from __future__ import annotations import os import pytest from pymatgen.io.qchem.sets import ( ForceSet, FreqSet, OptSet, PESScanSet, QChemDictSet, QCInput, SinglePointSet, TransitionStateSet, ) from pymatgen.util.testing import TEST_FILES_DIR, MatSciTest __author__ = "Samuel Blau, Brandon Wood, Shyam Dwaraknath, Evan Spotte-Smith, Ryan Kingsbury" __copyright__ = "Copyright 2018-2022, The Materials Project" __version__ = "0.1" __maintainer__ = "Samuel Blau" __email__ = "samblau1@gmail.com" TEST_DIR = f"{TEST_FILES_DIR}/io/qchem/new_qchem_files" class TestQChemDictSet(MatSciTest): def test_init(self): test_molecule = QCInput.from_file(f"{TEST_DIR}/pcm.qin").molecule test_dict_set = QChemDictSet( molecule=test_molecule, job_type="opt", basis_set="6-31G*", scf_algorithm="diis", ) ref_dict = { "job_type": "opt", "gen_scfman": "true", "basis": "6-31g*", "max_scf_cycles": "100", "method": "wb97mv", "scf_algorithm": "diis", "xc_grid": "3", "thresh": "14", "s2thresh": "16", "geom_opt_max_cycles": "200", "symmetry": "false", "sym_ignore": "true", "resp_charges": "true", } assert test_dict_set.rem == ref_dict assert test_dict_set.pcm == {} assert test_dict_set.solvent == {} assert test_dict_set.smx == {} assert test_dict_set.molecule == test_molecule def test_full_init(self): test_molecule = QCInput.from_file(f"{TEST_DIR}/pcm.qin").molecule test_dict_set = QChemDictSet( molecule=test_molecule, job_type="opt", basis_set="6-31g*", scf_algorithm="diis", dft_rung=2, pcm_dielectric=10.0, max_scf_cycles=35, ) ref_dict = { "job_type": "opt", "gen_scfman": "true", "basis": "6-31g*", "max_scf_cycles": "35", "method": "b97-d3", "dft_d": "d3_bj", "geom_opt_max_cycles": "200", "scf_algorithm": "diis", "xc_grid": "3", "thresh": "14", "s2thresh": "16", "solvent_method": "pcm", "symmetry": "false", "sym_ignore": "true", "resp_charges": "true", } assert test_dict_set.rem == ref_dict ref_dict = { "heavypoints": "194", "hpoints": "194", "radii": "uff", "theory": "cpcm", "vdwscale": "1.1", } assert test_dict_set.pcm == ref_dict assert test_dict_set.solvent == {"dielectric": "10.0"} assert test_dict_set.molecule == test_molecule test_dict_set = QChemDictSet( molecule=test_molecule, job_type="opt", basis_set="6-31g*", scf_algorithm="diis", dft_rung=2, smd_solvent="water", max_scf_cycles=35, ) ref_dict = { "job_type": "opt", "gen_scfman": "true", "basis": "6-31g*", "max_scf_cycles": "35", "method": "b97-d3", "dft_d": "d3_bj", "geom_opt_max_cycles": "200", "scf_algorithm": "diis", "xc_grid": "3", "thresh": "14", "s2thresh": "16", "solvent_method": "smd", "ideriv": "1", "symmetry": "false", "sym_ignore": "true", "resp_charges": "true", } assert test_dict_set.rem == ref_dict assert test_dict_set.smx == {"solvent": "water"} def test_overwrite_input(self): test_molecule = QCInput.from_file(f"{TEST_DIR}/pcm.qin").molecule overwrite_inputs = { "rem": { "method": "b3lyp", "basis": "6-31g*", "thresh": "10", "s2thresh": "12", "xc_grid": "000150000302", } } test_opt_set = OptSet(molecule=test_molecule, overwrite_inputs=overwrite_inputs) act_rem = { "job_type": "opt", "gen_scfman": "true", "basis": "6-31g*", "max_scf_cycles": "100", "method": "b3lyp", "scf_algorithm": "diis", "xc_grid": "000150000302", "geom_opt_max_cycles": "200", "thresh": "10", "s2thresh": "12", "symmetry": "false", "sym_ignore": "true", "resp_charges": "true", } assert act_rem == test_opt_set.rem def test_double_solvation(self): test_molecule = QCInput.from_file(f"{TEST_DIR}/pcm.qin").molecule raised_error = False dict_set = None try: dict_set = QChemDictSet( molecule=test_molecule, job_type="opt", basis_set="6-31g*", scf_algorithm="diis", dft_rung=1, pcm_dielectric=10.0, smd_solvent="water", max_scf_cycles=35, ) except ValueError: raised_error = True assert raised_error assert dict_set is None def test_pcm_write(self): test_molecule = QCInput.from_file(f"{TEST_DIR}/pcm.qin").molecule dict_set = QChemDictSet( molecule=test_molecule, job_type="opt", basis_set="6-31g*", scf_algorithm="diis", dft_rung=5, pcm_dielectric=10.0, max_scf_cycles=35, ) dict_set.write(f"{self.tmp_path}/mol.qin") test_dict = QCInput.from_file(f"{self.tmp_path}/mol.qin").as_dict() rem = { "job_type": "opt", "basis": "6-31G*", "max_scf_cycles": "35", "method": "wb97m(2)", "geom_opt_max_cycles": "200", "gen_scfman": "true", "scf_algorithm": "diis", "xc_grid": "3", "thresh": "14", "s2thresh": "16", "solvent_method": "pcm", "symmetry": "false", "sym_ignore": "true", "resp_charges": "true", } pcm = { "heavypoints": "194", "hpoints": "194", "radii": "uff", "theory": "cpcm", "vdwscale": "1.1", } qc_input = QCInput(molecule=test_molecule, rem=rem, pcm=pcm, solvent={"dielectric": 10.0}) for k, v in qc_input.as_dict().items(): assert v == test_dict[k] def test_isosvp_write(self): """Also tests overwrite_inputs with a RHOISO value.""" test_molecule = QCInput.from_file(f"{TEST_DIR}/pcm.qin").molecule dict_set = QChemDictSet( molecule=test_molecule, job_type="opt", basis_set="def2-SVPD", scf_algorithm="diis", dft_rung=4, isosvp_dielectric=62, max_scf_cycles=35, overwrite_inputs={"svp": {"RHOISO": 0.0009}}, ) dict_set.write(f"{self.tmp_path}/mol.qin") test_dict = QCInput.from_file(f"{self.tmp_path}/mol.qin").as_dict() rem = { "job_type": "opt", "basis": "def2-SVPD", "max_scf_cycles": "35", "method": "wb97mv", "geom_opt_max_cycles": "200", "gen_scfman": "false", "scf_algorithm": "diis", "xc_grid": "3", "thresh": "14", "s2thresh": "16", "solvent_method": "isosvp", "symmetry": "false", "sym_ignore": "true", "resp_charges": "true", } qc_input = QCInput( molecule=test_molecule, rem=rem, pcm_nonels=None, svp={ "RHOISO": 0.0009, "DIELST": 62, "NPTLEB": 1202, "ITRNGR": 2, "IROTGR": 2, }, ) for k, v in qc_input.as_dict().items(): assert v == test_dict[k] def test_smd_write(self): test_molecule = QCInput.from_file(f"{TEST_DIR}/pcm.qin").molecule dict_set = QChemDictSet( molecule=test_molecule, job_type="opt", basis_set="6-31g*", scf_algorithm="diis", dft_rung=4, smd_solvent="water", max_scf_cycles=35, ) dict_set.write(f"{self.tmp_path}/mol.qin") test_dict = QCInput.from_file(f"{self.tmp_path}/mol.qin").as_dict() rem = { "job_type": "opt", "basis": "6-31G*", "max_scf_cycles": "35", "method": "wb97mv", "geom_opt_max_cycles": "200", "gen_scfman": "true", "scf_algorithm": "diis", "xc_grid": "3", "thresh": "14", "s2thresh": "16", "solvent_method": "smd", "ideriv": "1", "symmetry": "false", "sym_ignore": "true", "resp_charges": "true", } qc_input = QCInput(molecule=test_molecule, rem=rem, smx={"solvent": "water"}) for k, v in qc_input.as_dict().items(): assert v == test_dict[k] def test_cmirs_write(self): """Also tests overwrite_inputs with a RHOISO value.""" test_molecule = QCInput.from_file(f"{TEST_DIR}/pcm.qin").molecule dict_set = QChemDictSet( molecule=test_molecule, job_type="opt", basis_set="def2-SVPD", scf_algorithm="diis", dft_rung=4, cmirs_solvent="water", max_scf_cycles=35, overwrite_inputs={"svp": {"RHOISO": 0.0005}}, ) dict_set.write(f"{self.tmp_path}/mol.qin") test_dict = QCInput.from_file(f"{self.tmp_path}/mol.qin").as_dict() rem = { "job_type": "opt", "basis": "def2-SVPD", "max_scf_cycles": "35", "method": "wb97mv", "geom_opt_max_cycles": "200", "gen_scfman": "false", "scf_algorithm": "diis", "xc_grid": "3", "thresh": "14", "s2thresh": "16", "solvent_method": "isosvp", "symmetry": "false", "sym_ignore": "true", "resp_charges": "true", } pcm_nonels = { "A": -0.006496, "B": 0.050833, "C": -566.7, "D": -30.503, "gamma": 3.2, "solvrho": 0.05, "Delta": 7, "GauLag_N": 40, } qc_input = QCInput( molecule=test_molecule, rem=rem, pcm_nonels=pcm_nonels, svp={ "RHOISO": 0.0005, "DIELST": 78.39, "NPTLEB": 1202, "ITRNGR": 2, "IROTGR": 2, "IPNRF": 1, "IDEFESR": 1, }, ) for k, v in qc_input.as_dict().items(): assert v == test_dict[k] def test_custom_smd_write(self): test_molecule = QCInput.from_file(f"{TEST_DIR}/pcm.qin").molecule dict_set = QChemDictSet( molecule=test_molecule, job_type="opt", basis_set="6-31g*", scf_algorithm="diis", dft_rung=4, smd_solvent="custom", custom_smd="90.00,1.415,0.00,0.735,20.2,0.00,0.00", max_scf_cycles=35, ) dict_set.write(f"{self.tmp_path}/mol.qin") test_dict = QCInput.from_file(f"{self.tmp_path}/mol.qin").as_dict() rem = { "job_type": "opt", "basis": "6-31G*", "max_scf_cycles": "35", "method": "wb97mv", "geom_opt_max_cycles": "200", "gen_scfman": "true", "scf_algorithm": "diis", "xc_grid": "3", "thresh": "14", "s2thresh": "16", "solvent_method": "smd", "ideriv": "1", "symmetry": "false", "sym_ignore": "true", "resp_charges": "true", } qc_input = QCInput(molecule=test_molecule, rem=rem, smx={"solvent": "other"}) for k, v in qc_input.as_dict().items(): assert v == test_dict[k] with open("solvent_data", encoding="utf-8") as sd: lines = sd.readlines() assert lines[0] == "90.00,1.415,0.00,0.735,20.2,0.00,0.00" os.remove("solvent_data") def test_output_wavefunction(self): """Test function for outputting *.wfn files""" test_molecule = QCInput.from_file(f"{TEST_DIR}/pcm.qin").molecule test_dict_set = QChemDictSet( molecule=test_molecule, job_type="opt", basis_set="6-31G*", scf_algorithm="diis", output_wavefunction=True, ) assert test_dict_set.rem["write_wfn"] == "wavefunction" def test_solvation_warnings(self): """Test warnings / errors resulting from nonsensical overwrite_inputs.""" test_molecule = QCInput.from_file(f"{TEST_DIR}/pcm.qin").molecule with pytest.raises(RuntimeError, match="CMIRS is only parameterized"): QChemDictSet( molecule=test_molecule, job_type="opt", basis_set="def2-SVPD", scf_algorithm="diis", dft_rung=5, cmirs_solvent="water", max_scf_cycles=35, overwrite_inputs={"svp": {"RHOISO": 0.0007}}, ) with pytest.warns(UserWarning, match="Setting IDEFESR=0"): QChemDictSet( molecule=test_molecule, job_type="opt", basis_set="def2-SVPD", scf_algorithm="diis", dft_rung=5, cmirs_solvent="water", max_scf_cycles=35, overwrite_inputs={"svp": {"IDEFESR": 0}}, ) with pytest.warns(UserWarning, match="Setting IDEFESR=1"): QChemDictSet( molecule=test_molecule, job_type="opt", basis_set="def2-SVPD", scf_algorithm="diis", dft_rung=5, isosvp_dielectric=78, max_scf_cycles=35, overwrite_inputs={"svp": {"IDEFESR": 1}}, ) with pytest.warns(UserWarning, match="Setting DIELST"): QChemDictSet( molecule=test_molecule, job_type="opt", basis_set="def2-SVPD", scf_algorithm="diis", dft_rung=5, pcm_dielectric=78, max_scf_cycles=35, overwrite_inputs={"svp": {"DIELST": 67}}, ) with pytest.warns(UserWarning, match="The solvent section will be ignored"): QChemDictSet( molecule=test_molecule, job_type="opt", basis_set="def2-SVPD", scf_algorithm="diis", dft_rung=5, isosvp_dielectric=78, max_scf_cycles=35, overwrite_inputs={"solvent": {"dielectric": 67}}, ) class TestSinglePointSet(MatSciTest): def test_init(self): test_molecule = QCInput.from_file(f"{TEST_DIR}/pcm.qin").molecule test_sp_set = SinglePointSet(molecule=test_molecule) ref_dict = { "job_type": "sp", "gen_scfman": "true", "basis": "def2-tzvpd", "max_scf_cycles": "100", "method": "wb97mv", "scf_algorithm": "diis", "xc_grid": "3", "thresh": "14", "s2thresh": "16", "symmetry": "false", "sym_ignore": "true", "resp_charges": "true", } assert test_sp_set.rem == ref_dict assert test_sp_set.pcm == {} assert test_sp_set.solvent == {} assert test_sp_set.molecule == test_molecule def test_scf_extra_print(self): test_molecule = QCInput.from_file(f"{TEST_DIR}/pcm.qin").molecule test_sp_set = SinglePointSet(molecule=test_molecule, extra_scf_print=True) ref_dict = { "job_type": "sp", "gen_scfman": "true", "basis": "def2-tzvpd", "max_scf_cycles": "100", "method": "wb97mv", "scf_algorithm": "diis", "xc_grid": "3", "thresh": "14", "s2thresh": "16", "symmetry": "false", "sym_ignore": "true", "resp_charges": "true", "scf_convergence": "8", "scf_final_print": "3", } assert test_sp_set.rem == ref_dict assert test_sp_set.pcm == {} assert test_sp_set.solvent == {} assert test_sp_set.molecule == test_molecule def test_pcm_init(self): test_molecule = QCInput.from_file(f"{TEST_DIR}/pcm.qin").molecule test_sp_set = SinglePointSet(molecule=test_molecule, pcm_dielectric=10.0) ref_dict = { "job_type": "sp", "gen_scfman": "true", "basis": "def2-tzvpd", "max_scf_cycles": "100", "method": "wb97mv", "scf_algorithm": "diis", "xc_grid": "3", "thresh": "14", "s2thresh": "16", "solvent_method": "pcm", "symmetry": "false", "sym_ignore": "true", "resp_charges": "true", } assert test_sp_set.rem == ref_dict ref_dict = { "heavypoints": "194", "hpoints": "194", "radii": "uff", "theory": "cpcm", "vdwscale": "1.1", } assert test_sp_set.pcm == ref_dict assert test_sp_set.solvent == {"dielectric": "10.0"} assert test_sp_set.molecule == test_molecule def test_isosvp_init(self): test_molecule = QCInput.from_file(f"{TEST_DIR}/pcm.qin").molecule test_sp_set = SinglePointSet(molecule=test_molecule, isosvp_dielectric=10.0) ref_dict = { "job_type": "sp", "gen_scfman": "false", "basis": "def2-tzvpd", "max_scf_cycles": "100", "method": "wb97mv", "scf_algorithm": "diis", "xc_grid": "3", "thresh": "14", "s2thresh": "16", "solvent_method": "isosvp", "symmetry": "false", "sym_ignore": "true", "resp_charges": "true", } assert test_sp_set.rem == ref_dict ref_dict = { "dielst": "10.0", "rhoiso": "0.001", "nptleb": "1202", "itrngr": "2", "irotgr": "2", } assert test_sp_set.svp == ref_dict assert test_sp_set.molecule == test_molecule def test_smd_init(self): test_molecule = QCInput.from_file(f"{TEST_DIR}/pcm.qin").molecule test_sp_set = SinglePointSet(molecule=test_molecule, smd_solvent="water") ref_dict = { "job_type": "sp", "gen_scfman": "true", "basis": "def2-tzvpd", "max_scf_cycles": "100", "method": "wb97mv", "scf_algorithm": "diis", "xc_grid": "3", "thresh": "14", "s2thresh": "16", "solvent_method": "smd", "ideriv": "1", "symmetry": "false", "sym_ignore": "true", "resp_charges": "true", } assert test_sp_set.rem == ref_dict assert test_sp_set.smx == {"solvent": "water"} assert test_sp_set.molecule == test_molecule def test_cmirs_init(self): test_molecule = QCInput.from_file(f"{TEST_DIR}/pcm.qin").molecule test_sp_set = SinglePointSet( molecule=test_molecule, cmirs_solvent="benzene", overwrite_inputs={"svp": {"RHOISO": 0.0005}}, ) ref_dict = { "job_type": "sp", "gen_scfman": "false", "basis": "def2-tzvpd", "max_scf_cycles": "100", "method": "wb97mv", "scf_algorithm": "diis", "xc_grid": "3", "thresh": "14", "s2thresh": "16", "solvent_method": "isosvp", "symmetry": "false", "sym_ignore": "true", "resp_charges": "true", } assert test_sp_set.rem == ref_dict ref_dict = { "dielst": "2.28", "rhoiso": "0.0005", "nptleb": "1202", "itrngr": "2", "irotgr": "2", "ipnrf": "1", "idefesr": "1", } assert test_sp_set.svp == ref_dict ref_dict = { "a": "-0.00572", "b": "0.01116", "c": None, "d": None, "gamma": None, "solvrho": "0.0421", "gaulag_n": "40", "delta": "7", } assert test_sp_set.pcm_nonels == ref_dict assert test_sp_set.molecule == test_molecule def test_plots_init(self): test_molecule = QCInput.from_file(f"{TEST_DIR}/pcm.qin").molecule test_sp_set = SinglePointSet(molecule=test_molecule, smd_solvent="water", plot_cubes=True) ref_dict = { "job_type": "sp", "gen_scfman": "true", "basis": "def2-tzvpd", "max_scf_cycles": "100", "method": "wb97mv", "scf_algorithm": "diis", "xc_grid": "3", "thresh": "14", "s2thresh": "16", "solvent_method": "smd", "ideriv": "1", "symmetry": "false", "sym_ignore": "true", "resp_charges": "true", "plots": "true", "make_cube_files": "true", } assert test_sp_set.rem == ref_dict assert test_sp_set.plots == {"grid_spacing": "0.05", "total_density": "0"} assert test_sp_set.smx == {"solvent": "water"} assert test_sp_set.molecule == test_molecule class TestOptSet(MatSciTest): def test_init(self): test_molecule = QCInput.from_file(f"{TEST_DIR}/pcm.qin").molecule test_opt_set = OptSet(molecule=test_molecule) ref_dict = { "job_type": "opt", "gen_scfman": "true", "basis": "def2-svpd", "max_scf_cycles": "100", "method": "wb97mv", "scf_algorithm": "diis", "xc_grid": "3", "thresh": "14", "s2thresh": "16", "geom_opt_max_cycles": "200", "symmetry": "false", "sym_ignore": "true", "resp_charges": "true", } assert test_opt_set.rem == ref_dict assert test_opt_set.pcm == {} assert test_opt_set.solvent == {} assert test_opt_set.smx == {} assert test_opt_set.molecule == test_molecule def test_pcm_init(self): test_molecule = QCInput.from_file(f"{TEST_DIR}/pcm.qin").molecule test_opt_set = OptSet(molecule=test_molecule, pcm_dielectric=10.0) ref_dict = { "job_type": "opt", "gen_scfman": "true", "basis": "def2-svpd", "max_scf_cycles": "100", "method": "wb97mv", "geom_opt_max_cycles": "200", "scf_algorithm": "diis", "xc_grid": "3", "thresh": "14", "s2thresh": "16", "solvent_method": "pcm", "symmetry": "false", "sym_ignore": "true", "resp_charges": "true", } assert test_opt_set.rem == ref_dict ref_dict = { "heavypoints": "194", "hpoints": "194", "radii": "uff", "theory": "cpcm", "vdwscale": "1.1", } assert test_opt_set.pcm == ref_dict assert test_opt_set.solvent == {"dielectric": "10.0"} assert test_opt_set.molecule == test_molecule def test_smd_init(self): test_molecule = QCInput.from_file(f"{TEST_DIR}/pcm.qin").molecule test_opt_set = OptSet(molecule=test_molecule, smd_solvent="water") ref_dict = { "job_type": "opt", "gen_scfman": "true", "basis": "def2-svpd", "max_scf_cycles": "100", "method": "wb97mv", "geom_opt_max_cycles": "200", "scf_algorithm": "diis", "xc_grid": "3", "thresh": "14", "s2thresh": "16", "solvent_method": "smd", "ideriv": "1", "symmetry": "false", "sym_ignore": "true", "resp_charges": "true", } assert test_opt_set.rem == ref_dict assert test_opt_set.smx == {"solvent": "water"} assert test_opt_set.molecule == test_molecule def test_overwrite_opt_input(self): test_molecule = QCInput.from_file(f"{TEST_DIR}/pcm.qin").molecule overwrite_inputs = {"opt": {"FIXED": ["1 XYZ", "2 XY"]}} test_opt_set = OptSet(molecule=test_molecule, overwrite_inputs=overwrite_inputs) act_opt = {"fixed": ["1 XYZ", "2 XY"]} assert act_opt == test_opt_set.opt def test_nbo_init(self): test_molecule = QCInput.from_file(f"{TEST_DIR}/pcm.qin").molecule test_opt_set = OptSet(molecule=test_molecule, nbo_params={}) ref_dict = { "job_type": "opt", "gen_scfman": "true", "geom_opt_max_cycles": "200", "basis": "def2-svpd", "max_scf_cycles": "100", "method": "wb97mv", "scf_algorithm": "diis", "xc_grid": "3", "thresh": "14", "s2thresh": "16", "symmetry": "false", "sym_ignore": "true", "resp_charges": "true", "nbo": "true", } assert test_opt_set.rem == ref_dict assert test_opt_set.nbo == {} assert test_opt_set.molecule == test_molecule def test_v5_vs_v6(self): test_molecule = QCInput.from_file(f"{TEST_DIR}/pcm.qin").molecule v5_opt_set = OptSet(molecule=test_molecule, qchem_version=5, basis_set="def2-tzvpd", geom_opt={}) ref_dict = { "job_type": "opt", "gen_scfman": "true", "geom_opt_max_cycles": "200", "basis": "def2-tzvpd", "max_scf_cycles": "100", "method": "wb97mv", "scf_algorithm": "diis", "xc_grid": "3", "thresh": "14", "s2thresh": "16", "symmetry": "false", "sym_ignore": "true", "resp_charges": "true", "geom_opt2": "3", } assert v5_opt_set.rem == ref_dict assert v5_opt_set.geom_opt == {"maxiter": "200"} assert v5_opt_set.molecule == test_molecule v6_opt_set = OptSet(molecule=test_molecule, qchem_version=6, basis_set="def2-tzvpd", geom_opt={}) ref_dict = { "job_type": "opt", "gen_scfman": "true", "geom_opt_max_cycles": "200", "basis": "def2-tzvpd", "max_scf_cycles": "100", "method": "wb97mv", "scf_algorithm": "diis", "xc_grid": "3", "thresh": "14", "s2thresh": "16", "symmetry": "false", "sym_ignore": "true", "resp_charges": "true", } assert v6_opt_set.rem == ref_dict ref_dict = { "maxiter": "200", "coordinates": "redundant", "max_displacement": "0.1", "optimization_restart": "false", } assert v6_opt_set.geom_opt == ref_dict assert v6_opt_set.molecule == test_molecule v6_opt_set_modified = OptSet( molecule=test_molecule, qchem_version=6, basis_set="def2-tzvpd", geom_opt={"coordinates": "delocalized", "initial_hessian": "read"}, ) ref_dict = { "maxiter": "200", "coordinates": "delocalized", "max_displacement": "0.1", "initial_hessian": "read", "optimization_restart": "false", } assert v6_opt_set_modified.geom_opt == ref_dict class TestTransitionStateSet(MatSciTest): def test_init(self): test_molecule = QCInput.from_file(f"{TEST_DIR}/pcm.qin").molecule test_ts_set = TransitionStateSet(molecule=test_molecule) ref_dict = { "job_type": "ts", "gen_scfman": "true", "basis": "def2-svpd", "max_scf_cycles": "100", "method": "wb97mv", "scf_algorithm": "diis", "xc_grid": "3", "thresh": "14", "s2thresh": "16", "geom_opt_max_cycles": "200", "resp_charges": "true", "sym_ignore": "true", "symmetry": "false", } assert test_ts_set.rem == ref_dict assert test_ts_set.pcm == {} assert test_ts_set.solvent == {} assert test_ts_set.smx == {} assert test_ts_set.molecule == test_molecule def test_pcm_init(self): test_molecule = QCInput.from_file(f"{TEST_DIR}/pcm.qin").molecule test_ts_set = TransitionStateSet(molecule=test_molecule, pcm_dielectric=10.0) ref_dict = { "job_type": "ts", "gen_scfman": "true", "basis": "def2-svpd", "max_scf_cycles": "100", "method": "wb97mv", "geom_opt_max_cycles": "200", "scf_algorithm": "diis", "xc_grid": "3", "thresh": "14", "s2thresh": "16", "solvent_method": "pcm", "resp_charges": "true", "sym_ignore": "true", "symmetry": "false", } assert test_ts_set.rem == ref_dict ref_dict = { "heavypoints": "194", "hpoints": "194", "radii": "uff", "theory": "cpcm", "vdwscale": "1.1", } assert test_ts_set.pcm == ref_dict assert test_ts_set.solvent == {"dielectric": "10.0"} assert test_ts_set.molecule == test_molecule def test_smd_init(self): test_molecule = QCInput.from_file(f"{TEST_DIR}/pcm.qin").molecule test_ts_set = TransitionStateSet(molecule=test_molecule, smd_solvent="water") ref_dict = { "job_type": "ts", "gen_scfman": "true", "basis": "def2-svpd", "max_scf_cycles": "100", "method": "wb97mv", "geom_opt_max_cycles": "200", "scf_algorithm": "diis", "xc_grid": "3", "thresh": "14", "s2thresh": "16", "solvent_method": "smd", "ideriv": "1", "resp_charges": "true", "sym_ignore": "true", "symmetry": "false", } assert test_ts_set.rem == ref_dict assert test_ts_set.smx == {"solvent": "water"} assert test_ts_set.molecule == test_molecule class TestForceSet(MatSciTest): def test_init(self): test_molecule = QCInput.from_file(f"{TEST_DIR}/pcm.qin").molecule test_forceset = ForceSet(molecule=test_molecule) ref_dict = { "job_type": "force", "gen_scfman": "true", "basis": "def2-tzvpd", "max_scf_cycles": "100", "method": "wb97mv", "scf_algorithm": "diis", "xc_grid": "3", "thresh": "14", "s2thresh": "16", "symmetry": "false", "sym_ignore": "true", "resp_charges": "true", } assert test_forceset.rem == ref_dict assert test_forceset.pcm == {} assert test_forceset.solvent == {} assert test_forceset.molecule == test_molecule def test_pcm_init(self): test_molecule = QCInput.from_file(f"{TEST_DIR}/pcm.qin").molecule test_forceset = ForceSet(molecule=test_molecule, pcm_dielectric=10.0) ref_dict = { "job_type": "force", "gen_scfman": "true", "basis": "def2-tzvpd", "max_scf_cycles": "100", "method": "wb97mv", "scf_algorithm": "diis", "xc_grid": "3", "thresh": "14", "s2thresh": "16", "solvent_method": "pcm", "symmetry": "false", "sym_ignore": "true", "resp_charges": "true", } assert test_forceset.rem == ref_dict ref_dict = { "heavypoints": "194", "hpoints": "194", "radii": "uff", "theory": "cpcm", "vdwscale": "1.1", } assert test_forceset.pcm == ref_dict assert test_forceset.solvent == {"dielectric": "10.0"} assert test_forceset.molecule == test_molecule def test_smd_init(self): test_molecule = QCInput.from_file(f"{TEST_DIR}/pcm.qin").molecule test_forceset = ForceSet(molecule=test_molecule, smd_solvent="water") ref_dict = { "job_type": "force", "gen_scfman": "true", "basis": "def2-tzvpd", "max_scf_cycles": "100", "method": "wb97mv", "scf_algorithm": "diis", "xc_grid": "3", "thresh": "14", "s2thresh": "16", "solvent_method": "smd", "ideriv": "1", "symmetry": "false", "sym_ignore": "true", "resp_charges": "true", } assert test_forceset.rem == ref_dict assert test_forceset.smx, {"solvent": "water"} assert test_forceset.molecule == test_molecule class TestPESScanSet(MatSciTest): def test_init(self): test_molecule = QCInput.from_file(f"{TEST_DIR}/pes_scan.qin").molecule test_pes_scan = PESScanSet(molecule=test_molecule, scan_variables={"stre": ["3 6 1.5 1.9 0.01"]}) ref_dict = { "job_type": "pes_scan", "gen_scfman": "true", "basis": "def2-svpd", "max_scf_cycles": "100", "geom_opt_max_cycles": "200", "method": "wb97mv", "scf_algorithm": "diis", "xc_grid": "3", "thresh": "14", "s2thresh": "16", "resp_charges": "true", "sym_ignore": "true", "symmetry": "false", } assert test_pes_scan.rem == ref_dict assert test_pes_scan.pcm == {} assert test_pes_scan.solvent == {} assert test_pes_scan.smx == {} assert test_pes_scan.scan == {"stre": ["3 6 1.5 1.9 0.01"]} assert test_pes_scan.molecule == test_molecule def test_pcm_init(self): test_molecule = QCInput.from_file(f"{TEST_DIR}/pes_scan.qin").molecule test_pes_scan = PESScanSet( molecule=test_molecule, pcm_dielectric=10.0, scan_variables={"stre": ["3 6 1.5 1.9 0.01"]}, ) ref_dict = { "job_type": "pes_scan", "gen_scfman": "true", "basis": "def2-svpd", "max_scf_cycles": "100", "geom_opt_max_cycles": "200", "method": "wb97mv", "scf_algorithm": "diis", "xc_grid": "3", "thresh": "14", "s2thresh": "16", "solvent_method": "pcm", "resp_charges": "true", "sym_ignore": "true", "symmetry": "false", } assert test_pes_scan.rem == ref_dict ref_dict = { "heavypoints": "194", "hpoints": "194", "radii": "uff", "theory": "cpcm", "vdwscale": "1.1", } assert test_pes_scan.pcm == ref_dict assert test_pes_scan.solvent == {"dielectric": "10.0"} assert test_pes_scan.scan == {"stre": ["3 6 1.5 1.9 0.01"]} assert test_pes_scan.molecule == test_molecule def test_smd_init(self): test_molecule = QCInput.from_file(f"{TEST_DIR}/pes_scan.qin").molecule test_pes_scan = PESScanSet( molecule=test_molecule, smd_solvent="water", scan_variables={"stre": ["3 6 1.5 1.9 0.01"]}, ) ref_dict = { "job_type": "pes_scan", "gen_scfman": "true", "basis": "def2-svpd", "max_scf_cycles": "100", "geom_opt_max_cycles": "200", "method": "wb97mv", "scf_algorithm": "diis", "xc_grid": "3", "thresh": "14", "s2thresh": "16", "solvent_method": "smd", "ideriv": "1", "resp_charges": "true", "sym_ignore": "true", "symmetry": "false", } assert test_pes_scan.rem == ref_dict assert test_pes_scan.smx == {"solvent": "water"} assert test_pes_scan.scan == {"stre": ["3 6 1.5 1.9 0.01"]} assert test_pes_scan.molecule == test_molecule class TestFreqSet(MatSciTest): def test_init(self): test_molecule = QCInput.from_file(f"{TEST_DIR}/pcm.qin").molecule test_freq_set = FreqSet(molecule=test_molecule) ref_dict = { "job_type": "freq", "gen_scfman": "true", "basis": "def2-svpd", "max_scf_cycles": "100", "method": "wb97mv", "scf_algorithm": "diis", "xc_grid": "3", "thresh": "14", "s2thresh": "16", "symmetry": "false", "sym_ignore": "true", "resp_charges": "true", } assert test_freq_set.rem == ref_dict assert test_freq_set.pcm == {} assert test_freq_set.solvent == {} assert test_freq_set.molecule == test_molecule def test_pcm_init(self): test_molecule = QCInput.from_file(f"{TEST_DIR}/pcm.qin").molecule test_freq_set = FreqSet(molecule=test_molecule, pcm_dielectric=10.0) ref_dict = { "job_type": "freq", "gen_scfman": "true", "basis": "def2-svpd", "max_scf_cycles": "100", "method": "wb97mv", "scf_algorithm": "diis", "xc_grid": "3", "thresh": "14", "s2thresh": "16", "solvent_method": "pcm", "symmetry": "false", "sym_ignore": "true", "resp_charges": "true", } assert test_freq_set.rem == ref_dict ref_dict = { "heavypoints": "194", "hpoints": "194", "radii": "uff", "theory": "cpcm", "vdwscale": "1.1", } assert test_freq_set.pcm == ref_dict assert test_freq_set.solvent == {"dielectric": "10.0"} assert test_freq_set.molecule == test_molecule def test_smd_init(self): test_molecule = QCInput.from_file(f"{TEST_DIR}/pcm.qin").molecule test_freq_set = FreqSet(molecule=test_molecule, smd_solvent="water") ref_dict = { "job_type": "freq", "gen_scfman": "true", "basis": "def2-svpd", "max_scf_cycles": "100", "method": "wb97mv", "scf_algorithm": "diis", "xc_grid": "3", "thresh": "14", "s2thresh": "16", "solvent_method": "smd", "ideriv": "1", "symmetry": "false", "sym_ignore": "true", "resp_charges": "true", } assert test_freq_set.rem == ref_dict assert test_freq_set.smx == {"solvent": "water"} assert test_freq_set.molecule == test_molecule