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<h1>Source code for pymatgen</h1><div class="highlight"><pre>
<span></span><span class="c1"># coding: utf-8</span>
<span class="c1"># Copyright (c) Pymatgen Development Team.</span>
<span class="c1"># Distributed under the terms of the MIT License.</span>
<span class="sd">"""</span>
<span class="sd">Pymatgen (Python Materials Genomics) is a robust, open-source Python library</span>
<span class="sd">for materials analysis. This is the root package.</span>
<span class="sd">"""</span>
<span class="c1"># Useful aliases for commonly used objects and modules.</span>
<span class="c1"># Allows from pymatgen import <class> for quick usage.</span>
<span class="kn">import</span> <span class="nn">os</span>
<span class="kn">import</span> <span class="nn">warnings</span>
<span class="kn">import</span> <span class="nn">ruamel.yaml</span> <span class="k">as</span> <span class="nn">yaml</span>
<span class="kn">from</span> <span class="nn">fnmatch</span> <span class="kn">import</span> <span class="n">fnmatch</span>
<span class="n">__author__</span> <span class="o">=</span> <span class="s2">"Pymatgen Development Team"</span>
<span class="n">__email__</span> <span class="o">=</span> <span class="s2">"pymatgen@googlegroups.com"</span>
<span class="n">__maintainer__</span> <span class="o">=</span> <span class="s2">"Shyue Ping Ong"</span>
<span class="n">__maintainer_email__</span> <span class="o">=</span> <span class="s2">"shyuep@gmail.com"</span>
<span class="n">__version__</span> <span class="o">=</span> <span class="s2">"2020.7.3"</span>
<span class="n">SETTINGS_FILE</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">expanduser</span><span class="p">(</span><span class="s2">"~"</span><span class="p">),</span> <span class="s2">".pmgrc.yaml"</span><span class="p">)</span>
<span class="k">def</span> <span class="nf">_load_pmg_settings</span><span class="p">():</span>
<span class="k">try</span><span class="p">:</span>
<span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">SETTINGS_FILE</span><span class="p">,</span> <span class="s2">"rt"</span><span class="p">)</span> <span class="k">as</span> <span class="n">f</span><span class="p">:</span>
<span class="n">d</span> <span class="o">=</span> <span class="n">yaml</span><span class="o">.</span><span class="n">safe_load</span><span class="p">(</span><span class="n">f</span><span class="p">)</span>
<span class="k">except</span> <span class="ne">IOError</span><span class="p">:</span>
<span class="c1"># If there are any errors, default to using environment variables</span>
<span class="c1"># if present.</span>
<span class="n">d</span> <span class="o">=</span> <span class="p">{}</span>
<span class="k">for</span> <span class="n">k</span><span class="p">,</span> <span class="n">v</span> <span class="ow">in</span> <span class="n">os</span><span class="o">.</span><span class="n">environ</span><span class="o">.</span><span class="n">items</span><span class="p">():</span>
<span class="k">if</span> <span class="n">k</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="s2">"PMG_"</span><span class="p">):</span>
<span class="n">d</span><span class="p">[</span><span class="n">k</span><span class="p">]</span> <span class="o">=</span> <span class="n">v</span>
<span class="k">elif</span> <span class="n">k</span> <span class="ow">in</span> <span class="p">[</span><span class="s2">"VASP_PSP_DIR"</span><span class="p">,</span> <span class="s2">"MAPI_KEY"</span><span class="p">,</span> <span class="s2">"DEFAULT_FUNCTIONAL"</span><span class="p">]:</span>
<span class="n">d</span><span class="p">[</span><span class="s2">"PMG_"</span> <span class="o">+</span> <span class="n">k</span><span class="p">]</span> <span class="o">=</span> <span class="n">v</span>
<span class="n">d</span> <span class="o">=</span> <span class="n">d</span> <span class="ow">or</span> <span class="p">{}</span>
<span class="k">return</span> <span class="nb">dict</span><span class="p">(</span><span class="n">d</span><span class="p">)</span>
<span class="n">SETTINGS</span> <span class="o">=</span> <span class="n">_load_pmg_settings</span><span class="p">()</span>
<span class="kn">from</span> <span class="nn">.core.periodic_table</span> <span class="kn">import</span> <span class="n">Element</span><span class="p">,</span> <span class="n">Specie</span><span class="p">,</span> <span class="n">DummySpecie</span>
<span class="kn">from</span> <span class="nn">.core.composition</span> <span class="kn">import</span> <span class="n">Composition</span>
<span class="kn">from</span> <span class="nn">.core.structure</span> <span class="kn">import</span> <span class="n">Structure</span><span class="p">,</span> <span class="n">IStructure</span><span class="p">,</span> <span class="n">Molecule</span><span class="p">,</span> <span class="n">IMolecule</span>
<span class="kn">from</span> <span class="nn">.core.lattice</span> <span class="kn">import</span> <span class="n">Lattice</span>
<span class="kn">from</span> <span class="nn">.core.sites</span> <span class="kn">import</span> <span class="n">Site</span><span class="p">,</span> <span class="n">PeriodicSite</span>
<span class="kn">from</span> <span class="nn">.core.operations</span> <span class="kn">import</span> <span class="n">SymmOp</span>
<span class="kn">from</span> <span class="nn">.core.units</span> <span class="kn">import</span> <span class="n">Unit</span><span class="p">,</span> <span class="n">FloatWithUnit</span><span class="p">,</span> <span class="n">ArrayWithUnit</span>
<span class="kn">from</span> <span class="nn">.electronic_structure.core</span> <span class="kn">import</span> <span class="n">Spin</span><span class="p">,</span> <span class="n">Orbital</span>
<span class="kn">from</span> <span class="nn">.ext.matproj</span> <span class="kn">import</span> <span class="n">MPRester</span>
<span class="kn">from</span> <span class="nn">monty.json</span> <span class="kn">import</span> <span class="n">MontyEncoder</span><span class="p">,</span> <span class="n">MontyDecoder</span><span class="p">,</span> <span class="n">MSONable</span>
<div class="viewcode-block" id="get_structure_from_mp"><a class="viewcode-back" href="../pymatgen.html#pymatgen.get_structure_from_mp">[docs]</a><span class="k">def</span> <span class="nf">get_structure_from_mp</span><span class="p">(</span><span class="n">formula</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Convenience method to get a crystal from the Materials Project database via</span>
<span class="sd"> the API. Requires PMG_MAPI_KEY to be set.</span>
<span class="sd"> Args:</span>
<span class="sd"> formula (str): A formula</span>
<span class="sd"> Returns:</span>
<span class="sd"> (Structure) The lowest energy structure in Materials Project with that</span>
<span class="sd"> formula.</span>
<span class="sd"> """</span>
<span class="n">m</span> <span class="o">=</span> <span class="n">MPRester</span><span class="p">()</span>
<span class="n">entries</span> <span class="o">=</span> <span class="n">m</span><span class="o">.</span><span class="n">get_entries</span><span class="p">(</span><span class="n">formula</span><span class="p">,</span> <span class="n">inc_structure</span><span class="o">=</span><span class="s2">"final"</span><span class="p">)</span>
<span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">entries</span><span class="p">)</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
<span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s2">"No structure with formula </span><span class="si">%s</span><span class="s2"> in Materials Project!"</span> <span class="o">%</span>
<span class="n">formula</span><span class="p">)</span>
<span class="k">elif</span> <span class="nb">len</span><span class="p">(</span><span class="n">entries</span><span class="p">)</span> <span class="o">></span> <span class="mi">1</span><span class="p">:</span>
<span class="n">warnings</span><span class="o">.</span><span class="n">warn</span><span class="p">(</span><span class="s2">"</span><span class="si">%d</span><span class="s2"> structures with formula </span><span class="si">%s</span><span class="s2"> found in Materials "</span>
<span class="s2">"Project. The lowest energy structure will be returned."</span> <span class="o">%</span>
<span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">entries</span><span class="p">),</span> <span class="n">formula</span><span class="p">))</span>
<span class="k">return</span> <span class="nb">min</span><span class="p">(</span><span class="n">entries</span><span class="p">,</span> <span class="n">key</span><span class="o">=</span><span class="k">lambda</span> <span class="n">e</span><span class="p">:</span> <span class="n">e</span><span class="o">.</span><span class="n">energy_per_atom</span><span class="p">)</span><span class="o">.</span><span class="n">structure</span></div>
<div class="viewcode-block" id="loadfn"><a class="viewcode-back" href="../pymatgen.html#pymatgen.loadfn">[docs]</a><span class="k">def</span> <span class="nf">loadfn</span><span class="p">(</span><span class="n">fname</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Convenience method to perform quick loading of data from a filename. The</span>
<span class="sd"> type of object returned depends the file type.</span>
<span class="sd"> Args:</span>
<span class="sd"> fname (string): A filename.</span>
<span class="sd"> Returns:</span>
<span class="sd"> Note that fname is matched using unix-style, i.e., fnmatch.</span>
<span class="sd"> (Structure) if *POSCAR*/*CONTCAR*/*.cif</span>
<span class="sd"> (Vasprun) *vasprun*</span>
<span class="sd"> (obj) if *json* (passthrough to monty.serialization.loadfn)</span>
<span class="sd"> """</span>
<span class="k">if</span> <span class="p">(</span><span class="n">fnmatch</span><span class="p">(</span><span class="n">fname</span><span class="p">,</span> <span class="s2">"*POSCAR*"</span><span class="p">)</span> <span class="ow">or</span> <span class="n">fnmatch</span><span class="p">(</span><span class="n">fname</span><span class="p">,</span> <span class="s2">"*CONTCAR*"</span><span class="p">)</span> <span class="ow">or</span>
<span class="s2">".cif"</span> <span class="ow">in</span> <span class="n">fname</span><span class="o">.</span><span class="n">lower</span><span class="p">())</span> <span class="ow">or</span> <span class="n">fnmatch</span><span class="p">(</span><span class="n">fname</span><span class="p">,</span> <span class="s2">"*.vasp"</span><span class="p">):</span>
<span class="k">return</span> <span class="n">Structure</span><span class="o">.</span><span class="n">from_file</span><span class="p">(</span><span class="n">fname</span><span class="p">)</span>
<span class="k">elif</span> <span class="n">fnmatch</span><span class="p">(</span><span class="n">fname</span><span class="p">,</span> <span class="s2">"*vasprun*"</span><span class="p">):</span>
<span class="kn">from</span> <span class="nn">pymatgen.io.vasp</span> <span class="kn">import</span> <span class="n">Vasprun</span>
<span class="k">return</span> <span class="n">Vasprun</span><span class="p">(</span><span class="n">fname</span><span class="p">)</span>
<span class="k">elif</span> <span class="n">fnmatch</span><span class="p">(</span><span class="n">fname</span><span class="p">,</span> <span class="s2">"*.json*"</span><span class="p">):</span>
<span class="kn">from</span> <span class="nn">monty.serialization</span> <span class="kn">import</span> <span class="n">loadfn</span>
<span class="k">return</span> <span class="n">loadfn</span><span class="p">(</span><span class="n">fname</span><span class="p">)</span></div>
</pre></div>
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