to this definition"></a></dt>
<dd><p>A bare-bones implementation of the formula for calculating the centroid of a 2D
polygon. Useful for calculating the location of an annotation on a chemical
potential domain within a 3D chemical potential diagram.</p>
<p>NOTE vertices must be ordered circumferentially!</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>vertices</strong> – array of 2-d coordinates corresponding to a polygon, ordered
circumferentially</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>Giving 2-d centroid coordinates.</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>np.ndarray</p>
</dd>
</dl>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="pymatgen.analysis.chempot_diagram.simple_pca">
<span class="sig-name descname"><span class="pre">simple_pca</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">data</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">ndarray</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">k</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">2</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">tuple</span><span class="p"><span class="pre">[</span></span><span class="pre">ndarray</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">ndarray</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">ndarray</span><span class="p"><span class="pre">]</span></span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/chempot_diagram.py#L646-L666"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.chempot_diagram.simple_pca" title="Link to this definition"></a></dt>
<dd><p>A bare-bones implementation of principal component analysis (PCA) used in the
ChemicalPotentialDiagram class for plotting.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>data</strong> – array of observations</p></li>
<li><p><strong>k</strong> – Number of principal components returned</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>projected data, eigenvalues, eigenvectors</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>tuple</p>
</dd>
</dl>
</dd></dl>
</section>
<section id="module-pymatgen.analysis.cost">
<span id="pymatgen-analysis-cost-module"></span><h2>pymatgen.analysis.cost module<a class="headerlink" href="#module-pymatgen.analysis.cost" title="Link to this heading"></a></h2>
<p>This module is used to estimate the cost of various compounds. Costs are taken
from the a CostDB instance, for example a CSV file via CostDBCSV.
For compounds with no cost listed, a Phase Diagram style convex hull
optimization is performed to determine a set of compositions that can be mixed
to give the desired compound with lowest total cost.</p>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.analysis.cost.CostAnalyzer">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">CostAnalyzer</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">costdb</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="#pymatgen.analysis.cost.CostDB" title="pymatgen.analysis.cost.CostDB"><span class="pre">CostDB</span></a></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/cost.py#L118-L174"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.cost.CostAnalyzer" title="Link to this definition"></a></dt>
<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></p>
<p>Given a CostDB, figures out the minimum cost solutions via convex hull.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>costdb</strong> (<a class="reference internal" href="#pymatgen.analysis.cost.CostDB" title="pymatgen.analysis.cost.CostDB"><em>CostDB</em></a>) – Cost database to use.</p>
</dd>
</dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.cost.CostAnalyzer.get_cost_per_kg">
<span class="sig-name descname"><span class="pre">get_cost_per_kg</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">comp</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/cost.py#L164-L174"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.cost.CostAnalyzer.get_cost_per_kg" title="Link to this definition"></a></dt>
<dd><p>Get best estimate of minimum cost/kg based on known data.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>comp</strong> (<em>CompositionLike</em>) – chemical formula</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>energy cost/kg</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>float</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.cost.CostAnalyzer.get_cost_per_mol">
<span class="sig-name descname"><span class="pre">get_cost_per_mol</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">comp</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">CompositionLike</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">float</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/cost.py#L151-L162"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.cost.CostAnalyzer.get_cost_per_mol" title="Link to this definition"></a></dt>
<dd><p>Get best estimate of minimum cost/mol based on known data.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>comp</strong> (<em>CompositionLike</em>) – chemical formula</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>energy cost/mol</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>float</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.cost.CostAnalyzer.get_lowest_decomposition">
<span class="sig-name descname"><span class="pre">get_lowest_decomposition</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">composition</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/cost.py#L128-L149"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.cost.CostAnalyzer.get_lowest_decomposition" title="Link to this definition"></a></dt>
<dd><p>Get the decomposition leading to lowest cost.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>composition</strong> – Composition as a pymatgen.core.structure.Composition</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>amount}</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>Decomposition as a dict of {Entry</p>
</dd>
</dl>
</dd></dl>
</dd></dl>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.analysis.cost.CostDB">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">CostDB</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/cost.py#L59-L74"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.cost.CostDB" title="Link to this definition"></a></dt>
<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">ABC</span></code></p>
<p>Abstract class for representing a Cost database.
Can be extended, e.g. for file-based or REST-based databases.</p>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.cost.CostDB.get_entries">
<em class="property"><span class="pre">abstract</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">get_entries</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">chemsys</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/cost.py#L65-L74"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.cost.CostDB.get_entries" title="Link to this definition"></a></dt>
<dd><p>For a given chemical system, return an array of CostEntries.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>chemsys</strong> (<em>list</em><em>[</em><em>SpeciesLike</em><em>]</em>) – Elements defining the chemical system.</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>list[CostEntries]</p>
</dd>
</dl>
</dd></dl>
</dd></dl>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.analysis.cost.CostDBCSV">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">CostDBCSV</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">filename</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/cost.py#L77-L107"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.cost.CostDBCSV" title="Link to this definition"></a></dt>
<dd><p>Bases: <a class="reference internal" href="#pymatgen.analysis.cost.CostDB" title="pymatgen.analysis.cost.CostDB"><code class="xref py py-class docutils literal notranslate"><span class="pre">CostDB</span></code></a></p>
<p>Read a CSV file to get costs. Format is formula,cost_per_kg,name,BibTeX.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>filename</strong> (<em>str</em>) – Filename of cost database.</p>
</dd>
</dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.cost.CostDBCSV.get_entries">
<span class="sig-name descname"><span class="pre">get_entries</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">chemsys</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/cost.py#L97-L107"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.cost.CostDBCSV.get_entries" title="Link to this definition"></a></dt>
<dd><p>For a given chemical system, return an array of CostEntries.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>chemsys</strong> (<em>list</em><em>[</em><a class="reference internal" href="pymatgen.core.html#pymatgen.core.periodic_table.Element" title="pymatgen.core.periodic_table.Element"><em>Element</em></a><em>]</em>) – Elements defining the chemical system.</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>array of CostEntries</p>
</dd>
</dl>
</dd></dl>
</dd></dl>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.analysis.cost.CostEntry">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">CostEntry</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">composition</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">cost</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">reference</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/cost.py#L38-L56"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.cost.CostEntry" title="Link to this definition"></a></dt>
<dd><p>Bases: <a class="reference internal" href="#pymatgen.analysis.phase_diagram.PDEntry" title="pymatgen.analysis.phase_diagram.PDEntry"><code class="xref py py-class docutils literal notranslate"><span class="pre">PDEntry</span></code></a></p>
<p>Extends PDEntry to include a BibTeX reference and include language about cost.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>composition</strong> (<a class="reference internal" href="pymatgen.core.html#pymatgen.core.composition.Composition" title="pymatgen.core.composition.Composition"><em>Composition</em></a>) – chemical composition of the entry</p></li>
<li><p><strong>cost</strong> (<em>float</em>) – per mol, NOT per kg of the full Composition</p></li>
<li><p><strong>name</strong> (<em>str</em>) – Optional parameter to name the entry. Defaults to the reduced
chemical formula as in PDEntry.</p></li>
<li><p><strong>reference</strong> (<em>str</em>) – Reference data as BiBTeX string.</p></li>
</ul>
</dd>
</dl>
</dd></dl>
</section>
<section id="module-pymatgen.analysis.dimensionality">
<span id="pymatgen-analysis-dimensionality-module"></span><h2>pymatgen.analysis.dimensionality module<a class="headerlink" href="#module-pymatgen.analysis.dimensionality" title="Link to this heading"></a></h2>
<p>This module provides functions to get the dimensionality of a structure.</p>
<p>A number of different algorithms are implemented. These are based on the
following publications:</p>
<dl class="simple">
<dt>get_dimensionality_larsen:</dt><dd><ul class="simple">
<li><p>P. M. Larsen, M. Pandey, M. Strange, K. W. Jacobsen. Definition of a
scoring parameter to identify low-dimensional materials components.
Phys. Rev. Materials 3, 034003 (2019).</p></li>
</ul>
</dd>
<dt>get_dimensionality_cheon:</dt><dd><ul class="simple">
<li><p>Cheon, G.; Duerloo, K.-A. N.; Sendek, A. D.; Porter, C.; Chen, Y.; Reed,
E. J. Data Mining for New Two- and One-Dimensional Weakly Bonded Solids
and Lattice-Commensurate Heterostructures. Nano Lett. 2017.</p></li>
</ul>
</dd>
<dt>get_dimensionality_gorai:</dt><dd><ul class="simple">
<li><p>Gorai, P., Toberer, E. & Stevanovic, V. Computational Identification of
Promising Thermoelectric Materials Among Known Quasi-2D Binary Compounds.
J. Mater. Chem. A 2, 4136 (2016).</p></li>
</ul>
</dd>
</dl>
<dl class="py function">
<dt class="sig sig-object py" id="pymatgen.analysis.dimensionality.calculate_dimensionality_of_site">
<span class="sig-name descname"><span class="pre">calculate_dimensionality_of_site</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">bonded_structure</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">site_index</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">inc_vertices</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/dimensionality.py#L169-L242"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.dimensionality.calculate_dimensionality_of_site" title="Link to this definition"></a></dt>
<dd><p>Calculate the dimensionality of the component containing the given site.</p>
<p>Implements directly the modified breadth-first-search algorithm described in
Algorithm 1 of:</p>
<p>P. M. Larsen, M. Pandey, M. Strange, K. W. Jacobsen. Definition of a
scoring parameter to identify low-dimensional materials components.
Phys. Rev. Materials 3, 034003 (2019).</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>bonded_structure</strong> (<a class="reference internal" href="#pymatgen.analysis.graphs.StructureGraph" title="pymatgen.analysis.graphs.StructureGraph"><em>StructureGraph</em></a>) – A structure with bonds, represented
as a pymatgen structure graph. For example, generated using the
CrystalNN.get_bonded_structure() method.</p></li>
<li><p><strong>site_index</strong> (<em>int</em>) – The index of a site in the component of interest.</p></li>
<li><p><strong>inc_vertices</strong> (<em>bool</em><em>, </em><em>optional</em>) – Whether to return the vertices (site
images) of the component.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p><dl class="simple">
<dt>If inc_vertices is False, the dimensionality of the</dt><dd><p>component will be returned as an int. If inc_vertices is true, the
function will return a tuple of (dimensionality, vertices), where
vertices is a list of tuples. E.g. [(0, 0, 0), (1, 1, 1)].</p>
</dd>
</dl>
</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>int | tuple</p>
</dd>
</dl>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="pymatgen.analysis.dimensionality.find_clusters">
<span class="sig-name descname"><span class="pre">find_clusters</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">struct</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">connected_matrix</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/dimensionality.py#L428-L479"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.dimensionality.find_clusters" title="Link to this definition"></a></dt>
<dd><p>Find bonded clusters of atoms in the structure with periodic boundary
conditions.</p>
<p>If there are atoms that are not bonded to anything, returns [0,1,0]. (For
faster computation time)</p>
<p>Author: Gowoon Cheon
Email: <a class="reference external" href="mailto:gcheon%40stanford.edu">gcheon<span>@</span>stanford<span>.</span>edu</a></p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>struct</strong> (<a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><em>Structure</em></a>) – Input structure</p></li>
<li><p><strong>connected_matrix</strong> – Must be made from the same structure with
find_connected_atoms() function.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>the size of the largest cluster in the crystal structure
min_cluster: the size of the smallest cluster in the crystal structure
clusters: list of bonded clusters found here, clusters are formatted as
sets of indices of atoms</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>max_cluster</p>
</dd>
</dl>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="pymatgen.analysis.dimensionality.find_connected_atoms">
<span class="sig-name descname"><span class="pre">find_connected_atoms</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">struct</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">tolerance</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0.45</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ldict</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/dimensionality.py#L381-L425"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.dimensionality.find_connected_atoms" title="Link to this definition"></a></dt>
<dd><p>Find bonded atoms and returns a adjacency matrix of bonded atoms.</p>
<p>Author: “Gowoon Cheon”
Email: “<a class="reference external" href="mailto:gcheon%40stanford.edu">gcheon<span>@</span>stanford<span>.</span>edu</a>”</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>struct</strong> (<a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><em>Structure</em></a>) – Input structure</p></li>
<li><p><strong>tolerance</strong> – length in angstroms used in finding bonded atoms. Two atoms
are considered bonded if (radius of atom 1) + (radius of atom 2) +
(tolerance) < (distance between atoms 1 and 2). Default
value = 0.45, the value used by JMol and Cheon et al.</p></li>
<li><p><strong>ldict</strong> – dictionary of bond lengths used in finding bonded atoms. Values
from JMol are used as default</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p><dl class="simple">
<dt>A numpy array of shape (number of atoms, number of atoms);</dt><dd><p>If any image of atom j is bonded to atom i with periodic boundary
conditions, the matrix element [atom i, atom j] is 1.</p>
</dd>
</dl>
</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>np.ndarray</p>
</dd>
</dl>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="pymatgen.analysis.dimensionality.get_dimensionality_cheon">
<span class="sig-name descname"><span class="pre">get_dimensionality_cheon</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">structure_raw</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">tolerance</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0.45</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ldict</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">standardize</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">larger_cell</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/dimensionality.py#L292-L378"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.dimensionality.get_dimensionality_cheon" title="Link to this definition"></a></dt>
<dd><p>Algorithm for finding the dimensions of connected subunits in a structure.
This method finds the dimensionality of the material even when the material
is not layered along low-index planes, or does not have flat
layers/molecular wires.</p>
<p>Author: “Gowoon Cheon”
Email: “<a class="reference external" href="mailto:gcheon%40stanford.edu">gcheon<span>@</span>stanford<span>.</span>edu</a>”</p>
<p>See details at :</p>
<p>Cheon, G.; Duerloo, K.-A. N.; Sendek, A. D.; Porter, C.; Chen, Y.; Reed,
E. J. Data Mining for New Two- and One-Dimensional Weakly Bonded Solids and
Lattice-Commensurate Heterostructures. Nano Lett. 2017.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>structure_raw</strong> (<a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><em>Structure</em></a>) – A pymatgen Structure object.</p></li>
<li><p><strong>tolerance</strong> (<em>float</em>) – length in angstroms used in finding bonded atoms.
Two atoms are considered bonded if (radius of atom 1) + (radius of
atom 2) + (tolerance) < (distance between atoms 1 and 2). Default
value = 0.45, the value used by JMol and Cheon et al.</p></li>
<li><p><strong>ldict</strong> (<em>dict</em>) – dictionary of bond lengths used in finding bonded atoms.
Values from JMol are used as default</p></li>
<li><p><strong>standardize</strong> – works with conventional standard structures if True. It is
recommended to keep this as True.</p></li>
<li><p><strong>larger_cell</strong> – <p>tests with 3x3x3 supercell instead of 2x2x2. Testing with
2x2x2 supercell is faster but misclassifies rare interpenetrated 3D</p>
<blockquote>
<div><p>structures. Testing with a larger cell circumvents this problem</p>
</div></blockquote>
</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p><dl class="simple">
<dt>dimension of the largest cluster as a string. If there are ions</dt><dd><p>or molecules it returns ‘intercalated ion/molecule’</p>
</dd>
</dl>
</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>str</p>
</dd>
</dl>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="pymatgen.analysis.dimensionality.get_dimensionality_gorai">
<span class="sig-name descname"><span class="pre">get_dimensionality_gorai</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">structure</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">max_hkl</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">2</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">el_radius_updates</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">min_slab_size</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">5</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">min_vacuum_size</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">5</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">standardize</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">bonds</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/dimensionality.py#L482-L544"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.dimensionality.get_dimensionality_gorai" title="Link to this definition"></a></dt>
<dd><p>This method returns whether a structure is 3D, 2D (layered), or 1D (linear
chains or molecules) according to the algorithm published in Gorai, P.,
Toberer, E. & Stevanovic, V. Computational Identification of Promising
Thermoelectric Materials Among Known Quasi-2D Binary Compounds. J. Mater.
Chem. A 2, 4136 (2016).</p>
<p>Note that a 1D structure detection might indicate problems in the bonding
algorithm, particularly for ionic crystals (e.g., NaCl)</p>
<p>Users can change the behavior of bonds detection by passing either
el_radius_updates to update atomic radii for auto-detection of max bond
distances, or bonds to explicitly specify max bond distances for atom pairs.
Note that if you pass both, el_radius_updates are ignored.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>structure</strong> (<a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><em>Structure</em></a>) – structure to analyze dimensionality for</p></li>
<li><p><strong>max_hkl</strong> (<em>int</em>) – max index of planes to look for layers</p></li>
<li><p><strong>el_radius_updates</strong> (<em>dict</em>) – symbol->float to update atomic radii</p></li>
<li><p><strong>min_slab_size</strong> (<em>float</em>) – internal surface construction parameter</p></li>
<li><p><strong>min_vacuum_size</strong> (<em>float</em>) – internal surface construction parameter</p></li>
<li><p><strong>standardize</strong> (<em>bool</em>) – whether to standardize the structure before
analysis. Set to False only if you already have the structure in a
convention where layers / chains will be along low <hkl> indexes.</p></li>
<li><p><strong>bonds</strong> (<em>dict</em><em>[</em><em>tuple</em><em>, </em><em>float</em><em>]</em>) – bonds are specified as a dict of 2-tuples of Species mapped to floats,
the max bonding distance. For example, PO4 groups may be
defined as {(“P”, “O”): 3}.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p><dl class="simple">
<dt>the dimensionality of the structure - 1 (molecules/chains),</dt><dd><p>2 (layered), or 3 (3D)</p>
</dd>
</dl>
</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>int</p>
</dd>
</dl>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="pymatgen.analysis.dimensionality.get_dimensionality_larsen">
<span class="sig-name descname"><span class="pre">get_dimensionality_larsen</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">bonded_structure</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/dimensionality.py#L44-L72"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.dimensionality.get_dimensionality_larsen" title="Link to this definition"></a></dt>
<dd><p>Gets the dimensionality of a bonded structure.</p>
<p>The dimensionality of the structure is the highest dimensionality of all
structure components. This method is very robust and can handle
many tricky structures, regardless of structure type or improper connections
due to periodic boundary conditions.</p>
<p>Requires a StructureGraph object as input. This can be generated using one
of the NearNeighbor classes. For example, using the CrystalNN class:</p>
<blockquote>
<div><p>bonded_structure = CrystalNN().get_bonded_structure(structure)</p>
</div></blockquote>
<p>Based on the modified breadth-first-search algorithm described in:</p>
<p>P. M. Larsen, M. Pandey, M. Strange, K. W. Jacobsen. Definition of a
scoring parameter to identify low-dimensional materials components.
Phys. Rev. Materials 3, 034003 (2019).</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>bonded_structure</strong> (<a class="reference internal" href="#pymatgen.analysis.graphs.StructureGraph" title="pymatgen.analysis.graphs.StructureGraph"><em>StructureGraph</em></a>) – A structure with bonds, represented
as a pymatgen structure graph. For example, generated using the
CrystalNN.get_bonded_structure() method.</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>The dimensionality of the structure.</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>int</p>
</dd>
</dl>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="pymatgen.analysis.dimensionality.get_structure_components">
<span class="sig-name descname"><span class="pre">get_structure_components</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">bonded_structure</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">inc_orientation</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">inc_site_ids</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">inc_molecule_graph</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/dimensionality.py#L75-L166"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.dimensionality.get_structure_components" title="Link to this definition"></a></dt>
<dd><p>Gets information on the components in a bonded structure.</p>
<p>Correctly determines the dimensionality of all structures, regardless of
structure type or improper connections due to periodic boundary conditions.</p>
<p>Requires a StructureGraph object as input. This can be generated using one
of the NearNeighbor classes. For example, using the CrystalNN class:</p>
<blockquote>
<div><p>bonded_structure = CrystalNN().get_bonded_structure(structure)</p>
</div></blockquote>
<p>Based on the modified breadth-first-search algorithm described in:</p>
<p>P. M. Larsen, M. Pandey, M. Strange, K. W. Jacobsen. Definition of a
scoring parameter to identify low-dimensional materials components.
Phys. Rev. Materials 3, 034003 (2019).</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>bonded_structure</strong> (<a class="reference internal" href="#pymatgen.analysis.graphs.StructureGraph" title="pymatgen.analysis.graphs.StructureGraph"><em>StructureGraph</em></a>) – A structure with bonds, represented
as a pymatgen structure graph. For example, generated using the
CrystalNN.get_bonded_structure() method.</p></li>
<li><p><strong>inc_orientation</strong> (<em>bool</em><em>, </em><em>optional</em>) – Whether to include the orientation
of the structure component. For surfaces, the miller index is given,
for one-dimensional structures, the direction of the chain is given.</p></li>
<li><p><strong>inc_site_ids</strong> (<em>bool</em><em>, </em><em>optional</em>) – Whether to include the site indices
of the sites in the structure component.</p></li>
<li><p><strong>inc_molecule_graph</strong> (<em>bool</em><em>, </em><em>optional</em>) – Whether to include MoleculeGraph
objects for zero-dimensional components.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p><dl class="simple">
<dt>Information on the components in a structure as a list</dt><dd><p>of dictionaries with the keys:</p>
<ul class="simple">
<li><dl class="simple">
<dt>”structure_graph”: A pymatgen StructureGraph object for the</dt><dd><p>component.</p>
</dd>
</dl>
</li>
<li><dl class="simple">
<dt>”dimensionality”: The dimensionality of the structure component as an</dt><dd><p>int.</p>
</dd>
</dl>
</li>
<li><dl class="simple">
<dt>”orientation”: If inc_orientation is <cite>True</cite>, the orientation of the</dt><dd><p>component as a tuple. E.g. (1, 1, 1)</p>
</dd>
</dl>
</li>
<li><dl class="simple">
<dt>”site_ids”: If inc_site_ids is <cite>True</cite>, the site indices of the</dt><dd><p>sites in the component as a tuple.</p>
</dd>
</dl>
</li>
<li><dl class="simple">
<dt>”molecule_graph”: If inc_molecule_graph is <cite>True</cite>, the site a</dt><dd><p>MoleculeGraph object for zero-dimensional components.</p>
</dd>
</dl>
</li>
</ul>
</dd>
</dl>
</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>list[dict]</p>
</dd>
</dl>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="pymatgen.analysis.dimensionality.zero_d_graph_to_molecule_graph">
<span class="sig-name descname"><span class="pre">zero_d_graph_to_molecule_graph</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">bonded_structure</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">graph</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/dimensionality.py#L245-L289"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.dimensionality.zero_d_graph_to_molecule_graph" title="Link to this definition"></a></dt>
<dd><p>Converts a zero-dimensional networkx Graph object into a MoleculeGraph.</p>
<p>Implements a similar breadth-first search to that in
calculate_dimensionality_of_site().</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>bonded_structure</strong> (<a class="reference internal" href="#pymatgen.analysis.graphs.StructureGraph" title="pymatgen.analysis.graphs.StructureGraph"><em>StructureGraph</em></a>) – A structure with bonds, represented
as a pymatgen structure graph. For example, generated using the
CrystalNN.get_bonded_structure() method.</p></li>
<li><p><strong>graph</strong> (<em>nx.Graph</em>) – A networkx <cite>Graph</cite> object for the component of
interest.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>A MoleculeGraph object of the component.</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p><a class="reference internal" href="#pymatgen.analysis.graphs.MoleculeGraph" title="pymatgen.analysis.graphs.MoleculeGraph">MoleculeGraph</a></p>
</dd>
</dl>
</dd></dl>
</section>
<section id="module-pymatgen.analysis.disorder">
<span id="pymatgen-analysis-disorder-module"></span><h2>pymatgen.analysis.disorder module<a class="headerlink" href="#module-pymatgen.analysis.disorder" title="Link to this heading"></a></h2>
<p>This module provides various methods to analyze order/disorder in materials.</p>
<dl class="py function">
<dt class="sig sig-object py" id="pymatgen.analysis.disorder.get_warren_cowley_parameters">
<span class="sig-name descname"><span class="pre">get_warren_cowley_parameters</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">structure</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><span class="pre">Structure</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">r</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">float</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">dr</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">float</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><span class="pre">tuple</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">float</span><span class="p"><span class="pre">]</span></span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/disorder.py#L13-L40"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.disorder.get_warren_cowley_parameters" title="Link to this definition"></a></dt>
<dd><p>Warren-Crowley parameters.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>structure</strong> – Pymatgen Structure.</p></li>
<li><p><strong>r</strong> – Radius</p></li>
<li><p><strong>dr</strong> – Shell width</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>-1.0, …}</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>Warren-Crowley parameters in the form of a dict, e.g. {(Element Mo, Element W)</p>
</dd>
</dl>
</dd></dl>
</section>
<section id="module-pymatgen.analysis.energy_models">
<span id="pymatgen-analysis-energy-models-module"></span><h2>pymatgen.analysis.energy_models module<a class="headerlink" href="#module-pymatgen.analysis.energy_models" title="Link to this heading"></a></h2>
<p>This module implements a EnergyModel abstract class and some basic
implementations. Basically, an EnergyModel is any model that returns an
“energy” for any given structure.</p>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.analysis.energy_models.EnergyModel">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">EnergyModel</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/energy_models.py#L25-L48"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.energy_models.EnergyModel" title="Link to this definition"></a></dt>
<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">MSONable</span></code>, <code class="xref py py-class docutils literal notranslate"><span class="pre">ABC</span></code></p>
<p>Abstract structure filter class.</p>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.energy_models.EnergyModel.from_dict">
<em class="property"><span class="pre">classmethod</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">from_dict</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">dct</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">dict</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">Self</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/energy_models.py#L39-L48"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.energy_models.EnergyModel.from_dict" title="Link to this definition"></a></dt>
<dd><dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>dct</strong> (<em>dict</em>) – Dict representation.</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>EnergyModel</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.energy_models.EnergyModel.get_energy">
<em class="property"><span class="pre">abstract</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">get_energy</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">structure</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">float</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/energy_models.py#L28-L37"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.energy_models.EnergyModel.get_energy" title="Link to this definition"></a></dt>
<dd><dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>structure</strong> – Structure.</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>Energy value</p>
</dd>
</dl>
</dd></dl>
</dd></dl>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.analysis.energy_models.EwaldElectrostaticModel">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">EwaldElectrostaticModel</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">real_space_cut</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">recip_space_cut</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">eta</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">acc_factor</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">8.0</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/energy_models.py#L51-L105"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.energy_models.EwaldElectrostaticModel" title="Link to this definition"></a></dt>
<dd><p>Bases: <a class="reference internal" href="#pymatgen.analysis.energy_models.EnergyModel" title="pymatgen.analysis.energy_models.EnergyModel"><code class="xref py py-class docutils literal notranslate"><span class="pre">EnergyModel</span></code></a></p>
<p>Wrapper around EwaldSum to calculate the electrostatic energy.</p>
<p>Initialize the model. Args have the same definitions as in
pymatgen.analysis.ewald.EwaldSummation.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>real_space_cut</strong> (<em>float</em>) – Real space cutoff radius dictating how
many terms are used in the real space sum. Defaults to None,
which means determine automatically using the formula given
in gulp 3.1 documentation.</p></li>
<li><p><strong>recip_space_cut</strong> (<em>float</em>) – Reciprocal space cutoff radius.
Defaults to None, which means determine automatically using
the formula given in gulp 3.1 documentation.</p></li>
<li><p><strong>eta</strong> (<em>float</em>) – Screening parameter. Defaults to None, which means
determine automatically.</p></li>
<li><p><strong>acc_factor</strong> (<em>float</em>) – No. of significant figures each sum is
converged to.</p></li>
</ul>
</dd>
</dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.energy_models.EwaldElectrostaticModel.as_dict">
<span class="sig-name descname"><span class="pre">as_dict</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/energy_models.py#L93-L105"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.energy_models.EwaldElectrostaticModel.as_dict" title="Link to this definition"></a></dt>
<dd><p>MSONable dict.</p>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.energy_models.EwaldElectrostaticModel.get_energy">
<span class="sig-name descname"><span class="pre">get_energy</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">structure</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><span class="pre">Structure</span></a></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/energy_models.py#L76-L91"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.energy_models.EwaldElectrostaticModel.get_energy" title="Link to this definition"></a></dt>
<dd><dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>structure</strong> – Structure.</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>Energy value</p>
</dd>
</dl>
</dd></dl>
</dd></dl>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.analysis.energy_models.IsingModel">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">IsingModel</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">j</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">max_radius</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/energy_models.py#L149-L184"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.energy_models.IsingModel" title="Link to this definition"></a></dt>
<dd><p>Bases: <a class="reference internal" href="#pymatgen.analysis.energy_models.EnergyModel" title="pymatgen.analysis.energy_models.EnergyModel"><code class="xref py py-class docutils literal notranslate"><span class="pre">EnergyModel</span></code></a></p>
<p>A very simple Ising model, with r^2 decay.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>j</strong> (<em>float</em>) – The interaction parameter. E = J * spin1 * spin2.</p></li>
<li><p><strong>radius</strong> (<em>float</em>) – max_radius for the interaction.</p></li>
</ul>
</dd>
</dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.energy_models.IsingModel.as_dict">
<span class="sig-name descname"><span class="pre">as_dict</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/energy_models.py#L177-L184"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.energy_models.IsingModel.as_dict" title="Link to this definition"></a></dt>
<dd><p>MSONable dict.</p>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.energy_models.IsingModel.get_energy">
<span class="sig-name descname"><span class="pre">get_energy</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">structure</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><span class="pre">Structure</span></a></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/energy_models.py#L161-L175"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.energy_models.IsingModel.get_energy" title="Link to this definition"></a></dt>
<dd><dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>structure</strong> – Structure.</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>Energy value</p>
</dd>
</dl>
</dd></dl>
</dd></dl>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.analysis.energy_models.NsitesModel">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">NsitesModel</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/energy_models.py#L187-L211"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.energy_models.NsitesModel" title="Link to this definition"></a></dt>
<dd><p>Bases: <a class="reference internal" href="#pymatgen.analysis.energy_models.EnergyModel" title="pymatgen.analysis.energy_models.EnergyModel"><code class="xref py py-class docutils literal notranslate"><span class="pre">EnergyModel</span></code></a></p>
<p>Sets the energy to the number of sites. More sites => higher “energy”.
Used to rank structures from smallest number of sites to largest number
of sites after enumeration.</p>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.energy_models.NsitesModel.as_dict">
<span class="sig-name descname"><span class="pre">as_dict</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/energy_models.py#L204-L211"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.energy_models.NsitesModel.as_dict" title="Link to this definition"></a></dt>
<dd><p>MSONable dict.</p>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.energy_models.NsitesModel.get_energy">
<span class="sig-name descname"><span class="pre">get_energy</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">structure</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><span class="pre">Structure</span></a></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/energy_models.py#L194-L202"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.energy_models.NsitesModel.get_energy" title="Link to this definition"></a></dt>
<dd><dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>structure</strong> – Structure.</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>Energy value</p>
</dd>
</dl>
</dd></dl>
</dd></dl>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.analysis.energy_models.SymmetryModel">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">SymmetryModel</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">symprec</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">float</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">0.1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">angle_tolerance</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">5</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/energy_models.py#L108-L146"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.energy_models.SymmetryModel" title="Link to this definition"></a></dt>
<dd><p>Bases: <a class="reference internal" href="#pymatgen.analysis.energy_models.EnergyModel" title="pymatgen.analysis.energy_models.EnergyModel"><code class="xref py py-class docutils literal notranslate"><span class="pre">EnergyModel</span></code></a></p>
<p>Sets the energy to the negative of the spacegroup number. Higher symmetry =>
lower “energy”.</p>
<p>Args have same meaning as in pymatgen.symmetry.SpacegroupAnalyzer.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>symprec</strong> (<em>float</em>) – Symmetry tolerance. Defaults to 0.1.</p></li>
<li><p><strong>angle_tolerance</strong> (<em>float</em>) – Tolerance for angles. Defaults to 5 degrees.</p></li>
</ul>
</dd>
</dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.energy_models.SymmetryModel.as_dict">
<span class="sig-name descname"><span class="pre">as_dict</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/energy_models.py#L136-L146"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.energy_models.SymmetryModel.as_dict" title="Link to this definition"></a></dt>
<dd><p>MSONable dict.</p>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.energy_models.SymmetryModel.get_energy">
<span class="sig-name descname"><span class="pre">get_energy</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">structure</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><span class="pre">Structure</span></a></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/energy_models.py#L125-L134"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.energy_models.SymmetryModel.get_energy" title="Link to this definition"></a></dt>
<dd><dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>structure</strong> – Structure.</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>Energy value</p>
</dd>
</dl>
</dd></dl>
</dd></dl>
</section>
<section id="module-pymatgen.analysis.eos">
<span id="pymatgen-analysis-eos-module"></span><h2>pymatgen.analysis.eos module<a class="headerlink" href="#module-pymatgen.analysis.eos" title="Link to this heading"></a></h2>
<p>This module implements various equation of states.</p>
<p>Note: Most of the code were initially adapted from ASE and deltafactor by
@gmatteo but has since undergone major refactoring.</p>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.analysis.eos.Birch">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">Birch</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">volumes</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">Sequence</span><span class="p"><span class="pre">[</span></span><span class="pre">float</span><span class="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="n"><span class="pre">energies</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">Sequence</span><span class="p"><span class="pre">[</span></span><span class="pre">float</span><span class="p"><span class="pre">]</span></span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/eos.py#L299-L313"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.eos.Birch" title="Link to this definition"></a></dt>
<dd><p>Bases: <a class="reference internal" href="#pymatgen.analysis.eos.EOSBase" title="pymatgen.analysis.eos.EOSBase"><code class="xref py py-class docutils literal notranslate"><span class="pre">EOSBase</span></code></a></p>
<p>Birch EOS.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>volumes</strong> (<em>Sequence</em><em>[</em><em>float</em><em>]</em>) – in Ang^3.</p></li>
<li><p><strong>energies</strong> (<em>Sequence</em><em>[</em><em>float</em><em>]</em>) – in eV.</p></li>
</ul>
</dd>
</dl>
</dd></dl>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.analysis.eos.BirchMurnaghan">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">BirchMurnaghan</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">volumes</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">Sequence</span><span class="p"><span class="pre">[</span></span><span class="pre">float</span><span class="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="n"><span class="pre">energies</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">Sequence</span><span class="p"><span class="pre">[</span></span><span class="pre">float</span><span class="p"><span class="pre">]</span></span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/eos.py#L316-L323"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.eos.BirchMurnaghan" title="Link to this definition"></a></dt>
<dd><p>Bases: <a class="reference internal" href="#pymatgen.analysis.eos.EOSBase" title="pymatgen.analysis.eos.EOSBase"><code class="xref py py-class docutils literal notranslate"><span class="pre">EOSBase</span></code></a></p>
<p>BirchMurnaghan EOS.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>volumes</strong> (<em>Sequence</em><em>[</em><em>float</em><em>]</em>) – in Ang^3.</p></li>
<li><p><strong>energies</strong> (<em>Sequence</em><em>[</em><em>float</em><em>]</em>) – in eV.</p></li>
</ul>
</dd>
</dl>
</dd></dl>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.analysis.eos.DeltaFactor">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">DeltaFactor</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">volumes</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">Sequence</span><span class="p"><span class="pre">[</span></span><span class="pre">float</span><span class="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="n"><span class="pre">energies</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">Sequence</span><span class="p"><span class="pre">[</span></span><span class="pre">float</span><span class="p"><span class="pre">]</span></span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/eos.py#L388-L424"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.eos.DeltaFactor" title="Link to this definition"></a></dt>
<dd><p>Bases: <a class="reference internal" href="#pymatgen.analysis.eos.PolynomialEOS" title="pymatgen.analysis.eos.PolynomialEOS"><code class="xref py py-class docutils literal notranslate"><span class="pre">PolynomialEOS</span></code></a></p>
<p>Fitting a polynomial EOS using delta factor.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>volumes</strong> (<em>Sequence</em><em>[</em><em>float</em><em>]</em>) – in Ang^3.</p></li>
<li><p><strong>energies</strong> (<em>Sequence</em><em>[</em><em>float</em><em>]</em>) – in eV.</p></li>
</ul>
</dd>
</dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.eos.DeltaFactor.fit">
<span class="sig-name descname"><span class="pre">fit</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">order</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">3</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">None</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/eos.py#L395-L399"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.eos.DeltaFactor.fit" title="Link to this definition"></a></dt>
<dd><p>Overridden since this eos works with volume**(2/3) instead of volume.</p>
</dd></dl>
</dd></dl>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.analysis.eos.EOS">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">EOS</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">eos_name</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">'murnaghan'</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/eos.py#L536-L602"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.eos.EOS" title="Link to this definition"></a></dt>
<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></p>
<p>Convenient wrapper. Retained in its original state to ensure backward
compatibility.</p>
<p>Fit equation of state for bulk systems.</p>
<p>The following equations are supported:</p>
<blockquote>
<div><p>murnaghan: PRB 28, 5480 (1983)</p>
<dl class="simple">
<dt>birch: Intermetallic compounds: Principles and Practice, Vol I:</dt><dd><p>Principles. pages 195-210</p>
</dd>
</dl>
<p>birch_murnaghan: PRB 70, 224107</p>
<p>pourier_tarantola: PRB 70, 224107</p>
<p>vinet: PRB 70, 224107</p>
<p>deltafactor</p>
<p>numerical_eos: 10.1103/PhysRevB.90.174107.</p>
</div></blockquote>
<p>Usage:</p>
<blockquote>
<div><p>eos = EOS(eos_name=’murnaghan’)
eos_fit = eos.fit(volumes, energies)
eos_fit.plot()</p>
</div></blockquote>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>eos_name</strong> (<em>str</em>) – Type of EOS to fit.</p>
</dd>
</dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.analysis.eos.EOS.MODELS">
<span class="sig-name descname"><span class="pre">MODELS</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">ClassVar</span><span class="p"><span class="pre">[</span></span><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">Any</span><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">]</span></span></em><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">{'birch':</span> <span class="pre"><class</span> <span class="pre">'pymatgen.analysis.eos.Birch'>,</span> <span class="pre">'birch_murnaghan':</span> <span class="pre"><class</span> <span class="pre">'pymatgen.analysis.eos.BirchMurnaghan'>,</span> <span class="pre">'deltafactor':</span> <span class="pre"><class</span> <span class="pre">'pymatgen.analysis.eos.DeltaFactor'>,</span> <span class="pre">'murnaghan':</span> <span class="pre"><class</span> <span class="pre">'pymatgen.analysis.eos.Murnaghan'>,</span> <span class="pre">'numerical_eos':</span> <span class="pre"><class</span> <span class="pre">'pymatgen.analysis.eos.NumericalEOS'>,</span> <span class="pre">'pourier_tarantola':</span> <span class="pre"><class</span> <span class="pre">'pymatgen.analysis.eos.PourierTarantola'>,</span> <span class="pre">'vinet':</span> <span class="pre"><class</span> <span class="pre">'pymatgen.analysis.eos.Vinet'>}</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/eos.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.eos.EOS.MODELS" title="Link to this definition"></a></dt>
<dd></dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.eos.EOS.fit">
<span class="sig-name descname"><span class="pre">fit</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">volumes</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">Sequence</span><span class="p"><span class="pre">[</span></span><span class="pre">float</span><span class="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="n"><span class="pre">energies</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">Sequence</span><span class="p"><span class="pre">[</span></span><span class="pre">float</span><span class="p"><span class="pre">]</span></span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><a class="reference internal" href="#pymatgen.analysis.eos.EOSBase" title="pymatgen.analysis.eos.EOSBase"><span class="pre">EOSBase</span></a></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/eos.py#L590-L602"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.eos.EOS.fit" title="Link to this definition"></a></dt>
<dd><p>Fit energies as function of volumes.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>volumes</strong> (<em>Sequence</em><em>[</em><em>float</em><em>]</em>) – in Ang^3</p></li>
<li><p><strong>energies</strong> (<em>Sequence</em><em>[</em><em>float</em><em>]</em>) – in eV</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>EOSBase object</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p><a class="reference internal" href="#pymatgen.analysis.eos.EOSBase" title="pymatgen.analysis.eos.EOSBase">EOSBase</a></p>
</dd>
</dl>
</dd></dl>
</dd></dl>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.analysis.eos.EOSBase">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">EOSBase</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">volumes</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">Sequence</span><span class="p"><span class="pre">[</span></span><span class="pre">float</span><span class="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="n"><span class="pre">energies</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">Sequence</span><span class="p"><span class="pre">[</span></span><span class="pre">float</span><span class="p"><span class="pre">]</span></span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/eos.py#L38-L287"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.eos.EOSBase" title="Link to this definition"></a></dt>
<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">ABC</span></code></p>
<p>Abstract class that must be subclassed by all equation of state
implementations.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>volumes</strong> (<em>Sequence</em><em>[</em><em>float</em><em>]</em>) – in Ang^3.</p></li>
<li><p><strong>energies</strong> (<em>Sequence</em><em>[</em><em>float</em><em>]</em>) – in eV.</p></li>
</ul>
</dd>
</dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.analysis.eos.EOSBase.b0">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">b0</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">float</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/eos.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.eos.EOSBase.b0" title="Link to this definition"></a></dt>
<dd><p>The bulk modulus in units of energy/unit of volume^3.</p>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.analysis.eos.EOSBase.b0_GPa">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">b0_GPa</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><a class="reference internal" href="pymatgen.core.html#pymatgen.core.units.FloatWithUnit" title="pymatgen.core.units.FloatWithUnit"><span class="pre">FloatWithUnit</span></a></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/eos.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.eos.EOSBase.b0_GPa" title="Link to this definition"></a></dt>
<dd><p>The bulk modulus in GPa. This assumes the energy and volumes are in eV and Ang^3.</p>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.analysis.eos.EOSBase.b1">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">b1</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/eos.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.eos.EOSBase.b1" title="Link to this definition"></a></dt>
<dd><p>The derivative of bulk modulus w.r.t. pressure(dimensionless).</p>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.analysis.eos.EOSBase.e0">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">e0</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">float</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/eos.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.eos.EOSBase.e0" title="Link to this definition"></a></dt>
<dd><p>The min energy.</p>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.eos.EOSBase.fit">
<span class="sig-name descname"><span class="pre">fit</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">None</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/eos.py#L96-L111"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.eos.EOSBase.fit" title="Link to this definition"></a></dt>
<dd><p>Do the fitting. Does least square fitting. If you want to use custom
fitting, must override this.</p>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.eos.EOSBase.func">
<span class="sig-name descname"><span class="pre">func</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">volume</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/eos.py#L125-L136"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.eos.EOSBase.func" title="Link to this definition"></a></dt>
<dd><p>The equation of state function with the parameters other than volume set
to the ones obtained from fitting.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>volume</strong> (<em>float</em><em> | </em><em>list</em><em>[</em><em>float</em><em>]</em>) – volumes in Ang^3</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>numpy.array</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.eos.EOSBase.plot">
<span class="sig-name descname"><span class="pre">plot</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">width</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">float</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">8</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">height</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">float</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ax</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">plt.Axes</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">dpi</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">float</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">plt.Axes</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/eos.py#L174-L229"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.eos.EOSBase.plot" title="Link to this definition"></a></dt>
<dd><p>Plot the equation of state.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>width</strong> (<em>float</em>) – Width of plot in inches. Defaults to 8in.</p></li>
<li><p><strong>height</strong> (<em>float</em>) – Height of plot in inches. Defaults to width *
golden ratio.</p></li>
<li><p><strong>ax</strong> (<em>plt.Axes</em>) – If supplied, changes will be made to the existing Axes.
Otherwise, new Axes will be created.</p></li>
<li><p><strong>dpi</strong> (<em>float</em>) – DPI.</p></li>
<li><p><strong>kwargs</strong> (<em>dict</em>) – additional args fed to pyplot.plot.
supported keys: style, color, text, label</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>The matplotlib axes.</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>plt.Axes</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.eos.EOSBase.plot_ax">
<span class="sig-name descname"><span class="pre">plot_ax</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">ax</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">plt.Axes</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">fontsize</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">float</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">12</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">plt.Figure</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../util/plotting.py#L231-L287"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.eos.EOSBase.plot_ax" title="Link to this definition"></a></dt>
<dd><p>Plot the equation of state on axis <cite>ax</cite>.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>ax</strong> – matplotlib Axes or None if a new figure should be created.</p></li>
<li><p><strong>fontsize</strong> – Legend fontsize.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>matplotlib figure.</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>plt.Figure</p>
</dd>
</dl>
<p>Keyword arguments controlling the display of the figure:</p>
<table class="docutils align-default">
<thead>
<tr class="row-odd"><th class="head"><p>kwargs</p></th>
<th class="head"><p>Meaning</p></th>
</tr>
</thead>
<tbody>
<tr class="row-even"><td><p>title</p></td>
<td><p>Title of the plot (Default: None).</p></td>
</tr>
<tr class="row-odd"><td><p>show</p></td>
<td><p>True to show the figure (default: True).</p></td>
</tr>
<tr class="row-even"><td><p>savefig</p></td>
<td><p>“abc.png” or “abc.eps” to save the figure to a file.</p></td>
</tr>
<tr class="row-odd"><td><p>size_kwargs</p></td>
<td><p>Dictionary with options passed to fig.set_size_inches
e.g. size_kwargs=dict(w=3, h=4)</p></td>
</tr>
<tr class="row-even"><td><p>tight_layout</p></td>
<td><p>True to call fig.tight_layout (default: False)</p></td>
</tr>
<tr class="row-odd"><td><p>ax_grid</p></td>
<td><p>True (False) to add (remove) grid from all axes in fig.
Default: None i.e. fig is left unchanged.</p></td>
</tr>
<tr class="row-even"><td><p>ax_annotate</p></td>
<td><p>Add labels to subplots e.g. (a), (b).
Default: False</p></td>
</tr>
<tr class="row-odd"><td><p>fig_close</p></td>
<td><p>Close figure. Default: False.</p></td>
</tr>
</tbody>
</table>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.analysis.eos.EOSBase.results">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">results</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">Any</span><span class="p"><span class="pre">]</span></span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/eos.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.eos.EOSBase.results" title="Link to this definition"></a></dt>
<dd><p>A summary dict.</p>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.analysis.eos.EOSBase.v0">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">v0</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/eos.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.eos.EOSBase.v0" title="Link to this definition"></a></dt>
<dd><p>The minimum or the reference volume in Ang^3.</p>
</dd></dl>
</dd></dl>
<dl class="py exception">
<dt class="sig sig-object py" id="pymatgen.analysis.eos.EOSError">
<em class="property"><span class="pre">exception</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">EOSError</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/eos.py#L605-L606"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.eos.EOSError" title="Link to this definition"></a></dt>
<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">Exception</span></code></p>
<p>Error class for EOS fitting.</p>
</dd></dl>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.analysis.eos.Murnaghan">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">Murnaghan</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">volumes</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">Sequence</span><span class="p"><span class="pre">[</span></span><span class="pre">float</span><span class="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="n"><span class="pre">energies</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">Sequence</span><span class="p"><span class="pre">[</span></span><span class="pre">float</span><span class="p"><span class="pre">]</span></span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/eos.py#L290-L296"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.eos.Murnaghan" title="Link to this definition"></a></dt>
<dd><p>Bases: <a class="reference internal" href="#pymatgen.analysis.eos.EOSBase" title="pymatgen.analysis.eos.EOSBase"><code class="xref py py-class docutils literal notranslate"><span class="pre">EOSBase</span></code></a></p>
<p>Murnaghan EOS.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>volumes</strong> (<em>Sequence</em><em>[</em><em>float</em><em>]</em>) – in Ang^3.</p></li>
<li><p><strong>energies</strong> (<em>Sequence</em><em>[</em><em>float</em><em>]</em>) – in eV.</p></li>
</ul>
</dd>
</dl>
</dd></dl>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.analysis.eos.NumericalEOS">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">NumericalEOS</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">volumes</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">Sequence</span><span class="p"><span class="pre">[</span></span><span class="pre">float</span><span class="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="n"><span class="pre">energies</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">Sequence</span><span class="p"><span class="pre">[</span></span><span class="pre">float</span><span class="p"><span class="pre">]</span></span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/eos.py#L427-L533"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.eos.NumericalEOS" title="Link to this definition"></a></dt>
<dd><p>Bases: <a class="reference internal" href="#pymatgen.analysis.eos.PolynomialEOS" title="pymatgen.analysis.eos.PolynomialEOS"><code class="xref py py-class docutils literal notranslate"><span class="pre">PolynomialEOS</span></code></a></p>
<p>A numerical EOS.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>volumes</strong> (<em>Sequence</em><em>[</em><em>float</em><em>]</em>) – in Ang^3.</p></li>
<li><p><strong>energies</strong> (<em>Sequence</em><em>[</em><em>float</em><em>]</em>) – in eV.</p></li>
</ul>
</dd>
</dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.eos.NumericalEOS.fit">
<span class="sig-name descname"><span class="pre">fit</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">min_ndata_factor</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">3</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">max_poly_order_factor</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">5</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">min_poly_order</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">2</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">None</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/eos.py#L430-L533"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.eos.NumericalEOS.fit" title="Link to this definition"></a></dt>
<dd><p>Fit the input data to the ‘numerical eos’, the equation of state employed
in the quasiharmonic Debye model described in the paper:
10.1103/PhysRevB.90.174107.</p>
<p>credits: Cormac Toher</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>min_ndata_factor</strong> (<em>int</em>) – parameter that controls the minimum number
of data points that will be used for fitting.
minimum number of data points = total data points-2*min_ndata_factor</p></li>
<li><p><strong>max_poly_order_factor</strong> (<em>int</em>) – parameter that limits the max order
of the polynomial used for fitting.
max_poly_order = number of data points used for fitting -
max_poly_order_factor</p></li>
<li><p><strong>min_poly_order</strong> (<em>int</em>) – minimum order of the polynomial to be
considered for fitting.</p></li>
</ul>
</dd>
</dl>
</dd></dl>
</dd></dl>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.analysis.eos.PolynomialEOS">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">PolynomialEOS</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">volumes</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">Sequence</span><span class="p"><span class="pre">[</span></span><span class="pre">float</span><span class="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="n"><span class="pre">energies</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">Sequence</span><span class="p"><span class="pre">[</span></span><span class="pre">float</span><span class="p"><span class="pre">]</span></span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/eos.py#L349-L385"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.eos.PolynomialEOS" title="Link to this definition"></a></dt>
<dd><p>Bases: <a class="reference internal" href="#pymatgen.analysis.eos.EOSBase" title="pymatgen.analysis.eos.EOSBase"><code class="xref py py-class docutils literal notranslate"><span class="pre">EOSBase</span></code></a></p>
<p>Derives from EOSBase. Polynomial based equations of states must subclass
this.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>volumes</strong> (<em>Sequence</em><em>[</em><em>float</em><em>]</em>) – in Ang^3.</p></li>
<li><p><strong>energies</strong> (<em>Sequence</em><em>[</em><em>float</em><em>]</em>) – in eV.</p></li>
</ul>
</dd>
</dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.eos.PolynomialEOS.fit">
<span class="sig-name descname"><span class="pre">fit</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">order</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">None</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/eos.py#L358-L366"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.eos.PolynomialEOS.fit" title="Link to this definition"></a></dt>
<dd><p>Do polynomial fitting and set the parameters. Uses numpy polyfit.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>order</strong> (<em>int</em>) – order of the fit polynomial</p>
</dd>
</dl>
</dd></dl>
</dd></dl>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.analysis.eos.PourierTarantola">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">PourierTarantola</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">volumes</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">Sequence</span><span class="p"><span class="pre">[</span></span><span class="pre">float</span><span class="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="n"><span class="pre">energies</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">Sequence</span><span class="p"><span class="pre">[</span></span><span class="pre">float</span><span class="p"><span class="pre">]</span></span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/eos.py#L326-L334"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.eos.PourierTarantola" title="Link to this definition"></a></dt>
<dd><p>Bases: <a class="reference internal" href="#pymatgen.analysis.eos.EOSBase" title="pymatgen.analysis.eos.EOSBase"><code class="xref py py-class docutils literal notranslate"><span class="pre">EOSBase</span></code></a></p>
<p>Pourier-Tarantola EOS.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>volumes</strong> (<em>Sequence</em><em>[</em><em>float</em><em>]</em>) – in Ang^3.</p></li>
<li><p><strong>energies</strong> (<em>Sequence</em><em>[</em><em>float</em><em>]</em>) – in eV.</p></li>
</ul>
</dd>
</dl>
</dd></dl>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.analysis.eos.Vinet">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">Vinet</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">volumes</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">Sequence</span><span class="p"><span class="pre">[</span></span><span class="pre">float</span><span class="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="n"><span class="pre">energies</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">Sequence</span><span class="p"><span class="pre">[</span></span><span class="pre">float</span><span class="p"><span class="pre">]</span></span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/eos.py#L337-L346"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.eos.Vinet" title="Link to this definition"></a></dt>
<dd><p>Bases: <a class="reference internal" href="#pymatgen.analysis.eos.EOSBase" title="pymatgen.analysis.eos.EOSBase"><code class="xref py py-class docutils literal notranslate"><span class="pre">EOSBase</span></code></a></p>
<p>Vinet EOS.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>volumes</strong> (<em>Sequence</em><em>[</em><em>float</em><em>]</em>) – in Ang^3.</p></li>
<li><p><strong>energies</strong> (<em>Sequence</em><em>[</em><em>float</em><em>]</em>) – in eV.</p></li>
</ul>
</dd>
</dl>
</dd></dl>
</section>
<section id="module-pymatgen.analysis.ewald">
<span id="pymatgen-analysis-ewald-module"></span><h2>pymatgen.analysis.ewald module<a class="headerlink" href="#module-pymatgen.analysis.ewald" title="Link to this heading"></a></h2>
<p>This module provides classes for calculating the Ewald sum of a structure.</p>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.analysis.ewald.EwaldMinimizer">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">EwaldMinimizer</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">matrix</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">m_list</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">num_to_return</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">algo</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/ewald.py#L469-L700"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.ewald.EwaldMinimizer" title="Link to this definition"></a></dt>
<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></p>
<p>This class determines the manipulations that will minimize an Ewald matrix,
given a list of possible manipulations. This class does not perform the
manipulations on a structure, but will return the list of manipulations
that should be done on one to produce the minimal structure. It returns the
manipulations for the n lowest energy orderings. This class should be used
to perform fractional species substitution or fractional species removal to
produce a new structure. These manipulations create large numbers of
candidate structures, and this class can be used to pick out those with the
lowest Ewald sum.</p>
<p>An alternative (possibly more intuitive) interface to this class is the
order disordered structure transformation.</p>
<p>Author - Will Richards</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>matrix</strong> – A matrix of the Ewald sum interaction energies. This is stored
in the class as a diagonally symmetric array and so
self._matrix will not be the same as the input matrix.</p></li>
<li><p><strong>m_list</strong> – list of manipulations. each item is of the form
(multiplication fraction, number_of_indices, indices, species)
These are sorted such that the first manipulation contains the
most permutations. this is actually evaluated last in the
recursion since I’m using pop.</p></li>
<li><p><strong>num_to_return</strong> – The minimizer will find the number_returned lowest
energy structures. This is likely to return a number of duplicate
structures so it may be necessary to overestimate and then
remove the duplicates later. (duplicate checking in this
process is extremely expensive).</p></li>
</ul>
</dd>
</dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.analysis.ewald.EwaldMinimizer.ALGO_BEST_FIRST">
<span class="sig-name descname"><span class="pre">ALGO_BEST_FIRST</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">2</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/ewald.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.ewald.EwaldMinimizer.ALGO_BEST_FIRST" title="Link to this definition"></a></dt>
<dd></dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.analysis.ewald.EwaldMinimizer.ALGO_COMPLETE">
<span class="sig-name descname"><span class="pre">ALGO_COMPLETE</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">1</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/ewald.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.ewald.EwaldMinimizer.ALGO_COMPLETE" title="Link to this definition"></a></dt>
<dd></dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.analysis.ewald.EwaldMinimizer.ALGO_FAST">
<span class="sig-name descname"><span class="pre">ALGO_FAST</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">0</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/ewald.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.ewald.EwaldMinimizer.ALGO_FAST" title="Link to this definition"></a></dt>
<dd></dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.analysis.ewald.EwaldMinimizer.ALGO_TIME_LIMIT">
<span class="sig-name descname"><span class="pre">ALGO_TIME_LIMIT</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">3</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/ewald.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.ewald.EwaldMinimizer.ALGO_TIME_LIMIT" title="Link to this definition"></a></dt>
<dd></dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.ewald.EwaldMinimizer.add_m_list">
<span class="sig-name descname"><span class="pre">add_m_list</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">matrix_sum</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">m_list</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/ewald.py#L553-L566"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.ewald.EwaldMinimizer.add_m_list" title="Link to this definition"></a></dt>
<dd><p>Add an m_list to the output_lists and updates the current
minimum if the list is full.</p>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.ewald.EwaldMinimizer.best_case">
<span class="sig-name descname"><span class="pre">best_case</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">matrix</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">m_list</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">indices_left</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/ewald.py#L568-L618"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.ewald.EwaldMinimizer.best_case" title="Link to this definition"></a></dt>
<dd><p>Compute a best case given a matrix and manipulation list.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>matrix</strong> – the current matrix (with some permutations already
performed)</p></li>
<li><p><strong>m_list</strong> – [(multiplication fraction, number_of_indices, indices,
species)] describing the manipulation</p></li>
<li><p><strong>indices</strong> – Set of indices which haven’t had a permutation
performed on them.</p></li>
</ul>
</dd>
</dl>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.analysis.ewald.EwaldMinimizer.best_m_list">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">best_m_list</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/ewald.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.ewald.EwaldMinimizer.best_m_list" title="Link to this definition"></a></dt>
<dd><p>The best manipulation list found.</p>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.ewald.EwaldMinimizer.get_next_index">
<em class="property"><span class="pre">classmethod</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">get_next_index</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">matrix</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">manipulation</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">indices_left</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/ewald.py#L620-L628"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.ewald.EwaldMinimizer.get_next_index" title="Link to this definition"></a></dt>
<dd><p>Get an index that should have the most negative effect on the
matrix sum.</p>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.ewald.EwaldMinimizer.minimize_matrix">
<span class="sig-name descname"><span class="pre">minimize_matrix</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/ewald.py#L545-L551"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.ewald.EwaldMinimizer.minimize_matrix" title="Link to this definition"></a></dt>
<dd><p>Get the permutations that produce the lowest
Ewald sum calls recursive function to iterate through permutations.</p>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.analysis.ewald.EwaldMinimizer.minimized_sum">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">minimized_sum</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/ewald.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.ewald.EwaldMinimizer.minimized_sum" title="Link to this definition"></a></dt>
<dd><p>The minimized Ewald sum.</p>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.analysis.ewald.EwaldMinimizer.output_lists">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">output_lists</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/ewald.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.ewald.EwaldMinimizer.output_lists" title="Link to this definition"></a></dt>
<dd><p>Output lists.</p>
</dd></dl>
</dd></dl>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.analysis.ewald.EwaldSummation">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">EwaldSummation</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">structure</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">real_space_cut</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">recip_space_cut</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">eta</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">acc_factor</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">12.0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">w</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0.7071067811865475</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">compute_forces</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/ewald.py#L35-L466"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.ewald.EwaldSummation" title="Link to this definition"></a></dt>
<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">MSONable</span></code></p>
<p>Calculates the electrostatic energy of a periodic array of charges using
the Ewald technique.</p>
<dl class="simple">
<dt>Ref:</dt><dd><p>Ewald summation techniques in perspective: a survey
Abdulnour Y. Toukmaji and John A. Board Jr.
DOI: 10.1016/0010-4655(96)00016-1
URL: <a class="reference external" href="http://www.ee.duke.edu/~ayt/ewaldpaper/ewaldpaper.html">http://www.ee.duke.edu/~ayt/ewaldpaper/ewaldpaper.html</a></p>
</dd>
</dl>
<p>This matrix can be used to do fast calculations of Ewald sums after species
removal.</p>
<p>E = E_recip + E_real + E_point</p>
<p>Atomic units used in the code, then converted to eV.</p>
<p>Initialize and calculate the Ewald sum. Default convergence
parameters have been specified, but you can override them if you wish.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>structure</strong> (<a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><em>Structure</em></a>) – Input structure that must have proper
Species on all sites, i.e. Element with oxidation state. Use
Structure.add_oxidation_state… for example.</p></li>
<li><p><strong>real_space_cut</strong> (<em>float</em>) – Real space cutoff radius dictating how
many terms are used in the real space sum. Defaults to None,
which means determine automatically using the formula given
in gulp 3.1 documentation.</p></li>
<li><p><strong>recip_space_cut</strong> (<em>float</em>) – Reciprocal space cutoff radius.
Defaults to None, which means determine automatically using
the formula given in gulp 3.1 documentation.</p></li>
<li><p><strong>eta</strong> (<em>float</em>) – The screening parameter. Defaults to None, which means
determine automatically.</p></li>
<li><p><strong>acc_factor</strong> (<em>float</em>) – No. of significant figures each sum is
converged to.</p></li>
<li><p><strong>w</strong> (<em>float</em>) – Weight parameter, w, has been included that represents
the relative computational expense of calculating a term in
real and reciprocal space. Default of 0.7 reproduces result
similar to GULP 4.2. This has little effect on the total
energy, but may influence speed of computation in large
systems. Note that this parameter is used only when the
cutoffs are set to None.</p></li>
<li><p><strong>compute_forces</strong> (<em>bool</em>) – Whether to compute forces. False by
default since it is usually not needed.</p></li>
</ul>
</dd>
</dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.analysis.ewald.EwaldSummation.CONV_FACT">
<span class="sig-name descname"><span class="pre">CONV_FACT</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">14.39964547842567</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/ewald.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.ewald.EwaldSummation.CONV_FACT" title="Link to this definition"></a></dt>
<dd></dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.ewald.EwaldSummation.as_dict">
<span class="sig-name descname"><span class="pre">as_dict</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">verbosity</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">0</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">dict</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/ewald.py#L415-L436"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.ewald.EwaldSummation.as_dict" title="Link to this definition"></a></dt>
<dd><p>JSON-serialization dict representation of EwaldSummation.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>verbosity</strong> (<em>int</em>) – Verbosity level. Default of 0 only includes the
matrix representation. Set to 1 for more details.</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.ewald.EwaldSummation.compute_partial_energy">
<span class="sig-name descname"><span class="pre">compute_partial_energy</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">removed_indices</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/ewald.py#L134-L140"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.ewald.EwaldSummation.compute_partial_energy" title="Link to this definition"></a></dt>
<dd><p>Get total Ewald energy for certain sites being removed, i.e. zeroed out.</p>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.ewald.EwaldSummation.compute_sub_structure">
<span class="sig-name descname"><span class="pre">compute_sub_structure</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">sub_structure</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">tol</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">float</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">0.001</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/ewald.py#L142-L184"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.ewald.EwaldSummation.compute_sub_structure" title="Link to this definition"></a></dt>
<dd><p>Get total Ewald energy for an sub structure in the same
lattice. The sub_structure must be a subset of the original
structure, with possible different charges.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>substructure</strong> (<a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><em>Structure</em></a>) – Substructure to compute Ewald sum for.</p></li>
<li><p><strong>tol</strong> (<em>float</em>) – Tolerance for site matching in fractional coordinates.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>Ewald sum of substructure.</p>
</dd>
</dl>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.analysis.ewald.EwaldSummation.eta">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">eta</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/ewald.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.ewald.EwaldSummation.eta" title="Link to this definition"></a></dt>
<dd><p>Eta value used in Ewald summation.</p>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.analysis.ewald.EwaldSummation.forces">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">forces</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/ewald.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.ewald.EwaldSummation.forces" title="Link to this definition"></a></dt>
<dd><p>The forces on each site as a Nx3 matrix. Each row corresponds to a site.</p>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.ewald.EwaldSummation.from_dict">
<em class="property"><span class="pre">classmethod</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">from_dict</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">dct</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">Any</span><span class="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="n"><span class="pre">fmt</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">Self</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/ewald.py#L438-L466"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.ewald.EwaldSummation.from_dict" title="Link to this definition"></a></dt>
<dd><p>Create an EwaldSummation instance from JSON-serialized dictionary.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>dct</strong> (<em>dict</em>) – Dictionary representation</p></li>
<li><p><strong>fmt</strong> (<em>str</em><em>, </em><em>optional</em>) – Unused. Defaults to None.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>class instance</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p><a class="reference internal" href="#pymatgen.analysis.ewald.EwaldSummation" title="pymatgen.analysis.ewald.EwaldSummation">EwaldSummation</a></p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.ewald.EwaldSummation.get_site_energy">
<span class="sig-name descname"><span class="pre">get_site_energy</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">site_index</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/ewald.py#L277-L292"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.ewald.EwaldSummation.get_site_energy" title="Link to this definition"></a></dt>
<dd><p>Compute the energy for a single site in the structure.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>site_index</strong> (<em>int</em>) – Index of site</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>Energy of that site</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>float</p>
</dd>
</dl>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.analysis.ewald.EwaldSummation.point_energy">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">point_energy</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/ewald.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.ewald.EwaldSummation.point_energy" title="Link to this definition"></a></dt>
<dd><p>The point energy.</p>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.analysis.ewald.EwaldSummation.point_energy_matrix">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">point_energy_matrix</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/ewald.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.ewald.EwaldSummation.point_energy_matrix" title="Link to this definition"></a></dt>
<dd><p>The point space matrix. A diagonal matrix with the point terms for each
site in the diagonal elements.</p>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.analysis.ewald.EwaldSummation.real_space_energy">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">real_space_energy</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/ewald.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.ewald.EwaldSummation.real_space_energy" title="Link to this definition"></a></dt>
<dd><p>The real space energy.</p>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.analysis.ewald.EwaldSummation.real_space_energy_matrix">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">real_space_energy_matrix</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/ewald.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.ewald.EwaldSummation.real_space_energy_matrix" title="Link to this definition"></a></dt>
<dd><p>The real space energy matrix. Each matrix element (i, j) corresponds to
the interaction energy between site i and site j in real space.</p>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.analysis.ewald.EwaldSummation.reciprocal_space_energy">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">reciprocal_space_energy</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/ewald.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.ewald.EwaldSummation.reciprocal_space_energy" title="Link to this definition"></a></dt>
<dd><p>The reciprocal space energy.</p>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.analysis.ewald.EwaldSummation.reciprocal_space_energy_matrix">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">reciprocal_space_energy_matrix</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/ewald.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.ewald.EwaldSummation.reciprocal_space_energy_matrix" title="Link to this definition"></a></dt>
<dd><p>The reciprocal space energy matrix. Each matrix element (i, j)
corresponds to the interaction energy between site i and site j in
reciprocal space.</p>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.analysis.ewald.EwaldSummation.total_energy">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">total_energy</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/ewald.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.ewald.EwaldSummation.total_energy" title="Link to this definition"></a></dt>
<dd><p>The total energy.</p>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.analysis.ewald.EwaldSummation.total_energy_matrix">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">total_energy_matrix</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/ewald.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.ewald.EwaldSummation.total_energy_matrix" title="Link to this definition"></a></dt>
<dd><p>The total energy matrix. Each matrix element (i, j) corresponds to the
total interaction energy between site i and site j.</p>
<p>Note that this does not include the charged-cell energy, which is only important
when the simulation cell is not charge balanced.</p>
</dd></dl>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="pymatgen.analysis.ewald.compute_average_oxidation_state">
<span class="sig-name descname"><span class="pre">compute_average_oxidation_state</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">site</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/ewald.py#L703-L724"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.ewald.compute_average_oxidation_state" title="Link to this definition"></a></dt>
<dd><p>Calculates the average oxidation state of a site.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>site</strong> – Site to compute average oxidation state</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>Average oxidation state of site.</p>
</dd>
</dl>
</dd></dl>
</section>
<section id="module-pymatgen.analysis.excitation">
<span id="pymatgen-analysis-excitation-module"></span><h2>pymatgen.analysis.excitation module<a class="headerlink" href="#module-pymatgen.analysis.excitation" title="Link to this heading"></a></h2>
<p>This module defines an excitation spectrum class.</p>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.analysis.excitation.ExcitationSpectrum">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">ExcitationSpectrum</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">x</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">y</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/excitation.py#L8-L26"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.excitation.ExcitationSpectrum" title="Link to this definition"></a></dt>
<dd><p>Bases: <a class="reference internal" href="pymatgen.core.html#pymatgen.core.spectrum.Spectrum" title="pymatgen.core.spectrum.Spectrum"><code class="xref py py-class docutils literal notranslate"><span class="pre">Spectrum</span></code></a></p>
<p>Basic excitation spectrum object.</p>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.analysis.excitation.ExcitationSpectrum.x">
<span class="sig-name descname"><span class="pre">x</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/excitation.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.excitation.ExcitationSpectrum.x" title="Link to this definition"></a></dt>
<dd><p>The sequence of energies.</p>
<dl class="field-list simple">
<dt class="field-odd">Type<span class="colon">:</span></dt>
<dd class="field-odd"><p>Sequence[float]</p>
</dd>
</dl>
</dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.analysis.excitation.ExcitationSpectrum.y">
<span class="sig-name descname"><span class="pre">y</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/excitation.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.excitation.ExcitationSpectrum.y" title="Link to this definition"></a></dt>
<dd><p>The sequence of mu(E).</p>
<dl class="field-list simple">
<dt class="field-odd">Type<span class="colon">:</span></dt>
<dd class="field-odd"><p>Sequence[float]</p>
</dd>
</dl>
</dd></dl>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>x</strong> – A sequence of x-ray energies in eV</p></li>
<li><p><strong>y</strong> – A sequence of intensity values.</p></li>
</ul>
</dd>
</dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.analysis.excitation.ExcitationSpectrum.XLABEL">
<span class="sig-name descname"><span class="pre">XLABEL</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">'Energy</span> <span class="pre">(eV)'</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/excitation.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.excitation.ExcitationSpectrum.XLABEL" title="Link to this definition"></a></dt>
<dd></dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.analysis.excitation.ExcitationSpectrum.YLABEL">
<span class="sig-name descname"><span class="pre">YLABEL</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">'Intensity'</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/excitation.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.excitation.ExcitationSpectrum.YLABEL" title="Link to this definition"></a></dt>
<dd></dd></dl>
</dd></dl>
</section>
<section id="module-pymatgen.analysis.fragmenter">
<span id="pymatgen-analysis-fragmenter-module"></span><h2>pymatgen.analysis.fragmenter module<a class="headerlink" href="#module-pymatgen.analysis.fragmenter" title="Link to this heading"></a></h2>
<p>Perform fragmentation of molecules.</p>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.analysis.fragmenter.Fragmenter">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">Fragmenter</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">molecule</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Molecule" title="pymatgen.core.structure.Molecule"><span class="pre">Molecule</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">edges</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">list</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">depth</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">open_rings</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_metal_edge_extender</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">opt_steps</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">10000</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">prev_unique_frag_dict</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">dict</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">assume_previous_thoroughness</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/fragmenter.py#L26-L291"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.fragmenter.Fragmenter" title="Link to this definition"></a></dt>
<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">MSONable</span></code></p>
<p>Molecule fragmenter class.</p>
<p>Standard constructor for molecule fragmentation.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>molecule</strong> (<a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Molecule" title="pymatgen.core.structure.Molecule"><em>Molecule</em></a>) – The molecule to fragment.</p></li>
<li><p><strong>edges</strong> (<em>list</em>) – List of index pairs that define graph edges, aka molecule bonds. If not set,
edges will be determined with OpenBabel. Defaults to None.</p></li>
<li><p><strong>depth</strong> (<em>int</em>) – The number of levels of iterative fragmentation to perform, where each level
will include fragments obtained by breaking one bond of a fragment one level up.
Defaults to 1. However, if set to 0, instead all possible fragments are generated
using an alternative, non-iterative scheme.</p></li>
<li><p><strong>open_rings</strong> (<em>bool</em>) – Whether or not to open any rings encountered during fragmentation.
Defaults to False. If true, any bond that fails to yield disconnected graphs when
broken is instead removed and the entire structure is optimized with OpenBabel in
order to obtain a good initial guess for an opened geometry that can then be put
back into QChem to be optimized without the ring just reforming.</p></li>
<li><p><strong>use_metal_edge_extender</strong> (<em>bool</em>) – Whether or not to attempt to add additional edges from
O, N, F, or Cl to any Li or Mg atoms present that OpenBabel may have missed. Defaults
to False. Most important for ionic bonding. Note that additional metal edges may yield
new “rings” (e.g. -C-O-Li-O- in LiEC) that will not play nicely with ring opening.</p></li>
<li><p><strong>opt_steps</strong> (<em>int</em>) – Number of optimization steps when opening rings. Defaults to 10000.</p></li>
<li><p><strong>prev_unique_frag_dict</strong> (<em>dict</em>) – A dictionary of previously identified unique fragments.
Defaults to None. Typically only used when trying to find the set of unique fragments
that come from multiple molecules.</p></li>
<li><p><strong>assume_previous_thoroughness</strong> (<em>bool</em>) – Whether or not to assume that a molecule / fragment
provided in prev_unique_frag_dict has all of its unique subfragments also provided in
prev_unique_frag_dict. Defaults to True. This is an essential optimization when trying
to find the set of unique fragments that come from multiple molecules if all of those
molecules are being fully iteratively fragmented. However, if you’re passing a
prev_unique_frag_dict which includes a molecule and its fragments that were generated
at insufficient depth to find all possible subfragments to a fragmentation calculation
of a different molecule that you aim to find all possible subfragments of and which has
common subfragments with the previous molecule, this optimization will cause you to
miss some unique subfragments.</p></li>
</ul>
</dd>
</dl>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="pymatgen.analysis.fragmenter.open_ring">
<span class="sig-name descname"><span class="pre">open_ring</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">mol_graph</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="#pymatgen.analysis.graphs.MoleculeGraph" title="pymatgen.analysis.graphs.MoleculeGraph"><span class="pre">MoleculeGraph</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">bond</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">list</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">opt_steps</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><a class="reference internal" href="#pymatgen.analysis.graphs.MoleculeGraph" title="pymatgen.analysis.graphs.MoleculeGraph"><span class="pre">MoleculeGraph</span></a></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/fragmenter.py#L294-L305"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.fragmenter.open_ring" title="Link to this definition"></a></dt>
<dd><p>Open a ring using OpenBabel’s local opt. Given a molecule graph and a bond,
convert the molecule graph into an OpenBabel molecule, remove
the given bond, perform the local opt with the number of steps determined by
self.steps, and then convert the resulting structure back into a molecule graph
to be returned.</p>
</dd></dl>
</section>
<section id="module-pymatgen.analysis.functional_groups">
<span id="pymatgen-analysis-functional-groups-module"></span><h2>pymatgen.analysis.functional_groups module<a class="headerlink" href="#module-pymatgen.analysis.functional_groups" title="Link to this heading"></a></h2>
<p>Determine functional groups present in a Molecule.</p>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.analysis.functional_groups.FunctionalGroupExtractor">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">FunctionalGroupExtractor</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">molecule</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">optimize</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/functional_groups.py#L27-L361"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.functional_groups.FunctionalGroupExtractor" title="Link to this definition"></a></dt>
<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></p>
<p>This class is used to algorithmically parse a molecule (represented by an
instance of pymatgen.analysis.graphs.MoleculeGraph) and determine arbitrary
functional groups.</p>
<p>Instantiation method for FunctionalGroupExtractor.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>molecule</strong> – Either a filename, a pymatgen.core.structure.Molecule
object, or a pymatgen.analysis.graphs.MoleculeGraph object.</p></li>
<li><p><strong>optimize</strong> – Default False. If True, then the input molecule will be
modified, adding Hydrogens, performing a simple conformer search, etc.</p></li>
</ul>
</dd>
</dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.functional_groups.FunctionalGroupExtractor.categorize_functional_groups">
<span class="sig-name descname"><span class="pre">categorize_functional_groups</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">groups</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/functional_groups.py#L320-L361"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.functional_groups.FunctionalGroupExtractor.categorize_functional_groups" title="Link to this definition"></a></dt>
<dd><p>Determine classes of functional groups present in a set.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>groups</strong> – Set of functional groups.</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>dict containing representations of the groups, the indices of
where the group occurs in the MoleculeGraph, and how many of each
type of group there is.</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.functional_groups.FunctionalGroupExtractor.get_all_functional_groups">
<span class="sig-name descname"><span class="pre">get_all_functional_groups</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">elements</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">func_groups</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">catch_basic</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/functional_groups.py#L293-L318"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.functional_groups.FunctionalGroupExtractor.get_all_functional_groups" title="Link to this definition"></a></dt>
<dd><p>Identify all functional groups (or all within a certain subset) in the
molecule, combining the methods described above.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>elements</strong> – List of elements that will qualify a carbon as special
(if only certain functional groups are of interest).
Default None.</p></li>
<li><p><strong>func_groups</strong> – List of strs representing the functional groups of
interest. Default to None, meaning that all of the functional groups
defined in this function will be sought.</p></li>
<li><p><strong>catch_basic</strong> – bool. If True, use get_basic_functional_groups and
other methods</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>list of sets of ints, representing groups of connected atoms</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.functional_groups.FunctionalGroupExtractor.get_basic_functional_groups">
<span class="sig-name descname"><span class="pre">get_basic_functional_groups</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">func_groups</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/functional_groups.py#L227-L291"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.functional_groups.FunctionalGroupExtractor.get_basic_functional_groups" title="Link to this definition"></a></dt>
<dd><p>Identify functional groups that cannot be identified by the Ertl method
of get_special_carbon and get_heteroatoms, such as benzene rings, methyl
groups, and ethyl groups.</p>
<p>TODO: Think of other functional groups that are important enough to be
added (ex: do we need ethyl, butyl, propyl?)</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>func_groups</strong> – List of strs representing the functional groups of
interest. Default to None, meaning that all of the functional groups
defined in this function will be sought.</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>list of sets of ints, representing groups of connected atoms</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.functional_groups.FunctionalGroupExtractor.get_heteroatoms">
<span class="sig-name descname"><span class="pre">get_heteroatoms</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">elements</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/functional_groups.py#L97-L118"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.functional_groups.FunctionalGroupExtractor.get_heteroatoms" title="Link to this definition"></a></dt>
<dd><p>Identify non-H, non-C atoms in the MoleculeGraph, returning a list of
their node indices.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>elements</strong> – List of elements to identify (if only certain</p></li>
<li><p><strong>interest</strong><strong>)</strong><strong>.</strong> (<em>functional groups are of</em>)</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>set of ints representing node indices</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.functional_groups.FunctionalGroupExtractor.get_special_carbon">
<span class="sig-name descname"><span class="pre">get_special_carbon</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">elements</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/functional_groups.py#L120-L191"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.functional_groups.FunctionalGroupExtractor.get_special_carbon" title="Link to this definition"></a></dt>
<dd><p>Identify Carbon atoms in the MoleculeGraph that fit the characteristics
defined Ertl (2017), returning a list of their node indices.</p>
<dl class="simple">
<dt>The conditions for marking carbon atoms are (quoted from Ertl):</dt><dd><p>“- atoms connected by non-aromatic double or triple bond to any
heteroatom
- atoms in nonaromatic carbon-carbon double or triple bonds
- acetal carbons, i.e. sp3 carbons connected to two or more oxygens,
nitrogens or sulfurs; these O, N or S atoms must have only single bonds
- all atoms in oxirane, aziridine and thiirane rings”</p>
</dd>
</dl>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>elements</strong> – List of elements that will qualify a carbon as special
(if only certain functional groups are of interest).
Default None.</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>set of ints representing node indices</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.functional_groups.FunctionalGroupExtractor.link_marked_atoms">
<span class="sig-name descname"><span class="pre">link_marked_atoms</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">atoms</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/functional_groups.py#L193-L225"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.functional_groups.FunctionalGroupExtractor.link_marked_atoms" title="Link to this definition"></a></dt>
<dd><p>Take a list of marked “interesting” atoms (heteroatoms, special carbons)
and attempt to connect them, returning a list of disjoint groups of
special atoms (and their connected hydrogens).</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>atoms</strong> – set of marked “interesting” atoms, presumably identified
using other functions in this class.</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>list of sets of ints, representing groups of connected atoms</p>
</dd>
</dl>
</dd></dl>
</dd></dl>
</section>
<section id="module-pymatgen.analysis.graphs">
<span id="pymatgen-analysis-graphs-module"></span><h2>pymatgen.analysis.graphs module<a class="headerlink" href="#module-pymatgen.analysis.graphs" title="Link to this heading"></a></h2>
<p>Module for graph representations of crystals and molecules.</p>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.analysis.graphs.ConnectedSite">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">ConnectedSite</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">site</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">jimage</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">index</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">weight</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">dist</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/graphs.py#L60-L65"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.graphs.ConnectedSite" title="Link to this definition"></a></dt>
<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">NamedTuple</span></code></p>
<p>Create new instance of ConnectedSite(site, jimage, index, weight, dist)</p>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.analysis.graphs.ConnectedSite.dist">
<span class="sig-name descname"><span class="pre">dist</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">float</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/graphs.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.graphs.ConnectedSite.dist" title="Link to this definition"></a></dt>
<dd><p>Alias for field number 4</p>
</dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.analysis.graphs.ConnectedSite.index">
<span class="sig-name descname"><span class="pre">index</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">Any</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/graphs.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.graphs.ConnectedSite.index" title="Link to this definition"></a></dt>
<dd><p>Alias for field number 2</p>
</dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.analysis.graphs.ConnectedSite.jimage">
<span class="sig-name descname"><span class="pre">jimage</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">Tuple3Ints</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/graphs.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.graphs.ConnectedSite.jimage" title="Link to this definition"></a></dt>
<dd><p>Alias for field number 1</p>
</dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.analysis.graphs.ConnectedSite.site">
<span class="sig-name descname"><span class="pre">site</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><a class="reference internal" href="pymatgen.core.html#pymatgen.core.sites.PeriodicSite" title="pymatgen.core.sites.PeriodicSite"><span class="pre">PeriodicSite</span></a></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/graphs.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.graphs.ConnectedSite.site" title="Link to this definition"></a></dt>
<dd><p>Alias for field number 0</p>
</dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.analysis.graphs.ConnectedSite.weight">
<span class="sig-name descname"><span class="pre">weight</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">float</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/graphs.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.graphs.ConnectedSite.weight" title="Link to this definition"></a></dt>
<dd><p>Alias for field number 3</p>
</dd></dl>
</dd></dl>
<dl class="py exception">
<dt class="sig sig-object py" id="pymatgen.analysis.graphs.MolGraphSplitError">
<em class="property"><span class="pre">exception</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">MolGraphSplitError</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/graphs.py#L1546-L1550"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.graphs.MolGraphSplitError" title="Link to this definition"></a></dt>
<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">Exception</span></code></p>
<p>Raised when a molecule graph is failed to split into two disconnected
subgraphs.</p>
</dd></dl>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.analysis.graphs.MoleculeGraph">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">MoleculeGraph</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">molecule</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">graph_data</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/graphs.py#L1553-L2868"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.graphs.MoleculeGraph" title="Link to this definition"></a></dt>
<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">MSONable</span></code></p>
<p>This is a class for annotating a Molecule with
bond information, stored in the form of a graph. A “bond” does
not necessarily have to be a chemical bond, but can store any
kind of information that connects two Sites.</p>
<p>If constructing this class manually, use the <cite>from_empty_graph</cite>
method or <cite>from_local_env_strategy</cite> method (using an algorithm
provided by the <cite>local_env</cite> module, such as O’Keeffe).</p>
<p>This class that contains connection information:
relationships between sites represented by a Graph structure,
and an associated structure object.</p>
<p>This class uses the NetworkX package to store and operate
on the graph itself, but contains a lot of helper methods
to make associating a graph with a given molecule easier.</p>
<p>Use cases for this include storing bonding information,
NMR J-couplings, Heisenberg exchange parameters, etc.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>molecule</strong> – Molecule object</p></li>
<li><p><strong>graph_data</strong> – dict containing graph information in
dict format (not intended to be constructed manually,
see as_dict method for format)</p></li>
</ul>
</dd>
</dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.graphs.MoleculeGraph.add_edge">
<span class="sig-name descname"><span class="pre">add_edge</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">from_index</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">to_index</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">weight</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">warn_duplicates</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">edge_properties</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/graphs.py#L1788-L1841"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.graphs.MoleculeGraph.add_edge" title="Link to this definition"></a></dt>
<dd><p>Add edge to graph.</p>
<p>Since physically a ‘bond’ (or other connection
between sites) doesn’t have a direction, from_index,
from_jimage can be swapped with to_index, to_jimage.</p>
<p>However, images will always be shifted so that
from_index < to_index and from_jimage becomes (0, 0, 0).</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>from_index</strong> – index of site connecting from</p></li>
<li><p><strong>to_index</strong> – index of site connecting to</p></li>
<li><p><strong>weight</strong> (<em>float</em>) – e.g. bond length</p></li>
<li><p><strong>warn_duplicates</strong> (<em>bool</em>) – if True, will warn if
trying to add duplicate edges (duplicate edges will not
be added in either case)</p></li>
<li><p><strong>edge_properties</strong> (<em>dict</em>) – any other information to
store on graph edges, similar to Structure’s site_properties</p></li>
</ul>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.graphs.MoleculeGraph.alter_edge">
<span class="sig-name descname"><span class="pre">alter_edge</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">from_index</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">to_index</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">new_weight</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">new_edge_properties</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/graphs.py#L1919-L1950"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.graphs.MoleculeGraph.alter_edge" title="Link to this definition"></a></dt>
<dd><p>Alters either the weight or the edge_properties of
an edge in the MoleculeGraph.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>from_index</strong> – int</p></li>
<li><p><strong>to_index</strong> – int</p></li>
<li><p><strong>new_weight</strong> – alter_edge does not require
that weight be altered. As such, by default, this
is None. If weight is to be changed, it should be a
float.</p></li>
<li><p><strong>new_edge_properties</strong> – alter_edge does not require
that edge_properties be altered. As such, by default,
this is None. If any edge properties are to be changed,
it should be a dictionary of edge properties to be changed.</p></li>
</ul>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.graphs.MoleculeGraph.as_dict">
<span class="sig-name descname"><span class="pre">as_dict</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/graphs.py#L2657-L2666"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.graphs.MoleculeGraph.as_dict" title="Link to this definition"></a></dt>
<dd><p>As in pymatgen.core.Molecule except
with using <cite>to_dict_of_dicts</cite> from NetworkX
to store graph information.</p>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.graphs.MoleculeGraph.break_edge">
<span class="sig-name descname"><span class="pre">break_edge</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">from_index</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">to_index</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">allow_reverse</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/graphs.py#L1952-L1979"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.graphs.MoleculeGraph.break_edge" title="Link to this definition"></a></dt>
<dd><p>Remove an edge from the MoleculeGraph.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>from_index</strong> – int</p></li>
<li><p><strong>to_index</strong> – int</p></li>
<li><p><strong>allow_reverse</strong> – If allow_reverse is True, then break_edge will
attempt to break both (from_index, to_index) and, failing that,
will attempt to break (to_index, from_index).</p></li>
</ul>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.graphs.MoleculeGraph.build_unique_fragments">
<span class="sig-name descname"><span class="pre">build_unique_fragments</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/graphs.py#L2118-L2184"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.graphs.MoleculeGraph.build_unique_fragments" title="Link to this definition"></a></dt>
<dd><p>Find all possible fragment combinations of the MoleculeGraphs (in other
words, all connected induced subgraphs).</p>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.graphs.MoleculeGraph.diff">
<span class="sig-name descname"><span class="pre">diff</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">other</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">strict</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/graphs.py#L2805-L2868"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.graphs.MoleculeGraph.diff" title="Link to this definition"></a></dt>
<dd><p>Compares two MoleculeGraphs. Returns dict with
keys ‘self’, ‘other’, ‘both’ with edges that are
present in only one MoleculeGraph (‘self’ and
‘other’), and edges that are present in both.</p>
<p>The Jaccard distance is a simple measure of the
dissimilarity between two MoleculeGraphs (ignoring
edge weights), and is defined by 1 - (size of the
intersection / size of the union) of the sets of
edges. This is returned with key ‘dist’.</p>
<p>Important note: all node indices are in terms
of the MoleculeGraph this method is called
from, not the ‘other’ MoleculeGraph: there
is no guarantee the node indices will be the
same if the underlying Molecules are ordered
differently.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>other</strong> – MoleculeGraph</p></li>
<li><p><strong>strict</strong> – if False, will compare bonds
from different Molecules, with node indices replaced by Species
strings, will not count number of occurrences of bonds</p></li>
</ul>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.graphs.MoleculeGraph.draw_graph_to_file">
<span class="sig-name descname"><span class="pre">draw_graph_to_file</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">filename</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'graph'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">diff</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">hide_unconnected_nodes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">hide_image_edges</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">edge_colors</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">node_labels</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">weight_labels</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">image_labels</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">color_scheme</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'VESTA'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">keep_dot</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">algo</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'fdp'</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/graphs.py#L2490-L2655"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.graphs.MoleculeGraph.draw_graph_to_file" title="Link to this definition"></a></dt>
<dd><p>Draws graph using GraphViz.</p>
<p>The networkx graph object itself can also be drawn
with networkx’s in-built graph drawing methods, but
note that this might give misleading results for
multigraphs (edges are super-imposed on each other).</p>
<p>If visualization is difficult to interpret,
<cite>hide_image_edges</cite> can help, especially in larger
graphs.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>filename</strong> – filename to output, will detect filetype
from extension (any graphviz filetype supported, such as
pdf or png)</p></li>
<li><p><strong>diff</strong> (<a class="reference internal" href="#pymatgen.analysis.graphs.StructureGraph" title="pymatgen.analysis.graphs.StructureGraph"><em>StructureGraph</em></a>) – an additional graph to
compare with, will color edges red that do not exist in diff
and edges green that are in diff graph but not in the
reference graph</p></li>
<li><p><strong>hide_unconnected_nodes</strong> – if True, hide unconnected nodes</p></li>
<li><p><strong>hide_image_edges</strong> – if True, do not draw edges that
go through periodic boundaries</p></li>
<li><p><strong>edge_colors</strong> (<em>bool</em>) – if True, use node colors to color edges</p></li>
<li><p><strong>node_labels</strong> (<em>bool</em>) – if True, label nodes with
species and site index</p></li>
<li><p><strong>weight_labels</strong> (<em>bool</em>) – if True, label edges with weights</p></li>
<li><p><strong>image_labels</strong> (<em>bool</em>) – if True, label edges with
their periodic images (usually only used for debugging,
edges to periodic images always appear as dashed lines)</p></li>
<li><p><strong>color_scheme</strong> (<em>str</em>) – “VESTA” or “JMOL”</p></li>
<li><p><strong>keep_dot</strong> (<em>bool</em>) – keep GraphViz .dot file for later visualization</p></li>
<li><p><strong>algo</strong> – any graphviz algo, “neato” (for simple graphs)
or “fdp” (for more crowded graphs) usually give good outputs</p></li>
</ul>
</dd>
</dl>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.analysis.graphs.MoleculeGraph.edge_weight_name">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">edge_weight_name</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/graphs.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.graphs.MoleculeGraph.edge_weight_name" title="Link to this definition"></a></dt>
<dd><p>Name of the edge weight property of graph.</p>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.analysis.graphs.MoleculeGraph.edge_weight_unit">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">edge_weight_unit</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/graphs.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.graphs.MoleculeGraph.edge_weight_unit" title="Link to this definition"></a></dt>
<dd><p>Units of the edge weight property of graph.</p>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.graphs.MoleculeGraph.find_rings">
<span class="sig-name descname"><span class="pre">find_rings</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">including</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">tuple</span><span class="p"><span class="pre">[</span></span><span class="pre">int</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">int</span><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">]</span></span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/graphs.py#L2387-L2433"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.graphs.MoleculeGraph.find_rings" title="Link to this definition"></a></dt>
<dd><p>Find ring structures in the MoleculeGraph.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>including</strong> (<em>list</em><em>[</em><em>int</em><em>]</em>) – list of site indices. If including is not None, then find_rings</p></li>
<li><p><strong>default</strong> (<em>will only return those rings including the specified sites. By</em>)</p></li>
<li><p><strong>parameter</strong> (<em>this</em>)</p></li>
<li><p><strong>None</strong> (<em>is</em>)</p></li>
<li><p><strong>returned.</strong> (<em>and all rings will be</em>)</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p><dl class="simple">
<dt>Each entry will be a ring (cycle, in graph theory terms)</dt><dd><p>including the index found in the Molecule. If there is no cycle including an index, the
value will be an empty list.</p>
</dd>
</dl>
</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>list[list[tuple[int, int]]]</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.graphs.MoleculeGraph.from_dict">
<em class="property"><span class="pre">classmethod</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">from_dict</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">dct</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">dict</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">Self</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/graphs.py#L2668-L2676"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.graphs.MoleculeGraph.from_dict" title="Link to this definition"></a></dt>
<dd><p>As in pymatgen.core.Molecule except
restoring graphs using <cite>from_dict_of_dicts</cite>
from NetworkX to restore graph information.</p>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.graphs.MoleculeGraph.from_edges">
<em class="property"><span class="pre">classmethod</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">from_edges</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">molecule</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Molecule" title="pymatgen.core.structure.Molecule"><span class="pre">Molecule</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">edges</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><span class="pre">tuple</span><span class="p"><span class="pre">[</span></span><span class="pre">int</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">int</span><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">None</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">dict</span><span class="p"><span class="pre">]</span></span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">Self</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/graphs.py#L1652-L1694"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.graphs.MoleculeGraph.from_edges" title="Link to this definition"></a></dt>
<dd><p>Constructor for MoleculeGraph, using pre-existing or pre-defined edges
with optional edge parameters.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>molecule</strong> – Molecule object</p></li>
<li><p><strong>edges</strong> – dict representing the bonds of the functional
group (format: {(u, v): props}, where props is a dictionary of
properties, including weight. Props should be None if no
additional properties are to be specified.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>A MoleculeGraph</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.graphs.MoleculeGraph.from_empty_graph">
<em class="property"><span class="pre">classmethod</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">from_empty_graph</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">molecule</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">name</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'bonds'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">edge_weight_name</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">edge_weight_units</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">Self</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/graphs.py#L1607-L1645"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.graphs.MoleculeGraph.from_empty_graph" title="Link to this definition"></a></dt>
<dd><p>Constructor for MoleculeGraph, returns a MoleculeGraph
object with an empty graph (no edges, only nodes defined
that correspond to Sites in Molecule).</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>molecule</strong> (<a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Molecule" title="pymatgen.core.structure.Molecule"><em>Molecule</em></a>)</p></li>
<li><p><strong>name</strong> (<em>str</em>) – name of graph, e.g. “bonds”</p></li>
<li><p><strong>edge_weight_name</strong> (<em>str</em>) – name of edge weights,
e.g. “bond_length” or “exchange_constant”</p></li>
<li><p><strong>edge_weight_units</strong> (<em>str</em>) – name of edge weight units</p></li>
<li><p><strong>"eV"</strong> (<em>e.g. "Å" or</em>)</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>MoleculeGraph</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.graphs.MoleculeGraph.from_local_env_strategy">
<em class="property"><span class="pre">classmethod</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">from_local_env_strategy</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">molecule</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">strategy</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">Self</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/graphs.py#L1701-L1766"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.graphs.MoleculeGraph.from_local_env_strategy" title="Link to this definition"></a></dt>
<dd><p>Constructor for MoleculeGraph, using a strategy
from pymatgen.analysis.local_env.</p>
<blockquote>
<div><p>molecule: Molecule object
strategy: an instance of a</p>
<blockquote>
<div><p>pymatgen.analysis.local_env.NearNeighbors object</p>
</div></blockquote>
</div></blockquote>
<dl class="field-list simple">
<dt class="field-odd">Returns<span class="colon">:</span></dt>
<dd class="field-odd"><p>mg, a MoleculeGraph</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.graphs.MoleculeGraph.get_connected_sites">
<span class="sig-name descname"><span class="pre">get_connected_sites</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">n</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/graphs.py#L2435-L2475"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.graphs.MoleculeGraph.get_connected_sites" title="Link to this definition"></a></dt>
<dd><p>Get a named tuple of neighbors of site n:
periodic_site, jimage, index, weight.
Index is the index of the corresponding site
in the original structure, weight can be
None if not defined.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>n</strong> – index of Site in Molecule</p></li>
<li><p><strong>jimage</strong> – lattice vector of site.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>list of ConnectedSite tuples,
sorted by closest first.</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.graphs.MoleculeGraph.get_coordination_of_site">
<span class="sig-name descname"><span class="pre">get_coordination_of_site</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">n</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">int</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/graphs.py#L2477-L2488"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.graphs.MoleculeGraph.get_coordination_of_site" title="Link to this definition"></a></dt>
<dd><p>Get the number of neighbors of site n.
In graph terms, simply returns degree
of node corresponding to site n.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>n</strong> – index of site</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>the number of neighbors of site n.</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>int</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.graphs.MoleculeGraph.get_disconnected_fragments">
<span class="sig-name descname"><span class="pre">get_disconnected_fragments</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">return_index_map</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/graphs.py#L1996-L2063"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.graphs.MoleculeGraph.get_disconnected_fragments" title="Link to this definition"></a></dt>
<dd><p>Determine if the MoleculeGraph is connected. If it is not, separate the
MoleculeGraph into different MoleculeGraphs, where each resulting MoleculeGraph is
a disconnected subgraph of the original. Currently, this function naively assigns
the charge of the total molecule to a single submolecule. A later effort will be
to actually accurately assign charge.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>return_index_map</strong> (<em>bool</em>) – If True, return a dictionary that maps the
new indices to the original indices. Defaults to False.</p>
</dd>
</dl>
<p>NOTE: This function does not modify the original MoleculeGraph. It creates a copy,
modifies that, and returns two or more new MoleculeGraph objects.</p>
<dl class="field-list simple">
<dt class="field-odd">Returns<span class="colon">:</span></dt>
<dd class="field-odd"><p>Each MoleculeGraph is a disconnected subgraph of the original MoleculeGraph.</p>
</dd>
<dt class="field-even">Return type<span class="colon">:</span></dt>
<dd class="field-even"><p>list[<a class="reference internal" href="#pymatgen.analysis.graphs.MoleculeGraph" title="pymatgen.analysis.graphs.MoleculeGraph">MoleculeGraph</a>]</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.graphs.MoleculeGraph.insert_node">
<span class="sig-name descname"><span class="pre">insert_node</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">idx</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">species</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">coords</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">validate_proximity</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">site_properties</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">edges</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/graphs.py#L1843-L1900"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.graphs.MoleculeGraph.insert_node" title="Link to this definition"></a></dt>
<dd><p>A wrapper around Molecule.insert(), which also incorporates the new
site into the MoleculeGraph.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>idx</strong> – Index at which to insert the new site</p></li>
<li><p><strong>species</strong> – Species for the new site</p></li>
<li><p><strong>coords</strong> – 3x1 array representing coordinates of the new site</p></li>
<li><p><strong>validate_proximity</strong> – For Molecule.insert(); if True (default
False), distance will be checked to ensure that site can be safely
added.</p></li>
<li><p><strong>site_properties</strong> – Site properties for Molecule</p></li>
<li><p><strong>edges</strong> – List of dicts representing edges to be added to the
MoleculeGraph. These edges must include the index of the new site i,
and all indices used for these edges should reflect the
MoleculeGraph AFTER the insertion, NOT before. Each dict should at
least have a “to_index” and “from_index” key, and can also have a
“weight” and a “properties” key.</p></li>
</ul>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.graphs.MoleculeGraph.isomorphic_to">
<span class="sig-name descname"><span class="pre">isomorphic_to</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">other</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="#pymatgen.analysis.graphs.MoleculeGraph" title="pymatgen.analysis.graphs.MoleculeGraph"><span class="pre">MoleculeGraph</span></a></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">bool</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/graphs.py#L2785-L2803"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.graphs.MoleculeGraph.isomorphic_to" title="Link to this definition"></a></dt>
<dd><p>Checks if the graphs of two MoleculeGraphs are isomorphic to one
another. In order to prevent problems with misdirected edges, both
graphs are converted into undirected nx.Graph objects.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>other</strong> – MoleculeGraph object to be compared.</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>bool</p>
</dd>
</dl>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.analysis.graphs.MoleculeGraph.name">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">name</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/graphs.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.graphs.MoleculeGraph.name" title="Link to this definition"></a></dt>
<dd><p>Name of graph.</p>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.graphs.MoleculeGraph.remove_nodes">
<span class="sig-name descname"><span class="pre">remove_nodes</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">indices</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">int</span><span class="p"><span class="pre">]</span></span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">None</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/graphs.py#L1981-L1994"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.graphs.MoleculeGraph.remove_nodes" title="Link to this definition"></a></dt>
<dd><p>A wrapper for Molecule.remove_sites().</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>indices</strong> – indices in the current Molecule (and graph) to be removed.</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.graphs.MoleculeGraph.replace_group">
<span class="sig-name descname"><span class="pre">replace_group</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">index</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">func_grp</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">strategy</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">bond_order</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">graph_dict</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">strategy_params</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/graphs.py#L2300-L2385"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.graphs.MoleculeGraph.replace_group" title="Link to this definition"></a></dt>
<dd><p>Builds off of Molecule.substitute and MoleculeGraph.substitute_group
to replace a functional group in self.molecule with a functional group.
This method also amends self.graph to incorporate the new functional
group.</p>
<p>TODO: Figure out how to replace into a ring structure.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>index</strong> – Index of atom to substitute.</p></li>
<li><p><strong>func_grp</strong> – Substituent molecule. There are three options:
1. Providing an actual molecule as the input. The first atom
must be a DummySpecies X, indicating the position of
nearest neighbor. The second atom must be the next
nearest atom. For example, for a methyl group
substitution, func_grp should be X-CH3, where X is the
first site and C is the second site. What the code will
do is to remove the index site, and connect the nearest
neighbor to the C atom in CH3. The X-C bond indicates the
directionality to connect the atoms.
2. A string name. The molecule will be obtained from the
relevant template in func_groups.json.
3. A MoleculeGraph object.</p></li>
<li><p><strong>strategy</strong> – Class from pymatgen.analysis.local_env.</p></li>
<li><p><strong>bond_order</strong> – A specified bond order to calculate the bond
length between the attached functional group and the nearest
neighbor site. Defaults to 1.</p></li>
<li><p><strong>graph_dict</strong> – Dictionary representing the bonds of the functional
group (format: {(u, v): props}, where props is a dictionary of
properties, including weight. If None, then the algorithm
will attempt to automatically determine bonds using one of
a list of strategies defined in pymatgen.analysis.local_env.</p></li>
<li><p><strong>strategy_params</strong> – dictionary of keyword arguments for strategy.
If None, default parameters will be used.</p></li>
</ul>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.graphs.MoleculeGraph.set_node_attributes">
<span class="sig-name descname"><span class="pre">set_node_attributes</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/graphs.py#L1902-L1917"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.graphs.MoleculeGraph.set_node_attributes" title="Link to this definition"></a></dt>
<dd><p>Replicates molecule site properties (specie, coords, etc.) in the
MoleculeGraph.</p>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.graphs.MoleculeGraph.sort">
<span class="sig-name descname"><span class="pre">sort</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">key</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">Callable</span><span class="p"><span class="pre">[</span></span><span class="p"><span class="pre">[</span></span><a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Molecule" title="pymatgen.core.structure.Molecule"><span class="pre">Molecule</span></a><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">float</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">reverse</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">None</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/graphs.py#L2726-L2756"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.graphs.MoleculeGraph.sort" title="Link to this definition"></a></dt>
<dd><p>Same as Molecule.sort(). Also remaps nodes in graph.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>key</strong> (<em>callable</em><em>, </em><em>optional</em>) – Sort key. Defaults to None.</p></li>
<li><p><strong>reverse</strong> (<em>bool</em><em>, </em><em>optional</em>) – Reverse sort order. Defaults to False.</p></li>
</ul>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.graphs.MoleculeGraph.split_molecule_subgraphs">
<span class="sig-name descname"><span class="pre">split_molecule_subgraphs</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">bonds</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">allow_reverse</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">alterations</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/graphs.py#L2065-L2116"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.graphs.MoleculeGraph.split_molecule_subgraphs" title="Link to this definition"></a></dt>
<dd><p>Split MoleculeGraph into two or more MoleculeGraphs by
breaking a set of bonds. This function uses
MoleculeGraph.break_edge repeatedly to create
disjoint graphs (two or more separate molecules).
This function does not only alter the graph
information, but also changes the underlying
Molecules.
If the bonds parameter does not include sufficient
bonds to separate two molecule fragments, then this
function will fail.
Currently, this function naively assigns the charge
of the total molecule to a single submolecule. A
later effort will be to actually accurately assign
charge.
NOTE: This function does not modify the original
MoleculeGraph. It creates a copy, modifies that, and
returns two or more new MoleculeGraph objects.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>bonds</strong> – list of tuples (from_index, to_index)
representing bonds to be broken to split the MoleculeGraph.</p></li>
<li><p><strong>alterations</strong> – a dict {(from_index, to_index): alt},
where alt is a dictionary including weight and/or edge
properties to be changed following the split.</p></li>
<li><p><strong>allow_reverse</strong> – If allow_reverse is True, then break_edge will
attempt to break both (from_index, to_index) and, failing that,
will attempt to break (to_index, from_index).</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>list of MoleculeGraphs.</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.graphs.MoleculeGraph.substitute_group">
<span class="sig-name descname"><span class="pre">substitute_group</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">index</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">func_grp</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">strategy</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">bond_order</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">graph_dict</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">strategy_params</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/graphs.py#L2186-L2298"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.graphs.MoleculeGraph.substitute_group" title="Link to this definition"></a></dt>
<dd><p>Builds off of Molecule.substitute to replace an atom in self.molecule
with a functional group. This method also amends self.graph to
incorporate the new functional group.</p>
<p>NOTE: using a MoleculeGraph will generally produce a different graph
compared with using a Molecule or str (when not using graph_dict).</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>index</strong> – Index of atom to substitute.</p></li>
<li><p><strong>func_grp</strong> – <p>Substituent molecule. There are three options:
1. Providing an actual molecule as the input. The first atom</p>
<blockquote>
<div><p>must be a DummySpecies X, indicating the position of
nearest neighbor. The second atom must be the next
nearest atom. For example, for a methyl group
substitution, func_grp should be X-CH3, where X is the
first site and C is the second site. What the code will
do is to remove the index site, and connect the nearest
neighbor to the C atom in CH3. The X-C bond indicates the
directionality to connect the atoms.</p>
</div></blockquote>
<ol class="arabic simple" start="2">
<li><dl class="simple">
<dt>A string name. The molecule will be obtained from the</dt><dd><p>relevant template in func_groups.json.</p>
</dd>
</dl>
</li>
<li><p>A MoleculeGraph object.</p></li>
</ol>
</p></li>
<li><p><strong>strategy</strong> – Class from pymatgen.analysis.local_env.</p></li>
<li><p><strong>bond_order</strong> – A specified bond order to calculate the bond
length between the attached functional group and the nearest
neighbor site. Defaults to 1.</p></li>
<li><p><strong>graph_dict</strong> – Dictionary representing the bonds of the functional
group (format: {(u, v): props}, where props is a dictionary of
properties, including weight. If None, then the algorithm
will attempt to automatically determine bonds using one of
a list of strategies defined in pymatgen.analysis.local_env.</p></li>
<li><p><strong>strategy_params</strong> – dictionary of keyword arguments for strategy.
If None, default parameters will be used.</p></li>
</ul>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.graphs.MoleculeGraph.with_edges">
<em class="property"><span class="pre">classmethod</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">with_edges</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">*</span></span><span class="n"><span class="pre">args</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../../../../monty/src/monty/dev.py#L1696-L1699"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.graphs.MoleculeGraph.with_edges" title="Link to this definition"></a></dt>
<dd></dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.graphs.MoleculeGraph.with_empty_graph">
<em class="property"><span class="pre">classmethod</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">with_empty_graph</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">*</span></span><span class="n"><span class="pre">args</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../../../../monty/src/monty/dev.py#L1647-L1650"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.graphs.MoleculeGraph.with_empty_graph" title="Link to this definition"></a></dt>
<dd></dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.graphs.MoleculeGraph.with_local_env_strategy">
<em class="property"><span class="pre">classmethod</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">with_local_env_strategy</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">*</span></span><span class="n"><span class="pre">args</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../../../../monty/src/monty/dev.py#L1768-L1771"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.graphs.MoleculeGraph.with_local_env_strategy" title="Link to this definition"></a></dt>
<dd></dd></dl>
</dd></dl>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.analysis.graphs.StructureGraph">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">StructureGraph</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">structure</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><span class="pre">Structure</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">graph_data</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">dict</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/graphs.py#L118-L1543"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.graphs.StructureGraph" title="Link to this definition"></a></dt>
<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">MSONable</span></code></p>
<p>This is a class for annotating a Structure with bond information, stored in the form
of a graph. A “bond” does not necessarily have to be a chemical bond, but can store
any kind of information that connects two Sites.</p>
<p>If constructing this class manually, use the from_empty_graph method or
from_local_env_strategy method (using an algorithm provided by the local_env
module, such as O’Keeffe).
This class that contains connection information: relationships between sites
represented by a Graph structure, and an associated structure object.</p>
<p>StructureGraph uses the NetworkX package to store and operate on the graph itself, but
contains a lot of helper methods to make associating a graph with a given
crystallographic structure easier.
Use cases for this include storing bonding information, NMR J-couplings,
Heisenberg exchange parameters, etc.
For periodic graphs, class stores information on the graph edges of what lattice
image the edge belongs to.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>structure</strong> (<a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><em>Structure</em></a>) – Structure object to be analyzed.</p></li>
<li><p><strong>graph_data</strong> (<em>dict</em>) – Dictionary containing graph information. Not intended to be
constructed manually see as_dict method for format.</p></li>
</ul>
</dd>
</dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.graphs.StructureGraph.add_edge">
<span class="sig-name descname"><span class="pre">add_edge</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">from_index</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">to_index</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">from_jimage</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">Tuple3Ints</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">(0,</span> <span class="pre">0,</span> <span class="pre">0)</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">to_jimage</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">Tuple3Ints</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">weight</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">float</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">warn_duplicates</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">edge_properties</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">dict</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">None</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/graphs.py#L333-L460"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.graphs.StructureGraph.add_edge" title="Link to this definition"></a></dt>
<dd><p>Add edge to graph.</p>
<p>Since physically a ‘bond’ (or other connection
between sites) doesn’t have a direction, from_index,
from_jimage can be swapped with to_index, to_jimage.</p>
<p>However, images will always be shifted so that
from_index < to_index and from_jimage becomes (0, 0, 0).</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>from_index</strong> – index of site connecting from</p></li>
<li><p><strong>to_index</strong> – index of site connecting to</p></li>
<li><p><strong>from_jimage</strong> (<em>tuple</em><em> of </em><em>ints</em>) – lattice vector of periodic
image, e.g. (1, 0, 0) for periodic image in +x direction</p></li>
<li><p><strong>to_jimage</strong> (<em>tuple</em><em> of </em><em>ints</em>) – lattice vector of image</p></li>
<li><p><strong>weight</strong> (<em>float</em>) – e.g. bond length</p></li>
<li><p><strong>warn_duplicates</strong> (<em>bool</em>) – if True, will warn if
trying to add duplicate edges (duplicate edges will not
be added in either case)</p></li>
<li><p><strong>edge_properties</strong> (<em>dict</em>) – any other information to
store on graph edges, similar to Structure’s site_properties</p></li>
</ul>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.graphs.StructureGraph.alter_edge">
<span class="sig-name descname"><span class="pre">alter_edge</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">from_index</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">to_index</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">to_jimage</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">tuple</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">new_weight</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">float</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">new_edge_properties</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">dict</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/graphs.py#L543-L587"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.graphs.StructureGraph.alter_edge" title="Link to this definition"></a></dt>
<dd><p>Alters either the weight or the edge_properties of
an edge in the StructureGraph.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>from_index</strong> – int</p></li>
<li><p><strong>to_index</strong> – int</p></li>
<li><p><strong>to_jimage</strong> – tuple</p></li>
<li><p><strong>new_weight</strong> – alter_edge does not require
that weight be altered. As such, by default, this
is None. If weight is to be changed, it should be a
float.</p></li>
<li><p><strong>new_edge_properties</strong> – alter_edge does not require
that edge_properties be altered. As such, by default,
this is None. If any edge properties are to be changed,
it should be a dictionary of edge properties to be changed.</p></li>
</ul>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.graphs.StructureGraph.as_dict">
<span class="sig-name descname"><span class="pre">as_dict</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">dict</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/graphs.py#L1072-L1083"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.graphs.StructureGraph.as_dict" title="Link to this definition"></a></dt>
<dd><p>As in pymatgen.core.Structure except
with using <cite>to_dict_of_dicts</cite> from NetworkX
to store graph information.</p>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.graphs.StructureGraph.break_edge">
<span class="sig-name descname"><span class="pre">break_edge</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">from_index</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">to_index</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">to_jimage</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">tuple</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">allow_reverse</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">None</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/graphs.py#L589-L635"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.graphs.StructureGraph.break_edge" title="Link to this definition"></a></dt>
<dd><p>Remove an edge from the StructureGraph. If no image is given, this method will fail.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>from_index</strong> – int</p></li>
<li><p><strong>to_index</strong> – int</p></li>
<li><p><strong>to_jimage</strong> – tuple</p></li>
<li><p><strong>allow_reverse</strong> – If allow_reverse is True, then break_edge will
attempt to break both (from_index, to_index) and, failing that,
will attempt to break (to_index, from_index).</p></li>
</ul>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.graphs.StructureGraph.diff">
<span class="sig-name descname"><span class="pre">diff</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">other</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="#pymatgen.analysis.graphs.StructureGraph" title="pymatgen.analysis.graphs.StructureGraph"><span class="pre">StructureGraph</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">strict</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">dict</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/graphs.py#L1399-L1462"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.graphs.StructureGraph.diff" title="Link to this definition"></a></dt>
<dd><p>Compares two StructureGraphs. Returns dict with
keys ‘self’, ‘other’, ‘both’ with edges that are
present in only one StructureGraph (‘self’ and
‘other’), and edges that are present in both.</p>
<p>The Jaccard distance is a simple measure of the
dissimilarity between two StructureGraphs (ignoring
edge weights), and is defined by 1 - (size of the
intersection / size of the union) of the sets of
edges. This is returned with key ‘dist’.</p>
<p>Important note: all node indices are in terms
of the StructureGraph this method is called
from, not the ‘other’ StructureGraph: there
is no guarantee the node indices will be the
same if the underlying Structures are ordered
differently.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>other</strong> – StructureGraph</p></li>
<li><p><strong>strict</strong> – if False, will compare bonds
from different Structures, with node indices
replaced by Species strings, will not count
number of occurrences of bonds</p></li>
</ul>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.graphs.StructureGraph.draw_graph_to_file">
<span class="sig-name descname"><span class="pre">draw_graph_to_file</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">filename</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">'graph'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">diff</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="#pymatgen.analysis.graphs.StructureGraph" title="pymatgen.analysis.graphs.StructureGraph"><span class="pre">StructureGraph</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">hide_unconnected_nodes</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">hide_image_edges</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">edge_colors</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">node_labels</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">weight_labels</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">image_labels</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">color_scheme</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">'VESTA'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">keep_dot</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">algo</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">'fdp'</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/graphs.py#L822-L986"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.graphs.StructureGraph.draw_graph_to_file" title="Link to this definition"></a></dt>
<dd><p>Draws graph using GraphViz.</p>
<p>The networkx graph object itself can also be drawn
with networkx’s in-built graph drawing methods, but
note that this might give misleading results for
multigraphs (edges are super-imposed on each other).</p>
<p>If visualization is difficult to interpret,
<cite>hide_image_edges</cite> can help, especially in larger
graphs.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>filename</strong> – filename to output, will detect filetype
from extension (any graphviz filetype supported, such as
pdf or png)</p></li>
<li><p><strong>diff</strong> (<a class="reference internal" href="#pymatgen.analysis.graphs.StructureGraph" title="pymatgen.analysis.graphs.StructureGraph"><em>StructureGraph</em></a>) – an additional graph to
compare with, will color edges red that do not exist in diff
and edges green that are in diff graph but not in the
reference graph</p></li>
<li><p><strong>hide_unconnected_nodes</strong> – if True, hide unconnected nodes</p></li>
<li><p><strong>hide_image_edges</strong> – if True, do not draw edges that
go through periodic boundaries</p></li>
<li><p><strong>edge_colors</strong> (<em>bool</em>) – if True, use node colors to color edges</p></li>
<li><p><strong>node_labels</strong> (<em>bool</em>) – if True, label nodes with species and site index</p></li>
<li><p><strong>weight_labels</strong> (<em>bool</em>) – if True, label edges with weights</p></li>
<li><p><strong>image_labels</strong> (<em>bool</em>) – if True, label edges with
their periodic images (usually only used for debugging,
edges to periodic images always appear as dashed lines)</p></li>
<li><p><strong>color_scheme</strong> (<em>str</em>) – “VESTA” or “JMOL”</p></li>
<li><p><strong>keep_dot</strong> (<em>bool</em>) – keep GraphViz .dot file for later visualization</p></li>
<li><p><strong>algo</strong> – any graphviz algo, “neato” (for simple graphs)
or “fdp” (for more crowded graphs) usually give good outputs</p></li>
</ul>
</dd>
</dl>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.analysis.graphs.StructureGraph.edge_weight_name">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">edge_weight_name</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">str</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/graphs.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.graphs.StructureGraph.edge_weight_name" title="Link to this definition"></a></dt>
<dd><p>Name of the edge weight property of graph.</p>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.analysis.graphs.StructureGraph.edge_weight_unit">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">edge_weight_unit</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/graphs.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.graphs.StructureGraph.edge_weight_unit" title="Link to this definition"></a></dt>
<dd><p>Units of the edge weight property of graph.</p>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.graphs.StructureGraph.from_dict">
<em class="property"><span class="pre">classmethod</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">from_dict</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">dct</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">dict</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">Self</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/graphs.py#L1085-L1091"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.graphs.StructureGraph.from_dict" title="Link to this definition"></a></dt>
<dd><p>As in pymatgen.core.Structure except restoring graphs using from_dict_of_dicts
from NetworkX to restore graph information.</p>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.graphs.StructureGraph.from_edges">
<em class="property"><span class="pre">classmethod</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">from_edges</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">structure</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><span class="pre">Structure</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">edges</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">dict</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">Self</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/graphs.py#L213-L265"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.graphs.StructureGraph.from_edges" title="Link to this definition"></a></dt>
<dd><p>Constructor for MoleculeGraph, using pre-existing or pre-defined edges
with optional edge parameters.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>structure</strong> – Structure object</p></li>
<li><p><strong>edges</strong> – dict representing the bonds of the functional
group (format: {(from_index, to_index, from_image, to_image): props},
where props is a dictionary of properties, including weight.
Props should be None if no additional properties are to be
specified.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>sg, a StructureGraph</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.graphs.StructureGraph.from_empty_graph">
<em class="property"><span class="pre">classmethod</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">from_empty_graph</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">structure</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><span class="pre">Structure</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">name</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">'bonds'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">edge_weight_name</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">edge_weight_units</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">Self</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/graphs.py#L164-L206"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.graphs.StructureGraph.from_empty_graph" title="Link to this definition"></a></dt>
<dd><p>Constructor for an empty StructureGraph, i.e. no edges, containing only nodes corresponding
to sites in Structure.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>structure</strong> – A pymatgen Structure object.</p></li>
<li><p><strong>name</strong> – Name of the graph, e.g. “bonds”.</p></li>
<li><p><strong>edge_weight_name</strong> – Name of the edge weights, e.g. “bond_length” or “exchange_constant”.</p></li>
<li><p><strong>edge_weight_units</strong> – Name of the edge weight units, e.g. “Å” or “eV”.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p><dl class="simple">
<dt>an empty graph with no edges, only nodes defined</dt><dd><p>that correspond to sites in Structure.</p>
</dd>
</dl>
</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p><a class="reference internal" href="#pymatgen.analysis.graphs.StructureGraph" title="pymatgen.analysis.graphs.StructureGraph">StructureGraph</a></p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.graphs.StructureGraph.from_local_env_strategy">
<em class="property"><span class="pre">classmethod</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">from_local_env_strategy</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">structure</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><span class="pre">Structure</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">strategy</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="#pymatgen.analysis.local_env.NearNeighbors" title="pymatgen.analysis.local_env.NearNeighbors"><span class="pre">NearNeighbors</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">weights</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">edge_properties</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">Self</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/graphs.py#L272-L311"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.graphs.StructureGraph.from_local_env_strategy" title="Link to this definition"></a></dt>
<dd><p>Constructor for StructureGraph, using a strategy
from pymatgen.analysis.local_env.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>structure</strong> – Structure object</p></li>
<li><p><strong>strategy</strong> – an instance of a pymatgen.analysis.local_env.NearNeighbors object</p></li>
<li><p><strong>weights</strong> (<em>bool</em>) – if True, use weights from local_env class (consult relevant class for their meaning)</p></li>
<li><p><strong>edge_properties</strong> (<em>bool</em>) – if True, edge_properties from neighbors will be used</p></li>
</ul>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.graphs.StructureGraph.get_connected_sites">
<span class="sig-name descname"><span class="pre">get_connected_sites</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">n</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">jimage</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">Tuple3Ints</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">(0,</span> <span class="pre">0,</span> <span class="pre">0)</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">list</span><span class="p"><span class="pre">[</span></span><a class="reference internal" href="#pymatgen.analysis.graphs.ConnectedSite" title="pymatgen.analysis.graphs.ConnectedSite"><span class="pre">ConnectedSite</span></a><span class="p"><span class="pre">]</span></span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/graphs.py#L758-L808"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.graphs.StructureGraph.get_connected_sites" title="Link to this definition"></a></dt>
<dd><p>Get a named tuple of neighbors of site n:
periodic_site, jimage, index, weight.
Index is the index of the corresponding site
in the original structure, weight can be
None if not defined.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>n</strong> – index of Site in Structure</p></li>
<li><p><strong>jimage</strong> – lattice vector of site</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>list of ConnectedSite tuples,
sorted by closest first.</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.graphs.StructureGraph.get_coordination_of_site">
<span class="sig-name descname"><span class="pre">get_coordination_of_site</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">n</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">int</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/graphs.py#L810-L820"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.graphs.StructureGraph.get_coordination_of_site" title="Link to this definition"></a></dt>
<dd><p>Get the number of neighbors of site n. In graph terms,
simply returns degree of node corresponding to site n.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>n</strong> – index of site</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>number of neighbors of site n.</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>int</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.graphs.StructureGraph.get_subgraphs_as_molecules">
<span class="sig-name descname"><span class="pre">get_subgraphs_as_molecules</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">use_weights</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">list</span><span class="p"><span class="pre">[</span></span><a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Molecule" title="pymatgen.core.structure.Molecule"><span class="pre">Molecule</span></a><span class="p"><span class="pre">]</span></span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/graphs.py#L1464-L1543"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.graphs.StructureGraph.get_subgraphs_as_molecules" title="Link to this definition"></a></dt>
<dd><p>Retrieve subgraphs as molecules, useful for extracting
molecules from periodic crystals.</p>
<p>Will only return unique molecules, not any duplicates
present in the crystal (a duplicate defined as an
isomorphic subgraph).</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>use_weights</strong> (<em>bool</em>) – If True, only treat subgraphs
as isomorphic if edges have the same weights. Typically,
this means molecules will need to have the same bond
lengths to be defined as duplicates, otherwise bond
lengths can differ. This is a fairly robust approach,
but will treat e.g. enantiomers as being duplicates.</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>list of unique Molecules in Structure</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.graphs.StructureGraph.insert_node">
<span class="sig-name descname"><span class="pre">insert_node</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">idx</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">species</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="pymatgen.core.html#pymatgen.core.periodic_table.Species" title="pymatgen.core.periodic_table.Species"><span class="pre">Species</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">coords</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">ArrayLike</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">coords_are_cartesian</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">validate_proximity</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">site_properties</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">dict</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">edges</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">list</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">dict</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">None</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/graphs.py#L462-L525"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.graphs.StructureGraph.insert_node" title="Link to this definition"></a></dt>
<dd><p>A wrapper around Molecule.insert(), which also incorporates the new
site into the MoleculeGraph.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>idx</strong> – Index at which to insert the new site</p></li>
<li><p><strong>species</strong> – Species for the new site</p></li>
<li><p><strong>coords</strong> – 3x1 array representing coordinates of the new site</p></li>
<li><p><strong>coords_are_cartesian</strong> – Whether coordinates are cartesian.
Defaults to False.</p></li>
<li><p><strong>validate_proximity</strong> – For Molecule.insert(); if True (default
False), distance will be checked to ensure that
site can be safely added.</p></li>
<li><p><strong>site_properties</strong> – Site properties for Molecule</p></li>
<li><p><strong>edges</strong> – List of dicts representing edges to be added to the</p></li>
<li><p><strong>i</strong> (<em>MoleculeGraph. These edges must include the index</em><em> of </em><em>the new site</em>)</p></li>
</ul>
</dd>
</dl>
<p>:param :
:param and all indices used for these edges should reflect the:
:param MoleculeGraph AFTER the insertion:
:param NOT before. Each dict should at:
:param least have a “to_index” and “from_index” key:
:param and can also have a:
:param “weight” and a “properties” key.:</p>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.analysis.graphs.StructureGraph.name">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">name</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">str</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/graphs.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.graphs.StructureGraph.name" title="Link to this definition"></a></dt>
<dd><p>Name of graph.</p>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.graphs.StructureGraph.remove_nodes">
<span class="sig-name descname"><span class="pre">remove_nodes</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">indices</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">Sequence</span><span class="p"><span class="pre">[</span></span><span class="pre">int</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span><span class="p"><span class="pre">]</span></span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">None</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/graphs.py#L637-L651"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.graphs.StructureGraph.remove_nodes" title="Link to this definition"></a></dt>
<dd><p>A wrapper for Molecule.remove_sites().</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>indices</strong> – list of indices in the current Molecule (and graph) to
be removed.</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.graphs.StructureGraph.set_node_attributes">
<span class="sig-name descname"><span class="pre">set_node_attributes</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">None</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/graphs.py#L527-L541"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.graphs.StructureGraph.set_node_attributes" title="Link to this definition"></a></dt>
<dd><p>Get each node a “specie” and a “coords” attribute, updated with the
current species and coordinates.</p>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.graphs.StructureGraph.sort">
<span class="sig-name descname"><span class="pre">sort</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">key</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">reverse</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">None</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/graphs.py#L1341-L1371"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.graphs.StructureGraph.sort" title="Link to this definition"></a></dt>
<dd><p>Same as Structure.sort(). Also remaps nodes in graph.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>key</strong> – key to sort by</p></li>
<li><p><strong>reverse</strong> – reverse sort order</p></li>
</ul>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.graphs.StructureGraph.substitute_group">
<span class="sig-name descname"><span class="pre">substitute_group</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">index</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">func_grp</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Molecule" title="pymatgen.core.structure.Molecule"><span class="pre">Molecule</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">str</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">strategy</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">Any</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">bond_order</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">graph_dict</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">dict</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">strategy_params</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">dict</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/graphs.py#L653-L756"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.graphs.StructureGraph.substitute_group" title="Link to this definition"></a></dt>
<dd><p>Builds off of Structure.substitute to replace an atom in self.structure
with a functional group. This method also amends self.graph to
incorporate the new functional group.</p>
<p>NOTE: Care must be taken to ensure that the functional group that is
substituted will not place atoms to close to each other, or violate the
dimensions of the Lattice.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>index</strong> – Index of atom to substitute.</p></li>
<li><p><strong>func_grp</strong> – <p>Substituent molecule. There are two options:
1. Providing an actual Molecule as the input. The first atom</p>
<blockquote>
<div><p>must be a DummySpecies X, indicating the position of
nearest neighbor. The second atom must be the next
nearest atom. For example, for a methyl group
substitution, func_grp should be X-CH3, where X is the
first site and C is the second site. What the code will
do is to remove the index site, and connect the nearest
neighbor to the C atom in CH3. The X-C bond indicates the
directionality to connect the atoms.</p>
</div></blockquote>
<ol class="arabic simple" start="2">
<li><dl class="simple">
<dt>A string name. The molecule will be obtained from the</dt><dd><p>relevant template in func_groups.json.</p>
</dd>
</dl>
</li>
</ol>
</p></li>
<li><p><strong>strategy</strong> – Class from pymatgen.analysis.local_env.</p></li>
<li><p><strong>bond_order</strong> – A specified bond order to calculate the bond
length between the attached functional group and the nearest
neighbor site. Defaults to 1.</p></li>
<li><p><strong>graph_dict</strong> – Dictionary representing the bonds of the functional
group (format: {(u, v): props}, where props is a dictionary of
properties, including weight. If None, then the algorithm
will attempt to automatically determine bonds using one of
a list of strategies defined in pymatgen.analysis.local_env.</p></li>
<li><p><strong>strategy_params</strong> – dictionary of keyword arguments for strategy.
If None, default parameters will be used.</p></li>
</ul>
</dd>
</dl>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.analysis.graphs.StructureGraph.types_and_weights_of_connections">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">types_and_weights_of_connections</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">dict</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/graphs.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.graphs.StructureGraph.types_and_weights_of_connections" title="Link to this definition"></a></dt>
<dd><p>Extract a dictionary summarizing the types and weights
of edges in the graph.</p>
<dl class="field-list simple">
<dt class="field-odd">Returns<span class="colon">:</span></dt>
<dd class="field-odd"><p>A dictionary with keys specifying the
species involved in a connection in alphabetical order
(e.g. string ‘Fe-O’) and values which are a list of
weights for those connections (e.g. bond lengths).</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.graphs.StructureGraph.types_of_coordination_environments">
<span class="sig-name descname"><span class="pre">types_of_coordination_environments</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">anonymous</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/graphs.py#L1032-L1070"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.graphs.StructureGraph.types_of_coordination_environments" title="Link to this definition"></a></dt>
<dd><p>Extract information on the different co-ordination environments
present in the graph.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>anonymous</strong> – if anonymous, will replace specie names with A, B, C, etc.</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>List of coordination environments, e.g. {‘Mo-S(6)’, ‘S-Mo(3)’}</p>
</dd>
</dl>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.analysis.graphs.StructureGraph.weight_statistics">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">weight_statistics</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">dict</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/graphs.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.graphs.StructureGraph.weight_statistics" title="Link to this definition"></a></dt>
<dd><p>Extract a statistical summary of edge weights present in
the graph.</p>
<dl class="field-list simple">
<dt class="field-odd">Returns<span class="colon">:</span></dt>
<dd class="field-odd"><p>A dict with an ‘all_weights’ list, ‘minimum’,
‘maximum’, ‘median’, ‘mean’, ‘std_dev’</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.graphs.StructureGraph.with_edges">
<em class="property"><span class="pre">classmethod</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">with_edges</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">*</span></span><span class="n"><span class="pre">args</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../../../../monty/src/monty/dev.py#L267-L270"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.graphs.StructureGraph.with_edges" title="Link to this definition"></a></dt>
<dd></dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.graphs.StructureGraph.with_empty_graph">
<em class="property"><span class="pre">classmethod</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">with_empty_graph</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">*</span></span><span class="n"><span class="pre">args</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../../../../monty/src/monty/dev.py#L208-L211"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.graphs.StructureGraph.with_empty_graph" title="Link to this definition"></a></dt>
<dd></dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.graphs.StructureGraph.with_local_env_strategy">
<em class="property"><span class="pre">classmethod</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">with_local_env_strategy</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">*</span></span><span class="n"><span class="pre">args</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../../../../monty/src/monty/dev.py#L313-L316"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.graphs.StructureGraph.with_local_env_strategy" title="Link to this definition"></a></dt>
<dd></dd></dl>
</dd></dl>
</section>
<section id="module-pymatgen.analysis.hhi">
<span id="pymatgen-analysis-hhi-module"></span><h2>pymatgen.analysis.hhi module<a class="headerlink" href="#module-pymatgen.analysis.hhi" title="Link to this heading"></a></h2>
<p>This module is used to estimate the Herfindahl-Hirschman Index, or HHI, of
chemical compounds. The HHI is a measure of how geographically confined or
dispersed the elements comprising a compound are. A low HHI is desirable
because it means the component elements are geographically dispersed.</p>
<p>Data/strategy from “Data-Driven Review of Thermoelectric Materials:
Performance and Resource Considerations” by Gaultois et al., published
in Chemistry of Materials (2013).</p>
</section>
<section id="module-pymatgen.analysis.interface_reactions">
<span id="pymatgen-analysis-interface-reactions-module"></span><h2>pymatgen.analysis.interface_reactions module<a class="headerlink" href="#module-pymatgen.analysis.interface_reactions" title="Link to this heading"></a></h2>
<p>This module provides a class to predict and analyze interfacial reactions between two
solids, with or without an open element (e.g., flowing O2).</p>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.analysis.interface_reactions.GrandPotentialInterfacialReactivity">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">GrandPotentialInterfacialReactivity</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">c1</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="pymatgen.core.html#pymatgen.core.composition.Composition" title="pymatgen.core.composition.Composition"><span class="pre">Composition</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">c2</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="pymatgen.core.html#pymatgen.core.composition.Composition" title="pymatgen.core.composition.Composition"><span class="pre">Composition</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">grand_pd</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="#pymatgen.analysis.phase_diagram.GrandPotentialPhaseDiagram" title="pymatgen.analysis.phase_diagram.GrandPotentialPhaseDiagram"><span class="pre">GrandPotentialPhaseDiagram</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">pd_non_grand</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="#pymatgen.analysis.phase_diagram.PhaseDiagram" title="pymatgen.analysis.phase_diagram.PhaseDiagram"><span class="pre">PhaseDiagram</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">include_no_mixing_energy</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">norm</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_hull_energy</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/interface_reactions.py#L610-L730"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.interface_reactions.GrandPotentialInterfacialReactivity" title="Link to this definition"></a></dt>
<dd><p>Bases: <a class="reference internal" href="#pymatgen.analysis.interface_reactions.InterfacialReactivity" title="pymatgen.analysis.interface_reactions.InterfacialReactivity"><code class="xref py py-class docutils literal notranslate"><span class="pre">InterfacialReactivity</span></code></a></p>
<p>Extends upon InterfacialReactivity to allow for modelling possible reactions
at the interface between two solids in the presence of an open element. The
thermodynamics of the open system are provided by the user via the
GrandPotentialPhaseDiagram class.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>c1</strong> – Reactant 1 composition</p></li>
<li><p><strong>c2</strong> – Reactant 2 composition</p></li>
<li><p><strong>grand_pd</strong> – Grand potential phase diagram object built from all elements in
composition c1 and c2.</p></li>
<li><p><strong>include_no_mixing_energy</strong> – No_mixing_energy for a reactant is the
opposite number of its energy above grand potential convex hull. In
cases where reactions involve elements reservoir, this param
determines whether no_mixing_energy of reactants will be included
in the final reaction energy calculation. By definition, if pd is
not a GrandPotentialPhaseDiagram object, this param is False.</p></li>
<li><p><strong>pd_non_grand</strong> – PhaseDiagram object but not
GrandPotentialPhaseDiagram object built from elements in c1 and c2.</p></li>
<li><p><strong>norm</strong> – Whether or not the total number of atoms in composition
of reactant will be normalized to 1.</p></li>
<li><p><strong>use_hull_energy</strong> – Whether or not use the convex hull energy for
a given composition for reaction energy calculation. If false,
the energy of ground state structure will be used instead.
Note that in case when ground state can not be found for a
composition, convex hull energy will be used associated with a
warning message.</p></li>
</ul>
</dd>
</dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.interface_reactions.GrandPotentialInterfacialReactivity.get_no_mixing_energy">
<span class="sig-name descname"><span class="pre">get_no_mixing_energy</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/interface_reactions.py#L683-L700"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.interface_reactions.GrandPotentialInterfacialReactivity.get_no_mixing_energy" title="Link to this definition"></a></dt>
<dd><p>Generate the opposite number of energy above grand potential
convex hull for both reactants.</p>
<dl class="field-list simple">
<dt class="field-odd">Returns<span class="colon">:</span></dt>
<dd class="field-odd"><p>[(reactant1, no_mixing_energy1),(reactant2,no_mixing_energy2)].</p>
</dd>
</dl>
</dd></dl>
</dd></dl>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.analysis.interface_reactions.InterfacialReactivity">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">InterfacialReactivity</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">c1</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="pymatgen.core.html#pymatgen.core.composition.Composition" title="pymatgen.core.composition.Composition"><span class="pre">Composition</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">c2</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="pymatgen.core.html#pymatgen.core.composition.Composition" title="pymatgen.core.composition.Composition"><span class="pre">Composition</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">pd</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="#pymatgen.analysis.phase_diagram.PhaseDiagram" title="pymatgen.analysis.phase_diagram.PhaseDiagram"><span class="pre">PhaseDiagram</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">norm</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_hull_energy</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/interface_reactions.py#L38-L607"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.interface_reactions.InterfacialReactivity" title="Link to this definition"></a></dt>
<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">MSONable</span></code></p>
<p>Model an interface between two solids and its possible reactions.
The two reactants are provided as Composition objects (c1 and c2), along with the
relevant compositional PhaseDiagram object. Possible reactions are calculated by
finding all points along a tie-line between c1 and c2 where there is a “kink” in
the phase diagram; i.e. a point or facet of the phase diagram.</p>
<p>Please consider citing one or both of the following papers if you use this code
in your own work.</p>
<p class="rubric">References</p>
<p>Richards, W. D., Miara, L. J., Wang, Y., Kim, J. C., &amp; Ceder, G. (2015).
Interface stability in solid-state batteries. Chemistry of Materials, 28(1),
266-273. <a class="reference external" href="https://doi.org/10.1021/acs.chemmater.5b04082">https://doi.org/10.1021/acs.chemmater.5b04082</a></p>
<p>Xiao, Y., Wang, Y., Bo, S.-H., Kim, J. C., Miara, L. J., &amp; Ceder, G. (2019).
Understanding interface stability in solid-state batteries.
Nature Reviews Materials, 5(2), 105-126.
<a class="reference external" href="https://doi.org/10.1038/s41578-019-0157-5">https://doi.org/10.1038/s41578-019-0157-5</a></p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>c1</strong> – Reactant 1 composition</p></li>
<li><p><strong>c2</strong> – Reactant 2 composition</p></li>
<li><p><strong>pd</strong> – Phase diagram object built from all elements in composition c1 and c2.</p></li>
<li><p><strong>norm</strong> – Whether or not the total number of atoms in composition
of reactant will be normalized to 1.</p></li>
<li><p><strong>use_hull_energy</strong> – Whether or not use the convex hull energy for
a given composition for reaction energy calculation. If false,
the energy of ground state structure will be used instead.
Note that in case when ground state can not be found for a
composition, convex hull energy will be used associated with a
warning message.</p></li>
</ul>
</dd>
</dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.analysis.interface_reactions.InterfacialReactivity.EV_TO_KJ_PER_MOL">
<span class="sig-name descname"><span class="pre">EV_TO_KJ_PER_MOL</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">96.4853</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/interface_reactions.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.interface_reactions.InterfacialReactivity.EV_TO_KJ_PER_MOL" title="Link to this definition"></a></dt>
<dd></dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.interface_reactions.InterfacialReactivity.get_chempot_correction">
<em class="property"><span class="pre">classmethod</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">get_chempot_correction</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">element</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">temp</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">float</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">pres</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">float</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/interface_reactions.py#L531-L577"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.interface_reactions.InterfacialReactivity.get_chempot_correction" title="Link to this definition"></a></dt>
<dd><p>Get the normalized correction term Δμ for chemical potential of a gas
phase consisting of element at given temperature and pressure,
referenced to that in the standard state (T_std = 298.15 K,
T_std = 1 bar). The gas phase is limited to be one of O2, N2, Cl2,
F2, H2. Calculation formula can be found in the documentation of
Materials Project website.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>element</strong> – The string representing the element.</p></li>
<li><p><strong>temp</strong> – The temperature of the gas phase in Kelvin.</p></li>
<li><p><strong>pres</strong> – The pressure of the gas phase in Pa. # codespell:ignore pres</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>The correction of chemical potential in eV/atom of the gas
phase at given temperature and pressure.</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.interface_reactions.InterfacialReactivity.get_critical_original_kink_ratio">
<span class="sig-name descname"><span class="pre">get_critical_original_kink_ratio</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/interface_reactions.py#L236-L252"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.interface_reactions.InterfacialReactivity.get_critical_original_kink_ratio" title="Link to this definition"></a></dt>
<dd><p>Get a list of molar mixing ratio for each kink between ORIGINAL
(instead of processed) reactant compositions. This is the
same list as mixing ratio obtained from get_kinks method
if self.norm = False.</p>
<dl class="field-list simple">
<dt class="field-odd">Returns<span class="colon">:</span></dt>
<dd class="field-odd"><p>A list of floats representing molar mixing ratios between
the original reactant compositions for each kink.</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.interface_reactions.InterfacialReactivity.get_dataframe">
<span class="sig-name descname"><span class="pre">get_dataframe</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">DataFrame</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/interface_reactions.py#L220-L234"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.interface_reactions.InterfacialReactivity.get_dataframe" title="Link to this definition"></a></dt>
<dd><p>Get a pandas DataFrame representation of the data produced by the
get_kinks() method.</p>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.interface_reactions.InterfacialReactivity.get_kinks">
<span class="sig-name descname"><span class="pre">get_kinks</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">tuple</span><span class="p"><span class="pre">[</span></span><span class="pre">int</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">float</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">float</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><a class="reference internal" href="#pymatgen.analysis.reaction_calculator.Reaction" title="pymatgen.analysis.reaction_calculator.Reaction"><span class="pre">Reaction</span></a><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">float</span><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">]</span></span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/interface_reactions.py#L134-L198"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.interface_reactions.InterfacialReactivity.get_kinks" title="Link to this definition"></a></dt>
<dd><p>Find all the kinks in mixing ratio where reaction products changes
along the tie-line of composition self.c1 and composition self.c2.</p>
<dl class="field-list simple">
<dt class="field-odd">Returns<span class="colon">:</span></dt>
<dd class="field-odd"><p>(index, mixing ratio, reaction energy in eV/atom, Reaction object, reaction
energy per mol of formula in kJ/mol).</p>
</dd>
<dt class="field-even">Return type<span class="colon">:</span></dt>
<dd class="field-even"><p>List object of tuples, each of which contains 5 elements</p>
</dd>
</dl>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.analysis.interface_reactions.InterfacialReactivity.labels">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">labels</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/interface_reactions.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.interface_reactions.InterfacialReactivity.labels" title="Link to this definition"></a></dt>
<dd><p>A dictionary containing kink information:
{index: ‘x= mixing_ratio energy= reaction_energy reaction_equation’}.
e.g. {1: ‘x= 0 energy = 0 Mn -> Mn’,</p>
<blockquote>
<div><p>2: ‘x= 0.5 energy = -15 O2 + Mn -> MnO2’,
3: ‘x= 1 energy = 0 O2 -> O2’}.</p>
</div></blockquote>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.analysis.interface_reactions.InterfacialReactivity.minimum">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">minimum</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/interface_reactions.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.interface_reactions.InterfacialReactivity.minimum" title="Link to this definition"></a></dt>
<dd><p>The minimum reaction energy E_min and corresponding mixing ratio x_min
as tuple[float, float]: (x_min, E_min).</p>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.interface_reactions.InterfacialReactivity.plot">
<span class="sig-name descname"><span class="pre">plot</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">backend</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">Literal</span><span class="p"><span class="pre">[</span></span><span class="s"><span class="pre">'plotly'</span></span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="s"><span class="pre">'matplotlib'</span></span><span class="p"><span class="pre">]</span></span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">'plotly'</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">Figure</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">plt.Figure</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/interface_reactions.py#L200-L218"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.interface_reactions.InterfacialReactivity.plot" title="Link to this definition"></a></dt>
<dd><p>Plots reaction energy as a function of mixing ratio x in self.c1 - self.c2 tie line.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>backend</strong> (<em>"plotly"</em><em> | </em><em>"matplotlib"</em>) – Plotting library used to create the plot. Defaults to
“plotly” but can also be “matplotlib”.</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>Plot of reaction energies as a function of mixing ratio</p>
</dd>
</dl>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.analysis.interface_reactions.InterfacialReactivity.products">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">products</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/interface_reactions.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.interface_reactions.InterfacialReactivity.products" title="Link to this definition"></a></dt>
<dd><p>List of formulas of potential products. e.g. [‘Li’,’O2’,’Mn’].</p>
</dd></dl>
</dd></dl>
</section>
<section id="module-pymatgen.analysis.local_env">
<span id="pymatgen-analysis-local-env-module"></span><h2>pymatgen.analysis.local_env module<a class="headerlink" href="#module-pymatgen.analysis.local_env" title="Link to this heading"></a></h2>
<p>This module provides classes to perform analyses of
the local environments (e.g., finding near neighbors)
of single sites in molecules and structures.</p>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.analysis.local_env.BrunnerNNReal">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">BrunnerNNReal</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">tol</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">float</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">0.0001</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">cutoff</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">8.0</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/local_env.py#L3587-L3655"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.local_env.BrunnerNNReal" title="Link to this definition"></a></dt>
<dd><p>Bases: <a class="reference internal" href="#pymatgen.analysis.local_env.NearNeighbors" title="pymatgen.analysis.local_env.NearNeighbors"><code class="xref py py-class docutils literal notranslate"><span class="pre">NearNeighbors</span></code></a></p>
<p>Determine coordination number using Brunner’s algorithm which counts the
atoms that are within the largest gap in differences in real space
interatomic distances. This algorithm uses Brunner’s method of
largest gap in interatomic distances.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>tol</strong> (<em>float</em>) – tolerance parameter for bond determination
(default: 1E-4).</p></li>
<li><p><strong>cutoff</strong> (<em>float</em>) – cutoff radius in Angstrom to look for near-neighbor
atoms. Defaults to 8.0.</p></li>
</ul>
</dd>
</dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.local_env.BrunnerNNReal.get_nn_info">
<span class="sig-name descname"><span class="pre">get_nn_info</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">structure</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><span class="pre">Structure</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">n</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/local_env.py#L3622-L3655"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.local_env.BrunnerNNReal.get_nn_info" title="Link to this definition"></a></dt>
<dd><p>Get all near-neighbor sites as well as the associated image locations
and weights of the site with index n in structure.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>structure</strong> (<a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><em>Structure</em></a>) – input structure.</p></li>
<li><p><strong>n</strong> (<em>int</em>) – index of site for which to determine near-neighbor sites.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p><dl class="simple">
<dt>tuples, each one</dt><dd><p>of which represents a coordinated site, its image location,
and its weight.</p>
</dd>
</dl>
</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>siw (list of tuples (<a class="reference internal" href="pymatgen.core.html#pymatgen.core.sites.Site" title="pymatgen.core.sites.Site">Site</a>, array, float))</p>
</dd>
</dl>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.analysis.local_env.BrunnerNNReal.molecules_allowed">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">molecules_allowed</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">bool</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/local_env.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.local_env.BrunnerNNReal.molecules_allowed" title="Link to this definition"></a></dt>
<dd><p>can this NearNeighbors class be used with Molecule
objects?</p>
<dl class="field-list simple">
<dt class="field-odd">Type<span class="colon">:</span></dt>
<dd class="field-odd"><p>Boolean property</p>
</dd>
</dl>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.analysis.local_env.BrunnerNNReal.structures_allowed">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">structures_allowed</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">bool</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/local_env.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.local_env.BrunnerNNReal.structures_allowed" title="Link to this definition"></a></dt>
<dd><p>can this NearNeighbors class be used with Structure
objects?</p>
<dl class="field-list simple">
<dt class="field-odd">Type<span class="colon">:</span></dt>
<dd class="field-odd"><p>Boolean property</p>
</dd>
</dl>
</dd></dl>
</dd></dl>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.analysis.local_env.BrunnerNNReciprocal">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">BrunnerNNReciprocal</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">tol</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">float</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">0.0001</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">cutoff</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">8.0</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/local_env.py#L3436-L3503"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.local_env.BrunnerNNReciprocal" title="Link to this definition"></a></dt>
<dd><p>Bases: <a class="reference internal" href="#pymatgen.analysis.local_env.NearNeighbors" title="pymatgen.analysis.local_env.NearNeighbors"><code class="xref py py-class docutils literal notranslate"><span class="pre">NearNeighbors</span></code></a></p>
<p>Determine coordination number using Brunner’s algorithm which counts the
atoms that are within the largest gap in differences in real space
interatomic distances. This algorithm uses Brunner’s method of
largest reciprocal gap in interatomic distances.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>tol</strong> (<em>float</em>) – tolerance parameter for bond determination
(default: 1E-4).</p></li>
<li><p><strong>cutoff</strong> (<em>float</em>) – cutoff radius in Angstrom to look for near-neighbor
atoms. Defaults to 8.0.</p></li>
</ul>
</dd>
</dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.local_env.BrunnerNNReciprocal.get_nn_info">
<span class="sig-name descname"><span class="pre">get_nn_info</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">structure</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><span class="pre">Structure</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">n</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/local_env.py#L3471-L3503"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.local_env.BrunnerNNReciprocal.get_nn_info" title="Link to this definition"></a></dt>
<dd><p>Get all near-neighbor sites as well as the associated image locations
and weights of the site with index n in structure.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>structure</strong> (<a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><em>Structure</em></a>) – input structure.</p></li>
<li><p><strong>n</strong> (<em>int</em>) – index of site for which to determine near-neighbor sites.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p><dl class="simple">
<dt>tuples, each one of which represents a</dt><dd><p>coordinated site, its image location, and its weight.</p>
</dd>
</dl>
</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>list[tuples[<a class="reference internal" href="pymatgen.core.html#pymatgen.core.sites.Site" title="pymatgen.core.sites.Site">Site</a>, array, float]]</p>
</dd>
</dl>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.analysis.local_env.BrunnerNNReciprocal.molecules_allowed">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">molecules_allowed</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">bool</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/local_env.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.local_env.BrunnerNNReciprocal.molecules_allowed" title="Link to this definition"></a></dt>
<dd><p>can this NearNeighbors class be used with Molecule
objects?</p>
<dl class="field-list simple">
<dt class="field-odd">Type<span class="colon">:</span></dt>
<dd class="field-odd"><p>Boolean property</p>
</dd>
</dl>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.analysis.local_env.BrunnerNNReciprocal.structures_allowed">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">structures_allowed</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">bool</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/local_env.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.local_env.BrunnerNNReciprocal.structures_allowed" title="Link to this definition"></a></dt>
<dd><p>can this NearNeighbors class be used with Structure
objects?</p>
<dl class="field-list simple">
<dt class="field-odd">Type<span class="colon">:</span></dt>
<dd class="field-odd"><p>Boolean property</p>
</dd>
</dl>
</dd></dl>
</dd></dl>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.analysis.local_env.BrunnerNNRelative">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">BrunnerNNRelative</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">tol</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">float</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">0.0001</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">cutoff</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">8.0</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/local_env.py#L3511-L3579"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.local_env.BrunnerNNRelative" title="Link to this definition"></a></dt>
<dd><p>Bases: <a class="reference internal" href="#pymatgen.analysis.local_env.NearNeighbors" title="pymatgen.analysis.local_env.NearNeighbors"><code class="xref py py-class docutils literal notranslate"><span class="pre">NearNeighbors</span></code></a></p>
<p>Determine coordination number using Brunner’s algorithm which counts the
atoms that are within the largest gap in differences in real space
interatomic distances. This algorithm uses Brunner’s method of
of largest relative gap in interatomic distances.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>tol</strong> (<em>float</em>) – tolerance parameter for bond determination
(default: 1E-4).</p></li>
<li><p><strong>cutoff</strong> (<em>float</em>) – cutoff radius in Angstrom to look for near-neighbor
atoms. Defaults to 8.0.</p></li>
</ul>
</dd>
</dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.local_env.BrunnerNNRelative.get_nn_info">
<span class="sig-name descname"><span class="pre">get_nn_info</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">structure</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><span class="pre">Structure</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">n</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/local_env.py#L3546-L3579"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.local_env.BrunnerNNRelative.get_nn_info" title="Link to this definition"></a></dt>
<dd><p>Get all near-neighbor sites as well as the associated image locations
and weights of the site with index n in structure.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>structure</strong> (<a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><em>Structure</em></a>) – input structure.</p></li>
<li><p><strong>n</strong> (<em>int</em>) – index of site for which to determine near-neighbor sites.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p><dl class="simple">
<dt>tuples, each one</dt><dd><p>of which represents a coordinated site, its image location,
and its weight.</p>
</dd>
</dl>
</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>siw (list of tuples (<a class="reference internal" href="pymatgen.core.html#pymatgen.core.sites.Site" title="pymatgen.core.sites.Site">Site</a>, array, float))</p>
</dd>
</dl>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.analysis.local_env.BrunnerNNRelative.molecules_allowed">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">molecules_allowed</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">bool</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/local_env.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.local_env.BrunnerNNRelative.molecules_allowed" title="Link to this definition"></a></dt>
<dd><p>can this NearNeighbors class be used with Molecule
objects?</p>
<dl class="field-list simple">
<dt class="field-odd">Type<span class="colon">:</span></dt>
<dd class="field-odd"><p>Boolean property</p>
</dd>
</dl>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.analysis.local_env.BrunnerNNRelative.structures_allowed">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">structures_allowed</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">bool</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/local_env.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.local_env.BrunnerNNRelative.structures_allowed" title="Link to this definition"></a></dt>
<dd><p>can this NearNeighbors class be used with Structure
objects?</p>
<dl class="field-list simple">
<dt class="field-odd">Type<span class="colon">:</span></dt>
<dd class="field-odd"><p>Boolean property</p>
</dd>
</dl>
</dd></dl>
</dd></dl>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.analysis.local_env.BrunnerNN_real">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">BrunnerNN_real</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">tol</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">float</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">0.0001</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">cutoff</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">8.0</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/local_env.py#L3658-L3660"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.local_env.BrunnerNN_real" title="Link to this definition"></a></dt>
<dd><p>Bases: <a class="reference internal" href="#pymatgen.analysis.local_env.BrunnerNNReal" title="pymatgen.analysis.local_env.BrunnerNNReal"><code class="xref py py-class docutils literal notranslate"><span class="pre">BrunnerNNReal</span></code></a></p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>tol</strong> (<em>float</em>) – tolerance parameter for bond determination
(default: 1E-4).</p></li>
<li><p><strong>cutoff</strong> (<em>float</em>) – cutoff radius in Angstrom to look for near-neighbor
atoms. Defaults to 8.0.</p></li>
</ul>
</dd>
</dl>
</dd></dl>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.analysis.local_env.BrunnerNN_reciprocal">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">BrunnerNN_reciprocal</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">tol</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">float</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">0.0001</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">cutoff</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">8.0</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/local_env.py#L3506-L3508"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.local_env.BrunnerNN_reciprocal" title="Link to this definition"></a></dt>
<dd><p>Bases: <a class="reference internal" href="#pymatgen.analysis.local_env.BrunnerNNReciprocal" title="pymatgen.analysis.local_env.BrunnerNNReciprocal"><code class="xref py py-class docutils literal notranslate"><span class="pre">BrunnerNNReciprocal</span></code></a></p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>tol</strong> (<em>float</em>) – tolerance parameter for bond determination
(default: 1E-4).</p></li>
<li><p><strong>cutoff</strong> (<em>float</em>) – cutoff radius in Angstrom to look for near-neighbor
atoms. Defaults to 8.0.</p></li>
</ul>
</dd>
</dl>
</dd></dl>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.analysis.local_env.BrunnerNN_relative">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">BrunnerNN_relative</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">tol</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">float</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">0.0001</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">cutoff</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">8.0</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/local_env.py#L3582-L3584"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.local_env.BrunnerNN_relative" title="Link to this definition"></a></dt>
<dd><p>Bases: <a class="reference internal" href="#pymatgen.analysis.local_env.BrunnerNNRelative" title="pymatgen.analysis.local_env.BrunnerNNRelative"><code class="xref py py-class docutils literal notranslate"><span class="pre">BrunnerNNRelative</span></code></a></p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>tol</strong> (<em>float</em>) – tolerance parameter for bond determination
(default: 1E-4).</p></li>
<li><p><strong>cutoff</strong> (<em>float</em>) – cutoff radius in Angstrom to look for near-neighbor
atoms. Defaults to 8.0.</p></li>
</ul>
</dd>
</dl>
</dd></dl>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.analysis.local_env.CovalentBondNN">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">CovalentBondNN</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">tol</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">float</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">0.2</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">order</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/local_env.py#L1582-L1734"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.local_env.CovalentBondNN" title="Link to this definition"></a></dt>
<dd><p>Bases: <a class="reference internal" href="#pymatgen.analysis.local_env.NearNeighbors" title="pymatgen.analysis.local_env.NearNeighbors"><code class="xref py py-class docutils literal notranslate"><span class="pre">NearNeighbors</span></code></a></p>
<p>Determine near-neighbor sites and bond orders using built-in
pymatgen.Molecule CovalentBond functionality.</p>
<p>NOTE: This strategy is only appropriate for molecules, and not for
structures.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>tol</strong> (<em>float</em>) – Tolerance for covalent bond checking.</p></li>
<li><p><strong>order</strong> (<em>bool</em>) – If True (default), this class will compute bond
orders. If False, bond lengths will be computed.</p></li>
</ul>
</dd>
</dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.analysis.local_env.CovalentBondNN.extend_structure_molecules">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">extend_structure_molecules</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">bool</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/local_env.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.local_env.CovalentBondNN.extend_structure_molecules" title="Link to this definition"></a></dt>
<dd><p>Do Molecules need to be converted to Structures to use
this NearNeighbors class? Note: this property is not defined for classes
for which molecules_allowed is False.</p>
<dl class="field-list simple">
<dt class="field-odd">Type<span class="colon">:</span></dt>
<dd class="field-odd"><p>Boolean property</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.local_env.CovalentBondNN.get_bonded_structure">
<span class="sig-name descname"><span class="pre">get_bonded_structure</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">structure</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><span class="pre">Structure</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">decorate</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><a class="reference internal" href="#pymatgen.analysis.graphs.MoleculeGraph" title="pymatgen.analysis.graphs.MoleculeGraph"><span class="pre">MoleculeGraph</span></a></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/local_env.py#L1672-L1696"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.local_env.CovalentBondNN.get_bonded_structure" title="Link to this definition"></a></dt>
<dd><p>Obtain a MoleculeGraph object using this NearNeighbor class.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>structure</strong> – Molecule object.</p></li>
<li><p><strong>decorate</strong> (<em>bool</em>) – whether to annotate site properties</p></li>
<li><p><strong>by</strong> (<em>with order parameters using neighbors determined</em>)</p></li>
<li><p><strong>class</strong> (<em>this NearNeighbor</em>)</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>object from pymatgen.analysis.graphs</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p><a class="reference internal" href="#pymatgen.analysis.graphs.MoleculeGraph" title="pymatgen.analysis.graphs.MoleculeGraph">MoleculeGraph</a></p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.local_env.CovalentBondNN.get_nn_info">
<span class="sig-name descname"><span class="pre">get_nn_info</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">structure</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><span class="pre">Structure</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">n</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/local_env.py#L1628-L1670"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.local_env.CovalentBondNN.get_nn_info" title="Link to this definition"></a></dt>
<dd><p>Get all near-neighbor sites and weights (orders) of bonds for a given
atom.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>structure</strong> – input Molecule.</p></li>
<li><p><strong>n</strong> – index of site for which to determine near neighbors.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>[dict] representing a neighboring site and the type of
bond present between site n and the neighboring site.</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.local_env.CovalentBondNN.get_nn_shell_info">
<span class="sig-name descname"><span class="pre">get_nn_shell_info</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">structure</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><span class="pre">Structure</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">site_idx</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">shell</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/local_env.py#L1698-L1734"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.local_env.CovalentBondNN.get_nn_shell_info" title="Link to this definition"></a></dt>
<dd><p>Get a certain nearest neighbor shell for a certain site.</p>
<p>Determines all non-backtracking paths through the neighbor network
computed by <cite>get_nn_info</cite>. The weight is determined by multiplying
the weight of the neighbor at each hop through the network. For
example, a 2nd-nearest-neighbor that has a weight of 1 from its
1st-nearest-neighbor and weight 0.5 from the original site will
be assigned a weight of 0.5.</p>
<p>As this calculation may involve computing the nearest neighbors of
atoms multiple times, the calculation starts by computing all of the
neighbor info and then calling <cite>_get_nn_shell_info</cite>. If you are likely
to call this method for more than one site, consider calling <cite>get_all_nn</cite>
first and then calling this protected method yourself.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>structure</strong> (<a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Molecule" title="pymatgen.core.structure.Molecule"><em>Molecule</em></a>) – Input structure</p></li>
<li><p><strong>site_idx</strong> (<em>int</em>) – index of site for which to determine neighbor
information.</p></li>
<li><p><strong>shell</strong> (<em>int</em>) – Which neighbor shell to retrieve (1 == 1st NN shell)</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p><dl class="simple">
<dt>list of dictionaries. Each entry in the list is information about</dt><dd><p>a certain neighbor in the structure, in the same format as
<cite>get_nn_info</cite>.</p>
</dd>
</dl>
</p>
</dd>
</dl>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.analysis.local_env.CovalentBondNN.molecules_allowed">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">molecules_allowed</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">bool</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/local_env.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.local_env.CovalentBondNN.molecules_allowed" title="Link to this definition"></a></dt>
<dd><p>can this NearNeighbors class be used with Molecule
objects?</p>
<dl class="field-list simple">
<dt class="field-odd">Type<span class="colon">:</span></dt>
<dd class="field-odd"><p>Boolean property</p>
</dd>
</dl>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.analysis.local_env.CovalentBondNN.structures_allowed">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">structures_allowed</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">bool</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/local_env.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.local_env.CovalentBondNN.structures_allowed" title="Link to this definition"></a></dt>
<dd><p>can this NearNeighbors class be used with Structure
objects?</p>
<dl class="field-list simple">
<dt class="field-odd">Type<span class="colon">:</span></dt>
<dd class="field-odd"><p>Boolean property</p>
</dd>
</dl>
</dd></dl>
</dd></dl>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.analysis.local_env.Critic2NN">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">Critic2NN</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/local_env.py#L4351-L4441"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.local_env.Critic2NN" title="Link to this definition"></a></dt>
<dd><p>Bases: <a class="reference internal" href="#pymatgen.analysis.local_env.NearNeighbors" title="pymatgen.analysis.local_env.NearNeighbors"><code class="xref py py-class docutils literal notranslate"><span class="pre">NearNeighbors</span></code></a></p>
<p>Performs a topological analysis using critic2 to obtain neighbor information, using a
sum of atomic charge densities. If an actual charge density is available (e.g. from a
VASP CHGCAR), see Critic2Caller directly instead.</p>
<p>Init for Critic2NN.</p>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.analysis.local_env.Critic2NN.extend_structure_molecules">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">extend_structure_molecules</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">bool</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/local_env.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.local_env.Critic2NN.extend_structure_molecules" title="Link to this definition"></a></dt>
<dd><p>Do Molecules need to be converted to Structures to use
this NearNeighbors class? Note: this property is not defined for classes
for which molecules_allowed is False.</p>
<dl class="field-list simple">
<dt class="field-odd">Type<span class="colon">:</span></dt>
<dd class="field-odd"><p>Boolean property</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.local_env.Critic2NN.get_bonded_structure">
<span class="sig-name descname"><span class="pre">get_bonded_structure</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">structure</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><span class="pre">Structure</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">decorate</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><a class="reference internal" href="#pymatgen.analysis.graphs.StructureGraph" title="pymatgen.analysis.graphs.StructureGraph"><span class="pre">StructureGraph</span></a></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/local_env.py#L4391-L4417"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.local_env.Critic2NN.get_bonded_structure" title="Link to this definition"></a></dt>
<dd><dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>structure</strong> (<a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><em>Structure</em></a>) – Input structure</p></li>
<li><p><strong>decorate</strong> (<em>bool</em><em>, </em><em>optional</em>) – Whether to decorate the structure. Defaults to False.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>Bonded structure</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p><a class="reference internal" href="#pymatgen.analysis.graphs.StructureGraph" title="pymatgen.analysis.graphs.StructureGraph">StructureGraph</a></p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.local_env.Critic2NN.get_nn_info">
<span class="sig-name descname"><span class="pre">get_nn_info</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">structure</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><span class="pre">Structure</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">n</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">dict</span><span class="p"><span class="pre">]</span></span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/local_env.py#L4419-L4441"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.local_env.Critic2NN.get_nn_info" title="Link to this definition"></a></dt>
<dd><p>Get all near-neighbor sites as well as the associated image locations
and weights of the site with index n in structure.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>structure</strong> (<a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><em>Structure</em></a>) – input structure.</p></li>
<li><p><strong>n</strong> (<em>int</em>) – index of site for which to determine near-neighbor sites.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p><dl class="simple">
<dt>tuples, each one</dt><dd><p>of which represents a coordinated site, its image location, and its weight.</p>
</dd>
</dl>
</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>siw (list of tuples (<a class="reference internal" href="pymatgen.core.html#pymatgen.core.sites.Site" title="pymatgen.core.sites.Site">Site</a>, array, float))</p>
</dd>
</dl>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.analysis.local_env.Critic2NN.molecules_allowed">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">molecules_allowed</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">bool</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/local_env.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.local_env.Critic2NN.molecules_allowed" title="Link to this definition"></a></dt>
<dd><p>can this NearNeighbors class be used with Molecule
objects?</p>
<dl class="field-list simple">
<dt class="field-odd">Type<span class="colon">:</span></dt>
<dd class="field-odd"><p>Boolean property</p>
</dd>
</dl>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.analysis.local_env.Critic2NN.structures_allowed">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">structures_allowed</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">bool</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/local_env.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.local_env.Critic2NN.structures_allowed" title="Link to this definition"></a></dt>
<dd><p>can this NearNeighbors class be used with Structure
objects?</p>
<dl class="field-list simple">
<dt class="field-odd">Type<span class="colon">:</span></dt>
<dd class="field-odd"><p>Boolean property</p>
</dd>
</dl>
</dd></dl>
</dd></dl>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.analysis.local_env.CrystalNN">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">CrystalNN</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">weighted_cn</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">cation_anion</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">distance_cutoffs</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">(0.5,</span> <span class="pre">1)</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">x_diff_weight</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">3.0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">porous_adjustment</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">search_cutoff</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">7</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">fingerprint_length</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/local_env.py#L3837-L4178"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.local_env.CrystalNN" title="Link to this definition"></a></dt>
<dd><p>Bases: <a class="reference internal" href="#pymatgen.analysis.local_env.NearNeighbors" title="pymatgen.analysis.local_env.NearNeighbors"><code class="xref py py-class docutils literal notranslate"><span class="pre">NearNeighbors</span></code></a></p>
<p>This is a custom near-neighbor method intended for use in all kinds of periodic structures
(metals, minerals, porous structures, etc). It is based on a Voronoi algorithm and uses the
solid angle weights to determine the probability of various coordination environments. The
algorithm can also modify probability using smooth distance cutoffs as well as Pauling
electronegativity differences. The output can either be the most probable coordination
environment or a weighted list of coordination environments.
Please note that the default weights have been benchmarked for inorganic crystal structures.
For MOFs or molecular crystals, weights and cutoffs likely will need to be adapted.
A starting point could be:
CrystalNN(x_diff_weight = 1.5, search_cutoff = 4.5).</p>
<p>Initialize CrystalNN with desired parameters. Default parameters assume
“chemical bond” type behavior is desired. For geometric neighbor
finding (e.g., structural framework), set (i) distance_cutoffs=None,
(ii) x_diff_weight=0 and (optionally) (iii) porous_adjustment=False
which will disregard the atomic identities and perform best for a purely
geometric match.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>weighted_cn</strong> (<em>bool</em>) – if set to True, will return fractional weights
for each potential near neighbor.</p></li>
<li><p><strong>cation_anion</strong> (<em>bool</em>) – if set True, will restrict bonding targets to
sites with opposite or zero charge. Requires an oxidation states
on all sites in the structure.</p></li>
<li><p><strong>distance_cutoffs</strong> (<em>[</em><em>float</em><em>, </em><em>float</em><em>]</em>) – <ul>
<li><p>if not None, penalizes neighbor</p></li>
</ul>
<p>distances greater than sum of covalent radii plus
distance_cutoffs[0]. Distances greater than covalent radii sum
plus distance_cutoffs[1] are enforced to have zero weight.</p>
</p></li>
<li><p><strong>x_diff_weight</strong> (<em>float</em>) – <ul>
<li><p>if multiple types of neighbor elements are</p></li>
</ul>
<p>possible, this sets preferences for targets with higher
electronegativity difference.</p>
</p></li>
<li><p><strong>porous_adjustment</strong> (<em>bool</em>) – <ul>
<li><p>if True, readjusts Voronoi weights to</p></li>
</ul>
<p>better describe layered / porous structures</p>
</p></li>
<li><p><strong>search_cutoff</strong> (<em>float</em>) – cutoff in Angstroms for initial neighbor
search; this will be adjusted if needed internally</p></li>
<li><p><strong>fingerprint_length</strong> (<em>int</em>) – if a fixed_length CN “fingerprint” is
desired from get_nn_data(), set this parameter</p></li>
</ul>
</dd>
</dl>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.analysis.local_env.CrystalNN.NNData">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">NNData</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">all_nninfo</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">cn_weights</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">cn_nninfo</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/local_env.py#L3851-L3854"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.local_env.CrystalNN.NNData" title="Link to this definition"></a></dt>
<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">NamedTuple</span></code></p>
<p>Create new instance of NNData(all_nninfo, cn_weights, cn_nninfo)</p>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.analysis.local_env.CrystalNN.NNData.all_nninfo">
<span class="sig-name descname"><span class="pre">all_nninfo</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">list</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/local_env.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.local_env.CrystalNN.NNData.all_nninfo" title="Link to this definition"></a></dt>
<dd><p>Alias for field number 0</p>
</dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.analysis.local_env.CrystalNN.NNData.cn_nninfo">
<span class="sig-name descname"><span class="pre">cn_nninfo</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">dict</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/local_env.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.local_env.CrystalNN.NNData.cn_nninfo" title="Link to this definition"></a></dt>
<dd><p>Alias for field number 2</p>
</dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.analysis.local_env.CrystalNN.NNData.cn_weights">
<span class="sig-name descname"><span class="pre">cn_weights</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">dict</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/local_env.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.local_env.CrystalNN.NNData.cn_weights" title="Link to this definition"></a></dt>
<dd><p>Alias for field number 1</p>
</dd></dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.local_env.CrystalNN.get_cn">
<span class="sig-name descname"><span class="pre">get_cn</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">structure</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><span class="pre">Structure</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">n</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">float</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/local_env.py#L4085-L4110"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.local_env.CrystalNN.get_cn" title="Link to this definition"></a></dt>
<dd><p>Get coordination number, CN, of site with index n in structure.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>structure</strong> (<a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><em>Structure</em></a>) – input structure.</p></li>
<li><p><strong>n</strong> (<em>int</em>) – index of site for which to determine CN.</p></li>
<li><p><strong>use_weights</strong> (<em>bool</em>) – flag indicating whether (True)
to use weights for computing the coordination number
or not (False, default: each coordinated site has equal
weight).</p></li>
<li><p><strong>on_disorder</strong> (<em>'take_majority_strict'</em><em> | </em><em>'take_majority_drop'</em><em> | </em><em>'take_max_species'</em><em> | </em><em>'error'</em>) – What to do when encountering a disordered structure. ‘error’ will raise ValueError.
‘take_majority_strict’ will use the majority specie on each site and raise
ValueError if no majority exists. ‘take_max_species’ will use the first max specie
on each site. For {{Fe: 0.4, O: 0.4, C: 0.2}}, ‘error’ and ‘take_majority_strict’
will raise ValueError, while ‘take_majority_drop’ ignores this site altogether and
‘take_max_species’ will use Fe as the site specie.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>coordination number.</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>float</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.local_env.CrystalNN.get_cn_dict">
<span class="sig-name descname"><span class="pre">get_cn_dict</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">structure</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><span class="pre">Structure</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">n</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_weights</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/local_env.py#L4112-L4129"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.local_env.CrystalNN.get_cn_dict" title="Link to this definition"></a></dt>
<dd><p>Get coordination number, CN, of each element bonded to site with index n in structure.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>structure</strong> (<a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><em>Structure</em></a>) – input structure</p></li>
<li><p><strong>n</strong> (<em>int</em>) – index of site for which to determine CN.</p></li>
<li><p><strong>use_weights</strong> (<em>bool</em>) – flag indicating whether (True)
to use weights for computing the coordination number
or not (False, default: each coordinated site has equal
weight).</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>coordination number and list of coordinated sites</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>dict[int, list[dict]]</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.local_env.CrystalNN.get_nn_data">
<span class="sig-name descname"><span class="pre">get_nn_data</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">structure</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><span class="pre">Structure</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">n</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">length</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/local_env.py#L3953-L4083"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.local_env.CrystalNN.get_nn_data" title="Link to this definition"></a></dt>
<dd><p>The main logic of the method to compute near neighbor.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>structure</strong> – (Structure) enclosing structure object</p></li>
<li><p><strong>n</strong> – (int) index of target site to get NN info for</p></li>
<li><p><strong>length</strong> – (int) if set, will return a fixed range of CN numbers</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p><ul class="simple">
<li><p>all near neighbor sites with weights</p></li>
<li><p>a dict of CN -> weight</p></li>
<li><p>a dict of CN -> associated near neighbor sites</p></li>
</ul>
</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>a namedtuple (<a class="reference internal" href="#pymatgen.analysis.local_env.CrystalNN.NNData" title="pymatgen.analysis.local_env.CrystalNN.NNData">NNData</a>) object that contains</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.local_env.CrystalNN.get_nn_info">
<span class="sig-name descname"><span class="pre">get_nn_info</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">structure</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><span class="pre">Structure</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">n</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">dict</span><span class="p"><span class="pre">]</span></span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/local_env.py#L3918-L3951"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.local_env.CrystalNN.get_nn_info" title="Link to this definition"></a></dt>
<dd><p>Get all near-neighbor information.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>structure</strong> – (Structure) pymatgen Structure</p></li>
<li><p><strong>n</strong> – (int) index of target site</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p><dl class="simple">
<dt>each dictionary provides information</dt><dd><p>about a single near neighbor, where key ‘site’ gives access to the
corresponding Site object, ‘image’ gives the image location, and
‘weight’ provides the weight that a given near-neighbor site contributes
to the coordination number (1 or smaller), ‘site_index’ gives index of
the corresponding site in the original structure.</p>
</dd>
</dl>
</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>siw (list[dict])</p>
</dd>
</dl>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.analysis.local_env.CrystalNN.molecules_allowed">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">molecules_allowed</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">bool</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/local_env.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.local_env.CrystalNN.molecules_allowed" title="Link to this definition"></a></dt>
<dd><p>can this NearNeighbors class be used with Molecule
objects?</p>
<dl class="field-list simple">
<dt class="field-odd">Type<span class="colon">:</span></dt>
<dd class="field-odd"><p>Boolean property</p>
</dd>
</dl>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.analysis.local_env.CrystalNN.structures_allowed">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">structures_allowed</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">bool</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/local_env.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.local_env.CrystalNN.structures_allowed" title="Link to this definition"></a></dt>
<dd><p>can this NearNeighbors class be used with Structure
objects?</p>
<dl class="field-list simple">
<dt class="field-odd">Type<span class="colon">:</span></dt>
<dd class="field-odd"><p>Boolean property</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.local_env.CrystalNN.transform_to_length">
<em class="property"><span class="pre">static</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">transform_to_length</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">nn_data</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">length</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/local_env.py#L4160-L4178"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.local_env.CrystalNN.transform_to_length" title="Link to this definition"></a></dt>
<dd><p>Given NNData, transforms data to the specified fingerprint length.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>nn_data</strong> – (NNData)</p></li>
<li><p><strong>length</strong> – (int) desired length of NNData.</p></li>
</ul>
</dd>
</dl>
</dd></dl>
</dd></dl>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.analysis.local_env.CutOffDictNN">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">CutOffDictNN</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cut_off_dict</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">dict</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/local_env.py#L4241-L4348"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.local_env.CutOffDictNN" title="Link to this definition"></a></dt>
<dd><p>Bases: <a class="reference internal" href="#pymatgen.analysis.local_env.NearNeighbors" title="pymatgen.analysis.local_env.NearNeighbors"><code class="xref py py-class docutils literal notranslate"><span class="pre">NearNeighbors</span></code></a></p>
<p>A basic NN class using a dictionary of fixed cut-off distances.
Only pairs of elements listed in the cut-off dictionary are considered
during construction of the neighbor lists.</p>
<p>Omit passing a dictionary for a Null/Empty NN class.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>cut_off_dict</strong> (<em>dict</em><em>[</em><em>str</em><em>, </em><em>float</em><em>]</em>) – a dictionary</p></li>
<li><p><strong>distances</strong> (<em>of cut-off</em>) – 2.0} for</p></li>
<li><p><strong>{</strong> (<em>e.g.</em>) – 2.0} for</p></li>
<li><p><strong>Angstroms.</strong> (<em>a maximum Fe-O bond length</em><em> of </em><em>2</em>)</p></li>
<li><p><strong>listed</strong> (<em>Bonds will only be created between pairs</em>)</p></li>
<li><p><strong>dictionary.</strong> (<em>in the cut-off</em>)</p></li>
<li><p><strong>decorated</strong> (<em>If your structure is oxidation state</em>)</p></li>
</ul>
</dd>
</dl>
<p>:param :
:param the cut-off distances will have to explicitly include:
:param the oxidation state: 2.0}.
:type the oxidation state: ‘Fe2+’, ‘O2-’
:param e.g. {: 2.0}.
:type e.g. {: ‘Fe2+’, ‘O2-’</p>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.analysis.local_env.CutOffDictNN.extend_structure_molecules">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">extend_structure_molecules</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">bool</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/local_env.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.local_env.CutOffDictNN.extend_structure_molecules" title="Link to this definition"></a></dt>
<dd><p>Do Molecules need to be converted to Structures to use
this NearNeighbors class? Note: this property is not defined for classes
for which molecules_allowed is False.</p>
<dl class="field-list simple">
<dt class="field-odd">Type<span class="colon">:</span></dt>
<dd class="field-odd"><p>Boolean property</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.local_env.CutOffDictNN.from_preset">
<em class="property"><span class="pre">classmethod</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">from_preset</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">preset</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">Self</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/local_env.py#L4298-L4314"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.local_env.CutOffDictNN.from_preset" title="Link to this definition"></a></dt>
<dd><p>Initialize a CutOffDictNN according to a preset set of cutoffs.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>preset</strong> (<em>str</em>) – A preset name. The list of supported presets are:
- “vesta_2019”: The distance cutoffs used by the VESTA visualisation program.</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>A CutOffDictNN using the preset cut-off dictionary.</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.local_env.CutOffDictNN.get_nn_info">
<span class="sig-name descname"><span class="pre">get_nn_info</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">structure</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><span class="pre">Structure</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">n</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">dict</span><span class="p"><span class="pre">]</span></span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/local_env.py#L4316-L4348"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.local_env.CutOffDictNN.get_nn_info" title="Link to this definition"></a></dt>
<dd><p>Get all near-neighbor sites as well as the associated image locations
and weights of the site with index n in structure.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>structure</strong> (<a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><em>Structure</em></a>) – input structure.</p></li>
<li><p><strong>n</strong> (<em>int</em>) – index of site for which to determine near-neighbor sites.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p><dl class="simple">
<dt>tuples, each one of which</dt><dd><p>represents a coordinated site, its image location, and its weight.</p>
</dd>
</dl>
</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>siw (list of tuples (<a class="reference internal" href="pymatgen.core.html#pymatgen.core.sites.Site" title="pymatgen.core.sites.Site">Site</a>, array, float))</p>
</dd>
</dl>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.analysis.local_env.CutOffDictNN.molecules_allowed">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">molecules_allowed</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">bool</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/local_env.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.local_env.CutOffDictNN.molecules_allowed" title="Link to this definition"></a></dt>
<dd><p>can this NearNeighbors class be used with Molecule
objects?</p>
<dl class="field-list simple">
<dt class="field-odd">Type<span class="colon">:</span></dt>
<dd class="field-odd"><p>Boolean property</p>
</dd>
</dl>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.analysis.local_env.CutOffDictNN.structures_allowed">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">structures_allowed</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">bool</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/local_env.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.local_env.CutOffDictNN.structures_allowed" title="Link to this definition"></a></dt>
<dd><p>can this NearNeighbors class be used with Structure
objects?</p>
<dl class="field-list simple">
<dt class="field-odd">Type<span class="colon">:</span></dt>
<dd class="field-odd"><p>Boolean property</p>
</dd>
</dl>
</dd></dl>
</dd></dl>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.analysis.local_env.EconNN">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">EconNN</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">tol</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">float</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">0.2</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">cutoff</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">float</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">10.0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">cation_anion</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_fictive_radius</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/local_env.py#L3663-L3775"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.local_env.EconNN" title="Link to this definition"></a></dt>
<dd><p>Bases: <a class="reference internal" href="#pymatgen.analysis.local_env.NearNeighbors" title="pymatgen.analysis.local_env.NearNeighbors"><code class="xref py py-class docutils literal notranslate"><span class="pre">NearNeighbors</span></code></a></p>
<p>Determines the average effective coordination number for each cation in a
given structure using Hoppe’s algorithm.</p>
<p>This method follows the procedure outlined in:</p>
<p>Hoppe, Rudolf. “Effective coordination numbers (ECoN) and mean fictive ionic
radii (MEFIR).” Zeitschrift für Kristallographie-Crystalline Materials
150.1-4 (1979): 23-52.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>tol</strong> – Tolerance parameter for bond determination.</p></li>
<li><p><strong>cutoff</strong> – Cutoff radius in Angstrom to look for near-neighbor atoms.</p></li>
<li><p><strong>cation_anion</strong> – If set to True, will restrict bonding targets to
sites with opposite or zero charge. Requires an oxidation states
on all sites in the structure.</p></li>
<li><p><strong>use_fictive_radius</strong> – Whether to use the fictive radius in the
EcoN calculation. If False, the bond distance will be used.</p></li>
</ul>
</dd>
</dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.analysis.local_env.EconNN.extend_structure_molecules">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">extend_structure_molecules</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">bool</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/local_env.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.local_env.EconNN.extend_structure_molecules" title="Link to this definition"></a></dt>
<dd><p>Do Molecules need to be converted to Structures to use
this NearNeighbors class? Note: this property is not defined for classes
for which molecules_allowed is False.</p>
<dl class="field-list simple">
<dt class="field-odd">Type<span class="colon">:</span></dt>
<dd class="field-odd"><p>Boolean property</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.local_env.EconNN.get_nn_info">
<span class="sig-name descname"><span class="pre">get_nn_info</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">structure</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><span class="pre">Structure</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">n</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/local_env.py#L3722-L3775"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.local_env.EconNN.get_nn_info" title="Link to this definition"></a></dt>
<dd><p>Get all near-neighbor sites as well as the associated image locations
and weights of the site with index n in structure.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>structure</strong> (<a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><em>Structure</em></a>) – input structure.</p></li>
<li><p><strong>n</strong> (<em>int</em>) – index of site for which to determine near-neighbor sites.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p><dl class="simple">
<dt>tuples, each one</dt><dd><p>of which represents a coordinated site, its image location,
and its weight.</p>
</dd>
</dl>
</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>siw (list of tuples (<a class="reference internal" href="pymatgen.core.html#pymatgen.core.sites.Site" title="pymatgen.core.sites.Site">Site</a>, array, float))</p>
</dd>
</dl>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.analysis.local_env.EconNN.molecules_allowed">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">molecules_allowed</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">bool</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/local_env.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.local_env.EconNN.molecules_allowed" title="Link to this definition"></a></dt>
<dd><p>can this NearNeighbors class be used with Molecule
objects?</p>
<dl class="field-list simple">
<dt class="field-odd">Type<span class="colon">:</span></dt>
<dd class="field-odd"><p>Boolean property</p>
</dd>
</dl>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.analysis.local_env.EconNN.structures_allowed">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">structures_allowed</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">bool</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/local_env.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.local_env.EconNN.structures_allowed" title="Link to this definition"></a></dt>
<dd><p>can this NearNeighbors class be used with Structure
objects?</p>
<dl class="field-list simple">
<dt class="field-odd">Type<span class="colon">:</span></dt>
<dd class="field-odd"><p>Boolean property</p>
</dd>
</dl>
</dd></dl>
</dd></dl>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.analysis.local_env.IsayevNN">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">IsayevNN</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">tol</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">float</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">0.25</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">targets</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="pymatgen.core.html#pymatgen.core.periodic_table.Element" title="pymatgen.core.periodic_table.Element"><span class="pre">Element</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">list</span><span class="p"><span class="pre">[</span></span><a class="reference internal" href="pymatgen.core.html#pymatgen.core.periodic_table.Element" title="pymatgen.core.periodic_table.Element"><span class="pre">Element</span></a><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">cutoff</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">float</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">13.0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">allow_pathological</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">extra_nn_info</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">compute_adj_neighbors</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/local_env.py#L1066-L1176"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.local_env.IsayevNN" title="Link to this definition"></a></dt>
<dd><p>Bases: <a class="reference internal" href="#pymatgen.analysis.local_env.VoronoiNN" title="pymatgen.analysis.local_env.VoronoiNN"><code class="xref py py-class docutils literal notranslate"><span class="pre">VoronoiNN</span></code></a></p>
<p>Uses the algorithm defined in 10.1038/ncomms15679.</p>
<p>Sites are considered neighbors if (i) they share a Voronoi facet and (ii) the
bond distance is less than the sum of the Cordero covalent radii + 0.25 Å.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>tol</strong> – Tolerance in Å for bond distances that are considered coordinated.</p></li>
<li><p><strong>targets</strong> – Target element(s).</p></li>
<li><p><strong>cutoff</strong> – Cutoff radius in Angstrom to look for near-neighbor atoms.</p></li>
<li><p><strong>allow_pathological</strong> – Whether to allow infinite vertices in Voronoi
coordination.</p></li>
<li><p><strong>extra_nn_info</strong> – Add all polyhedron info to <cite>get_nn_info</cite>.</p></li>
<li><p><strong>compute_adj_neighbors</strong> – Whether to compute which neighbors are adjacent. Turn
off for faster performance.</p></li>
</ul>
</dd>
</dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.local_env.IsayevNN.get_all_nn_info">
<span class="sig-name descname"><span class="pre">get_all_nn_info</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">structure</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><span class="pre">Structure</span></a></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">Any</span><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">]</span></span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/local_env.py#L1125-L1135"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.local_env.IsayevNN.get_all_nn_info" title="Link to this definition"></a></dt>
<dd><dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>structure</strong> (<a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><em>Structure</em></a>) – input structure.</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>List of near neighbor information for each site. See get_nn_info for the
format of the data for each site.</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.local_env.IsayevNN.get_nn_info">
<span class="sig-name descname"><span class="pre">get_nn_info</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">structure</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><span class="pre">Structure</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">n</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">Any</span><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">]</span></span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/local_env.py#L1102-L1123"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.local_env.IsayevNN.get_nn_info" title="Link to this definition"></a></dt>
<dd><p>Get all near-neighbor site information.</p>
<p>Gets the associated image locations and weights of the site with index n
in structure using Voronoi decomposition and distance cutoff.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>structure</strong> – Input structure.</p></li>
<li><p><strong>n</strong> – Index of site for which to determine near-neighbor sites.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p><p>List of dicts containing the near-neighbor information. Each dict has the
keys:</p>
<ul class="simple">
<li><p>”site”: The near-neighbor site.</p></li>
<li><p>”image”: The periodic image of the near-neighbor site.</p></li>
<li><p>”weight”: The face weight of the Voronoi decomposition.</p></li>
<li><p>”site_index”: The index of the near-neighbor site in the original
structure.</p></li>
</ul>
</p>
</dd>
</dl>
</dd></dl>
</dd></dl>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.analysis.local_env.JmolNN">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">JmolNN</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">tol</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">float</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">0.45</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">min_bond_distance</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">float</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">0.4</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">el_radius_updates</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><span class="pre">SpeciesLike</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">float</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/local_env.py#L1211-L1323"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.local_env.JmolNN" title="Link to this definition"></a></dt>
<dd><p>Bases: <a class="reference internal" href="#pymatgen.analysis.local_env.NearNeighbors" title="pymatgen.analysis.local_env.NearNeighbors"><code class="xref py py-class docutils literal notranslate"><span class="pre">NearNeighbors</span></code></a></p>
<p>Determine near-neighbor sites and coordination number using an emulation
of Jmol’s default autoBond() algorithm. This version of the algorithm
does not take into account any information regarding known charge
states.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>tol</strong> (<em>float</em>) – tolerance parameter for bond determination
Defaults to 0.56.</p></li>
<li><p><strong>min_bond_distance</strong> (<em>float</em>) – minimum bond distance for consideration
Defaults to 0.4.</p></li>
<li><p><strong>el_radius_updates</strong> (<em>dict</em>) – symbol->float to override default atomic
radii table values.</p></li>
</ul>
</dd>
</dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.analysis.local_env.JmolNN.extend_structure_molecules">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">extend_structure_molecules</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">bool</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/local_env.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.local_env.JmolNN.extend_structure_molecules" title="Link to this definition"></a></dt>
<dd><p>Do Molecules need to be converted to Structures to use
this NearNeighbors class? Note: this property is not defined for classes
for which molecules_allowed is False.</p>
<dl class="field-list simple">
<dt class="field-odd">Type<span class="colon">:</span></dt>
<dd class="field-odd"><p>Boolean property</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.local_env.JmolNN.get_max_bond_distance">
<span class="sig-name descname"><span class="pre">get_max_bond_distance</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">el1_sym</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">el2_sym</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/local_env.py#L1270-L1281"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.local_env.JmolNN.get_max_bond_distance" title="Link to this definition"></a></dt>
<dd><p>Use Jmol algorithm to determine bond length from atomic parameters.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>el1_sym</strong> (<em>str</em>) – symbol of atom 1</p></li>
<li><p><strong>el2_sym</strong> (<em>str</em>) – symbol of atom 2.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>max bond length</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>float</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.local_env.JmolNN.get_nn_info">
<span class="sig-name descname"><span class="pre">get_nn_info</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">structure</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><span class="pre">Structure</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">n</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/local_env.py#L1283-L1323"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.local_env.JmolNN.get_nn_info" title="Link to this definition"></a></dt>
<dd><p>Get all near-neighbor sites as well as the associated image locations
and weights of the site with index n using the bond identification
algorithm underlying Jmol.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>structure</strong> (<a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><em>Structure</em></a>) – input structure.</p></li>
<li><p><strong>n</strong> (<em>int</em>) – index of site for which to determine near
neighbors.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p><dl class="simple">
<dt>tuples, each one</dt><dd><p>of which represents a neighbor site, its image location,
and its weight.</p>
</dd>
</dl>
</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>siw (list of tuples (<a class="reference internal" href="pymatgen.core.html#pymatgen.core.sites.Site" title="pymatgen.core.sites.Site">Site</a>, array, float))</p>
</dd>
</dl>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.analysis.local_env.JmolNN.molecules_allowed">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">molecules_allowed</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">bool</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/local_env.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.local_env.JmolNN.molecules_allowed" title="Link to this definition"></a></dt>
<dd><p>can this NearNeighbors class be used with Molecule
objects?</p>
<dl class="field-list simple">
<dt class="field-odd">Type<span class="colon">:</span></dt>
<dd class="field-odd"><p>Boolean property</p>
</dd>
</dl>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.analysis.local_env.JmolNN.structures_allowed">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">structures_allowed</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">bool</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/local_env.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.local_env.JmolNN.structures_allowed" title="Link to this definition"></a></dt>
<dd><p>can this NearNeighbors class be used with Structure
objects?</p>
<dl class="field-list simple">
<dt class="field-odd">Type<span class="colon">:</span></dt>
<dd class="field-odd"><p>Boolean property</p>
</dd>
</dl>
</dd></dl>
</dd></dl>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.analysis.local_env.LocalStructOrderParams">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">LocalStructOrderParams</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">types</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="n"><span class="pre">parameters</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">float</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">cutoff</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">float</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">-10.0</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/local_env.py#L2165-L3433"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.local_env.LocalStructOrderParams" title="Link to this definition"></a></dt>
<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></p>
<p>This class permits the calculation of various types of local
structure order parameters.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>types</strong> (<em>list</em><em>[</em><em>str</em><em>]</em>) – <p>the types of order parameters to be calculated.
Note that multiple mentions of the same type may occur.
Currently available types recognize following environments:</p>
<blockquote>
<div><dl class="simple">
<dt>”cn”: simple coordination number—normalized</dt><dd><p>if desired;</p>
</dd>
</dl>
<p>”sgl_bd”: single bonds;
“bent”: bent (angular) coordinations</p>
<blockquote>
<div><p>(Zimmermann & Jain, in progress, 2017);</p>
</div></blockquote>
<p>”T”: T-shape coordinations;
“see_saw_rect”: see saw-like coordinations;
“tet”: tetrahedra</p>
<blockquote>
<div><p>(Zimmermann et al., submitted, 2017);</p>
</div></blockquote>
<dl class="simple">
<dt>”oct”: octahedra</dt><dd><p>(Zimmermann et al., submitted, 2017);</p>
</dd>
<dt>”bcc”: body-centered cubic environments (Peters,</dt><dd><ol class="upperalpha simple" start="10">
<li><p>Chem. Phys., 131, 244103, 2009);</p></li>
</ol>
</dd>
</dl>
<p>”tri_plan”: trigonal planar environments;
“sq_plan”: square planar environments;
“pent_plan”: pentagonal planar environments;
“tri_pyr”: trigonal pyramids (coordinated atom is in</p>
<blockquote>
<div><p>the center of the basal plane);</p>
</div></blockquote>
<p>”sq_pyr”: square pyramids;
“pent_pyr”: pentagonal pyramids;
“hex_pyr”: hexagonal pyramids;
“tri_bipyr”: trigonal bipyramids;
“sq_bipyr”: square bipyramids;
“pent_bipyr”: pentagonal bipyramids;
“hex_bipyr”: hexagonal bipyramids;
“cuboct”: cuboctahedra;
“q2”: motif-unspecific bond orientational order</p>
<blockquote>
<div><p>parameter (BOOP) of weight l=2 (Steinhardt
et al., Phys. Rev. B, 28, 784-805, 1983);</p>
</div></blockquote>
<p>”q4”: BOOP of weight l=4;
“q6”: BOOP of weight l=6.
“reg_tri”: regular triangle with varying height</p>
<blockquote>
<div><p>to basal plane;</p>
</div></blockquote>
<p>”sq”: square coordination (cf., “reg_tri”);
“oct_legacy”: original Peters-style OP recognizing</p>
<blockquote>
<div><p>octahedral coordination environments
(Zimmermann et al., J. Am. Chem. Soc.,
137, 13352-13361, 2015) that can, however,
produce small negative values sometimes.</p>
</div></blockquote>
<p>”sq_pyr_legacy”: square pyramids (legacy);</p>
</div></blockquote>
</p></li>
<li><p><strong>parameters</strong> (<em>list</em><em>[</em><em>dict</em><em>]</em>) – <p>float-type parameters associated with the
definitions of the different order parameters
(length of list = number of OPs). If an entry
is None, default values are used that are read from
the op_params.yaml file. With few exceptions, 9 different
parameters are used across all OPs:</p>
<blockquote>
<div><dl class="simple">
<dt>”norm”: normalizing constant (used in “cn”</dt><dd><p>(default value: 1)).</p>
</dd>
<dt>”TA”: target angle (TA) in fraction of 180 degrees</dt><dd><p>(“bent” (1), “tet” (0.6081734479693927),
“tri_plan” (0.66666666667), “pent_plan” (0.6),
“sq_pyr_legacy” (0.5)).</p>
</dd>
<dt>”IGW_TA”: inverse Gaussian width (IGW) for penalizing</dt><dd><p>angles away from the target angle in inverse
fractions of 180 degrees to (“bent” and “tet” (15),
“tri_plan” (13.5), “pent_plan” (18),
“sq_pyr_legacy” (30)).</p>
</dd>
<dt>”IGW_EP”: IGW for penalizing angles away from the</dt><dd><p>equatorial plane (EP) at 90 degrees (“T”, “see_saw_rect”,
“oct”, “sq_plan”, “tri_pyr”, “sq_pyr”, “pent_pyr”,
“hex_pyr”, “tri_bipyr”, “sq_bipyr”, “pent_bipyr”,
“hex_bipyr”, and “oct_legacy” (18)).</p>
</dd>
<dt>”fac_AA”: factor applied to azimuth angle (AA) in cosine</dt><dd><p>term (“T”, “tri_plan”, and “sq_plan” (1), “tet”,
“tri_pyr”, and “tri_bipyr” (1.5), “oct”, “sq_pyr”,
“sq_bipyr”, and “oct_legacy” (2), “pent_pyr”
and “pent_bipyr” (2.5), “hex_pyr” and
“hex_bipyr” (3)).</p>
</dd>
<dt>”exp_cos_AA”: exponent applied to cosine term of AA</dt><dd><p>(“T”, “tet”, “oct”, “tri_plan”, “sq_plan”,
“tri_pyr”, “sq_pyr”, “pent_pyr”, “hex_pyr”,
“tri_bipyr”, “sq_bipyr”, “pent_bipyr”, “hex_bipyr”,
and “oct_legacy” (2)).</p>
</dd>
<dt>”min_SPP”: smallest angle (in radians) to consider</dt><dd><p>a neighbor to be
at South pole position (“see_saw_rect”, “oct”, “bcc”,
“sq_plan”, “tri_bipyr”, “sq_bipyr”, “pent_bipyr”,
“hex_bipyr”, “cuboct”, and “oct_legacy”
(2.792526803190927)).</p>
</dd>
<dt>”IGW_SPP”: IGW for penalizing angles away from South</dt><dd><p>pole position (“see_saw_rect”, “oct”, “bcc”, “sq_plan”,
“tri_bipyr”, “sq_bipyr”, “pent_bipyr”, “hex_bipyr”,
“cuboct”, and “oct_legacy” (15)).</p>
</dd>
<dt>”w_SPP”: weight for South pole position relative to</dt><dd><p>equatorial positions (“see_saw_rect” and “sq_plan” (1),
“cuboct” (1.8), “tri_bipyr” (2), “oct”,
“sq_bipyr”, and “oct_legacy” (3), “pent_bipyr” (4),
“hex_bipyr” (5), “bcc” (6)).</p>
</dd>
</dl>
</div></blockquote>
</p></li>
<li><p><strong>cutoff</strong> (<em>float</em>) – Cutoff radius to determine which nearest
neighbors are supposed to contribute to the order
parameters. If the value is negative the neighboring
sites found by distance and cutoff radius are further
pruned using the get_nn method from the
VoronoiNN class.</p></li>
</ul>
</dd>
</dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.local_env.LocalStructOrderParams.compute_trigonometric_terms">
<span class="sig-name descname"><span class="pre">compute_trigonometric_terms</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">thetas</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">phis</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/local_env.py#L2415-L2449"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.local_env.LocalStructOrderParams.compute_trigonometric_terms" title="Link to this definition"></a></dt>
<dd><p>Compute trigonometric terms that are required to calculate
bond orientational order parameters using internal variables.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>thetas</strong> (<em>[</em><em>float</em><em>]</em>) – polar angles of all neighbors in radians.</p></li>
<li><p><strong>phis</strong> (<em>[</em><em>float</em><em>]</em>) – azimuth angles of all neighbors in radians.
The list of
azimuth angles of all neighbors in radians. The list of
azimuth angles is expected to have the same size as the
list of polar angles; otherwise, a ValueError is raised.
Also, the two lists of angles have to be coherent in
order. That is, it is expected that the order in the list
of azimuth angles corresponds to a distinct sequence of
neighbors. And, this sequence has to equal the sequence
of neighbors in the list of polar angles.</p></li>
</ul>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.local_env.LocalStructOrderParams.get_order_parameters">
<span class="sig-name descname"><span class="pre">get_order_parameters</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">structure</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><span class="pre">Structure</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">n</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">indices_neighs</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">int</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">tol</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">float</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">0.0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">target_spec</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="pymatgen.core.html#pymatgen.core.periodic_table.Species" title="pymatgen.core.periodic_table.Species"><span class="pre">Species</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/local_env.py#L2830-L3433"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.local_env.LocalStructOrderParams.get_order_parameters" title="Link to this definition"></a></dt>
<dd><p>Compute all order parameters of site n.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>structure</strong> (<a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><em>Structure</em></a>) – input structure.</p></li>
<li><p><strong>n</strong> (<em>int</em>) – index of site in input structure,
for which OPs are to be
calculated. Note that we do not use the sites iterator
here, but directly access sites via struct[index].</p></li>
<li><p><strong>indices_neighs</strong> (<em>list</em><em>[</em><em>int</em><em>]</em>) – list of indices of those neighbors
in Structure object
structure that are to be considered for OP computation.
This optional argument overwrites the way neighbors are
to be determined as defined in the constructor (i.e.,
Voronoi coordination finder via negative cutoff radius
vs constant cutoff radius if cutoff was positive).
We do not use information about the underlying
structure lattice if the neighbor indices are explicitly
provided. This has two important consequences. First,
the input Structure object can, in fact, be a
simple list of Site objects. Second, no nearest images
of neighbors are determined when providing an index list.
Note furthermore that this neighbor
determination type ignores the optional target_spec
argument.</p></li>
<li><p><strong>tol</strong> (<em>float</em>) – threshold of weight
(= solid angle / maximal solid angle)
to determine if a particular pair is
considered neighbors; this is relevant only in the case
when Voronoi polyhedra are used to determine coordination</p></li>
<li><p><strong>target_spec</strong> (<a class="reference internal" href="pymatgen.core.html#pymatgen.core.periodic_table.Species" title="pymatgen.core.periodic_table.Species"><em>Species</em></a>) – target species to be considered
when calculating the order
parameters of site n; None includes all species of input
structure.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>representing order parameters. Should it not be
possible to compute a given OP for a conceptual reason, the
corresponding entry is None instead of a float. For Steinhardt
et al.’s bond orientational OPs and the other geometric OPs
(“tet”, “oct”, “bcc”, etc.),
this can happen if there is a single
neighbor around site n in the structure because that
does not permit calculation of angles between multiple
neighbors.</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>[floats]</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.local_env.LocalStructOrderParams.get_parameters">
<span class="sig-name descname"><span class="pre">get_parameters</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">index</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">int</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">float</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/local_env.py#L2813-L2828"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.local_env.LocalStructOrderParams.get_parameters" title="Link to this definition"></a></dt>
<dd><p>Get parameters associated with calculation of the order
parameter that was defined at the index provided.</p>
<p>Attention: the parameters do not need to equal those originally
inputted because of processing out of efficiency reasons.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>index</strong> (<em>int</em>) – index of order parameter for which to return associated params.</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>parameters of a given OP.</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>dict[str, float]</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.local_env.LocalStructOrderParams.get_q2">
<span class="sig-name descname"><span class="pre">get_q2</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">thetas</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">phis</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/local_env.py#L2451-L2516"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.local_env.LocalStructOrderParams.get_q2" title="Link to this definition"></a></dt>
<dd><p>Calculates the value of the bond orientational order parameter of
weight l=2. If the function is called with non-empty lists of
polar and azimuthal angles the corresponding trigonometric terms
are computed afresh. Otherwise, it is expected that the
compute_trigonometric_terms function has been just called.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>thetas</strong> (<em>[</em><em>float</em><em>]</em>) – polar angles of all neighbors in radians.</p></li>
<li><p><strong>phis</strong> (<em>[</em><em>float</em><em>]</em>) – azimuth angles of all neighbors in radians.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p><dl class="simple">
<dt>bond orientational order parameter of weight l=2</dt><dd><p>corresponding to the input angles thetas and phis.</p>
</dd>
</dl>
</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>float</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.local_env.LocalStructOrderParams.get_q4">
<span class="sig-name descname"><span class="pre">get_q4</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">thetas</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">phis</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/local_env.py#L2518-L2625"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.local_env.LocalStructOrderParams.get_q4" title="Link to this definition"></a></dt>
<dd><p>Calculates the value of the bond orientational order parameter of
weight l=4. If the function is called with non-empty lists of
polar and azimuthal angles the corresponding trigonometric terms
are computed afresh. Otherwise, it is expected that the
compute_trigonometric_terms function has been just called.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>thetas</strong> (<em>[</em><em>float</em><em>]</em>) – polar angles of all neighbors in radians.</p></li>
<li><p><strong>phis</strong> (<em>[</em><em>float</em><em>]</em>) – azimuth angles of all neighbors in radians.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p><dl class="simple">
<dt>bond orientational order parameter of weight l=4</dt><dd><p>corresponding to the input angles thetas and phis.</p>
</dd>
</dl>
</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>float</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.local_env.LocalStructOrderParams.get_q6">
<span class="sig-name descname"><span class="pre">get_q6</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">thetas</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">phis</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/local_env.py#L2627-L2796"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.local_env.LocalStructOrderParams.get_q6" title="Link to this definition"></a></dt>
<dd><p>Calculates the value of the bond orientational order parameter of
weight l=6. If the function is called with non-empty lists of
polar and azimuthal angles the corresponding trigonometric terms
are computed afresh. Otherwise, it is expected that the
compute_trigonometric_terms function has been just called.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>thetas</strong> (<em>[</em><em>float</em><em>]</em>) – polar angles of all neighbors in radians.</p></li>
<li><p><strong>phis</strong> (<em>[</em><em>float</em><em>]</em>) – azimuth angles of all neighbors in radians.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p><dl class="simple">
<dt>bond orientational order parameter of weight l=6</dt><dd><p>corresponding to the input angles thetas and phis.</p>
</dd>
</dl>
</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>float</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.local_env.LocalStructOrderParams.get_type">
<span class="sig-name descname"><span class="pre">get_type</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">index</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/local_env.py#L2798-L2811"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.local_env.LocalStructOrderParams.get_type" title="Link to this definition"></a></dt>
<dd><p>Get type of order parameter at the index provided and
represented by a short string.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>index</strong> (<em>int</em>) – index of order parameter for which type is
to be returned.</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>OP type.</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>str</p>
</dd>
</dl>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.analysis.local_env.LocalStructOrderParams.last_nneigh">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">last_nneigh</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/local_env.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.local_env.LocalStructOrderParams.last_nneigh" title="Link to this definition"></a></dt>
<dd><p>Number of neighbors encountered during the most recent order parameter calculation.
A value of -1 indicates that no such calculation has yet been performed for this instance.</p>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.analysis.local_env.LocalStructOrderParams.num_ops">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">num_ops</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">int</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/local_env.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.local_env.LocalStructOrderParams.num_ops" title="Link to this definition"></a></dt>
<dd><p>Number of different order parameters that are targeted to be calculated.</p>
</dd></dl>
</dd></dl>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.analysis.local_env.MinimumDistanceNN">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">MinimumDistanceNN</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">tol</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">float</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">0.1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">cutoff</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">10</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">get_all_sites</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/local_env.py#L1326-L1416"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.local_env.MinimumDistanceNN" title="Link to this definition"></a></dt>
<dd><p>Bases: <a class="reference internal" href="#pymatgen.analysis.local_env.NearNeighbors" title="pymatgen.analysis.local_env.NearNeighbors"><code class="xref py py-class docutils literal notranslate"><span class="pre">NearNeighbors</span></code></a></p>
<p>Determine near-neighbor sites and coordination number using the
nearest neighbor(s) at distance, d_min, plus all neighbors
within a distance (1 + tol) * d_min, where tol is a
(relative) distance tolerance parameter.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>tol</strong> (<em>float</em>) – tolerance parameter for neighbor identification
(default: 0.1).</p></li>
<li><p><strong>cutoff</strong> (<em>float</em>) – cutoff radius in Angstrom to look for trial
near-neighbor sites (default: 10).</p></li>
<li><p><strong>get_all_sites</strong> (<em>bool</em>) – If this is set to True then the neighbor
sites are only determined by the cutoff radius, tol is ignored.</p></li>
</ul>
</dd>
</dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.analysis.local_env.MinimumDistanceNN.extend_structure_molecules">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">extend_structure_molecules</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">bool</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/local_env.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.local_env.MinimumDistanceNN.extend_structure_molecules" title="Link to this definition"></a></dt>
<dd><p>Do Molecules need to be converted to Structures to use
this NearNeighbors class? Note: this property is not defined for classes
for which molecules_allowed is False.</p>
<dl class="field-list simple">
<dt class="field-odd">Type<span class="colon">:</span></dt>
<dd class="field-odd"><p>Boolean property</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.local_env.MinimumDistanceNN.get_nn_info">
<span class="sig-name descname"><span class="pre">get_nn_info</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">structure</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><span class="pre">Structure</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">n</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">Any</span><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">]</span></span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/local_env.py#L1373-L1416"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.local_env.MinimumDistanceNN.get_nn_info" title="Link to this definition"></a></dt>
<dd><p>Get all near-neighbor sites as well as the associated image locations
and weights of the site with index n using the closest neighbor
distance-based method.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>structure</strong> (<a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><em>Structure</em></a>) – input structure.</p></li>
<li><p><strong>n</strong> (<em>int</em>) – index of site for which to determine near
neighbors.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p><dl class="simple">
<dt>dicts with (Site, array, float) each one of which represents a</dt><dd><p>neighbor site, its image location, and its weight.</p>
</dd>
</dl>
</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>siw (list[dict])</p>
</dd>
</dl>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.analysis.local_env.MinimumDistanceNN.molecules_allowed">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">molecules_allowed</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">bool</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/local_env.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.local_env.MinimumDistanceNN.molecules_allowed" title="Link to this definition"></a></dt>
<dd><p>can this NearNeighbors class be used with Molecule
objects?</p>
<dl class="field-list simple">
<dt class="field-odd">Type<span class="colon">:</span></dt>
<dd class="field-odd"><p>Boolean property</p>
</dd>
</dl>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.analysis.local_env.MinimumDistanceNN.structures_allowed">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">structures_allowed</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">bool</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/local_env.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.local_env.MinimumDistanceNN.structures_allowed" title="Link to this definition"></a></dt>
<dd><p>can this NearNeighbors class be used with Structure
objects?</p>
<dl class="field-list simple">
<dt class="field-odd">Type<span class="colon">:</span></dt>
<dd class="field-odd"><p>Boolean property</p>
</dd>
</dl>
</dd></dl>
</dd></dl>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.analysis.local_env.MinimumOKeeffeNN">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">MinimumOKeeffeNN</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">tol</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">float</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">0.1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">cutoff</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">10</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/local_env.py#L1737-L1828"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.local_env.MinimumOKeeffeNN" title="Link to this definition"></a></dt>
<dd><p>Bases: <a class="reference internal" href="#pymatgen.analysis.local_env.NearNeighbors" title="pymatgen.analysis.local_env.NearNeighbors"><code class="xref py py-class docutils literal notranslate"><span class="pre">NearNeighbors</span></code></a></p>
<p>Determine near-neighbor sites and coordination number using the
neighbor(s) at closest relative distance, d_min_OKeffee, plus some
relative tolerance, where bond valence parameters from O’Keeffe’s
bond valence method (J. Am. Chem. Soc. 1991, 3226-3229) are used
to calculate relative distances.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>tol</strong> (<em>float</em>) – tolerance parameter for neighbor identification
(default: 0.1).</p></li>
<li><p><strong>cutoff</strong> (<em>float</em>) – cutoff radius in Angstrom to look for trial
near-neighbor sites (default: 10).</p></li>
</ul>
</dd>
</dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.analysis.local_env.MinimumOKeeffeNN.extend_structure_molecules">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">extend_structure_molecules</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">bool</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/local_env.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.local_env.MinimumOKeeffeNN.extend_structure_molecules" title="Link to this definition"></a></dt>
<dd><p>Do Molecules need to be converted to Structures to use
this NearNeighbors class? Note: this property is not defined for classes
for which molecules_allowed is False.</p>
<dl class="field-list simple">
<dt class="field-odd">Type<span class="colon">:</span></dt>
<dd class="field-odd"><p>Boolean property</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.local_env.MinimumOKeeffeNN.get_nn_info">
<span class="sig-name descname"><span class="pre">get_nn_info</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">structure</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><span class="pre">Structure</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">n</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/local_env.py#L1782-L1828"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.local_env.MinimumOKeeffeNN.get_nn_info" title="Link to this definition"></a></dt>
<dd><p>Get all near-neighbor sites as well as the associated image locations
and weights of the site with index n using the closest relative
neighbor distance-based method with O’Keeffe parameters.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>structure</strong> (<a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><em>Structure</em></a>) – input structure.</p></li>
<li><p><strong>n</strong> (<em>int</em>) – index of site for which to determine near
neighbors.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p><dl class="simple">
<dt>tuples, each one</dt><dd><p>of which represents a neighbor site, its image location,
and its weight.</p>
</dd>
</dl>
</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>siw (list of tuples (<a class="reference internal" href="pymatgen.core.html#pymatgen.core.sites.Site" title="pymatgen.core.sites.Site">Site</a>, array, float))</p>
</dd>
</dl>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.analysis.local_env.MinimumOKeeffeNN.molecules_allowed">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">molecules_allowed</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">bool</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/local_env.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.local_env.MinimumOKeeffeNN.molecules_allowed" title="Link to this definition"></a></dt>
<dd><p>can this NearNeighbors class be used with Molecule
objects?</p>
<dl class="field-list simple">
<dt class="field-odd">Type<span class="colon">:</span></dt>
<dd class="field-odd"><p>Boolean property</p>
</dd>
</dl>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.analysis.local_env.MinimumOKeeffeNN.structures_allowed">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">structures_allowed</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">bool</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/local_env.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.local_env.MinimumOKeeffeNN.structures_allowed" title="Link to this definition"></a></dt>
<dd><p>can this NearNeighbors class be used with Structure
objects?</p>
<dl class="field-list simple">
<dt class="field-odd">Type<span class="colon">:</span></dt>
<dd class="field-odd"><p>Boolean property</p>
</dd>
</dl>
</dd></dl>
</dd></dl>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.analysis.local_env.MinimumVIRENN">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">MinimumVIRENN</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">tol</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">float</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">0.1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">cutoff</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">10</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/local_env.py#L1831-L1905"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.local_env.MinimumVIRENN" title="Link to this definition"></a></dt>
<dd><p>Bases: <a class="reference internal" href="#pymatgen.analysis.local_env.NearNeighbors" title="pymatgen.analysis.local_env.NearNeighbors"><code class="xref py py-class docutils literal notranslate"><span class="pre">NearNeighbors</span></code></a></p>
<p>Determine near-neighbor sites and coordination number using the
neighbor(s) at closest relative distance, d_min_VIRE, plus some
relative tolerance, where atom radii from the
ValenceIonicRadiusEvaluator (VIRE) are used
to calculate relative distances.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>tol</strong> (<em>float</em>) – tolerance parameter for neighbor identification
(default: 0.1).</p></li>
<li><p><strong>cutoff</strong> (<em>float</em>) – cutoff radius in Angstrom to look for trial
near-neighbor sites (default: 10).</p></li>
</ul>
</dd>
</dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.local_env.MinimumVIRENN.get_nn_info">
<span class="sig-name descname"><span class="pre">get_nn_info</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">structure</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><span class="pre">Structure</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">n</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/local_env.py#L1867-L1905"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.local_env.MinimumVIRENN.get_nn_info" title="Link to this definition"></a></dt>
<dd><p>Get all near-neighbor sites as well as the associated image locations
and weights of the site with index n using the closest relative
neighbor distance-based method with VIRE atomic/ionic radii.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>structure</strong> (<a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><em>Structure</em></a>) – input structure.</p></li>
<li><p><strong>n</strong> (<em>int</em>) – index of site for which to determine near
neighbors.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p><dl class="simple">
<dt>tuples, each one</dt><dd><p>of which represents a neighbor site, its image location,
and its weight.</p>
</dd>
</dl>
</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>siw (list of tuples (<a class="reference internal" href="pymatgen.core.html#pymatgen.core.sites.Site" title="pymatgen.core.sites.Site">Site</a>, array, float))</p>
</dd>
</dl>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.analysis.local_env.MinimumVIRENN.molecules_allowed">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">molecules_allowed</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">bool</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/local_env.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.local_env.MinimumVIRENN.molecules_allowed" title="Link to this definition"></a></dt>
<dd><p>can this NearNeighbors class be used with Molecule
objects?</p>
<dl class="field-list simple">
<dt class="field-odd">Type<span class="colon">:</span></dt>
<dd class="field-odd"><p>Boolean property</p>
</dd>
</dl>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.analysis.local_env.MinimumVIRENN.structures_allowed">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">structures_allowed</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">bool</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/local_env.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.local_env.MinimumVIRENN.structures_allowed" title="Link to this definition"></a></dt>
<dd><p>can this NearNeighbors class be used with Structure
objects?</p>
<dl class="field-list simple">
<dt class="field-odd">Type<span class="colon">:</span></dt>
<dd class="field-odd"><p>Boolean property</p>
</dd>
</dl>
</dd></dl>
</dd></dl>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.analysis.local_env.NearNeighbors">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">NearNeighbors</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/local_env.py#L243-L691"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.local_env.NearNeighbors" title="Link to this definition"></a></dt>
<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></p>
<p>Base class to determine near neighbors that typically include nearest
neighbors and others that are within some tolerable distance.</p>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.analysis.local_env.NearNeighbors.extend_structure_molecules">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">extend_structure_molecules</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">bool</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/local_env.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.local_env.NearNeighbors.extend_structure_molecules" title="Link to this definition"></a></dt>
<dd><p>Do Molecules need to be converted to Structures to use
this NearNeighbors class? Note: this property is not defined for classes
for which molecules_allowed is False.</p>
<dl class="field-list simple">
<dt class="field-odd">Type<span class="colon">:</span></dt>
<dd class="field-odd"><p>Boolean property</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.local_env.NearNeighbors.get_all_nn_info">
<span class="sig-name descname"><span class="pre">get_all_nn_info</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">structure</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><span class="pre">Structure</span></a></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/local_env.py#L424-L434"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.local_env.NearNeighbors.get_all_nn_info" title="Link to this definition"></a></dt>
<dd><p>Get a listing of all neighbors for all sites in a structure.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>structure</strong> (<a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><em>Structure</em></a>) – Input structure</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p><dl class="simple">
<dt>List of NN site information for each site in the structure. Each</dt><dd><p>entry has the same format as <cite>get_nn_info</cite></p>
</dd>
</dl>
</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.local_env.NearNeighbors.get_bonded_structure">
<span class="sig-name descname"><span class="pre">get_bonded_structure</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">structure</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><span class="pre">Structure</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">decorate</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">weights</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">edge_properties</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">on_disorder</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">on_disorder_options</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">'take_majority_strict'</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><a class="reference internal" href="#pymatgen.analysis.graphs.StructureGraph" title="pymatgen.analysis.graphs.StructureGraph"><span class="pre">StructureGraph</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference internal" href="#pymatgen.analysis.graphs.MoleculeGraph" title="pymatgen.analysis.graphs.MoleculeGraph"><span class="pre">MoleculeGraph</span></a></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/local_env.py#L604-L652"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.local_env.NearNeighbors.get_bonded_structure" title="Link to this definition"></a></dt>
<dd><p>Obtain a StructureGraph object using this NearNeighbor class. Requires pip install networkx.</p>
<p>NOTE: The StructureGraph will not contain sites or bonds that are equivalent under lattice
vector translations. For more details please see the following discussion:
<a class="reference external" href="https://github.com/materialsproject/pymatgen/issues/3888">https://github.com/materialsproject/pymatgen/issues/3888</a></p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>structure</strong> – Structure object.</p></li>
<li><p><strong>decorate</strong> (<em>bool</em>) – whether to annotate site properties with order parameters using neighbors
determined by this NearNeighbor class</p></li>
<li><p><strong>weights</strong> (<em>bool</em>) – whether to include edge weights from NearNeighbor class in StructureGraph</p></li>
<li><p><strong>edge_properties</strong> (<em>bool</em>)</p></li>
<li><p><strong>on_disorder</strong> (<em>'take_majority_strict'</em><em> | </em><em>'take_majority_drop'</em><em> | </em><em>'take_max_species'</em><em> | </em><em>'error'</em>) – What to do when encountering a disordered structure. ‘error’ will raise ValueError.
‘take_majority_strict’ will use the majority specie on each site and raise
ValueError if no majority exists. ‘take_max_species’ will use the first max specie
on each site. For {{Fe: 0.4, O: 0.4, C: 0.2}}, ‘error’ and ‘take_majority_strict’
will raise ValueError, while ‘take_majority_drop’ ignores this site altogether and
‘take_max_species’ will use Fe as the site specie.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>object from pymatgen.analysis.graphs</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p><a class="reference internal" href="#pymatgen.analysis.graphs.StructureGraph" title="pymatgen.analysis.graphs.StructureGraph">StructureGraph</a></p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.local_env.NearNeighbors.get_cn">
<span class="sig-name descname"><span class="pre">get_cn</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">structure</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><span class="pre">Structure</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">n</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_weights</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">Literal</span><span class="p"><span class="pre">[</span></span><span class="k"><span class="pre">False</span></span><span class="p"><span class="pre">]</span></span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">on_disorder</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">Literal</span><span class="p"><span class="pre">[</span></span><span class="s"><span class="pre">'take_majority_strict'</span></span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="s"><span class="pre">'take_majority_drop'</span></span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="s"><span class="pre">'take_max_species'</span></span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="s"><span class="pre">'error'</span></span><span class="p"><span class="pre">]</span></span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">'take_majority_strict'</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">int</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/local_env.py#L305-L332"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.local_env.NearNeighbors.get_cn" title="Link to this definition"></a></dt>
<dt class="sig sig-object py">
<span class="sig-name descname"><span class="pre">get_cn</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">structure</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><span class="pre">Structure</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">n</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_weights</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">Literal</span><span class="p"><span class="pre">[</span></span><span class="k"><span class="pre">True</span></span><span class="p"><span class="pre">]</span></span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">on_disorder</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">Literal</span><span class="p"><span class="pre">[</span></span><span class="s"><span class="pre">'take_majority_strict'</span></span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="s"><span class="pre">'take_majority_drop'</span></span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="s"><span class="pre">'take_max_species'</span></span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="s"><span class="pre">'error'</span></span><span class="p"><span class="pre">]</span></span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">'take_majority_strict'</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">float</span></span></span></dt>
<dd><p>Get coordination number, CN, of site with index n in structure.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>structure</strong> (<a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><em>Structure</em></a>) – input structure.</p></li>
<li><p><strong>n</strong> (<em>int</em>) – index of site for which to determine CN.</p></li>
<li><p><strong>use_weights</strong> (<em>bool</em>) – flag indicating whether (True) to use weights for computing the coordination
number or not (False, default: each coordinated site has equal weight).</p></li>
<li><p><strong>on_disorder</strong> (<em>'take_majority_strict'</em><em> | </em><em>'take_majority_drop'</em><em> | </em><em>'take_max_species'</em><em> | </em><em>'error'</em>) – What to do when encountering a disordered structure. ‘error’ will raise ValueError.
‘take_majority_strict’ will use the majority specie on each site and raise
ValueError if no majority exists. ‘take_max_species’ will use the first max specie
on each site. For {{Fe: 0.4, O: 0.4, C: 0.2}}, ‘error’ and ‘take_majority_strict’
will raise ValueError, while ‘take_majority_drop’ ignores this site altogether and
‘take_max_species’ will use Fe as the site specie.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>coordination number (float if weighted)</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>int | float</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.local_env.NearNeighbors.get_cn_dict">
<span class="sig-name descname"><span class="pre">get_cn_dict</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">structure</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><span class="pre">Structure</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">n</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_weights</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/local_env.py#L334-L362"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.local_env.NearNeighbors.get_cn_dict" title="Link to this definition"></a></dt>
<dd><p>Get coordination number, CN, of each element bonded to site with index n in structure.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>structure</strong> (<a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><em>Structure</em></a>) – input structure</p></li>
<li><p><strong>n</strong> (<em>int</em>) – index of site for which to determine CN.</p></li>
<li><p><strong>use_weights</strong> (<em>bool</em>) – flag indicating whether (True)
to use weights for computing the coordination number
or not (False, default: each coordinated site has equal
weight).</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>coordination number of each element bonded to site with index n in structure.</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>dict[str, float]</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.local_env.NearNeighbors.get_local_order_parameters">
<span class="sig-name descname"><span class="pre">get_local_order_parameters</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">structure</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><span class="pre">Structure</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">n</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/local_env.py#L654-L691"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.local_env.NearNeighbors.get_local_order_parameters" title="Link to this definition"></a></dt>
<dd><p>Calculate those local structure order parameters for
the given site whose ideal CN corresponds to the
underlying motif (e.g., CN=4, then calculate the
square planar, tetrahedral, see-saw-like,
rectangular see-saw-like order parameters).</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>structure</strong> – Structure object</p></li>
<li><p><strong>n</strong> (<em>int</em>) – site index.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p><dl class="simple">
<dt>A dict of order parameters (values) and the</dt><dd><p>underlying motif type (keys; for example, tetrahedral).</p>
</dd>
</dl>
</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>dict[str, float]</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.local_env.NearNeighbors.get_nn">
<span class="sig-name descname"><span class="pre">get_nn</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">structure</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><span class="pre">Structure</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">n</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/local_env.py#L364-L375"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.local_env.NearNeighbors.get_nn" title="Link to this definition"></a></dt>
<dd><p>Get near neighbors of site with index n in structure.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>structure</strong> (<a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><em>Structure</em></a>) – input structure.</p></li>
<li><p><strong>n</strong> (<em>int</em>) – index of site in structure for which to determine
neighbors.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>near neighbors.</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>sites (list of Site objects)</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.local_env.NearNeighbors.get_nn_images">
<span class="sig-name descname"><span class="pre">get_nn_images</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">structure</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><span class="pre">Structure</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">n</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/local_env.py#L390-L403"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.local_env.NearNeighbors.get_nn_images" title="Link to this definition"></a></dt>
<dd><p>Get image location of all near neighbors of site with index n in
structure.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>structure</strong> (<a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><em>Structure</em></a>) – input structure.</p></li>
<li><p><strong>n</strong> (<em>int</em>) – index of site for which to determine the image
location of near neighbors.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p><dl class="simple">
<dt>image locations of</dt><dd><p>near neighbors.</p>
</dd>
</dl>
</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>images (list of 3D integer array)</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.local_env.NearNeighbors.get_nn_info">
<span class="sig-name descname"><span class="pre">get_nn_info</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">structure</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><span class="pre">Structure</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">n</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">dict</span><span class="p"><span class="pre">]</span></span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/local_env.py#L405-L422"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.local_env.NearNeighbors.get_nn_info" title="Link to this definition"></a></dt>
<dd><p>Get all near-neighbor sites as well as the associated image locations
and weights of the site with index n.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>structure</strong> (<a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><em>Structure</em></a>) – input structure.</p></li>
<li><p><strong>n</strong> (<em>int</em>) – index of site for which to determine near-neighbor
information.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p><dl class="simple">
<dt>each dictionary provides information</dt><dd><p>about a single near neighbor, where key ‘site’ gives access to the
corresponding Site object, ‘image’ gives the image location, and
‘weight’ provides the weight that a given near-neighbor site contributes
to the coordination number (1 or smaller), ‘site_index’ gives index of
the corresponding site in the original structure.</p>
</dd>
</dl>
</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>siw (list[dict])</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.local_env.NearNeighbors.get_nn_shell_info">
<span class="sig-name descname"><span class="pre">get_nn_shell_info</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">structure</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><span class="pre">Structure</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">site_idx</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">shell</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/local_env.py#L436-L477"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.local_env.NearNeighbors.get_nn_shell_info" title="Link to this definition"></a></dt>
<dd><p>Get a certain nearest neighbor shell for a certain site.</p>
<p>Determines all non-backtracking paths through the neighbor network
computed by <cite>get_nn_info</cite>. The weight is determined by multiplying
the weight of the neighbor at each hop through the network. For
example, a 2nd-nearest-neighbor that has a weight of 1 from its
1st-nearest-neighbor and weight 0.5 from the original site will
be assigned a weight of 0.5.</p>
<p>As this calculation may involve computing the nearest neighbors of
atoms multiple times, the calculation starts by computing all of the
neighbor info and then calling <cite>_get_nn_shell_info</cite>. If you are likely
to call this method for more than one site, consider calling <cite>get_all_nn</cite>
first and then calling this protected method yourself.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>structure</strong> (<a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><em>Structure</em></a>) – Input structure</p></li>
<li><p><strong>site_idx</strong> (<em>int</em>) – index of site for which to determine neighbor
information.</p></li>
<li><p><strong>shell</strong> (<em>int</em>) – Which neighbor shell to retrieve (1 == 1st NN shell)</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p><dl class="simple">
<dt>list of dictionaries. Each entry in the list is information about</dt><dd><p>a certain neighbor in the structure, in the same format as
<cite>get_nn_info</cite>.</p>
</dd>
</dl>
</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.local_env.NearNeighbors.get_weights_of_nn_sites">
<span class="sig-name descname"><span class="pre">get_weights_of_nn_sites</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">structure</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><span class="pre">Structure</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">n</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/local_env.py#L377-L388"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.local_env.NearNeighbors.get_weights_of_nn_sites" title="Link to this definition"></a></dt>
<dd><p>Get weight associated with each near neighbor of site with
index n in structure.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>structure</strong> (<a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><em>Structure</em></a>) – input structure.</p></li>
<li><p><strong>n</strong> (<em>int</em>) – index of site for which to determine the weights.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>near-neighbor weights.</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>weights (list of floats)</p>
</dd>
</dl>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.analysis.local_env.NearNeighbors.molecules_allowed">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">molecules_allowed</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">bool</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/local_env.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.local_env.NearNeighbors.molecules_allowed" title="Link to this definition"></a></dt>
<dd><p>can this NearNeighbors class be used with Molecule
objects?</p>
<dl class="field-list simple">
<dt class="field-odd">Type<span class="colon">:</span></dt>
<dd class="field-odd"><p>Boolean property</p>
</dd>
</dl>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.analysis.local_env.NearNeighbors.structures_allowed">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">structures_allowed</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">bool</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/local_env.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.local_env.NearNeighbors.structures_allowed" title="Link to this definition"></a></dt>
<dd><p>can this NearNeighbors class be used with Structure
objects?</p>
<dl class="field-list simple">
<dt class="field-odd">Type<span class="colon">:</span></dt>
<dd class="field-odd"><p>Boolean property</p>
</dd>
</dl>
</dd></dl>
</dd></dl>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.analysis.local_env.OpenBabelNN">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">OpenBabelNN</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">order</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/local_env.py#L1419-L1579"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.local_env.OpenBabelNN" title="Link to this definition"></a></dt>
<dd><p>Bases: <a class="reference internal" href="#pymatgen.analysis.local_env.NearNeighbors" title="pymatgen.analysis.local_env.NearNeighbors"><code class="xref py py-class docutils literal notranslate"><span class="pre">NearNeighbors</span></code></a></p>
<p>Determine near-neighbor sites and bond orders using OpenBabel API.</p>
<p>NOTE: This strategy is only appropriate for molecules, and not for
structures.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>order</strong> (<em>bool</em>) – True if bond order should be returned as a weight, False</p></li>
<li><p><strong>weight.</strong> (<em>if bond length should be used as a</em>)</p></li>
</ul>
</dd>
</dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.analysis.local_env.OpenBabelNN.extend_structure_molecules">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">extend_structure_molecules</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">bool</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/local_env.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.local_env.OpenBabelNN.extend_structure_molecules" title="Link to this definition"></a></dt>
<dd><p>Do Molecules need to be converted to Structures to use
this NearNeighbors class? Note: this property is not defined for classes
for which molecules_allowed is False.</p>
<dl class="field-list simple">
<dt class="field-odd">Type<span class="colon">:</span></dt>
<dd class="field-odd"><p>Boolean property</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.local_env.OpenBabelNN.get_bonded_structure">
<span class="sig-name descname"><span class="pre">get_bonded_structure</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">structure</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><span class="pre">Structure</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">decorate</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><a class="reference internal" href="#pymatgen.analysis.graphs.StructureGraph" title="pymatgen.analysis.graphs.StructureGraph"><span class="pre">StructureGraph</span></a></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/local_env.py#L1515-L1541"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.local_env.OpenBabelNN.get_bonded_structure" title="Link to this definition"></a></dt>
<dd><p>Obtain a MoleculeGraph object using this NearNeighbor
class. Requires the optional dependency networkx
(pip install networkx).</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>structure</strong> – Molecule object.</p></li>
<li><p><strong>decorate</strong> (<em>bool</em>) – whether to annotate site properties</p></li>
<li><p><strong>by</strong> (<em>with order parameters using neighbors determined</em>)</p></li>
<li><p><strong>class</strong> (<em>this NearNeighbor</em>)</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>object from pymatgen.analysis.graphs</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p><a class="reference internal" href="#pymatgen.analysis.graphs.MoleculeGraph" title="pymatgen.analysis.graphs.MoleculeGraph">MoleculeGraph</a></p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.local_env.OpenBabelNN.get_nn_info">
<span class="sig-name descname"><span class="pre">get_nn_info</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">structure</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><span class="pre">Structure</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">n</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/local_env.py#L1466-L1513"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.local_env.OpenBabelNN.get_nn_info" title="Link to this definition"></a></dt>
<dd><p>Get all near-neighbor sites and weights (orders) of bonds for a given
atom.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>structure</strong> – Molecule object.</p></li>
<li><p><strong>n</strong> – index of site for which to determine near neighbors.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>representing a neighboring site and the type of
bond present between site n and the neighboring site.</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>dict</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.local_env.OpenBabelNN.get_nn_shell_info">
<span class="sig-name descname"><span class="pre">get_nn_shell_info</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">structure</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><span class="pre">Structure</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">site_idx</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">shell</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/local_env.py#L1543-L1579"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.local_env.OpenBabelNN.get_nn_shell_info" title="Link to this definition"></a></dt>
<dd><p>Get a certain nearest neighbor shell for a certain site.</p>
<p>Determines all non-backtracking paths through the neighbor network
computed by <cite>get_nn_info</cite>. The weight is determined by multiplying
the weight of the neighbor at each hop through the network. For
example, a 2nd-nearest-neighbor that has a weight of 1 from its
1st-nearest-neighbor and weight 0.5 from the original site will
be assigned a weight of 0.5.</p>
<p>As this calculation may involve computing the nearest neighbors of
atoms multiple times, the calculation starts by computing all of the
neighbor info and then calling <cite>_get_nn_shell_info</cite>. If you are likely
to call this method for more than one site, consider calling <cite>get_all_nn</cite>
first and then calling this protected method yourself.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>structure</strong> (<a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Molecule" title="pymatgen.core.structure.Molecule"><em>Molecule</em></a>) – Input structure</p></li>
<li><p><strong>site_idx</strong> (<em>int</em>) – index of site for which to determine neighbor
information.</p></li>
<li><p><strong>shell</strong> (<em>int</em>) – Which neighbor shell to retrieve (1 == 1st NN shell)</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p><dl class="simple">
<dt>list of dictionaries. Each entry in the list is information about</dt><dd><p>a certain neighbor in the structure, in the same format as
<cite>get_nn_info</cite>.</p>
</dd>
</dl>
</p>
</dd>
</dl>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.analysis.local_env.OpenBabelNN.molecules_allowed">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">molecules_allowed</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">bool</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/local_env.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.local_env.OpenBabelNN.molecules_allowed" title="Link to this definition"></a></dt>
<dd><p>can this NearNeighbors class be used with Molecule
objects?</p>
<dl class="field-list simple">
<dt class="field-odd">Type<span class="colon">:</span></dt>
<dd class="field-odd"><p>Boolean property</p>
</dd>
</dl>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.analysis.local_env.OpenBabelNN.structures_allowed">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">structures_allowed</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">bool</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/local_env.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.local_env.OpenBabelNN.structures_allowed" title="Link to this definition"></a></dt>
<dd><p>can this NearNeighbors class be used with Structure
objects?</p>
<dl class="field-list simple">
<dt class="field-odd">Type<span class="colon">:</span></dt>
<dd class="field-odd"><p>Boolean property</p>
</dd>
</dl>
</dd></dl>
</dd></dl>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.analysis.local_env.ValenceIonicRadiusEvaluator">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">ValenceIonicRadiusEvaluator</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">structure</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><span class="pre">Structure</span></a></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/local_env.py#L69-L198"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.local_env.ValenceIonicRadiusEvaluator" title="Link to this definition"></a></dt>
<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></p>
<p>Computes site valences and ionic radii for a structure using bond valence
analyzer.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>structure</strong> – pymatgen Structure.</p>
</dd>
</dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.analysis.local_env.ValenceIonicRadiusEvaluator.radii">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">radii</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/local_env.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.local_env.ValenceIonicRadiusEvaluator.radii" title="Link to this definition"></a></dt>
<dd><p>List of ionic radii of elements in the order of sites.</p>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.analysis.local_env.ValenceIonicRadiusEvaluator.structure">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">structure</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/local_env.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.local_env.ValenceIonicRadiusEvaluator.structure" title="Link to this definition"></a></dt>
<dd><p>Oxidation state decorated structure.</p>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.analysis.local_env.ValenceIonicRadiusEvaluator.valences">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">valences</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/local_env.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.local_env.ValenceIonicRadiusEvaluator.valences" title="Link to this definition"></a></dt>
<dd><p>List of oxidation states of elements in the order of sites.</p>
</dd></dl>
</dd></dl>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.analysis.local_env.VoronoiNN">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">VoronoiNN</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">tol</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">targets</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">cutoff</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">13.0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">allow_pathological</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">weight</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'solid_angle'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">extra_nn_info</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">compute_adj_neighbors</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/local_env.py#L694-L1063"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.local_env.VoronoiNN" title="Link to this definition"></a></dt>
<dd><p>Bases: <a class="reference internal" href="#pymatgen.analysis.local_env.NearNeighbors" title="pymatgen.analysis.local_env.NearNeighbors"><code class="xref py py-class docutils literal notranslate"><span class="pre">NearNeighbors</span></code></a></p>
<p>Uses a Voronoi algorithm to determine near neighbors for each site in a
structure.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>tol</strong> (<em>float</em>) – tolerance parameter for near-neighbor finding. Faces that are
smaller than <cite>tol</cite> fraction of the largest face are not included in the
tessellation. (default: 0).</p></li>
<li><p><strong>targets</strong> (<a class="reference internal" href="pymatgen.core.html#pymatgen.core.periodic_table.Element" title="pymatgen.core.periodic_table.Element"><em>Element</em></a><em> or </em><em>list</em><em> of </em><em>Elements</em>) – target element(s).</p></li>
<li><p><strong>cutoff</strong> (<em>float</em>) – cutoff radius in Angstrom to look for near-neighbor
atoms. Defaults to 13.0.</p></li>
<li><p><strong>allow_pathological</strong> (<em>bool</em>) – whether to allow infinite vertices in
determination of Voronoi coordination.</p></li>
<li><p><strong>weight</strong> (<em>string</em>) – available in get_voronoi_polyhedra)</p></li>
<li><p><strong>extra_nn_info</strong> (<em>bool</em>)</p></li>
<li><p><strong>compute_adj_neighbors</strong> (<em>bool</em>) – adjacent. Turn off for faster performance.</p></li>
</ul>
</dd>
</dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.local_env.VoronoiNN.get_all_nn_info">
<span class="sig-name descname"><span class="pre">get_all_nn_info</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">structure</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><span class="pre">Structure</span></a></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/local_env.py#L1019-L1028"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.local_env.VoronoiNN.get_all_nn_info" title="Link to this definition"></a></dt>
<dd><dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>structure</strong> (<a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><em>Structure</em></a>) – input structure.</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>All nn info for all sites.</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.local_env.VoronoiNN.get_all_voronoi_polyhedra">
<span class="sig-name descname"><span class="pre">get_all_voronoi_polyhedra</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">structure</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><span class="pre">Structure</span></a></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/local_env.py#L805-L867"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.local_env.VoronoiNN.get_all_voronoi_polyhedra" title="Link to this definition"></a></dt>
<dd><p>Get the Voronoi polyhedra for all site in a simulation cell.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>structure</strong> (<a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><em>Structure</em></a>) – Structure to be evaluated</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p><p>A dict of sites sharing a common Voronoi facet with the site
n mapped to a directory containing statistics about the facet:</p>
<blockquote>
<div><ul class="simple">
<li><p>solid_angle - Solid angle subtended by face</p></li>
<li><dl class="simple">
<dt>angle_normalized - Solid angle normalized such that the</dt><dd><p>faces with the largest</p>
</dd>
</dl>
</li>
<li><p>area - Area of the facet</p></li>
<li><p>face_dist - Distance between site n and the facet</p></li>
<li><p>volume - Volume of Voronoi cell for this face</p></li>
<li><p>n_verts - Number of vertices on the facet</p></li>
</ul>
</div></blockquote>
</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.local_env.VoronoiNN.get_nn_info">
<span class="sig-name descname"><span class="pre">get_nn_info</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">structure</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><span class="pre">Structure</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">n</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/local_env.py#L999-L1017"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.local_env.VoronoiNN.get_nn_info" title="Link to this definition"></a></dt>
<dd><p>Get all near-neighbor sites as well as the associated image locations
and weights of the site with index n in structure
using Voronoi decomposition.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>structure</strong> (<a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><em>Structure</em></a>) – input structure.</p></li>
<li><p><strong>n</strong> (<em>int</em>) – index of site for which to determine near-neighbor sites.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p><dl class="simple">
<dt>tuples, each one</dt><dd><p>of which represents a coordinated site, its image location,
and its weight.</p>
</dd>
</dl>
</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>siw (list of tuples (<a class="reference internal" href="pymatgen.core.html#pymatgen.core.sites.Site" title="pymatgen.core.sites.Site">Site</a>, array, float))</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.local_env.VoronoiNN.get_voronoi_polyhedra">
<span class="sig-name descname"><span class="pre">get_voronoi_polyhedra</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">structure</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><span class="pre">Structure</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">n</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/local_env.py#L751-L803"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.local_env.VoronoiNN.get_voronoi_polyhedra" title="Link to this definition"></a></dt>
<dd><p>Get a weighted polyhedra around a site.</p>
<p>See ref: A Proposed Rigorous Definition of Coordination Number,
M. O’Keeffe, Acta Cryst. (1979). A35, 772-775</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>structure</strong> (<a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><em>Structure</em></a>) – structure for which to evaluate the
coordination environment.</p></li>
<li><p><strong>n</strong> (<em>int</em>) – site index.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p><p>A dict of sites sharing a common Voronoi facet with the site
n mapped to a directory containing statistics about the facet:</p>
<blockquote>
<div><ul class="simple">
<li><p>solid_angle - Solid angle subtended by face</p></li>
<li><dl class="simple">
<dt>angle_normalized - Solid angle normalized such that the</dt><dd><p>faces with the largest</p>
</dd>
</dl>
</li>
<li><p>area - Area of the facet</p></li>
<li><p>face_dist - Distance between site n and the facet</p></li>
<li><p>volume - Volume of Voronoi cell for this face</p></li>
<li><p>n_verts - Number of vertices on the facet</p></li>
</ul>
</div></blockquote>
</p>
</dd>
</dl>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.analysis.local_env.VoronoiNN.molecules_allowed">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">molecules_allowed</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">bool</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/local_env.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.local_env.VoronoiNN.molecules_allowed" title="Link to this definition"></a></dt>
<dd><p>can this NearNeighbors class be used with Molecule
objects?</p>
<dl class="field-list simple">
<dt class="field-odd">Type<span class="colon">:</span></dt>
<dd class="field-odd"><p>Boolean property</p>
</dd>
</dl>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.analysis.local_env.VoronoiNN.structures_allowed">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">structures_allowed</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">bool</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/local_env.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.local_env.VoronoiNN.structures_allowed" title="Link to this definition"></a></dt>
<dd><p>can this NearNeighbors class be used with Structure
objects?</p>
<dl class="field-list simple">
<dt class="field-odd">Type<span class="colon">:</span></dt>
<dd class="field-odd"><p>Boolean property</p>
</dd>
</dl>
</dd></dl>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="pymatgen.analysis.local_env.get_neighbors_of_site_with_index">
<span class="sig-name descname"><span class="pre">get_neighbors_of_site_with_index</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">struct</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">n</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">approach</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'min_dist'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">delta</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0.1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">cutoff</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">10</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/local_env.py#L2041-L2069"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.local_env.get_neighbors_of_site_with_index" title="Link to this definition"></a></dt>
<dd><p>Get the neighbors of a given site using a specific neighbor-finding method.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>struct</strong> (<a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><em>Structure</em></a>) – input structure.</p></li>
<li><p><strong>n</strong> (<em>int</em>) – index of site in Structure object for which motif type
is to be determined.</p></li>
<li><p><strong>approach</strong> (<em>str</em>) – type of neighbor-finding approach, where
“min_dist” will use the MinimumDistanceNN class,
“voronoi” the VoronoiNN class, “min_OKeeffe” the
MinimumOKeeffe class, and “min_VIRE” the MinimumVIRENN class.</p></li>
<li><p><strong>delta</strong> (<em>float</em>) – tolerance involved in neighbor finding.</p></li>
<li><p><strong>cutoff</strong> (<em>float</em>) – radius to find tentative neighbors.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>neighbor sites.</p>
</dd>
</dl>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="pymatgen.analysis.local_env.get_okeeffe_distance_prediction">
<span class="sig-name descname"><span class="pre">get_okeeffe_distance_prediction</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">el1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">el2</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/local_env.py#L2015-L2038"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.local_env.get_okeeffe_distance_prediction" title="Link to this definition"></a></dt>
<dd><p>Get an estimate of the bond valence parameter (bond length) using
the derived parameters from ‘Atoms Sizes and Bond Lengths in Molecules
and Crystals’ (O’Keeffe & Brese, 1991). The estimate is based on two
experimental parameters: r and c. The value for r is based off radius,
while c is (usually) the Allred-Rochow electronegativity. Values used
are <em>not</em> generated from pymatgen, and are found in
‘okeeffe_params.json’.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>el1</strong> (<a class="reference internal" href="pymatgen.core.html#pymatgen.core.periodic_table.Element" title="pymatgen.core.periodic_table.Element"><em>Element</em></a>) – two Element objects</p></li>
<li><p><strong>el2</strong> (<a class="reference internal" href="pymatgen.core.html#pymatgen.core.periodic_table.Element" title="pymatgen.core.periodic_table.Element"><em>Element</em></a>) – two Element objects</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>a float value of the predicted bond length</p>
</dd>
</dl>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="pymatgen.analysis.local_env.get_okeeffe_params">
<span class="sig-name descname"><span class="pre">get_okeeffe_params</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">el_symbol</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/local_env.py#L1993-L2012"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.local_env.get_okeeffe_params" title="Link to this definition"></a></dt>
<dd><p>Get the elemental parameters related to atom size and electronegativity which are
used for estimating bond-valence parameters (bond length) of pairs of atoms on the
basis of data provided in ‘Atoms Sizes and Bond Lengths in Molecules and Crystals’
(O’Keeffe & Brese, 1991).</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>el_symbol</strong> (<em>str</em>) – element symbol.</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>atom-size (‘r’) and electronegativity-related (‘c’) parameter.</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>dict</p>
</dd>
</dl>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="pymatgen.analysis.local_env.gramschmidt">
<span class="sig-name descname"><span class="pre">gramschmidt</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">vin</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">uin</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/local_env.py#L2147-L2162"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.local_env.gramschmidt" title="Link to this definition"></a></dt>
<dd><p>Get that part of the first input vector
that is orthogonal to the second input vector.
The output vector is not normalized.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>vin</strong> (<em>numpy array</em>) – first input vector</p></li>
<li><p><strong>uin</strong> (<em>numpy array</em>) – second input vector</p></li>
</ul>
</dd>
</dl>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="pymatgen.analysis.local_env.metal_edge_extender">
<span class="sig-name descname"><span class="pre">metal_edge_extender</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">mol_graph</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">cutoff</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">float</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">2.5</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">metals</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">list</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">tuple</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">('Li',</span> <span class="pre">'Mg',</span> <span class="pre">'Ca',</span> <span class="pre">'Zn',</span> <span class="pre">'B',</span> <span class="pre">'Al')</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">coordinators</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">list</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">tuple</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">('O',</span> <span class="pre">'N',</span> <span class="pre">'F',</span> <span class="pre">'S',</span> <span class="pre">'Cl')</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/local_env.py#L4469-L4541"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.local_env.metal_edge_extender" title="Link to this definition"></a></dt>
<dd><p>Identify and add missed coordinate bond edges for metals.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>mol_graph</strong> – pymatgen.analysis.graphs.MoleculeGraph object</p></li>
<li><p><strong>cutoff</strong> – cutoff in Angstrom. Metal-coordinator sites that are closer
together than this value will be considered coordination bonds.
If the MoleculeGraph contains a metal, but no coordination bonds are found
with the chosen cutoff, the cutoff will be increased by 1 Angstrom
and another attempt will be made to identify coordination bonds.</p></li>
<li><p><strong>metals</strong> – Species considered metals for the purpose of identifying
missed coordinate bond edges. The set {“Li”, “Mg”, “Ca”, “Zn”, “B”, “Al”}
(default) corresponds to the settings used in the LIBE dataset.
Alternatively, set to None to cause any Species classified as a metal
by Specie.is_metal to be considered a metal.</p></li>
<li><p><strong>coordinators</strong> – Possible coordinating species to consider when identifying
missed coordinate bonds. The default set {“O”, “N”, “F”, “S”, “Cl”} was
used in the LIBE dataset.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p><dl class="simple">
<dt>pymatgen.analysis.graphs.MoleculeGraph object with additional</dt><dd><p>metal bonds (if any found) added</p>
</dd>
</dl>
</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>mol_graph</p>
</dd>
</dl>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="pymatgen.analysis.local_env.oxygen_edge_extender">
<span class="sig-name descname"><span class="pre">oxygen_edge_extender</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">mol_graph</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="#pymatgen.analysis.graphs.MoleculeGraph" title="pymatgen.analysis.graphs.MoleculeGraph"><span class="pre">MoleculeGraph</span></a></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><a class="reference internal" href="#pymatgen.analysis.graphs.MoleculeGraph" title="pymatgen.analysis.graphs.MoleculeGraph"><span class="pre">MoleculeGraph</span></a></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/local_env.py#L4444-L4466"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.local_env.oxygen_edge_extender" title="Link to this definition"></a></dt>
<dd><p>Identify and add missed O-C or O-H bonds. This is particularly
important when oxygen is forming three bonds, e.g. in H3O+ or XOH2+.
See <a class="reference external" href="https://github.com/materialsproject/pymatgen/pull/2903">https://github.com/materialsproject/pymatgen/pull/2903</a> for details.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>mol_graph</strong> (<a class="reference internal" href="#pymatgen.analysis.graphs.MoleculeGraph" title="pymatgen.analysis.graphs.MoleculeGraph"><em>MoleculeGraph</em></a>) – molecule graph to extend</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>object with additional O-C or O-H bonds added (if any found)</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p><a class="reference internal" href="#pymatgen.analysis.graphs.MoleculeGraph" title="pymatgen.analysis.graphs.MoleculeGraph">MoleculeGraph</a></p>
</dd>
</dl>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="pymatgen.analysis.local_env.site_is_of_motif_type">
<span class="sig-name descname"><span class="pre">site_is_of_motif_type</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">struct</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">n</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">approach</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'min_dist'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">delta</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0.1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">cutoff</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">10</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">thresh</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/local_env.py#L2072-L2144"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.local_env.site_is_of_motif_type" title="Link to this definition"></a></dt>
<dd><p>Get the motif type of the site with index n in structure struct;
currently featuring “tetrahedral”, “octahedral”, “bcc”, and “cp”
(close-packed: fcc and hcp) as well as “square pyramidal” and
“trigonal bipyramidal”. If the site is not recognized,
“unrecognized” is returned. If a site should be assigned to two
different motifs, “multiple assignments” is returned.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>struct</strong> (<a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><em>Structure</em></a>) – input structure.</p></li>
<li><p><strong>n</strong> (<em>int</em>) – index of site in Structure object for which motif type
is to be determined.</p></li>
<li><p><strong>approach</strong> (<em>str</em>) – type of neighbor-finding approach, where
“min_dist” will use the MinimumDistanceNN class,
“voronoi” the VoronoiNN class, “min_OKeeffe” the
MinimumOKeeffe class, and “min_VIRE” the MinimumVIRENN class.</p></li>
<li><p><strong>delta</strong> (<em>float</em>) – tolerance involved in neighbor finding.</p></li>
<li><p><strong>cutoff</strong> (<em>float</em>) – radius to find tentative neighbors.</p></li>
<li><p><strong>thresh</strong> (<em>dict</em>) – thresholds for motif criteria (currently, required
keys and their default values are “qtet”: 0.5,
“qoct”: 0.5, “qbcc”: 0.5, “q6”: 0.4).</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>motif type</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>str</p>
</dd>
</dl>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="pymatgen.analysis.local_env.solid_angle">
<span class="sig-name descname"><span class="pre">solid_angle</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">center</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">coords</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/local_env.py#L1940-L1973"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.local_env.solid_angle" title="Link to this definition"></a></dt>
<dd><p>Helper method to calculate the solid angle of a set of coords from the
center.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>center</strong> (<em>3x1 array</em>) – Center to measure solid angle from.</p></li>
<li><p><strong>coords</strong> (<em>Nx3 array</em>) – List of coords to determine solid angle.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>The solid angle.</p>
</dd>
</dl>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="pymatgen.analysis.local_env.vol_tetra">
<span class="sig-name descname"><span class="pre">vol_tetra</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">vt1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">vt2</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">vt3</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">vt4</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/local_env.py#L1976-L1990"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.local_env.vol_tetra" title="Link to this definition"></a></dt>
<dd><p>Calculate the volume of a tetrahedron, given the four vertices of vt1,
vt2, vt3 and vt4.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>vt1</strong> (<em>array-like</em>) – coordinates of vertex 1.</p></li>
<li><p><strong>vt2</strong> (<em>array-like</em>) – coordinates of vertex 2.</p></li>
<li><p><strong>vt3</strong> (<em>array-like</em>) – coordinates of vertex 3.</p></li>
<li><p><strong>vt4</strong> (<em>array-like</em>) – coordinates of vertex 4.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>volume of the tetrahedron.</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>float</p>
</dd>
</dl>
</dd></dl>
</section>
<section id="module-pymatgen.analysis.molecule_matcher">
<span id="pymatgen-analysis-molecule-matcher-module"></span><h2>pymatgen.analysis.molecule_matcher module<a class="headerlink" href="#module-pymatgen.analysis.molecule_matcher" title="Link to this heading"></a></h2>
<p>This module provides classes to perform fitting of molecule with arbitrary
atom orders.
This module is supposed to perform exact comparisons without the atom order
correspondence prerequisite, while molecule_structure_comparator is supposed
to do rough comparisons with the atom order correspondence prerequisite.</p>
<p>The implementation is based on an excellent python package called <cite>rmsd</cite> that
you can find at <a class="reference external" href="https://github.com/charnley/rmsd">https://github.com/charnley/rmsd</a>.</p>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.analysis.molecule_matcher.AbstractMolAtomMapper">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">AbstractMolAtomMapper</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/molecule_matcher.py#L48-L107"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.molecule_matcher.AbstractMolAtomMapper" title="Link to this definition"></a></dt>
<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">MSONable</span></code>, <code class="xref py py-class docutils literal notranslate"><span class="pre">ABC</span></code></p>
<p>Abstract molecular atom order mapping class. A mapping will be able to
find the uniform atom order of two molecules that can pair the
geometrically equivalent atoms.</p>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.molecule_matcher.AbstractMolAtomMapper.from_dict">
<em class="property"><span class="pre">classmethod</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">from_dict</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">dct</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">dict</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">Self</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/molecule_matcher.py#L86-L107"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.molecule_matcher.AbstractMolAtomMapper.from_dict" title="Link to this definition"></a></dt>
<dd><dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>dct</strong> (<em>dict</em>) – Dict representation.</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>AbstractMolAtomMapper</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.molecule_matcher.AbstractMolAtomMapper.get_molecule_hash">
<em class="property"><span class="pre">abstract</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">get_molecule_hash</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">mol</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/molecule_matcher.py#L73-L84"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.molecule_matcher.AbstractMolAtomMapper.get_molecule_hash" title="Link to this definition"></a></dt>
<dd><p>Defines a hash for molecules. This allows molecules to be grouped
efficiently for comparison.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>mol</strong> – The molecule. OpenBabel OBMol or pymatgen Molecule object</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>A hashable object. Examples can be string formulas, etc.</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.molecule_matcher.AbstractMolAtomMapper.uniform_labels">
<em class="property"><span class="pre">abstract</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">uniform_labels</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">mol1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">mol2</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/molecule_matcher.py#L55-L71"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.molecule_matcher.AbstractMolAtomMapper.uniform_labels" title="Link to this definition"></a></dt>
<dd><p>Pair the geometrically equivalent atoms of the molecules.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>mol1</strong> – First molecule. OpenBabel OBMol or pymatgen Molecule object.</p></li>
<li><p><strong>mol2</strong> – Second molecule. OpenBabel OBMol or pymatgen Molecule object.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p><dl class="simple">
<dt>if uniform atom order is found. list1 and list2</dt><dd><p>are for mol1 and mol2, respectively. Their length equal
to the number of atoms. They represents the uniform atom order
of the two molecules. The value of each element is the original
atom index in mol1 or mol2 of the current atom in uniform atom order.
(None, None) if uniform atom is not available.</p>
</dd>
</dl>
</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>tuple[list1, list2]</p>
</dd>
</dl>
</dd></dl>
</dd></dl>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.analysis.molecule_matcher.BruteForceOrderMatcher">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">BruteForceOrderMatcher</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">target</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Molecule" title="pymatgen.core.structure.Molecule"><span class="pre">Molecule</span></a></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/molecule_matcher.py#L826-L934"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.molecule_matcher.BruteForceOrderMatcher" title="Link to this definition"></a></dt>
<dd><p>Bases: <a class="reference internal" href="#pymatgen.analysis.molecule_matcher.KabschMatcher" title="pymatgen.analysis.molecule_matcher.KabschMatcher"><code class="xref py py-class docutils literal notranslate"><span class="pre">KabschMatcher</span></code></a></p>
<p>Finding the best match between molecules by selecting molecule order
with the smallest RMSD from all the possible order combinations.</p>
<p class="rubric">Notes</p>
<p>When aligning molecules, the atoms of the two molecules <strong>must</strong> have same number
of atoms from the same species.</p>
<p>Constructor of the matcher object.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>target</strong> – a <cite>Molecule</cite> object used as a target during the alignment</p>
</dd>
</dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.molecule_matcher.BruteForceOrderMatcher.fit">
<span class="sig-name descname"><span class="pre">fit</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">p</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Molecule" title="pymatgen.core.structure.Molecule"><span class="pre">Molecule</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">ignore_warning</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/molecule_matcher.py#L904-L924"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.molecule_matcher.BruteForceOrderMatcher.fit" title="Link to this definition"></a></dt>
<dd><p>Order, rotate and transform <cite>p</cite> molecule according to the best match.</p>
<p>A <cite>ValueError</cite> will be raised when the total number of possible combinations
become unfeasible (more than a million combinations).</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>p</strong> – a <cite>Molecule</cite> object what will be matched with the target one.</p></li>
<li><p><strong>ignore_warning</strong> – ignoring error when the number of combination is too large</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>Rotated and translated of the <cite>p</cite> <cite>Molecule</cite> object
rmsd: Root-mean-square-deviation between <cite>p_prime</cite> and the <cite>target</cite></p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>p_prime</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.molecule_matcher.BruteForceOrderMatcher.match">
<span class="sig-name descname"><span class="pre">match</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">mol</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Molecule" title="pymatgen.core.structure.Molecule"><span class="pre">Molecule</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">ignore_warning</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">tuple</span><span class="p"><span class="pre">[</span></span><span class="pre">ndarray</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">ndarray</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">ndarray</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">float</span><span class="p"><span class="pre">]</span></span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/molecule_matcher.py#L835-L902"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.molecule_matcher.BruteForceOrderMatcher.match" title="Link to this definition"></a></dt>
<dd><p>Similar as <cite>KabschMatcher.match</cite> but this method also finds the order of
atoms which belongs to the best match.</p>
<p>A <cite>ValueError</cite> will be raised when the total number of possible combinations
become unfeasible (more than a million combination).</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>mol</strong> – a <cite>Molecule</cite> object what will be matched with the target one.</p></li>
<li><p><strong>ignore_warning</strong> – ignoring error when the number of combination is too large</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>The indices of atoms
U: 3x3 rotation matrix
V: Translation vector
rmsd: Root mean squared deviation between P and Q</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>inds</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.molecule_matcher.BruteForceOrderMatcher.permutations">
<em class="property"><span class="pre">static</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">permutations</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">atoms</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/molecule_matcher.py#L926-L934"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.molecule_matcher.BruteForceOrderMatcher.permutations" title="Link to this definition"></a></dt>
<dd><p>Generate all the possible permutations of atom order. To achieve better
performance all the cases where the atoms are different has been ignored.</p>
</dd></dl>
</dd></dl>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.analysis.molecule_matcher.GeneticOrderMatcher">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">GeneticOrderMatcher</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">target</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Molecule" title="pymatgen.core.structure.Molecule"><span class="pre">Molecule</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">threshold</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">float</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/molecule_matcher.py#L1149-L1301"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.molecule_matcher.GeneticOrderMatcher" title="Link to this definition"></a></dt>
<dd><p>Bases: <a class="reference internal" href="#pymatgen.analysis.molecule_matcher.KabschMatcher" title="pymatgen.analysis.molecule_matcher.KabschMatcher"><code class="xref py py-class docutils literal notranslate"><span class="pre">KabschMatcher</span></code></a></p>
<p>This method was inspired by genetic algorithms and tries to match molecules
based on their already matched fragments.</p>
<p>It uses the fact that when two molecule is matching their sub-structures have to match as well.
The main idea here is that in each iteration (generation) we can check the match of all possible
fragments and ignore those which are not feasible.</p>
<p>Although in the worst case this method has N! complexity (same as the brute force one),
in practice it performs much faster because many of the combination can be eliminated
during the fragment matching.</p>
<p class="rubric">Notes</p>
<p>This method very robust and returns with all the possible orders.</p>
<p>There is a well known weakness/corner case: The case when there is
a outlier with large deviation with a small index might be ignored.
This happens due to the nature of the average function
used to calculate the RMSD for the fragments.</p>
<p>When aligning molecules, the atoms of the two molecules <strong>must</strong> have the
same number of atoms from the same species.</p>
<p>Constructor of the matcher object.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>target</strong> – a <cite>Molecule</cite> object used as a target during the alignment</p></li>
<li><p><strong>threshold</strong> – value used to match fragments and prune configuration</p></li>
</ul>
</dd>
</dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.molecule_matcher.GeneticOrderMatcher.fit">
<span class="sig-name descname"><span class="pre">fit</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">p</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Molecule" title="pymatgen.core.structure.Molecule"><span class="pre">Molecule</span></a></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/molecule_matcher.py#L1209-L1235"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.molecule_matcher.GeneticOrderMatcher.fit" title="Link to this definition"></a></dt>
<dd><p>Order, rotate and transform all of the matched <cite>p</cite> molecule
according to the given <cite>threshold</cite>.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>p</strong> – a <cite>Molecule</cite> object what will be matched with the target one.</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p><dl class="simple">
<dt>possible matches where the elements are:</dt><dd><p>p_prime: Rotated and translated of the <cite>p</cite> <cite>Molecule</cite> object
rmsd: Root-mean-square-deviation between <cite>p_prime</cite> and the <cite>target</cite></p>
</dd>
</dl>
</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>list[tuple[<a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Molecule" title="pymatgen.core.structure.Molecule">Molecule</a>, float]]</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.molecule_matcher.GeneticOrderMatcher.match">
<span class="sig-name descname"><span class="pre">match</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">p</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Molecule" title="pymatgen.core.structure.Molecule"><span class="pre">Molecule</span></a></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/molecule_matcher.py#L1184-L1207"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.molecule_matcher.GeneticOrderMatcher.match" title="Link to this definition"></a></dt>
<dd><p>Similar as <cite>KabschMatcher.match</cite> but this method also finds all of the
possible atomic orders according to the <cite>threshold</cite>.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>p</strong> – a <cite>Molecule</cite> object what will be matched with the target one.</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>inds: The indices of atoms
U: 3x3 rotation matrix
V: Translation vector
rmsd: Root mean squared deviation between P and Q</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>Array of the possible matches where the elements are</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.molecule_matcher.GeneticOrderMatcher.permutations">
<span class="sig-name descname"><span class="pre">permutations</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">p</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Molecule" title="pymatgen.core.structure.Molecule"><span class="pre">Molecule</span></a></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/molecule_matcher.py#L1237-L1301"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.molecule_matcher.GeneticOrderMatcher.permutations" title="Link to this definition"></a></dt>
<dd><p>Generate all of possible permutations of atom order according the threshold.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>p</strong> – a <cite>Molecule</cite> object what will be matched with the target one.</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>Array of index arrays</p>
</dd>
</dl>
</dd></dl>
</dd></dl>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.analysis.molecule_matcher.HungarianOrderMatcher">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">HungarianOrderMatcher</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">target</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Molecule" title="pymatgen.core.structure.Molecule"><span class="pre">Molecule</span></a></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/molecule_matcher.py#L937-L1146"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.molecule_matcher.HungarianOrderMatcher" title="Link to this definition"></a></dt>
<dd><p>Bases: <a class="reference internal" href="#pymatgen.analysis.molecule_matcher.KabschMatcher" title="pymatgen.analysis.molecule_matcher.KabschMatcher"><code class="xref py py-class docutils literal notranslate"><span class="pre">KabschMatcher</span></code></a></p>
<p>Pre-align the molecules based on their principal inertia
axis and then re-orders the input atom list using the Hungarian method.</p>
<p class="rubric">Notes</p>
<p>This method cannot guarantee the best match but is very fast.</p>
<p>When aligning molecules, the atoms of the two molecules <strong>must</strong> have same number
of atoms from the same species.</p>
<p>Constructor of the matcher object.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>target</strong> – a <cite>Molecule</cite> object used as a target during the alignment</p>
</dd>
</dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.molecule_matcher.HungarianOrderMatcher.fit">
<span class="sig-name descname"><span class="pre">fit</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">p</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Molecule" title="pymatgen.core.structure.Molecule"><span class="pre">Molecule</span></a></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/molecule_matcher.py#L1000-L1017"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.molecule_matcher.HungarianOrderMatcher.fit" title="Link to this definition"></a></dt>
<dd><p>Order, rotate and transform <cite>p</cite> molecule according to the best match.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>p</strong> – a <cite>Molecule</cite> object what will be matched with the target one.</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>Rotated and translated of the <cite>p</cite> <cite>Molecule</cite> object
rmsd: Root-mean-square-deviation between <cite>p_prime</cite> and the <cite>target</cite></p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>p_prime</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.molecule_matcher.HungarianOrderMatcher.get_principal_axis">
<em class="property"><span class="pre">static</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">get_principal_axis</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">coords</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">weights</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/molecule_matcher.py#L1090-L1116"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.molecule_matcher.HungarianOrderMatcher.get_principal_axis" title="Link to this definition"></a></dt>
<dd><p>Get the molecule’s principal axis.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>coords</strong> – coordinates of atoms</p></li>
<li><p><strong>weights</strong> – the weight use for calculating the inertia tensor</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>Array of dim 3 containing the principal axis</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.molecule_matcher.HungarianOrderMatcher.match">
<span class="sig-name descname"><span class="pre">match</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">p</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Molecule" title="pymatgen.core.structure.Molecule"><span class="pre">Molecule</span></a></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/molecule_matcher.py#L948-L998"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.molecule_matcher.HungarianOrderMatcher.match" title="Link to this definition"></a></dt>
<dd><p>Similar as <cite>KabschMatcher.match</cite> but this method also finds the order of
atoms which belongs to the best match.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>p</strong> – a <cite>Molecule</cite> object what will be matched with the target one.</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>The indices of atoms
U: 3x3 rotation matrix
V: Translation vector
rmsd: Root mean squared deviation between P and Q</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>inds</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.molecule_matcher.HungarianOrderMatcher.permutations">
<em class="property"><span class="pre">static</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">permutations</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">p_atoms</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">p_centroid</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">p_weights</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">q_atoms</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">q_centroid</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">q_weights</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/molecule_matcher.py#L1019-L1088"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.molecule_matcher.HungarianOrderMatcher.permutations" title="Link to this definition"></a></dt>
<dd><p>Generate two possible permutations of atom order. This method uses the principle component
of the inertia tensor to pre-align the molecules and hungarian method to determine the order.
There are always two possible permutation depending on the way to pre-aligning the molecules.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>p_atoms</strong> – atom numbers</p></li>
<li><p><strong>p_centroid</strong> – array of atom positions</p></li>
<li><p><strong>p_weights</strong> – array of atom weights</p></li>
<li><p><strong>q_atoms</strong> – atom numbers</p></li>
<li><p><strong>q_centroid</strong> – array of atom positions</p></li>
<li><p><strong>q_weights</strong> – array of atom weights</p></li>
</ul>
</dd>
<dt class="field-even">Yields<span class="colon">:</span></dt>
<dd class="field-even"><p><em>perm_inds</em> – array of atoms’ order</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.molecule_matcher.HungarianOrderMatcher.rotation_matrix_vectors">
<em class="property"><span class="pre">static</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">rotation_matrix_vectors</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">v1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">v2</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/molecule_matcher.py#L1118-L1146"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.molecule_matcher.HungarianOrderMatcher.rotation_matrix_vectors" title="Link to this definition"></a></dt>
<dd><p>Get the rotation matrix that rotates v1 onto v2 using
Rodrigues’ rotation formula.</p>
<p>See more: <a class="reference external" href="https://math.stackexchange.com/a/476311">https://math.stackexchange.com/a/476311</a></p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>v1</strong> – initial vector</p></li>
<li><p><strong>v2</strong> – target vector</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>3x3 rotation matrix</p>
</dd>
</dl>
</dd></dl>
</dd></dl>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.analysis.molecule_matcher.InchiMolAtomMapper">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">InchiMolAtomMapper</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">angle_tolerance</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">10.0</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/molecule_matcher.py#L200-L561"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.molecule_matcher.InchiMolAtomMapper" title="Link to this definition"></a></dt>
<dd><p>Bases: <a class="reference internal" href="#pymatgen.analysis.molecule_matcher.AbstractMolAtomMapper" title="pymatgen.analysis.molecule_matcher.AbstractMolAtomMapper"><code class="xref py py-class docutils literal notranslate"><span class="pre">AbstractMolAtomMapper</span></code></a></p>
<p>Pair atoms by inchi labels.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>angle_tolerance</strong> (<em>float</em>) – Angle threshold to assume linear molecule. In degrees.</p>
</dd>
</dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.molecule_matcher.InchiMolAtomMapper.as_dict">
<span class="sig-name descname"><span class="pre">as_dict</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/molecule_matcher.py#L211-L218"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.molecule_matcher.InchiMolAtomMapper.as_dict" title="Link to this definition"></a></dt>
<dd><p>Get MSONable dict.</p>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.molecule_matcher.InchiMolAtomMapper.from_dict">
<em class="property"><span class="pre">classmethod</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">from_dict</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">dct</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">dict</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">Self</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/molecule_matcher.py#L220-L229"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.molecule_matcher.InchiMolAtomMapper.from_dict" title="Link to this definition"></a></dt>
<dd><dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>dct</strong> (<em>dict</em>) – Dict Representation.</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>InchiMolAtomMapper</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.molecule_matcher.InchiMolAtomMapper.get_molecule_hash">
<span class="sig-name descname"><span class="pre">get_molecule_hash</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">mol</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/molecule_matcher.py#L558-L561"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.molecule_matcher.InchiMolAtomMapper.get_molecule_hash" title="Link to this definition"></a></dt>
<dd><p>Return inchi as molecular hash.</p>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.molecule_matcher.InchiMolAtomMapper.uniform_labels">
<span class="sig-name descname"><span class="pre">uniform_labels</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">mol1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">mol2</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/molecule_matcher.py#L514-L556"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.molecule_matcher.InchiMolAtomMapper.uniform_labels" title="Link to this definition"></a></dt>
<dd><dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>mol1</strong> (<a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Molecule" title="pymatgen.core.structure.Molecule"><em>Molecule</em></a>) – Molecule 1</p></li>
<li><p><strong>mol2</strong> (<a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Molecule" title="pymatgen.core.structure.Molecule"><em>Molecule</em></a>) – Molecule 2.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>Labels</p>
</dd>
</dl>
</dd></dl>
</dd></dl>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.analysis.molecule_matcher.IsomorphismMolAtomMapper">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">IsomorphismMolAtomMapper</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/molecule_matcher.py#L110-L197"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.molecule_matcher.IsomorphismMolAtomMapper" title="Link to this definition"></a></dt>
<dd><p>Bases: <a class="reference internal" href="#pymatgen.analysis.molecule_matcher.AbstractMolAtomMapper" title="pymatgen.analysis.molecule_matcher.AbstractMolAtomMapper"><code class="xref py py-class docutils literal notranslate"><span class="pre">AbstractMolAtomMapper</span></code></a></p>
<p>Pair atoms by isomorphism permutations in the OpenBabel::OBAlign class.</p>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.molecule_matcher.IsomorphismMolAtomMapper.as_dict">
<span class="sig-name descname"><span class="pre">as_dict</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/molecule_matcher.py#L180-L186"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.molecule_matcher.IsomorphismMolAtomMapper.as_dict" title="Link to this definition"></a></dt>
<dd><p>Get MSONable dict.</p>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.molecule_matcher.IsomorphismMolAtomMapper.from_dict">
<em class="property"><span class="pre">classmethod</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">from_dict</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">dct</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">dict</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">Self</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/molecule_matcher.py#L188-L197"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.molecule_matcher.IsomorphismMolAtomMapper.from_dict" title="Link to this definition"></a></dt>
<dd><dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>dct</strong> (<em>dict</em>) – Dict representation.</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>IsomorphismMolAtomMapper</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.molecule_matcher.IsomorphismMolAtomMapper.get_molecule_hash">
<span class="sig-name descname"><span class="pre">get_molecule_hash</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">mol</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/molecule_matcher.py#L171-L178"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.molecule_matcher.IsomorphismMolAtomMapper.get_molecule_hash" title="Link to this definition"></a></dt>
<dd><p>Return inchi as molecular hash.</p>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.molecule_matcher.IsomorphismMolAtomMapper.uniform_labels">
<span class="sig-name descname"><span class="pre">uniform_labels</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">mol1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">mol2</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/molecule_matcher.py#L113-L169"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.molecule_matcher.IsomorphismMolAtomMapper.uniform_labels" title="Link to this definition"></a></dt>
<dd><p>Pair the geometrically equivalent atoms of the molecules.
Calculate RMSD on all possible isomorphism mappings and return mapping
with the least RMSD.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>mol1</strong> – First molecule. OpenBabel OBMol or pymatgen Molecule object.</p></li>
<li><p><strong>mol2</strong> – Second molecule. OpenBabel OBMol or pymatgen Molecule object.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p><dl class="simple">
<dt>if uniform atom order is found. list1 and list2</dt><dd><p>are for mol1 and mol2, respectively. Their length equal
to the number of atoms. They represents the uniform atom order
of the two molecules. The value of each element is the original
atom index in mol1 or mol2 of the current atom in uniform atom order.
(None, None) if uniform atom is not available.</p>
</dd>
</dl>
</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>tuple[list1, list2]</p>
</dd>
</dl>
</dd></dl>
</dd></dl>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.analysis.molecule_matcher.KabschMatcher">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">KabschMatcher</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">target</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Molecule" title="pymatgen.core.structure.Molecule"><span class="pre">Molecule</span></a></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/molecule_matcher.py#L714-L823"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.molecule_matcher.KabschMatcher" title="Link to this definition"></a></dt>
<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">MSONable</span></code></p>
<p>Molecule matcher using Kabsch algorithm.</p>
<p>The Kabsch algorithm capable aligning two molecules by finding the parameters
(translation, rotation) which minimize the root-mean-square-deviation (RMSD) of
two molecules which are topologically (atom types, geometry) similar two each other.</p>
<p class="rubric">Notes</p>
<p>When aligning molecules, the atoms of the two molecules <strong>must</strong> be in the same
order for the results to be sensible.</p>
<p>Constructor of the matcher object.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>target</strong> – a <cite>Molecule</cite> object used as a target during the alignment</p>
</dd>
</dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.molecule_matcher.KabschMatcher.fit">
<span class="sig-name descname"><span class="pre">fit</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">p</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Molecule" title="pymatgen.core.structure.Molecule"><span class="pre">Molecule</span></a></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/molecule_matcher.py#L774-L792"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.molecule_matcher.KabschMatcher.fit" title="Link to this definition"></a></dt>
<dd><p>Rotate and transform <cite>p</cite> molecule according to the best match.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>p</strong> – a <cite>Molecule</cite> object what will be matched with the target one.</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>Rotated and translated of the <cite>p</cite> <cite>Molecule</cite> object
rmsd: Root-mean-square-deviation between <cite>p_prime</cite> and the <cite>target</cite></p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>p_prime</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.molecule_matcher.KabschMatcher.kabsch">
<em class="property"><span class="pre">static</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">kabsch</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">P</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">ndarray</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">Q</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">ndarray</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/molecule_matcher.py#L794-L823"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.molecule_matcher.KabschMatcher.kabsch" title="Link to this definition"></a></dt>
<dd><p>The Kabsch algorithm is a method for calculating the optimal rotation matrix
that minimizes the root mean squared deviation (RMSD) between two paired sets of points
P and Q, centered around the their centroid.</p>
<p>For more info see:
- <a class="reference external" href="https://wikipedia.org/wiki/Kabsch_algorithm">https://wikipedia.org/wiki/Kabsch_algorithm</a> and
- <a class="reference external" href="https://cnx.org/contents/HV-RsdwL@23/Molecular-Distance-Measures">https://cnx.org/contents/HV-RsdwL@23/Molecular-Distance-Measures</a></p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>P</strong> – Nx3 matrix, where N is the number of points.</p></li>
<li><p><strong>Q</strong> – Nx3 matrix, where N is the number of points.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>3x3 rotation matrix</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>U</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.molecule_matcher.KabschMatcher.match">
<span class="sig-name descname"><span class="pre">match</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">p</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Molecule" title="pymatgen.core.structure.Molecule"><span class="pre">Molecule</span></a></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/molecule_matcher.py#L734-L772"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.molecule_matcher.KabschMatcher.match" title="Link to this definition"></a></dt>
<dd><p>Using the Kabsch algorithm the alignment of two molecules (P, Q)
happens in three steps:
- translate the P and Q into their centroid
- compute of the optimal rotation matrix (U) using Kabsch algorithm
- compute the translation (V) and rmsd.</p>
<p>The function returns the rotation matrix (U), translation vector (V),
and RMSD between Q and P’, where P’ is:</p>
<blockquote>
<div><p>P’ = P * U + V</p>
</div></blockquote>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>p</strong> – a <cite>Molecule</cite> object what will be matched with the target one.</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>Rotation matrix (D,D)
V: Translation vector (D)
RMSD : Root mean squared deviation between P and Q</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>U</p>
</dd>
</dl>
</dd></dl>
</dd></dl>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.analysis.molecule_matcher.MoleculeMatcher">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">MoleculeMatcher</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">tolerance</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">float</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">0.01</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">mapper</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/molecule_matcher.py#L564-L711"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.molecule_matcher.MoleculeMatcher" title="Link to this definition"></a></dt>
<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">MSONable</span></code></p>
<p>Match molecules and identify whether molecules are the same.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>tolerance</strong> (<em>float</em>) – RMSD difference threshold whether two molecules are
different</p></li>
<li><p><strong>mapper</strong> (<a class="reference internal" href="#pymatgen.analysis.molecule_matcher.AbstractMolAtomMapper" title="pymatgen.analysis.molecule_matcher.AbstractMolAtomMapper"><em>AbstractMolAtomMapper</em></a>) – MolAtomMapper object that is able to map the atoms of two
molecule to uniform order.</p></li>
</ul>
</dd>
</dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.molecule_matcher.MoleculeMatcher.as_dict">
<span class="sig-name descname"><span class="pre">as_dict</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/molecule_matcher.py#L689-L697"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.molecule_matcher.MoleculeMatcher.as_dict" title="Link to this definition"></a></dt>
<dd><p>Get MSONable dict.</p>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.molecule_matcher.MoleculeMatcher.fit">
<span class="sig-name descname"><span class="pre">fit</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">mol1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">mol2</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/molecule_matcher.py#L583-L593"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.molecule_matcher.MoleculeMatcher.fit" title="Link to this definition"></a></dt>
<dd><p>Fit two molecules.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>mol1</strong> – First molecule. OpenBabel OBMol or pymatgen Molecule object</p></li>
<li><p><strong>mol2</strong> – Second molecule. OpenBabel OBMol or pymatgen Molecule object</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>True if two molecules are the same.</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>bool</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.molecule_matcher.MoleculeMatcher.from_dict">
<em class="property"><span class="pre">classmethod</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">from_dict</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">dct</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">dict</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">Self</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/molecule_matcher.py#L699-L711"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.molecule_matcher.MoleculeMatcher.from_dict" title="Link to this definition"></a></dt>
<dd><dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>dct</strong> (<em>dict</em>) – Dict representation.</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>MoleculeMatcher</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.molecule_matcher.MoleculeMatcher.get_rmsd">
<span class="sig-name descname"><span class="pre">get_rmsd</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">mol1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">mol2</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/molecule_matcher.py#L595-L605"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.molecule_matcher.MoleculeMatcher.get_rmsd" title="Link to this definition"></a></dt>
<dd><p>Get RMSD between two molecule with arbitrary atom order.</p>
<dl class="field-list simple">
<dt class="field-odd">Returns<span class="colon">:</span></dt>
<dd class="field-odd"><p>RMSD if topology of the two molecules are the same
Infinite if the topology is different</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.molecule_matcher.MoleculeMatcher.group_molecules">
<span class="sig-name descname"><span class="pre">group_molecules</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">mol_list</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/molecule_matcher.py#L647-L687"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.molecule_matcher.MoleculeMatcher.group_molecules" title="Link to this definition"></a></dt>
<dd><p>Group molecules by structural equality.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>mol_list</strong> – List of OpenBabel OBMol or pymatgen objects</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>A list of lists of matched molecules
Assumption: if s1=s2 and s2=s3, then s1=s3
This may not be true for small tolerances.</p>
</dd>
</dl>
</dd></dl>
</dd></dl>
</section>
<section id="module-pymatgen.analysis.molecule_structure_comparator">
<span id="pymatgen-analysis-molecule-structure-comparator-module"></span><h2>pymatgen.analysis.molecule_structure_comparator module<a class="headerlink" href="#module-pymatgen.analysis.molecule_structure_comparator" title="Link to this heading"></a></h2>
<p>This module provides classes to comparison the structures of the two
molecule. As long as the two molecule have the same bond connection tables,
the molecules are deemed to be same. The atom in the two molecule must be
paired accordingly.
This module is supposed to perform rough comparisons with the atom order
correspondence prerequisite, while molecule_matcher is supposed to do exact
comparisons without the atom order correspondence prerequisite.</p>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.analysis.molecule_structure_comparator.CovalentRadius">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">CovalentRadius</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/molecule_structure_comparator.py#L34-L139"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.molecule_structure_comparator.CovalentRadius" title="Link to this definition"></a></dt>
<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></p>
<p>Covalent radius of the elements.</p>
<p>Beatriz C. et al. Dalton Trans. 2008, 2832-2838. <a class="reference external" href="https://doi.org/10.1039/b801115j">https://doi.org/10.1039/b801115j</a></p>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.analysis.molecule_structure_comparator.CovalentRadius.radius">
<span class="sig-name descname"><span class="pre">radius</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">ClassVar</span></em><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">{'Ac':</span> <span class="pre">2.15,</span> <span class="pre">'Ag':</span> <span class="pre">1.45,</span> <span class="pre">'Al':</span> <span class="pre">1.21,</span> <span class="pre">'Am':</span> <span class="pre">1.8,</span> <span class="pre">'Ar':</span> <span class="pre">1.06,</span> <span class="pre">'As':</span> <span class="pre">1.19,</span> <span class="pre">'At':</span> <span class="pre">1.5,</span> <span class="pre">'Au':</span> <span class="pre">1.36,</span> <span class="pre">'B':</span> <span class="pre">0.84,</span> <span class="pre">'Ba':</span> <span class="pre">2.15,</span> <span class="pre">'Be':</span> <span class="pre">0.96,</span> <span class="pre">'Bi':</span> <span class="pre">1.48,</span> <span class="pre">'Br':</span> <span class="pre">1.2,</span> <span class="pre">'C':</span> <span class="pre">0.73,</span> <span class="pre">'Ca':</span> <span class="pre">1.76,</span> <span class="pre">'Cd':</span> <span class="pre">1.44,</span> <span class="pre">'Ce':</span> <span class="pre">2.04,</span> <span class="pre">'Cl':</span> <span class="pre">1.02,</span> <span class="pre">'Cm':</span> <span class="pre">1.69,</span> <span class="pre">'Co':</span> <span class="pre">1.38,</span> <span class="pre">'Cr':</span> <span class="pre">1.39,</span> <span class="pre">'Cs':</span> <span class="pre">2.44,</span> <span class="pre">'Cu':</span> <span class="pre">1.32,</span> <span class="pre">'Dy':</span> <span class="pre">1.92,</span> <span class="pre">'Er':</span> <span class="pre">1.89,</span> <span class="pre">'Eu':</span> <span class="pre">1.98,</span> <span class="pre">'F':</span> <span class="pre">0.57,</span> <span class="pre">'Fe':</span> <span class="pre">1.42,</span> <span class="pre">'Fr':</span> <span class="pre">2.6,</span> <span class="pre">'Ga':</span> <span class="pre">1.22,</span> <span class="pre">'Gd':</span> <span class="pre">1.96,</span> <span class="pre">'Ge':</span> <span class="pre">1.2,</span> <span class="pre">'H':</span> <span class="pre">0.31,</span> <span class="pre">'He':</span> <span class="pre">0.28,</span> <span class="pre">'Hf':</span> <span class="pre">1.75,</span> <span class="pre">'Hg':</span> <span class="pre">1.32,</span> <span class="pre">'Ho':</span> <span class="pre">1.92,</span> <span class="pre">'I':</span> <span class="pre">1.39,</span> <span class="pre">'In':</span> <span class="pre">1.42,</span> <span class="pre">'Ir':</span> <span class="pre">1.41,</span> <span class="pre">'K':</span> <span class="pre">2.03,</span> <span class="pre">'Kr':</span> <span class="pre">1.16,</span> <span class="pre">'La':</span> <span class="pre">2.07,</span> <span class="pre">'Li':</span> <span class="pre">1.28,</span> <span class="pre">'Lu':</span> <span class="pre">1.87,</span> <span class="pre">'Mg':</span> <span class="pre">1.41,</span> <span class="pre">'Mn':</span> <span class="pre">1.5,</span> <span class="pre">'Mo':</span> <span class="pre">1.54,</span> <span class="pre">'N':</span> <span class="pre">0.71,</span> <span class="pre">'Na':</span> <span class="pre">1.66,</span> <span class="pre">'Nb':</span> <span class="pre">1.64,</span> <span class="pre">'Nd':</span> <span class="pre">2.01,</span> <span class="pre">'Ne':</span> <span class="pre">0.58,</span> <span class="pre">'Ni':</span> <span class="pre">1.24,</span> <span class="pre">'Np':</span> <span class="pre">1.9,</span> <span class="pre">'O':</span> <span class="pre">0.66,</span> <span class="pre">'Os':</span> <span class="pre">1.44,</span> <span class="pre">'P':</span> <span class="pre">1.07,</span> <span class="pre">'Pa':</span> <span class="pre">2,</span> <span class="pre">'Pb':</span> <span class="pre">1.46,</span> <span class="pre">'Pd':</span> <span class="pre">1.39,</span> <span class="pre">'Pm':</span> <span class="pre">1.99,</span> <span class="pre">'Po':</span> <span class="pre">1.4,</span> <span class="pre">'Pr':</span> <span class="pre">2.03,</span> <span class="pre">'Pt':</span> <span class="pre">1.36,</span> <span class="pre">'Pu':</span> <span class="pre">1.87,</span> <span class="pre">'Ra':</span> <span class="pre">2.21,</span> <span class="pre">'Rb':</span> <span class="pre">2.2,</span> <span class="pre">'Re':</span> <span class="pre">1.51,</span> <span class="pre">'Rh':</span> <span class="pre">1.42,</span> <span class="pre">'Rn':</span> <span class="pre">1.5,</span> <span class="pre">'Ru':</span> <span class="pre">1.46,</span> <span class="pre">'S':</span> <span class="pre">1.05,</span> <span class="pre">'Sb':</span> <span class="pre">1.39,</span> <span class="pre">'Sc':</span> <span class="pre">1.7,</span> <span class="pre">'Se':</span> <span class="pre">1.2,</span> <span class="pre">'Si':</span> <span class="pre">1.11,</span> <span class="pre">'Sm':</span> <span class="pre">1.98,</span> <span class="pre">'Sn':</span> <span class="pre">1.39,</span> <span class="pre">'Sr':</span> <span class="pre">1.95,</span> <span class="pre">'Ta':</span> <span class="pre">1.7,</span> <span class="pre">'Tb':</span> <span class="pre">1.94,</span> <span class="pre">'Tc':</span> <span class="pre">1.47,</span> <span class="pre">'Te':</span> <span class="pre">1.38,</span> <span class="pre">'Th':</span> <span class="pre">2.06,</span> <span class="pre">'Ti':</span> <span class="pre">1.6,</span> <span class="pre">'Tl':</span> <span class="pre">1.45,</span> <span class="pre">'Tm':</span> <span class="pre">1.9,</span> <span class="pre">'U':</span> <span class="pre">1.96,</span> <span class="pre">'V':</span> <span class="pre">1.53,</span> <span class="pre">'W':</span> <span class="pre">1.62,</span> <span class="pre">'Xe':</span> <span class="pre">1.4,</span> <span class="pre">'Y':</span> <span class="pre">1.9,</span> <span class="pre">'Yb':</span> <span class="pre">1.87,</span> <span class="pre">'Zn':</span> <span class="pre">1.22,</span> <span class="pre">'Zr':</span> <span class="pre">1.75}</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/molecule_structure_comparator.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.molecule_structure_comparator.CovalentRadius.radius" title="Link to this definition"></a></dt>
<dd></dd></dl>
</dd></dl>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.analysis.molecule_structure_comparator.MoleculeStructureComparator">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">MoleculeStructureComparator</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">bond_length_cap</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0.3</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">covalent_radius</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">{'Ac':</span> <span class="pre">2.15,</span> <span class="pre">'Ag':</span> <span class="pre">1.45,</span> <span class="pre">'Al':</span> <span class="pre">1.21,</span> <span class="pre">'Am':</span> <span class="pre">1.8,</span> <span class="pre">'Ar':</span> <span class="pre">1.06,</span> <span class="pre">'As':</span> <span class="pre">1.19,</span> <span class="pre">'At':</span> <span class="pre">1.5,</span> <span class="pre">'Au':</span> <span class="pre">1.36,</span> <span class="pre">'B':</span> <span class="pre">0.84,</span> <span class="pre">'Ba':</span> <span class="pre">2.15,</span> <span class="pre">'Be':</span> <span class="pre">0.96,</span> <span class="pre">'Bi':</span> <span class="pre">1.48,</span> <span class="pre">'Br':</span> <span class="pre">1.2,</span> <span class="pre">'C':</span> <span class="pre">0.73,</span> <span class="pre">'Ca':</span> <span class="pre">1.76,</span> <span class="pre">'Cd':</span> <span class="pre">1.44,</span> <span class="pre">'Ce':</span> <span class="pre">2.04,</span> <span class="pre">'Cl':</span> <span class="pre">1.02,</span> <span class="pre">'Cm':</span> <span class="pre">1.69,</span> <span class="pre">'Co':</span> <span class="pre">1.38,</span> <span class="pre">'Cr':</span> <span class="pre">1.39,</span> <span class="pre">'Cs':</span> <span class="pre">2.44,</span> <span class="pre">'Cu':</span> <span class="pre">1.32,</span> <span class="pre">'Dy':</span> <span class="pre">1.92,</span> <span class="pre">'Er':</span> <span class="pre">1.89,</span> <span class="pre">'Eu':</span> <span class="pre">1.98,</span> <span class="pre">'F':</span> <span class="pre">0.57,</span> <span class="pre">'Fe':</span> <span class="pre">1.42,</span> <span class="pre">'Fr':</span> <span class="pre">2.6,</span> <span class="pre">'Ga':</span> <span class="pre">1.22,</span> <span class="pre">'Gd':</span> <span class="pre">1.96,</span> <span class="pre">'Ge':</span> <span class="pre">1.2,</span> <span class="pre">'H':</span> <span class="pre">0.31,</span> <span class="pre">'He':</span> <span class="pre">0.28,</span> <span class="pre">'Hf':</span> <span class="pre">1.75,</span> <span class="pre">'Hg':</span> <span class="pre">1.32,</span> <span class="pre">'Ho':</span> <span class="pre">1.92,</span> <span class="pre">'I':</span> <span class="pre">1.39,</span> <span class="pre">'In':</span> <span class="pre">1.42,</span> <span class="pre">'Ir':</span> <span class="pre">1.41,</span> <span class="pre">'K':</span> <span class="pre">2.03,</span> <span class="pre">'Kr':</span> <span class="pre">1.16,</span> <span class="pre">'La':</span> <span class="pre">2.07,</span> <span class="pre">'Li':</span> <span class="pre">1.28,</span> <span class="pre">'Lu':</span> <span class="pre">1.87,</span> <span class="pre">'Mg':</span> <span class="pre">1.41,</span> <span class="pre">'Mn':</span> <span class="pre">1.5,</span> <span class="pre">'Mo':</span> <span class="pre">1.54,</span> <span class="pre">'N':</span> <span class="pre">0.71,</span> <span class="pre">'Na':</span> <span class="pre">1.66,</span> <span class="pre">'Nb':</span> <span class="pre">1.64,</span> <span class="pre">'Nd':</span> <span class="pre">2.01,</span> <span class="pre">'Ne':</span> <span class="pre">0.58,</span> <span class="pre">'Ni':</span> <span class="pre">1.24,</span> <span class="pre">'Np':</span> <span class="pre">1.9,</span> <span class="pre">'O':</span> <span class="pre">0.66,</span> <span class="pre">'Os':</span> <span class="pre">1.44,</span> <span class="pre">'P':</span> <span class="pre">1.07,</span> <span class="pre">'Pa':</span> <span class="pre">2,</span> <span class="pre">'Pb':</span> <span class="pre">1.46,</span> <span class="pre">'Pd':</span> <span class="pre">1.39,</span> <span class="pre">'Pm':</span> <span class="pre">1.99,</span> <span class="pre">'Po':</span> <span class="pre">1.4,</span> <span class="pre">'Pr':</span> <span class="pre">2.03,</span> <span class="pre">'Pt':</span> <span class="pre">1.36,</span> <span class="pre">'Pu':</span> <span class="pre">1.87,</span> <span class="pre">'Ra':</span> <span class="pre">2.21,</span> <span class="pre">'Rb':</span> <span class="pre">2.2,</span> <span class="pre">'Re':</span> <span class="pre">1.51,</span> <span class="pre">'Rh':</span> <span class="pre">1.42,</span> <span class="pre">'Rn':</span> <span class="pre">1.5,</span> <span class="pre">'Ru':</span> <span class="pre">1.46,</span> <span class="pre">'S':</span> <span class="pre">1.05,</span> <span class="pre">'Sb':</span> <span class="pre">1.39,</span> <span class="pre">'Sc':</span> <span class="pre">1.7,</span> <span class="pre">'Se':</span> <span class="pre">1.2,</span> <span class="pre">'Si':</span> <span class="pre">1.11,</span> <span class="pre">'Sm':</span> <span class="pre">1.98,</span> <span class="pre">'Sn':</span> <span class="pre">1.39,</span> <span class="pre">'Sr':</span> <span class="pre">1.95,</span> <span class="pre">'Ta':</span> <span class="pre">1.7,</span> <span class="pre">'Tb':</span> <span class="pre">1.94,</span> <span class="pre">'Tc':</span> <span class="pre">1.47,</span> <span class="pre">'Te':</span> <span class="pre">1.38,</span> <span class="pre">'Th':</span> <span class="pre">2.06,</span> <span class="pre">'Ti':</span> <span class="pre">1.6,</span> <span class="pre">'Tl':</span> <span class="pre">1.45,</span> <span class="pre">'Tm':</span> <span class="pre">1.9,</span> <span class="pre">'U':</span> <span class="pre">1.96,</span> <span class="pre">'V':</span> <span class="pre">1.53,</span> <span class="pre">'W':</span> <span class="pre">1.62,</span> <span class="pre">'Xe':</span> <span class="pre">1.4,</span> <span class="pre">'Y':</span> <span class="pre">1.9,</span> <span class="pre">'Yb':</span> <span class="pre">1.87,</span> <span class="pre">'Zn':</span> <span class="pre">1.22,</span> <span class="pre">'Zr':</span> <span class="pre">1.75}</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">priority_bonds</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">priority_cap</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0.8</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ignore_ionic_bond</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">bond_13_cap</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0.05</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/molecule_structure_comparator.py#L142-L300"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.molecule_structure_comparator.MoleculeStructureComparator" title="Link to this definition"></a></dt>
<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">MSONable</span></code></p>
<p>Check whether the connection tables of the two molecules are the
same. The atom in the two molecule must be paired accordingly.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>bond_length_cap</strong> – The ratio of the elongation of the bond to be
acknowledged. If the distance between two atoms is less than (
empirical covalent bond length) X (1 + bond_length_cap), the bond
between the two atoms will be acknowledged.</p></li>
<li><p><strong>covalent_radius</strong> – The covalent radius of the atoms.
dict (element symbol -> radius)</p></li>
<li><p><strong>priority_bonds</strong> – The bonds that are known to be existed in the initial
molecule. Such bonds will be acknowledged in a loose criteria.
The index should start from 0.</p></li>
<li><p><strong>priority_cap</strong> – The ratio of the elongation of the bond to be
acknowledged for the priority bonds.</p></li>
</ul>
</dd>
</dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.molecule_structure_comparator.MoleculeStructureComparator.are_equal">
<span class="sig-name descname"><span class="pre">are_equal</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">mol1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">mol2</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">bool</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/molecule_structure_comparator.py#L197-L207"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.molecule_structure_comparator.MoleculeStructureComparator.are_equal" title="Link to this definition"></a></dt>
<dd><p>Compare the bond table of the two molecules.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>mol1</strong> – first molecule. pymatgen Molecule object.</p></li>
<li><p><strong>mol2</strong> – second molecules. pymatgen Molecule object.</p></li>
</ul>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.molecule_structure_comparator.MoleculeStructureComparator.as_dict">
<span class="sig-name descname"><span class="pre">as_dict</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/molecule_structure_comparator.py#L274-L284"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.molecule_structure_comparator.MoleculeStructureComparator.as_dict" title="Link to this definition"></a></dt>
<dd><p>Get MSONable dict.</p>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.molecule_structure_comparator.MoleculeStructureComparator.from_dict">
<em class="property"><span class="pre">classmethod</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">from_dict</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">dct</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">dict</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">Self</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/molecule_structure_comparator.py#L286-L300"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.molecule_structure_comparator.MoleculeStructureComparator.from_dict" title="Link to this definition"></a></dt>
<dd><dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>dct</strong> (<em>dict</em>) – Dict representation.</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>MoleculeStructureComparator</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.molecule_structure_comparator.MoleculeStructureComparator.get_13_bonds">
<em class="property"><span class="pre">static</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">get_13_bonds</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">priority_bonds</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/molecule_structure_comparator.py#L209-L225"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.molecule_structure_comparator.MoleculeStructureComparator.get_13_bonds" title="Link to this definition"></a></dt>
<dd><dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>priority_bonds</strong> (<em>list</em><em>[</em><em>tuple</em><em>]</em>) – 12 bonds</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>13 bonds</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>tuple</p>
</dd>
</dl>
</dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.analysis.molecule_structure_comparator.MoleculeStructureComparator.halogen_list">
<span class="sig-name descname"><span class="pre">halogen_list</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">('F',</span> <span class="pre">'Cl',</span> <span class="pre">'Br',</span> <span class="pre">'I')</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/molecule_structure_comparator.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.molecule_structure_comparator.MoleculeStructureComparator.halogen_list" title="Link to this definition"></a></dt>
<dd></dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.analysis.molecule_structure_comparator.MoleculeStructureComparator.ionic_element_list">
<span class="sig-name descname"><span class="pre">ionic_element_list</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">('Na',</span> <span class="pre">'Mg',</span> <span class="pre">'Al',</span> <span class="pre">'Sc',</span> <span class="pre">'V',</span> <span class="pre">'Cr',</span> <span class="pre">'Mn',</span> <span class="pre">'Fe',</span> <span class="pre">'Co',</span> <span class="pre">'Ni',</span> <span class="pre">'Cu',</span> <span class="pre">'Zn',</span> <span class="pre">'Ga',</span> <span class="pre">'Rb',</span> <span class="pre">'Sr')</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/molecule_structure_comparator.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.molecule_structure_comparator.MoleculeStructureComparator.ionic_element_list" title="Link to this definition"></a></dt>
<dd></dd></dl>
</dd></dl>
</section>
<section id="module-pymatgen.analysis.nmr">
<span id="pymatgen-analysis-nmr-module"></span><h2>pymatgen.analysis.nmr module<a class="headerlink" href="#module-pymatgen.analysis.nmr" title="Link to this heading"></a></h2>
<p>A module for NMR analysis.</p>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.analysis.nmr.ChemicalShielding">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">ChemicalShielding</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cs_matrix</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">vscale</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/nmr.py#L28-L135"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.nmr.ChemicalShielding" title="Link to this definition"></a></dt>
<dd><p>Bases: <a class="reference internal" href="pymatgen.core.html#pymatgen.core.tensors.SquareTensor" title="pymatgen.core.tensors.SquareTensor"><code class="xref py py-class docutils literal notranslate"><span class="pre">SquareTensor</span></code></a></p>
<p>This class extends the SquareTensor to perform extra analysis unique to
NMR Chemical shielding tensors.</p>
<p>Three notations to describe chemical shielding tensor (RK Harris; Magn. Resonance
Chem. 2008, 46, 582-598; DOI: 10.1002/mrc.2225) are supported.</p>
<p>Authors: Shyam Dwaraknath, Xiaohui Qu</p>
<p>Create a Chemical Shielding tensor.
Note that the constructor uses __new__
rather than __init__ according to the standard method of
subclassing numpy ndarrays.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>cs_matrix</strong> (<em>1x3</em><em> or </em><em>3x3 array-like</em>) – the 3x3 array-like
representing the chemical shielding tensor
or a 1x3 array of the primary sigma values corresponding
to the principal axis system</p></li>
<li><p><strong>vscale</strong> (<em>6x1 array-like</em>) – 6x1 array-like scaling the
Voigt notation vector with the tensor entries</p></li>
</ul>
</dd>
</dl>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.analysis.nmr.ChemicalShielding.HaeberlenNotation">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">HaeberlenNotation</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">sigma_iso</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">delta_sigma_iso</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">zeta</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">eta</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/nmr.py#L40-L44"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.nmr.ChemicalShielding.HaeberlenNotation" title="Link to this definition"></a></dt>
<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">NamedTuple</span></code></p>
<p>Create new instance of HaeberlenNotation(sigma_iso, delta_sigma_iso, zeta, eta)</p>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.analysis.nmr.ChemicalShielding.HaeberlenNotation.delta_sigma_iso">
<span class="sig-name descname"><span class="pre">delta_sigma_iso</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">Any</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/nmr.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.nmr.ChemicalShielding.HaeberlenNotation.delta_sigma_iso" title="Link to this definition"></a></dt>
<dd><p>Alias for field number 1</p>
</dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.analysis.nmr.ChemicalShielding.HaeberlenNotation.eta">
<span class="sig-name descname"><span class="pre">eta</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">Any</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/nmr.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.nmr.ChemicalShielding.HaeberlenNotation.eta" title="Link to this definition"></a></dt>
<dd><p>Alias for field number 3</p>
</dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.analysis.nmr.ChemicalShielding.HaeberlenNotation.sigma_iso">
<span class="sig-name descname"><span class="pre">sigma_iso</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">Any</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/nmr.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.nmr.ChemicalShielding.HaeberlenNotation.sigma_iso" title="Link to this definition"></a></dt>
<dd><p>Alias for field number 0</p>
</dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.analysis.nmr.ChemicalShielding.HaeberlenNotation.zeta">
<span class="sig-name descname"><span class="pre">zeta</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">Any</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/nmr.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.nmr.ChemicalShielding.HaeberlenNotation.zeta" title="Link to this definition"></a></dt>
<dd><p>Alias for field number 2</p>
</dd></dl>
</dd></dl>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.analysis.nmr.ChemicalShielding.MarylandNotation">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">MarylandNotation</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">sigma_iso</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">omega</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">kappa</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/nmr.py#L52-L55"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.nmr.ChemicalShielding.MarylandNotation" title="Link to this definition"></a></dt>
<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">NamedTuple</span></code></p>
<p>Create new instance of MarylandNotation(sigma_iso, omega, kappa)</p>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.analysis.nmr.ChemicalShielding.MarylandNotation.kappa">
<span class="sig-name descname"><span class="pre">kappa</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">Any</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/nmr.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.nmr.ChemicalShielding.MarylandNotation.kappa" title="Link to this definition"></a></dt>
<dd><p>Alias for field number 2</p>
</dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.analysis.nmr.ChemicalShielding.MarylandNotation.omega">
<span class="sig-name descname"><span class="pre">omega</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">Any</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/nmr.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.nmr.ChemicalShielding.MarylandNotation.omega" title="Link to this definition"></a></dt>
<dd><p>Alias for field number 1</p>
</dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.analysis.nmr.ChemicalShielding.MarylandNotation.sigma_iso">
<span class="sig-name descname"><span class="pre">sigma_iso</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">Any</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/nmr.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.nmr.ChemicalShielding.MarylandNotation.sigma_iso" title="Link to this definition"></a></dt>
<dd><p>Alias for field number 0</p>
</dd></dl>
</dd></dl>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.analysis.nmr.ChemicalShielding.MehringNotation">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">MehringNotation</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">sigma_iso</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">sigma_11</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">sigma_22</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">sigma_33</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/nmr.py#L46-L50"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.nmr.ChemicalShielding.MehringNotation" title="Link to this definition"></a></dt>
<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">NamedTuple</span></code></p>
<p>Create new instance of MehringNotation(sigma_iso, sigma_11, sigma_22, sigma_33)</p>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.analysis.nmr.ChemicalShielding.MehringNotation.sigma_11">
<span class="sig-name descname"><span class="pre">sigma_11</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">Any</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/nmr.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.nmr.ChemicalShielding.MehringNotation.sigma_11" title="Link to this definition"></a></dt>
<dd><p>Alias for field number 1</p>
</dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.analysis.nmr.ChemicalShielding.MehringNotation.sigma_22">
<span class="sig-name descname"><span class="pre">sigma_22</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">Any</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/nmr.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.nmr.ChemicalShielding.MehringNotation.sigma_22" title="Link to this definition"></a></dt>
<dd><p>Alias for field number 2</p>
</dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.analysis.nmr.ChemicalShielding.MehringNotation.sigma_33">
<span class="sig-name descname"><span class="pre">sigma_33</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">Any</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/nmr.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.nmr.ChemicalShielding.MehringNotation.sigma_33" title="Link to this definition"></a></dt>
<dd><p>Alias for field number 3</p>
</dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.analysis.nmr.ChemicalShielding.MehringNotation.sigma_iso">
<span class="sig-name descname"><span class="pre">sigma_iso</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">Any</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/nmr.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.nmr.ChemicalShielding.MehringNotation.sigma_iso" title="Link to this definition"></a></dt>
<dd><p>Alias for field number 0</p>
</dd></dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.nmr.ChemicalShielding.from_maryland_notation">
<em class="property"><span class="pre">classmethod</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">from_maryland_notation</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">sigma_iso</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">omega</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">kappa</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">Self</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/nmr.py#L119-L135"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.nmr.ChemicalShielding.from_maryland_notation" title="Link to this definition"></a></dt>
<dd><p>Initialize from Maryland notation.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>sigma_iso</strong> (<em>float</em>) – isotropic chemical shielding</p></li>
<li><p><strong>omega</strong> (<em>float</em>) – anisotropy</p></li>
<li><p><strong>kappa</strong> (<em>float</em>) – asymmetry parameter</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>ChemicalShielding</p>
</dd>
</dl>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.analysis.nmr.ChemicalShielding.haeberlen_values">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">haeberlen_values</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/nmr.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.nmr.ChemicalShielding.haeberlen_values" title="Link to this definition"></a></dt>
<dd><p>The Chemical shielding tensor in Haeberlen Notation.</p>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.analysis.nmr.ChemicalShielding.maryland_values">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">maryland_values</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/nmr.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.nmr.ChemicalShielding.maryland_values" title="Link to this definition"></a></dt>
<dd><p>The Chemical shielding tensor in Maryland Notation.</p>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.analysis.nmr.ChemicalShielding.mehring_values">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">mehring_values</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/nmr.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.nmr.ChemicalShielding.mehring_values" title="Link to this definition"></a></dt>
<dd><p>The Chemical shielding tensor in Mehring Notation.</p>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.analysis.nmr.ChemicalShielding.principal_axis_system">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">principal_axis_system</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/nmr.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.nmr.ChemicalShielding.principal_axis_system" title="Link to this definition"></a></dt>
<dd><p>A chemical shielding tensor aligned to the principle axis system
so that only the 3 diagonal components are non-zero.</p>
</dd></dl>
</dd></dl>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.analysis.nmr.ElectricFieldGradient">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">ElectricFieldGradient</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">efg_matrix</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">vscale</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/nmr.py#L138-L243"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.nmr.ElectricFieldGradient" title="Link to this definition"></a></dt>
<dd><p>Bases: <a class="reference internal" href="pymatgen.core.html#pymatgen.core.tensors.SquareTensor" title="pymatgen.core.tensors.SquareTensor"><code class="xref py py-class docutils literal notranslate"><span class="pre">SquareTensor</span></code></a></p>
<p>This class extends the SquareTensor to perform extra analysis unique to
NMR Electric Field Gradient tensors in units of V/Angstrom^2.</p>
<p>Authors: Shyam Dwaraknath, Xiaohui Qu</p>
<p>Create a Chemical Shielding tensor.
Note that the constructor uses __new__
rather than __init__ according to the standard method of
subclassing numpy ndarrays.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>efg_matrix</strong> (<em>1x3</em><em> or </em><em>3x3 array-like</em>) – the 3x3 array-like
representing the electric field tensor
or a 1x3 array of the primary values corresponding
to the principal axis system</p></li>
<li><p><strong>vscale</strong> (<em>6x1 array-like</em>) – 6x1 array-like scaling the
Voigt notation vector with the tensor entries</p></li>
</ul>
</dd>
</dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.analysis.nmr.ElectricFieldGradient.V_xx">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">V_xx</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/nmr.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.nmr.ElectricFieldGradient.V_xx" title="Link to this definition"></a></dt>
<dd><p>First diagonal element.</p>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.analysis.nmr.ElectricFieldGradient.V_yy">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">V_yy</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/nmr.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.nmr.ElectricFieldGradient.V_yy" title="Link to this definition"></a></dt>
<dd><p>Second diagonal element.</p>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.analysis.nmr.ElectricFieldGradient.V_zz">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">V_zz</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/nmr.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.nmr.ElectricFieldGradient.V_zz" title="Link to this definition"></a></dt>
<dd><p>Third diagonal element.</p>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.analysis.nmr.ElectricFieldGradient.asymmetry">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">asymmetry</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/nmr.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.nmr.ElectricFieldGradient.asymmetry" title="Link to this definition"></a></dt>
<dd><p>Asymmetry of the electric field tensor defined as (V_yy - V_xx)/V_zz.</p>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.nmr.ElectricFieldGradient.coupling_constant">
<span class="sig-name descname"><span class="pre">coupling_constant</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">specie</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/nmr.py#L201-L243"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.nmr.ElectricFieldGradient.coupling_constant" title="Link to this definition"></a></dt>
<dd><p>Compute the coupling constant C_q as defined in:</p>
<blockquote>
<div><p>Wasylishen R E, Ashbrook S E, Wimperis S. NMR of quadrupolar nuclei
in solid materials[M]. John Wiley & Sons, 2012. (Chapter 3.2).</p>
</div></blockquote>
<dl>
<dt>C_q for a specific atom type for this electric field tensor:</dt><dd><blockquote>
<div><p>C_q=e*Q*V_zz/h</p>
</div></blockquote>
<p>h: Planck’s constant
Q: nuclear electric quadrupole moment in mb (millibarn
e: elementary proton charge</p>
</dd>
</dl>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>specie</strong> – flexible input to specify the species at this site.
Can take a isotope or element string, Species object,
or Site object</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>the coupling constant as a FloatWithUnit in MHz</p>
</dd>
</dl>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.analysis.nmr.ElectricFieldGradient.principal_axis_system">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">principal_axis_system</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/nmr.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.nmr.ElectricFieldGradient.principal_axis_system" title="Link to this definition"></a></dt>
<dd><p>An electric field gradient tensor aligned to the principle axis system so that
only the 3 diagonal components are non-zero.</p>
</dd></dl>
</dd></dl>
</section>
<section id="module-pymatgen.analysis.phase_diagram">
<span id="pymatgen-analysis-phase-diagram-module"></span><h2>pymatgen.analysis.phase_diagram module<a class="headerlink" href="#module-pymatgen.analysis.phase_diagram" title="Link to this heading"></a></h2>
<p>This module defines tools to generate and analyze phase diagrams.</p>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.analysis.phase_diagram.CompoundPhaseDiagram">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">CompoundPhaseDiagram</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entries</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">terminal_compositions</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">normalize_terminal_compositions</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/phase_diagram.py#L1460-L1583"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.phase_diagram.CompoundPhaseDiagram" title="Link to this definition"></a></dt>
<dd><p>Bases: <a class="reference internal" href="#pymatgen.analysis.phase_diagram.PhaseDiagram" title="pymatgen.analysis.phase_diagram.PhaseDiagram"><code class="xref py py-class docutils literal notranslate"><span class="pre">PhaseDiagram</span></code></a></p>
<p>Generates phase diagrams from compounds as terminations instead of
elements.</p>
<p>Initialize a CompoundPhaseDiagram.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>entries</strong> (<em>[</em><a class="reference internal" href="#pymatgen.analysis.phase_diagram.PDEntry" title="pymatgen.analysis.phase_diagram.PDEntry"><em>PDEntry</em></a><em>]</em>) – Sequence of input entries. For example,
if you want a Li2O-P2O5 phase diagram, you might have all
Li-P-O entries as an input.</p></li>
<li><p><strong>terminal_compositions</strong> (<em>list</em><em>[</em><a class="reference internal" href="pymatgen.core.html#pymatgen.core.composition.Composition" title="pymatgen.core.composition.Composition"><em>Composition</em></a><em>]</em>) – Terminal compositions of
phase space. In the Li2O-P2O5 example, these will be the
Li2O and P2O5 compositions.</p></li>
<li><p><strong>normalize_terminal_compositions</strong> (<em>bool</em>) – Whether to normalize the
terminal compositions to a per atom basis. If normalized,
the energy above hulls will be consistent
for comparison across systems. Non-normalized terminals are
more intuitive in terms of compositional breakdowns.</p></li>
</ul>
</dd>
</dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.analysis.phase_diagram.CompoundPhaseDiagram.amount_tol">
<span class="sig-name descname"><span class="pre">amount_tol</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">1e-05</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/phase_diagram.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.phase_diagram.CompoundPhaseDiagram.amount_tol" title="Link to this definition"></a></dt>
<dd></dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.phase_diagram.CompoundPhaseDiagram.as_dict">
<span class="sig-name descname"><span class="pre">as_dict</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/phase_diagram.py#L1562-L1570"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.phase_diagram.CompoundPhaseDiagram.as_dict" title="Link to this definition"></a></dt>
<dd><p>Get MSONable dict representation of CompoundPhaseDiagram.</p>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.phase_diagram.CompoundPhaseDiagram.from_dict">
<em class="property"><span class="pre">classmethod</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">from_dict</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">dct</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">dict</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">Self</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/phase_diagram.py#L1572-L1583"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.phase_diagram.CompoundPhaseDiagram.from_dict" title="Link to this definition"></a></dt>
<dd><dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>dct</strong> (<em>dict</em>) – dictionary representation of CompoundPhaseDiagram.</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>CompoundPhaseDiagram</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.phase_diagram.CompoundPhaseDiagram.num2str">
<em class="property"><span class="pre">static</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">num2str</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">num</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/phase_diagram.py#L1492-L1518"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.phase_diagram.CompoundPhaseDiagram.num2str" title="Link to this definition"></a></dt>
<dd><p>Convert number to a list of letter(s). First letter must be <cite>f</cite>.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>int</strong> (<em>num</em>) – Number to convert</p>
</dd>
<dt class="field-even">Return type<span class="colon">:</span></dt>
<dd class="field-even"><p>str</p>
</dd>
</dl>
<p>:return Converted string</p>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.phase_diagram.CompoundPhaseDiagram.transform_entries">
<span class="sig-name descname"><span class="pre">transform_entries</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entries</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">terminal_compositions</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/phase_diagram.py#L1520-L1560"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.phase_diagram.CompoundPhaseDiagram.transform_entries" title="Link to this definition"></a></dt>
<dd><p>Method to transform all entries to the composition coordinate in the
terminal compositions. If the entry does not fall within the space
defined by the terminal compositions, they are excluded. For example,
Li3PO4 is mapped into a Li2O:1.5, P2O5:0.5 composition. The terminal
compositions are represented by DummySpecies.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>entries</strong> – Sequence of all input entries</p></li>
<li><p><strong>terminal_compositions</strong> – Terminal compositions of phase space.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>Sequence of TransformedPDEntries falling within the phase space.</p>
</dd>
</dl>
</dd></dl>
</dd></dl>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.analysis.phase_diagram.GrandPotPDEntry">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">GrandPotPDEntry</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entry</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">chempots</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">name</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/phase_diagram.py#L121-L203"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.phase_diagram.GrandPotPDEntry" title="Link to this definition"></a></dt>
<dd><p>Bases: <a class="reference internal" href="#pymatgen.analysis.phase_diagram.PDEntry" title="pymatgen.analysis.phase_diagram.PDEntry"><code class="xref py py-class docutils literal notranslate"><span class="pre">PDEntry</span></code></a></p>
<p>A grand potential pd entry object encompassing all relevant data for phase
diagrams. Chemical potentials are given as a element-chemical potential
dict.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>entry</strong> – A PDEntry-like object.</p></li>
<li><p><strong>chempots</strong> – Chemical potential specification as {Element: float}.</p></li>
<li><p><strong>name</strong> – Optional parameter to name the entry. Defaults to the reduced
chemical formula of the original entry.</p></li>
</ul>
</dd>
</dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.phase_diagram.GrandPotPDEntry.as_dict">
<span class="sig-name descname"><span class="pre">as_dict</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/phase_diagram.py#L182-L190"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.phase_diagram.GrandPotPDEntry.as_dict" title="Link to this definition"></a></dt>
<dd><p>Get MSONable dict representation of GrandPotPDEntry.</p>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.analysis.phase_diagram.GrandPotPDEntry.chemical_energy">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">chemical_energy</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/phase_diagram.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.phase_diagram.GrandPotPDEntry.chemical_energy" title="Link to this definition"></a></dt>
<dd><p>The chemical energy term mu*N in the grand potential.</p>
<dl class="field-list simple">
<dt class="field-odd">Returns<span class="colon">:</span></dt>
<dd class="field-odd"><p>The chemical energy term mu*N in the grand potential</p>
</dd>
</dl>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.analysis.phase_diagram.GrandPotPDEntry.composition">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">composition</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><a class="reference internal" href="pymatgen.core.html#pymatgen.core.composition.Composition" title="pymatgen.core.composition.Composition"><span class="pre">Composition</span></a></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/phase_diagram.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.phase_diagram.GrandPotPDEntry.composition" title="Link to this definition"></a></dt>
<dd><p>The composition after removing free species.</p>
<dl class="field-list simple">
<dt class="field-odd">Returns<span class="colon">:</span></dt>
<dd class="field-odd"><p>Composition</p>
</dd>
</dl>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.analysis.phase_diagram.GrandPotPDEntry.energy">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">energy</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">float</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/phase_diagram.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.phase_diagram.GrandPotPDEntry.energy" title="Link to this definition"></a></dt>
<dd><p>Grand potential energy.</p>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.phase_diagram.GrandPotPDEntry.from_dict">
<em class="property"><span class="pre">classmethod</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">from_dict</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">dct</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">dict</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">Self</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/phase_diagram.py#L192-L203"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.phase_diagram.GrandPotPDEntry.from_dict" title="Link to this definition"></a></dt>
<dd><dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>dct</strong> (<em>dict</em>) – dictionary representation of GrandPotPDEntry.</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>GrandPotPDEntry</p>
</dd>
</dl>
</dd></dl>
</dd></dl>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.analysis.phase_diagram.GrandPotentialPhaseDiagram">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">GrandPotentialPhaseDiagram</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entries</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">chempots</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">elements</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">*</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">computed_data</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/phase_diagram.py#L1365-L1457"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.phase_diagram.GrandPotentialPhaseDiagram" title="Link to this definition"></a></dt>
<dd><p>Bases: <a class="reference internal" href="#pymatgen.analysis.phase_diagram.PhaseDiagram" title="pymatgen.analysis.phase_diagram.PhaseDiagram"><code class="xref py py-class docutils literal notranslate"><span class="pre">PhaseDiagram</span></code></a></p>
<p>A class representing a Grand potential phase diagram. Grand potential phase
diagrams are essentially phase diagrams that are open to one or more
components. To construct such phase diagrams, the relevant free energy is
the grand potential, which can be written as the Legendre transform of the
Gibbs free energy as follows.</p>
<p>Grand potential = G - u_X N_X</p>
<p>The algorithm is based on the work in the following papers:</p>
<ol class="arabic simple">
<li><p>S. P. Ong, L. Wang, B. Kang, and G. Ceder, Li-Fe-P-O2 Phase Diagram from
First Principles Calculations. Chem. Mater., 2008, 20(5), 1798-1807.
doi:10.1021/cm702327g</p></li>
<li><p>S. P. Ong, A. Jain, G. Hautier, B. Kang, G. Ceder, Thermal stabilities
of delithiated olivine MPO4 (M=Fe, Mn) cathodes investigated using first
principles calculations. Electrochem. Comm., 2010, 12(3), 427-430.
doi:10.1016/j.elecom.2010.01.010</p></li>
</ol>
<p>Standard constructor for grand potential phase diagram.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>entries</strong> (<em>[</em><a class="reference internal" href="#pymatgen.analysis.phase_diagram.PDEntry" title="pymatgen.analysis.phase_diagram.PDEntry"><em>PDEntry</em></a><em>]</em>) – A list of PDEntry-like objects having an
energy, energy_per_atom and composition.</p></li>
<li><p><strong>(</strong><strong>{Element</strong> (<em>chempots</em>) – float}): Specify the chemical potentials
of the open elements.</p></li>
<li><p><strong>elements</strong> (<em>[</em><a class="reference internal" href="pymatgen.core.html#pymatgen.core.periodic_table.Element" title="pymatgen.core.periodic_table.Element"><em>Element</em></a><em>]</em>) – Optional list of elements in the phase
diagram. If set to None, the elements are determined from
the entries themselves.</p></li>
<li><p><strong>computed_data</strong> (<em>dict</em>) – A dict containing pre-computed data. This allows
PhaseDiagram object to be reconstituted without performing the
expensive convex hull computation. The dict is the output from the
PhaseDiagram._compute() method and is stored in PhaseDiagram.computed_data
when generated for the first time.</p></li>
</ul>
</dd>
</dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.phase_diagram.GrandPotentialPhaseDiagram.as_dict">
<span class="sig-name descname"><span class="pre">as_dict</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/phase_diagram.py#L1436-L1444"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.phase_diagram.GrandPotentialPhaseDiagram.as_dict" title="Link to this definition"></a></dt>
<dd><p>Get MSONable dict representation of GrandPotentialPhaseDiagram.</p>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.phase_diagram.GrandPotentialPhaseDiagram.from_dict">
<em class="property"><span class="pre">classmethod</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">from_dict</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">dct</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">dict</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">Self</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/phase_diagram.py#L1446-L1457"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.phase_diagram.GrandPotentialPhaseDiagram.from_dict" title="Link to this definition"></a></dt>
<dd><dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>dct</strong> (<em>dict</em>) – dictionary representation of GrandPotentialPhaseDiagram.</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>GrandPotentialPhaseDiagram</p>
</dd>
</dl>
</dd></dl>
</dd></dl>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.analysis.phase_diagram.PDEntry">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">PDEntry</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">composition</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="pymatgen.core.html#pymatgen.core.composition.Composition" title="pymatgen.core.composition.Composition"><span class="pre">Composition</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">energy</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">float</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">name</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">attribute</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">object</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/phase_diagram.py#L55-L118"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.phase_diagram.PDEntry" title="Link to this definition"></a></dt>
<dd><p>Bases: <a class="reference internal" href="pymatgen.entries.html#pymatgen.entries.Entry" title="pymatgen.entries.Entry"><code class="xref py py-class docutils literal notranslate"><span class="pre">Entry</span></code></a></p>
<p>An object encompassing all relevant data for phase diagrams.</p>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.analysis.phase_diagram.PDEntry.composition">
<span class="sig-name descname"><span class="pre">composition</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/phase_diagram.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.phase_diagram.PDEntry.composition" title="Link to this definition"></a></dt>
<dd><p>The composition associated with the PDEntry.</p>
<dl class="field-list simple">
<dt class="field-odd">Type<span class="colon">:</span></dt>
<dd class="field-odd"><p><a class="reference internal" href="pymatgen.core.html#pymatgen.core.composition.Composition" title="pymatgen.core.composition.Composition">Composition</a></p>
</dd>
</dl>
</dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.analysis.phase_diagram.PDEntry.energy">
<span class="sig-name descname"><span class="pre">energy</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/phase_diagram.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.phase_diagram.PDEntry.energy" title="Link to this definition"></a></dt>
<dd><p>The energy associated with the entry.</p>
<dl class="field-list simple">
<dt class="field-odd">Type<span class="colon">:</span></dt>
<dd class="field-odd"><p>float</p>
</dd>
</dl>
</dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.analysis.phase_diagram.PDEntry.name">
<span class="sig-name descname"><span class="pre">name</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/phase_diagram.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.phase_diagram.PDEntry.name" title="Link to this definition"></a></dt>
<dd><p>A name for the entry. This is the string shown in the phase diagrams.
By default, this is the reduced formula for the composition, but can be
set to some other string for display purposes.</p>
<dl class="field-list simple">
<dt class="field-odd">Type<span class="colon">:</span></dt>
<dd class="field-odd"><p>str</p>
</dd>
</dl>
</dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.analysis.phase_diagram.PDEntry.attribute">
<span class="sig-name descname"><span class="pre">attribute</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/phase_diagram.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.phase_diagram.PDEntry.attribute" title="Link to this definition"></a></dt>
<dd><p>A arbitrary attribute. Can be used to specify that the
entry is a newly found compound, or to specify a particular label for
the entry, etc. An attribute can be anything but must be MSONable.</p>
<dl class="field-list simple">
<dt class="field-odd">Type<span class="colon">:</span></dt>
<dd class="field-odd"><p>MSONable</p>
</dd>
</dl>
</dd></dl>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>composition</strong> (<a class="reference internal" href="pymatgen.core.html#pymatgen.core.composition.Composition" title="pymatgen.core.composition.Composition"><em>Composition</em></a>) – Composition</p></li>
<li><p><strong>energy</strong> (<em>float</em>) – Energy for composition.</p></li>
<li><p><strong>name</strong> (<em>str</em>) – Optional parameter to name the entry. Defaults
to the reduced chemical formula.</p></li>
<li><p><strong>attribute</strong> – Optional attribute of the entry. Must be MSONable.</p></li>
</ul>
</dd>
</dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.phase_diagram.PDEntry.as_dict">
<span class="sig-name descname"><span class="pre">as_dict</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/phase_diagram.py#L100-L102"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.phase_diagram.PDEntry.as_dict" title="Link to this definition"></a></dt>
<dd><p>Get MSONable dict representation of PDEntry.</p>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="id0">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">energy</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">float</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/phase_diagram.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#id0" title="Link to this definition"></a></dt>
<dd><p>The entry’s energy.</p>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.phase_diagram.PDEntry.from_dict">
<em class="property"><span class="pre">classmethod</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">from_dict</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">dct</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">dict</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">Self</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/phase_diagram.py#L104-L118"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.phase_diagram.PDEntry.from_dict" title="Link to this definition"></a></dt>
<dd><dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>dct</strong> (<em>dict</em>) – dictionary representation of PDEntry.</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>PDEntry</p>
</dd>
</dl>
</dd></dl>
</dd></dl>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.analysis.phase_diagram.PDPlotter">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">PDPlotter</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">phasediagram</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="#pymatgen.analysis.phase_diagram.PhaseDiagram" title="pymatgen.analysis.phase_diagram.PhaseDiagram"><span class="pre">PhaseDiagram</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">show_unstable</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">float</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">0.2</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">backend</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">Literal</span><span class="p"><span class="pre">[</span></span><span class="s"><span class="pre">'plotly'</span></span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="s"><span class="pre">'matplotlib'</span></span><span class="p"><span class="pre">]</span></span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">'plotly'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ternary_style</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">Literal</span><span class="p"><span class="pre">[</span></span><span class="s"><span class="pre">'2d'</span></span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="s"><span class="pre">'3d'</span></span><span class="p"><span class="pre">]</span></span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">'2d'</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">plotkwargs</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/phase_diagram.py#L2190-L3853"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.phase_diagram.PDPlotter" title="Link to this definition"></a></dt>
<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></p>
<p>A plotting class for compositional phase diagrams.</p>
<p>To use, initialize this class with a PhaseDiagram object containing 1-4 components
and call get_plot() or show().</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>phasediagram</strong> (<a class="reference internal" href="#pymatgen.analysis.phase_diagram.PhaseDiagram" title="pymatgen.analysis.phase_diagram.PhaseDiagram"><em>PhaseDiagram</em></a>) – PhaseDiagram object (must be 1-4 components).</p></li>
<li><p><strong>show_unstable</strong> (<em>float</em>) – Whether unstable (above the hull) phases will be
plotted. If a number > 0 is entered, all phases with
e_hull < show_unstable (eV/atom) will be shown.</p></li>
<li><p><strong>backend</strong> (<em>"plotly"</em><em> | </em><em>"matplotlib"</em>) – Python package to use for plotting.
Defaults to “plotly”.</p></li>
<li><p><strong>ternary_style</strong> (<em>"2d"</em><em> | </em><em>"3d"</em>) – Ternary phase diagrams are typically plotted in
two-dimensions (2d), but can be plotted in three dimensions (3d) to visualize
the depth of the hull. This argument only applies when backend=”plotly”.
Defaults to “2d”.</p></li>
<li><p><strong>**plotkwargs</strong> (<em>dict</em>) – <p>Keyword args passed to matplotlib.pyplot.plot (only
applies when backend=”matplotlib”). Can be used to customize markers
etc. If not set, the default is:</p>
<blockquote>
<div><dl class="simple">
<dt>{</dt><dd><p>“markerfacecolor”: “#4daf4a”,
“markersize”: 10,
“linewidth”: 3</p>
</dd>
</dl>
<p>}.</p>
</div></blockquote>
</p></li>
</ul>
</dd>
</dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.phase_diagram.PDPlotter.get_chempot_range_map_plot">
<span class="sig-name descname"><span class="pre">get_chempot_range_map_plot</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">elements</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">referenced</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/phase_diagram.py#L2446-L2548"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.phase_diagram.PDPlotter.get_chempot_range_map_plot" title="Link to this definition"></a></dt>
<dd><p>Get a plot of the chemical potential range _map. Currently works
only for 3-component PDs.</p>
<p>Note: this functionality is now included in the ChemicalPotentialDiagram
class (pymatgen.analysis.chempot_diagram).</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>elements</strong> – Sequence of elements to be considered as independent
variables. e.g. if you want to show the stability ranges of
all Li-Co-O phases w.r.t. to uLi and uO, you will supply
[Element(“Li”), Element(“O”)]</p></li>
<li><p><strong>referenced</strong> – if True, gives the results with a reference being the
energy of the elemental phase. If False, gives absolute values.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>matplotlib axes object.</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>plt.Axes</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.phase_diagram.PDPlotter.get_contour_pd_plot">
<span class="sig-name descname"><span class="pre">get_contour_pd_plot</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/phase_diagram.py#L2550-L2582"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.phase_diagram.PDPlotter.get_contour_pd_plot" title="Link to this definition"></a></dt>
<dd><p>Plot a contour phase diagram plot, where phase triangles are colored
according to degree of instability by interpolation. Currently only
works for 3-component phase diagrams.</p>
<dl class="field-list simple">
<dt class="field-odd">Returns<span class="colon">:</span></dt>
<dd class="field-odd"><p>A matplotlib plot object.</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.phase_diagram.PDPlotter.get_plot">
<span class="sig-name descname"><span class="pre">get_plot</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">label_stable</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">label_unstable</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ordering</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">Sequence</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">energy_colormap</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">process_attributes</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ax</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">plt.Axes</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">label_uncertainties</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">fill</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">highlight_entries</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">Collection</span><span class="p"><span class="pre">[</span></span><a class="reference internal" href="#pymatgen.analysis.phase_diagram.PDEntry" title="pymatgen.analysis.phase_diagram.PDEntry"><span class="pre">PDEntry</span></a><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">go.Figure</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">plt.Axes</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/phase_diagram.py#L2246-L2326"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.phase_diagram.PDPlotter.get_plot" title="Link to this definition"></a></dt>
<dd><dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>label_stable</strong> – Whether to label stable compounds.</p></li>
<li><p><strong>label_unstable</strong> – Whether to label unstable compounds.</p></li>
<li><p><strong>ordering</strong> – Ordering of vertices, given as a list [‘Up’,
‘Left’,’Right’] (matplotlib only).</p></li>
<li><p><strong>energy_colormap</strong> – Colormap for coloring energy (matplotlib only).</p></li>
<li><p><strong>process_attributes</strong> – Whether to process the attributes (matplotlib only).</p></li>
<li><p><strong>ax</strong> – Existing matplotlib Axes object if plotting multiple phase diagrams
(matplotlib only).</p></li>
<li><p><strong>label_uncertainties</strong> – Whether to add error bars to the hull.
For binaries, this also shades the hull with the uncertainty window.
(plotly only).</p></li>
<li><p><strong>fill</strong> – Whether to shade the hull. For ternary_2d and quaternary plots, this
colors facets arbitrarily for visual clarity. For ternary_3d plots, this
shades the hull by formation energy (plotly only).</p></li>
<li><p><strong>highlight_entries</strong> – Entries to highlight in the plot (plotly only). This will
create a new marker trace that is separate from the other entries.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>Plotly figure or matplotlib axes object depending on backend.</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>go.Figure | plt.Axes</p>
</dd>
</dl>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.analysis.phase_diagram.PDPlotter.pd_plot_data">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">pd_plot_data</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/phase_diagram.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.phase_diagram.PDPlotter.pd_plot_data" title="Link to this definition"></a></dt>
<dd><p>Plotting data for phase diagram. Cached for repetitive calls.</p>
<p>2-comp - Full hull with energies
3/4-comp - Projection into 2D or 3D Gibbs triangles</p>
<dl class="field-list simple">
<dt class="field-odd">Returns<span class="colon">:</span></dt>
<dd class="field-odd"><p><ul class="simple">
<li><p>lines is a list of list of coordinates for lines in the PD.</p></li>
<li><dl class="simple">
<dt>stable_entries is a dict of {coordinates<span class="classifier">entry} for each stable node</span></dt><dd><p>in the phase diagram. (Each coordinate can only have one
stable phase)</p>
</dd>
</dl>
</li>
<li><dl class="simple">
<dt>unstable_entries is a dict of {entry: coordinates} for all unstable</dt><dd><p>nodes in the phase diagram.</p>
</dd>
</dl>
</li>
</ul>
</p>
</dd>
<dt class="field-even">Return type<span class="colon">:</span></dt>
<dd class="field-even"><p>A tuple containing three objects (lines, stable_entries, unstable_entries)</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.phase_diagram.PDPlotter.plot_chempot_range_map">
<span class="sig-name descname"><span class="pre">plot_chempot_range_map</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">elements</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">referenced</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">None</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/phase_diagram.py#L2428-L2444"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.phase_diagram.PDPlotter.plot_chempot_range_map" title="Link to this definition"></a></dt>
<dd><p>Plot the chemical potential range _map using matplotlib. Currently works only for
3-component PDs. This shows the plot but does not return it.</p>
<p>Note: this functionality is now included in the ChemicalPotentialDiagram
class (pymatgen.analysis.chempot_diagram).</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>elements</strong> – Sequence of elements to be considered as independent
variables. e.g. if you want to show the stability ranges of
all Li-Co-O phases w.r.t. to uLi and uO, you will supply
[Element(“Li”), Element(“O”)]</p></li>
<li><p><strong>referenced</strong> – if True, gives the results with a reference being the
energy of the elemental phase. If False, gives absolute values.</p></li>
</ul>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.phase_diagram.PDPlotter.plot_element_profile">
<span class="sig-name descname"><span class="pre">plot_element_profile</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">element</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">comp</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">show_label_index</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">xlim</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">5</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/phase_diagram.py#L2363-L2426"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.phase_diagram.PDPlotter.plot_element_profile" title="Link to this definition"></a></dt>
<dd><p>Draw the element profile plot for a composition varying different
chemical potential of an element.</p>
<p>X value is the negative value of the chemical potential reference to
elemental chemical potential. For example, if choose Element(“Li”),
X= -(μLi-μLi0), which corresponds to the voltage versus metal anode.
Y values represent for the number of element uptake in this composition
(unit: per atom). All reactions are printed to help choosing the
profile steps you want to show label in the plot.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>element</strong> (<a class="reference internal" href="pymatgen.core.html#pymatgen.core.periodic_table.Element" title="pymatgen.core.periodic_table.Element"><em>Element</em></a>) – An element of which the chemical potential is
considered. It also must be in the phase diagram.</p></li>
<li><p><strong>comp</strong> (<a class="reference internal" href="pymatgen.core.html#pymatgen.core.composition.Composition" title="pymatgen.core.composition.Composition"><em>Composition</em></a>) – A composition.</p></li>
<li><p><strong>show_label_index</strong> (<em>list</em><em> of </em><em>integers</em>) – The labels for reaction products
you want to show in the plot. Default to None (not showing any
annotation for reaction products). For the profile steps you want
to show the labels, just add it to the show_label_index. The
profile step counts from zero. For example, you can set
show_label_index=[0, 2, 5] to label profile step 0,2,5.</p></li>
<li><p><strong>xlim</strong> (<em>float</em>) – The max x value. x value is from 0 to xlim. Default to
5 eV.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>Plot of element profile evolution by varying the chemical potential
of an element.</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.phase_diagram.PDPlotter.show">
<span class="sig-name descname"><span class="pre">show</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">*</span></span><span class="n"><span class="pre">args</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">None</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/phase_diagram.py#L2328-L2341"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.phase_diagram.PDPlotter.show" title="Link to this definition"></a></dt>
<dd><p>Draw the phase diagram with the provided arguments and display it. This shows
the figure but does not return it.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>*args</strong> – Passed to get_plot.</p></li>
<li><p><strong>**kwargs</strong> – Passed to get_plot.</p></li>
</ul>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.phase_diagram.PDPlotter.write_image">
<span class="sig-name descname"><span class="pre">write_image</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">stream</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">StringIO</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">image_format</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">'svg'</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">None</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/phase_diagram.py#L2343-L2361"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.phase_diagram.PDPlotter.write_image" title="Link to this definition"></a></dt>
<dd><p>Directly save the plot to a file. This is a wrapper for calling plt.savefig() or
fig.write_image(), depending on the backend. For more customization, it is
recommended to call those methods directly.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>stream</strong> (<em>str</em><em> | </em><em>StringIO</em>) – Filename or StringIO stream.</p></li>
<li><p><strong>image_format</strong> (<em>str</em>) – Can be any supported image format for the plotting backend.
Defaults to ‘svg’ (vector graphics).</p></li>
<li><p><strong>**kwargs</strong> – Optinoal kwargs passed to the get_plot function.</p></li>
</ul>
</dd>
</dl>
</dd></dl>
</dd></dl>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.analysis.phase_diagram.PatchedPhaseDiagram">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">PatchedPhaseDiagram</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entries</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">Sequence</span><span class="p"><span class="pre">[</span></span><a class="reference internal" href="#pymatgen.analysis.phase_diagram.PDEntry" title="pymatgen.analysis.phase_diagram.PDEntry"><span class="pre">PDEntry</span></a><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">set</span><span class="p"><span class="pre">[</span></span><a class="reference internal" href="#pymatgen.analysis.phase_diagram.PDEntry" title="pymatgen.analysis.phase_diagram.PDEntry"><span class="pre">PDEntry</span></a><span class="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="n"><span class="pre">elements</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">Sequence</span><span class="p"><span class="pre">[</span></span><a class="reference internal" href="pymatgen.core.html#pymatgen.core.periodic_table.Element" title="pymatgen.core.periodic_table.Element"><span class="pre">Element</span></a><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">keep_all_spaces</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">verbose</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/phase_diagram.py#L1586-L1931"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.phase_diagram.PatchedPhaseDiagram" title="Link to this definition"></a></dt>
<dd><p>Bases: <a class="reference internal" href="#pymatgen.analysis.phase_diagram.PhaseDiagram" title="pymatgen.analysis.phase_diagram.PhaseDiagram"><code class="xref py py-class docutils literal notranslate"><span class="pre">PhaseDiagram</span></code></a></p>
<p>Computing the Convex Hull of a large set of data in multiple dimensions is
highly expensive. This class acts to breakdown large chemical spaces into
smaller chemical spaces which can be computed much more quickly due to having
both reduced dimensionality and data set sizes.</p>
<dl class="py attribute">
<dt class="sig sig-object py">
<span class="sig-name descname"><span class="pre">subspaces</span> <span class="pre">({str</span></span></dt>
<dd><p>{Element, }}): Dictionary of the sets of elements for each of the
PhaseDiagrams within the PatchedPhaseDiagram.</p>
</dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py">
<span class="sig-name descname"><span class="pre">pds</span> <span class="pre">({str</span></span></dt>
<dd><p>PhaseDiagram}): Dictionary of PhaseDiagrams within the
PatchedPhaseDiagram.</p>
</dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.analysis.phase_diagram.PatchedPhaseDiagram.all_entries">
<span class="sig-name descname"><span class="pre">all_entries</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/phase_diagram.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.phase_diagram.PatchedPhaseDiagram.all_entries" title="Link to this definition"></a></dt>
<dd><p>All entries provided for Phase Diagram construction.
Note that this does not mean that all these entries are actually used in
the phase diagram. For example, this includes the positive formation energy
entries that are filtered out before Phase Diagram construction.</p>
<dl class="field-list simple">
<dt class="field-odd">Type<span class="colon">:</span></dt>
<dd class="field-odd"><p>list[<a class="reference internal" href="#pymatgen.analysis.phase_diagram.PDEntry" title="pymatgen.analysis.phase_diagram.PDEntry">PDEntry</a>]</p>
</dd>
</dl>
</dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.analysis.phase_diagram.PatchedPhaseDiagram.min_entries">
<span class="sig-name descname"><span class="pre">min_entries</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/phase_diagram.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.phase_diagram.PatchedPhaseDiagram.min_entries" title="Link to this definition"></a></dt>
<dd><p>List of the lowest energy entries for each composition
in the data provided for Phase Diagram construction.</p>
<dl class="field-list simple">
<dt class="field-odd">Type<span class="colon">:</span></dt>
<dd class="field-odd"><p>list[<a class="reference internal" href="#pymatgen.analysis.phase_diagram.PDEntry" title="pymatgen.analysis.phase_diagram.PDEntry">PDEntry</a>]</p>
</dd>
</dl>
</dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.analysis.phase_diagram.PatchedPhaseDiagram.el_refs">
<span class="sig-name descname"><span class="pre">el_refs</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/phase_diagram.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.phase_diagram.PatchedPhaseDiagram.el_refs" title="Link to this definition"></a></dt>
<dd><p>List of elemental references for the phase diagrams.
These are entries corresponding to the lowest energy element entries for
simple compositional phase diagrams.</p>
<dl class="field-list simple">
<dt class="field-odd">Type<span class="colon">:</span></dt>
<dd class="field-odd"><p>list[<a class="reference internal" href="#pymatgen.analysis.phase_diagram.PDEntry" title="pymatgen.analysis.phase_diagram.PDEntry">PDEntry</a>]</p>
</dd>
</dl>
</dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.analysis.phase_diagram.PatchedPhaseDiagram.elements">
<span class="sig-name descname"><span class="pre">elements</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/phase_diagram.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.phase_diagram.PatchedPhaseDiagram.elements" title="Link to this definition"></a></dt>
<dd><p>List of elements in the phase diagram.</p>
<dl class="field-list simple">
<dt class="field-odd">Type<span class="colon">:</span></dt>
<dd class="field-odd"><p>list[<a class="reference internal" href="pymatgen.core.html#pymatgen.core.periodic_table.Element" title="pymatgen.core.periodic_table.Element">Element</a>]</p>
</dd>
</dl>
</dd></dl>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>entries</strong> (<em>list</em><em>[</em><a class="reference internal" href="#pymatgen.analysis.phase_diagram.PDEntry" title="pymatgen.analysis.phase_diagram.PDEntry"><em>PDEntry</em></a><em>]</em>) – A list of PDEntry-like objects having an
energy, energy_per_atom and composition.</p></li>
<li><p><strong>elements</strong> (<em>list</em><em>[</em><a class="reference internal" href="pymatgen.core.html#pymatgen.core.periodic_table.Element" title="pymatgen.core.periodic_table.Element"><em>Element</em></a><em>]</em><em>, </em><em>optional</em>) – Optional list of elements in the phase
diagram. If set to None, the elements are determined from
the entries themselves and are sorted alphabetically.
If specified, element ordering (e.g. for pd coordinates)
is preserved.</p></li>
<li><p><strong>keep_all_spaces</strong> (<em>bool</em>) – Pass True to keep chemical spaces that are subspaces
of other spaces.</p></li>
<li><p><strong>verbose</strong> (<em>bool</em>) – Whether to show progress bar during convex hull construction.</p></li>
</ul>
</dd>
</dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.phase_diagram.PatchedPhaseDiagram.as_dict">
<span class="sig-name descname"><span class="pre">as_dict</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">Any</span><span class="p"><span class="pre">]</span></span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/phase_diagram.py#L1720-L1742"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.phase_diagram.PatchedPhaseDiagram.as_dict" title="Link to this definition"></a></dt>
<dd><p>Write the entries and elements used to construct the PatchedPhaseDiagram
to a dictionary.</p>
<p>NOTE unlike PhaseDiagram the computation involved in constructing the
PatchedPhaseDiagram is not saved on serialization. This is done because
hierarchically calling the <cite>PhaseDiagram.as_dict()</cite> method would break the
link in memory between entries in overlapping patches leading to a
ballooning of the amount of memory used.</p>
<p>NOTE For memory efficiency the best way to store patched phase diagrams is
via pickling. As this allows all the entries in overlapping patches to share
the same id in memory when unpickling.</p>
<dl class="field-list simple">
<dt class="field-odd">Returns<span class="colon">:</span></dt>
<dd class="field-odd"><p>MSONable dictionary representation of PatchedPhaseDiagram.</p>
</dd>
<dt class="field-even">Return type<span class="colon">:</span></dt>
<dd class="field-even"><p>dict[str, Any]</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.phase_diagram.PatchedPhaseDiagram.from_dict">
<em class="property"><span class="pre">classmethod</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">from_dict</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">dct</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">dict</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">Self</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/phase_diagram.py#L1744-L1766"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.phase_diagram.PatchedPhaseDiagram.from_dict" title="Link to this definition"></a></dt>
<dd><p>Reconstruct PatchedPhaseDiagram from dictionary serialization.</p>
<p>NOTE unlike PhaseDiagram the computation involved in constructing the
PatchedPhaseDiagram is not saved on serialization. This is done because
hierarchically calling the <cite>PhaseDiagram.as_dict()</cite> method would break the
link in memory between entries in overlapping patches leading to a
ballooning of the amount of memory used.</p>
<p>NOTE For memory efficiency the best way to store patched phase diagrams is
via pickling. As this allows all the entries in overlapping patches to share
the same id in memory when unpickling.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>dct</strong> (<em>dict</em>) – dictionary representation of PatchedPhaseDiagram.</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>PatchedPhaseDiagram</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.phase_diagram.PatchedPhaseDiagram.get_all_chempots">
<span class="sig-name descname"><span class="pre">get_all_chempots</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/phase_diagram.py#L1905-L1907"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.phase_diagram.PatchedPhaseDiagram.get_all_chempots" title="Link to this definition"></a></dt>
<dd><p>Not Implemented - See PhaseDiagram.</p>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.phase_diagram.PatchedPhaseDiagram.get_chempot_range_map">
<span class="sig-name descname"><span class="pre">get_chempot_range_map</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/phase_diagram.py#L1921-L1923"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.phase_diagram.PatchedPhaseDiagram.get_chempot_range_map" title="Link to this definition"></a></dt>
<dd><p>Not Implemented - See PhaseDiagram.</p>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.phase_diagram.PatchedPhaseDiagram.get_chempot_range_stability_phase">
<span class="sig-name descname"><span class="pre">get_chempot_range_stability_phase</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/phase_diagram.py#L1929-L1931"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.phase_diagram.PatchedPhaseDiagram.get_chempot_range_stability_phase" title="Link to this definition"></a></dt>
<dd><p>Not Implemented - See PhaseDiagram.</p>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.phase_diagram.PatchedPhaseDiagram.get_composition_chempots">
<span class="sig-name descname"><span class="pre">get_composition_chempots</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/phase_diagram.py#L1901-L1903"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.phase_diagram.PatchedPhaseDiagram.get_composition_chempots" title="Link to this definition"></a></dt>
<dd><p>Not Implemented - See PhaseDiagram.</p>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.phase_diagram.PatchedPhaseDiagram.get_critical_compositions">
<span class="sig-name descname"><span class="pre">get_critical_compositions</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/phase_diagram.py#L1913-L1915"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.phase_diagram.PatchedPhaseDiagram.get_critical_compositions" title="Link to this definition"></a></dt>
<dd><p>Not Implemented - See PhaseDiagram.</p>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.phase_diagram.PatchedPhaseDiagram.get_decomp_and_e_above_hull">
<span class="sig-name descname"><span class="pre">get_decomp_and_e_above_hull</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entry</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="#pymatgen.analysis.phase_diagram.PDEntry" title="pymatgen.analysis.phase_diagram.PDEntry"><span class="pre">PDEntry</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">allow_negative</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">check_stable</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">on_error</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">Literal</span><span class="p"><span class="pre">[</span></span><span class="s"><span class="pre">'raise'</span></span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="s"><span class="pre">'warn'</span></span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="s"><span class="pre">'ignore'</span></span><span class="p"><span class="pre">]</span></span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">'raise'</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">tuple</span><span class="p"><span class="pre">[</span></span><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><a class="reference internal" href="#pymatgen.analysis.phase_diagram.PDEntry" title="pymatgen.analysis.phase_diagram.PDEntry"><span class="pre">PDEntry</span></a><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">float</span><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">float</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">tuple</span><span class="p"><span class="pre">[</span></span><span class="pre">None</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">None</span><span class="p"><span class="pre">]</span></span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/phase_diagram.py#L1854-L1869"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.phase_diagram.PatchedPhaseDiagram.get_decomp_and_e_above_hull" title="Link to this definition"></a></dt>
<dd><p>Same as method on parent class PhaseDiagram except check_stable defaults to False
for speed. See <a class="reference external" href="https://github.com/materialsproject/pymatgen/issues/2840">https://github.com/materialsproject/pymatgen/issues/2840</a> for details.</p>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.phase_diagram.PatchedPhaseDiagram.get_decomposition">
<span class="sig-name descname"><span class="pre">get_decomposition</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">comp</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="pymatgen.core.html#pymatgen.core.composition.Composition" title="pymatgen.core.composition.Composition"><span class="pre">Composition</span></a></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><a class="reference internal" href="#pymatgen.analysis.phase_diagram.PDEntry" title="pymatgen.analysis.phase_diagram.PDEntry"><span class="pre">PDEntry</span></a><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">float</span><span class="p"><span class="pre">]</span></span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/phase_diagram.py#L1819-L1836"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.phase_diagram.PatchedPhaseDiagram.get_decomposition" title="Link to this definition"></a></dt>
<dd><p>See PhaseDiagram.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>comp</strong> (<a class="reference internal" href="pymatgen.core.html#pymatgen.core.composition.Composition" title="pymatgen.core.composition.Composition"><em>Composition</em></a>) – A composition</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>amount} where amount
is the amount of the fractional composition.</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>Decomposition as a dict of {PDEntry</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.phase_diagram.PatchedPhaseDiagram.get_element_profile">
<span class="sig-name descname"><span class="pre">get_element_profile</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/phase_diagram.py#L1917-L1919"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.phase_diagram.PatchedPhaseDiagram.get_element_profile" title="Link to this definition"></a></dt>
<dd><p>Not Implemented - See PhaseDiagram.</p>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.phase_diagram.PatchedPhaseDiagram.get_equilibrium_reaction_energy">
<span class="sig-name descname"><span class="pre">get_equilibrium_reaction_energy</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entry</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="pymatgen.entries.html#pymatgen.entries.Entry" title="pymatgen.entries.Entry"><span class="pre">Entry</span></a></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">float</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/phase_diagram.py#L1838-L1852"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.phase_diagram.PatchedPhaseDiagram.get_equilibrium_reaction_energy" title="Link to this definition"></a></dt>
<dd><p>See PhaseDiagram.</p>
<p>NOTE this is only approximately the same as the what we would get
from <cite>PhaseDiagram</cite> as we make use of the slsqp approach inside
get_phase_separation_energy().</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>entry</strong> (<a class="reference internal" href="#pymatgen.analysis.phase_diagram.PDEntry" title="pymatgen.analysis.phase_diagram.PDEntry"><em>PDEntry</em></a>) – A PDEntry like object</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>Equilibrium reaction energy of entry. Stable entries should have
equilibrium reaction energy <= 0. The energy is given per atom.</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.phase_diagram.PatchedPhaseDiagram.get_pd_for_entry">
<span class="sig-name descname"><span class="pre">get_pd_for_entry</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entry</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="pymatgen.entries.html#pymatgen.entries.Entry" title="pymatgen.entries.Entry"><span class="pre">Entry</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference internal" href="pymatgen.core.html#pymatgen.core.composition.Composition" title="pymatgen.core.composition.Composition"><span class="pre">Composition</span></a></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><a class="reference internal" href="#pymatgen.analysis.phase_diagram.PhaseDiagram" title="pymatgen.analysis.phase_diagram.PhaseDiagram"><span class="pre">PhaseDiagram</span></a></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/phase_diagram.py#L1796-L1817"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.phase_diagram.PatchedPhaseDiagram.get_pd_for_entry" title="Link to this definition"></a></dt>
<dd><p>Get the possible phase diagrams for an entry.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>entry</strong> (<a class="reference internal" href="#pymatgen.analysis.phase_diagram.PDEntry" title="pymatgen.analysis.phase_diagram.PDEntry"><em>PDEntry</em></a><em> | </em><a class="reference internal" href="pymatgen.core.html#pymatgen.core.composition.Composition" title="pymatgen.core.composition.Composition"><em>Composition</em></a>) – A PDEntry or Composition-like object</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>phase diagram that the entry is part of</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p><a class="reference internal" href="#pymatgen.analysis.phase_diagram.PhaseDiagram" title="pymatgen.analysis.phase_diagram.PhaseDiagram">PhaseDiagram</a></p>
</dd>
<dt class="field-even">Raises<span class="colon">:</span></dt>
<dd class="field-even"><p><strong>ValueError</strong> – If no suitable PhaseDiagram is found for the entry.</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.phase_diagram.PatchedPhaseDiagram.get_transition_chempots">
<span class="sig-name descname"><span class="pre">get_transition_chempots</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/phase_diagram.py#L1909-L1911"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.phase_diagram.PatchedPhaseDiagram.get_transition_chempots" title="Link to this definition"></a></dt>
<dd><p>Not Implemented - See PhaseDiagram.</p>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.phase_diagram.PatchedPhaseDiagram.getmu_vertices_stability_phase">
<span class="sig-name descname"><span class="pre">getmu_vertices_stability_phase</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/phase_diagram.py#L1925-L1927"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.phase_diagram.PatchedPhaseDiagram.getmu_vertices_stability_phase" title="Link to this definition"></a></dt>
<dd><p>Not Implemented - See PhaseDiagram.</p>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.phase_diagram.PatchedPhaseDiagram.remove_redundant_spaces">
<em class="property"><span class="pre">static</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">remove_redundant_spaces</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">spaces</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">keep_all_spaces</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/phase_diagram.py#L1768-L1781"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.phase_diagram.PatchedPhaseDiagram.remove_redundant_spaces" title="Link to this definition"></a></dt>
<dd></dd></dl>
</dd></dl>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.analysis.phase_diagram.PhaseDiagram">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">PhaseDiagram</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entries</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">Sequence</span><span class="p"><span class="pre">[</span></span><a class="reference internal" href="#pymatgen.analysis.phase_diagram.PDEntry" title="pymatgen.analysis.phase_diagram.PDEntry"><span class="pre">PDEntry</span></a><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">set</span><span class="p"><span class="pre">[</span></span><a class="reference internal" href="#pymatgen.analysis.phase_diagram.PDEntry" title="pymatgen.analysis.phase_diagram.PDEntry"><span class="pre">PDEntry</span></a><span class="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="n"><span class="pre">elements</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">Sequence</span><span class="p"><span class="pre">[</span></span><a class="reference internal" href="pymatgen.core.html#pymatgen.core.periodic_table.Element" title="pymatgen.core.periodic_table.Element"><span class="pre">Element</span></a><span class="p"><span class="pre">]</span></span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">*</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">computed_data</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">Any</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/phase_diagram.py#L293-L1362"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.phase_diagram.PhaseDiagram" title="Link to this definition"></a></dt>
<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">MSONable</span></code></p>
<p>Simple phase diagram class taking in elements and entries as inputs.
The algorithm is based on the work in the following papers:</p>
<ol class="arabic">
<li><ol class="upperalpha simple" start="19">
<li><ol class="upperalpha simple" start="16">
<li><p>Ong, L. Wang, B. Kang, and G. Ceder, Li-Fe-P-O2 Phase Diagram from</p></li>
</ol>
</li>
</ol>
<blockquote>
<div><p>First Principles Calculations. Chem. Mater., 2008, 20(5), 1798-1807.
doi:10.1021/cm702327g</p>
</div></blockquote>
</li>
<li><ol class="upperalpha simple" start="19">
<li><ol class="upperalpha simple" start="16">
<li><p>Ong, A. Jain, G. Hautier, B. Kang, G. Ceder, Thermal stabilities</p></li>
</ol>
</li>
</ol>
<blockquote>
<div><p>of delithiated olivine MPO4 (M=Fe, Mn) cathodes investigated using first
principles calculations. Electrochem. Comm., 2010, 12(3), 427-430.
doi:10.1016/j.elecom.2010.01.010</p>
</div></blockquote>
</li>
</ol>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.analysis.phase_diagram.PhaseDiagram.dim">
<span class="sig-name descname"><span class="pre">dim</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/phase_diagram.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.phase_diagram.PhaseDiagram.dim" title="Link to this definition"></a></dt>
<dd><p>The dimensionality of the phase diagram.</p>
<dl class="field-list simple">
<dt class="field-odd">Type<span class="colon">:</span></dt>
<dd class="field-odd"><p>int</p>
</dd>
</dl>
</dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.analysis.phase_diagram.PhaseDiagram.elements">
<span class="sig-name descname"><span class="pre">elements</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/phase_diagram.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.phase_diagram.PhaseDiagram.elements" title="Link to this definition"></a></dt>
<dd><p>Elements in the phase diagram.</p>
</dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.analysis.phase_diagram.PhaseDiagram.el_refs">
<span class="sig-name descname"><span class="pre">el_refs</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/phase_diagram.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.phase_diagram.PhaseDiagram.el_refs" title="Link to this definition"></a></dt>
<dd><p>List of elemental references for the phase diagrams. These are
entries corresponding to the lowest energy element entries for simple
compositional phase diagrams.</p>
</dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.analysis.phase_diagram.PhaseDiagram.all_entries">
<span class="sig-name descname"><span class="pre">all_entries</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/phase_diagram.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.phase_diagram.PhaseDiagram.all_entries" title="Link to this definition"></a></dt>
<dd><p>All entries provided for Phase Diagram construction. Note that this
does not mean that all these entries are actually used in the phase
diagram. For example, this includes the positive formation energy
entries that are filtered out before Phase Diagram construction.</p>
</dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.analysis.phase_diagram.PhaseDiagram.qhull_entries">
<span class="sig-name descname"><span class="pre">qhull_entries</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/phase_diagram.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.phase_diagram.PhaseDiagram.qhull_entries" title="Link to this definition"></a></dt>
<dd><p>Actual entries used in convex hull. Excludes all positive formation
energy entries.</p>
</dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.analysis.phase_diagram.PhaseDiagram.qhull_data">
<span class="sig-name descname"><span class="pre">qhull_data</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/phase_diagram.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.phase_diagram.PhaseDiagram.qhull_data" title="Link to this definition"></a></dt>
<dd><p>Data used in the convex hull operation. This is essentially a matrix of
composition data and energy per atom values created from qhull_entries.</p>
</dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.analysis.phase_diagram.PhaseDiagram.facets">
<span class="sig-name descname"><span class="pre">facets</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/phase_diagram.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.phase_diagram.PhaseDiagram.facets" title="Link to this definition"></a></dt>
<dd><p>Facets of the phase diagram in the form of [[1,2,3],[4,5,6]…].
For a ternary, it is the indices (references to qhull_entries and
qhull_data) for the vertices of the phase triangles. Similarly
extended to higher D simplices for higher dimensions.</p>
</dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.analysis.phase_diagram.PhaseDiagram.simplices">
<span class="sig-name descname"><span class="pre">simplices</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/phase_diagram.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.phase_diagram.PhaseDiagram.simplices" title="Link to this definition"></a></dt>
<dd><p>The simplices of the phase diagram as a list of np.ndarray, i.e.,
the list of stable compositional coordinates in the phase diagram.</p>
</dd></dl>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>entries</strong> (<em>list</em><em>[</em><a class="reference internal" href="#pymatgen.analysis.phase_diagram.PDEntry" title="pymatgen.analysis.phase_diagram.PDEntry"><em>PDEntry</em></a><em>]</em>) – A list of PDEntry-like objects having an
energy, energy_per_atom and composition.</p></li>
<li><p><strong>elements</strong> (<em>list</em><em>[</em><a class="reference internal" href="pymatgen.core.html#pymatgen.core.periodic_table.Element" title="pymatgen.core.periodic_table.Element"><em>Element</em></a><em>]</em>) – Optional list of elements in the phase
diagram. If set to None, the elements are determined from
the entries themselves and are sorted alphabetically.
If specified, element ordering (e.g. for pd coordinates)
is preserved.</p></li>
<li><p><strong>computed_data</strong> (<em>dict</em>) – A dict containing pre-computed data. This allows
PhaseDiagram object to be reconstituted without performing the
expensive convex hull computation. The dict is the output from the
PhaseDiagram._compute() method and is stored in PhaseDiagram.computed_data
when generated for the first time.</p></li>
</ul>
</dd>
</dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.analysis.phase_diagram.PhaseDiagram.all_entries_hulldata">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">all_entries_hulldata</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/phase_diagram.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.phase_diagram.PhaseDiagram.all_entries_hulldata" title="Link to this definition"></a></dt>
<dd><p>The ndarray used to construct the convex hull.</p>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.phase_diagram.PhaseDiagram.as_dict">
<span class="sig-name descname"><span class="pre">as_dict</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/phase_diagram.py#L390-L398"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.phase_diagram.PhaseDiagram.as_dict" title="Link to this definition"></a></dt>
<dd><p>Get MSONable dict representation of PhaseDiagram.</p>
</dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.analysis.phase_diagram.PhaseDiagram.formation_energy_tol">
<span class="sig-name descname"><span class="pre">formation_energy_tol</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">1e-11</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/phase_diagram.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.phase_diagram.PhaseDiagram.formation_energy_tol" title="Link to this definition"></a></dt>
<dd></dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.phase_diagram.PhaseDiagram.from_dict">
<em class="property"><span class="pre">classmethod</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">from_dict</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">dct</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">Any</span><span class="p"><span class="pre">]</span></span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">Self</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/phase_diagram.py#L400-L412"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.phase_diagram.PhaseDiagram.from_dict" title="Link to this definition"></a></dt>
<dd><dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>dct</strong> (<em>dict</em>) – dictionary representation of PhaseDiagram.</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>PhaseDiagram</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.phase_diagram.PhaseDiagram.get_all_chempots">
<span class="sig-name descname"><span class="pre">get_all_chempots</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">comp</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/phase_diagram.py#L980-L996"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.phase_diagram.PhaseDiagram.get_all_chempots" title="Link to this definition"></a></dt>
<dd><p>Get chemical potentials at a given composition.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>comp</strong> (<a class="reference internal" href="pymatgen.core.html#pymatgen.core.composition.Composition" title="pymatgen.core.composition.Composition"><em>Composition</em></a>) – Composition</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>Chemical potentials.</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.phase_diagram.PhaseDiagram.get_chempot_range_map">
<span class="sig-name descname"><span class="pre">get_chempot_range_map</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">elements</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">Sequence</span><span class="p"><span class="pre">[</span></span><a class="reference internal" href="pymatgen.core.html#pymatgen.core.periodic_table.Element" title="pymatgen.core.periodic_table.Element"><span class="pre">Element</span></a><span class="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="n"><span class="pre">referenced</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">joggle</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><a class="reference internal" href="pymatgen.core.html#pymatgen.core.periodic_table.Element" title="pymatgen.core.periodic_table.Element"><span class="pre">Element</span></a><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">list</span><span class="p"><span class="pre">[</span></span><a class="reference internal" href="pymatgen.util.html#pymatgen.util.coord.Simplex" title="pymatgen.util.coord.Simplex"><span class="pre">Simplex</span></a><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">]</span></span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/phase_diagram.py#L1133-L1185"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.phase_diagram.PhaseDiagram.get_chempot_range_map" title="Link to this definition"></a></dt>
<dd><p>Get a chemical potential range map for each stable entry.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>elements</strong> – Sequence of elements to be considered as independent variables.
e.g. if you want to show the stability ranges
of all Li-Co-O phases with respect to mu_Li and mu_O, you will supply
[Element(“Li”), Element(“O”)]</p></li>
<li><p><strong>referenced</strong> – If True, gives the results with a reference being the
energy of the elemental phase. If False, gives absolute values.</p></li>
<li><p><strong>joggle</strong> (<em>bool</em>) – Whether to joggle the input to avoid precision
errors.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>[simplices]}. The list of
simplices are the sides of the N-1 dim polytope bounding the
allowable chemical potential range of each entry.</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>Returns a dict of the form {entry</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.phase_diagram.PhaseDiagram.get_chempot_range_stability_phase">
<span class="sig-name descname"><span class="pre">get_chempot_range_stability_phase</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">target_comp</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">open_elt</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/phase_diagram.py#L1245-L1296"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.phase_diagram.PhaseDiagram.get_chempot_range_stability_phase" title="Link to this definition"></a></dt>
<dd><p>Get a set of chemical potentials corresponding to the max and min
chemical potential of the open element for a given composition. It is
quite common to have for instance a ternary oxide (e.g., ABO3) for
which you want to know what are the A and B chemical potential leading
to the highest and lowest oxygen chemical potential (reducing and
oxidizing conditions). This is useful for defect computations.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>target_comp</strong> – A Composition object</p></li>
<li><p><strong>open_elt</strong> – Element that you want to constrain to be max or min</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>A dictionary of the form {Element: (min_mu, max_mu)}
where min_mu and max_mu are the minimum and maximum chemical potentials
for the given element (as “absolute” values, i.e. not referenced to 0).</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>dict[<a class="reference internal" href="pymatgen.core.html#pymatgen.core.periodic_table.Element" title="pymatgen.core.periodic_table.Element">Element</a>, (float, float)]</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.phase_diagram.PhaseDiagram.get_composition_chempots">
<span class="sig-name descname"><span class="pre">get_composition_chempots</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">comp</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/phase_diagram.py#L968-L978"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.phase_diagram.PhaseDiagram.get_composition_chempots" title="Link to this definition"></a></dt>
<dd><p>Get the chemical potentials for all elements at a given composition.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>comp</strong> (<a class="reference internal" href="pymatgen.core.html#pymatgen.core.composition.Composition" title="pymatgen.core.composition.Composition"><em>Composition</em></a>) – Composition</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>Dictionary of chemical potentials.</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.phase_diagram.PhaseDiagram.get_critical_compositions">
<span class="sig-name descname"><span class="pre">get_critical_compositions</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">comp1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">comp2</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/phase_diagram.py#L1026-L1084"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.phase_diagram.PhaseDiagram.get_critical_compositions" title="Link to this definition"></a></dt>
<dd><p>Get the critical compositions along the tieline between two
compositions. I.e. where the decomposition products change.
The endpoints are also returned.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>comp1</strong> (<a class="reference internal" href="pymatgen.core.html#pymatgen.core.composition.Composition" title="pymatgen.core.composition.Composition"><em>Composition</em></a>) – First composition to define the tieline</p></li>
<li><p><strong>comp2</strong> (<a class="reference internal" href="pymatgen.core.html#pymatgen.core.composition.Composition" title="pymatgen.core.composition.Composition"><em>Composition</em></a>) – Second composition to define the tieline</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p><dl class="simple">
<dt>list of critical compositions. All are of</dt><dd><p>the form x * comp1 + (1-x) * comp2</p>
</dd>
</dl>
</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>[(<a class="reference internal" href="pymatgen.core.html#pymatgen.core.composition.Composition" title="pymatgen.core.composition.Composition">Composition</a>)]</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.phase_diagram.PhaseDiagram.get_decomp_and_e_above_hull">
<span class="sig-name descname"><span class="pre">get_decomp_and_e_above_hull</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entry</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="#pymatgen.analysis.phase_diagram.PDEntry" title="pymatgen.analysis.phase_diagram.PDEntry"><span class="pre">PDEntry</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">allow_negative</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">check_stable</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">on_error</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">Literal</span><span class="p"><span class="pre">[</span></span><span class="s"><span class="pre">'raise'</span></span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="s"><span class="pre">'warn'</span></span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="s"><span class="pre">'ignore'</span></span><span class="p"><span class="pre">]</span></span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">'raise'</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">tuple</span><span class="p"><span class="pre">[</span></span><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><a class="reference internal" href="#pymatgen.analysis.phase_diagram.PDEntry" title="pymatgen.analysis.phase_diagram.PDEntry"><span class="pre">PDEntry</span></a><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">float</span><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">float</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">tuple</span><span class="p"><span class="pre">[</span></span><span class="pre">None</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">None</span><span class="p"><span class="pre">]</span></span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/phase_diagram.py#L716-L774"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.phase_diagram.PhaseDiagram.get_decomp_and_e_above_hull" title="Link to this definition"></a></dt>
<dd><p>Provides the decomposition and energy above convex hull for an entry.
Due to caching, can be much faster if entries with the same composition
are processed together.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>entry</strong> (<a class="reference internal" href="#pymatgen.analysis.phase_diagram.PDEntry" title="pymatgen.analysis.phase_diagram.PDEntry"><em>PDEntry</em></a>) – A PDEntry like object</p></li>
<li><p><strong>allow_negative</strong> (<em>bool</em>) – Whether to allow negative e_above_hulls. Used to
calculate equilibrium reaction energies. Defaults to False.</p></li>
<li><p><strong>check_stable</strong> (<em>bool</em>) – Whether to first check whether an entry is stable.
In normal circumstances, this is the faster option since checking for
stable entries is relatively fast. However, if you have a huge proportion
of unstable entries, then this check can slow things down. You should then
set this to False.</p></li>
<li><p><strong>on_error</strong> (<em>'raise'</em><em> | </em><em>'warn'</em><em> | </em><em>'ignore'</em>) – What to do if no valid decomposition was
found. ‘raise’ will throw ValueError. ‘warn’ will print return (None, None).
‘ignore’ just returns (None, None). Defaults to ‘raise’.</p></li>
</ul>
</dd>
<dt class="field-even">Raises<span class="colon">:</span></dt>
<dd class="field-even"><p><strong>ValueError</strong> – If on_error is ‘raise’ and no valid decomposition exists in this
phase diagram for given entry.</p>
</dd>
<dt class="field-odd">Returns<span class="colon">:</span></dt>
<dd class="field-odd"><p><dl class="simple">
<dt>The decomposition is provided</dt><dd><p>as a dict of {PDEntry: amount} where amount is the amount of the
fractional composition. Stable entries should have energy above
convex hull of 0. The energy is given per atom.</p>
</dd>
</dl>
</p>
</dd>
<dt class="field-even">Return type<span class="colon">:</span></dt>
<dd class="field-even"><p>tuple[decomp, energy_above_hull]</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.phase_diagram.PhaseDiagram.get_decomp_and_hull_energy_per_atom">
<span class="sig-name descname"><span class="pre">get_decomp_and_hull_energy_per_atom</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">comp</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="pymatgen.core.html#pymatgen.core.composition.Composition" title="pymatgen.core.composition.Composition"><span class="pre">Composition</span></a></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">tuple</span><span class="p"><span class="pre">[</span></span><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><a class="reference internal" href="#pymatgen.analysis.phase_diagram.PDEntry" title="pymatgen.analysis.phase_diagram.PDEntry"><span class="pre">PDEntry</span></a><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">float</span><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">float</span><span class="p"><span class="pre">]</span></span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/phase_diagram.py#L684-L693"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.phase_diagram.PhaseDiagram.get_decomp_and_hull_energy_per_atom" title="Link to this definition"></a></dt>
<dd><dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>comp</strong> (<a class="reference internal" href="pymatgen.core.html#pymatgen.core.composition.Composition" title="pymatgen.core.composition.Composition"><em>Composition</em></a>) – Input composition.</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>Energy of lowest energy equilibrium at desired composition per atom</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.phase_diagram.PhaseDiagram.get_decomp_and_phase_separation_energy">
<span class="sig-name descname"><span class="pre">get_decomp_and_phase_separation_energy</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entry</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="#pymatgen.analysis.phase_diagram.PDEntry" title="pymatgen.analysis.phase_diagram.PDEntry"><span class="pre">PDEntry</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">space_limit</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">200</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">stable_only</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">tols</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">Sequence</span><span class="p"><span class="pre">[</span></span><span class="pre">float</span><span class="p"><span class="pre">]</span></span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">(1e-08,)</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">maxiter</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">1000</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">Any</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">tuple</span><span class="p"><span class="pre">[</span></span><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><a class="reference internal" href="#pymatgen.analysis.phase_diagram.PDEntry" title="pymatgen.analysis.phase_diagram.PDEntry"><span class="pre">PDEntry</span></a><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">float</span><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">float</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">tuple</span><span class="p"><span class="pre">[</span></span><span class="pre">None</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">None</span><span class="p"><span class="pre">]</span></span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/phase_diagram.py#L819-L937"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.phase_diagram.PhaseDiagram.get_decomp_and_phase_separation_energy" title="Link to this definition"></a></dt>
<dd><p>Provides the combination of entries in the PhaseDiagram that gives the
lowest formation enthalpy with the same composition as the given entry
excluding entries with the same composition and the energy difference
per atom between the given entry and the energy of the combination found.</p>
<p>For unstable entries that are not polymorphs of stable entries (or completely
novel entries) this is simply the energy above (or below) the convex hull.</p>
<p>For entries with the same composition as one of the stable entries in the
phase diagram setting <cite>stable_only</cite> to <cite>False</cite> (Default) allows for entries
not previously on the convex hull to be considered in the combination.
In this case the energy returned is what is referred to as the decomposition
enthalpy in:</p>
<ol class="arabic simple">
<li><dl class="simple">
<dt>Bartel, C., Trewartha, A., Wang, Q., Dunn, A., Jain, A., Ceder, G.,</dt><dd><p>A critical examination of compound stability predictions from
machine-learned formation energies, npj Computational Materials 6, 97 (2020)</p>
</dd>
</dl>
</li>
</ol>
<p>For stable entries setting <cite>stable_only</cite> to <cite>True</cite> returns the same energy
as <cite>get_equilibrium_reaction_energy</cite>. This function is based on a constrained
optimization rather than recalculation of the convex hull making it
algorithmically cheaper. However, if <cite>tol</cite> is too loose there is potential
for this algorithm to converge to a different solution.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>entry</strong> (<a class="reference internal" href="#pymatgen.analysis.phase_diagram.PDEntry" title="pymatgen.analysis.phase_diagram.PDEntry"><em>PDEntry</em></a>) – A PDEntry like object.</p></li>
<li><p><strong>space_limit</strong> (<em>int</em>) – The maximum number of competing entries to consider
before calculating a second convex hull to reducing the complexity
of the optimization.</p></li>
<li><p><strong>stable_only</strong> (<em>bool</em>) – Only use stable materials as competing entries.</p></li>
<li><p><strong>tols</strong> (<em>list</em><em>[</em><em>float</em><em>]</em>) – Tolerances for convergence of the SLSQP optimization
when finding the equilibrium reaction. Tighter tolerances tested first.</p></li>
<li><p><strong>maxiter</strong> (<em>int</em>) – The maximum number of iterations of the SLSQP optimizer
when finding the equilibrium reaction.</p></li>
<li><p><strong>**kwargs</strong> – Passed to get_decomp_and_e_above_hull.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p><dl class="simple">
<dt>The decomposition is given as a dict of {PDEntry, amount}</dt><dd><p>for all entries in the decomp reaction where amount is the amount of the
fractional composition. The phase separation energy is given per atom.</p>
</dd>
</dl>
</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>tuple[decomp, energy]</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.phase_diagram.PhaseDiagram.get_decomposition">
<span class="sig-name descname"><span class="pre">get_decomposition</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">comp</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="pymatgen.core.html#pymatgen.core.composition.Composition" title="pymatgen.core.composition.Composition"><span class="pre">Composition</span></a></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><a class="reference internal" href="#pymatgen.analysis.phase_diagram.PDEntry" title="pymatgen.analysis.phase_diagram.PDEntry"><span class="pre">PDEntry</span></a><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">float</span><span class="p"><span class="pre">]</span></span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/phase_diagram.py#L665-L682"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.phase_diagram.PhaseDiagram.get_decomposition" title="Link to this definition"></a></dt>
<dd><p>Provides the decomposition at a particular composition.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>comp</strong> (<a class="reference internal" href="pymatgen.core.html#pymatgen.core.composition.Composition" title="pymatgen.core.composition.Composition"><em>Composition</em></a>) – A composition</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>amount} where amount
is the amount of the fractional composition.</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>Decomposition as a dict of {PDEntry</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.phase_diagram.PhaseDiagram.get_e_above_hull">
<span class="sig-name descname"><span class="pre">get_e_above_hull</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entry</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="#pymatgen.analysis.phase_diagram.PDEntry" title="pymatgen.analysis.phase_diagram.PDEntry"><span class="pre">PDEntry</span></a></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">Any</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">float</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/phase_diagram.py#L776-L788"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.phase_diagram.PhaseDiagram.get_e_above_hull" title="Link to this definition"></a></dt>
<dd><p>Provides the energy above convex hull for an entry.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>entry</strong> (<a class="reference internal" href="#pymatgen.analysis.phase_diagram.PDEntry" title="pymatgen.analysis.phase_diagram.PDEntry"><em>PDEntry</em></a>) – A PDEntry like object.</p></li>
<li><p><strong>**kwargs</strong> – Passed to get_decomp_and_e_above_hull().</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p><dl class="simple">
<dt>Energy above convex hull of entry. Stable entries should have</dt><dd><p>energy above hull of 0. The energy is given per atom.</p>
</dd>
</dl>
</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>float | None</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.phase_diagram.PhaseDiagram.get_element_profile">
<span class="sig-name descname"><span class="pre">get_element_profile</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">element</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">comp</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">comp_tol</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1e-05</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/phase_diagram.py#L1086-L1131"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.phase_diagram.PhaseDiagram.get_element_profile" title="Link to this definition"></a></dt>
<dd><p>Provides the element evolution data for a composition. For example, can be used
to analyze Li conversion voltages by varying mu_Li and looking at the phases
formed. Also can be used to analyze O2 evolution by varying mu_O2.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>element</strong> – An element. Must be in the phase diagram.</p></li>
<li><p><strong>comp</strong> – A Composition</p></li>
<li><p><strong>comp_tol</strong> – The tolerance to use when calculating decompositions.
Phases with amounts less than this tolerance are excluded.
Defaults to 1e-5.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>[ {‘chempot’: -10.487582, ‘evolution’: -2.0,
‘reaction’: Reaction Object], …]</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>Evolution data as a list of dictionaries of the following format</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.phase_diagram.PhaseDiagram.get_equilibrium_reaction_energy">
<span class="sig-name descname"><span class="pre">get_equilibrium_reaction_energy</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entry</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="#pymatgen.analysis.phase_diagram.PDEntry" title="pymatgen.analysis.phase_diagram.PDEntry"><span class="pre">PDEntry</span></a></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">float</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/phase_diagram.py#L790-L817"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.phase_diagram.PhaseDiagram.get_equilibrium_reaction_energy" title="Link to this definition"></a></dt>
<dd><p>Provides the reaction energy of a stable entry from the neighboring
equilibrium stable entries (also known as the inverse distance to
hull).</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>entry</strong> (<a class="reference internal" href="#pymatgen.analysis.phase_diagram.PDEntry" title="pymatgen.analysis.phase_diagram.PDEntry"><em>PDEntry</em></a>) – A PDEntry like object</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p><dl class="simple">
<dt>Equilibrium reaction energy of entry. Stable entries should have</dt><dd><p>equilibrium reaction energy <= 0. The energy is given per atom.</p>
</dd>
</dl>
</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>float | None</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.phase_diagram.PhaseDiagram.get_form_energy">
<span class="sig-name descname"><span class="pre">get_form_energy</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entry</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="#pymatgen.analysis.phase_diagram.PDEntry" title="pymatgen.analysis.phase_diagram.PDEntry"><span class="pre">PDEntry</span></a></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">float</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/phase_diagram.py#L562-L573"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.phase_diagram.PhaseDiagram.get_form_energy" title="Link to this definition"></a></dt>
<dd><p>Get the formation energy for an entry (NOT normalized) from the
elemental references.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>entry</strong> (<a class="reference internal" href="#pymatgen.analysis.phase_diagram.PDEntry" title="pymatgen.analysis.phase_diagram.PDEntry"><em>PDEntry</em></a>) – A PDEntry-like object.</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>Formation energy from the elemental references.</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>float</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.phase_diagram.PhaseDiagram.get_form_energy_per_atom">
<span class="sig-name descname"><span class="pre">get_form_energy_per_atom</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entry</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="#pymatgen.analysis.phase_diagram.PDEntry" title="pymatgen.analysis.phase_diagram.PDEntry"><span class="pre">PDEntry</span></a></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">float</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/phase_diagram.py#L575-L585"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.phase_diagram.PhaseDiagram.get_form_energy_per_atom" title="Link to this definition"></a></dt>
<dd><p>Get the formation energy per atom for an entry from the
elemental references.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>entry</strong> (<a class="reference internal" href="#pymatgen.analysis.phase_diagram.PDEntry" title="pymatgen.analysis.phase_diagram.PDEntry"><em>PDEntry</em></a>) – An PDEntry-like object</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>Formation energy <strong>per atom</strong> from the elemental references.</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.phase_diagram.PhaseDiagram.get_hull_energy">
<span class="sig-name descname"><span class="pre">get_hull_energy</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">comp</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="pymatgen.core.html#pymatgen.core.composition.Composition" title="pymatgen.core.composition.Composition"><span class="pre">Composition</span></a></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">float</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/phase_diagram.py#L705-L714"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.phase_diagram.PhaseDiagram.get_hull_energy" title="Link to this definition"></a></dt>
<dd><dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>comp</strong> (<a class="reference internal" href="pymatgen.core.html#pymatgen.core.composition.Composition" title="pymatgen.core.composition.Composition"><em>Composition</em></a>) – Input composition.</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p><dl class="simple">
<dt>Energy of lowest energy equilibrium at desired composition. Not</dt><dd><p>normalized by atoms, i.e. E(Li4O2) = 2 * E(Li2O)</p>
</dd>
</dl>
</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.phase_diagram.PhaseDiagram.get_hull_energy_per_atom">
<span class="sig-name descname"><span class="pre">get_hull_energy_per_atom</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">comp</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="pymatgen.core.html#pymatgen.core.composition.Composition" title="pymatgen.core.composition.Composition"><span class="pre">Composition</span></a></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">float</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/phase_diagram.py#L695-L703"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.phase_diagram.PhaseDiagram.get_hull_energy_per_atom" title="Link to this definition"></a></dt>
<dd><dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>comp</strong> (<a class="reference internal" href="pymatgen.core.html#pymatgen.core.composition.Composition" title="pymatgen.core.composition.Composition"><em>Composition</em></a>) – Input composition.</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>Energy of lowest energy equilibrium at desired composition.</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.phase_diagram.PhaseDiagram.get_phase_separation_energy">
<span class="sig-name descname"><span class="pre">get_phase_separation_energy</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entry</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/phase_diagram.py#L939-L966"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.phase_diagram.PhaseDiagram.get_phase_separation_energy" title="Link to this definition"></a></dt>
<dd><p>Provides the energy to the convex hull for the given entry. For stable entries
already in the phase diagram the algorithm provides the phase separation energy
which is referred to as the decomposition enthalpy in:</p>
<ol class="arabic simple">
<li><dl class="simple">
<dt>Bartel, C., Trewartha, A., Wang, Q., Dunn, A., Jain, A., Ceder, G.,</dt><dd><p>A critical examination of compound stability predictions from
machine-learned formation energies, npj Computational Materials 6, 97 (2020)</p>
</dd>
</dl>
</li>
</ol>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>entry</strong> (<a class="reference internal" href="#pymatgen.analysis.phase_diagram.PDEntry" title="pymatgen.analysis.phase_diagram.PDEntry"><em>PDEntry</em></a>) – A PDEntry like object</p></li>
<li><p><strong>**kwargs</strong> – <p>Keyword args passed to <cite>get_decomp_and_decomp_energy</cite>
space_limit (int): The maximum number of competing entries to consider.
stable_only (bool): Only use stable materials as competing entries
tol (float): The tolerance for convergence of the SLSQP optimization</p>
<blockquote>
<div><p>when finding the equilibrium reaction.</p>
</div></blockquote>
<dl class="simple">
<dt>maxiter (int): The maximum number of iterations of the SLSQP optimizer</dt><dd><p>when finding the equilibrium reaction.</p>
</dd>
</dl>
</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>phase separation energy per atom of entry. Stable entries should have
energies <= 0, Stable elemental entries should have energies = 0 and
unstable entries should have energies > 0. Entries that have the same
composition as a stable energy may have positive or negative phase
separation energies depending on their own energy.</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.phase_diagram.PhaseDiagram.get_plot">
<span class="sig-name descname"><span class="pre">get_plot</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">show_unstable</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">float</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">0.2</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">backend</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">Literal</span><span class="p"><span class="pre">[</span></span><span class="s"><span class="pre">'plotly'</span></span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="s"><span class="pre">'matplotlib'</span></span><span class="p"><span class="pre">]</span></span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">'plotly'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ternary_style</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">Literal</span><span class="p"><span class="pre">[</span></span><span class="s"><span class="pre">'2d'</span></span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="s"><span class="pre">'3d'</span></span><span class="p"><span class="pre">]</span></span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">'2d'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">label_stable</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">label_unstable</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ordering</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">Sequence</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">energy_colormap</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">process_attributes</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ax</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">plt.Axes</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">label_uncertainties</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">fill</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/phase_diagram.py#L1298-L1362"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.phase_diagram.PhaseDiagram.get_plot" title="Link to this definition"></a></dt>
<dd><p>Convenient wrapper for PDPlotter. Initializes a PDPlotter object and calls
get_plot() with provided combined arguments.</p>
<p>Plotting is only supported for phase diagrams with <=4 elements (unary,
binary, ternary, or quaternary systems).</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>show_unstable</strong> (<em>float</em>) – Whether unstable (above the hull) phases will be
plotted. If a number > 0 is entered, all phases with
e_hull < show_unstable (eV/atom) will be shown.</p></li>
<li><p><strong>backend</strong> (<em>"plotly"</em><em> | </em><em>"matplotlib"</em>) – Python package to use for plotting.
Defaults to “plotly”.</p></li>
<li><p><strong>ternary_style</strong> (<em>"2d"</em><em> | </em><em>"3d"</em>) – Ternary phase diagrams are typically plotted in
two-dimensions (2d), but can be plotted in three dimensions (3d) to visualize
the depth of the hull. This argument only applies when backend=”plotly”.
Defaults to “2d”.</p></li>
<li><p><strong>label_stable</strong> – Whether to label stable compounds.</p></li>
<li><p><strong>label_unstable</strong> – Whether to label unstable compounds.</p></li>
<li><p><strong>ordering</strong> – Ordering of vertices (matplotlib backend only).</p></li>
<li><p><strong>energy_colormap</strong> – Colormap for coloring energy (matplotlib backend only).</p></li>
<li><p><strong>process_attributes</strong> – Whether to process the attributes (matplotlib
backend only).</p></li>
<li><p><strong>ax</strong> – Existing Axes object if plotting multiple phase diagrams (matplotlib backend only).</p></li>
<li><p><strong>label_uncertainties</strong> – Whether to add error bars to the hull (plotly
backend only). For binaries, this also shades the hull with the
uncertainty window.</p></li>
<li><p><strong>fill</strong> – Whether to shade the hull. For ternary_2d and quaternary plots, this
colors facets arbitrarily for visual clarity. For ternary_3d plots, this
shades the hull by formation energy (plotly backend only).</p></li>
<li><p><strong>**kwargs</strong> (<em>dict</em>) – Keyword args passed to PDPlotter.get_plot(). Can be used to customize markers
etc. If not set, the default is { “markerfacecolor”: “#4daf4a”, “markersize”: 10, “linewidth”: 3 }</p></li>
</ul>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.phase_diagram.PhaseDiagram.get_reference_energy">
<span class="sig-name descname"><span class="pre">get_reference_energy</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">comp</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="pymatgen.core.html#pymatgen.core.composition.Composition" title="pymatgen.core.composition.Composition"><span class="pre">Composition</span></a></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">float</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/phase_diagram.py#L540-L549"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.phase_diagram.PhaseDiagram.get_reference_energy" title="Link to this definition"></a></dt>
<dd><p>Sum of elemental reference energies over all elements in a composition.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>comp</strong> (<a class="reference internal" href="pymatgen.core.html#pymatgen.core.composition.Composition" title="pymatgen.core.composition.Composition"><em>Composition</em></a>) – Input composition.</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>Reference energy</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>float</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.phase_diagram.PhaseDiagram.get_reference_energy_per_atom">
<span class="sig-name descname"><span class="pre">get_reference_energy_per_atom</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">comp</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="pymatgen.core.html#pymatgen.core.composition.Composition" title="pymatgen.core.composition.Composition"><span class="pre">Composition</span></a></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">float</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/phase_diagram.py#L551-L560"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.phase_diagram.PhaseDiagram.get_reference_energy_per_atom" title="Link to this definition"></a></dt>
<dd><p>Sum of elemental reference energies over all elements in a composition.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>comp</strong> (<a class="reference internal" href="pymatgen.core.html#pymatgen.core.composition.Composition" title="pymatgen.core.composition.Composition"><em>Composition</em></a>) – Input composition.</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>Reference energy per atom</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>float</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.phase_diagram.PhaseDiagram.get_transition_chempots">
<span class="sig-name descname"><span class="pre">get_transition_chempots</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">element</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/phase_diagram.py#L998-L1024"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.phase_diagram.PhaseDiagram.get_transition_chempots" title="Link to this definition"></a></dt>
<dd><p>Get the critical chemical potentials for an element in the Phase
Diagram.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>element</strong> – An element. Has to be in the PD in the first place.</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>A sorted sequence of critical chemical potentials, from less
negative to more negative.</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.phase_diagram.PhaseDiagram.getmu_vertices_stability_phase">
<span class="sig-name descname"><span class="pre">getmu_vertices_stability_phase</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">target_comp</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">dep_elt</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">tol_en</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0.01</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/phase_diagram.py#L1187-L1243"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.phase_diagram.PhaseDiagram.getmu_vertices_stability_phase" title="Link to this definition"></a></dt>
<dd><p>Get a set of chemical potentials corresponding to the vertices of
the simplex in the chemical potential phase diagram.
The simplex is built using all elements in the target_composition
except dep_elt.
The chemical potential of dep_elt is computed from the target
composition energy.
This method is useful to get the limiting conditions for
defects computations for instance.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>target_comp</strong> – A Composition object</p></li>
<li><p><strong>dep_elt</strong> – the element for which the chemical potential is computed
from the energy of the stable phase at the target composition</p></li>
<li><p><strong>tol_en</strong> – a tolerance on the energy to set</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>mu}]: An array of conditions on simplex vertices for
which each element has a chemical potential set to a given
value. “absolute” values (i.e., not referenced to element energies)</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>[{Element</p>
</dd>
</dl>
</dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.analysis.phase_diagram.PhaseDiagram.numerical_tol">
<span class="sig-name descname"><span class="pre">numerical_tol</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">1e-08</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/phase_diagram.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.phase_diagram.PhaseDiagram.numerical_tol" title="Link to this definition"></a></dt>
<dd></dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.phase_diagram.PhaseDiagram.pd_coords">
<span class="sig-name descname"><span class="pre">pd_coords</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">comp</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="pymatgen.core.html#pymatgen.core.composition.Composition" title="pymatgen.core.composition.Composition"><span class="pre">Composition</span></a></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">ndarray</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/phase_diagram.py#L488-L502"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.phase_diagram.PhaseDiagram.pd_coords" title="Link to this definition"></a></dt>
<dd><p>The phase diagram is generated in a reduced dimensional space
(n_elements - 1). This function returns the coordinates in that space.
These coordinates are compatible with the stored simplex objects.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>comp</strong> (<a class="reference internal" href="pymatgen.core.html#pymatgen.core.composition.Composition" title="pymatgen.core.composition.Composition"><em>Composition</em></a>) – A composition</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>The coordinates for a given composition in the PhaseDiagram’s basis</p>
</dd>
</dl>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.analysis.phase_diagram.PhaseDiagram.stable_entries">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">stable_entries</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">set</span><span class="p"><span class="pre">[</span></span><a class="reference internal" href="pymatgen.entries.html#pymatgen.entries.Entry" title="pymatgen.entries.Entry"><span class="pre">Entry</span></a><span class="p"><span class="pre">]</span></span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/phase_diagram.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.phase_diagram.PhaseDiagram.stable_entries" title="Link to this definition"></a></dt>
<dd><p>Returns:
set[Entry]: of stable entries in the phase diagram.</p>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.analysis.phase_diagram.PhaseDiagram.unstable_entries">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">unstable_entries</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">set</span><span class="p"><span class="pre">[</span></span><a class="reference internal" href="pymatgen.entries.html#pymatgen.entries.Entry" title="pymatgen.entries.Entry"><span class="pre">Entry</span></a><span class="p"><span class="pre">]</span></span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/phase_diagram.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.phase_diagram.PhaseDiagram.unstable_entries" title="Link to this definition"></a></dt>
<dd><p>Returns:
set[Entry]: unstable entries in the phase diagram. Includes positive formation energy entries.</p>
</dd></dl>
</dd></dl>
<dl class="py exception">
<dt class="sig sig-object py" id="pymatgen.analysis.phase_diagram.PhaseDiagramError">
<em class="property"><span class="pre">exception</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">PhaseDiagramError</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/phase_diagram.py#L2084-L2085"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.phase_diagram.PhaseDiagramError" title="Link to this definition"></a></dt>
<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">Exception</span></code></p>
<p>An exception class for Phase Diagram generation.</p>
</dd></dl>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.analysis.phase_diagram.ReactionDiagram">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">ReactionDiagram</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entry1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entry2</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">all_entries</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">tol</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">float</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">0.0001</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">float_fmt</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'%.4f'</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/phase_diagram.py#L1934-L2081"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.phase_diagram.ReactionDiagram" title="Link to this definition"></a></dt>
<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></p>
<p>Analyzes the possible reactions between a pair of compounds, e.g.
an electrolyte and an electrode.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>entry1</strong> (<a class="reference internal" href="pymatgen.entries.html#pymatgen.entries.computed_entries.ComputedEntry" title="pymatgen.entries.computed_entries.ComputedEntry"><em>ComputedEntry</em></a>) – Entry for 1st component. Note that
corrections, if any, must already be pre-applied. This is to
give flexibility for different kinds of corrections, e.g.
if a particular entry is fitted to an experimental data (such
as EC molecule).</p></li>
<li><p><strong>entry2</strong> (<a class="reference internal" href="pymatgen.entries.html#pymatgen.entries.computed_entries.ComputedEntry" title="pymatgen.entries.computed_entries.ComputedEntry"><em>ComputedEntry</em></a>) – Entry for 2nd component. Note that
corrections must already be pre-applied. This is to
give flexibility for different kinds of corrections, e.g.
if a particular entry is fitted to an experimental data (such
as EC molecule).</p></li>
<li><p><strong>all_entries</strong> (<em>[</em><a class="reference internal" href="pymatgen.entries.html#pymatgen.entries.computed_entries.ComputedEntry" title="pymatgen.entries.computed_entries.ComputedEntry"><em>ComputedEntry</em></a><em>]</em>) – All other entries to be
considered in the analysis. Note that corrections, if any,
must already be pre-applied.</p></li>
<li><p><strong>tol</strong> (<em>float</em>) – Tolerance to be used to determine validity of reaction. Defaults to 1e-4.</p></li>
<li><p><strong>float_fmt</strong> (<em>str</em>) – Formatting string to be applied to all floats. Determines
number of decimal places in reaction string. Defaults to “%.4f”.</p></li>
</ul>
</dd>
</dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.phase_diagram.ReactionDiagram.get_compound_pd">
<span class="sig-name descname"><span class="pre">get_compound_pd</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/phase_diagram.py#L2061-L2081"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.phase_diagram.ReactionDiagram.get_compound_pd" title="Link to this definition"></a></dt>
<dd><p>Get the CompoundPhaseDiagram object, which can then be used for
plotting.</p>
<dl class="field-list simple">
<dt class="field-odd">Returns<span class="colon">:</span></dt>
<dd class="field-odd"><p>CompoundPhaseDiagram</p>
</dd>
</dl>
</dd></dl>
</dd></dl>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.analysis.phase_diagram.TransformedPDEntry">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">TransformedPDEntry</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entry</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">sp_mapping</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">name</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/phase_diagram.py#L206-L286"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.phase_diagram.TransformedPDEntry" title="Link to this definition"></a></dt>
<dd><p>Bases: <a class="reference internal" href="#pymatgen.analysis.phase_diagram.PDEntry" title="pymatgen.analysis.phase_diagram.PDEntry"><code class="xref py py-class docutils literal notranslate"><span class="pre">PDEntry</span></code></a></p>
<p>This class represents a TransformedPDEntry, which allows for a PDEntry to be
transformed to a different composition coordinate space. It is used in the
construction of phase diagrams that do not have elements as the terminal
compositions.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>entry</strong> (<a class="reference internal" href="#pymatgen.analysis.phase_diagram.PDEntry" title="pymatgen.analysis.phase_diagram.PDEntry"><em>PDEntry</em></a>) – Original entry to be transformed.</p></li>
<li><p><strong>(</strong><strong>{Composition</strong> (<em>sp_mapping</em>) – DummySpecies}): dictionary mapping Terminal Compositions to Dummy Species.</p></li>
</ul>
</dd>
</dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.analysis.phase_diagram.TransformedPDEntry.amount_tol">
<span class="sig-name descname"><span class="pre">amount_tol</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">1e-05</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/phase_diagram.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.phase_diagram.TransformedPDEntry.amount_tol" title="Link to this definition"></a></dt>
<dd></dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.phase_diagram.TransformedPDEntry.as_dict">
<span class="sig-name descname"><span class="pre">as_dict</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/phase_diagram.py#L265-L272"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.phase_diagram.TransformedPDEntry.as_dict" title="Link to this definition"></a></dt>
<dd><p>Get MSONable dict representation of TransformedPDEntry.</p>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.analysis.phase_diagram.TransformedPDEntry.composition">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">composition</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><a class="reference internal" href="pymatgen.core.html#pymatgen.core.composition.Composition" title="pymatgen.core.composition.Composition"><span class="pre">Composition</span></a></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/phase_diagram.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.phase_diagram.TransformedPDEntry.composition" title="Link to this definition"></a></dt>
<dd><p>The composition in the dummy species space.</p>
<dl class="field-list simple">
<dt class="field-odd">Returns<span class="colon">:</span></dt>
<dd class="field-odd"><p>Composition</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.phase_diagram.TransformedPDEntry.from_dict">
<em class="property"><span class="pre">classmethod</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">from_dict</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">dct</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">dict</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">Self</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/phase_diagram.py#L274-L286"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.phase_diagram.TransformedPDEntry.from_dict" title="Link to this definition"></a></dt>
<dd><dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>dct</strong> (<em>dict</em>) – dictionary representation of TransformedPDEntry.</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>TransformedPDEntry</p>
</dd>
</dl>
</dd></dl>
</dd></dl>
<dl class="py exception">
<dt class="sig sig-object py" id="pymatgen.analysis.phase_diagram.TransformedPDEntryError">
<em class="property"><span class="pre">exception</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">TransformedPDEntryError</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/phase_diagram.py#L289-L290"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.phase_diagram.TransformedPDEntryError" title="Link to this definition"></a></dt>
<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">Exception</span></code></p>
<p>An exception class for TransformedPDEntry.</p>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="pymatgen.analysis.phase_diagram.get_facets">
<span class="sig-name descname"><span class="pre">get_facets</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">qhull_data</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">ArrayLike</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">joggle</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">ConvexHull</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/phase_diagram.py#L2088-L2103"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.phase_diagram.get_facets" title="Link to this definition"></a></dt>
<dd><p>Get the simplex facets for the Convex hull.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>qhull_data</strong> (<em>np.ndarray</em>) – The data from which to construct the convex
hull as a Nxd array (N being number of data points and d being the
dimension)</p></li>
<li><p><strong>joggle</strong> (<em>bool</em>) – Whether to joggle the input to avoid precision
errors.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>with list of simplices of the convex hull.</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>scipy.spatial.ConvexHull</p>
</dd>
</dl>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="pymatgen.analysis.phase_diagram.order_phase_diagram">
<span class="sig-name descname"><span class="pre">order_phase_diagram</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">lines</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">stable_entries</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">unstable_entries</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ordering</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/phase_diagram.py#L3911-L4068"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.phase_diagram.order_phase_diagram" title="Link to this definition"></a></dt>
<dd><p>Orders the entries (their coordinates) in a phase diagram plot according
to the user specified ordering.
Ordering should be given as [‘Up’, ‘Left’, ‘Right’], where Up,
Left and Right are the names of the entries in the upper, left and right
corners of the triangle respectively.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>lines</strong> – list of list of coordinates for lines in the PD.</p></li>
<li><p><strong>stable_entries</strong> – {coordinate : entry} for each stable node in the
phase diagram. (Each coordinate can only have one stable phase)</p></li>
<li><p><strong>unstable_entries</strong> – {entry: coordinates} for all unstable nodes in the
phase diagram.</p></li>
<li><p><strong>ordering</strong> – Ordering of the phase diagram, given as a list [‘Up’,
‘Left’,’Right’]</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p><ul class="simple">
<li><p>new_lines is a list of list of coordinates for lines in the PD.</p></li>
<li><p>new_stable_entries is a {coordinate: entry} for each stable node</p></li>
</ul>
<p>in the phase diagram. (Each coordinate can only have one
stable phase)
- new_unstable_entries is a {entry: coordinates} for all unstable
nodes in the phase diagram.</p>
</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>tuple[list, dict, dict]</p>
</dd>
</dl>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="pymatgen.analysis.phase_diagram.tet_coord">
<span class="sig-name descname"><span class="pre">tet_coord</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">coord</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/phase_diagram.py#L3889-L3908"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.phase_diagram.tet_coord" title="Link to this definition"></a></dt>
<dd><p>Convert a 3D coordinate into a tetrahedron based coordinate system for a
prettier phase diagram.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>coord</strong> – coordinate used in the convex hull computation.</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>coordinates in a tetrahedron-based coordinate system.</p>
</dd>
</dl>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="pymatgen.analysis.phase_diagram.triangular_coord">
<span class="sig-name descname"><span class="pre">triangular_coord</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">coord</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/phase_diagram.py#L3872-L3886"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.phase_diagram.triangular_coord" title="Link to this definition"></a></dt>
<dd><p>Convert a 2D coordinate into a triangle-based coordinate system for a
prettier phase diagram.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>coord</strong> – coordinate used in the convex hull computation.</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>coordinates in a triangular-based coordinate system.</p>
</dd>
</dl>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="pymatgen.analysis.phase_diagram.uniquelines">
<span class="sig-name descname"><span class="pre">uniquelines</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">q</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/phase_diagram.py#L3856-L3869"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.phase_diagram.uniquelines" title="Link to this definition"></a></dt>
<dd><p>Given all the facets, convert it into a set of unique lines. Specifically
used for converting convex hull facets into line pairs of coordinates.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>q</strong> – A 2-dim sequence, where each row represents a facet. e.g.
[[1,2,3],[3,6,7],…]</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>A set of tuple of lines. e.g. ((1,2), (1,3), (2,3), ….)</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>setoflines</p>
</dd>
</dl>
</dd></dl>
</section>
<section id="module-pymatgen.analysis.piezo">
<span id="pymatgen-analysis-piezo-module"></span><h2>pymatgen.analysis.piezo module<a class="headerlink" href="#module-pymatgen.analysis.piezo" title="Link to this heading"></a></h2>
<p>This module provides classes for the Piezoelectric tensor.</p>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.analysis.piezo.PiezoTensor">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">PiezoTensor</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">input_array</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">ArrayLike</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">tol</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">float</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">0.001</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/piezo.py#L25-L64"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.piezo.PiezoTensor" title="Link to this definition"></a></dt>
<dd><p>Bases: <a class="reference internal" href="pymatgen.core.html#pymatgen.core.tensors.Tensor" title="pymatgen.core.tensors.Tensor"><code class="xref py py-class docutils literal notranslate"><span class="pre">Tensor</span></code></a></p>
<p>This class describes the 3x6 piezo tensor in Voigt notation.</p>
<p>Create an PiezoTensor object. The constructor throws an error if
the shape of the input_matrix argument is not 3x3x3, i.e. in true
tensor notation. Note that the constructor uses __new__ rather than
__init__ according to the standard method of subclassing numpy
ndarrays.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>input_matrix</strong> (<em>3x3x3 array-like</em>) – the 3x6 array-like
representing the piezo tensor</p>
</dd>
</dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.piezo.PiezoTensor.from_vasp_voigt">
<em class="property"><span class="pre">classmethod</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">from_vasp_voigt</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">input_vasp_array</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">ArrayLike</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">Self</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/piezo.py#L45-L64"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.piezo.PiezoTensor.from_vasp_voigt" title="Link to this definition"></a></dt>
<dd><dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>input_vasp_array</strong> (<em>ArrayLike</em>) – Voigt form of tensor.</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>PiezoTensor</p>
</dd>
</dl>
</dd></dl>
</dd></dl>
</section>
<section id="module-pymatgen.analysis.piezo_sensitivity">
<span id="pymatgen-analysis-piezo-sensitivity-module"></span><h2>pymatgen.analysis.piezo_sensitivity module<a class="headerlink" href="#module-pymatgen.analysis.piezo_sensitivity" title="Link to this heading"></a></h2>
<p>Piezo sensitivity analysis module.</p>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.analysis.piezo_sensitivity.BornEffectiveCharge">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">BornEffectiveCharge</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">structure</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><span class="pre">Structure</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">bec</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">pointops</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">tol</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">float</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">0.001</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/piezo_sensitivity.py#L33-L161"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.piezo_sensitivity.BornEffectiveCharge" title="Link to this definition"></a></dt>
<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></p>
<p>This class describes the Nx3x3 born effective charge tensor.</p>
<p>Create an BornEffectiveChargeTensor object defined by a
structure, point operations of the structure’s atomic sites.
Note that the constructor uses __new__ rather than __init__
according to the standard method of subclassing numpy ndarrays.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>input_matrix</strong> (<em>Nx3x3 array-like</em>) – the Nx3x3 array-like
representing the born effective charge tensor</p>
</dd>
</dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.piezo_sensitivity.BornEffectiveCharge.get_BEC_operations">
<span class="sig-name descname"><span class="pre">get_BEC_operations</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">eigtol</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1e-05</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">opstol</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0.001</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/piezo_sensitivity.py#L54-L109"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.piezo_sensitivity.BornEffectiveCharge.get_BEC_operations" title="Link to this definition"></a></dt>
<dd><p>Get the symmetry operations which maps the tensors
belonging to equivalent sites onto each other in the form
[site index 1, site index 2, [Symmops mapping from site
index 1 to site index 2]].</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>eigtol</strong> (<em>float</em>) – tolerance for determining if two sites are</p></li>
<li><p><strong>symmetry</strong> (<em>related by</em>)</p></li>
<li><p><strong>opstol</strong> (<em>float</em>) – tolerance for determining if a symmetry</p></li>
<li><p><strong>sites</strong> (<em>operation relates two</em>)</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>list of symmetry operations mapping equivalent sites and
the indexes of those sites.</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.piezo_sensitivity.BornEffectiveCharge.get_rand_BEC">
<span class="sig-name descname"><span class="pre">get_rand_BEC</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">max_charge</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/piezo_sensitivity.py#L111-L161"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.piezo_sensitivity.BornEffectiveCharge.get_rand_BEC" title="Link to this definition"></a></dt>
<dd><p>Generate a random born effective charge tensor which obeys a structure’s
symmetry and the acoustic sum rule.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>max_charge</strong> (<em>float</em>) – maximum born effective charge value</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>np.array Born effective charge tensor</p>
</dd>
</dl>
</dd></dl>
</dd></dl>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.analysis.piezo_sensitivity.ForceConstantMatrix">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">ForceConstantMatrix</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">structure</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><span class="pre">Structure</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">fcm</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">pointops</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">sharedops</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">tol</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">float</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">0.001</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/piezo_sensitivity.py#L254-L633"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.piezo_sensitivity.ForceConstantMatrix" title="Link to this definition"></a></dt>
<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></p>
<p>This class describes the NxNx3x3 force constant matrix defined by a
structure, point operations of the structure’s atomic sites, and the
shared symmetry operations between pairs of atomic sites.</p>
<p>Create an ForceConstantMatrix object.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>input_matrix</strong> (<em>NxNx3x3 array-like</em>) – the NxNx3x3 array-like
representing the force constant matrix</p>
</dd>
</dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.piezo_sensitivity.ForceConstantMatrix.get_FCM_operations">
<span class="sig-name descname"><span class="pre">get_FCM_operations</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">eigtol</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1e-05</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">opstol</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1e-05</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/piezo_sensitivity.py#L275-L346"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.piezo_sensitivity.ForceConstantMatrix.get_FCM_operations" title="Link to this definition"></a></dt>
<dd><p>Get the symmetry operations which maps the tensors
belonging to equivalent sites onto each other in the form
[site index 1a, site index 1b, site index 2a, site index 2b,
[Symmops mapping from site index 1a, 1b to site index 2a, 2b]].</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>eigtol</strong> (<em>float</em>) – tolerance for determining if two sites are</p></li>
<li><p><strong>symmetry</strong> (<em>related by</em>)</p></li>
<li><p><strong>opstol</strong> (<em>float</em>) – tolerance for determining if a symmetry</p></li>
<li><p><strong>sites</strong> (<em>operation relates two</em>)</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>list of symmetry operations mapping equivalent sites and
the indexes of those sites.</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.piezo_sensitivity.ForceConstantMatrix.get_asum_FCM">
<span class="sig-name descname"><span class="pre">get_asum_FCM</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">fcm</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">ndarray</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">numiter</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">15</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/piezo_sensitivity.py#L504-L587"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.piezo_sensitivity.ForceConstantMatrix.get_asum_FCM" title="Link to this definition"></a></dt>
<dd><p>Generate a symmetrized force constant matrix that obeys the objects symmetry
constraints and obeys the acoustic sum rule through an iterative procedure.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>fcm</strong> (<em>numpy array</em>) – 3Nx3N unsymmetrized force constant matrix</p></li>
<li><p><strong>numiter</strong> (<em>int</em>) – number of iterations to attempt to obey the acoustic sum
rule</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>numpy array representing the force constant matrix</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.piezo_sensitivity.ForceConstantMatrix.get_rand_FCM">
<span class="sig-name descname"><span class="pre">get_rand_FCM</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">asum</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">15</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">force</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">10</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../../../../monty/src/monty/dev.py#L589-L633"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.piezo_sensitivity.ForceConstantMatrix.get_rand_FCM" title="Link to this definition"></a></dt>
<dd><p>Generate a symmetrized force constant matrix from an unsymmetrized matrix
that has no unstable modes and also obeys the acoustic sum rule through an
iterative procedure.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>force</strong> (<em>float</em>) – maximum force constant</p></li>
<li><p><strong>asum</strong> (<em>int</em>) – number of iterations to attempt to obey the acoustic sum
rule</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>NxNx3x3 np.array representing the force constant matrix</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.piezo_sensitivity.ForceConstantMatrix.get_stable_FCM">
<span class="sig-name descname"><span class="pre">get_stable_FCM</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">fcm</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">fcmasum</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">10</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/piezo_sensitivity.py#L456-L500"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.piezo_sensitivity.ForceConstantMatrix.get_stable_FCM" title="Link to this definition"></a></dt>
<dd><p>Generate a symmetrized force constant matrix that obeys the objects symmetry
constraints, has no unstable modes and also obeys the acoustic sum rule through an
iterative procedure.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>fcm</strong> (<em>numpy array</em>) – unsymmetrized force constant matrix</p></li>
<li><p><strong>fcmasum</strong> (<em>int</em>) – number of iterations to attempt to obey the acoustic sum
rule</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>3Nx3N numpy array representing the force constant matrix</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.piezo_sensitivity.ForceConstantMatrix.get_symmetrized_FCM">
<span class="sig-name descname"><span class="pre">get_symmetrized_FCM</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">unsymmetrized_fcm</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">max_force</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/piezo_sensitivity.py#L403-L454"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.piezo_sensitivity.ForceConstantMatrix.get_symmetrized_FCM" title="Link to this definition"></a></dt>
<dd><p>Generate a symmetrized force constant matrix from an unsymmetrized matrix.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>unsymmetrized_fcm</strong> (<em>numpy array</em>) – unsymmetrized force constant matrix</p></li>
<li><p><strong>max_charge</strong> (<em>float</em>) – maximum born effective charge value</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>3Nx3N numpy array representing the force constant matrix</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.piezo_sensitivity.ForceConstantMatrix.get_unstable_FCM">
<span class="sig-name descname"><span class="pre">get_unstable_FCM</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">max_force</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/piezo_sensitivity.py#L348-L401"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.piezo_sensitivity.ForceConstantMatrix.get_unstable_FCM" title="Link to this definition"></a></dt>
<dd><p>Generate an unsymmetrized force constant matrix.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>max_charge</strong> (<em>float</em>) – maximum born effective charge value</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>numpy array representing the force constant matrix</p>
</dd>
</dl>
</dd></dl>
</dd></dl>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.analysis.piezo_sensitivity.InternalStrainTensor">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">InternalStrainTensor</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">structure</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><span class="pre">Structure</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">ist</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">pointops</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">tol</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">float</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">0.001</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/piezo_sensitivity.py#L164-L251"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.piezo_sensitivity.InternalStrainTensor" title="Link to this definition"></a></dt>
<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></p>
<p>This class describes the Nx3x3x3 internal tensor defined by a
structure, point operations of the structure’s atomic sites.</p>
<p>Create an InternalStrainTensor object.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>input_matrix</strong> (<em>Nx3x3x3 array-like</em>) – the Nx3x3x3 array-like
representing the internal strain tensor</p>
</dd>
</dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.piezo_sensitivity.InternalStrainTensor.get_IST_operations">
<span class="sig-name descname"><span class="pre">get_IST_operations</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">opstol</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0.001</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">list</span><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">]</span></span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/piezo_sensitivity.py#L187-L221"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.piezo_sensitivity.InternalStrainTensor.get_IST_operations" title="Link to this definition"></a></dt>
<dd><p>Get the symmetry operations which maps the tensors
belonging to equivalent sites onto each other in the form
[site index 1, site index 2, [SymmOps mapping from site
index 1 to site index 2]].</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>opstol</strong> (<em>float</em>) – tolerance for determining if a symmetry</p></li>
<li><p><strong>sites</strong> (<em>operation relates two</em>)</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>symmetry operations mapping equivalent sites and the indexes of those sites.</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>list[list[list]]</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.piezo_sensitivity.InternalStrainTensor.get_rand_IST">
<span class="sig-name descname"><span class="pre">get_rand_IST</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">max_force</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/piezo_sensitivity.py#L223-L251"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.piezo_sensitivity.InternalStrainTensor.get_rand_IST" title="Link to this definition"></a></dt>
<dd><p>Generate a random internal strain tensor which obeys a structure’s
symmetry and the acoustic sum rule.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>max_force</strong> (<em>float</em>) – maximum born effective charge value</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>InternalStrainTensor</p>
</dd>
</dl>
</dd></dl>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="pymatgen.analysis.piezo_sensitivity.get_piezo">
<span class="sig-name descname"><span class="pre">get_piezo</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">BEC</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">IST</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">FCM</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">rcond</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0.0001</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/piezo_sensitivity.py#L636-L660"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.piezo_sensitivity.get_piezo" title="Link to this definition"></a></dt>
<dd><p>Generate a random piezoelectric tensor based on a structure and corresponding
symmetry.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>BEC</strong> (<em>numpy array</em>) – Nx3x3 array representing the born effective charge tensor</p></li>
<li><p><strong>IST</strong> (<em>numpy array</em>) – Nx3x3x3 array representing the internal strain tensor</p></li>
<li><p><strong>FCM</strong> (<em>numpy array</em>) – NxNx3x3 array representing the born effective charge tensor</p></li>
<li><p><strong>rcondy</strong> (<em>float</em>) – condition for excluding eigenvalues in the pseudoinverse</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>3x3x3 calculated Piezo tensor</p>
</dd>
</dl>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="pymatgen.analysis.piezo_sensitivity.rand_piezo">
<span class="sig-name descname"><span class="pre">rand_piezo</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">struct</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">pointops</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">sharedops</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">BEC</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">IST</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">FCM</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">anumiter</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">10</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../../../../monty/src/monty/dev.py#L663-L696"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.piezo_sensitivity.rand_piezo" title="Link to this definition"></a></dt>
<dd><p>Generate a random piezoelectric tensor based on a structure and corresponding
symmetry.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>struct</strong> (<em>pymatgen structure</em>) – structure whose symmetry operations the piezo tensor must obey</p></li>
<li><p><strong>pointops</strong> – list of point operations obeyed by a single atomic site</p></li>
<li><p><strong>sharedops</strong> – list of point operations shared by a pair of atomic sites</p></li>
<li><p><strong>BEC</strong> (<em>numpy array</em>) – Nx3x3 array representing the born effective charge tensor</p></li>
<li><p><strong>IST</strong> (<em>numpy array</em>) – Nx3x3x3 array representing the internal strain tensor</p></li>
<li><p><strong>FCM</strong> (<em>numpy array</em>) – NxNx3x3 array representing the born effective charge tensor</p></li>
<li><p><strong>anumiter</strong> (<em>int</em>) – number of iterations for acoustic sum rule convergence</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>list in the form of [Nx3x3 random born effective charge tenosr,
Nx3x3x3 random internal strain tensor, NxNx3x3 random force constant matrix, 3x3x3 piezo tensor]</p>
</dd>
</dl>
</dd></dl>
</section>
<section id="module-pymatgen.analysis.pourbaix_diagram">
<span id="pymatgen-analysis-pourbaix-diagram-module"></span><h2>pymatgen.analysis.pourbaix_diagram module<a class="headerlink" href="#module-pymatgen.analysis.pourbaix_diagram" title="Link to this heading"></a></h2>
<p>This module is intended to be used to compute Pourbaix diagrams of arbitrary compositions
and formation energies.</p>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.analysis.pourbaix_diagram.IonEntry">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">IonEntry</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">ion</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="pymatgen.core.html#pymatgen.core.ion.Ion" title="pymatgen.core.ion.Ion"><span class="pre">Ion</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">energy</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">float</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">name</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">attribute</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/pourbaix_diagram.py#L360-L400"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.pourbaix_diagram.IonEntry" title="Link to this definition"></a></dt>
<dd><p>Bases: <a class="reference internal" href="#pymatgen.analysis.phase_diagram.PDEntry" title="pymatgen.analysis.phase_diagram.PDEntry"><code class="xref py py-class docutils literal notranslate"><span class="pre">PDEntry</span></code></a></p>
<p>Object similar to PDEntry, but contains an Ion object instead of a
Composition object.</p>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.analysis.pourbaix_diagram.IonEntry.name">
<span class="sig-name descname"><span class="pre">name</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/pourbaix_diagram.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.pourbaix_diagram.IonEntry.name" title="Link to this definition"></a></dt>
<dd><p>A name for the entry. This is the string shown in the phase diagrams.
By default, this is the reduced formula for the composition, but can be
set to some other string for display purposes.</p>
<dl class="field-list simple">
<dt class="field-odd">Type<span class="colon">:</span></dt>
<dd class="field-odd"><p>str</p>
</dd>
</dl>
</dd></dl>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>ion</strong> – Ion object</p></li>
<li><p><strong>energy</strong> – Energy for composition.</p></li>
<li><p><strong>name</strong> – Optional parameter to name the entry. Defaults to the
chemical formula.</p></li>
<li><p><strong>attribute</strong> – Optional attribute of the entry, e.g. band gap.</p></li>
</ul>
</dd>
</dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.pourbaix_diagram.IonEntry.as_dict">
<span class="sig-name descname"><span class="pre">as_dict</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><span class="pre">Literal</span><span class="p"><span class="pre">[</span></span><span class="s"><span class="pre">'ion'</span></span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="s"><span class="pre">'energy'</span></span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="s"><span class="pre">'name'</span></span><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">Any</span><span class="p"><span class="pre">]</span></span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/pourbaix_diagram.py#L398-L400"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.pourbaix_diagram.IonEntry.as_dict" title="Link to this definition"></a></dt>
<dd><p>Create a dict of composition, energy, and ion name.</p>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.pourbaix_diagram.IonEntry.from_dict">
<em class="property"><span class="pre">classmethod</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">from_dict</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">dct</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">dict</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">Self</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/pourbaix_diagram.py#L388-L396"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.pourbaix_diagram.IonEntry.from_dict" title="Link to this definition"></a></dt>
<dd><p>Get an IonEntry object from a dict.</p>
</dd></dl>
</dd></dl>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.analysis.pourbaix_diagram.MultiEntry">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">MultiEntry</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entry_list</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">Sequence</span><span class="p"><span class="pre">[</span></span><a class="reference internal" href="#pymatgen.analysis.pourbaix_diagram.PourbaixEntry" title="pymatgen.analysis.pourbaix_diagram.PourbaixEntry"><span class="pre">PourbaixEntry</span></a><span class="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="n"><span class="pre">weights</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">float</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/pourbaix_diagram.py#L277-L355"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.pourbaix_diagram.MultiEntry" title="Link to this definition"></a></dt>
<dd><p>Bases: <a class="reference internal" href="#pymatgen.analysis.pourbaix_diagram.PourbaixEntry" title="pymatgen.analysis.pourbaix_diagram.PourbaixEntry"><code class="xref py py-class docutils literal notranslate"><span class="pre">PourbaixEntry</span></code></a></p>
<p>PourbaixEntry-like object for constructing multi-elemental Pourbaix diagrams.</p>
<p>Initialize a MultiEntry.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>entry_list</strong> (<em>Sequence</em><em>[</em><a class="reference internal" href="#pymatgen.analysis.pourbaix_diagram.PourbaixEntry" title="pymatgen.analysis.pourbaix_diagram.PourbaixEntry"><em>PourbaixEntry</em></a><em>]</em>) – Component PourbaixEntries.</p></li>
<li><p><strong>weights</strong> (<em>list</em><em>[</em><em>float</em><em>]</em>) – Weights associated with each entry. Default is None</p></li>
</ul>
</dd>
</dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.pourbaix_diagram.MultiEntry.as_dict">
<span class="sig-name descname"><span class="pre">as_dict</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">Any</span><span class="p"><span class="pre">]</span></span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/pourbaix_diagram.py#L336-L343"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.pourbaix_diagram.MultiEntry.as_dict" title="Link to this definition"></a></dt>
<dd><p>Get MSONable dict.</p>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.pourbaix_diagram.MultiEntry.from_dict">
<em class="property"><span class="pre">classmethod</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">from_dict</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">dct</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">dict</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">Self</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/pourbaix_diagram.py#L345-L355"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.pourbaix_diagram.MultiEntry.from_dict" title="Link to this definition"></a></dt>
<dd><dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>dct</strong> (<em>dict</em>) – Dict representation.</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>MultiEntry</p>
</dd>
</dl>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.analysis.pourbaix_diagram.MultiEntry.name">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">name</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">str</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/pourbaix_diagram.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.pourbaix_diagram.MultiEntry.name" title="Link to this definition"></a></dt>
<dd><p>MultiEntry name, i.e. the name of each entry joined by ‘ + ‘.</p>
</dd></dl>
</dd></dl>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.analysis.pourbaix_diagram.PourbaixDiagram">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">PourbaixDiagram</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entries</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">list</span><span class="p"><span class="pre">[</span></span><a class="reference internal" href="#pymatgen.analysis.pourbaix_diagram.PourbaixEntry" title="pymatgen.analysis.pourbaix_diagram.PourbaixEntry"><span class="pre">PourbaixEntry</span></a><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">list</span><span class="p"><span class="pre">[</span></span><a class="reference internal" href="#pymatgen.analysis.pourbaix_diagram.MultiEntry" title="pymatgen.analysis.pourbaix_diagram.MultiEntry"><span class="pre">MultiEntry</span></a><span class="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="n"><span class="pre">comp_dict</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">float</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">conc_dict</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">float</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">filter_solids</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">nproc</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/pourbaix_diagram.py#L432-L965"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.pourbaix_diagram.PourbaixDiagram" title="Link to this definition"></a></dt>
<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">MSONable</span></code></p>
<p>Create a Pourbaix diagram from entries.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>entries</strong> (<em>[</em><a class="reference internal" href="#pymatgen.analysis.pourbaix_diagram.PourbaixEntry" title="pymatgen.analysis.pourbaix_diagram.PourbaixEntry"><em>PourbaixEntry</em></a><em>] or </em><em>[</em><a class="reference internal" href="#pymatgen.analysis.pourbaix_diagram.MultiEntry" title="pymatgen.analysis.pourbaix_diagram.MultiEntry"><em>MultiEntry</em></a><em>]</em>) – Entries list
containing Solids and Ions or a list of MultiEntries</p></li>
<li><p><strong>comp_dict</strong> (<em>dict</em><em>[</em><em>str</em><em>, </em><em>float</em><em>]</em>) – Dictionary of compositions,
defaults to equal parts of each elements</p></li>
<li><p><strong>conc_dict</strong> (<em>dict</em><em>[</em><em>str</em><em>, </em><em>float</em><em>]</em>) – Dictionary of ion concentrations,
defaults to 1e-6 for each element</p></li>
<li><p><strong>filter_solids</strong> (<em>bool</em>) – applying this filter to a Pourbaix
diagram ensures all included solid phases are filtered by
stability on the compositional phase diagram. Defaults to True.
The practical consequence of this is that highly oxidized or reduced
phases that might show up in experiments due to kinetic limitations
on oxygen/hydrogen evolution won’t appear in the diagram, but they are
not actually “stable” (and are frequently overstabilized from DFT errors).
Hence, including only the stable solid phases generally leads to the
most accurate Pourbaix diagrams.</p></li>
<li><p><strong>nproc</strong> (<em>int</em>) – number of processes to generate multi-entries with
in parallel. Defaults to None (serial processing).</p></li>
</ul>
</dd>
</dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.analysis.pourbaix_diagram.PourbaixDiagram.all_entries">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">all_entries</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">list</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/pourbaix_diagram.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.pourbaix_diagram.PourbaixDiagram.all_entries" title="Link to this definition"></a></dt>
<dd><p>All entries used to generate the Pourbaix diagram.</p>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.pourbaix_diagram.PourbaixDiagram.as_dict">
<span class="sig-name descname"><span class="pre">as_dict</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">Any</span><span class="p"><span class="pre">]</span></span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/pourbaix_diagram.py#L939-L948"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.pourbaix_diagram.PourbaixDiagram.as_dict" title="Link to this definition"></a></dt>
<dd><p>Get MSONable dict.</p>
</dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.analysis.pourbaix_diagram.PourbaixDiagram.elements_ho">
<span class="sig-name descname"><span class="pre">elements_ho</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">ClassVar</span><span class="p"><span class="pre">[</span></span><span class="pre">set</span><span class="p"><span class="pre">[</span></span><a class="reference internal" href="pymatgen.core.html#pymatgen.core.periodic_table.Element" title="pymatgen.core.periodic_table.Element"><span class="pre">Element</span></a><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">]</span></span></em><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">{Element</span> <span class="pre">H,</span> <span class="pre">Element</span> <span class="pre">O}</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/pourbaix_diagram.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.pourbaix_diagram.PourbaixDiagram.elements_ho" title="Link to this definition"></a></dt>
<dd></dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.pourbaix_diagram.PourbaixDiagram.find_stable_entry">
<span class="sig-name descname"><span class="pre">find_stable_entry</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">pH</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">float</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">V</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">float</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><a class="reference internal" href="#pymatgen.analysis.pourbaix_diagram.PourbaixEntry" title="pymatgen.analysis.pourbaix_diagram.PourbaixEntry"><span class="pre">PourbaixEntry</span></a></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/pourbaix_diagram.py#L843-L854"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.pourbaix_diagram.PourbaixDiagram.find_stable_entry" title="Link to this definition"></a></dt>
<dd><p>Find stable entry at a pH,V condition.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>pH</strong> (<em>float</em>) – pH to find stable entry</p></li>
<li><p><strong>V</strong> (<em>float</em>) – V to find stable entry.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>stable entry at pH, V</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p><a class="reference internal" href="#pymatgen.analysis.pourbaix_diagram.PourbaixEntry" title="pymatgen.analysis.pourbaix_diagram.PourbaixEntry">PourbaixEntry</a></p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.pourbaix_diagram.PourbaixDiagram.from_dict">
<em class="property"><span class="pre">classmethod</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">from_dict</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">dct</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">dict</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">Self</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/pourbaix_diagram.py#L950-L965"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.pourbaix_diagram.PourbaixDiagram.from_dict" title="Link to this definition"></a></dt>
<dd><dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>dct</strong> (<em>dict</em>) – Dict representation.</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>PourbaixDiagram</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.pourbaix_diagram.PourbaixDiagram.get_decomposition_energy">
<span class="sig-name descname"><span class="pre">get_decomposition_energy</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entry</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="#pymatgen.analysis.pourbaix_diagram.PourbaixEntry" title="pymatgen.analysis.pourbaix_diagram.PourbaixEntry"><span class="pre">PourbaixEntry</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">pH</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">float</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">V</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">float</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">NDArray</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/pourbaix_diagram.py#L856-L889"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.pourbaix_diagram.PourbaixDiagram.get_decomposition_energy" title="Link to this definition"></a></dt>
<dd><p>Find decomposition to most stable entries in eV/atom,
supports vectorized inputs for pH and V.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>entry</strong> (<a class="reference internal" href="#pymatgen.analysis.pourbaix_diagram.PourbaixEntry" title="pymatgen.analysis.pourbaix_diagram.PourbaixEntry"><em>PourbaixEntry</em></a>) – PourbaixEntry corresponding to
compound to find the decomposition for</p></li>
<li><p><strong>pH</strong> (<em>float</em>) – pH at which to find the decomposition</p></li>
<li><p><strong>V</strong> (<em>float</em>) – voltage at which to find the decomposition</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p><dl class="simple">
<dt>Decomposition energy for the entry, i.e. the energy above</dt><dd><p>the “Pourbaix hull” in eV/atom at the given conditions</p>
</dd>
</dl>
</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.pourbaix_diagram.PourbaixDiagram.get_hull_energy">
<span class="sig-name descname"><span class="pre">get_hull_energy</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">pH</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">float</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">float</span><span class="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="n"><span class="pre">V</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">float</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">float</span><span class="p"><span class="pre">]</span></span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">NDArray</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/pourbaix_diagram.py#L891-L903"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.pourbaix_diagram.PourbaixDiagram.get_hull_energy" title="Link to this definition"></a></dt>
<dd><p>Get the minimum energy of the Pourbaix “basin” that is formed
from the stable Pourbaix planes. Vectorized.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>pH</strong> (<em>float</em><em> | </em><em>list</em><em>[</em><em>float</em><em>]</em>) – pH at which to find the hull energy</p></li>
<li><p><strong>V</strong> (<em>float</em><em> | </em><em>list</em><em>[</em><em>float</em><em>]</em>) – V at which to find the hull energy</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>minimum Pourbaix energy at conditions</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>np.array</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.pourbaix_diagram.PourbaixDiagram.get_pourbaix_domains">
<em class="property"><span class="pre">static</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">get_pourbaix_domains</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">pourbaix_entries</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">list</span><span class="p"><span class="pre">[</span></span><a class="reference internal" href="#pymatgen.analysis.pourbaix_diagram.PourbaixEntry" title="pymatgen.analysis.pourbaix_diagram.PourbaixEntry"><span class="pre">PourbaixEntry</span></a><span class="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="n"><span class="pre">limits</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">float</span><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">tuple</span><span class="p"><span class="pre">[</span></span><span class="pre">dict</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">dict</span><span class="p"><span class="pre">]</span></span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/pourbaix_diagram.py#L753-L841"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.pourbaix_diagram.PourbaixDiagram.get_pourbaix_domains" title="Link to this definition"></a></dt>
<dd><p>Get a set of Pourbaix stable domains (i.e. polygons) in
pH-V space from a list of pourbaix_entries.</p>
<p>This function works by using scipy’s HalfspaceIntersection
function to construct all of the 2-D polygons that form the
boundaries of the planes corresponding to individual entry
gibbs free energies as a function of pH and V. Hyperplanes
of the form a*pH + b*V + 1 - g(0, 0) are constructed and
supplied to HalfspaceIntersection, which then finds the
boundaries of each Pourbaix region using the intersection
points.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>pourbaix_entries</strong> (<em>list</em><em>[</em><a class="reference internal" href="#pymatgen.analysis.pourbaix_diagram.PourbaixEntry" title="pymatgen.analysis.pourbaix_diagram.PourbaixEntry"><em>PourbaixEntry</em></a><em>]</em>) – Pourbaix entries
with which to construct stable Pourbaix domains</p></li>
<li><p><strong>limits</strong> (<em>list</em><em>[</em><em>list</em><em>[</em><em>float</em><em>]</em><em>]</em>) – limits in which to do the pourbaix
analysis</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>The first dict is of form: {entry: [boundary_points]}.
The list of boundary points are the sides of the N-1
dim polytope bounding the allowable ph-V range of each entry.</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>tuple[dict[<a class="reference internal" href="#pymatgen.analysis.pourbaix_diagram.PourbaixEntry" title="pymatgen.analysis.pourbaix_diagram.PourbaixEntry">PourbaixEntry</a>, list], dict[<a class="reference internal" href="#pymatgen.analysis.pourbaix_diagram.PourbaixEntry" title="pymatgen.analysis.pourbaix_diagram.PourbaixEntry">PourbaixEntry</a>, NDArray]</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.pourbaix_diagram.PourbaixDiagram.get_stable_entry">
<span class="sig-name descname"><span class="pre">get_stable_entry</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">pH</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">float</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">V</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">float</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><a class="reference internal" href="#pymatgen.analysis.pourbaix_diagram.PourbaixEntry" title="pymatgen.analysis.pourbaix_diagram.PourbaixEntry"><span class="pre">PourbaixEntry</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference internal" href="#pymatgen.analysis.pourbaix_diagram.MultiEntry" title="pymatgen.analysis.pourbaix_diagram.MultiEntry"><span class="pre">MultiEntry</span></a></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/pourbaix_diagram.py#L905-L917"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.pourbaix_diagram.PourbaixDiagram.get_stable_entry" title="Link to this definition"></a></dt>
<dd><p>Get the stable entry at a given pH, V condition.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>pH</strong> (<em>float</em>) – pH at a given condition</p></li>
<li><p><strong>V</strong> (<em>float</em>) – V at a given condition</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p><dl class="simple">
<dt>Pourbaix or multi-entry</dt><dd><p>corresponding to the minimum energy entry at a given pH, V condition</p>
</dd>
</dl>
</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p><a class="reference internal" href="#pymatgen.analysis.pourbaix_diagram.PourbaixEntry" title="pymatgen.analysis.pourbaix_diagram.PourbaixEntry">PourbaixEntry</a> | <a class="reference internal" href="#pymatgen.analysis.pourbaix_diagram.MultiEntry" title="pymatgen.analysis.pourbaix_diagram.MultiEntry">MultiEntry</a></p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.pourbaix_diagram.PourbaixDiagram.process_multientry">
<em class="property"><span class="pre">static</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">process_multientry</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entry_list</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">Sequence</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">prod_comp</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="pymatgen.core.html#pymatgen.core.composition.Composition" title="pymatgen.core.composition.Composition"><span class="pre">Composition</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">coeff_threshold</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">float</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">0.0001</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><a class="reference internal" href="#pymatgen.analysis.pourbaix_diagram.MultiEntry" title="pymatgen.analysis.pourbaix_diagram.MultiEntry"><span class="pre">MultiEntry</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/pourbaix_diagram.py#L713-L751"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.pourbaix_diagram.PourbaixDiagram.process_multientry" title="Link to this definition"></a></dt>
<dd><p>Static method for finding a multientry based on
a list of entries and a product composition.
Essentially checks to see if a valid aqueous
reaction exists between the entries and the
product composition and returns a MultiEntry
with weights according to the coefficients if so.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>entry_list</strong> (<em>Sequence</em><em>[</em><a class="reference internal" href="pymatgen.entries.html#pymatgen.entries.Entry" title="pymatgen.entries.Entry"><em>Entry</em></a><em>]</em>) – Entries from which to
create a MultiEntry</p></li>
<li><p><strong>prod_comp</strong> (<a class="reference internal" href="pymatgen.core.html#pymatgen.core.composition.Composition" title="pymatgen.core.composition.Composition"><em>Composition</em></a>) – composition constraint for setting
weights of MultiEntry</p></li>
<li><p><strong>coeff_threshold</strong> (<em>float</em>) – threshold of stoichiometric
coefficients to filter, if weights are lower than
this value, the entry is not returned</p></li>
</ul>
</dd>
</dl>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.analysis.pourbaix_diagram.PourbaixDiagram.stable_entries">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">stable_entries</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">list</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/pourbaix_diagram.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.pourbaix_diagram.PourbaixDiagram.stable_entries" title="Link to this definition"></a></dt>
<dd><p>The stable entries in the Pourbaix diagram.</p>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.analysis.pourbaix_diagram.PourbaixDiagram.unprocessed_entries">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">unprocessed_entries</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">list</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/pourbaix_diagram.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.pourbaix_diagram.PourbaixDiagram.unprocessed_entries" title="Link to this definition"></a></dt>
<dd><p>Unprocessed entries.</p>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.analysis.pourbaix_diagram.PourbaixDiagram.unstable_entries">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">unstable_entries</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">list</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/pourbaix_diagram.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.pourbaix_diagram.PourbaixDiagram.unstable_entries" title="Link to this definition"></a></dt>
<dd><p>All unstable entries in the Pourbaix diagram.</p>
</dd></dl>
</dd></dl>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.analysis.pourbaix_diagram.PourbaixEntry">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">PourbaixEntry</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entry</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="pymatgen.entries.html#pymatgen.entries.computed_entries.ComputedEntry" title="pymatgen.entries.computed_entries.ComputedEntry"><span class="pre">ComputedEntry</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference internal" href="pymatgen.entries.html#pymatgen.entries.computed_entries.ComputedStructureEntry" title="pymatgen.entries.computed_entries.ComputedStructureEntry"><span class="pre">ComputedStructureEntry</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">entry_id</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">concentration</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">float</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">1e-06</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/pourbaix_diagram.py#L80-L274"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.pourbaix_diagram.PourbaixEntry" title="Link to this definition"></a></dt>
<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">MSONable</span></code>, <a class="reference internal" href="pymatgen.util.html#pymatgen.util.string.Stringify" title="pymatgen.util.string.Stringify"><code class="xref py py-class docutils literal notranslate"><span class="pre">Stringify</span></code></a></p>
<p>An object encompassing all data relevant to a solid or ion
in a Pourbaix diagram. Each bulk solid/ion has an energy
g of the form: e = e0 + 0.0591 log10(conc) - nO mu_H2O
+ (nH - 2nO) pH + phi (-nH + 2nO + q).</p>
<p>Note that the energies corresponding to the input entries
should be formation energies with respect to hydrogen and
oxygen gas in order for the Pourbaix diagram formalism to
work. This may be changed to be more flexible in the future.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>entry</strong> (<a class="reference internal" href="pymatgen.entries.html#pymatgen.entries.computed_entries.ComputedEntry" title="pymatgen.entries.computed_entries.ComputedEntry"><em>ComputedEntry</em></a><em> | </em><a class="reference internal" href="pymatgen.entries.html#pymatgen.entries.computed_entries.ComputedStructureEntry" title="pymatgen.entries.computed_entries.ComputedStructureEntry"><em>ComputedStructureEntry</em></a><em> | </em><a class="reference internal" href="#pymatgen.analysis.phase_diagram.PDEntry" title="pymatgen.analysis.phase_diagram.PDEntry"><em>PDEntry</em></a><em> | </em><a class="reference internal" href="#pymatgen.analysis.pourbaix_diagram.IonEntry" title="pymatgen.analysis.pourbaix_diagram.IonEntry"><em>IonEntry</em></a>) – An entry object</p></li>
<li><p><strong>entry_id</strong> (<em>str</em>) – A string id for the entry</p></li>
<li><p><strong>concentration</strong> (<em>float</em>) – Concentration of the entry in M. Defaults to 1e-6.</p></li>
</ul>
</dd>
</dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.pourbaix_diagram.PourbaixEntry.as_dict">
<span class="sig-name descname"><span class="pre">as_dict</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/pourbaix_diagram.py#L225-L241"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.pourbaix_diagram.PourbaixEntry.as_dict" title="Link to this definition"></a></dt>
<dd><p>Get dict which contains Pourbaix Entry data.
Note that the pH, voltage, H2O factors are always calculated when
constructing a PourbaixEntry object.</p>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.analysis.pourbaix_diagram.PourbaixEntry.composition">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">composition</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><a class="reference internal" href="pymatgen.core.html#pymatgen.core.composition.Composition" title="pymatgen.core.composition.Composition"><span class="pre">Composition</span></a></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/pourbaix_diagram.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.pourbaix_diagram.PourbaixEntry.composition" title="Link to this definition"></a></dt>
<dd><p>Composition.</p>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.analysis.pourbaix_diagram.PourbaixEntry.conc_term">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">conc_term</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">float</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/pourbaix_diagram.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.pourbaix_diagram.PourbaixEntry.conc_term" title="Link to this definition"></a></dt>
<dd><p>The concentration contribution to the free energy. Should only be present
when there are ions in the entry.</p>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.analysis.pourbaix_diagram.PourbaixEntry.elements">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">elements</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">list</span><span class="p"><span class="pre">[</span></span><a class="reference internal" href="pymatgen.core.html#pymatgen.core.periodic_table.Element" title="pymatgen.core.periodic_table.Element"><span class="pre">Element</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference internal" href="pymatgen.core.html#pymatgen.core.periodic_table.Species" title="pymatgen.core.periodic_table.Species"><span class="pre">Species</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference internal" href="pymatgen.core.html#pymatgen.core.periodic_table.DummySpecies" title="pymatgen.core.periodic_table.DummySpecies"><span class="pre">DummySpecies</span></a><span class="p"><span class="pre">]</span></span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/pourbaix_diagram.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.pourbaix_diagram.PourbaixEntry.elements" title="Link to this definition"></a></dt>
<dd><p>Elements in the entry.</p>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.analysis.pourbaix_diagram.PourbaixEntry.energy">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">energy</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">float</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/pourbaix_diagram.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.pourbaix_diagram.PourbaixEntry.energy" title="Link to this definition"></a></dt>
<dd><p>Total energy of the Pourbaix entry (at pH, V = 0 vs. SHE).</p>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.pourbaix_diagram.PourbaixEntry.energy_at_conditions">
<span class="sig-name descname"><span class="pre">energy_at_conditions</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">pH</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">float</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">V</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">float</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">float</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/pourbaix_diagram.py#L173-L183"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.pourbaix_diagram.PourbaixEntry.energy_at_conditions" title="Link to this definition"></a></dt>
<dd><p>Get free energy for a given pH and V.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>pH</strong> (<em>float</em>) – pH at which to evaluate free energy</p></li>
<li><p><strong>V</strong> (<em>float</em>) – voltage at which to evaluate free energy</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>free energy at conditions</p>
</dd>
</dl>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.analysis.pourbaix_diagram.PourbaixEntry.energy_per_atom">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">energy_per_atom</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">float</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/pourbaix_diagram.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.pourbaix_diagram.PourbaixEntry.energy_per_atom" title="Link to this definition"></a></dt>
<dd><p>Energy per atom of the Pourbaix entry.</p>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.pourbaix_diagram.PourbaixEntry.from_dict">
<em class="property"><span class="pre">classmethod</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">from_dict</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">dct</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">dict</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">Self</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/pourbaix_diagram.py#L243-L252"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.pourbaix_diagram.PourbaixEntry.from_dict" title="Link to this definition"></a></dt>
<dd><p>Invokes a PourbaixEntry from a dictionary.</p>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.pourbaix_diagram.PourbaixEntry.get_element_fraction">
<span class="sig-name descname"><span class="pre">get_element_fraction</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">element</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="pymatgen.core.html#pymatgen.core.periodic_table.Element" title="pymatgen.core.periodic_table.Element"><span class="pre">Element</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">str</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">float</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/pourbaix_diagram.py#L185-L195"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.pourbaix_diagram.PourbaixEntry.get_element_fraction" title="Link to this definition"></a></dt>
<dd><p>Get the elemental fraction of a given non-OH element.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>element</strong> (<a class="reference internal" href="pymatgen.core.html#pymatgen.core.periodic_table.Element" title="pymatgen.core.periodic_table.Element"><em>Element</em></a><em> or </em><em>str</em>) – string or element corresponding
to element to get from composition</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>fraction of element / sum(all non-OH elements)</p>
</dd>
</dl>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.analysis.pourbaix_diagram.PourbaixEntry.nH2O">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">nH2O</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">float</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/pourbaix_diagram.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.pourbaix_diagram.PourbaixEntry.nH2O" title="Link to this definition"></a></dt>
<dd><p>The number of H2O.</p>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.analysis.pourbaix_diagram.PourbaixEntry.nPhi">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">nPhi</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">float</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/pourbaix_diagram.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.pourbaix_diagram.PourbaixEntry.nPhi" title="Link to this definition"></a></dt>
<dd><p>The number of electrons.</p>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.analysis.pourbaix_diagram.PourbaixEntry.name">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">name</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">str</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/pourbaix_diagram.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.pourbaix_diagram.PourbaixEntry.name" title="Link to this definition"></a></dt>
<dd><p>The entry’s name.</p>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.analysis.pourbaix_diagram.PourbaixEntry.normalization_factor">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">normalization_factor</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">float</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/pourbaix_diagram.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.pourbaix_diagram.PourbaixEntry.normalization_factor" title="Link to this definition"></a></dt>
<dd><p>Sum of number of atoms minus the number of H and O in composition.</p>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.analysis.pourbaix_diagram.PourbaixEntry.normalized_energy">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">normalized_energy</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">float</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/pourbaix_diagram.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.pourbaix_diagram.PourbaixEntry.normalized_energy" title="Link to this definition"></a></dt>
<dd><p>Energy normalized by number of non H or O atoms, e.g.
for Zn2O6, energy / 2 or for AgTe3(OH)3, energy / 4.</p>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.pourbaix_diagram.PourbaixEntry.normalized_energy_at_conditions">
<span class="sig-name descname"><span class="pre">normalized_energy_at_conditions</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">pH</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">float</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">V</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">float</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">float</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/pourbaix_diagram.py#L204-L215"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.pourbaix_diagram.PourbaixEntry.normalized_energy_at_conditions" title="Link to this definition"></a></dt>
<dd><p>Energy at an electrochemical condition, compatible with
numpy arrays for pH/V input.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>pH</strong> (<em>float</em>) – pH at condition</p></li>
<li><p><strong>V</strong> (<em>float</em>) – applied potential at condition</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>energy normalized by number of non-O/H atoms at condition</p>
</dd>
</dl>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.analysis.pourbaix_diagram.PourbaixEntry.npH">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">npH</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">float</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/pourbaix_diagram.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.pourbaix_diagram.PourbaixEntry.npH" title="Link to this definition"></a></dt>
<dd><p>The number of H.</p>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.analysis.pourbaix_diagram.PourbaixEntry.num_atoms">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">num_atoms</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">float</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/pourbaix_diagram.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.pourbaix_diagram.PourbaixEntry.num_atoms" title="Link to this definition"></a></dt>
<dd><p>Number of atoms in current formula. Useful for normalization.</p>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.pourbaix_diagram.PourbaixEntry.to_pretty_string">
<span class="sig-name descname"><span class="pre">to_pretty_string</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">str</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/pourbaix_diagram.py#L269-L274"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.pourbaix_diagram.PourbaixEntry.to_pretty_string" title="Link to this definition"></a></dt>
<dd><p>A pretty string representation.</p>
</dd></dl>
</dd></dl>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.analysis.pourbaix_diagram.PourbaixPlotter">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">PourbaixPlotter</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">pourbaix_diagram</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="#pymatgen.analysis.pourbaix_diagram.PourbaixDiagram" title="pymatgen.analysis.pourbaix_diagram.PourbaixDiagram"><span class="pre">PourbaixDiagram</span></a></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/pourbaix_diagram.py#L968-L1138"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.pourbaix_diagram.PourbaixPlotter" title="Link to this definition"></a></dt>
<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></p>
<p>A plotter class for phase diagrams.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>pourbaix_diagram</strong> (<a class="reference internal" href="#pymatgen.analysis.pourbaix_diagram.PourbaixDiagram" title="pymatgen.analysis.pourbaix_diagram.PourbaixDiagram"><em>PourbaixDiagram</em></a>) – A PourbaixDiagram object.</p>
</dd>
</dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.pourbaix_diagram.PourbaixPlotter.domain_vertices">
<span class="sig-name descname"><span class="pre">domain_vertices</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entry</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">list</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/pourbaix_diagram.py#L1129-L1138"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.pourbaix_diagram.PourbaixPlotter.domain_vertices" title="Link to this definition"></a></dt>
<dd><p>Get the vertices of the Pourbaix domain.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>entry</strong> – Entry for which domain vertices are desired</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>list of vertices</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.pourbaix_diagram.PourbaixPlotter.get_pourbaix_plot">
<span class="sig-name descname"><span class="pre">get_pourbaix_plot</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">limits</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">tuple</span><span class="p"><span class="pre">[</span></span><span class="pre">tuple</span><span class="p"><span class="pre">[</span></span><span class="pre">float</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">float</span><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">tuple</span><span class="p"><span class="pre">[</span></span><span class="pre">float</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">float</span><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">title</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">''</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">label_domains</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">label_fontsize</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">20</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">show_water_lines</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">show_neutral_axes</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ax</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">plt.Axes</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">plt.Axes</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/pourbaix_diagram.py#L1007-L1077"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.pourbaix_diagram.PourbaixPlotter.get_pourbaix_plot" title="Link to this definition"></a></dt>
<dd><p>Plot Pourbaix diagram.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>limits</strong> – tuple containing limits of the Pourbaix diagram
of the form ((xlo, xhi), (ylo, yhi)).</p></li>
<li><p><strong>title</strong> (<em>str</em>) – Title to display on plot</p></li>
<li><p><strong>label_domains</strong> (<em>bool</em>) – whether to label Pourbaix domains</p></li>
<li><p><strong>label_fontsize</strong> – font size for domain labels</p></li>
<li><p><strong>show_water_lines</strong> – whether to show dashed lines indicating the region
of water stability.</p></li>
<li><p><strong>lines</strong> (<em>show_neutral_axes; whether to show dashed horizontal and vertical</em>) – at 0 V and pH 7, respectively.</p></li>
<li><p><strong>ax</strong> (<em>Axes</em>) – Matplotlib Axes instance for plotting</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>matplotlib Axes object with Pourbaix diagram</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>Axes</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.pourbaix_diagram.PourbaixPlotter.plot_entry_stability">
<span class="sig-name descname"><span class="pre">plot_entry_stability</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entry</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">Any</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">pH_range</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">tuple</span><span class="p"><span class="pre">[</span></span><span class="pre">float</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">float</span><span class="p"><span class="pre">]</span></span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">(-2,</span> <span class="pre">16)</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">pH_resolution</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">100</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">V_range</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">tuple</span><span class="p"><span class="pre">[</span></span><span class="pre">float</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">float</span><span class="p"><span class="pre">]</span></span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">(-3,</span> <span class="pre">3)</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">V_resolution</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">100</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">e_hull_max</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">float</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">cmap</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">'RdYlBu_r'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ax</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">plt.Axes</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">Any</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">plt.Axes</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/pourbaix_diagram.py#L1079-L1127"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.pourbaix_diagram.PourbaixPlotter.plot_entry_stability" title="Link to this definition"></a></dt>
<dd><p>Plots the stability of an entry in the Pourbaix diagram.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>entry</strong> (<em>Any</em>) – The entry to plot stability for.</p></li>
<li><p><strong>pH_range</strong> (<em>tuple</em><em>[</em><em>float</em><em>, </em><em>float</em><em>]</em>) – pH range for the plot. Defaults to (-2, 16).</p></li>
<li><p><strong>pH_resolution</strong> (<em>int</em>) – pH resolution. Defaults to 100.</p></li>
<li><p><strong>V_range</strong> (<em>tuple</em><em>[</em><em>float</em><em>, </em><em>float</em><em>]</em>) – Voltage range for the plot. Defaults to (-3, 3).</p></li>
<li><p><strong>V_resolution</strong> (<em>int</em>) – Voltage resolution. Defaults to 100.</p></li>
<li><p><strong>e_hull_max</strong> (<em>float</em>) – Maximum energy above the hull. Defaults to 1.</p></li>
<li><p><strong>cmap</strong> (<em>str</em>) – Colormap for the plot. Defaults to “RdYlBu_r”.</p></li>
<li><p><strong>ax</strong> (<em>Axes</em><em>, </em><em>optional</em>) – Existing matplotlib Axes object for plotting. Defaults to None.</p></li>
<li><p><strong>**kwargs</strong> (<em>Any</em>) – Additional keyword arguments passed to <cite>get_pourbaix_plot</cite>.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>Matplotlib Axes object with the plotted stability.</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>plt.Axes</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.pourbaix_diagram.PourbaixPlotter.show">
<span class="sig-name descname"><span class="pre">show</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">*</span></span><span class="n"><span class="pre">args</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">None</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/pourbaix_diagram.py#L997-L1005"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.pourbaix_diagram.PourbaixPlotter.show" title="Link to this definition"></a></dt>
<dd><p>Show the Pourbaix plot.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>*args</strong> – args to get_pourbaix_plot</p></li>
<li><p><strong>**kwargs</strong> – kwargs to get_pourbaix_plot</p></li>
</ul>
</dd>
</dl>
</dd></dl>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="pymatgen.analysis.pourbaix_diagram.ion_or_solid_comp_object">
<span class="sig-name descname"><span class="pre">ion_or_solid_comp_object</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">formula</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><a class="reference internal" href="pymatgen.core.html#pymatgen.core.composition.Composition" title="pymatgen.core.composition.Composition"><span class="pre">Composition</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference internal" href="pymatgen.core.html#pymatgen.core.ion.Ion" title="pymatgen.core.ion.Ion"><span class="pre">Ion</span></a></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/pourbaix_diagram.py#L403-L421"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.pourbaix_diagram.ion_or_solid_comp_object" title="Link to this definition"></a></dt>
<dd><p>Get an Ion or Composition from a formula.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>formula</strong> (<em>str</em>) – Formula. E.g. of ion: NaOH(aq), Na[+], Na+;
E.g. of solid: Fe2O3(s), Fe(s), Na2O.</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>Composition/Ion object.</p>
</dd>
</dl>
</dd></dl>
</section>
<section id="module-pymatgen.analysis.prototypes">
<span id="pymatgen-analysis-prototypes-module"></span><h2>pymatgen.analysis.prototypes module<a class="headerlink" href="#module-pymatgen.analysis.prototypes" title="Link to this heading"></a></h2>
<p>This module is intended to match crystal structures against known crystallographic “prototype”
structures.</p>
<p>In this module, the AflowPrototypeMatcher uses the AFLOW LIBRARY OF CRYSTALLOGRAPHIC PROTOTYPES.
If using this particular class, please cite their publication appropriately:</p>
<p>Mehl, M. J., Hicks, D., Toher, C., Levy, O., Hanson, R. M., Hart, G., & Curtarolo, S. (2017).
The AFLOW library of crystallographic prototypes: part 1.
Computational Materials Science, 136, S1-S828.
<a class="reference external" href="https://doi.org/10.1016/j.commatsci.2017.01.017">https://doi.org/10.1016/j.commatsci.2017.01.017</a></p>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.analysis.prototypes.AflowPrototypeMatcher">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">AflowPrototypeMatcher</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">initial_ltol</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">float</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">0.2</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">initial_stol</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">float</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">0.3</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">initial_angle_tol</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">float</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">5</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/prototypes.py#L31-L133"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.prototypes.AflowPrototypeMatcher" title="Link to this definition"></a></dt>
<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></p>
<p>This class will match structures to their crystal prototypes, and will
attempt to group species together to match structures derived from
prototypes (e.g. an A_xB_1-x_C from a binary prototype), and will
give these the names the “-like” suffix.</p>
<p>This class uses data from the AFLOW LIBRARY OF CRYSTALLOGRAPHIC PROTOTYPES.
If using this class, please cite their publication appropriately:</p>
<p>Mehl, M. J., Hicks, D., Toher, C., Levy, O., Hanson, R. M., Hart, G., & Curtarolo, S. (2017).
The AFLOW library of crystallographic prototypes: part 1.
Computational Materials Science, 136, S1-S828.
<a class="reference external" href="https://doi.org/10.1016/j.commatsci.2017.01.017">https://doi.org/10.1016/j.commatsci.2017.01.017</a></p>
<p>Tolerances as defined in StructureMatcher. Tolerances will be
gradually decreased until only a single match is found (if possible).</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>initial_ltol</strong> (<em>float</em>) – fractional length tolerance.</p></li>
<li><p><strong>initial_stol</strong> (<em>float</em>) – site tolerance.</p></li>
<li><p><strong>initial_angle_tol</strong> (<em>float</em>) – angle tolerance.</p></li>
</ul>
</dd>
</dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.prototypes.AflowPrototypeMatcher.get_prototypes">
<span class="sig-name descname"><span class="pre">get_prototypes</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">structure</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><span class="pre">Structure</span></a></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">dict</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/prototypes.py#L114-L133"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.prototypes.AflowPrototypeMatcher.get_prototypes" title="Link to this definition"></a></dt>
<dd><p>Get prototype(s) structures for a given input structure. If you use this method in
your work, please cite the appropriate AFLOW publication:</p>
<blockquote>
<div><p>Mehl, M. J., Hicks, D., Toher, C., Levy, O., Hanson, R. M., Hart, G., & Curtarolo,
S. (2017). The AFLOW library of crystallographic prototypes: part 1. Computational
Materials Science, 136, S1-S828. <a class="reference external" href="https://doi.org/10.1016/j.commatsci.2017.01.017">https://doi.org/10.1016/j.commatsci.2017.01.017</a></p>
</div></blockquote>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>structure</strong> (<a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><em>Structure</em></a>) – structure to match</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p><dl class="simple">
<dt>A list of dicts with keys “snl” for the matched prototype and</dt><dd><p>”tags”, a dict of tags (“mineral”, “strukturbericht” and “aflow”) of that
prototype. This should be a list containing just a single entry, but it is
possible a material can match multiple prototypes.</p>
</dd>
</dl>
</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>list[dict] | None</p>
</dd>
</dl>
</dd></dl>
</dd></dl>
</section>
<section id="module-pymatgen.analysis.quasiharmonic">
<span id="pymatgen-analysis-quasiharmonic-module"></span><h2>pymatgen.analysis.quasiharmonic module<a class="headerlink" href="#module-pymatgen.analysis.quasiharmonic" title="Link to this heading"></a></h2>
<p>This module implements the Quasi-harmonic Debye approximation that can
be used to compute thermal properties.</p>
<p>See the following papers for more info:</p>
<blockquote>
<div><p><a class="reference external" href="https://doi.org/10.1016/j.comphy.2003.12.001">https://doi.org/10.1016/j.comphy.2003.12.001</a> (2004)
<a class="reference external" href="https://doi.org/10.1103/PhysRevB.90.174107">https://doi.org/10.1103/PhysRevB.90.174107</a> (2014)</p>
</div></blockquote>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.analysis.quasiharmonic.QuasiHarmonicDebyeApprox">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">QuasiHarmonicDebyeApprox</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">energies</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">volumes</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">structure</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">t_min</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">300.0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">t_step</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">100</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">t_max</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">300.0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">eos</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'vinet'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">pressure</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0.0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">poisson</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0.25</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_mie_gruneisen</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">anharmonic_contribution</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/quasiharmonic.py#L42-L459"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.quasiharmonic.QuasiHarmonicDebyeApprox" title="Link to this definition"></a></dt>
<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></p>
<p>Quasi-harmonic approximation.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>energies</strong> (<em>list</em>) – list of DFT energies in eV</p></li>
<li><p><strong>volumes</strong> (<em>list</em>) – list of volumes in Ang^3</p></li>
<li><p><strong>structure</strong> (<a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><em>Structure</em></a>) – pymatgen structure object</p></li>
<li><p><strong>t_min</strong> (<em>float</em>) – min temperature</p></li>
<li><p><strong>t_step</strong> (<em>float</em>) – temperature step</p></li>
<li><p><strong>t_max</strong> (<em>float</em>) – max temperature</p></li>
<li><p><strong>eos</strong> (<em>str</em>) – <p>equation of state used for fitting the energies and the volumes.
options supported by pymatgen: “quadratic”, “murnaghan”, “birch”,</p>
<blockquote>
<div><p>”birch_murnaghan”, “pourier_tarantola”, “vinet”, “deltafactor”, “numerical_eos”</p>
</div></blockquote>
</p></li>
<li><p><strong>pressure</strong> (<em>float</em>) – in GPa, optional.</p></li>
<li><p><strong>poisson</strong> (<em>float</em>) – poisson ratio.</p></li>
<li><p><strong>use_mie_gruneisen</strong> (<em>bool</em>) – whether or not to use the mie-gruneisen
formulation to compute the gruneisen parameter.
The default is the slater-gamma formulation.</p></li>
<li><p><strong>anharmonic_contribution</strong> (<em>bool</em>) – whether or not to consider the anharmonic
contribution to the Debye temperature. Cannot be used with
use_mie_gruneisen. Defaults to False.</p></li>
</ul>
</dd>
</dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.quasiharmonic.QuasiHarmonicDebyeApprox.debye_integral">
<em class="property"><span class="pre">static</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">debye_integral</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">y</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/quasiharmonic.py#L247-L266"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.quasiharmonic.QuasiHarmonicDebyeApprox.debye_integral" title="Link to this definition"></a></dt>
<dd><p>Debye integral. Eq(5) in doi.org/10.1016/j.comphy.2003.12.001.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>y</strong> (<em>float</em>) – Debye temperature / T, upper limit</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>unitless</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>float</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.quasiharmonic.QuasiHarmonicDebyeApprox.debye_temperature">
<span class="sig-name descname"><span class="pre">debye_temperature</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">volume</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">float</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">float</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/quasiharmonic.py#L215-L245"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.quasiharmonic.QuasiHarmonicDebyeApprox.debye_temperature" title="Link to this definition"></a></dt>
<dd><p>Calculates the Debye temperature.
Eq(6) in doi.org/10.1016/j.comphy.2003.12.001. Thanks to Joey.</p>
<p>Eq(6) above is equivalent to Eq(3) in doi.org/10.1103/PhysRevB.37.790
which does not consider anharmonic effects. Eq(20) in the same paper
and Eq(18) in doi.org/10.1016/j.commatsci.2009.12.006 both consider
anharmonic contributions to the Debye temperature through the Gruneisen
parameter at 0K (Gruneisen constant).</p>
<p>The anharmonic contribution is toggled by setting the anharmonic_contribution
to True or False in the QuasiHarmonicDebyeApprox constructor.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>volume</strong> (<em>float</em>) – in Ang^3</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>Debye temperature in K</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>float</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.quasiharmonic.QuasiHarmonicDebyeApprox.get_summary_dict">
<span class="sig-name descname"><span class="pre">get_summary_dict</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/quasiharmonic.py#L444-L459"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.quasiharmonic.QuasiHarmonicDebyeApprox.get_summary_dict" title="Link to this definition"></a></dt>
<dd><p>Get a dict with a summary of the computed properties.</p>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.quasiharmonic.QuasiHarmonicDebyeApprox.gruneisen_parameter">
<span class="sig-name descname"><span class="pre">gruneisen_parameter</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">temperature</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">volume</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/quasiharmonic.py#L268-L421"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.quasiharmonic.QuasiHarmonicDebyeApprox.gruneisen_parameter" title="Link to this definition"></a></dt>
<dd><dl>
<dt>Slater-gamma formulation(the default):</dt><dd><dl class="simple">
<dt>gruneisen parameter = - d log(theta)/ d log(V) = - (1/6 + 0.5 d log(B)/ d log(V))</dt><dd><p>= - (1/6 + 0.5 V/B dB/dV), where dB/dV = d^2E/dV^2 + V * d^3E/dV^3.</p>
</dd>
</dl>
</dd>
<dt>Mie-gruneisen formulation:</dt><dd><p>Eq(31) in doi.org/10.1016/j.comphy.2003.12.001
Eq(7) in Blanco et. al. Journal of Molecular Structure (Theochem)</p>
<blockquote>
<div><p>368 (1996) 245-255</p>
</div></blockquote>
<dl class="simple">
<dt>Also see J.P. Poirier, Introduction to the Physics of the Earth’s</dt><dd><p>Interior, 2nd ed. (Cambridge University Press, Cambridge,
2000) Eq(3.53)</p>
</dd>
</dl>
</dd>
</dl>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>temperature</strong> (<em>float</em>) – temperature in K</p></li>
<li><p><strong>volume</strong> (<em>float</em>) – in Ang^3</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>unitless</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>float</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.quasiharmonic.QuasiHarmonicDebyeApprox.optimize_gibbs_free_energy">
<span class="sig-name descname"><span class="pre">optimize_gibbs_free_energy</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/quasiharmonic.py#L120-L144"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.quasiharmonic.QuasiHarmonicDebyeApprox.optimize_gibbs_free_energy" title="Link to this definition"></a></dt>
<dd><p>Evaluate the Gibbs free energy as a function of V, T and P i.e
G(V, T, P), minimize G(V, T, P) w.r.t. V for each T and store the
optimum values.</p>
<dl class="simple">
<dt>Note: The data points for which the equation of state fitting fails</dt><dd><p>are skipped.</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.quasiharmonic.QuasiHarmonicDebyeApprox.optimizer">
<span class="sig-name descname"><span class="pre">optimizer</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">temperature</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/quasiharmonic.py#L146-L179"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.quasiharmonic.QuasiHarmonicDebyeApprox.optimizer" title="Link to this definition"></a></dt>
<dd><p>Evaluate G(V, T, P) at the given temperature(and pressure) and minimize it w.r.t. V.</p>
<ol class="arabic simple">
<li><p>Compute the vibrational Helmholtz free energy, A_vib.</p></li>
<li><dl class="simple">
<dt>Compute the Gibbs free energy as a function of volume, temperature</dt><dd><p>and pressure, G(V,T,P).</p>
</dd>
</dl>
</li>
<li><dl class="simple">
<dt>Perform an equation of state fit to get the functional form of</dt><dd><p>Gibbs free energy:G(V, T, P).</p>
</dd>
</dl>
</li>
<li><p>Finally G(V, P, T) is minimized with respect to V.</p></li>
</ol>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>temperature</strong> (<em>float</em>) – temperature in K</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>G_opt(V_opt, T, P) in eV and V_opt in Ang^3.</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>float, float</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.quasiharmonic.QuasiHarmonicDebyeApprox.thermal_conductivity">
<span class="sig-name descname"><span class="pre">thermal_conductivity</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">temperature</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">float</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">volume</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">float</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">float</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/quasiharmonic.py#L423-L442"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.quasiharmonic.QuasiHarmonicDebyeApprox.thermal_conductivity" title="Link to this definition"></a></dt>
<dd><p>Eq(17) in 10.1103/PhysRevB.90.174107.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>temperature</strong> (<em>float</em>) – temperature in K</p></li>
<li><p><strong>volume</strong> (<em>float</em>) – in Ang^3</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>thermal conductivity in W/K/m</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>float</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.quasiharmonic.QuasiHarmonicDebyeApprox.vibrational_free_energy">
<span class="sig-name descname"><span class="pre">vibrational_free_energy</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">temperature</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">volume</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/quasiharmonic.py#L181-L197"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.quasiharmonic.QuasiHarmonicDebyeApprox.vibrational_free_energy" title="Link to this definition"></a></dt>
<dd><p>Vibrational Helmholtz free energy, A_vib(V, T).
Eq(4) in doi.org/10.1016/j.comphy.2003.12.001.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>temperature</strong> (<em>float</em>) – temperature in K</p></li>
<li><p><strong>volume</strong> (<em>float</em>)</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>vibrational free energy in eV</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>float</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.quasiharmonic.QuasiHarmonicDebyeApprox.vibrational_internal_energy">
<span class="sig-name descname"><span class="pre">vibrational_internal_energy</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">temperature</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">volume</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/quasiharmonic.py#L199-L213"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.quasiharmonic.QuasiHarmonicDebyeApprox.vibrational_internal_energy" title="Link to this definition"></a></dt>
<dd><p>Vibrational internal energy, U_vib(V, T).
Eq(4) in doi.org/10.1016/j.comphy.2003.12.001.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>temperature</strong> (<em>float</em>) – temperature in K</p></li>
<li><p><strong>volume</strong> (<em>float</em>) – in Ang^3</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>vibrational internal energy in eV</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>float</p>
</dd>
</dl>
</dd></dl>
</dd></dl>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.analysis.quasiharmonic.QuasiharmonicDebyeApprox">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">QuasiharmonicDebyeApprox</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">energies</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">volumes</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">structure</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">t_min</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">300.0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">t_step</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">100</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">t_max</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">300.0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">eos</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'vinet'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">pressure</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0.0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">poisson</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0.25</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_mie_gruneisen</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">anharmonic_contribution</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/quasiharmonic.py#L462-L468"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.quasiharmonic.QuasiharmonicDebyeApprox" title="Link to this definition"></a></dt>
<dd><p>Bases: <a class="reference internal" href="#pymatgen.analysis.quasiharmonic.QuasiHarmonicDebyeApprox" title="pymatgen.analysis.quasiharmonic.QuasiHarmonicDebyeApprox"><code class="xref py py-class docutils literal notranslate"><span class="pre">QuasiHarmonicDebyeApprox</span></code></a></p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>energies</strong> (<em>list</em>) – list of DFT energies in eV</p></li>
<li><p><strong>volumes</strong> (<em>list</em>) – list of volumes in Ang^3</p></li>
<li><p><strong>structure</strong> (<a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><em>Structure</em></a>) – pymatgen structure object</p></li>
<li><p><strong>t_min</strong> (<em>float</em>) – min temperature</p></li>
<li><p><strong>t_step</strong> (<em>float</em>) – temperature step</p></li>
<li><p><strong>t_max</strong> (<em>float</em>) – max temperature</p></li>
<li><p><strong>eos</strong> (<em>str</em>) – <p>equation of state used for fitting the energies and the volumes.
options supported by pymatgen: “quadratic”, “murnaghan”, “birch”,</p>
<blockquote>
<div><p>”birch_murnaghan”, “pourier_tarantola”, “vinet”, “deltafactor”, “numerical_eos”</p>
</div></blockquote>
</p></li>
<li><p><strong>pressure</strong> (<em>float</em>) – in GPa, optional.</p></li>
<li><p><strong>poisson</strong> (<em>float</em>) – poisson ratio.</p></li>
<li><p><strong>use_mie_gruneisen</strong> (<em>bool</em>) – whether or not to use the mie-gruneisen
formulation to compute the gruneisen parameter.
The default is the slater-gamma formulation.</p></li>
<li><p><strong>anharmonic_contribution</strong> (<em>bool</em>) – whether or not to consider the anharmonic
contribution to the Debye temperature. Cannot be used with
use_mie_gruneisen. Defaults to False.</p></li>
</ul>
</dd>
</dl>
</dd></dl>
</section>
<section id="module-pymatgen.analysis.quasirrho">
<span id="pymatgen-analysis-quasirrho-module"></span><h2>pymatgen.analysis.quasirrho module<a class="headerlink" href="#module-pymatgen.analysis.quasirrho" title="Link to this heading"></a></h2>
<p>A module to calculate free energies using the Quasi-Rigid Rotor Harmonic
Oscillator approximation. Modified from a script by Steven Wheeler.
See: Grimme, S. Chem. Eur. J. 2012, 18, 9955.</p>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.analysis.quasirrho.QuasiRRHO">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">QuasiRRHO</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">mol</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Molecule" title="pymatgen.core.structure.Molecule"><span class="pre">Molecule</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">frequencies</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">float</span><span class="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="n"><span class="pre">energy</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">float</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">mult</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">sigma_r</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">float</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">temp</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">float</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">298.15</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">press</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">float</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">101317</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">v0</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">float</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">100</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/quasirrho.py#L79-L263"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.quasirrho.QuasiRRHO" title="Link to this definition"></a></dt>
<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></p>
<p>Calculate thermochemistry using Grimme’s Quasi-RRHO approximation.
All outputs are in atomic units, e.g. energy outputs are in Hartrees.
Citation: Grimme, S. Chemistry - A European Journal 18, 9955-9964 (2012).</p>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.analysis.quasirrho.QuasiRRHO.temp">
<span class="sig-name descname"><span class="pre">temp</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/quasirrho.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.quasirrho.QuasiRRHO.temp" title="Link to this definition"></a></dt>
<dd><p>Temperature [K]</p>
<dl class="field-list simple">
<dt class="field-odd">Type<span class="colon">:</span></dt>
<dd class="field-odd"><p>float</p>
</dd>
</dl>
</dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.analysis.quasirrho.QuasiRRHO.press">
<span class="sig-name descname"><span class="pre">press</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/quasirrho.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.quasirrho.QuasiRRHO.press" title="Link to this definition"></a></dt>
<dd><p>Pressure [Pa]</p>
<dl class="field-list simple">
<dt class="field-odd">Type<span class="colon">:</span></dt>
<dd class="field-odd"><p>float</p>
</dd>
</dl>
</dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.analysis.quasirrho.QuasiRRHO.v0">
<span class="sig-name descname"><span class="pre">v0</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/quasirrho.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.quasirrho.QuasiRRHO.v0" title="Link to this definition"></a></dt>
<dd><p>Cutoff frequency for Quasi-RRHO method [1/cm]</p>
<dl class="field-list simple">
<dt class="field-odd">Type<span class="colon">:</span></dt>
<dd class="field-odd"><p>float</p>
</dd>
</dl>
</dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.analysis.quasirrho.QuasiRRHO.entropy_quasiRRHO">
<span class="sig-name descname"><span class="pre">entropy_quasiRRHO</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/quasirrho.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.quasirrho.QuasiRRHO.entropy_quasiRRHO" title="Link to this definition"></a></dt>
<dd><p>Quasi-RRHO entropy [Ha/K]</p>
<dl class="field-list simple">
<dt class="field-odd">Type<span class="colon">:</span></dt>
<dd class="field-odd"><p>float</p>
</dd>
</dl>
</dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.analysis.quasirrho.QuasiRRHO.entropy_ho">
<span class="sig-name descname"><span class="pre">entropy_ho</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/quasirrho.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.quasirrho.QuasiRRHO.entropy_ho" title="Link to this definition"></a></dt>
<dd><p>Total entropy calculated with a harmonic
oscillator approximation for the vibrational entropy [Ha/K]</p>
<dl class="field-list simple">
<dt class="field-odd">Type<span class="colon">:</span></dt>
<dd class="field-odd"><p>float</p>
</dd>
</dl>
</dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.analysis.quasirrho.QuasiRRHO.h_corrected">
<span class="sig-name descname"><span class="pre">h_corrected</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/quasirrho.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.quasirrho.QuasiRRHO.h_corrected" title="Link to this definition"></a></dt>
<dd><p>Thermal correction to the enthalpy [Ha]</p>
<dl class="field-list simple">
<dt class="field-odd">Type<span class="colon">:</span></dt>
<dd class="field-odd"><p>float</p>
</dd>
</dl>
</dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.analysis.quasirrho.QuasiRRHO.free_energy_quasiRRHO">
<span class="sig-name descname"><span class="pre">free_energy_quasiRRHO</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/quasirrho.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.quasirrho.QuasiRRHO.free_energy_quasiRRHO" title="Link to this definition"></a></dt>
<dd><p>Quasi-RRHO free energy [Ha]</p>
<dl class="field-list simple">
<dt class="field-odd">Type<span class="colon">:</span></dt>
<dd class="field-odd"><p>float</p>
</dd>
</dl>
</dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.analysis.quasirrho.QuasiRRHO.free_energy_ho">
<span class="sig-name descname"><span class="pre">free_energy_ho</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/quasirrho.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.quasirrho.QuasiRRHO.free_energy_ho" title="Link to this definition"></a></dt>
<dd><p>Free energy calculated without the Quasi-RRHO
method, i.e. with a harmonic oscillator approximation for the
vibrational entropy [Ha]</p>
<dl class="field-list simple">
<dt class="field-odd">Type<span class="colon">:</span></dt>
<dd class="field-odd"><p>float</p>
</dd>
</dl>
</dd></dl>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>mol</strong> (<a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Molecule" title="pymatgen.core.structure.Molecule"><em>Molecule</em></a>) – Pymatgen molecule</p></li>
<li><p><strong>frequencies</strong> (<em>list</em>) – List of frequencies (float) [cm^-1]</p></li>
<li><p><strong>energy</strong> (<em>float</em>) – Electronic energy [Ha]</p></li>
<li><p><strong>mult</strong> (<em>int</em>) – Spin multiplicity</p></li>
<li><p><strong>sigma_r</strong> (<em>int</em>) – Rotational symmetry number. Defaults to 1.</p></li>
<li><p><strong>temp</strong> (<em>float</em>) – Temperature [K]. Defaults to 298.15.</p></li>
<li><p><strong>press</strong> (<em>float</em>) – Pressure [Pa]. Defaults to 101_317.</p></li>
<li><p><strong>v0</strong> (<em>float</em>) – Cutoff frequency for Quasi-RRHO method [cm^-1]. Defaults to 100.</p></li>
</ul>
</dd>
</dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.quasirrho.QuasiRRHO.from_gaussian_output">
<em class="property"><span class="pre">classmethod</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">from_gaussian_output</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">output</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="pymatgen.io.html#pymatgen.io.gaussian.GaussianOutput" title="pymatgen.io.gaussian.GaussianOutput"><span class="pre">GaussianOutput</span></a></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">Self</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/quasirrho.py#L142-L155"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.quasirrho.QuasiRRHO.from_gaussian_output" title="Link to this definition"></a></dt>
<dd><dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>output</strong> (<a class="reference internal" href="pymatgen.io.html#pymatgen.io.gaussian.GaussianOutput" title="pymatgen.io.gaussian.GaussianOutput"><em>GaussianOutput</em></a>) – Pymatgen GaussianOutput object.</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>QuasiRRHO class instantiated from a Gaussian Output</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p><a class="reference internal" href="#pymatgen.analysis.quasirrho.QuasiRRHO" title="pymatgen.analysis.quasirrho.QuasiRRHO">QuasiRRHO</a></p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.quasirrho.QuasiRRHO.from_qc_output">
<em class="property"><span class="pre">classmethod</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">from_qc_output</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">output</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="pymatgen.io.qchem.html#pymatgen.io.qchem.outputs.QCOutput" title="pymatgen.io.qchem.outputs.QCOutput"><span class="pre">QCOutput</span></a></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">Self</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/quasirrho.py#L157-L174"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.quasirrho.QuasiRRHO.from_qc_output" title="Link to this definition"></a></dt>
<dd><dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>output</strong> (<a class="reference internal" href="pymatgen.io.qchem.html#pymatgen.io.qchem.outputs.QCOutput" title="pymatgen.io.qchem.outputs.QCOutput"><em>QCOutput</em></a>) – Pymatgen QCOutput object.</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>QuasiRRHO class instantiated from a QChem Output</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p><a class="reference internal" href="#pymatgen.analysis.quasirrho.QuasiRRHO" title="pymatgen.analysis.quasirrho.QuasiRRHO">QuasiRRHO</a></p>
</dd>
</dl>
</dd></dl>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="pymatgen.analysis.quasirrho.get_avg_mom_inertia">
<span class="sig-name descname"><span class="pre">get_avg_mom_inertia</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">mol</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/quasirrho.py#L50-L76"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.quasirrho.get_avg_mom_inertia" title="Link to this definition"></a></dt>
<dd><p>Calculate the average moment of inertia of a molecule.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>mol</strong> (<a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Molecule" title="pymatgen.core.structure.Molecule"><em>Molecule</em></a>) – Pymatgen Molecule</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>average moment of inertia, eigenvalues of the inertia tensor</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>int, list</p>
</dd>
</dl>
</dd></dl>
</section>
<section id="module-pymatgen.analysis.reaction_calculator">
<span id="pymatgen-analysis-reaction-calculator-module"></span><h2>pymatgen.analysis.reaction_calculator module<a class="headerlink" href="#module-pymatgen.analysis.reaction_calculator" title="Link to this heading"></a></h2>
<p>This module provides classes that define a chemical reaction.</p>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.analysis.reaction_calculator.BalancedReaction">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">BalancedReaction</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reactants_coeffs</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">Mapping</span><span class="p"><span class="pre">[</span></span><span class="pre">CompositionLike</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">int</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">float</span><span class="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="n"><span class="pre">products_coeffs</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">Mapping</span><span class="p"><span class="pre">[</span></span><span class="pre">CompositionLike</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">int</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">float</span><span class="p"><span class="pre">]</span></span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/reaction_calculator.py#L35-L291"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.reaction_calculator.BalancedReaction" title="Link to this definition"></a></dt>
<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">MSONable</span></code></p>
<p>Represent a complete chemical reaction.</p>
<p>Reactants and products to be specified as dict of {Composition: coeff}.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>reactants_coeffs</strong> (<em>dict</em><em>[</em><a class="reference internal" href="pymatgen.core.html#pymatgen.core.composition.Composition" title="pymatgen.core.composition.Composition"><em>Composition</em></a><em>, </em><em>float</em><em>]</em>) – Reactants as dict of {Composition: amt}.</p></li>
<li><p><strong>products_coeffs</strong> (<em>dict</em><em>[</em><a class="reference internal" href="pymatgen.core.html#pymatgen.core.composition.Composition" title="pymatgen.core.composition.Composition"><em>Composition</em></a><em>, </em><em>float</em><em>]</em>) – Products as dict of {Composition: amt}.</p></li>
</ul>
</dd>
</dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.analysis.reaction_calculator.BalancedReaction.TOLERANCE">
<span class="sig-name descname"><span class="pre">TOLERANCE</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">1e-06</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/reaction_calculator.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.reaction_calculator.BalancedReaction.TOLERANCE" title="Link to this definition"></a></dt>
<dd></dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.analysis.reaction_calculator.BalancedReaction.all_comp">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">all_comp</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">list</span><span class="p"><span class="pre">[</span></span><a class="reference internal" href="pymatgen.core.html#pymatgen.core.composition.Composition" title="pymatgen.core.composition.Composition"><span class="pre">Composition</span></a><span class="p"><span class="pre">]</span></span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/reaction_calculator.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.reaction_calculator.BalancedReaction.all_comp" title="Link to this definition"></a></dt>
<dd><p>List of all compositions in the reaction.</p>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.reaction_calculator.BalancedReaction.as_dict">
<span class="sig-name descname"><span class="pre">as_dict</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">dict</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/reaction_calculator.py#L247-L257"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.reaction_calculator.BalancedReaction.as_dict" title="Link to this definition"></a></dt>
<dd><dl class="field-list simple">
<dt class="field-odd">Returns<span class="colon">:</span></dt>
<dd class="field-odd"><p>A dictionary representation of BalancedReaction.</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.reaction_calculator.BalancedReaction.as_entry">
<span class="sig-name descname"><span class="pre">as_entry</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">energies</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><a class="reference internal" href="pymatgen.entries.html#pymatgen.entries.computed_entries.ComputedEntry" title="pymatgen.entries.computed_entries.ComputedEntry"><span class="pre">ComputedEntry</span></a></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/reaction_calculator.py#L238-L245"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.reaction_calculator.BalancedReaction.as_entry" title="Link to this definition"></a></dt>
<dd><p>Get a ComputedEntry representation of the reaction.</p>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.reaction_calculator.BalancedReaction.calculate_energy">
<span class="sig-name descname"><span class="pre">calculate_energy</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">energies</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><a class="reference internal" href="pymatgen.core.html#pymatgen.core.composition.Composition" title="pymatgen.core.composition.Composition"><span class="pre">Composition</span></a><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">ufloat</span><span class="p"><span class="pre">]</span></span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">ufloat</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/reaction_calculator.py#L110-L121"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.reaction_calculator.BalancedReaction.calculate_energy" title="Link to this definition"></a></dt>
<dt class="sig sig-object py">
<span class="sig-name descname"><span class="pre">calculate_energy</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">energies</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><a class="reference internal" href="pymatgen.core.html#pymatgen.core.composition.Composition" title="pymatgen.core.composition.Composition"><span class="pre">Composition</span></a><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">float</span><span class="p"><span class="pre">]</span></span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">float</span></span></span></dt>
<dd><p>Calculates the energy of the reaction.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>(</strong><strong>{Composition</strong> (<em>energies</em>) – float}): Energy for each composition.
E.g ., {comp1: energy1, comp2: energy2}.</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>reaction energy as a float.</p>
</dd>
</dl>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.analysis.reaction_calculator.BalancedReaction.coeffs">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">coeffs</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">float</span><span class="p"><span class="pre">]</span></span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/reaction_calculator.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.reaction_calculator.BalancedReaction.coeffs" title="Link to this definition"></a></dt>
<dd><p>Final coefficients of the calculated reaction.</p>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.analysis.reaction_calculator.BalancedReaction.elements">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">elements</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">list</span><span class="p"><span class="pre">[</span></span><a class="reference internal" href="pymatgen.core.html#pymatgen.core.periodic_table.Element" title="pymatgen.core.periodic_table.Element"><span class="pre">Element</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference internal" href="pymatgen.core.html#pymatgen.core.periodic_table.Species" title="pymatgen.core.periodic_table.Species"><span class="pre">Species</span></a><span class="p"><span class="pre">]</span></span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/reaction_calculator.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.reaction_calculator.BalancedReaction.elements" title="Link to this definition"></a></dt>
<dd><p>List of elements in the reaction.</p>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.reaction_calculator.BalancedReaction.from_dict">
<em class="property"><span class="pre">classmethod</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">from_dict</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">dct</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">dict</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">Self</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/reaction_calculator.py#L259-L270"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.reaction_calculator.BalancedReaction.from_dict" title="Link to this definition"></a></dt>
<dd><dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>dct</strong> (<em>dict</em>) – from as_dict().</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>BalancedReaction</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.reaction_calculator.BalancedReaction.from_str">
<em class="property"><span class="pre">classmethod</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">from_str</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">rxn_str</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">Self</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/reaction_calculator.py#L272-L291"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.reaction_calculator.BalancedReaction.from_str" title="Link to this definition"></a></dt>
<dd><p>Generate a balanced reaction from a string. The reaction must
already be balanced.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>rxn_string</strong> (<em>str</em>) – The reaction string. For example, “4 Li + O2 -> 2Li2O”</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>BalancedReaction</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.reaction_calculator.BalancedReaction.get_coeff">
<span class="sig-name descname"><span class="pre">get_coeff</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">comp</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="pymatgen.core.html#pymatgen.core.composition.Composition" title="pymatgen.core.composition.Composition"><span class="pre">Composition</span></a></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">float</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/reaction_calculator.py#L188-L190"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.reaction_calculator.BalancedReaction.get_coeff" title="Link to this definition"></a></dt>
<dd><p>Get coefficient for a particular composition.</p>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.reaction_calculator.BalancedReaction.get_el_amount">
<span class="sig-name descname"><span class="pre">get_el_amount</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">element</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="pymatgen.core.html#pymatgen.core.periodic_table.Element" title="pymatgen.core.periodic_table.Element"><span class="pre">Element</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference internal" href="pymatgen.core.html#pymatgen.core.periodic_table.Species" title="pymatgen.core.periodic_table.Species"><span class="pre">Species</span></a></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">float</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/reaction_calculator.py#L152-L161"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.reaction_calculator.BalancedReaction.get_el_amount" title="Link to this definition"></a></dt>
<dd><p>Get the amount of the element in the reaction.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>element</strong> (<em>SpeciesLike</em>) – Element in the reaction</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>Amount of that element in the reaction.</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.reaction_calculator.BalancedReaction.normalize_to">
<span class="sig-name descname"><span class="pre">normalize_to</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">comp</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="pymatgen.core.html#pymatgen.core.composition.Composition" title="pymatgen.core.composition.Composition"><span class="pre">Composition</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">factor</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">float</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">1</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">None</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/reaction_calculator.py#L123-L134"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.reaction_calculator.BalancedReaction.normalize_to" title="Link to this definition"></a></dt>
<dd><p>Normalizes the reaction to one of the compositions.
By default, normalizes such that the composition given has a
coefficient of 1. Another factor can be specified.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>comp</strong> (<a class="reference internal" href="pymatgen.core.html#pymatgen.core.composition.Composition" title="pymatgen.core.composition.Composition"><em>Composition</em></a>) – Composition to normalize to</p></li>
<li><p><strong>factor</strong> (<em>float</em>) – Factor to normalize to. Defaults to 1.</p></li>
</ul>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.reaction_calculator.BalancedReaction.normalize_to_element">
<span class="sig-name descname"><span class="pre">normalize_to_element</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">element</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="pymatgen.core.html#pymatgen.core.periodic_table.Species" title="pymatgen.core.periodic_table.Species"><span class="pre">Species</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference internal" href="pymatgen.core.html#pymatgen.core.periodic_table.Element" title="pymatgen.core.periodic_table.Element"><span class="pre">Element</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">factor</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">float</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">1</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">None</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/reaction_calculator.py#L136-L150"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.reaction_calculator.BalancedReaction.normalize_to_element" title="Link to this definition"></a></dt>
<dd><p>Normalizes the reaction to one of the elements.
By default, normalizes such that the amount of the element is 1.
Another factor can be specified.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>element</strong> (<em>SpeciesLike</em>) – Element to normalize to.</p></li>
<li><p><strong>factor</strong> (<em>float</em>) – Factor to normalize to. Defaults to 1.</p></li>
</ul>
</dd>
</dl>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.analysis.reaction_calculator.BalancedReaction.normalized_repr">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">normalized_repr</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">str</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/reaction_calculator.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.reaction_calculator.BalancedReaction.normalized_repr" title="Link to this definition"></a></dt>
<dd><p>A normalized representation of the reaction. All factors are converted
to lowest common factors.</p>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.reaction_calculator.BalancedReaction.normalized_repr_and_factor">
<span class="sig-name descname"><span class="pre">normalized_repr_and_factor</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">tuple</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">float</span><span class="p"><span class="pre">]</span></span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/reaction_calculator.py#L192-L197"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.reaction_calculator.BalancedReaction.normalized_repr_and_factor" title="Link to this definition"></a></dt>
<dd><p>Normalized representation for a reaction
For example, <code class="docutils literal notranslate"><span class="pre">4</span> <span class="pre">Li</span> <span class="pre">+</span> <span class="pre">2</span> <span class="pre">O</span> <span class="pre">-></span> <span class="pre">2Li2O</span></code> becomes <code class="docutils literal notranslate"><span class="pre">2</span> <span class="pre">Li</span> <span class="pre">+</span> <span class="pre">O</span> <span class="pre">-></span> <span class="pre">Li2O</span></code>.</p>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.analysis.reaction_calculator.BalancedReaction.products">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">products</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">list</span><span class="p"><span class="pre">[</span></span><a class="reference internal" href="pymatgen.core.html#pymatgen.core.composition.Composition" title="pymatgen.core.composition.Composition"><span class="pre">Composition</span></a><span class="p"><span class="pre">]</span></span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/reaction_calculator.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.reaction_calculator.BalancedReaction.products" title="Link to this definition"></a></dt>
<dd><p>List of products.</p>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.analysis.reaction_calculator.BalancedReaction.reactants">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">reactants</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">list</span><span class="p"><span class="pre">[</span></span><a class="reference internal" href="pymatgen.core.html#pymatgen.core.composition.Composition" title="pymatgen.core.composition.Composition"><span class="pre">Composition</span></a><span class="p"><span class="pre">]</span></span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/reaction_calculator.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.reaction_calculator.BalancedReaction.reactants" title="Link to this definition"></a></dt>
<dd><p>List of reactants.</p>
</dd></dl>
</dd></dl>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.analysis.reaction_calculator.ComputedReaction">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">ComputedReaction</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reactant_entries</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">list</span><span class="p"><span class="pre">[</span></span><a class="reference internal" href="pymatgen.entries.html#pymatgen.entries.computed_entries.ComputedEntry" title="pymatgen.entries.computed_entries.ComputedEntry"><span class="pre">ComputedEntry</span></a><span class="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="n"><span class="pre">product_entries</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">list</span><span class="p"><span class="pre">[</span></span><a class="reference internal" href="pymatgen.entries.html#pymatgen.entries.computed_entries.ComputedEntry" title="pymatgen.entries.computed_entries.ComputedEntry"><span class="pre">ComputedEntry</span></a><span class="p"><span class="pre">]</span></span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/reaction_calculator.py#L425-L516"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.reaction_calculator.ComputedReaction" title="Link to this definition"></a></dt>
<dd><p>Bases: <a class="reference internal" href="#pymatgen.analysis.reaction_calculator.Reaction" title="pymatgen.analysis.reaction_calculator.Reaction"><code class="xref py py-class docutils literal notranslate"><span class="pre">Reaction</span></code></a></p>
<p>Convenience class to generate a reaction from ComputedEntry objects, with
some additional attributes, such as a reaction energy based on computed
energies.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>reactant_entries</strong> (<em>[</em><a class="reference internal" href="pymatgen.entries.html#pymatgen.entries.computed_entries.ComputedEntry" title="pymatgen.entries.computed_entries.ComputedEntry"><em>ComputedEntry</em></a><em>]</em>) – List of reactant_entries.</p></li>
<li><p><strong>product_entries</strong> (<em>[</em><a class="reference internal" href="pymatgen.entries.html#pymatgen.entries.computed_entries.ComputedEntry" title="pymatgen.entries.computed_entries.ComputedEntry"><em>ComputedEntry</em></a><em>]</em>) – List of product_entries.</p></li>
</ul>
</dd>
</dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.analysis.reaction_calculator.ComputedReaction.all_entries">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">all_entries</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/reaction_calculator.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.reaction_calculator.ComputedReaction.all_entries" title="Link to this definition"></a></dt>
<dd><p>Equivalent of all_comp but returns entries, in the same order as the
coefficients.</p>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.reaction_calculator.ComputedReaction.as_dict">
<span class="sig-name descname"><span class="pre">as_dict</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">dict</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/reaction_calculator.py#L493-L503"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.reaction_calculator.ComputedReaction.as_dict" title="Link to this definition"></a></dt>
<dd><dl class="field-list simple">
<dt class="field-odd">Returns<span class="colon">:</span></dt>
<dd class="field-odd"><p>A dictionary representation of ComputedReaction.</p>
</dd>
</dl>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.analysis.reaction_calculator.ComputedReaction.calculated_reaction_energy">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">calculated_reaction_energy</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">float</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/reaction_calculator.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.reaction_calculator.ComputedReaction.calculated_reaction_energy" title="Link to this definition"></a></dt>
<dd><p>Returns:
float: The calculated reaction energy.</p>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.analysis.reaction_calculator.ComputedReaction.calculated_reaction_energy_uncertainty">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">calculated_reaction_energy_uncertainty</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">float</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/reaction_calculator.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.reaction_calculator.ComputedReaction.calculated_reaction_energy_uncertainty" title="Link to this definition"></a></dt>
<dd><p>Calculates the uncertainty in the reaction energy based on the uncertainty in the
energies of the products and reactants.</p>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.reaction_calculator.ComputedReaction.from_dict">
<em class="property"><span class="pre">classmethod</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">from_dict</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">dct</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">dict</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">Self</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/reaction_calculator.py#L505-L516"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.reaction_calculator.ComputedReaction.from_dict" title="Link to this definition"></a></dt>
<dd><dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>dct</strong> (<em>dict</em>) – from as_dict().</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>A ComputedReaction object.</p>
</dd>
</dl>
</dd></dl>
</dd></dl>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.analysis.reaction_calculator.Reaction">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">Reaction</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">reactants</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">list</span><span class="p"><span class="pre">[</span></span><a class="reference internal" href="pymatgen.core.html#pymatgen.core.composition.Composition" title="pymatgen.core.composition.Composition"><span class="pre">Composition</span></a><span class="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="n"><span class="pre">products</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">list</span><span class="p"><span class="pre">[</span></span><a class="reference internal" href="pymatgen.core.html#pymatgen.core.composition.Composition" title="pymatgen.core.composition.Composition"><span class="pre">Composition</span></a><span class="p"><span class="pre">]</span></span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/reaction_calculator.py#L294-L404"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.reaction_calculator.Reaction" title="Link to this definition"></a></dt>
<dd><p>Bases: <a class="reference internal" href="#pymatgen.analysis.reaction_calculator.BalancedReaction" title="pymatgen.analysis.reaction_calculator.BalancedReaction"><code class="xref py py-class docutils literal notranslate"><span class="pre">BalancedReaction</span></code></a></p>
<p>A more flexible class representing a Reaction. The reaction amounts will
be automatically balanced. Reactants and products can swap sides so that
all coefficients are positive, however this class will find the solution
with the minimum number of swaps and coefficients of 0. Normalizes so that
the <em>FIRST</em> product (or products, if underdetermined) has a coefficient of one.</p>
<p>Reactants and products to be specified as list of
pymatgen.core.structure.Composition. e.g. [comp1, comp2].</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>reactants</strong> (<em>[</em><a class="reference internal" href="pymatgen.core.html#pymatgen.core.composition.Composition" title="pymatgen.core.composition.Composition"><em>Composition</em></a><em>]</em>) – List of reactants.</p></li>
<li><p><strong>products</strong> (<em>[</em><a class="reference internal" href="pymatgen.core.html#pymatgen.core.composition.Composition" title="pymatgen.core.composition.Composition"><em>Composition</em></a><em>]</em>) – List of products.</p></li>
</ul>
</dd>
</dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.reaction_calculator.Reaction.as_dict">
<span class="sig-name descname"><span class="pre">as_dict</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">dict</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/reaction_calculator.py#L381-L391"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.reaction_calculator.Reaction.as_dict" title="Link to this definition"></a></dt>
<dd><dl class="field-list simple">
<dt class="field-odd">Returns<span class="colon">:</span></dt>
<dd class="field-odd"><p>A dictionary representation of Reaction.</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.reaction_calculator.Reaction.copy">
<span class="sig-name descname"><span class="pre">copy</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">Self</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/reaction_calculator.py#L377-L379"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.reaction_calculator.Reaction.copy" title="Link to this definition"></a></dt>
<dd><p>Get a copy of the Reaction object.</p>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.reaction_calculator.Reaction.from_dict">
<em class="property"><span class="pre">classmethod</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">from_dict</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">dct</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">dict</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">Self</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/reaction_calculator.py#L393-L404"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.reaction_calculator.Reaction.from_dict" title="Link to this definition"></a></dt>
<dd><dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>dct</strong> (<em>dict</em>) – from as_dict().</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>Reaction</p>
</dd>
</dl>
</dd></dl>
</dd></dl>
<dl class="py exception">
<dt class="sig sig-object py" id="pymatgen.analysis.reaction_calculator.ReactionError">
<em class="property"><span class="pre">exception</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">ReactionError</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">msg</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/reaction_calculator.py#L407-L422"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.reaction_calculator.ReactionError" title="Link to this definition"></a></dt>
<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">Exception</span></code></p>
<p>Exception class for Reactions. Allows more information in exception
messages to cover situations not covered by standard exception classes.</p>
<p>Create a ReactionError.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>msg</strong> (<em>str</em>) – More information about the ReactionError.</p>
</dd>
</dl>
</dd></dl>
</section>
<section id="module-pymatgen.analysis.structure_analyzer">
<span id="pymatgen-analysis-structure-analyzer-module"></span><h2>pymatgen.analysis.structure_analyzer module<a class="headerlink" href="#module-pymatgen.analysis.structure_analyzer" title="Link to this heading"></a></h2>
<p>This module provides classes to perform topological analyses of structures.</p>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.analysis.structure_analyzer.OxideType">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">OxideType</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">structure</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><span class="pre">Structure</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">relative_cutoff</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1.1</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/structure_analyzer.py#L408-L489"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.structure_analyzer.OxideType" title="Link to this definition"></a></dt>
<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></p>
<p>Separate class for determining oxide type.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>structure</strong> – Input structure.</p></li>
<li><p><strong>relative_cutoff</strong> – Relative_cutoff * act. cutoff stipulates the max.
distance two O atoms must be from each other. Default value is
1.1. At most 1.1 is recommended, nothing larger, otherwise the
script cannot distinguish between superoxides and peroxides.</p></li>
</ul>
</dd>
</dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.structure_analyzer.OxideType.parse_oxide">
<span class="sig-name descname"><span class="pre">parse_oxide</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">tuple</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">int</span><span class="p"><span class="pre">]</span></span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/structure_analyzer.py#L424-L489"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.structure_analyzer.OxideType.parse_oxide" title="Link to this definition"></a></dt>
<dd><p>Determines if an oxide is a peroxide/superoxide/ozonide/normal oxide.</p>
<dl class="field-list simple">
<dt class="field-odd">Returns<span class="colon">:</span></dt>
<dd class="field-odd"><p><dl class="simple">
<dt>Type of oxide (ozonide/peroxide/superoxide/hydroxide/None) and number of</dt><dd><p>peroxide/superoxide/hydroxide bonds in structure.</p>
</dd>
</dl>
</p>
</dd>
<dt class="field-even">Return type<span class="colon">:</span></dt>
<dd class="field-even"><p>tuple[str, int]</p>
</dd>
</dl>
</dd></dl>
</dd></dl>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.analysis.structure_analyzer.RelaxationAnalyzer">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">RelaxationAnalyzer</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">initial_structure</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><span class="pre">Structure</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">final_structure</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><span class="pre">Structure</span></a></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/structure_analyzer.py#L171-L234"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.structure_analyzer.RelaxationAnalyzer" title="Link to this definition"></a></dt>
<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></p>
<p>This class analyzes the relaxation in a calculation.</p>
<p>Please note that the input and final structures should have the same
ordering of sites. This is typically the case for most computational codes.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>initial_structure</strong> (<a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><em>Structure</em></a>) – Initial input structure to
calculation.</p></li>
<li><p><strong>final_structure</strong> (<a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><em>Structure</em></a>) – Final output structure from
calculation.</p></li>
</ul>
</dd>
<dt class="field-even">Raises<span class="colon">:</span></dt>
<dd class="field-even"><p><strong>ValueError</strong> – If initial and final structures have different formulas.</p>
</dd>
</dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.structure_analyzer.RelaxationAnalyzer.get_percentage_bond_dist_changes">
<span class="sig-name descname"><span class="pre">get_percentage_bond_dist_changes</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">max_radius</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">float</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">3.0</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><span class="pre">int</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><span class="pre">int</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">float</span><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">]</span></span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/structure_analyzer.py#L212-L234"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.structure_analyzer.RelaxationAnalyzer.get_percentage_bond_dist_changes" title="Link to this definition"></a></dt>
<dd><p>Get the percentage bond distance changes for each site up to a
maximum radius for nearest neighbors.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>max_radius</strong> (<em>float</em>) – Maximum radius to search for nearest
neighbors. This radius is applied to the initial structure,
not the final structure.</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p><dl class="simple">
<dt>Bond distance changes in the form {index1: {index2: 0.011, …}}.</dt><dd><p>For economy of representation, the index1 is always less than index2, i.e., since bonding
between site1 and site_n is the same as bonding between site_n and site1, there is no
reason to duplicate the information or computation.</p>
</dd>
</dl>
</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>dict[int, dict[int, float]]</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.structure_analyzer.RelaxationAnalyzer.get_percentage_lattice_parameter_changes">
<span class="sig-name descname"><span class="pre">get_percentage_lattice_parameter_changes</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">float</span><span class="p"><span class="pre">]</span></span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/structure_analyzer.py#L200-L210"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.structure_analyzer.RelaxationAnalyzer.get_percentage_lattice_parameter_changes" title="Link to this definition"></a></dt>
<dd><p>Get the percentage lattice parameter changes.</p>
<dl class="field-list simple">
<dt class="field-odd">Returns<span class="colon">:</span></dt>
<dd class="field-odd"><p><dl class="simple">
<dt>Percent changes in lattice parameter, e.g.</dt><dd><p>{‘a’: 0.012, ‘b’: 0.021, ‘c’: -0.031} implies a change of 1.2%,
2.1% and -3.1% in the a, b and c lattice parameters respectively.</p>
</dd>
</dl>
</p>
</dd>
<dt class="field-even">Return type<span class="colon">:</span></dt>
<dd class="field-even"><p>dict[str, float]</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.structure_analyzer.RelaxationAnalyzer.get_percentage_volume_change">
<span class="sig-name descname"><span class="pre">get_percentage_volume_change</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">float</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/structure_analyzer.py#L192-L198"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.structure_analyzer.RelaxationAnalyzer.get_percentage_volume_change" title="Link to this definition"></a></dt>
<dd><p>Get the percentage volume change.</p>
<dl class="field-list simple">
<dt class="field-odd">Returns<span class="colon">:</span></dt>
<dd class="field-odd"><p>Volume change in percent. 0.055 means a 5.5% increase.</p>
</dd>
<dt class="field-even">Return type<span class="colon">:</span></dt>
<dd class="field-even"><p>float</p>
</dd>
</dl>
</dd></dl>
</dd></dl>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.analysis.structure_analyzer.VoronoiAnalyzer">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">VoronoiAnalyzer</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cutoff</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">5.0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">qhull_options</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'Qbb</span> <span class="pre">Qc</span> <span class="pre">Qz'</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/structure_analyzer.py#L55-L168"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.structure_analyzer.VoronoiAnalyzer" title="Link to this definition"></a></dt>
<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></p>
<p>Performs a statistical analysis of Voronoi polyhedra around each site.
Each Voronoi polyhedron is described using Schaefli notation.
That is a set of indices {c_i} where c_i is the number of faces with i
number of vertices. E.g. for a bcc crystal, there is only one polyhedron
notation of which is [0,6,0,8,0,0,…].
In perfect crystals, these also corresponds to the Wigner-Seitz cells.
For distorted-crystals, liquids or amorphous structures, rather than one-type,
there is a statistical distribution of polyhedra.
See ref: Microstructure and its relaxation in Fe-B amorphous system
simulated by molecular dynamics,</p>
<blockquote>
<div><p>Stepanyuk et al., J. Non-cryst. Solids (1993), 159, 80-87.</p>
</div></blockquote>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>cutoff</strong> (<em>float</em>) – cutoff distance to search for neighbors of a given atom
(default = 5.0)</p></li>
<li><p><strong>qhull_options</strong> (<em>str</em>) – options to pass to qhull (optional).</p></li>
</ul>
</dd>
</dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.structure_analyzer.VoronoiAnalyzer.analyze">
<span class="sig-name descname"><span class="pre">analyze</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">structure</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><span class="pre">Structure</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">n</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/structure_analyzer.py#L80-L109"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.structure_analyzer.VoronoiAnalyzer.analyze" title="Link to this definition"></a></dt>
<dd><p>Performs Voronoi analysis and returns the polyhedra around atom n
in Schlaefli notation.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>structure</strong> (<a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><em>Structure</em></a>) – structure to analyze</p></li>
<li><p><strong>n</strong> (<em>int</em>) – index of the center atom in structure</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p><dl class="simple">
<dt><c3,c4,c6,c6,c7,c8,c9,c10></dt><dd><p>where c_i denotes number of facets with i vertices.</p>
</dd>
</dl>
</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>voronoi index of n</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.structure_analyzer.VoronoiAnalyzer.analyze_structures">
<span class="sig-name descname"><span class="pre">analyze_structures</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">structures</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">step_freq</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">10</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">most_frequent_polyhedra</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">15</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/structure_analyzer.py#L111-L144"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.structure_analyzer.VoronoiAnalyzer.analyze_structures" title="Link to this definition"></a></dt>
<dd><p>Perform Voronoi analysis on a list of Structures.
Note that this might take a significant amount of time depending on the
size and number of structures.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>structures</strong> (<em>list</em>) – list of Structures</p></li>
<li><p><strong>(</strong><strong>float</strong> (<em>cutoff</em>) – cutoff distance around an atom to search for
neighbors</p></li>
<li><p><strong>step_freq</strong> (<em>int</em>) – perform analysis every step_freq steps</p></li>
<li><p><strong>qhull_options</strong> (<em>str</em>) – options to pass to qhull</p></li>
<li><p><strong>most_frequent_polyhedra</strong> (<em>int</em>) – this many unique polyhedra with
highest frequencies is stored.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>A list of tuples in the form (voronoi_index,frequency)</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.structure_analyzer.VoronoiAnalyzer.plot_vor_analysis">
<em class="property"><span class="pre">static</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">plot_vor_analysis</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">voronoi_ensemble</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">tuple</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">float</span><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">]</span></span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">Axes</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/structure_analyzer.py#L146-L168"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.structure_analyzer.VoronoiAnalyzer.plot_vor_analysis" title="Link to this definition"></a></dt>
<dd><p>Plot the Voronoi analysis.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>voronoi_ensemble</strong> (<em>list</em><em>[</em><em>tuple</em><em>[</em><em>str</em><em>, </em><em>float</em><em>]</em><em>]</em>) – List of tuples containing labels and
values for Voronoi analysis.</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>Matplotlib Axes object with the plotted Voronoi analysis.</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>plt.Axes</p>
</dd>
</dl>
</dd></dl>
</dd></dl>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.analysis.structure_analyzer.VoronoiConnectivity">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">VoronoiConnectivity</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">structure</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><span class="pre">Structure</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">cutoff</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">10</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/structure_analyzer.py#L237-L338"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.structure_analyzer.VoronoiConnectivity" title="Link to this definition"></a></dt>
<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></p>
<p>Computes the solid angles swept out by the shared face of the voronoi
polyhedron between two sites.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>structure</strong> (<a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><em>Structure</em></a>) – Input structure</p></li>
<li><p><strong>cutoff</strong> (<em>float</em>)</p></li>
</ul>
</dd>
</dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.analysis.structure_analyzer.VoronoiConnectivity.connectivity_array">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">connectivity_array</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/structure_analyzer.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.structure_analyzer.VoronoiConnectivity.connectivity_array" title="Link to this definition"></a></dt>
<dd><p>The connectivity array of shape [atom_i, atom_j, image_j]. atom_i is the index of the
atom in the input structure. Since the second atom can be outside of the unit cell, it
must be described by both an atom index and an image index. Array data is the solid
angle of polygon between atom_i and image_j of atom_j.</p>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.structure_analyzer.VoronoiConnectivity.get_connections">
<span class="sig-name descname"><span class="pre">get_connections</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/structure_analyzer.py#L312-L323"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.structure_analyzer.VoronoiConnectivity.get_connections" title="Link to this definition"></a></dt>
<dd><p>Get a list of site pairs that are Voronoi Neighbors, along
with their real-space distances.</p>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.structure_analyzer.VoronoiConnectivity.get_sitej">
<span class="sig-name descname"><span class="pre">get_sitej</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">site_index</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">image_index</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/structure_analyzer.py#L325-L338"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.structure_analyzer.VoronoiConnectivity.get_sitej" title="Link to this definition"></a></dt>
<dd><p>Assuming there is some value in the connectivity array at indices
(1, 3, 12). site_i can be obtained directly from the input structure
(structure[1]). site_j can be obtained by passing 3, 12 to this function.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>site_index</strong> (<em>int</em>) – index of the site (3 in the example)</p></li>
<li><p><strong>image_index</strong> (<em>int</em>) – index of the image (12 in the example)</p></li>
</ul>
</dd>
</dl>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.analysis.structure_analyzer.VoronoiConnectivity.max_connectivity">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">max_connectivity</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/structure_analyzer.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.structure_analyzer.VoronoiConnectivity.max_connectivity" title="Link to this definition"></a></dt>
<dd><p>The 2d array [site_i, site_j] that represents the maximum connectivity of
site i to any periodic image of site j.</p>
</dd></dl>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="pymatgen.analysis.structure_analyzer.average_coordination_number">
<span class="sig-name descname"><span class="pre">average_coordination_number</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">structures</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">freq</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">10</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/structure_analyzer.py#L26-L52"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.structure_analyzer.average_coordination_number" title="Link to this definition"></a></dt>
<dd><p>Calculates the ensemble averaged Voronoi coordination numbers
of a list of Structures using VoronoiNN.
Typically used for analyzing the output of a Molecular Dynamics run.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>structures</strong> (<em>list</em>) – list of Structures.</p></li>
<li><p><strong>freq</strong> (<em>int</em>) – sampling frequency of coordination number [every freq steps].</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>Dictionary of elements as keys and average coordination numbers as values.</p>
</dd>
</dl>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="pymatgen.analysis.structure_analyzer.contains_peroxide">
<span class="sig-name descname"><span class="pre">contains_peroxide</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">structure</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">relative_cutoff</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1.1</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/structure_analyzer.py#L392-L405"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.structure_analyzer.contains_peroxide" title="Link to this definition"></a></dt>
<dd><p>Determines if a structure contains peroxide anions.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>structure</strong> (<a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><em>Structure</em></a>) – Input structure.</p></li>
<li><p><strong>relative_cutoff</strong> – The peroxide bond distance is 1.49 Angstrom.
Relative_cutoff * 1.49 stipulates the maximum distance two O
atoms must be to each other to be considered a peroxide.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>True if structure contains a peroxide anion.</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>bool</p>
</dd>
</dl>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="pymatgen.analysis.structure_analyzer.get_max_bond_lengths">
<span class="sig-name descname"><span class="pre">get_max_bond_lengths</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">structure</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">el_radius_updates</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/structure_analyzer.py#L367-L389"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.structure_analyzer.get_max_bond_lengths" title="Link to this definition"></a></dt>
<dd><p>Provides max bond length estimates for a structure based on the JMol
table and algorithms.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>structure</strong> – (structure)</p></li>
<li><p><strong>el_radius_updates</strong> – (dict) symbol->float to update atom_ic radii</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>The two elements are ordered by Z.</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>dict[(Element1, Element2)], float]</p>
</dd>
</dl>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="pymatgen.analysis.structure_analyzer.oxide_type">
<span class="sig-name descname"><span class="pre">oxide_type</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">structure</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><span class="pre">Structure</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">relative_cutoff</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">float</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">1.1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">return_nbonds</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">tuple</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">int</span><span class="p"><span class="pre">]</span></span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/structure_analyzer.py#L492-L507"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.structure_analyzer.oxide_type" title="Link to this definition"></a></dt>
<dd><p>Determines if an oxide is a peroxide/superoxide/ozonide/normal oxide.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>structure</strong> (<a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><em>Structure</em></a>) – Input structure.</p></li>
<li><p><strong>relative_cutoff</strong> (<em>float</em>) – Relative_cutoff * act. cutoff stipulates the
max distance two O atoms must be from each other.</p></li>
<li><p><strong>return_nbonds</strong> (<em>bool</em>) – Should number of bonds be requested?</p></li>
</ul>
</dd>
</dl>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="pymatgen.analysis.structure_analyzer.solid_angle">
<span class="sig-name descname"><span class="pre">solid_angle</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">center</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">coords</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/structure_analyzer.py#L341-L364"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.structure_analyzer.solid_angle" title="Link to this definition"></a></dt>
<dd><p>Helper method to calculate the solid angle of a set of coords from the center.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>center</strong> (<em>3x1 array</em>) – Center to measure solid angle from.</p></li>
<li><p><strong>coords</strong> (<em>Nx3 array</em>) – List of coords to determine solid angle.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>The solid angle.</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>float</p>
</dd>
</dl>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="pymatgen.analysis.structure_analyzer.sulfide_type">
<span class="sig-name descname"><span class="pre">sulfide_type</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">structure</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/structure_analyzer.py#L510-L561"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.structure_analyzer.sulfide_type" title="Link to this definition"></a></dt>
<dd><p>Determines if a structure is a sulfide/polysulfide/sulfate.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>structure</strong> (<a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><em>Structure</em></a>) – Input structure.</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>sulfide/polysulfide or None if structure is a sulfate.</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>str</p>
</dd>
</dl>
</dd></dl>
</section>
<section id="module-pymatgen.analysis.structure_matcher">
<span id="pymatgen-analysis-structure-matcher-module"></span><h2>pymatgen.analysis.structure_matcher module<a class="headerlink" href="#module-pymatgen.analysis.structure_matcher" title="Link to this heading"></a></h2>
<p>This module provides classes to perform fitting of structures.</p>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.analysis.structure_matcher.AbstractComparator">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">AbstractComparator</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/structure_matcher.py#L61-L135"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.structure_matcher.AbstractComparator" title="Link to this definition"></a></dt>
<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">MSONable</span></code>, <code class="xref py py-class docutils literal notranslate"><span class="pre">ABC</span></code></p>
<p>Abstract Comparator class. A Comparator defines how sites are compared in
a structure.</p>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.structure_matcher.AbstractComparator.are_equal">
<em class="property"><span class="pre">abstract</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">are_equal</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">sp1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">sp2</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">bool</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/structure_matcher.py#L67-L85"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.structure_matcher.AbstractComparator.are_equal" title="Link to this definition"></a></dt>
<dd><p>Defines how the species of two sites are considered equal. For
example, one can consider sites to have the same species only when
the species are exactly the same, i.e., Fe2+ matches Fe2+ but not
Fe3+. Or one can define that only the element matters,
and all oxidation state information are ignored.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>sp1</strong> – First species. A dict of {specie/element: amt} as per the
definition in Site and PeriodicSite.</p></li>
<li><p><strong>sp2</strong> – Second species. A dict of {specie/element: amt} as per the
definition in Site and PeriodicSite.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>True if species are considered equal.</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>bool</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.structure_matcher.AbstractComparator.as_dict">
<span class="sig-name descname"><span class="pre">as_dict</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/structure_matcher.py#L129-L135"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.structure_matcher.AbstractComparator.as_dict" title="Link to this definition"></a></dt>
<dd><p>MSONable dict.</p>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.structure_matcher.AbstractComparator.from_dict">
<em class="property"><span class="pre">classmethod</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">from_dict</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">dct</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">dict</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">Self</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/structure_matcher.py#L107-L127"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.structure_matcher.AbstractComparator.from_dict" title="Link to this definition"></a></dt>
<dd><dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>dct</strong> (<em>dict</em>) – Dict representation.</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>Comparator.</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.structure_matcher.AbstractComparator.get_hash">
<em class="property"><span class="pre">abstract</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">get_hash</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">composition</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/structure_matcher.py#L87-L105"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.structure_matcher.AbstractComparator.get_hash" title="Link to this definition"></a></dt>
<dd><p>Defines a hash to group structures. This allows structures to be
grouped efficiently for comparison. The hash must be invariant under
supercell creation. (e.g. composition is not a good hash, but
fractional_composition might be). Reduced formula is not a good formula,
due to weird behavior with fractional occupancy.</p>
<p>Composition is used here instead of structure because for anonymous
matches it is much quicker to apply a substitution to a composition
object than a structure object.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>composition</strong> (<a class="reference internal" href="pymatgen.core.html#pymatgen.core.composition.Composition" title="pymatgen.core.composition.Composition"><em>Composition</em></a>) – composition of the structure</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>A hashable object. Examples can be string formulas, integers etc.</p>
</dd>
</dl>
</dd></dl>
</dd></dl>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.analysis.structure_matcher.ElementComparator">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">ElementComparator</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/structure_matcher.py#L200-L226"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.structure_matcher.ElementComparator" title="Link to this definition"></a></dt>
<dd><p>Bases: <a class="reference internal" href="#pymatgen.analysis.structure_matcher.AbstractComparator" title="pymatgen.analysis.structure_matcher.AbstractComparator"><code class="xref py py-class docutils literal notranslate"><span class="pre">AbstractComparator</span></code></a></p>
<p>A Comparator that matches elements. i.e. oxidation states are
ignored.</p>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.structure_matcher.ElementComparator.are_equal">
<span class="sig-name descname"><span class="pre">are_equal</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">sp1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">sp2</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">bool</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/structure_matcher.py#L206-L222"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.structure_matcher.ElementComparator.are_equal" title="Link to this definition"></a></dt>
<dd><p>True if element:amounts are exactly the same, i.e.,
oxidation state is not considered.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>sp1</strong> – First species. A dict of {specie/element: amt} as per the
definition in Site and PeriodicSite.</p></li>
<li><p><strong>sp2</strong> – Second species. A dict of {specie/element: amt} as per the
definition in Site and PeriodicSite.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>True if species are the same based on element and amounts.</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>bool</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.structure_matcher.ElementComparator.get_hash">
<span class="sig-name descname"><span class="pre">get_hash</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">composition</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/structure_matcher.py#L224-L226"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.structure_matcher.ElementComparator.get_hash" title="Link to this definition"></a></dt>
<dd><p>Get the fractional element composition.</p>
</dd></dl>
</dd></dl>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.analysis.structure_matcher.FrameworkComparator">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">FrameworkComparator</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/structure_matcher.py#L229-L248"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.structure_matcher.FrameworkComparator" title="Link to this definition"></a></dt>
<dd><p>Bases: <a class="reference internal" href="#pymatgen.analysis.structure_matcher.AbstractComparator" title="pymatgen.analysis.structure_matcher.AbstractComparator"><code class="xref py py-class docutils literal notranslate"><span class="pre">AbstractComparator</span></code></a></p>
<p>A Comparator that matches sites, regardless of species.</p>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.structure_matcher.FrameworkComparator.are_equal">
<span class="sig-name descname"><span class="pre">are_equal</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">sp1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">sp2</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">bool</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/structure_matcher.py#L232-L244"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.structure_matcher.FrameworkComparator.are_equal" title="Link to this definition"></a></dt>
<dd><p>True if there are atoms on both sites.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>sp1</strong> – First species. A dict of {specie/element: amt} as per the
definition in Site and PeriodicSite.</p></li>
<li><p><strong>sp2</strong> – Second species. A dict of {specie/element: amt} as per the
definition in Site and PeriodicSite.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>True always</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.structure_matcher.FrameworkComparator.get_hash">
<span class="sig-name descname"><span class="pre">get_hash</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">composition</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/structure_matcher.py#L246-L248"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.structure_matcher.FrameworkComparator.get_hash" title="Link to this definition"></a></dt>
<dd><p>No hash possible.</p>
</dd></dl>
</dd></dl>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.analysis.structure_matcher.OccupancyComparator">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">OccupancyComparator</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/structure_matcher.py#L279-L308"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.structure_matcher.OccupancyComparator" title="Link to this definition"></a></dt>
<dd><p>Bases: <a class="reference internal" href="#pymatgen.analysis.structure_matcher.AbstractComparator" title="pymatgen.analysis.structure_matcher.AbstractComparator"><code class="xref py py-class docutils literal notranslate"><span class="pre">AbstractComparator</span></code></a></p>
<p>A Comparator that matches occupancies on sites,
irrespective of the species of those sites.</p>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.structure_matcher.OccupancyComparator.are_equal">
<span class="sig-name descname"><span class="pre">are_equal</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">sp1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">sp2</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">bool</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/structure_matcher.py#L285-L296"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.structure_matcher.OccupancyComparator.are_equal" title="Link to this definition"></a></dt>
<dd><dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>sp1</strong> – First species. A dict of {specie/element: amt} as per the
definition in Site and PeriodicSite.</p></li>
<li><p><strong>sp2</strong> – Second species. A dict of {specie/element: amt} as per the
definition in Site and PeriodicSite.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>True if sets of occupancies (amt) are equal on both sites.</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>bool</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.structure_matcher.OccupancyComparator.get_hash">
<span class="sig-name descname"><span class="pre">get_hash</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">composition</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/structure_matcher.py#L298-L308"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.structure_matcher.OccupancyComparator.get_hash" title="Link to this definition"></a></dt>
<dd><dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>composition</strong> – Composition.</p>
</dd>
</dl>
<p>TODO: might need a proper hash method</p>
<dl class="field-list simple">
<dt class="field-odd">Returns<span class="colon">:</span></dt>
<dd class="field-odd"><p><ol class="arabic simple">
<li><p>Difficult to define sensible hash</p></li>
</ol>
</p>
</dd>
</dl>
</dd></dl>
</dd></dl>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.analysis.structure_matcher.OrderDisorderElementComparator">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">OrderDisorderElementComparator</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/structure_matcher.py#L251-L276"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.structure_matcher.OrderDisorderElementComparator" title="Link to this definition"></a></dt>
<dd><p>Bases: <a class="reference internal" href="#pymatgen.analysis.structure_matcher.AbstractComparator" title="pymatgen.analysis.structure_matcher.AbstractComparator"><code class="xref py py-class docutils literal notranslate"><span class="pre">AbstractComparator</span></code></a></p>
<p>A Comparator that matches sites, given some overlap in the element
composition.</p>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.structure_matcher.OrderDisorderElementComparator.are_equal">
<span class="sig-name descname"><span class="pre">are_equal</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">sp1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">sp2</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">bool</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/structure_matcher.py#L257-L272"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.structure_matcher.OrderDisorderElementComparator.are_equal" title="Link to this definition"></a></dt>
<dd><p>True if there is some overlap in composition between the species.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>sp1</strong> – First species. A dict of {specie/element: amt} as per the
definition in Site and PeriodicSite.</p></li>
<li><p><strong>sp2</strong> – Second species. A dict of {specie/element: amt} as per the
definition in Site and PeriodicSite.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>True always</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.structure_matcher.OrderDisorderElementComparator.get_hash">
<span class="sig-name descname"><span class="pre">get_hash</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">composition</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/structure_matcher.py#L274-L276"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.structure_matcher.OrderDisorderElementComparator.get_hash" title="Link to this definition"></a></dt>
<dd><p>Get the fractional composition.</p>
</dd></dl>
</dd></dl>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.analysis.structure_matcher.SiteOrderedIStructure">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">SiteOrderedIStructure</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">lattice</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">ArrayLike</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference internal" href="pymatgen.core.html#pymatgen.core.lattice.Lattice" title="pymatgen.core.lattice.Lattice"><span class="pre">Lattice</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">species</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">Sequence</span><span class="p"><span class="pre">[</span></span><span class="pre">CompositionLike</span><span class="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="n"><span class="pre">coords</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">Sequence</span><span class="p"><span class="pre">[</span></span><span class="pre">ArrayLike</span><span class="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="n"><span class="pre">charge</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">float</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">validate_proximity</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">to_unit_cell</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">coords_are_cartesian</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">site_properties</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">dict</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">labels</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">Sequence</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">properties</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">dict</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/structure_matcher.py#L37-L58"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.structure_matcher.SiteOrderedIStructure" title="Link to this definition"></a></dt>
<dd><p>Bases: <a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.IStructure" title="pymatgen.core.structure.IStructure"><code class="xref py py-class docutils literal notranslate"><span class="pre">IStructure</span></code></a></p>
<p>Imutable structure where the order of sites matters.</p>
<p>In caching reduced structures (see <cite>StructureMatcher._get_reduced_structure</cite>)
the order of input sites can be important.
In general, the order of sites in a structure does not matter, but when
a method like <cite>StructureMatcher.get_s2_like_s1</cite> tries to put s2’s sites in
the same order as s1, the site order matters.</p>
<p>Create a periodic structure.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>lattice</strong> (<em>Lattice/3x3 array</em>) – The lattice, either as a
pymatgen.core.Lattice or
simply as any 2D array. Each row should correspond to a lattice
vector. e.g. [[10,0,0], [20,10,0], [0,0,30]] specifies a
lattice with lattice vectors [10,0,0], [20,10,0] and [0,0,30].</p></li>
<li><p><strong>species</strong> (<em>[</em><a class="reference internal" href="pymatgen.core.html#pymatgen.core.periodic_table.Species" title="pymatgen.core.periodic_table.Species"><em>Species</em></a><em>]</em>) – <p>Sequence of species on each site. Can take in
flexible input, including:</p>
<ol class="lowerroman simple">
<li><p>A sequence of element / species specified either as string
symbols, e.g. [“Li”, “Fe2+”, “P”, …] or atomic numbers,
e.g. (3, 56, …) or actual Element or Species objects.</p></li>
<li><p>List of dict of elements/species and occupancies, e.g.
[{“Fe” : 0.5, “Mn”:0.5}, …]. This allows the setup of
disordered structures.</p></li>
</ol>
</p></li>
<li><p><strong>coords</strong> (<em>Nx3 array</em>) – list of fractional/Cartesian coordinates of
each species.</p></li>
<li><p><strong>charge</strong> (<em>int</em>) – overall charge of the structure. Defaults to behavior
in SiteCollection where total charge is the sum of the oxidation
states.</p></li>
<li><p><strong>validate_proximity</strong> (<em>bool</em>) – Whether to check if there are sites
that are less than 0.01 Ang apart. Defaults to False.</p></li>
<li><p><strong>to_unit_cell</strong> (<em>bool</em>) – Whether to map all sites into the unit cell,
i.e. fractional coords between 0 and 1. Defaults to False.</p></li>
<li><p><strong>coords_are_cartesian</strong> (<em>bool</em>) – Set to True if you are providing
coordinates in Cartesian coordinates. Defaults to False.</p></li>
<li><p><strong>site_properties</strong> (<em>dict</em>) – Properties associated with the sites as a
dict of sequences, e.g. {“magmom”:[5, 5, 5, 5]}. The sequences
have to be the same length as the atomic species and
fractional_coords. Defaults to None for no properties.</p></li>
<li><p><strong>labels</strong> (<em>list</em><em>[</em><em>str</em><em>]</em>) – Labels associated with the sites as a
list of strings, e.g. [‘Li1’, ‘Li2’]. Must have the same
length as the species and fractional coords. Defaults to
None for no labels.</p></li>
<li><p><strong>properties</strong> (<em>dict</em>) – Properties associated with the whole structure.
Will be serialized when writing the structure to JSON or YAML but is
lost when converting to other formats.</p></li>
</ul>
</dd>
</dl>
</dd></dl>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.analysis.structure_matcher.SpeciesComparator">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">SpeciesComparator</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/structure_matcher.py#L138-L158"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.structure_matcher.SpeciesComparator" title="Link to this definition"></a></dt>
<dd><p>Bases: <a class="reference internal" href="#pymatgen.analysis.structure_matcher.AbstractComparator" title="pymatgen.analysis.structure_matcher.AbstractComparator"><code class="xref py py-class docutils literal notranslate"><span class="pre">AbstractComparator</span></code></a></p>
<p>A Comparator that matches species exactly. The default used in StructureMatcher.</p>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.structure_matcher.SpeciesComparator.are_equal">
<span class="sig-name descname"><span class="pre">are_equal</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">sp1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">sp2</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">bool</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/structure_matcher.py#L141-L154"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.structure_matcher.SpeciesComparator.are_equal" title="Link to this definition"></a></dt>
<dd><p>True if species are exactly the same, i.e., Fe2+ == Fe2+ but not Fe3+.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>sp1</strong> – First species. A dict of {specie/element: amt} as per the
definition in Site and PeriodicSite.</p></li>
<li><p><strong>sp2</strong> – Second species. A dict of {specie/element: amt} as per the
definition in Site and PeriodicSite.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>True if species are equal.</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>bool</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.structure_matcher.SpeciesComparator.get_hash">
<span class="sig-name descname"><span class="pre">get_hash</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">composition</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="pymatgen.core.html#pymatgen.core.composition.Composition" title="pymatgen.core.composition.Composition"><span class="pre">Composition</span></a></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/structure_matcher.py#L156-L158"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.structure_matcher.SpeciesComparator.get_hash" title="Link to this definition"></a></dt>
<dd><p>Get the fractional composition.</p>
</dd></dl>
</dd></dl>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.analysis.structure_matcher.SpinComparator">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">SpinComparator</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/structure_matcher.py#L161-L197"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.structure_matcher.SpinComparator" title="Link to this definition"></a></dt>
<dd><p>Bases: <a class="reference internal" href="#pymatgen.analysis.structure_matcher.AbstractComparator" title="pymatgen.analysis.structure_matcher.AbstractComparator"><code class="xref py py-class docutils literal notranslate"><span class="pre">AbstractComparator</span></code></a></p>
<p>A Comparator that matches magnetic structures to their inverse spins.
This comparator is primarily used to filter magnetically ordered
structures with opposite spins, which are equivalent.</p>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.structure_matcher.SpinComparator.are_equal">
<span class="sig-name descname"><span class="pre">are_equal</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">sp1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">sp2</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">bool</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/structure_matcher.py#L168-L193"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.structure_matcher.SpinComparator.are_equal" title="Link to this definition"></a></dt>
<dd><p>True if species are exactly the same, i.e., Fe2+ == Fe2+ but not
Fe3+. and the spins are reversed. i.e., spin up maps to spin down,
and vice versa.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>sp1</strong> – First species. A dict of {specie/element: amt} as per the
definition in Site and PeriodicSite.</p></li>
<li><p><strong>sp2</strong> – Second species. A dict of {specie/element: amt} as per the
definition in Site and PeriodicSite.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>True if species are equal.</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>bool</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.structure_matcher.SpinComparator.get_hash">
<span class="sig-name descname"><span class="pre">get_hash</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">composition</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/structure_matcher.py#L195-L197"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.structure_matcher.SpinComparator.get_hash" title="Link to this definition"></a></dt>
<dd><p>Get the fractional composition.</p>
</dd></dl>
</dd></dl>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.analysis.structure_matcher.StructureMatcher">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">StructureMatcher</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">ltol</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">float</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">0.2</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">stol</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">float</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">0.3</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">angle_tol</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">float</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">5</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">primitive_cell</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">scale</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">attempt_supercell</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">allow_subset</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">comparator</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="#pymatgen.analysis.structure_matcher.AbstractComparator" title="pymatgen.analysis.structure_matcher.AbstractComparator"><span class="pre">AbstractComparator</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">supercell_size</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">Literal</span><span class="p"><span class="pre">[</span></span><span class="s"><span class="pre">'num_sites'</span></span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="s"><span class="pre">'num_atoms'</span></span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="s"><span class="pre">'volume'</span></span><span class="p"><span class="pre">]</span></span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">'num_sites'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ignored_species</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">Sequence</span><span class="p"><span class="pre">[</span></span><span class="pre">SpeciesLike</span><span class="p"><span class="pre">]</span></span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">()</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/structure_matcher.py#L311-L1239"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.structure_matcher.StructureMatcher" title="Link to this definition"></a></dt>
<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">MSONable</span></code></p>
<p>Match structures by similarity.</p>
<p>Algorithm:
1. Given two structures: s1 and s2
2. Optional: Reduce to primitive cells.
3. If the number of sites do not match, return False
4. Reduce to s1 and s2 to Niggli Cells
5. Optional: Scale s1 and s2 to same volume.
6. Optional: Remove oxidation states associated with sites
7. Find all possible lattice vectors for s2 within shell of ltol.
8. For s1, translate an atom in the smallest set to the origin
9. For s2: find all valid lattices from permutations of the list</p>
<blockquote>
<div><p>of lattice vectors (invalid if: det(Lattice Matrix) < half
volume of original s2 lattice)</p>
</div></blockquote>
<ol class="arabic" start="10">
<li><p>For each valid lattice:</p>
<ol class="loweralpha">
<li><p>If the lattice angles of are within tolerance of s1,
basis change s2 into new lattice.</p></li>
<li><p>For each atom in the smallest set of s2:</p>
<blockquote>
<div><p>i. Translate to origin and compare fractional sites in
structure within a fractional tolerance.
ii. If true:</p>
<blockquote>
<div><p>ia. Convert both lattices to Cartesian and place
both structures on an average lattice
ib. Compute and return the average and max rms
displacement between the two structures normalized
by the average free length per atom</p>
<dl class="simple">
<dt>if fit function called:</dt><dd><p>if normalized max rms displacement is less than
stol. Return True</p>
</dd>
<dt>if get_rms_dist function called:</dt><dd><p>if normalized average rms displacement is less
than the stored rms displacement, store and
continue. (This function will search all possible
lattices for the smallest average rms displacement
between the two structures)</p>
</dd>
</dl>
</div></blockquote>
</div></blockquote>
</li>
</ol>
</li>
</ol>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>ltol</strong> (<em>float</em>) – Fractional length tolerance. Default is 0.2.</p></li>
<li><p><strong>stol</strong> (<em>float</em>) – Site tolerance. Defined as the fraction of the
average free length per atom := ( V / Nsites ) ** (1/3)
Default is 0.3.</p></li>
<li><p><strong>angle_tol</strong> (<em>float</em>) – Angle tolerance in degrees. Default is 5 degrees.</p></li>
<li><p><strong>primitive_cell</strong> (<em>bool</em>) – If true: input structures will be reduced to
primitive cells prior to matching. Default to True.</p></li>
<li><p><strong>scale</strong> (<em>bool</em>) – Input structures are scaled to equivalent volume if
true; For exact matching, set to False.</p></li>
<li><p><strong>attempt_supercell</strong> (<em>bool</em>) – If set to True and number of sites in
cells differ after a primitive cell reduction (divisible by an
integer) attempts to generate a supercell transformation of the
smaller cell which is equivalent to the larger structure.</p></li>
<li><p><strong>allow_subset</strong> (<em>bool</em>) – Allow one structure to match to the subset of
another structure. Eg. Matching of an ordered structure onto a
disordered one, or matching a delithiated to a lithiated
structure. This option cannot be combined with
attempt_supercell, or with structure grouping.</p></li>
<li><p><strong>comparator</strong> (<em>Comparator</em>) – <p>A comparator object implementing an equals
method that declares equivalency of sites. Default is
SpeciesComparator, which implies rigid species
mapping, i.e., Fe2+ only matches Fe2+ and not Fe3+.</p>
<p>Other comparators are provided, e.g. ElementComparator which
matches only the elements and not the species.</p>
<p>The reason why a comparator object is used instead of
supplying a comparison function is that it is not possible to
pickle a function, which makes it otherwise difficult to use
StructureMatcher with Python’s multiprocessing.</p>
</p></li>
<li><p><strong>supercell_size</strong> (<em>str</em><em> or </em><em>list</em>) – Method to use for determining the
size of a supercell (if applicable). Possible values are
‘num_sites’, ‘num_atoms’, ‘volume’, or an element or list of elements
present in both structures.</p></li>
<li><p><strong>ignored_species</strong> (<em>list</em>) – A list of ions to be ignored in matching.
Useful for matching structures that have similar frameworks
except for certain ions, e.g. Li-ion intercalation frameworks.
This is more useful than allow_subset because it allows better
control over what species are ignored in the matching.</p></li>
</ul>
</dd>
</dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.structure_matcher.StructureMatcher.as_dict">
<span class="sig-name descname"><span class="pre">as_dict</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/structure_matcher.py#L866-L882"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.structure_matcher.StructureMatcher.as_dict" title="Link to this definition"></a></dt>
<dd><p>MSONable dict.</p>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.structure_matcher.StructureMatcher.fit">
<span class="sig-name descname"><span class="pre">fit</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">struct1</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><span class="pre">Structure</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">struct2</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><span class="pre">Structure</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">symmetric</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">skip_structure_reduction</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">bool</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/structure_matcher.py#L591-L641"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.structure_matcher.StructureMatcher.fit" title="Link to this definition"></a></dt>
<dd><p>Fit two structures.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>struct1</strong> (<a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><em>Structure</em></a>) – 1st structure</p></li>
<li><p><strong>struct2</strong> (<a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><em>Structure</em></a>) – 2nd structure</p></li>
<li><p><strong>symmetric</strong> (<em>bool</em>) – Defaults to False
If True, check the equality both ways.
This only impacts a small percentage of structures</p></li>
<li><p><strong>skip_structure_reduction</strong> (<em>bool</em>) – Defaults to False
If True, skip to get a primitive structure and perform Niggli reduction for struct1 and struct2</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>True if the structures are equivalent</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>bool</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.structure_matcher.StructureMatcher.fit_anonymous">
<span class="sig-name descname"><span class="pre">fit_anonymous</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">struct1</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><span class="pre">Structure</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">struct2</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><span class="pre">Structure</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">niggli</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">skip_structure_reduction</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">bool</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/structure_matcher.py#L1076-L1102"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.structure_matcher.StructureMatcher.fit_anonymous" title="Link to this definition"></a></dt>
<dd><p>Performs an anonymous fitting, which allows distinct species in one structure to map
to another. e.g. to compare if the Li2O and Na2O structures are similar.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>struct1</strong> (<a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><em>Structure</em></a>) – 1st structure</p></li>
<li><p><strong>struct2</strong> (<a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><em>Structure</em></a>) – 2nd structure</p></li>
<li><p><strong>niggli</strong> (<em>bool</em>) – If true, perform Niggli reduction for struct1 and struct2</p></li>
<li><p><strong>skip_structure_reduction</strong> (<em>bool</em>) – Defaults to False
If True, skip to get a primitive structure and perform Niggli reduction for struct1 and struct2</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>True if a species mapping can map struct1 to struct2</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>bool</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.structure_matcher.StructureMatcher.from_dict">
<em class="property"><span class="pre">classmethod</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">from_dict</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">dct</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">dict</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">Self</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/structure_matcher.py#L884-L904"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.structure_matcher.StructureMatcher.from_dict" title="Link to this definition"></a></dt>
<dd><dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>dct</strong> (<em>dict</em>) – Dict representation.</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>StructureMatcher</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.structure_matcher.StructureMatcher.get_all_anonymous_mappings">
<span class="sig-name descname"><span class="pre">get_all_anonymous_mappings</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">struct1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">struct2</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">niggli</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">include_dist</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/structure_matcher.py#L1050-L1074"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.structure_matcher.StructureMatcher.get_all_anonymous_mappings" title="Link to this definition"></a></dt>
<dd><p>Performs an anonymous fitting, which allows distinct species in one
structure to map to another. Returns a dictionary of species
substitutions that are within tolerance.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>struct1</strong> (<a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><em>Structure</em></a>) – 1st structure</p></li>
<li><p><strong>struct2</strong> (<a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><em>Structure</em></a>) – 2nd structure</p></li>
<li><p><strong>niggli</strong> (<em>bool</em>) – Find niggli cell in preprocessing</p></li>
<li><p><strong>include_dist</strong> (<em>bool</em>) – Return the maximin distance with each mapping</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>list of species mappings that map struct1 to struct2.</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.structure_matcher.StructureMatcher.get_best_electronegativity_anonymous_mapping">
<span class="sig-name descname"><span class="pre">get_best_electronegativity_anonymous_mapping</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">struct1</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><span class="pre">Structure</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">struct2</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><span class="pre">Structure</span></a></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">dict</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/structure_matcher.py#L1018-L1048"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.structure_matcher.StructureMatcher.get_best_electronegativity_anonymous_mapping" title="Link to this definition"></a></dt>
<dd><p>Performs an anonymous fitting, which allows distinct species in one
structure to map to another. e.g. to compare if the Li2O and Na2O
structures are similar. If multiple substitutions are within tolerance
this will return the one which minimizes the difference in
electronegativity between the matches species.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>struct1</strong> (<a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><em>Structure</em></a>) – 1st structure</p></li>
<li><p><strong>struct2</strong> (<a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><em>Structure</em></a>) – 2nd structure</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>Mapping of struct1 species to struct2 species.</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>dict[<a class="reference internal" href="pymatgen.core.html#pymatgen.core.periodic_table.Element" title="pymatgen.core.periodic_table.Element">Element</a>, <a class="reference internal" href="pymatgen.core.html#pymatgen.core.periodic_table.Element" title="pymatgen.core.periodic_table.Element">Element</a>] | None</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.structure_matcher.StructureMatcher.get_mapping">
<span class="sig-name descname"><span class="pre">get_mapping</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">superset</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">subset</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/structure_matcher.py#L1212-L1239"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.structure_matcher.StructureMatcher.get_mapping" title="Link to this definition"></a></dt>
<dd><p>Calculate the mapping from superset to subset.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>superset</strong> (<a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><em>Structure</em></a>) – Structure containing at least the sites in
subset (within the structure matching tolerance)</p></li>
<li><p><strong>subset</strong> (<a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><em>Structure</em></a>) – Structure containing some of the sites in
superset (within the structure matching tolerance)</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>numpy array such that superset.sites[mapping] is within matching
tolerance of subset.sites or None if no such mapping is possible</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.structure_matcher.StructureMatcher.get_rms_anonymous">
<span class="sig-name descname"><span class="pre">get_rms_anonymous</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">struct1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">struct2</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/structure_matcher.py#L993-L1016"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.structure_matcher.StructureMatcher.get_rms_anonymous" title="Link to this definition"></a></dt>
<dd><p>Performs an anonymous fitting, which allows distinct species in one
structure to map to another. e.g. to compare if the Li2O and Na2O
structures are similar.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>struct1</strong> (<a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><em>Structure</em></a>) – 1st structure</p></li>
<li><p><strong>struct2</strong> (<a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><em>Structure</em></a>) – 2nd structure</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p><dl class="simple">
<dt>1st element is min_rms, 2nd is min_mapping.</dt><dd><p>min_rms is the minimum RMS distance, and min_mapping is the corresponding
minimal species mapping that would map struct1 to struct2. (None, None) is
returned if the minimax_rms exceeds the threshold.</p>
</dd>
</dl>
</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>tuple[float, float] | tuple[None, None]</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.structure_matcher.StructureMatcher.get_rms_dist">
<span class="sig-name descname"><span class="pre">get_rms_dist</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">struct1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">struct2</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/structure_matcher.py#L643-L663"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.structure_matcher.StructureMatcher.get_rms_dist" title="Link to this definition"></a></dt>
<dd><p>Calculate RMS displacement between two structures.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>struct1</strong> (<a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><em>Structure</em></a>) – 1st structure</p></li>
<li><p><strong>struct2</strong> (<a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><em>Structure</em></a>) – 2nd structure</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>rms displacement normalized by (Vol / nsites) ** (1/3)
and maximum distance between paired sites. If no matching
lattice is found None is returned.</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.structure_matcher.StructureMatcher.get_s2_like_s1">
<span class="sig-name descname"><span class="pre">get_s2_like_s1</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">struct1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">struct2</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">include_ignored_species</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/structure_matcher.py#L1169-L1210"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.structure_matcher.StructureMatcher.get_s2_like_s1" title="Link to this definition"></a></dt>
<dd><p>Performs transformations on struct2 to put it in a basis similar to
struct1 (without changing any of the inter-site distances).</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>struct1</strong> (<a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><em>Structure</em></a>) – Reference structure</p></li>
<li><p><strong>struct2</strong> (<a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><em>Structure</em></a>) – Structure to transform.</p></li>
<li><p><strong>include_ignored_species</strong> (<em>bool</em>) – Defaults to True,
the ignored_species is also transformed to the struct1
lattice orientation, though obviously there is no direct
matching to existing sites.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>A structure object similar to struct1, obtained by making a
supercell, sorting, and translating struct2.</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.structure_matcher.StructureMatcher.get_supercell_matrix">
<span class="sig-name descname"><span class="pre">get_supercell_matrix</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">supercell</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">struct</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">ndarray</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/structure_matcher.py#L1104-L1121"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.structure_matcher.StructureMatcher.get_supercell_matrix" title="Link to this definition"></a></dt>
<dd><p>Get the matrix for transforming struct to supercell. This
can be used for very distorted ‘supercells’ where the primitive cell
is impossible to find.</p>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.structure_matcher.StructureMatcher.get_transformation">
<span class="sig-name descname"><span class="pre">get_transformation</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">struct1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">struct2</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/structure_matcher.py#L1123-L1167"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.structure_matcher.StructureMatcher.get_transformation" title="Link to this definition"></a></dt>
<dd><p>Get the supercell transformation, fractional translation vector,
and a mapping to transform struct2 to be similar to struct1.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>struct1</strong> (<a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><em>Structure</em></a>) – Reference structure</p></li>
<li><p><strong>struct2</strong> (<a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><em>Structure</em></a>) – Structure to transform.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p><p>supercell matrix
vector (np.array(3)): fractional translation vector
mapping (list[int | None]):</p>
<blockquote>
<div><p>The first len(struct1) items of the mapping vector are the
indices of struct1’s corresponding sites in struct2 (or None
if there is no corresponding site), and the other items are
the remaining site indices of struct2.</p>
</div></blockquote>
</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>supercell (np.array(3, 3))</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.structure_matcher.StructureMatcher.group_structures">
<span class="sig-name descname"><span class="pre">group_structures</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">s_list</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">anonymous</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/structure_matcher.py#L806-L864"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.structure_matcher.StructureMatcher.group_structures" title="Link to this definition"></a></dt>
<dd><p>Given a list of structures, use fit to group
them by structural equality.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>s_list</strong> (<em>[</em><a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><em>Structure</em></a><em>]</em>) – List of structures to be grouped</p></li>
<li><p><strong>anonymous</strong> (<em>bool</em>) – Whether to use anonymous mode.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>A list of lists of matched structures
Assumption: if s1 == s2 but s1 != s3, than s2 and s3 will be put
in different groups without comparison.</p>
</dd>
</dl>
</dd></dl>
</dd></dl>
</section>
<section id="module-pymatgen.analysis.surface_analysis">
<span id="pymatgen-analysis-surface-analysis-module"></span><h2>pymatgen.analysis.surface_analysis module<a class="headerlink" href="#module-pymatgen.analysis.surface_analysis" title="Link to this heading"></a></h2>
<p>This module defines tools to analyze surface and adsorption related
quantities as well as related plots. If you use this module, please
consider citing the following works:</p>
<blockquote>
<div><ol class="upperalpha simple" start="18">
<li><p>Tran, Z. Xu, B. Radhakrishnan, D. Winston, W. Sun, K. A. Persson,</p></li>
</ol>
<p>S. P. Ong, “Surface Energies of Elemental Crystals”, Scientific
Data, 2016, 3:160080, doi: 10.1038/sdata.2016.80.</p>
<p>and</p>
<p>Kang, S., Mo, Y., Ong, S. P., & Ceder, G. (2014). Nanoscale
stabilization of sodium oxides: Implications for Na-O2 batteries.
Nano Letters, 14(2), 1016-1020. <a class="reference external" href="https://doi.org/10.1021/nl404557w">https://doi.org/10.1021/nl404557w</a></p>
<p>and</p>
<dl class="simple">
<dt>Montoya, J. H., & Persson, K. A. (2017). A high-throughput framework</dt><dd><p>for determining adsorption energies on solid surfaces. Npj
Computational Materials, 3(1), 14.
<a class="reference external" href="https://doi.org/10.1038/s41524-017-0017-z">https://doi.org/10.1038/s41524-017-0017-z</a></p>
</dd>
</dl>
</div></blockquote>
<p>Todo:
- Still assumes individual elements have their own chempots</p>
<blockquote>
<div><p>in a molecular adsorbate instead of considering a single
chempot for a single molecular adsorbate. E.g. for an OH
adsorbate, the surface energy is a function of delu_O and
delu_H instead of delu_OH</p>
</div></blockquote>
<ul class="simple">
<li><dl class="simple">
<dt>Need a method to automatically get chempot range when</dt><dd><p>dealing with non-stoichiometric slabs</p>
</dd>
</dl>
</li>
<li><dl class="simple">
<dt>Simplify the input for SurfaceEnergyPlotter such that the</dt><dd><p>user does not need to generate a dict</p>
</dd>
</dl>
</li>
</ul>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.analysis.surface_analysis.NanoscaleStability">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">NanoscaleStability</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">se_analyzers</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">symprec</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1e-05</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/surface_analysis.py#L1604-L1886"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.surface_analysis.NanoscaleStability" title="Link to this definition"></a></dt>
<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></p>
<p>A class for analyzing the stability of nanoparticles of different
polymorphs with respect to size. The Wulff shape will be the model for the
nanoparticle. Stability will be determined by an energetic competition between the
weighted surface energy (surface energy of the Wulff shape) and the bulk energy. A
future release will include a 2D phase diagram (e.g. w.r.t. size vs chempot for adsorbed
or non-stoichiometric surfaces). Based on the following work:</p>
<dl class="simple">
<dt>Kang, S., Mo, Y., Ong, S. P., & Ceder, G. (2014). Nanoscale</dt><dd><p>stabilization of sodium oxides: Implications for Na-O2
batteries. Nano Letters, 14(2), 1016-1020.
<a class="reference external" href="https://doi.org/10.1021/nl404557w">https://doi.org/10.1021/nl404557w</a></p>
</dd>
</dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.analysis.surface_analysis.NanoscaleStability.se_analyzers">
<span class="sig-name descname"><span class="pre">se_analyzers</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/surface_analysis.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.surface_analysis.NanoscaleStability.se_analyzers" title="Link to this definition"></a></dt>
<dd><p>Each item corresponds to a different polymorph.</p>
<dl class="field-list simple">
<dt class="field-odd">Type<span class="colon">:</span></dt>
<dd class="field-odd"><p>list[<a class="reference internal" href="#pymatgen.analysis.surface_analysis.SurfaceEnergyPlotter" title="pymatgen.analysis.surface_analysis.SurfaceEnergyPlotter">SurfaceEnergyPlotter</a>]</p>
</dd>
</dl>
</dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.analysis.surface_analysis.NanoscaleStability.symprec">
<span class="sig-name descname"><span class="pre">symprec</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/surface_analysis.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.surface_analysis.NanoscaleStability.symprec" title="Link to this definition"></a></dt>
<dd><p>Tolerance for symmetry finding. See WulffShape.</p>
<dl class="field-list simple">
<dt class="field-odd">Type<span class="colon">:</span></dt>
<dd class="field-odd"><p>float</p>
</dd>
</dl>
</dd></dl>
<p>Analyzes the nanoscale stability of different polymorphs.</p>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.surface_analysis.NanoscaleStability.bulk_gform">
<em class="property"><span class="pre">static</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">bulk_gform</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">bulk_entry</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/surface_analysis.py#L1729-L1739"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.surface_analysis.NanoscaleStability.bulk_gform" title="Link to this definition"></a></dt>
<dd><p>Get the formation energy of the bulk.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>bulk_entry</strong> (<a class="reference internal" href="pymatgen.entries.html#pymatgen.entries.computed_entries.ComputedStructureEntry" title="pymatgen.entries.computed_entries.ComputedStructureEntry"><em>ComputedStructureEntry</em></a>) – Entry of the corresponding bulk.</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>bulk formation energy (in eV)</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>float</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.surface_analysis.NanoscaleStability.plot_all_stability_map">
<span class="sig-name descname"><span class="pre">plot_all_stability_map</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">max_r</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">increments</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">50</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">delu_dict</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">delu_default</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ax</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">labels</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">from_sphere_area</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">e_units</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'keV'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">r_units</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'nanometers'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">normalize</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">scale_per_atom</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/surface_analysis.py#L1833-L1886"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.surface_analysis.NanoscaleStability.plot_all_stability_map" title="Link to this definition"></a></dt>
<dd><dl class="simple">
<dt>Get the plot of the formation energy of a particles</dt><dd><p>of different polymorphs against its effect radius.</p>
</dd>
</dl>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>max_r</strong> (<em>float</em>) – The maximum radius of the particle to plot up to.</p></li>
<li><p><strong>increments</strong> (<em>int</em>) – Number of plot points</p></li>
<li><p><strong>delu_dict</strong> (<em>dict</em>) – Dictionary of the chemical potentials to be set as
constant. Note the key should be a sympy Symbol object of the
format: Symbol(“delu_el”) where el is the name of the element.</p></li>
<li><p><strong>delu_default</strong> (<em>float</em>) – Default value for all unset chemical potentials</p></li>
<li><p><strong>plt</strong> (<em>pyplot</em>) – Plot</p></li>
<li><p><strong>labels</strong> (<em>list</em>) – List of labels for each plot, corresponds to the
list of se_analyzers</p></li>
<li><p><strong>from_sphere_area</strong> (<em>bool</em>) – There are two ways to calculate the bulk
formation energy. Either by treating the volume and thus surface
area of the particle as a perfect sphere, or as a Wulff shape.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>matplotlib Axes object</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>plt.Axes</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.surface_analysis.NanoscaleStability.plot_one_stability_map">
<span class="sig-name descname"><span class="pre">plot_one_stability_map</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">analyzer</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">max_r</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">delu_dict</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">label</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">''</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">increments</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">50</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">delu_default</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ax</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">from_sphere_area</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">e_units</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'keV'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">r_units</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'nanometers'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">normalize</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">scale_per_atom</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/surface_analysis.py#L1766-L1831"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.surface_analysis.NanoscaleStability.plot_one_stability_map" title="Link to this definition"></a></dt>
<dd><dl class="simple">
<dt>Get the plot of the formation energy of a particle against its</dt><dd><p>effect radius.</p>
</dd>
</dl>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>analyzer</strong> (<a class="reference internal" href="#pymatgen.analysis.surface_analysis.SurfaceEnergyPlotter" title="pymatgen.analysis.surface_analysis.SurfaceEnergyPlotter"><em>SurfaceEnergyPlotter</em></a>) – Analyzer associated with the
first polymorph</p></li>
<li><p><strong>max_r</strong> (<em>float</em>) – The maximum radius of the particle to plot up to.</p></li>
<li><p><strong>delu_dict</strong> (<em>dict</em>) – Dictionary of the chemical potentials to be set as
constant. Note the key should be a sympy Symbol object of the
format: Symbol(“delu_el”) where el is the name of the element.</p></li>
<li><p><strong>label</strong> (<em>str</em>) – Label of the plot for legend</p></li>
<li><p><strong>increments</strong> (<em>int</em>) – Number of plot points</p></li>
<li><p><strong>delu_default</strong> (<em>float</em>) – Default value for all unset chemical potentials</p></li>
<li><p><strong>plt</strong> (<em>pyplot</em>) – Plot</p></li>
<li><p><strong>from_sphere_area</strong> (<em>bool</em>) – There are two ways to calculate the bulk
formation energy. Either by treating the volume and thus surface
area of the particle as a perfect sphere, or as a Wulff shape.</p></li>
<li><p><strong>r_units</strong> (<em>str</em>) – Can be nanometers or Angstrom</p></li>
<li><p><strong>e_units</strong> (<em>str</em>) – Can be keV or eV</p></li>
<li><p><strong>normalize</strong> (<em>str</em>) – Whether or not to normalize energy by volume</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>matplotlib Axes object</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>plt.Axes</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.surface_analysis.NanoscaleStability.scaled_wulff">
<span class="sig-name descname"><span class="pre">scaled_wulff</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">wulff_shape</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">r</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/surface_analysis.py#L1741-L1764"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.surface_analysis.NanoscaleStability.scaled_wulff" title="Link to this definition"></a></dt>
<dd><dl class="simple">
<dt>Scales the Wulff shape with an effective radius r. Note that the resulting</dt><dd><p>Wulff does not necessarily have the same effective radius as the one
provided. The Wulff shape is scaled by its surface energies where first
the surface energies are scale by the minimum surface energy and then
multiplied by the given effective radius.</p>
</dd>
</dl>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>wulff_shape</strong> (<a class="reference internal" href="#pymatgen.analysis.wulff.WulffShape" title="pymatgen.analysis.wulff.WulffShape"><em>WulffShape</em></a>) – Initial, unscaled WulffShape</p></li>
<li><p><strong>r</strong> (<em>float</em>) – Arbitrary effective radius of the WulffShape</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>WulffShape (scaled by r)</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.surface_analysis.NanoscaleStability.solve_equilibrium_point">
<span class="sig-name descname"><span class="pre">solve_equilibrium_point</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">analyzer1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">analyzer2</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">delu_dict</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">delu_default</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">units</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'nanometers'</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/surface_analysis.py#L1631-L1664"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.surface_analysis.NanoscaleStability.solve_equilibrium_point" title="Link to this definition"></a></dt>
<dd><p>Get the radial size of two particles where equilibrium is reached between both
particles. NOTE: the solution here is not the same as the solution visualized in
the plot because solving for r requires that both the total surface area and
volume of the particles are functions of r.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>analyzer1</strong> (<a class="reference internal" href="#pymatgen.analysis.surface_analysis.SurfaceEnergyPlotter" title="pymatgen.analysis.surface_analysis.SurfaceEnergyPlotter"><em>SurfaceEnergyPlotter</em></a>) – Analyzer associated with the
first polymorph</p></li>
<li><p><strong>analyzer2</strong> (<a class="reference internal" href="#pymatgen.analysis.surface_analysis.SurfaceEnergyPlotter" title="pymatgen.analysis.surface_analysis.SurfaceEnergyPlotter"><em>SurfaceEnergyPlotter</em></a>) – Analyzer associated with the
second polymorph</p></li>
<li><p><strong>delu_dict</strong> (<em>dict</em>) – Dictionary of the chemical potentials to be set as
constant. Note the key should be a sympy Symbol object of the
format: Symbol(“delu_el”) where el is the name of the element.</p></li>
<li><p><strong>delu_default</strong> (<em>float</em>) – Default value for all unset chemical potentials</p></li>
<li><p><strong>units</strong> (<em>str</em>) – Can be nanometers or Angstrom</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>Particle radius in nm or Angstrom</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>float</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.surface_analysis.NanoscaleStability.wulff_gform_and_r">
<span class="sig-name descname"><span class="pre">wulff_gform_and_r</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">wulff_shape</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">bulk_entry</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">r</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">from_sphere_area</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">r_units</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'nanometers'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">e_units</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'keV'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">normalize</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">scale_per_atom</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/surface_analysis.py#L1666-L1727"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.surface_analysis.NanoscaleStability.wulff_gform_and_r" title="Link to this definition"></a></dt>
<dd><p>Calculates the formation energy of the particle with arbitrary radius r.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>wulff_shape</strong> (<a class="reference internal" href="#pymatgen.analysis.wulff.WulffShape" title="pymatgen.analysis.wulff.WulffShape"><em>WulffShape</em></a>) – Initial unscaled WulffShape</p></li>
<li><p><strong>bulk_entry</strong> (<a class="reference internal" href="pymatgen.entries.html#pymatgen.entries.computed_entries.ComputedStructureEntry" title="pymatgen.entries.computed_entries.ComputedStructureEntry"><em>ComputedStructureEntry</em></a>) – Entry of the corresponding bulk.</p></li>
<li><p><strong>r</strong> (<em>float</em><em> (</em><em>Ang</em><em>)</em>) – Arbitrary effective radius of the WulffShape</p></li>
<li><p><strong>from_sphere_area</strong> (<em>bool</em>) – There are two ways to calculate the bulk
formation energy. Either by treating the volume and thus surface
area of the particle as a perfect sphere, or as a Wulff shape.</p></li>
<li><p><strong>r_units</strong> (<em>str</em>) – Can be nanometers or Angstrom</p></li>
<li><p><strong>e_units</strong> (<em>str</em>) – Can be keV or eV</p></li>
<li><p><strong>normalize</strong> (<em>bool</em>) – Whether or not to normalize energy by volume</p></li>
<li><p><strong>scale_per_atom</strong> (<em>True</em>) – Whether or not to normalize by number of
atoms in the particle</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>particle formation energy (float in keV), effective radius</p>
</dd>
</dl>
</dd></dl>
</dd></dl>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.analysis.surface_analysis.SlabEntry">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">SlabEntry</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">structure</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">energy</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">miller_index</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">correction</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0.0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">parameters</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entry_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">label</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">adsorbates</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">clean_entry</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">marker</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">color</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/surface_analysis.py#L68-L346"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.surface_analysis.SlabEntry" title="Link to this definition"></a></dt>
<dd><p>Bases: <a class="reference internal" href="pymatgen.entries.html#pymatgen.entries.computed_entries.ComputedStructureEntry" title="pymatgen.entries.computed_entries.ComputedStructureEntry"><code class="xref py py-class docutils literal notranslate"><span class="pre">ComputedStructureEntry</span></code></a></p>
<dl class="simple">
<dt>A ComputedStructureEntry object encompassing all data relevant to a</dt><dd><p>slab for analyzing surface thermodynamics.</p>
</dd>
</dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.analysis.surface_analysis.SlabEntry.miller_index">
<span class="sig-name descname"><span class="pre">miller_index</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/surface_analysis.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.surface_analysis.SlabEntry.miller_index" title="Link to this definition"></a></dt>
<dd><p>Miller index of plane parallel to surface.</p>
<dl class="field-list simple">
<dt class="field-odd">Type<span class="colon">:</span></dt>
<dd class="field-odd"><p>tuple</p>
</dd>
</dl>
</dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.analysis.surface_analysis.SlabEntry.label">
<span class="sig-name descname"><span class="pre">label</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/surface_analysis.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.surface_analysis.SlabEntry.label" title="Link to this definition"></a></dt>
<dd><p>Brief description for this slab.</p>
<dl class="field-list simple">
<dt class="field-odd">Type<span class="colon">:</span></dt>
<dd class="field-odd"><p>str</p>
</dd>
</dl>
</dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.analysis.surface_analysis.SlabEntry.adsorbates">
<span class="sig-name descname"><span class="pre">adsorbates</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/surface_analysis.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.surface_analysis.SlabEntry.adsorbates" title="Link to this definition"></a></dt>
<dd><p>List of ComputedStructureEntry for the types of adsorbates.</p>
<dl class="field-list simple">
<dt class="field-odd">Type<span class="colon">:</span></dt>
<dd class="field-odd"><p>list</p>
</dd>
</dl>
</dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.analysis.surface_analysis.SlabEntry.clean_entry">
<span class="sig-name descname"><span class="pre">clean_entry</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/surface_analysis.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.surface_analysis.SlabEntry.clean_entry" title="Link to this definition"></a></dt>
<dd><p>SlabEntry for the corresponding clean slab for an adsorbed slab.</p>
<dl class="field-list simple">
<dt class="field-odd">Type<span class="colon">:</span></dt>
<dd class="field-odd"><p><a class="reference internal" href="#pymatgen.analysis.surface_analysis.SlabEntry" title="pymatgen.analysis.surface_analysis.SlabEntry">SlabEntry</a></p>
</dd>
</dl>
</dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.analysis.surface_analysis.SlabEntry.ads_entries_dict">
<span class="sig-name descname"><span class="pre">ads_entries_dict</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/surface_analysis.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.surface_analysis.SlabEntry.ads_entries_dict" title="Link to this definition"></a></dt>
<dd><p>Dictionary where the key is the reduced composition of the
adsorbate entry and value is the entry itself.</p>
<dl class="field-list simple">
<dt class="field-odd">Type<span class="colon">:</span></dt>
<dd class="field-odd"><p>dict</p>
</dd>
</dl>
</dd></dl>
<p>Make a SlabEntry containing all relevant surface thermodynamics data.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>structure</strong> (<a class="reference internal" href="pymatgen.core.html#pymatgen.core.surface.Slab" title="pymatgen.core.surface.Slab"><em>Slab</em></a>) – The primary slab associated with this entry.</p></li>
<li><p><strong>energy</strong> (<em>float</em>) – Energy from total energy calculation</p></li>
<li><p><strong>miller_index</strong> (<em>tuple</em><em>(</em><em>h</em><em>, </em><em>k</em><em>, </em><em>l</em><em>)</em>) – Miller index of plane parallel
to surface</p></li>
<li><p><strong>correction</strong> (<em>float</em>) – See ComputedSlabEntry</p></li>
<li><p><strong>parameters</strong> (<em>dict</em>) – See ComputedSlabEntry</p></li>
<li><p><strong>data</strong> (<em>dict</em>) – See ComputedSlabEntry</p></li>
<li><p><strong>entry_id</strong> (<em>str</em>) – See ComputedSlabEntry</p></li>
<li><p><strong>data</strong> – See ComputedSlabEntry</p></li>
<li><p><strong>entry_id</strong> – See ComputedSlabEntry</p></li>
<li><p><strong>label</strong> (<em>str</em>) – Any particular label for this slab, e.g. “Tasker 2”,
“non-stoichiometric”, “reconstructed”</p></li>
<li><p><strong>adsorbates</strong> (<em>[</em><a class="reference internal" href="pymatgen.entries.html#pymatgen.entries.computed_entries.ComputedStructureEntry" title="pymatgen.entries.computed_entries.ComputedStructureEntry"><em>ComputedStructureEntry</em></a><em>]</em>) – List of reference entries
for the adsorbates on the slab, can be an isolated molecule
(e.g. O2 for O or O2 adsorption), a bulk structure (eg. fcc
Cu for Cu adsorption) or anything.</p></li>
<li><p><strong>clean_entry</strong> (<a class="reference internal" href="pymatgen.entries.html#pymatgen.entries.computed_entries.ComputedStructureEntry" title="pymatgen.entries.computed_entries.ComputedStructureEntry"><em>ComputedStructureEntry</em></a>) – If the SlabEntry is for an
adsorbed slab, this is the corresponding SlabEntry for the
clean slab</p></li>
<li><p><strong>marker</strong> (<em>str</em>) – Custom marker for gamma plots (”–” and “-” are typical)</p></li>
<li><p><strong>color</strong> (<em>str</em><em> or </em><em>rgba</em>) – Custom color for gamma plots</p></li>
</ul>
</dd>
</dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.analysis.surface_analysis.SlabEntry.Nads_in_slab">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">Nads_in_slab</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/surface_analysis.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.surface_analysis.SlabEntry.Nads_in_slab" title="Link to this definition"></a></dt>
<dd><p>The TOTAL number of adsorbates in the slab on BOTH sides.</p>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.analysis.surface_analysis.SlabEntry.Nsurfs_ads_in_slab">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">Nsurfs_ads_in_slab</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/surface_analysis.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.surface_analysis.SlabEntry.Nsurfs_ads_in_slab" title="Link to this definition"></a></dt>
<dd><p>The TOTAL number of adsorbed surfaces in the slab.</p>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.surface_analysis.SlabEntry.as_dict">
<span class="sig-name descname"><span class="pre">as_dict</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/surface_analysis.py#L140-L150"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.surface_analysis.SlabEntry.as_dict" title="Link to this definition"></a></dt>
<dd><p>Get dict which contains Slab Entry data.</p>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.analysis.surface_analysis.SlabEntry.cleaned_up_slab">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">cleaned_up_slab</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/surface_analysis.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.surface_analysis.SlabEntry.cleaned_up_slab" title="Link to this definition"></a></dt>
<dd><p>A slab with the adsorbates removed.</p>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.analysis.surface_analysis.SlabEntry.create_slab_label">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">create_slab_label</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/surface_analysis.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.surface_analysis.SlabEntry.create_slab_label" title="Link to this definition"></a></dt>
<dd><p>A label (str) for this particular slab based on composition, coverage and Miller index.</p>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.surface_analysis.SlabEntry.from_computed_structure_entry">
<em class="property"><span class="pre">classmethod</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">from_computed_structure_entry</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">entry</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">miller_index</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">label</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">adsorbates</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">clean_entry</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">Self</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/surface_analysis.py#L327-L346"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.surface_analysis.SlabEntry.from_computed_structure_entry" title="Link to this definition"></a></dt>
<dd><p>Get SlabEntry from a ComputedStructureEntry.</p>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.surface_analysis.SlabEntry.from_dict">
<em class="property"><span class="pre">classmethod</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">from_dict</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">dct</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">dict</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">Self</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/surface_analysis.py#L276-L293"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.surface_analysis.SlabEntry.from_dict" title="Link to this definition"></a></dt>
<dd><p>Get a SlabEntry by reading in an dictionary.</p>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.analysis.surface_analysis.SlabEntry.get_monolayer">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">get_monolayer</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/surface_analysis.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.surface_analysis.SlabEntry.get_monolayer" title="Link to this definition"></a></dt>
<dd><p>The primitive unit surface area density of the adsorbate.</p>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.analysis.surface_analysis.SlabEntry.get_unit_primitive_area">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">get_unit_primitive_area</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/surface_analysis.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.surface_analysis.SlabEntry.get_unit_primitive_area" title="Link to this definition"></a></dt>
<dd><p>The surface area of the adsorbed system per unit area of the primitive slab system.</p>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.surface_analysis.SlabEntry.gibbs_binding_energy">
<span class="sig-name descname"><span class="pre">gibbs_binding_energy</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">eads</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/surface_analysis.py#L152-L166"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.surface_analysis.SlabEntry.gibbs_binding_energy" title="Link to this definition"></a></dt>
<dd><p>Get the adsorption energy or Gibbs binding energy of an adsorbate on a surface.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>eads</strong> (<em>bool</em>) – Whether to calculate the adsorption energy
(True) or the binding energy (False) which is just
adsorption energy normalized by number of adsorbates.</p>
</dd>
</dl>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.analysis.surface_analysis.SlabEntry.surface_area">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">surface_area</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/surface_analysis.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.surface_analysis.SlabEntry.surface_area" title="Link to this definition"></a></dt>
<dd><p>Calculate the surface area of the slab.</p>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.surface_analysis.SlabEntry.surface_energy">
<span class="sig-name descname"><span class="pre">surface_energy</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">ucell_entry</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ref_entries</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/surface_analysis.py#L168-L233"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.surface_analysis.SlabEntry.surface_energy" title="Link to this definition"></a></dt>
<dd><p>Calculates the surface energy of this SlabEntry.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>ucell_entry</strong> (<em>entry</em>) – An entry object for the bulk</p></li>
<li><p><strong>(</strong><strong>list</strong> (<em>ref_entries</em>) – [entry]): A list of entries for each type
of element to be used as a reservoir for non-stoichiometric
systems. The length of this list MUST be n-1 where n is the
number of different elements in the bulk entry. The chempot
of the element ref_entry that is not in the list will be
treated as a variable.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>The surface energy of the slab.</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>float</p>
</dd>
</dl>
</dd></dl>
</dd></dl>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.analysis.surface_analysis.SurfaceEnergyPlotter">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">SurfaceEnergyPlotter</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">all_slab_entries</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ucell_entry</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ref_entries</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/surface_analysis.py#L349-L1303"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.surface_analysis.SurfaceEnergyPlotter" title="Link to this definition"></a></dt>
<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></p>
<p>A class used for generating plots to analyze the thermodynamics of surfaces
of a material. Produces stability maps of different slab configurations,
phases diagrams of two parameters to determine stability of configurations
(future release), and Wulff shapes.</p>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.analysis.surface_analysis.SurfaceEnergyPlotter.all_slab_entries">
<span class="sig-name descname"><span class="pre">all_slab_entries</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/surface_analysis.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.surface_analysis.SurfaceEnergyPlotter.all_slab_entries" title="Link to this definition"></a></dt>
<dd><p>Either a list of SlabEntry objects (note for a list, the
SlabEntry must have the adsorbates and clean_entry parameter plugged in) or a Nested
dictionary containing a list of entries for slab calculations as
items and the corresponding Miller index of the slab as the key.
To account for adsorption, each value is a sub-dictionary with the
entry of a clean slab calculation as the sub-key and a list of
entries for adsorption calculations as the sub-value. The sub-value
can contain different adsorption configurations such as a different
site or a different coverage, however, ordinarily only the most stable
configuration for a particular coverage will be considered as the
function of the adsorbed surface energy has an intercept dependent on
the adsorption energy (ie an adsorption site with a higher adsorption
energy will always provide a higher surface energy than a site with a
lower adsorption energy). An example parameter is provided:
{(h1,k1,l1): {clean_entry1: [ads_entry1, ads_entry2, …], clean_entry2: […], …}, (h2,k2,l2): {…}}
where clean_entry1 can be a pristine surface and clean_entry2 can be a
reconstructed surface while ads_entry1 can be adsorption at site 1 with
a 2x2 coverage while ads_entry2 can have a 3x3 coverage. If adsorption
entries are present (i.e. if all_slab_entries[(h,k,l)][clean_entry1]), we
consider adsorption in all plots and analysis for this particular facet.</p>
<dl class="field-list simple">
<dt class="field-odd">Type<span class="colon">:</span></dt>
<dd class="field-odd"><p>dict | list</p>
</dd>
</dl>
</dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.analysis.surface_analysis.SurfaceEnergyPlotter.color_dict">
<span class="sig-name descname"><span class="pre">color_dict</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/surface_analysis.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.surface_analysis.SurfaceEnergyPlotter.color_dict" title="Link to this definition"></a></dt>
<dd><p>Dictionary of colors (r,g,b,a) when plotting surface energy stability.
The keys are individual surface entries where clean surfaces have a solid color while
the corresponding adsorbed surface will be transparent.</p>
<dl class="field-list simple">
<dt class="field-odd">Type<span class="colon">:</span></dt>
<dd class="field-odd"><p>dict</p>
</dd>
</dl>
</dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.analysis.surface_analysis.SurfaceEnergyPlotter.ucell_entry">
<span class="sig-name descname"><span class="pre">ucell_entry</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/surface_analysis.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.surface_analysis.SurfaceEnergyPlotter.ucell_entry" title="Link to this definition"></a></dt>
<dd><p>ComputedStructureEntry of the bulk reference for
this particular material.</p>
<dl class="field-list simple">
<dt class="field-odd">Type<span class="colon">:</span></dt>
<dd class="field-odd"><p><a class="reference internal" href="pymatgen.entries.html#pymatgen.entries.computed_entries.ComputedStructureEntry" title="pymatgen.entries.computed_entries.ComputedStructureEntry">ComputedStructureEntry</a></p>
</dd>
</dl>
</dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.analysis.surface_analysis.SurfaceEnergyPlotter.ref_entries">
<span class="sig-name descname"><span class="pre">ref_entries</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/surface_analysis.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.surface_analysis.SurfaceEnergyPlotter.ref_entries" title="Link to this definition"></a></dt>
<dd><p>List of ComputedStructureEntries to be used for calculating chemical potential.</p>
<dl class="field-list simple">
<dt class="field-odd">Type<span class="colon">:</span></dt>
<dd class="field-odd"><p>list</p>
</dd>
</dl>
</dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.analysis.surface_analysis.SurfaceEnergyPlotter.facet_color_dict">
<span class="sig-name descname"><span class="pre">facet_color_dict</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/surface_analysis.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.surface_analysis.SurfaceEnergyPlotter.facet_color_dict" title="Link to this definition"></a></dt>
<dd><p>Randomly generated dictionary of colors associated with each facet.</p>
<dl class="field-list simple">
<dt class="field-odd">Type<span class="colon">:</span></dt>
<dd class="field-odd"><p>dict</p>
</dd>
</dl>
</dd></dl>
<dl class="simple">
<dt>Object for plotting surface energy in different ways for clean and</dt><dd><p>adsorbed surfaces.</p>
</dd>
</dl>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>all_slab_entries</strong> (<em>dict</em><em> or </em><em>list</em>) – Dictionary or list containing
all entries for slab calculations. See attributes.</p></li>
<li><p><strong>ucell_entry</strong> (<a class="reference internal" href="pymatgen.entries.html#pymatgen.entries.computed_entries.ComputedStructureEntry" title="pymatgen.entries.computed_entries.ComputedStructureEntry"><em>ComputedStructureEntry</em></a>) – ComputedStructureEntry
of the bulk reference for this particular material.</p></li>
<li><p><strong>ref_entries</strong> (<em>[</em><em>ComputedStructureEntries</em><em>]</em>) – A list of entries for
each type of element to be used as a reservoir for
non-stoichiometric systems. The length of this list MUST be
n-1 where n is the number of different elements in the bulk
entry. The bulk energy term in the grand surface potential can
be defined by a summation of the chemical potentials for each
element in the system. As the bulk energy is already provided,
one can solve for one of the chemical potentials as a function
of the other chemical potentials and bulk energy. i.e. there
are n-1 variables (chempots). e.g. if your ucell_entry is for
LiFePO4 than your ref_entries should have an entry for Li, Fe,
and P if you want to use the chempot of O as the variable.</p></li>
</ul>
</dd>
</dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.surface_analysis.SurfaceEnergyPlotter.BE_vs_clean_SE">
<span class="sig-name descname"><span class="pre">BE_vs_clean_SE</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">delu_dict</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">delu_default</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">plot_eads</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">annotate_monolayer</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">JPERM2</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/surface_analysis.py#L1092-L1139"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.surface_analysis.SurfaceEnergyPlotter.BE_vs_clean_SE" title="Link to this definition"></a></dt>
<dd><dl class="simple">
<dt>For each facet, plot the clean surface energy against the most</dt><dd><p>stable binding energy.</p>
</dd>
</dl>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>delu_dict</strong> (<em>dict</em>) – Dictionary of the chemical potentials to be set as
constant. Note the key should be a sympy Symbol object of the
format: Symbol(“delu_el”) where el is the name of the element.</p></li>
<li><p><strong>delu_default</strong> (<em>float</em>) – Default value for all unset chemical potentials</p></li>
<li><p><strong>plot_eads</strong> (<em>bool</em>) – Option to plot the adsorption energy (binding
energy multiplied by number of adsorbates) instead.</p></li>
<li><p><strong>annotate_monolayer</strong> (<em>bool</em>) – Whether or not to label each data point
with its monolayer (adsorbate density per unit primiitve area)</p></li>
<li><p><strong>JPERM2</strong> (<em>bool</em>) – Whether to plot surface energy in /m^2 (True) or
eV/A^2 (False)</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p><dl class="simple">
<dt>Plot of clean surface energy vs binding energy for</dt><dd><p>all facets.</p>
</dd>
</dl>
</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>Plot</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.surface_analysis.SurfaceEnergyPlotter.area_frac_vs_chempot_plot">
<span class="sig-name descname"><span class="pre">area_frac_vs_chempot_plot</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">ref_delu</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">Symbol</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">chempot_range</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">float</span><span class="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="n"><span class="pre">delu_dict</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><span class="pre">Symbol</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">float</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">delu_default</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">float</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">increments</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">int</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">10</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">no_clean</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">no_doped</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">Axes</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/surface_analysis.py#L541-L621"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.surface_analysis.SurfaceEnergyPlotter.area_frac_vs_chempot_plot" title="Link to this definition"></a></dt>
<dd><p>1D plot. Plots the change in the area contribution
of each facet as a function of chemical potential.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>ref_delu</strong> (<em>Symbol</em>) – The free variable chempot with the format:
Symbol(“delu_el”) where el is the name of the element.</p></li>
<li><p><strong>chempot_range</strong> (<em>list</em><em>[</em><em>float</em><em>]</em>) – Min/max range of chemical potential to plot along.</p></li>
<li><p><strong>delu_dict</strong> (<em>dict</em><em>[</em><em>Symbol</em><em>, </em><em>float</em><em>]</em>) – Dictionary of the chemical potentials to be set as
constant. Note the key should be a sympy Symbol object of the
format: Symbol(“delu_el”) where el is the name of the element.</p></li>
<li><p><strong>delu_default</strong> (<em>float</em>) – Default value for all unset chemical potentials.</p></li>
<li><p><strong>increments</strong> (<em>int</em>) – Number of data points between min/max or point
of intersection. Defaults to 10 points.</p></li>
<li><p><strong>no_clean</strong> (<em>bool</em>) – Some parameter, description missing.</p></li>
<li><p><strong>no_doped</strong> (<em>bool</em>) – Some parameter, description missing.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>Plot of area frac on the Wulff shape for each facet vs chemical potential.</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>plt.Axes</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.surface_analysis.SurfaceEnergyPlotter.chempot_plot_addons">
<em class="property"><span class="pre">static</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">chempot_plot_addons</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">ax</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">xrange</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ref_el</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">pad</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">2.4</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">rect</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ylim</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/surface_analysis.py#L1056-L1090"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.surface_analysis.SurfaceEnergyPlotter.chempot_plot_addons" title="Link to this definition"></a></dt>
<dd><p>Helper function to a chempot plot look nicer.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>plt</strong> (<em>Plot</em>)</p></li>
<li><p><strong>xrange</strong> (<em>list</em>) – xlim parameter</p></li>
<li><p><strong>ref_el</strong> (<em>str</em>) – Element of the referenced chempot.</p></li>
<li><p><strong>axes</strong> (<em>axes</em>)</p></li>
<li><p><strong>pad</strong> (<em>float</em>)</p></li>
<li><p><strong>rect</strong> (<em>list</em>) – For tight layout</p></li>
<li><p><strong>ylim</strong> (<em>ylim parameter</em>)</p></li>
</ul>
</dd>
</dl>
<p>return (Plot): Modified plot with addons.
return (Plot): Modified plot with addons.</p>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.surface_analysis.SurfaceEnergyPlotter.chempot_vs_gamma">
<span class="sig-name descname"><span class="pre">chempot_vs_gamma</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">ref_delu</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">chempot_range</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">miller_index</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">delu_dict</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">delu_default</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">JPERM2</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">show_unstable</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ylim</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">plt</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">no_clean</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">no_doped</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_entry_labels</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">no_label</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/surface_analysis.py#L896-L1017"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.surface_analysis.SurfaceEnergyPlotter.chempot_vs_gamma" title="Link to this definition"></a></dt>
<dd><dl class="simple">
<dt>Plots the surface energy as a function of chemical potential.</dt><dd><p>Each facet will be associated with its own distinct colors.
Dashed lines will represent stoichiometries different from that
of the mpid’s compound. Transparent lines indicates adsorption.</p>
</dd>
</dl>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>ref_delu</strong> (<em>sympy Symbol</em>) – The range stability of each slab is based
on the chempot range of this chempot. Should be a sympy Symbol
object of the format: Symbol(“delu_el”) where el is the name of
the element</p></li>
<li><p><strong>chempot_range</strong> (<em>[</em><em>max_chempot</em><em>, </em><em>min_chempot</em><em>]</em>) – Range to consider the
stability of the slabs.</p></li>
<li><p><strong>miller_index</strong> (<em>list</em>) – Miller index for a specific facet to get a
dictionary for.</p></li>
<li><p><strong>delu_dict</strong> (<em>dict</em>) – Dictionary of the chemical potentials to be set as
constant. Note the key should be a sympy Symbol object of the
format: Symbol(“delu_el”) where el is the name of the element.</p></li>
<li><p><strong>delu_default</strong> (<em>float</em>) – Default value for all unset chemical potentials</p></li>
<li><p><strong>JPERM2</strong> (<em>bool</em>) – Whether to plot surface energy in /m^2 (True) or
eV/A^2 (False)</p></li>
<li><p><strong>show_unstable</strong> (<em>bool</em>) – Whether or not to show parts of the surface
energy plot outside the region of stability.</p></li>
<li><p><strong>ylim</strong> (<em>[</em><em>ymax</em><em>, </em><em>ymin</em><em>]</em>) – Range of y axis</p></li>
<li><p><strong>no_doped</strong> (<em>bool</em>) – Whether to plot for the clean slabs only.</p></li>
<li><p><strong>no_clean</strong> (<em>bool</em>) – Whether to plot for the doped slabs only.</p></li>
<li><p><strong>use_entry_labels</strong> (<em>bool</em>) – If True, will label each slab configuration
according to their given label in the SlabEntry object.</p></li>
<li><p><strong>no_label</strong> (<em>bool</em>) – Option to turn off labels.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>Plot of surface energy vs chempot for all entries.</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>Plot</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.surface_analysis.SurfaceEnergyPlotter.chempot_vs_gamma_plot_one">
<span class="sig-name descname"><span class="pre">chempot_vs_gamma_plot_one</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">ax</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">Axes</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">entry</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="#pymatgen.analysis.surface_analysis.SlabEntry" title="pymatgen.analysis.surface_analysis.SlabEntry"><span class="pre">SlabEntry</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">ref_delu</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">Symbol</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">chempot_range</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">list</span><span class="p"><span class="pre">[</span></span><span class="pre">float</span><span class="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="n"><span class="pre">delu_dict</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><span class="pre">Symbol</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">float</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">delu_default</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">float</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">label</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">''</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">JPERM2</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">Axes</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/surface_analysis.py#L834-L894"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.surface_analysis.SurfaceEnergyPlotter.chempot_vs_gamma_plot_one" title="Link to this definition"></a></dt>
<dd><p>Helper function to help plot the surface energy of a
single SlabEntry as a function of chemical potential.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>ax</strong> (<em>plt.Axes</em>) – Matplotlib Axes instance for plotting.</p></li>
<li><p><strong>entry</strong> – Entry of the slab whose surface energy we want
to plot. (Add appropriate description for type)</p></li>
<li><p><strong>ref_delu</strong> (<em>Symbol</em>) – The range stability of each slab is based
on the chempot range of this chempot.</p></li>
<li><p><strong>chempot_range</strong> (<em>list</em><em>[</em><em>float</em><em>]</em>) – Range to consider the stability of the slabs.</p></li>
<li><p><strong>delu_dict</strong> (<em>dict</em><em>[</em><em>Symbol</em><em>, </em><em>float</em><em>]</em>) – Dictionary of the chemical potentials.</p></li>
<li><p><strong>delu_default</strong> (<em>float</em>) – Default value for all unset chemical potentials.</p></li>
<li><p><strong>label</strong> (<em>str</em>) – Label of the slab for the legend.</p></li>
<li><p><strong>JPERM2</strong> (<em>bool</em>) – Whether to plot surface energy in /m^2 (True) or
eV/A^2 (False).</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>Plot of surface energy vs chemical potential for one entry.</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>plt.Axes</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.surface_analysis.SurfaceEnergyPlotter.color_palette_dict">
<span class="sig-name descname"><span class="pre">color_palette_dict</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">alpha</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0.35</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/surface_analysis.py#L796-L832"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.surface_analysis.SurfaceEnergyPlotter.color_palette_dict" title="Link to this definition"></a></dt>
<dd><p>Helper function to assign each facet a unique color using a dictionary.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>alpha</strong> (<em>float</em>) – Degree of transparency</p>
</dd>
</dl>
<dl class="simple">
<dt>return (dict): Dictionary of colors (r,g,b,a) when plotting surface</dt><dd><p>energy stability. The keys are individual surface entries where
clean surfaces have a solid color while the corresponding adsorbed
surface will be transparent.</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.surface_analysis.SurfaceEnergyPlotter.get_stable_entry_at_u">
<span class="sig-name descname"><span class="pre">get_stable_entry_at_u</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">miller_index</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">delu_dict</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">delu_default</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">no_doped</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">no_clean</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">tuple</span><span class="p"><span class="pre">[</span></span><a class="reference internal" href="#pymatgen.analysis.surface_analysis.SlabEntry" title="pymatgen.analysis.surface_analysis.SlabEntry"><span class="pre">SlabEntry</span></a><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">float</span><span class="p"><span class="pre">]</span></span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/surface_analysis.py#L446-L497"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.surface_analysis.SurfaceEnergyPlotter.get_stable_entry_at_u" title="Link to this definition"></a></dt>
<dd><dl class="simple">
<dt>Get the entry corresponding to the most stable slab for a particular</dt><dd><p>facet at a specific chempot. We assume that surface energy is constant
so all free variables must be set with delu_dict, otherwise they are
assumed to be equal to delu_default.</p>
</dd>
</dl>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>miller_index</strong> (<em>(</em><em>h</em><em>,</em><em>k</em><em>,</em><em>l</em><em>)</em>) – The facet to find the most stable slab in</p></li>
<li><p><strong>delu_dict</strong> (<em>dict</em>) – Dictionary of the chemical potentials to be set as
constant. Note the key should be a sympy Symbol object of the
format: Symbol(“delu_el”) where el is the name of the element.</p></li>
<li><p><strong>delu_default</strong> (<em>float</em>) – Default value for all unset chemical potentials</p></li>
<li><p><strong>no_doped</strong> (<em>bool</em>) – Consider stability of clean slabs only.</p></li>
<li><p><strong>no_clean</strong> (<em>bool</em>) – Consider stability of doped slabs only.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>The most stable slab entry and its surface energy.</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>tuple[<a class="reference internal" href="#pymatgen.analysis.surface_analysis.SlabEntry" title="pymatgen.analysis.surface_analysis.SlabEntry">SlabEntry</a>, float]</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.surface_analysis.SurfaceEnergyPlotter.get_surface_equilibrium">
<span class="sig-name descname"><span class="pre">get_surface_equilibrium</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">slab_entries</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">delu_dict</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/surface_analysis.py#L623-L664"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.surface_analysis.SurfaceEnergyPlotter.get_surface_equilibrium" title="Link to this definition"></a></dt>
<dd><dl class="simple">
<dt>Takes in a list of SlabEntries and calculates the chemical potentials</dt><dd><p>at which all slabs in the list coexists simultaneously. Useful for
building surface phase diagrams. Note that to solve for x equations
(x slab_entries), there must be x free variables (chemical potentials).
Adjust delu_dict as need be to get the correct number of free variables.</p>
</dd>
</dl>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>slab_entries</strong> (<em>array</em>) – The coefficients of the first equation</p></li>
<li><p><strong>delu_dict</strong> (<em>dict</em>) – Dictionary of the chemical potentials to be set as
constant. Note the key should be a sympy Symbol object of the
format: Symbol(“delu_el”) where el is the name of the element.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p><dl class="simple">
<dt>Array containing a solution to x equations with x</dt><dd><p>variables (x-1 chemical potential and 1 surface energy)</p>
</dd>
</dl>
</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>array</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.surface_analysis.SurfaceEnergyPlotter.monolayer_vs_BE">
<span class="sig-name descname"><span class="pre">monolayer_vs_BE</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">plot_eads</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/surface_analysis.py#L1019-L1054"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.surface_analysis.SurfaceEnergyPlotter.monolayer_vs_BE" title="Link to this definition"></a></dt>
<dd><dl class="simple">
<dt>Plots the binding energy as a function of monolayers (ML), i.e.</dt><dd><p>the fractional area adsorbate density for all facets. For each
facet at a specific monolayer, only plot the lowest binding energy.</p>
</dd>
</dl>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>plot_eads</strong> (<em>bool</em>) – Option to plot the adsorption energy (binding
energy multiplied by number of adsorbates) instead.</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>Plot of binding energy vs monolayer for all facets.</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>Plot</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.surface_analysis.SurfaceEnergyPlotter.set_all_variables">
<span class="sig-name descname"><span class="pre">set_all_variables</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">delu_dict</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">delu_default</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/surface_analysis.py#L1279-L1303"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.surface_analysis.SurfaceEnergyPlotter.set_all_variables" title="Link to this definition"></a></dt>
<dd><dl class="simple">
<dt>Set all chemical potential values and returns a dictionary where</dt><dd><p>the key is a sympy Symbol and the value is a float (chempot).</p>
</dd>
</dl>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>entry</strong> (<a class="reference internal" href="#pymatgen.analysis.surface_analysis.SlabEntry" title="pymatgen.analysis.surface_analysis.SlabEntry"><em>SlabEntry</em></a>) – Computed structure entry of the slab</p></li>
<li><p><strong>delu_dict</strong> (<em>dict</em>) – Dictionary of the chemical potentials to be set as
constant. Note the key should be a sympy Symbol object of the
format: Symbol(“delu_el”) where el is the name of the element.</p></li>
<li><p><strong>delu_default</strong> (<em>float</em>) – Default value for all unset chemical potentials</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>Dictionary of set chemical potential values</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.surface_analysis.SurfaceEnergyPlotter.stable_u_range_dict">
<span class="sig-name descname"><span class="pre">stable_u_range_dict</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">chempot_range</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ref_delu</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">no_doped</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">no_clean</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">delu_dict</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">miller_index</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">()</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">dmu_at_0</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">return_se_dict</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/surface_analysis.py#L666-L794"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.surface_analysis.SurfaceEnergyPlotter.stable_u_range_dict" title="Link to this definition"></a></dt>
<dd><p>Creates a dictionary where each entry is a key pointing to a
chemical potential range where the surface of that entry is stable.
Does so by enumerating through all possible solutions (intersect)
for surface energies of a specific facet.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>chempot_range</strong> (<em>[</em><em>max_chempot</em><em>, </em><em>min_chempot</em><em>]</em>) – Range to consider the
stability of the slabs.</p></li>
<li><p><strong>ref_delu</strong> (<em>sympy Symbol</em>) – The range stability of each slab is based
on the chempot range of this chempot. Should be a sympy Symbol
object of the format: Symbol(“delu_el”) where el is the name of
the element</p></li>
<li><p><strong>no_doped</strong> (<em>bool</em>) – Consider stability of clean slabs only.</p></li>
<li><p><strong>no_clean</strong> (<em>bool</em>) – Consider stability of doped slabs only.</p></li>
<li><p><strong>delu_dict</strong> (<em>dict</em>) – Dictionary of the chemical potentials to be set as
constant. Note the key should be a sympy Symbol object of the
format: Symbol(“delu_el”) where el is the name of the element.</p></li>
<li><p><strong>miller_index</strong> (<em>list</em>) – Miller index for a specific facet to get a
dictionary for.</p></li>
<li><p><strong>dmu_at_0</strong> (<em>bool</em>) – If True, if the surface energies corresponding to
the chemical potential range is between a negative and positive
value, the value is a list of three chemical potentials with the
one in the center corresponding a surface energy of 0. Uselful
in identifying unphysical ranges of surface energies and their
chemical potential range.</p></li>
<li><p><strong>return_se_dict</strong> (<em>bool</em>) – Whether or not to return the corresponding
dictionary of surface energies</p></li>
</ul>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.surface_analysis.SurfaceEnergyPlotter.surface_chempot_range_map">
<span class="sig-name descname"><span class="pre">surface_chempot_range_map</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">elements</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">miller_index</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ranges</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">incr</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">50</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">no_doped</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">no_clean</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">delu_dict</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ax</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">annotate</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">show_unphysical_only</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">fontsize</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">10</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">Axes</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/surface_analysis.py#L1141-L1277"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.surface_analysis.SurfaceEnergyPlotter.surface_chempot_range_map" title="Link to this definition"></a></dt>
<dd><dl class="simple">
<dt>Adapted from the get_chempot_range_map() method in the PhaseDiagram</dt><dd><p>class. Plot the chemical potential range map based on surface
energy stability. Currently works only for 2-component PDs. At
the moment uses a brute force method by enumerating through the
range of the first element chempot with a specified increment
and determines the chempot range of the second element for each
SlabEntry. Future implementation will determine the chempot range
map first by solving systems of equations up to 3 instead of 2.</p>
</dd>
</dl>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>elements</strong> (<em>list</em>) – Sequence of elements to be considered as independent
variables. e.g. if you want to show the stability ranges of
all Li-Co-O phases w.r.t. to duLi and duO, you will supply
[Element(“Li”), Element(“O”)]</p></li>
<li><p><strong>miller_index</strong> (<em>[</em><em>h</em><em>, </em><em>k</em><em>, </em><em>l</em><em>]</em>) – Miller index of the surface we are interested in</p></li>
<li><p><strong>ranges</strong> (<em>[</em><em>[</em><em>range1</em><em>]</em><em>, </em><em>[</em><em>range2</em><em>]</em><em>]</em>) – List of chempot ranges (max and min values)
for the first and second element.</p></li>
<li><p><strong>incr</strong> (<em>int</em>) – Number of points to sample along the range of the first chempot</p></li>
<li><p><strong>no_doped</strong> (<em>bool</em>) – Whether or not to include doped systems.</p></li>
<li><p><strong>no_clean</strong> (<em>bool</em>) – Whether or not to include clean systems.</p></li>
<li><p><strong>delu_dict</strong> (<em>dict</em>) – Dictionary of the chemical potentials to be set as
constant. Note the key should be a sympy Symbol object of the
format: Symbol(“delu_el”) where el is the name of the element.</p></li>
<li><p><strong>ax</strong> (<em>plt.Axes</em>) – Axes object to plot on. If None, will create a new plot.</p></li>
<li><p><strong>annotate</strong> (<em>bool</em>) – Whether to annotate each “phase” with the label of
the entry. If no label, uses the reduced formula</p></li>
<li><p><strong>show_unphysical_only</strong> (<em>bool</em>) – Whether to only show the shaded region where
surface energy is negative. Useful for drawing other chempot range maps.</p></li>
<li><p><strong>fontsize</strong> (<em>int</em>) – Font size of the annotation</p></li>
</ul>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.surface_analysis.SurfaceEnergyPlotter.wulff_from_chempot">
<span class="sig-name descname"><span class="pre">wulff_from_chempot</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">delu_dict</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">delu_default</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">symprec</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1e-05</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">no_clean</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">no_doped</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><a class="reference internal" href="#pymatgen.analysis.wulff.WulffShape" title="pymatgen.analysis.wulff.WulffShape"><span class="pre">WulffShape</span></a></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/surface_analysis.py#L499-L539"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.surface_analysis.SurfaceEnergyPlotter.wulff_from_chempot" title="Link to this definition"></a></dt>
<dd><p>Method to get the Wulff shape at a specific chemical potential.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>delu_dict</strong> (<em>dict</em>) – Dictionary of the chemical potentials to be set as
constant. Note the key should be a sympy Symbol object of the
format: Symbol(“delu_el”) where el is the name of the element.</p></li>
<li><p><strong>delu_default</strong> (<em>float</em>) – Default value for all unset chemical potentials</p></li>
<li><p><strong>symprec</strong> (<em>float</em>) – See WulffShape.</p></li>
<li><p><strong>no_doped</strong> (<em>bool</em>) – Consider stability of clean slabs only.</p></li>
<li><p><strong>no_clean</strong> (<em>bool</em>) – Consider stability of doped slabs only.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>The WulffShape at u_ref and u_ads.</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p><a class="reference internal" href="#pymatgen.analysis.wulff.WulffShape" title="pymatgen.analysis.wulff.WulffShape">WulffShape</a></p>
</dd>
</dl>
</dd></dl>
</dd></dl>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.analysis.surface_analysis.WorkFunctionAnalyzer">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">WorkFunctionAnalyzer</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">structure</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><span class="pre">Structure</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">locpot_along_c</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">efermi</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">shift</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">blength</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">3.5</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/surface_analysis.py#L1335-L1601"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.surface_analysis.WorkFunctionAnalyzer" title="Link to this definition"></a></dt>
<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></p>
<p>A class used for calculating the work function from a slab model and
visualizing the behavior of the local potential along the slab.</p>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.analysis.surface_analysis.WorkFunctionAnalyzer.efermi">
<span class="sig-name descname"><span class="pre">efermi</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/surface_analysis.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.surface_analysis.WorkFunctionAnalyzer.efermi" title="Link to this definition"></a></dt>
<dd><p>The Fermi energy.</p>
<dl class="field-list simple">
<dt class="field-odd">Type<span class="colon">:</span></dt>
<dd class="field-odd"><p>float</p>
</dd>
</dl>
</dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.analysis.surface_analysis.WorkFunctionAnalyzer.locpot_along_c">
<span class="sig-name descname"><span class="pre">locpot_along_c</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/surface_analysis.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.surface_analysis.WorkFunctionAnalyzer.locpot_along_c" title="Link to this definition"></a></dt>
<dd><p>Local potential in eV along points along the c axis.</p>
<dl class="field-list simple">
<dt class="field-odd">Type<span class="colon">:</span></dt>
<dd class="field-odd"><p>list</p>
</dd>
</dl>
</dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.analysis.surface_analysis.WorkFunctionAnalyzer.vacuum_locpot">
<span class="sig-name descname"><span class="pre">vacuum_locpot</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/surface_analysis.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.surface_analysis.WorkFunctionAnalyzer.vacuum_locpot" title="Link to this definition"></a></dt>
<dd><p>The maximum local potential along the c direction for the slab model,
i.e. the potential at the vacuum.</p>
<dl class="field-list simple">
<dt class="field-odd">Type<span class="colon">:</span></dt>
<dd class="field-odd"><p>float</p>
</dd>
</dl>
</dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.analysis.surface_analysis.WorkFunctionAnalyzer.work_function">
<span class="sig-name descname"><span class="pre">work_function</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/surface_analysis.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.surface_analysis.WorkFunctionAnalyzer.work_function" title="Link to this definition"></a></dt>
<dd><p>The minimum energy needed to move an electron from the surface to infinity.
Defined as the difference between the potential at the vacuum and the Fermi energy.</p>
<dl class="field-list simple">
<dt class="field-odd">Type<span class="colon">:</span></dt>
<dd class="field-odd"><p>float</p>
</dd>
</dl>
</dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.analysis.surface_analysis.WorkFunctionAnalyzer.slab">
<span class="sig-name descname"><span class="pre">slab</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/surface_analysis.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.surface_analysis.WorkFunctionAnalyzer.slab" title="Link to this definition"></a></dt>
<dd><p>The slab structure model.</p>
<dl class="field-list simple">
<dt class="field-odd">Type<span class="colon">:</span></dt>
<dd class="field-odd"><p><a class="reference internal" href="pymatgen.core.html#pymatgen.core.surface.Slab" title="pymatgen.core.surface.Slab">Slab</a></p>
</dd>
</dl>
</dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.analysis.surface_analysis.WorkFunctionAnalyzer.along_c">
<span class="sig-name descname"><span class="pre">along_c</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/surface_analysis.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.surface_analysis.WorkFunctionAnalyzer.along_c" title="Link to this definition"></a></dt>
<dd><p>Points along the c direction with same increments as the locpot in the c axis.</p>
<dl class="field-list simple">
<dt class="field-odd">Type<span class="colon">:</span></dt>
<dd class="field-odd"><p>list</p>
</dd>
</dl>
</dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.analysis.surface_analysis.WorkFunctionAnalyzer.ave_locpot">
<span class="sig-name descname"><span class="pre">ave_locpot</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/surface_analysis.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.surface_analysis.WorkFunctionAnalyzer.ave_locpot" title="Link to this definition"></a></dt>
<dd><p>Mean of the minimum and maximum (vacuum) locpot along c.</p>
<dl class="field-list simple">
<dt class="field-odd">Type<span class="colon">:</span></dt>
<dd class="field-odd"><p>float</p>
</dd>
</dl>
</dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.analysis.surface_analysis.WorkFunctionAnalyzer.sorted_sites">
<span class="sig-name descname"><span class="pre">sorted_sites</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/surface_analysis.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.surface_analysis.WorkFunctionAnalyzer.sorted_sites" title="Link to this definition"></a></dt>
<dd><p>List of sites from the slab sorted along the c direction.</p>
<dl class="field-list simple">
<dt class="field-odd">Type<span class="colon">:</span></dt>
<dd class="field-odd"><p>list</p>
</dd>
</dl>
</dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.analysis.surface_analysis.WorkFunctionAnalyzer.ave_bulk_p">
<span class="sig-name descname"><span class="pre">ave_bulk_p</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/surface_analysis.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.surface_analysis.WorkFunctionAnalyzer.ave_bulk_p" title="Link to this definition"></a></dt>
<dd><p>The average locpot of the slab region along the c direction.</p>
<dl class="field-list simple">
<dt class="field-odd">Type<span class="colon">:</span></dt>
<dd class="field-odd"><p>float</p>
</dd>
</dl>
</dd></dl>
<p>Initialize the WorkFunctionAnalyzer class.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>structure</strong> (<a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><em>Structure</em></a>) – Structure object modelling the surface</p></li>
<li><p><strong>locpot_along_c</strong> (<em>list</em>) – Local potential along the c direction</p></li>
<li><p><strong>outcar</strong> (<em>MSONable</em>) – Outcar vasp output object</p></li>
<li><p><strong>shift</strong> (<em>float</em>) – Parameter to translate the slab (and
therefore the vacuum) of the slab structure, thereby
translating the plot along the x axis.</p></li>
<li><p><strong>blength</strong> (<em>float</em><em> (</em><em>Ang</em><em>)</em>) – The longest bond length in the material.
Used to handle pbc for noncontiguous slab layers</p></li>
</ul>
</dd>
</dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.surface_analysis.WorkFunctionAnalyzer.from_files">
<em class="property"><span class="pre">classmethod</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">from_files</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">poscar_filename</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">locpot_filename</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">outcar_filename</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">shift</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">blength</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">3.5</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">Self</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/surface_analysis.py#L1578-L1601"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.surface_analysis.WorkFunctionAnalyzer.from_files" title="Link to this definition"></a></dt>
<dd><p>Initialize a WorkFunctionAnalyzer from POSCAR, LOCPOT, and OUTCAR files.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>poscar_filename</strong> (<em>str</em>) – The path to the POSCAR file.</p></li>
<li><p><strong>locpot_filename</strong> (<em>str</em>) – The path to the LOCPOT file.</p></li>
<li><p><strong>outcar_filename</strong> (<em>str</em>) – The path to the OUTCAR file.</p></li>
<li><p><strong>shift</strong> (<em>float</em>) – The shift value. Defaults to 0.</p></li>
<li><p><strong>blength</strong> (<em>float</em>) – The longest bond length in the material.
Used to handle pbc for noncontiguous slab layers. Defaults to 3.5.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>A WorkFunctionAnalyzer instance.</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p><a class="reference internal" href="#pymatgen.analysis.surface_analysis.WorkFunctionAnalyzer" title="pymatgen.analysis.surface_analysis.WorkFunctionAnalyzer">WorkFunctionAnalyzer</a></p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.surface_analysis.WorkFunctionAnalyzer.get_labels">
<span class="sig-name descname"><span class="pre">get_labels</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">plt</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">label_fontsize</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">10</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/surface_analysis.py#L1475-L1548"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.surface_analysis.WorkFunctionAnalyzer.get_labels" title="Link to this definition"></a></dt>
<dd><p>Handles the optional labelling of the plot with relevant quantities.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>plt</strong> (<em>plt</em>) – Plot of the locpot vs c axis</p></li>
<li><p><strong>label_fontsize</strong> (<em>float</em>) – Fontsize of labels</p></li>
</ul>
</dd>
</dl>
<p>Returns Labelled plt.</p>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.surface_analysis.WorkFunctionAnalyzer.get_locpot_along_slab_plot">
<span class="sig-name descname"><span class="pre">get_locpot_along_slab_plot</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">label_energies</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">plt</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">label_fontsize</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">10</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/surface_analysis.py#L1422-L1473"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.surface_analysis.WorkFunctionAnalyzer.get_locpot_along_slab_plot" title="Link to this definition"></a></dt>
<dd><dl class="simple">
<dt>Get a plot of the local potential (eV) vs the</dt><dd><p>position along the c axis of the slab model (Ang).</p>
</dd>
</dl>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>label_energies</strong> (<em>bool</em>) – Whether to label relevant energy
quantities such as the work function, Fermi energy,
vacuum locpot, bulk-like locpot</p></li>
<li><p><strong>plt</strong> (<em>plt</em>) – Matplotlib pyplot object</p></li>
<li><p><strong>label_fontsize</strong> (<em>float</em>) – Fontsize of labels</p></li>
</ul>
</dd>
</dl>
<p>Returns plt of the locpot vs c axis</p>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.surface_analysis.WorkFunctionAnalyzer.is_converged">
<span class="sig-name descname"><span class="pre">is_converged</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">min_points_frac</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0.015</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">tol</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">float</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">0.0025</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/surface_analysis.py#L1550-L1576"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.surface_analysis.WorkFunctionAnalyzer.is_converged" title="Link to this definition"></a></dt>
<dd><dl class="simple">
<dt>A well converged work function should have a flat electrostatic</dt><dd><p>potential within some distance (min_point) about where the peak
electrostatic potential is found along the c direction of the
slab. This is dependent on the size of the slab.</p>
</dd>
</dl>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>min_point</strong> (<em>fractional coordinates</em>) – The number of data points
+/- the point of where the electrostatic potential is at
its peak along the c direction.</p></li>
<li><p><strong>tol</strong> (<em>float</em>) – If the electrostatic potential stays the same
within this tolerance, within the min_points, it is converged.</p></li>
</ul>
</dd>
</dl>
<p>Returns a bool (whether or not the work function is converged)</p>
</dd></dl>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="pymatgen.analysis.surface_analysis.entry_dict_from_list">
<span class="sig-name descname"><span class="pre">entry_dict_from_list</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">all_slab_entries</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">dict</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/surface_analysis.py#L1306-L1332"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.surface_analysis.entry_dict_from_list" title="Link to this definition"></a></dt>
<dd><p>Converts a list of SlabEntry to an appropriate dictionary. It is
assumed that if there is no adsorbate, then it is a clean SlabEntry
and that adsorbed SlabEntry has the clean_entry parameter set.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>all_slab_entries</strong> (<em>list</em>) – List of SlabEntry objects</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p><dl class="simple">
<dt>Dictionary of SlabEntry with the Miller index as the main</dt><dd><p>key to a dictionary with a clean SlabEntry as the key to a
list of adsorbed SlabEntry.</p>
</dd>
</dl>
</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>dict</p>
</dd>
</dl>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="pymatgen.analysis.surface_analysis.sub_chempots">
<span class="sig-name descname"><span class="pre">sub_chempots</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">gamma_dict</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">chempots</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/surface_analysis.py#L1889-L1914"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.surface_analysis.sub_chempots" title="Link to this definition"></a></dt>
<dd><dl class="simple">
<dt>Uses dot product of numpy array to sub chemical potentials</dt><dd><p>into the surface grand potential. This is much faster
than using the subs function in sympy.</p>
</dd>
</dl>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>gamma_dict</strong> (<em>dict</em>) – Surface grand potential equation
as a coefficient dictionary</p></li>
<li><p><strong>chempots</strong> (<em>dict</em>) – Dictionary assigning each chemical
potential (key) in gamma a value</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>Surface energy as a float</p>
</dd>
</dl>
</dd></dl>
</section>
<section id="module-pymatgen.analysis.thermochemistry">
<span id="pymatgen-analysis-thermochemistry-module"></span><h2>pymatgen.analysis.thermochemistry module<a class="headerlink" href="#module-pymatgen.analysis.thermochemistry" title="Link to this heading"></a></h2>
<p>A module to perform experimental thermochemical data analysis.</p>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.analysis.thermochemistry.ThermoData">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">ThermoData</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">data_type</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">cpdname</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">phaseinfo</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">formula</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">value</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ref</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">''</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">''</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">temp_range</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">(298,</span> <span class="pre">298)</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">uncertainty</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/thermochemistry.py#L22-L124"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.thermochemistry.ThermoData" title="Link to this definition"></a></dt>
<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></p>
<p>Container for experimental thermo-chemical data.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>data_type</strong> – The thermochemical data type. Should be one of the
following: fH - Formation enthalpy, S - Entropy,
A, B, C, D, E, F, G, H - variables for use in the various
equations for generating formation enthalpies or Cp at
various temperatures.</p></li>
<li><p><strong>cpdname</strong> (<em>str</em>) – A name for the compound. For example, hematite for
Fe2O3.</p></li>
<li><p><strong>phaseinfo</strong> (<em>str</em>) – Denoting the phase. For example, “solid”, “liquid”,
“gas” or “tetragonal”.</p></li>
<li><p><strong>formula</strong> (<em>str</em>) – A proper string formula, e.g. Fe2O3</p></li>
<li><p><strong>value</strong> (<em>float</em>) – The value of the data.</p></li>
<li><p><strong>ref</strong> (<em>str</em>) – A reference, if any, for the data.</p></li>
<li><p><strong>method</strong> (<em>str</em>) – The method by which the data was determined,
if available.</p></li>
<li><p><strong>temp_range</strong> (<em>[</em><em>float</em><em>, </em><em>float</em><em>]</em>) – Temperature range of validity for the
data in Kelvin. Defaults to 298 K only.</p></li>
<li><p><strong>uncertainty</strong> (<em>float</em>) – An uncertainty for the data, if available.</p></li>
</ul>
</dd>
</dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.thermochemistry.ThermoData.as_dict">
<span class="sig-name descname"><span class="pre">as_dict</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/thermochemistry.py#L91-L105"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.thermochemistry.ThermoData.as_dict" title="Link to this definition"></a></dt>
<dd><p>Get MSONable dict.</p>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.thermochemistry.ThermoData.from_dict">
<em class="property"><span class="pre">classmethod</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">from_dict</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">dct</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">dict</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">Self</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/thermochemistry.py#L70-L89"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.thermochemistry.ThermoData.from_dict" title="Link to this definition"></a></dt>
<dd><dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>dct</strong> (<em>dict</em>) – Dict representation.</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>ThermoData</p>
</dd>
</dl>
</dd></dl>
</dd></dl>
</section>
<section id="module-pymatgen.analysis.transition_state">
<span id="pymatgen-analysis-transition-state-module"></span><h2>pymatgen.analysis.transition_state module<a class="headerlink" href="#module-pymatgen.analysis.transition_state" title="Link to this heading"></a></h2>
<p>Some reimplementation of Henkelman’s Transition State Analysis utilities,
which are originally in Perl. Additional features beyond those offered by
Henkelman’s utilities will be added.</p>
<p>This allows the usage and customization in Python.</p>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.analysis.transition_state.NEBAnalysis">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">NEBAnalysis</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">r</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">energies</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">forces</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">structures</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">spline_options</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/transition_state.py#L29-L292"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.transition_state.NEBAnalysis" title="Link to this definition"></a></dt>
<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">MSONable</span></code></p>
<p>An NEBAnalysis class.</p>
<p>Initialize an NEBAnalysis from the cumulative root mean squared distances
between structures, the energies, the forces, the structures and the
interpolation_order for the analysis.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>r</strong> – Root mean square distances between structures</p></li>
<li><p><strong>energies</strong> – Energies of each structure along reaction coordinate</p></li>
<li><p><strong>forces</strong> – Tangent forces along the reaction coordinate.</p></li>
<li><p><strong>structures</strong> (<em>[</em><a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><em>Structure</em></a><em>]</em>) – List of Structures along reaction
coordinate.</p></li>
<li><p><strong>spline_options</strong> (<em>dict</em>) – Options for cubic spline. For example,
{“saddle_point”: “zero_slope”} forces the slope at the saddle to
be zero.</p></li>
</ul>
</dd>
</dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.transition_state.NEBAnalysis.as_dict">
<span class="sig-name descname"><span class="pre">as_dict</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/transition_state.py#L278-L292"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.transition_state.NEBAnalysis.as_dict" title="Link to this definition"></a></dt>
<dd><p>Dict representation of NEBAnalysis.</p>
<dl class="field-list simple">
<dt class="field-odd">Returns<span class="colon">:</span></dt>
<dd class="field-odd"><p>JSON-serializable dict representation.</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.transition_state.NEBAnalysis.from_dir">
<em class="property"><span class="pre">classmethod</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">from_dir</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">root_dir</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">relaxation_dirs</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">Self</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/transition_state.py#L204-L276"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.transition_state.NEBAnalysis.from_dir" title="Link to this definition"></a></dt>
<dd><p>Initialize a NEBAnalysis object from a directory of a NEB run.
Note that OUTCARs must be present in all image directories. For the
terminal OUTCARs from relaxation calculations, you can specify the
locations using relaxation_dir. If these are not specified, the code
will attempt to look for the OUTCARs in 00 and 0n directories,
followed by subdirs “start”, “end” or “initial”, “final” in the
root_dir. These are just some typical conventions used
preferentially in Shyue Ping’s MAVRL research group. For the
non-terminal points, the CONTCAR is read to obtain structures. For
terminal points, the POSCAR is used. The image directories are
assumed to be the only directories that can be resolved to integers.
e.g. “00”, “01”, “02”, “03”, “04”, “05”, “06”. The minimum
sub-directory structure that can be parsed is of the following form (
a 5-image example is shown):</p>
<p>00:
- POSCAR
- OUTCAR
01, 02, 03, 04, 05:
- CONTCAR
- OUTCAR
06:
- POSCAR
- OUTCAR</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>root_dir</strong> (<em>str</em>) – Path to the root directory of the NEB calculation.</p></li>
<li><p><strong>relaxation_dirs</strong> (<em>tuple</em>) – This specifies the starting and ending
relaxation directories from which the OUTCARs are read for the
terminal points for the energies.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>NEBAnalysis object.</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.transition_state.NEBAnalysis.from_outcars">
<em class="property"><span class="pre">classmethod</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">from_outcars</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">outcars</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">structures</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">Self</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/transition_state.py#L86-L133"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.transition_state.NEBAnalysis.from_outcars" title="Link to this definition"></a></dt>
<dd><p>Initialize an NEBAnalysis from Outcar and Structure objects. Use
the static constructors, e.g. from_dir instead if you
prefer to have these automatically generated from a directory of NEB
calculations.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>outcars</strong> (<em>[</em><a class="reference internal" href="pymatgen.io.vasp.html#pymatgen.io.vasp.outputs.Outcar" title="pymatgen.io.vasp.outputs.Outcar"><em>Outcar</em></a><em>]</em>) – List of Outcar objects. Note that these have
to be ordered from start to end along reaction coordinates.</p></li>
<li><p><strong>structures</strong> (<em>[</em><a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure"><em>Structure</em></a><em>]</em>) – List of Structures along reaction
coordinate. Must be same length as outcar.</p></li>
<li><p><strong>interpolation_order</strong> (<em>int</em>) – Order of polynomial to use to
interpolate between images. Same format as order parameter in
scipy.interpolate.PiecewisePolynomial.</p></li>
</ul>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.transition_state.NEBAnalysis.get_extrema">
<span class="sig-name descname"><span class="pre">get_extrema</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">normalize_rxn_coordinate</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/transition_state.py#L135-L157"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.transition_state.NEBAnalysis.get_extrema" title="Link to this definition"></a></dt>
<dd><p>Get the positions of the extrema along the MEP. Both local
minimums and maximums are returned.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>normalize_rxn_coordinate</strong> (<em>bool</em>) – Whether to normalize the
reaction coordinate to between 0 and 1. Defaults to True.</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>where the extrema are given as [(x1, y1), (x2, y2), …].</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>tuple[min_extrema, max_extrema]</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.transition_state.NEBAnalysis.get_plot">
<span class="sig-name descname"><span class="pre">get_plot</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">normalize_rxn_coordinate</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">label_barrier</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">bool</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">Axes</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/transition_state.py#L159-L202"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.transition_state.NEBAnalysis.get_plot" title="Link to this definition"></a></dt>
<dd><p>Get an NEB plot. Uses Henkelman’s approach of spline fitting
each section of the reaction path based on tangent force and energies.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>normalize_rxn_coordinate</strong> (<em>bool</em>) – Whether to normalize the
reaction coordinate to between 0 and 1. Defaults to True.</p></li>
<li><p><strong>label_barrier</strong> (<em>bool</em>) – Whether to label the maximum barrier. Defaults to True.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>matplotlib axes object.</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>plt.Axes</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.transition_state.NEBAnalysis.setup_spline">
<span class="sig-name descname"><span class="pre">setup_spline</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">spline_options</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/transition_state.py#L60-L84"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.transition_state.NEBAnalysis.setup_spline" title="Link to this definition"></a></dt>
<dd><p>Setup of the options for the spline interpolation.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>spline_options</strong> (<em>dict</em>) – Options for cubic spline. For example,
{“saddle_point”: “zero_slope”} forces the slope at the saddle to
be zero.</p>
</dd>
</dl>
</dd></dl>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="pymatgen.analysis.transition_state.combine_neb_plots">
<span class="sig-name descname"><span class="pre">combine_neb_plots</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">neb_analyses</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">arranged_neb_analyses</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">reverse_plot</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/transition_state.py#L295-L396"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.transition_state.combine_neb_plots" title="Link to this definition"></a></dt>
<dd><p>neb_analyses: a list of NEBAnalysis objects.</p>
<p>arranged_neb_analyses: The code connects two end points with the
smallest-energy difference. If all end points have very close energies, it’s
likely to result in an inaccurate connection. Manually arrange neb_analyses
if the combined plot is not as expected compared with all individual plots.
e.g. if there are two NEBAnalysis objects to combine, arrange in such a
way that the end-point energy of the first NEBAnalysis object is the
start-point energy of the second NEBAnalysis object.
Note that the barrier labeled in y-axis in the combined plot might be
different from that in the individual plot due to the reference energy used.
reverse_plot: reverse the plot or percolation direction.</p>
<dl class="field-list simple">
<dt class="field-odd">Returns<span class="colon">:</span></dt>
<dd class="field-odd"><p>a NEBAnalysis object</p>
</dd>
</dl>
</dd></dl>
</section>
<section id="module-pymatgen.analysis.wulff">
<span id="pymatgen-analysis-wulff-module"></span><h2>pymatgen.analysis.wulff module<a class="headerlink" href="#module-pymatgen.analysis.wulff" title="Link to this heading"></a></h2>
<p>This module define a WulffShape class to generate the Wulff shape from
a lattice, a list of indices and their corresponding surface energies,
and the total area and volume of the Wulff shape, the weighted surface energy,
the anisotropy and shape_factor can also be calculated.
In support of plotting from a given view in terms of miller index.</p>
<p>The lattice is from the conventional unit cell, and (hkil) for hexagonal
lattices.</p>
<p>If you use this code extensively, consider citing the following:</p>
<p>Tran, R.; Xu, Z.; Radhakrishnan, B.; Winston, D.; Persson, K. A.; Ong, S. P.
(2016). Surface energies of elemental crystals. Scientific Data.</p>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.analysis.wulff.WulffFacet">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">WulffFacet</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">normal</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">e_surf</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">normal_pt</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">dual_pt</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">index</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">m_ind_orig</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">miller</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/wulff.py#L72-L94"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.wulff.WulffFacet" title="Link to this definition"></a></dt>
<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></p>
<p>Helper container for each Wulff plane.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>normal</strong></p></li>
<li><p><strong>e_surf</strong></p></li>
<li><p><strong>normal_pt</strong></p></li>
<li><p><strong>dual_pt</strong></p></li>
<li><p><strong>index</strong></p></li>
<li><p><strong>m_ind_orig</strong></p></li>
<li><p><strong>miller</strong></p></li>
</ul>
</dd>
</dl>
</dd></dl>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.analysis.wulff.WulffShape">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">WulffShape</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">lattice</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="pymatgen.core.html#pymatgen.core.lattice.Lattice" title="pymatgen.core.lattice.Lattice"><span class="pre">Lattice</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">miller_list</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">e_surf_list</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">symprec</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1e-05</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/wulff.py#L97-L750"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.wulff.WulffShape" title="Link to this definition"></a></dt>
<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></p>
<p>Generate Wulff Shape from list of miller index and surface energies,
with given conventional unit cell.
surface energy (Jm^2) is the length of normal.</p>
<p>Wulff shape is the convex hull.
Based on:
<a class="reference external" href="https://docs.scipy.org/doc/scipy/reference/generated/scipy.spatial.ConvexHull.html">https://docs.scipy.org/doc/scipy/reference/generated/scipy.spatial.ConvexHull.html</a></p>
<dl class="simple">
<dt>Process:</dt><dd><ol class="arabic simple">
<li><p>get Wulff simplices</p></li>
<li><p>label with color</p></li>
<li><p>get wulff_area and other properties</p></li>
</ol>
</dd>
</dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.analysis.wulff.WulffShape.debug">
<span class="sig-name descname"><span class="pre">debug</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/wulff.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.wulff.WulffShape.debug" title="Link to this definition"></a></dt>
<dd><p>Whether to print debug information.</p>
<dl class="field-list simple">
<dt class="field-odd">Type<span class="colon">:</span></dt>
<dd class="field-odd"><p>bool</p>
</dd>
</dl>
</dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.analysis.wulff.WulffShape.alpha">
<span class="sig-name descname"><span class="pre">alpha</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/wulff.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.wulff.WulffShape.alpha" title="Link to this definition"></a></dt>
<dd><p>Transparency of the Wulff shape.</p>
<dl class="field-list simple">
<dt class="field-odd">Type<span class="colon">:</span></dt>
<dd class="field-odd"><p>float</p>
</dd>
</dl>
</dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.analysis.wulff.WulffShape.color_set">
<span class="sig-name descname"><span class="pre">color_set</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/wulff.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.wulff.WulffShape.color_set" title="Link to this definition"></a></dt>
<dd><p>colors to use for facets.</p>
<dl class="field-list simple">
<dt class="field-odd">Type<span class="colon">:</span></dt>
<dd class="field-odd"><p>list</p>
</dd>
</dl>
</dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.analysis.wulff.WulffShape.grid_off">
<span class="sig-name descname"><span class="pre">grid_off</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/wulff.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.wulff.WulffShape.grid_off" title="Link to this definition"></a></dt>
<dd><p>Whether to turn off the grid.</p>
<dl class="field-list simple">
<dt class="field-odd">Type<span class="colon">:</span></dt>
<dd class="field-odd"><p>bool</p>
</dd>
</dl>
</dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.analysis.wulff.WulffShape.axis_off">
<span class="sig-name descname"><span class="pre">axis_off</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/wulff.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.wulff.WulffShape.axis_off" title="Link to this definition"></a></dt>
<dd><p>Whether to turn off the axis.</p>
<dl class="field-list simple">
<dt class="field-odd">Type<span class="colon">:</span></dt>
<dd class="field-odd"><p>bool</p>
</dd>
</dl>
</dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.analysis.wulff.WulffShape.show_area">
<span class="sig-name descname"><span class="pre">show_area</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/wulff.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.wulff.WulffShape.show_area" title="Link to this definition"></a></dt>
<dd><p>Whether to show the area of each facet.</p>
<dl class="field-list simple">
<dt class="field-odd">Type<span class="colon">:</span></dt>
<dd class="field-odd"><p>bool</p>
</dd>
</dl>
</dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.analysis.wulff.WulffShape.off_color">
<span class="sig-name descname"><span class="pre">off_color</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/wulff.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.wulff.WulffShape.off_color" title="Link to this definition"></a></dt>
<dd><p>Color of facets not on the Wulff shape.</p>
<dl class="field-list simple">
<dt class="field-odd">Type<span class="colon">:</span></dt>
<dd class="field-odd"><p>str</p>
</dd>
</dl>
</dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.analysis.wulff.WulffShape.structure">
<span class="sig-name descname"><span class="pre">structure</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/wulff.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.wulff.WulffShape.structure" title="Link to this definition"></a></dt>
<dd><p>Input conventional unit cell (with H) from lattice.</p>
<dl class="field-list simple">
<dt class="field-odd">Type<span class="colon">:</span></dt>
<dd class="field-odd"><p><a class="reference internal" href="pymatgen.core.html#pymatgen.core.structure.Structure" title="pymatgen.core.structure.Structure">Structure</a></p>
</dd>
</dl>
</dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.analysis.wulff.WulffShape.miller_list">
<span class="sig-name descname"><span class="pre">miller_list</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/wulff.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.wulff.WulffShape.miller_list" title="Link to this definition"></a></dt>
<dd><p>input Miller indices, for hcp in the form of hkil.</p>
<dl class="field-list simple">
<dt class="field-odd">Type<span class="colon">:</span></dt>
<dd class="field-odd"><p>list</p>
</dd>
</dl>
</dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.analysis.wulff.WulffShape.hkl_list">
<span class="sig-name descname"><span class="pre">hkl_list</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/wulff.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.wulff.WulffShape.hkl_list" title="Link to this definition"></a></dt>
<dd><p>Modified Miller indices in the same order as input_miller.</p>
<dl class="field-list simple">
<dt class="field-odd">Type<span class="colon">:</span></dt>
<dd class="field-odd"><p>list</p>
</dd>
</dl>
</dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.analysis.wulff.WulffShape.e_surf_list">
<span class="sig-name descname"><span class="pre">e_surf_list</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/wulff.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.wulff.WulffShape.e_surf_list" title="Link to this definition"></a></dt>
<dd><p>input surface energies in the same order as input_miller.</p>
<dl class="field-list simple">
<dt class="field-odd">Type<span class="colon">:</span></dt>
<dd class="field-odd"><p>list</p>
</dd>
</dl>
</dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.analysis.wulff.WulffShape.lattice">
<span class="sig-name descname"><span class="pre">lattice</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/wulff.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.wulff.WulffShape.lattice" title="Link to this definition"></a></dt>
<dd><p>Input lattice for the conventional unit cell.</p>
<dl class="field-list simple">
<dt class="field-odd">Type<span class="colon">:</span></dt>
<dd class="field-odd"><p><a class="reference internal" href="pymatgen.core.html#pymatgen.core.lattice.Lattice" title="pymatgen.core.lattice.Lattice">Lattice</a></p>
</dd>
</dl>
</dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.analysis.wulff.WulffShape.facets">
<span class="sig-name descname"><span class="pre">facets</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/wulff.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.wulff.WulffShape.facets" title="Link to this definition"></a></dt>
<dd><p>WulffFacet objects considering symmetry.</p>
<dl class="field-list simple">
<dt class="field-odd">Type<span class="colon">:</span></dt>
<dd class="field-odd"><p>list</p>
</dd>
</dl>
</dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.analysis.wulff.WulffShape.dual_cv_simp">
<span class="sig-name descname"><span class="pre">dual_cv_simp</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/wulff.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.wulff.WulffShape.dual_cv_simp" title="Link to this definition"></a></dt>
<dd><p>Simplices from the dual convex hull (dual_pt).</p>
<dl class="field-list simple">
<dt class="field-odd">Type<span class="colon">:</span></dt>
<dd class="field-odd"><p>list</p>
</dd>
</dl>
</dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.analysis.wulff.WulffShape.wulff_pt_list">
<span class="sig-name descname"><span class="pre">wulff_pt_list</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/wulff.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.wulff.WulffShape.wulff_pt_list" title="Link to this definition"></a></dt>
<dd><p>Wulff points.</p>
<dl class="field-list simple">
<dt class="field-odd">Type<span class="colon">:</span></dt>
<dd class="field-odd"><p>list</p>
</dd>
</dl>
</dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.analysis.wulff.WulffShape.wulff_cv_simp">
<span class="sig-name descname"><span class="pre">wulff_cv_simp</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/wulff.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.wulff.WulffShape.wulff_cv_simp" title="Link to this definition"></a></dt>
<dd><p>Simplices from the convex hull of wulff_pt_list.</p>
<dl class="field-list simple">
<dt class="field-odd">Type<span class="colon">:</span></dt>
<dd class="field-odd"><p>list</p>
</dd>
</dl>
</dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.analysis.wulff.WulffShape.on_wulff">
<span class="sig-name descname"><span class="pre">on_wulff</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/wulff.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.wulff.WulffShape.on_wulff" title="Link to this definition"></a></dt>
<dd><p>List for all input_miller, True if on the Wulff shape.</p>
<dl class="field-list simple">
<dt class="field-odd">Type<span class="colon">:</span></dt>
<dd class="field-odd"><p>list</p>
</dd>
</dl>
</dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.analysis.wulff.WulffShape.color_area">
<span class="sig-name descname"><span class="pre">color_area</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/wulff.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.wulff.WulffShape.color_area" title="Link to this definition"></a></dt>
<dd><p>List for all input_miller, total area on the Wulff shape, off_wulff = 0.</p>
<dl class="field-list simple">
<dt class="field-odd">Type<span class="colon">:</span></dt>
<dd class="field-odd"><p>list</p>
</dd>
</dl>
</dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.analysis.wulff.WulffShape.miller_area">
<span class="sig-name descname"><span class="pre">miller_area</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/wulff.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.wulff.WulffShape.miller_area" title="Link to this definition"></a></dt>
<dd><p>Dictionary of Miller indices and their corresponding areas.</p>
<dl class="field-list simple">
<dt class="field-odd">Type<span class="colon">:</span></dt>
<dd class="field-odd"><p>dict</p>
</dd>
</dl>
</dd></dl>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>lattice</strong> – Lattice object of the conventional unit cell</p></li>
<li><p><strong>miller_list</strong> (<em>[</em><em>(</em><em>hkl</em>) – list of hkl or hkil for hcp</p></li>
<li><p><strong>e_surf_list</strong> (<em>[</em><em>float</em><em>]</em>) – list of corresponding surface energies</p></li>
<li><p><strong>symprec</strong> (<em>float</em>) – for reciprocal lattice operation, default is 1e-5.</p></li>
</ul>
</dd>
</dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.analysis.wulff.WulffShape.anisotropy">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">anisotropy</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">float</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/wulff.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.wulff.WulffShape.anisotropy" title="Link to this definition"></a></dt>
<dd><p>Returns:
float: Coefficient of Variation from weighted surface energy. The ideal sphere is 0.</p>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.analysis.wulff.WulffShape.area_fraction_dict">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">area_fraction_dict</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><span class="pre">tuple</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">float</span><span class="p"><span class="pre">]</span></span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/wulff.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.wulff.WulffShape.area_fraction_dict" title="Link to this definition"></a></dt>
<dd><p>Returns:
dict: {hkl: area_hkl/total area on wulff}.</p>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.analysis.wulff.WulffShape.effective_radius">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">effective_radius</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">float</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/wulff.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.wulff.WulffShape.effective_radius" title="Link to this definition"></a></dt>
<dd><p>Radius of the WulffShape (in Angstroms) when the WulffShape is approximated as a sphere.</p>
<dl class="field-list simple">
<dt class="field-odd">Returns<span class="colon">:</span></dt>
<dd class="field-odd"><p>radius R_eff</p>
</dd>
<dt class="field-even">Return type<span class="colon">:</span></dt>
<dd class="field-even"><p>float</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.wulff.WulffShape.get_line_in_facet">
<span class="sig-name descname"><span class="pre">get_line_in_facet</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">facet</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/wulff.py#L315-L340"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.wulff.WulffShape.get_line_in_facet" title="Link to this definition"></a></dt>
<dd><p>Get the sorted pts in a facet used to draw a line.</p>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.wulff.WulffShape.get_plot">
<span class="sig-name descname"><span class="pre">get_plot</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">color_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'PuBu'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">grid_off</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">axis_off</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">show_area</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">alpha</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">off_color</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'red'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">direction</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">bar_pos</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">(0.75,</span> <span class="pre">0.15,</span> <span class="pre">0.05,</span> <span class="pre">0.65)</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">bar_on</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">units_in_JPERM2</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">legend_on</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">aspect_ratio</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">(8,</span> <span class="pre">8)</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">custom_colors</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/wulff.py#L342-L481"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.wulff.WulffShape.get_plot" title="Link to this definition"></a></dt>
<dd><p>Get the Wulff shape plot.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>color_set</strong> – default is ‘PuBu’</p></li>
<li><p><strong>grid_off</strong> (<em>bool</em>) – default is True</p></li>
<li><p><strong>axis_off</strong> (<em>bool</em>) – default is True</p></li>
<li><p><strong>show_area</strong> (<em>bool</em>) – default is False</p></li>
<li><p><strong>alpha</strong> (<em>float</em>) – chosen from 0 to 1 (float), default is 1</p></li>
<li><p><strong>off_color</strong> – Default color for facets not present on the Wulff shape.</p></li>
<li><p><strong>direction</strong> – default is (1, 1, 1)</p></li>
<li><p><strong>bar_pos</strong> – default is [0.75, 0.15, 0.05, 0.65]</p></li>
<li><p><strong>bar_on</strong> (<em>bool</em>) – default is False</p></li>
<li><p><strong>legend_on</strong> (<em>bool</em>) – default is True</p></li>
<li><p><strong>aspect_ratio</strong> – default is (8, 8)</p></li>
<li><p><strong>(</strong><strong>{</strong><strong>(</strong><strong>h</strong> (<em>custom_colors</em>) – [r,g,b,alpha]}): Customize color of each
facet with a dictionary. The key is the corresponding Miller
index and value is the color. Undefined facets will use default
color site. Note: If you decide to set your own colors, it
probably won’t make any sense to have the color bar on.</p></li>
<li><p><strong>k</strong> – [r,g,b,alpha]}): Customize color of each
facet with a dictionary. The key is the corresponding Miller
index and value is the color. Undefined facets will use default
color site. Note: If you decide to set your own colors, it
probably won’t make any sense to have the color bar on.</p></li>
<li><p><strong>l}</strong> – [r,g,b,alpha]}): Customize color of each
facet with a dictionary. The key is the corresponding Miller
index and value is the color. Undefined facets will use default
color site. Note: If you decide to set your own colors, it
probably won’t make any sense to have the color bar on.</p></li>
<li><p><strong>units_in_JPERM2</strong> (<em>bool</em>) – Units of surface energy, defaults to
Joules per square meter (True)</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>3D plot of the Wulff shape.</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>mpl_toolkits.mplot3d.Axes3D</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.wulff.WulffShape.get_plotly">
<span class="sig-name descname"><span class="pre">get_plotly</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">color_set</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'PuBu'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">off_color</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'red'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">alpha</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">custom_colors</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">units_in_JPERM2</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/wulff.py#L483-L617"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.wulff.WulffShape.get_plotly" title="Link to this definition"></a></dt>
<dd><p>Get the Wulff shape as a plotly Figure object.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>color_set</strong> – default is ‘PuBu’</p></li>
<li><p><strong>alpha</strong> (<em>float</em>) – chosen from 0 to 1 (float), default is 1</p></li>
<li><p><strong>off_color</strong> – Default color for facets not present on the Wulff shape.</p></li>
<li><p><strong>(</strong><strong>{</strong><strong>(</strong><strong>h</strong> (<em>custom_colors</em>) – [r,g,b,alpha}): Customize color of each
facet with a dictionary. The key is the corresponding Miller
index and value is the color. Undefined facets will use default
color site. Note: If you decide to set your own colors, it
probably won’t make any sense to have the color bar on.</p></li>
<li><p><strong>k</strong> – [r,g,b,alpha}): Customize color of each
facet with a dictionary. The key is the corresponding Miller
index and value is the color. Undefined facets will use default
color site. Note: If you decide to set your own colors, it
probably won’t make any sense to have the color bar on.</p></li>
<li><p><strong>l}</strong> – [r,g,b,alpha}): Customize color of each
facet with a dictionary. The key is the corresponding Miller
index and value is the color. Undefined facets will use default
color site. Note: If you decide to set your own colors, it
probably won’t make any sense to have the color bar on.</p></li>
<li><p><strong>units_in_JPERM2</strong> (<em>bool</em>) – Units of surface energy, defaults to
Joules per square meter (True)</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>(plotly.graph_objects.Figure)</p>
</dd>
</dl>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.analysis.wulff.WulffShape.miller_area_dict">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">miller_area_dict</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><span class="pre">tuple</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">float</span><span class="p"><span class="pre">]</span></span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/wulff.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.wulff.WulffShape.miller_area_dict" title="Link to this definition"></a></dt>
<dd><p>area_hkl on wulff}.</p>
<dl class="field-list simple">
<dt class="field-odd">Type<span class="colon">:</span></dt>
<dd class="field-odd"><p>{hkl</p>
</dd>
</dl>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.analysis.wulff.WulffShape.miller_energy_dict">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">miller_energy_dict</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">dict</span><span class="p"><span class="pre">[</span></span><span class="pre">tuple</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">float</span><span class="p"><span class="pre">]</span></span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/wulff.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.wulff.WulffShape.miller_energy_dict" title="Link to this definition"></a></dt>
<dd><p>surface energy_hkl}.</p>
<dl class="field-list simple">
<dt class="field-odd">Type<span class="colon">:</span></dt>
<dd class="field-odd"><p>{hkl</p>
</dd>
</dl>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.analysis.wulff.WulffShape.shape_factor">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">shape_factor</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">float</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/wulff.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.wulff.WulffShape.shape_factor" title="Link to this definition"></a></dt>
<dd><p>Determine the critical nucleus size.
A large shape factor indicates great anisotropy.
See Ballufi, R. W., Allen, S. M. & Carter, W. C. Kinetics</p>
<blockquote>
<div><p>of Materials. (John Wiley & Sons, 2005), p.461.</p>
</div></blockquote>
<dl class="field-list simple">
<dt class="field-odd">Returns<span class="colon">:</span></dt>
<dd class="field-odd"><p>Shape factor.</p>
</dd>
<dt class="field-even">Return type<span class="colon">:</span></dt>
<dd class="field-even"><p>float</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.wulff.WulffShape.show">
<span class="sig-name descname"><span class="pre">show</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">*</span></span><span class="n"><span class="pre">args</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/wulff.py#L306-L313"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.wulff.WulffShape.show" title="Link to this definition"></a></dt>
<dd><p>Show the Wulff plot.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>*args</strong> – Passed to get_plot.</p></li>
<li><p><strong>**kwargs</strong> – Passed to get_plot.</p></li>
</ul>
</dd>
</dl>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.analysis.wulff.WulffShape.surface_area">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">surface_area</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">float</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/wulff.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.wulff.WulffShape.surface_area" title="Link to this definition"></a></dt>
<dd><p>Total surface area of Wulff shape.</p>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.analysis.wulff.WulffShape.tot_corner_sites">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">tot_corner_sites</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/wulff.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.wulff.WulffShape.tot_corner_sites" title="Link to this definition"></a></dt>
<dd><p>The number of vertices in the convex hull.
Useful for identifying catalytically active sites.</p>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.analysis.wulff.WulffShape.tot_edges">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">tot_edges</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/wulff.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.wulff.WulffShape.tot_edges" title="Link to this definition"></a></dt>
<dd><p>The number of edges in the convex hull.
Useful for identifying catalytically active sites.</p>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.analysis.wulff.WulffShape.total_surface_energy">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">total_surface_energy</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">float</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/wulff.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.wulff.WulffShape.total_surface_energy" title="Link to this definition"></a></dt>
<dd><p>Total surface energy of the Wulff shape.</p>
<dl class="field-list simple">
<dt class="field-odd">Returns<span class="colon">:</span></dt>
<dd class="field-odd"><p>sum(surface_energy_hkl * area_hkl)</p>
</dd>
<dt class="field-even">Return type<span class="colon">:</span></dt>
<dd class="field-even"><p>float</p>
</dd>
</dl>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.analysis.wulff.WulffShape.volume">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">volume</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">float</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/wulff.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.wulff.WulffShape.volume" title="Link to this definition"></a></dt>
<dd><p>Volume of the Wulff shape.</p>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.analysis.wulff.WulffShape.weighted_surface_energy">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">weighted_surface_energy</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">float</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/wulff.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.wulff.WulffShape.weighted_surface_energy" title="Link to this definition"></a></dt>
<dd><p>Returns:
sum(surface_energy_hkl * area_hkl)/ sum(area_hkl).</p>
</dd></dl>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="pymatgen.analysis.wulff.get_tri_area">
<span class="sig-name descname"><span class="pre">get_tri_area</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">pts</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/wulff.py#L58-L69"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.wulff.get_tri_area" title="Link to this definition"></a></dt>
<dd><p>Given a list of coords for 3 points,
Compute the area of this triangle.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>pts</strong> – [a, b, c] three points</p>
</dd>
</dl>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="pymatgen.analysis.wulff.hkl_tuple_to_str">
<span class="sig-name descname"><span class="pre">hkl_tuple_to_str</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">hkl</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/wulff.py#L47-L55"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.wulff.hkl_tuple_to_str" title="Link to this definition"></a></dt>
<dd><p>Prepare for display on plots “(hkl)” for surfaces.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>hkl</strong> – in the form of [h, k, l] or (h, k, l).</p>
</dd>
</dl>
</dd></dl>
</section>
<section id="module-pymatgen.analysis.xps">
<span id="pymatgen-analysis-xps-module"></span><h2>pymatgen.analysis.xps module<a class="headerlink" href="#module-pymatgen.analysis.xps" title="Link to this heading"></a></h2>
<p>This is a module for XPS analysis. It is modelled after the Galore package (<a class="reference external" href="https://github.com/SMTG-UCL/galore">https://github.com/SMTG-UCL/galore</a>), but
with some modifications for easier analysis from pymatgen itself. Please cite the following original work if you use
this:</p>
<blockquote>
<div><p>Adam J. Jackson, Alex M. Ganose, Anna Regoutz, Russell G. Egdell, David O. Scanlon (2018). Galore: Broadening and
weighting for simulation of photoelectron spectroscopy. Journal of Open Source Software, 3(26), 773,
doi: 10.21105/joss.007733</p>
</div></blockquote>
<p>You may wish to look at the optional dependency galore for more functionality such as plotting and other cross-sections.
Note that the atomic_subshell_photoionization_cross_sections.csv has been reparsed from the original compilation:</p>
<blockquote>
<div><p>Yeh, J. J.; Lindau, I. Atomic Subshell Photoionization Cross Sections and Asymmetry Parameters: 1 ⩽ Z ⩽ 103.
Atomic Data and Nuclear Data Tables 1985, 32 (1), 1-155. <a class="reference external" href="https://doi.org/10.1016/0092-640X(85)90016-6">https://doi.org/10.1016/0092-640X(85)90016-6</a>.</p>
</div></blockquote>
<p>This version contains all detailed information for all orbitals.</p>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.analysis.xps.XPS">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">XPS</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">x</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">NDArray</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">y</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">NDArray</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">*</span></span><span class="n"><span class="pre">args</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/xps.py#L74-L100"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.xps.XPS" title="Link to this definition"></a></dt>
<dd><p>Bases: <a class="reference internal" href="pymatgen.core.html#pymatgen.core.spectrum.Spectrum" title="pymatgen.core.spectrum.Spectrum"><code class="xref py py-class docutils literal notranslate"><span class="pre">Spectrum</span></code></a></p>
<p>An X-ray photoelectron spectra.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>x</strong> (<em>ndarray</em>) – A ndarray of N values.</p></li>
<li><p><strong>y</strong> (<em>ndarray</em>) – A ndarray of N x k values. The first dimension must be
the same as that of x. Each of the k values are interpreted as separate.</p></li>
<li><p><strong>*args</strong> – All subclasses should provide args other than x and y
when calling super, e.g. super().__init__(
x, y, arg1, arg2, kwarg1=val1, ..). This guarantees the +, -, <a href="#id1"><span class="problematic" id="id2">*</span></a>,
etc. operators work properly.</p></li>
<li><p><strong>**kwargs</strong> – Same as that for <a href="#id3"><span class="problematic" id="id4">*</span></a>args.</p></li>
</ul>
</dd>
</dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.analysis.xps.XPS.XLABEL">
<span class="sig-name descname"><span class="pre">XLABEL</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">'Binding</span> <span class="pre">Energy</span> <span class="pre">(eV)'</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/xps.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.xps.XPS.XLABEL" title="Link to this definition"></a></dt>
<dd></dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.analysis.xps.XPS.YLABEL">
<span class="sig-name descname"><span class="pre">YLABEL</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">'Intensity'</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/xps.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.xps.XPS.YLABEL" title="Link to this definition"></a></dt>
<dd></dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.xps.XPS.from_dos">
<em class="property"><span class="pre">classmethod</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">from_dos</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">dos</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="pymatgen.electronic_structure.html#pymatgen.electronic_structure.dos.CompleteDos" title="pymatgen.electronic_structure.dos.CompleteDos"><span class="pre">CompleteDos</span></a></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">Self</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/xps.py#L80-L100"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.xps.XPS.from_dos" title="Link to this definition"></a></dt>
<dd><dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>dos</strong> – CompleteDos object with project element-orbital DOS.</p></li>
<li><p><strong>Vasprun.get_complete_dos.</strong> (<em>Can be obtained from</em>)</p></li>
<li><p><strong>sigma</strong> – Smearing for Gaussian.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>X-ray photoelectron spectrum.</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p><a class="reference internal" href="#pymatgen.analysis.xps.XPS" title="pymatgen.analysis.xps.XPS">XPS</a></p>
</dd>
</dl>
</dd></dl>
</dd></dl>
</section>
</section>
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