4075885785

Build Type

push

github

Committed by Shyue Ping Ong

Commit Message

Merge branch 'master' of github.com:materialsproject/pymatgen

Run Details

96 of 96 new or added lines in 27 files covered. (100.0%)

81013 of 102710 relevant lines covered (78.88%)

0.79 hits per line

Source File
Press 'n' to go to next uncovered line, 'b' for previous

72.82

/pymatgen/io/qchem/tests/test_outputs.py

# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.


from __future__ import annotations

import os
import unittest

from monty.serialization import dumpfn, loadfn

from pymatgen.core.structure import Molecule
from pymatgen.io.qchem.outputs import QCOutput, check_for_structure_changes
from pymatgen.util.testing import PymatgenTest

try:
    from openbabel import openbabel
except ImportError:
    openbabel = None

__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"

single_job_dict = loadfn(os.path.join(os.path.dirname(__file__), "single_job.json"))
multi_job_dict = loadfn(os.path.join(os.path.dirname(__file__), "multi_job.json"))

property_list = {
    "errors",
    "multiple_outputs",
    "completion",
    "unrestricted",
    "using_GEN_SCFMAN",
    "final_energy",
    "S2",
    "optimization",
    "energy_trajectory",
    "opt_constraint",
    "frequency_job",
    "charge",
    "multiplicity",
    "species",
    "initial_geometry",
    "initial_molecule",
    "SCF",
    "Mulliken",
    "optimized_geometry",
    "optimized_zmat",
    "molecule_from_optimized_geometry",
    "last_geometry",
    "molecule_from_last_geometry",
    "geometries",
    "gradients",
    "frequency_mode_vectors",
    "walltime",
    "cputime",
    "point_group",
    "frequencies",
    "IR_intens",
    "IR_active",
    "g_electrostatic",
    "g_cavitation",
    "g_dispersion",
    "g_repulsion",
    "total_contribution_pcm",
    "ZPE",
    "trans_enthalpy",
    "vib_enthalpy",
    "rot_enthalpy",
    "gas_constant",
    "trans_entropy",
    "vib_entropy",
    "rot_entropy",
    "total_entropy",
    "total_enthalpy",
    "warnings",
    "SCF_energy_in_the_final_basis_set",
    "Total_energy_in_the_final_basis_set",
    "solvent_method",
    "solvent_data",
    "using_dft_d3",
    "single_point_job",
    "force_job",
    "pcm_gradients",
    "CDS_gradients",
    "RESP",
    "trans_dip",
    "transition_state",
    "scan_job",
    "optimized_geometries",
    "molecules_from_optimized_geometries",
    "scan_energies",
    "scan_constraint_sets",
    "hf_scf_energy",
    "mp2_energy",
    "ccsd_correlation_energy",
    "ccsd_total_energy",
    "ccsd(t)_correlation_energy",
    "ccsd(t)_total_energy",
    "alpha_fock_matrix",
    "beta_fock_matrix",
    "alpha_eigenvalues",
    "beta_eigenvalues",
    "alpha_coeff_matrix",
    "beta_coeff_matrix",
    "final_soln_phase_e",
    "solute_internal_e",
    "total_solvation_free_e",
    "change_solute_internal_e",
    "reaction_field_free_e",
    "isosvp_dielectric",
    "dispersion_e",
    "exchange_e",
    "min_neg_field_e",
    "max_pos_field_e",
    "norm_of_stepsize",
    "version",
    "dipoles",
    "gap_info",
}

if openbabel is not None:
    property_list.add("structure_change")

single_job_out_names = {
    "unable_to_determine_lambda_in_geom_opt.qcout",
    "thiophene_wfs_5_carboxyl.qcout",
    "hf.qcout",
    "hf_opt_failed.qcout",
    "no_reading.qcout",
    "exit_code_134.qcout",
    "negative_eigen.qcout",
    "insufficient_memory.qcout",
    "freq_seg_too_small.qcout",
    "crowd_gradient_number.qcout",
    "quinoxaline_anion.qcout",
    "tfsi_nbo.qcout",
    "crowd_nbo_charges.qcout",
    "h2o_aimd.qcout",
    "quinoxaline_anion.qcout",
    "crowd_gradient_number.qcout",
    "bsse.qcout",
    "thiophene_wfs_5_carboxyl.qcout",
    "time_nan_values.qcout",
    "pt_dft_180.0.qcout",
    "qchem_energies/hf-rimp2.qcout",
    "qchem_energies/hf_b3lyp.qcout",
    "qchem_energies/hf_ccsd(t).qcout",
    "qchem_energies/hf_cosmo.qcout",
    "qchem_energies/hf_hf.qcout",
    "qchem_energies/hf_lxygjos.qcout",
    "qchem_energies/hf_mosmp2.qcout",
    "qchem_energies/hf_mp2.qcout",
    "qchem_energies/hf_qcisd(t).qcout",
    "qchem_energies/hf_riccsd(t).qcout",
    "qchem_energies/hf_tpssh.qcout",
    "qchem_energies/hf_xyg3.qcout",
    "qchem_energies/hf_xygjos.qcout",
    "qchem_energies/hf_wb97xd_gen_scfman.qcout",
    "new_qchem_files/pt_n2_n_wb_180.0.qcout",
    "new_qchem_files/pt_n2_trip_wb_90.0.qcout",
    "new_qchem_files/pt_n2_gs_rimp2_pvqz_90.0.qcout",
    "new_qchem_files/VC_solv_eps10.2.qcout",
    "crazy_scf_values.qcout",
    "new_qchem_files/N2.qcout",
    "new_qchem_files/julian.qcout.gz",
    "new_qchem_files/Frequency_no_equal.qout",
    "new_qchem_files/gdm.qout",
    "new_qchem_files/DinfH.qout",
    "new_qchem_files/mpi_error.qout",
    "new_qchem_files/molecule_read_error.qout",
    "new_qchem_files/basis_not_supported.qout",
    "new_qchem_files/lebdevpts.qout",
    "new_qchem_files/Optimization_no_equal.qout",
    "new_qchem_files/2068.qout",
    "new_qchem_files/2620.qout",
    "new_qchem_files/1746.qout",
    "new_qchem_files/1570.qout",
    "new_qchem_files/1570_2.qout",
    "new_qchem_files/single_point.qout",
    "new_qchem_files/roothaan_diis_gdm.qout",
    "new_qchem_files/pes_scan_single_variable.qout",
    "new_qchem_files/pes_scan_double_variable.qout",
    "new_qchem_files/ts.out",
    "new_qchem_files/ccsd.qout",
    "new_qchem_files/ccsdt.qout",
    "extra_scf_print.qcout",
    "new_qchem_files/cmirs_benzene_single.qcout",
    "new_qchem_files/cmirs_dielst10_single.qcout",
    "new_qchem_files/cmirs_water_single.qcout",
    "new_qchem_files/isosvp_water_single.qcout",
    "new_qchem_files/isosvp_dielst10_single.qcout",
    "new_qchem_files/custom_gdm_gdmqls_opt.qout",
    "new_qchem_files/unable.qout",
    "new_qchem_files/unexpected_ts.out",
    "new_qchem_files/svd_failed.qout",
    "new_qchem_files/v6_old_driver.out",
    "new_qchem_files/gap.qout",
    "new_qchem_files/3C.qout",
    "new_qchem_files/hyper.qout",
    "new_qchem_files/os_gap.qout",
}

multi_job_out_names = {
    "not_enough_total_memory.qcout",
    "new_qchem_files/VC_solv_eps10.qcout",
    "new_qchem_files/MECLi_solv_eps10.qcout",
    "pcm_solvent_deprecated.qcout",
    "qchem43_batch_job.qcout",
    "ferrocenium_1pos.qcout",
    "CdBr2.qcout",
    "killed.qcout",
    "aux_mpi_time_mol.qcout",
    "new_qchem_files/VCLi_solv_eps10.qcout",
    "new_qchem_files/cmirs_benzene.qcout",
    "new_qchem_files/cmirs_dielst10.qcout",
    "new_qchem_files/isosvp_water.qcout",
    "new_qchem_files/isosvp_dielst10.qcout",
}


class TestQCOutput(PymatgenTest):
    @staticmethod
    def generate_single_job_dict():
        """
        Used to generate test dictionary for single jobs.
        """
        single_job_dict = {}
        for file in single_job_out_names:
            single_job_dict[file] = QCOutput(os.path.join(PymatgenTest.TEST_FILES_DIR, "molecules", file)).data
        dumpfn(single_job_dict, "single_job.json")

    @staticmethod
    def generate_multi_job_dict():
        """
        Used to generate test dictionary for multiple jobs.
        """
        multi_job_dict = {}
        for file in multi_job_out_names:
            outputs = QCOutput.multiple_outputs_from_file(
                QCOutput, os.path.join(PymatgenTest.TEST_FILES_DIR, "molecules", file), keep_sub_files=False
            )
            data = []
            for sub_output in outputs:
                data.append(sub_output.data)
            multi_job_dict[file] = data
        dumpfn(multi_job_dict, "multi_job.json")

    def _test_property(self, key, single_outs, multi_outs):
        for name, outdata in single_outs.items():
            try:
                assert outdata.get(key) == single_job_dict[name].get(key)
            except ValueError:
                try:
                    self.assertArrayEqual(outdata.get(key), single_job_dict[name].get(key))
                except AssertionError:
                    raise RuntimeError("Issue with file: " + name + " Exiting...")
            except AssertionError:
                raise RuntimeError("Issue with file: " + name + " Exiting...")
        for name, outputs in multi_outs.items():
            for ii, sub_output in enumerate(outputs):
                try:
                    assert sub_output.data.get(key) == multi_job_dict[name][ii].get(key)
                except ValueError:
                    self.assertArrayEqual(sub_output.data.get(key), multi_job_dict[name][ii].get(key))

    @unittest.skipIf(openbabel is None, "OpenBabel not installed.")
    def test_all(self):
        self.maxDiff = None
        single_outs = {}
        for file in single_job_out_names:
            single_outs[file] = QCOutput(os.path.join(PymatgenTest.TEST_FILES_DIR, "molecules", file)).data

        multi_outs = {}
        for file in multi_job_out_names:
            multi_outs[file] = QCOutput.multiple_outputs_from_file(
                QCOutput, os.path.join(PymatgenTest.TEST_FILES_DIR, "molecules", file), keep_sub_files=False
            )

        for key in property_list:
            print("Testing ", key)
            self._test_property(key, single_outs, multi_outs)

    @unittest.skipIf((openbabel is None), "OpenBabel not installed.")
    def test_structural_change(self):
        t1 = Molecule.from_file(os.path.join(PymatgenTest.TEST_FILES_DIR, "molecules", "structural_change", "t1.xyz"))
        t2 = Molecule.from_file(os.path.join(PymatgenTest.TEST_FILES_DIR, "molecules", "structural_change", "t2.xyz"))
        t3 = Molecule.from_file(os.path.join(PymatgenTest.TEST_FILES_DIR, "molecules", "structural_change", "t3.xyz"))

        thio_1 = Molecule.from_file(
            os.path.join(PymatgenTest.TEST_FILES_DIR, "molecules", "structural_change", "thiophene1.xyz")
        )
        thio_2 = Molecule.from_file(
            os.path.join(PymatgenTest.TEST_FILES_DIR, "molecules", "structural_change", "thiophene2.xyz")
        )

        frag_1 = Molecule.from_file(
            os.path.join(
                PymatgenTest.TEST_FILES_DIR, "molecules", "new_qchem_files", "test_structure_change", "frag_1.xyz"
            )
        )
        frag_2 = Molecule.from_file(
            os.path.join(
                PymatgenTest.TEST_FILES_DIR, "molecules", "new_qchem_files", "test_structure_change", "frag_2.xyz"
            )
        )

        assert check_for_structure_changes(t1, t1) == "no_change"
        assert check_for_structure_changes(t2, t3) == "no_change"
        assert check_for_structure_changes(t1, t2) == "fewer_bonds"
        assert check_for_structure_changes(t2, t1) == "more_bonds"

        assert check_for_structure_changes(thio_1, thio_2) == "unconnected_fragments"

        assert check_for_structure_changes(frag_1, frag_2) == "bond_change"

    def test_NBO_parsing(self):
        data = QCOutput(os.path.join(PymatgenTest.TEST_FILES_DIR, "molecules", "new_qchem_files", "nbo.qout")).data
        assert len(data["nbo_data"]["natural_populations"]) == 3
        assert len(data["nbo_data"]["hybridization_character"]) == 6
        assert len(data["nbo_data"]["perturbation_energy"]) == 2
        assert data["nbo_data"]["natural_populations"][0]["Density"][5] == -0.08624
        assert data["nbo_data"]["hybridization_character"][4]["atom 2 pol coeff"][35] == "-0.7059"
        next_to_last = list(data["nbo_data"]["perturbation_energy"][-1]["fock matrix element"])[-2]
        assert data["nbo_data"]["perturbation_energy"][-1]["fock matrix element"][next_to_last] == 0.071
        assert data["nbo_data"]["perturbation_energy"][0]["acceptor type"][0] == "RY*"

    def test_NBO7_parsing(self):
        data = QCOutput(os.path.join(PymatgenTest.TEST_FILES_DIR, "molecules", "new_qchem_files", "nbo7_1.qout")).data
        assert data["nbo_data"]["perturbation_energy"][0]["perturbation energy"][9] == 15.73
        assert len(data["nbo_data"]["perturbation_energy"][0]["donor bond index"]) == 84
        assert len(data["nbo_data"]["perturbation_energy"][1]["donor bond index"]) == 29

        data = QCOutput(os.path.join(PymatgenTest.TEST_FILES_DIR, "molecules", "new_qchem_files", "nbo7_2.qout")).data
        assert data["nbo_data"]["perturbation_energy"][0]["perturbation energy"][13] == 32.93
        assert data["nbo_data"]["perturbation_energy"][0]["acceptor type"][13] == "LV"
        assert data["nbo_data"]["perturbation_energy"][0]["acceptor type"][12] == "RY"
        assert data["nbo_data"]["perturbation_energy"][0]["acceptor atom 1 symbol"][12] == "Mg"

        data = QCOutput(os.path.join(PymatgenTest.TEST_FILES_DIR, "molecules", "new_qchem_files", "nbo7_3.qout")).data
        assert data["nbo_data"]["perturbation_energy"][0]["perturbation energy"][13] == 34.54
        assert data["nbo_data"]["perturbation_energy"][0]["acceptor type"][13] == "BD*"
        assert data["nbo_data"]["perturbation_energy"][0]["acceptor atom 1 symbol"][13] == "B"
        assert data["nbo_data"]["perturbation_energy"][0]["acceptor atom 2 symbol"][13] == "Mg"
        assert data["nbo_data"]["perturbation_energy"][0]["acceptor atom 2 number"][13] == 3

    def test_NBO5_vs_NBO7_hybridization_character(self):
        data5 = QCOutput(os.path.join(PymatgenTest.TEST_FILES_DIR, "molecules", "new_qchem_files", "nbo5_1.qout")).data
        data7 = QCOutput(os.path.join(PymatgenTest.TEST_FILES_DIR, "molecules", "new_qchem_files", "nbo7_1.qout")).data
        assert len(data5["nbo_data"]["hybridization_character"]) == len(data7["nbo_data"]["hybridization_character"])
        assert (
            data5["nbo_data"]["hybridization_character"][4]["atom 2 pol coeff"][9]
            == data7["nbo_data"]["hybridization_character"][4]["atom 2 pol coeff"][9]
        )
        assert (
            data5["nbo_data"]["hybridization_character"][0]["s"][0]
            == data7["nbo_data"]["hybridization_character"][0]["s"][0]
        )
        assert data5["nbo_data"]["hybridization_character"][1]["bond index"][7] == "149"
        assert data7["nbo_data"]["hybridization_character"][1]["bond index"][7] == "21"

    def test_NBO7_infinite_e2pert(self):
        data = QCOutput(os.path.join(PymatgenTest.TEST_FILES_DIR, "molecules", "new_qchem_files", "nbo7_inf.qout")).data
        assert data["nbo_data"]["perturbation_energy"][0]["perturbation energy"][0] == float("inf")

    def test_isosvp_water(self):
        data = QCOutput(
            os.path.join(PymatgenTest.TEST_FILES_DIR, "molecules", "new_qchem_files", "isosvp_water_single.qcout")
        ).data
        assert data["solvent_method"] == "ISOSVP"

        # ISOSVP parameters
        assert data["solvent_data"]["isosvp"]["isosvp_dielectric"] == 78.39
        assert data["solvent_data"]["isosvp"]["final_soln_phase_e"] == -40.4850599393
        assert data["solvent_data"]["isosvp"]["solute_internal_e"] == -40.4846329762
        assert data["solvent_data"]["isosvp"]["change_solute_internal_e"] == 0.0000121967
        assert data["solvent_data"]["isosvp"]["reaction_field_free_e"] == -0.0004269631
        assert data["solvent_data"]["isosvp"]["total_solvation_free_e"] == -0.0004147664

        # CMIRS parameters
        assert data["solvent_data"]["cmirs"]["CMIRS_enabled"] is False

    def test_isosvp_dielst10(self):
        data = QCOutput(
            os.path.join(PymatgenTest.TEST_FILES_DIR, "molecules", "new_qchem_files", "isosvp_dielst10_single.qcout")
        ).data
        assert data["solvent_method"] == "ISOSVP"

        # ISOSVP parameters
        assert data["solvent_data"]["isosvp"]["isosvp_dielectric"] == 10
        assert data["solvent_data"]["isosvp"]["final_soln_phase_e"] == -40.4850012952
        assert data["solvent_data"]["isosvp"]["solute_internal_e"] == -40.4846362547
        assert data["solvent_data"]["isosvp"]["change_solute_internal_e"] == 0.0000089182
        assert data["solvent_data"]["isosvp"]["reaction_field_free_e"] == -0.0003650405
        assert data["solvent_data"]["isosvp"]["total_solvation_free_e"] == -0.0003561223

        # CMIRS parameters
        assert data["solvent_data"]["cmirs"]["CMIRS_enabled"] is False

    def test_cmirs_benzene(self):
        data = QCOutput(
            os.path.join(PymatgenTest.TEST_FILES_DIR, "molecules", "new_qchem_files", "cmirs_benzene_single.qcout")
        ).data
        assert data["solvent_method"] == "ISOSVP"
        assert data["solvent_data"]["isosvp"]["isosvp_dielectric"] == 2.28
        assert data["solvent_data"]["cmirs"]["CMIRS_enabled"] is True
        assert data["solvent_data"]["cmirs"]["dispersion_e"] == 0.6955542829
        assert data["solvent_data"]["cmirs"]["exchange_e"] == 0.2654553686
        assert data["solvent_data"]["cmirs"]["min_neg_field_e"] == 0.0006019665
        assert data["solvent_data"]["cmirs"]["max_pos_field_e"] == 0.0178177740

    def test_cmirs_dielst10(self):
        data = QCOutput(
            os.path.join(PymatgenTest.TEST_FILES_DIR, "molecules", "new_qchem_files", "cmirs_dielst10_single.qcout")
        ).data
        assert data["solvent_method"] == "ISOSVP"
        assert data["solvent_data"]["isosvp"]["isosvp_dielectric"] == 10
        assert data["solvent_data"]["cmirs"]["CMIRS_enabled"] is True
        assert data["solvent_data"]["cmirs"]["dispersion_e"] == 0.6955550107
        assert data["solvent_data"]["cmirs"]["exchange_e"] == 0.2652679507
        assert data["solvent_data"]["cmirs"]["min_neg_field_e"] == 0.0005235850
        assert data["solvent_data"]["cmirs"]["max_pos_field_e"] == 0.0179866718

    def test_cmirs_water(self):
        data = QCOutput(
            os.path.join(PymatgenTest.TEST_FILES_DIR, "molecules", "new_qchem_files", "cmirs_water_single.qcout")
        ).data
        assert data["solvent_method"] == "ISOSVP"

        # ISOSVP parameters
        assert data["solvent_data"]["isosvp"]["isosvp_dielectric"] == 78.39
        assert data["solvent_data"]["isosvp"]["final_soln_phase_e"] == -40.4752415075
        assert data["solvent_data"]["isosvp"]["solute_internal_e"] == -40.4748535587
        assert data["solvent_data"]["isosvp"]["change_solute_internal_e"] == 0.0000122982
        assert data["solvent_data"]["isosvp"]["reaction_field_free_e"] == -0.0003879488
        assert data["solvent_data"]["isosvp"]["total_solvation_free_e"] == 0.0037602703

        # CMIRS parameters
        assert data["solvent_data"]["cmirs"]["CMIRS_enabled"] is True
        assert data["solvent_data"]["cmirs"]["dispersion_e"] == 0.6722278965
        assert data["solvent_data"]["cmirs"]["exchange_e"] == 0.2652032616
        assert data["solvent_data"]["cmirs"]["min_neg_field_e"] == 0.0004967767
        assert data["solvent_data"]["cmirs"]["max_pos_field_e"] == 0.0180445935

    def test_NBO_hyperbonds(self):
        data = QCOutput(os.path.join(PymatgenTest.TEST_FILES_DIR, "molecules", "new_qchem_files", "hyper.qout")).data
        assert len(data["nbo_data"]["hyperbonds"][0]["hyperbond index"].keys()) == 2
        assert data["nbo_data"]["hyperbonds"][0]["BD(A-B)"][1] == 106
        assert data["nbo_data"]["hyperbonds"][0]["bond atom 2 symbol"][0] == "C"
        assert data["nbo_data"]["hyperbonds"][0]["occ"][1] == 3.0802

    def test_NBO_3C(self):
        data = QCOutput(os.path.join(PymatgenTest.TEST_FILES_DIR, "molecules", "new_qchem_files", "3C.qout")).data
        assert len(data["nbo_data"]["hybridization_character"]) == 3
        assert data["nbo_data"]["hybridization_character"][2]["type"][0] == "3C"
        assert data["nbo_data"]["hybridization_character"][2]["type"][10] == "3Cn"
        assert data["nbo_data"]["hybridization_character"][2]["type"][20] == "3C*"
        assert data["nbo_data"]["hybridization_character"][2]["atom 3 pol coeff"][15] == "0.3643"
        assert data["nbo_data"]["hybridization_character"][2]["atom 3 polarization"][8] == "56.72"
        assert data["nbo_data"]["hybridization_character"][2]["atom 3 symbol"][3] == "B"
        assert data["nbo_data"]["perturbation_energy"][0]["donor atom 2 number"][2592] == 36
        assert data["nbo_data"]["perturbation_energy"][0]["donor atom 2 symbol"][2125] == "B12"
        assert data["nbo_data"]["perturbation_energy"][0]["donor atom 2 number"][2593] == "info_is_from_3C"
        assert data["nbo_data"]["perturbation_energy"][0]["acceptor type"][723] == "3C*"
        assert data["nbo_data"]["perturbation_energy"][0]["perturbation energy"][3209] == 3.94


if __name__ == "__main__":
    unittest.main()

1	# Copyright (c) Pymatgen Development Team.
2	# Distributed under the terms of the MIT License.
3
4
5	from __future__ import annotations	1✔
6
7	import os	1✔
8	import unittest	1✔
9
10	from monty.serialization import dumpfn, loadfn	1✔
11
12	from pymatgen.core.structure import Molecule	1✔
13	from pymatgen.io.qchem.outputs import QCOutput, check_for_structure_changes	1✔
14	from pymatgen.util.testing import PymatgenTest	1✔
15
16	try:	1✔
17	from openbabel import openbabel	1✔
18	except ImportError:	1✔
19	openbabel = None	1✔
20
21	__author__ = "Samuel Blau, Brandon Wood, Shyam Dwaraknath, Evan Spotte-Smith, Ryan Kingsbury"	1✔
22	__copyright__ = "Copyright 2018-2022, The Materials Project"	1✔
23	__version__ = "0.1"	1✔
24	__maintainer__ = "Samuel Blau"	1✔
25	__email__ = "samblau1@gmail.com"	1✔
26
27	single_job_dict = loadfn(os.path.join(os.path.dirname(__file__), "single_job.json"))	1✔
28	multi_job_dict = loadfn(os.path.join(os.path.dirname(__file__), "multi_job.json"))	1✔
29
30	property_list = {	1✔
31	"errors",
32	"multiple_outputs",
33	"completion",
34	"unrestricted",
35	"using_GEN_SCFMAN",
36	"final_energy",
37	"S2",
38	"optimization",
39	"energy_trajectory",
40	"opt_constraint",
41	"frequency_job",
42	"charge",
43	"multiplicity",
44	"species",
45	"initial_geometry",
46	"initial_molecule",
47	"SCF",
48	"Mulliken",
49	"optimized_geometry",
50	"optimized_zmat",
51	"molecule_from_optimized_geometry",
52	"last_geometry",
53	"molecule_from_last_geometry",
54	"geometries",
55	"gradients",
56	"frequency_mode_vectors",
57	"walltime",
58	"cputime",
59	"point_group",
60	"frequencies",
61	"IR_intens",
62	"IR_active",
63	"g_electrostatic",
64	"g_cavitation",
65	"g_dispersion",
66	"g_repulsion",
67	"total_contribution_pcm",
68	"ZPE",
69	"trans_enthalpy",
70	"vib_enthalpy",
71	"rot_enthalpy",
72	"gas_constant",
73	"trans_entropy",
74	"vib_entropy",
75	"rot_entropy",
76	"total_entropy",
77	"total_enthalpy",
78	"warnings",
79	"SCF_energy_in_the_final_basis_set",
80	"Total_energy_in_the_final_basis_set",
81	"solvent_method",
82	"solvent_data",
83	"using_dft_d3",
84	"single_point_job",
85	"force_job",
86	"pcm_gradients",
87	"CDS_gradients",
88	"RESP",
89	"trans_dip",
90	"transition_state",
91	"scan_job",
92	"optimized_geometries",
93	"molecules_from_optimized_geometries",
94	"scan_energies",
95	"scan_constraint_sets",
96	"hf_scf_energy",
97	"mp2_energy",
98	"ccsd_correlation_energy",
99	"ccsd_total_energy",
100	"ccsd(t)_correlation_energy",
101	"ccsd(t)_total_energy",
102	"alpha_fock_matrix",
103	"beta_fock_matrix",
104	"alpha_eigenvalues",
105	"beta_eigenvalues",
106	"alpha_coeff_matrix",
107	"beta_coeff_matrix",
108	"final_soln_phase_e",
109	"solute_internal_e",
110	"total_solvation_free_e",
111	"change_solute_internal_e",
112	"reaction_field_free_e",
113	"isosvp_dielectric",
114	"dispersion_e",
115	"exchange_e",
116	"min_neg_field_e",
117	"max_pos_field_e",
118	"norm_of_stepsize",
119	"version",
120	"dipoles",
121	"gap_info",
122	}
123
124	if openbabel is not None:	1✔
125	property_list.add("structure_change")	×
126
127	single_job_out_names = {	1✔
128	"unable_to_determine_lambda_in_geom_opt.qcout",
129	"thiophene_wfs_5_carboxyl.qcout",
130	"hf.qcout",
131	"hf_opt_failed.qcout",
132	"no_reading.qcout",
133	"exit_code_134.qcout",
134	"negative_eigen.qcout",
135	"insufficient_memory.qcout",
136	"freq_seg_too_small.qcout",
137	"crowd_gradient_number.qcout",
138	"quinoxaline_anion.qcout",
139	"tfsi_nbo.qcout",
140	"crowd_nbo_charges.qcout",
141	"h2o_aimd.qcout",
142	"quinoxaline_anion.qcout",
143	"crowd_gradient_number.qcout",
144	"bsse.qcout",
145	"thiophene_wfs_5_carboxyl.qcout",
146	"time_nan_values.qcout",
147	"pt_dft_180.0.qcout",
148	"qchem_energies/hf-rimp2.qcout",
149	"qchem_energies/hf_b3lyp.qcout",
150	"qchem_energies/hf_ccsd(t).qcout",
151	"qchem_energies/hf_cosmo.qcout",
152	"qchem_energies/hf_hf.qcout",
153	"qchem_energies/hf_lxygjos.qcout",
154	"qchem_energies/hf_mosmp2.qcout",
155	"qchem_energies/hf_mp2.qcout",
156	"qchem_energies/hf_qcisd(t).qcout",
157	"qchem_energies/hf_riccsd(t).qcout",
158	"qchem_energies/hf_tpssh.qcout",
159	"qchem_energies/hf_xyg3.qcout",
160	"qchem_energies/hf_xygjos.qcout",
161	"qchem_energies/hf_wb97xd_gen_scfman.qcout",
162	"new_qchem_files/pt_n2_n_wb_180.0.qcout",
163	"new_qchem_files/pt_n2_trip_wb_90.0.qcout",
164	"new_qchem_files/pt_n2_gs_rimp2_pvqz_90.0.qcout",
165	"new_qchem_files/VC_solv_eps10.2.qcout",
166	"crazy_scf_values.qcout",
167	"new_qchem_files/N2.qcout",
168	"new_qchem_files/julian.qcout.gz",
169	"new_qchem_files/Frequency_no_equal.qout",
170	"new_qchem_files/gdm.qout",
171	"new_qchem_files/DinfH.qout",
172	"new_qchem_files/mpi_error.qout",
173	"new_qchem_files/molecule_read_error.qout",
174	"new_qchem_files/basis_not_supported.qout",
175	"new_qchem_files/lebdevpts.qout",
176	"new_qchem_files/Optimization_no_equal.qout",
177	"new_qchem_files/2068.qout",
178	"new_qchem_files/2620.qout",
179	"new_qchem_files/1746.qout",
180	"new_qchem_files/1570.qout",
181	"new_qchem_files/1570_2.qout",
182	"new_qchem_files/single_point.qout",
183	"new_qchem_files/roothaan_diis_gdm.qout",
184	"new_qchem_files/pes_scan_single_variable.qout",
185	"new_qchem_files/pes_scan_double_variable.qout",
186	"new_qchem_files/ts.out",
187	"new_qchem_files/ccsd.qout",
188	"new_qchem_files/ccsdt.qout",
189	"extra_scf_print.qcout",
190	"new_qchem_files/cmirs_benzene_single.qcout",
191	"new_qchem_files/cmirs_dielst10_single.qcout",
192	"new_qchem_files/cmirs_water_single.qcout",
193	"new_qchem_files/isosvp_water_single.qcout",
194	"new_qchem_files/isosvp_dielst10_single.qcout",
195	"new_qchem_files/custom_gdm_gdmqls_opt.qout",
196	"new_qchem_files/unable.qout",
197	"new_qchem_files/unexpected_ts.out",
198	"new_qchem_files/svd_failed.qout",
199	"new_qchem_files/v6_old_driver.out",
200	"new_qchem_files/gap.qout",
201	"new_qchem_files/3C.qout",
202	"new_qchem_files/hyper.qout",
203	"new_qchem_files/os_gap.qout",
204	}
205
206	multi_job_out_names = {	1✔
207	"not_enough_total_memory.qcout",
208	"new_qchem_files/VC_solv_eps10.qcout",
209	"new_qchem_files/MECLi_solv_eps10.qcout",
210	"pcm_solvent_deprecated.qcout",
211	"qchem43_batch_job.qcout",
212	"ferrocenium_1pos.qcout",
213	"CdBr2.qcout",
214	"killed.qcout",
215	"aux_mpi_time_mol.qcout",
216	"new_qchem_files/VCLi_solv_eps10.qcout",
217	"new_qchem_files/cmirs_benzene.qcout",
218	"new_qchem_files/cmirs_dielst10.qcout",
219	"new_qchem_files/isosvp_water.qcout",
220	"new_qchem_files/isosvp_dielst10.qcout",
221	}
222
223
224	class TestQCOutput(PymatgenTest):	1✔
225	@staticmethod	1✔
226	def generate_single_job_dict():	1✔
227	"""
228	Used to generate test dictionary for single jobs.
229	"""
230	single_job_dict = {}	×
231	for file in single_job_out_names:	×
232	single_job_dict[file] = QCOutput(os.path.join(PymatgenTest.TEST_FILES_DIR, "molecules", file)).data	×
233	dumpfn(single_job_dict, "single_job.json")	×
234
235	@staticmethod	1✔
236	def generate_multi_job_dict():	1✔
237	"""
238	Used to generate test dictionary for multiple jobs.
239	"""
240	multi_job_dict = {}	×
241	for file in multi_job_out_names:	×
242	outputs = QCOutput.multiple_outputs_from_file(	×
243	QCOutput, os.path.join(PymatgenTest.TEST_FILES_DIR, "molecules", file), keep_sub_files=False
244	)
245	data = []	×
246	for sub_output in outputs:	×
247	data.append(sub_output.data)	×
248	multi_job_dict[file] = data	×
249	dumpfn(multi_job_dict, "multi_job.json")	×
250
251	def _test_property(self, key, single_outs, multi_outs):	1✔
252	for name, outdata in single_outs.items():	×
253	try:	×
254	assert outdata.get(key) == single_job_dict[name].get(key)	×
255	except ValueError:	×
256	try:	×
257	self.assertArrayEqual(outdata.get(key), single_job_dict[name].get(key))	×
258	except AssertionError:	×
259	raise RuntimeError("Issue with file: " + name + " Exiting...")	×
260	except AssertionError:	×
261	raise RuntimeError("Issue with file: " + name + " Exiting...")	×
262	for name, outputs in multi_outs.items():	×
263	for ii, sub_output in enumerate(outputs):	×
264	try:	×
265	assert sub_output.data.get(key) == multi_job_dict[name][ii].get(key)	×
266	except ValueError:	×
267	self.assertArrayEqual(sub_output.data.get(key), multi_job_dict[name][ii].get(key))	×
268
269	@unittest.skipIf(openbabel is None, "OpenBabel not installed.")	1✔
270	def test_all(self):	1✔
271	self.maxDiff = None	×
272	single_outs = {}	×
273	for file in single_job_out_names:	×
274	single_outs[file] = QCOutput(os.path.join(PymatgenTest.TEST_FILES_DIR, "molecules", file)).data	×
275
276	multi_outs = {}	×
277	for file in multi_job_out_names:	×
278	multi_outs[file] = QCOutput.multiple_outputs_from_file(	×
279	QCOutput, os.path.join(PymatgenTest.TEST_FILES_DIR, "molecules", file), keep_sub_files=False
280	)
281
282	for key in property_list:	×
283	print("Testing ", key)	×
284	self._test_property(key, single_outs, multi_outs)	×
285
286	@unittest.skipIf((openbabel is None), "OpenBabel not installed.")	1✔
287	def test_structural_change(self):	1✔
288	t1 = Molecule.from_file(os.path.join(PymatgenTest.TEST_FILES_DIR, "molecules", "structural_change", "t1.xyz"))	×
289	t2 = Molecule.from_file(os.path.join(PymatgenTest.TEST_FILES_DIR, "molecules", "structural_change", "t2.xyz"))	×
290	t3 = Molecule.from_file(os.path.join(PymatgenTest.TEST_FILES_DIR, "molecules", "structural_change", "t3.xyz"))	×
291
292	thio_1 = Molecule.from_file(	×
293	os.path.join(PymatgenTest.TEST_FILES_DIR, "molecules", "structural_change", "thiophene1.xyz")
294	)
295	thio_2 = Molecule.from_file(	×
296	os.path.join(PymatgenTest.TEST_FILES_DIR, "molecules", "structural_change", "thiophene2.xyz")
297	)
298
299	frag_1 = Molecule.from_file(	×
300	os.path.join(
301	PymatgenTest.TEST_FILES_DIR, "molecules", "new_qchem_files", "test_structure_change", "frag_1.xyz"
302	)
303	)
304	frag_2 = Molecule.from_file(	×
305	os.path.join(
306	PymatgenTest.TEST_FILES_DIR, "molecules", "new_qchem_files", "test_structure_change", "frag_2.xyz"
307	)
308	)
309
310	assert check_for_structure_changes(t1, t1) == "no_change"	×
311	assert check_for_structure_changes(t2, t3) == "no_change"	×
312	assert check_for_structure_changes(t1, t2) == "fewer_bonds"	×
313	assert check_for_structure_changes(t2, t1) == "more_bonds"	×
314
315	assert check_for_structure_changes(thio_1, thio_2) == "unconnected_fragments"	×
316
317	assert check_for_structure_changes(frag_1, frag_2) == "bond_change"	×
318
319	def test_NBO_parsing(self):	1✔
320	data = QCOutput(os.path.join(PymatgenTest.TEST_FILES_DIR, "molecules", "new_qchem_files", "nbo.qout")).data	1✔
321	assert len(data["nbo_data"]["natural_populations"]) == 3	1✔
322	assert len(data["nbo_data"]["hybridization_character"]) == 6	1✔
323	assert len(data["nbo_data"]["perturbation_energy"]) == 2	1✔
324	assert data["nbo_data"]["natural_populations"][0]["Density"][5] == -0.08624	1✔
325	assert data["nbo_data"]["hybridization_character"][4]["atom 2 pol coeff"][35] == "-0.7059"	1✔
326	next_to_last = list(data["nbo_data"]["perturbation_energy"][-1]["fock matrix element"])[-2]	1✔
327	assert data["nbo_data"]["perturbation_energy"][-1]["fock matrix element"][next_to_last] == 0.071	1✔
328	assert data["nbo_data"]["perturbation_energy"][0]["acceptor type"][0] == "RY*"	1✔
329
330	def test_NBO7_parsing(self):	1✔
331	data = QCOutput(os.path.join(PymatgenTest.TEST_FILES_DIR, "molecules", "new_qchem_files", "nbo7_1.qout")).data	1✔
332	assert data["nbo_data"]["perturbation_energy"][0]["perturbation energy"][9] == 15.73	1✔
333	assert len(data["nbo_data"]["perturbation_energy"][0]["donor bond index"]) == 84	1✔
334	assert len(data["nbo_data"]["perturbation_energy"][1]["donor bond index"]) == 29	1✔
335
336	data = QCOutput(os.path.join(PymatgenTest.TEST_FILES_DIR, "molecules", "new_qchem_files", "nbo7_2.qout")).data	1✔
337	assert data["nbo_data"]["perturbation_energy"][0]["perturbation energy"][13] == 32.93	1✔
338	assert data["nbo_data"]["perturbation_energy"][0]["acceptor type"][13] == "LV"	1✔
339	assert data["nbo_data"]["perturbation_energy"][0]["acceptor type"][12] == "RY"	1✔
340	assert data["nbo_data"]["perturbation_energy"][0]["acceptor atom 1 symbol"][12] == "Mg"	1✔
341
342	data = QCOutput(os.path.join(PymatgenTest.TEST_FILES_DIR, "molecules", "new_qchem_files", "nbo7_3.qout")).data	1✔
343	assert data["nbo_data"]["perturbation_energy"][0]["perturbation energy"][13] == 34.54	1✔
344	assert data["nbo_data"]["perturbation_energy"][0]["acceptor type"][13] == "BD*"	1✔
345	assert data["nbo_data"]["perturbation_energy"][0]["acceptor atom 1 symbol"][13] == "B"	1✔
346	assert data["nbo_data"]["perturbation_energy"][0]["acceptor atom 2 symbol"][13] == "Mg"	1✔
347	assert data["nbo_data"]["perturbation_energy"][0]["acceptor atom 2 number"][13] == 3	1✔
348
349	def test_NBO5_vs_NBO7_hybridization_character(self):	1✔
350	data5 = QCOutput(os.path.join(PymatgenTest.TEST_FILES_DIR, "molecules", "new_qchem_files", "nbo5_1.qout")).data	1✔
351	data7 = QCOutput(os.path.join(PymatgenTest.TEST_FILES_DIR, "molecules", "new_qchem_files", "nbo7_1.qout")).data	1✔
352	assert len(data5["nbo_data"]["hybridization_character"]) == len(data7["nbo_data"]["hybridization_character"])	1✔
353	assert (	1✔
354	data5["nbo_data"]["hybridization_character"][4]["atom 2 pol coeff"][9]
355	== data7["nbo_data"]["hybridization_character"][4]["atom 2 pol coeff"][9]
356	)
357	assert (	1✔
358	data5["nbo_data"]["hybridization_character"][0]["s"][0]
359	== data7["nbo_data"]["hybridization_character"][0]["s"][0]
360	)
361	assert data5["nbo_data"]["hybridization_character"][1]["bond index"][7] == "149"	1✔
362	assert data7["nbo_data"]["hybridization_character"][1]["bond index"][7] == "21"	1✔
363
364	def test_NBO7_infinite_e2pert(self):	1✔
365	data = QCOutput(os.path.join(PymatgenTest.TEST_FILES_DIR, "molecules", "new_qchem_files", "nbo7_inf.qout")).data	1✔
366	assert data["nbo_data"]["perturbation_energy"][0]["perturbation energy"][0] == float("inf")	1✔
367
368	def test_isosvp_water(self):	1✔
369	data = QCOutput(	1✔
370	os.path.join(PymatgenTest.TEST_FILES_DIR, "molecules", "new_qchem_files", "isosvp_water_single.qcout")
371	).data
372	assert data["solvent_method"] == "ISOSVP"	1✔
373
374	# ISOSVP parameters
375	assert data["solvent_data"]["isosvp"]["isosvp_dielectric"] == 78.39	1✔
376	assert data["solvent_data"]["isosvp"]["final_soln_phase_e"] == -40.4850599393	1✔
377	assert data["solvent_data"]["isosvp"]["solute_internal_e"] == -40.4846329762	1✔
378	assert data["solvent_data"]["isosvp"]["change_solute_internal_e"] == 0.0000121967	1✔
379	assert data["solvent_data"]["isosvp"]["reaction_field_free_e"] == -0.0004269631	1✔
380	assert data["solvent_data"]["isosvp"]["total_solvation_free_e"] == -0.0004147664	1✔
381
382	# CMIRS parameters
383	assert data["solvent_data"]["cmirs"]["CMIRS_enabled"] is False	1✔
384
385	def test_isosvp_dielst10(self):	1✔
386	data = QCOutput(	1✔
387	os.path.join(PymatgenTest.TEST_FILES_DIR, "molecules", "new_qchem_files", "isosvp_dielst10_single.qcout")
388	).data
389	assert data["solvent_method"] == "ISOSVP"	1✔
390
391	# ISOSVP parameters
392	assert data["solvent_data"]["isosvp"]["isosvp_dielectric"] == 10	1✔
393	assert data["solvent_data"]["isosvp"]["final_soln_phase_e"] == -40.4850012952	1✔
394	assert data["solvent_data"]["isosvp"]["solute_internal_e"] == -40.4846362547	1✔
395	assert data["solvent_data"]["isosvp"]["change_solute_internal_e"] == 0.0000089182	1✔
396	assert data["solvent_data"]["isosvp"]["reaction_field_free_e"] == -0.0003650405	1✔
397	assert data["solvent_data"]["isosvp"]["total_solvation_free_e"] == -0.0003561223	1✔
398
399	# CMIRS parameters
400	assert data["solvent_data"]["cmirs"]["CMIRS_enabled"] is False	1✔
401
402	def test_cmirs_benzene(self):	1✔
403	data = QCOutput(	1✔
404	os.path.join(PymatgenTest.TEST_FILES_DIR, "molecules", "new_qchem_files", "cmirs_benzene_single.qcout")
405	).data
406	assert data["solvent_method"] == "ISOSVP"	1✔
407	assert data["solvent_data"]["isosvp"]["isosvp_dielectric"] == 2.28	1✔
408	assert data["solvent_data"]["cmirs"]["CMIRS_enabled"] is True	1✔
409	assert data["solvent_data"]["cmirs"]["dispersion_e"] == 0.6955542829	1✔
410	assert data["solvent_data"]["cmirs"]["exchange_e"] == 0.2654553686	1✔
411	assert data["solvent_data"]["cmirs"]["min_neg_field_e"] == 0.0006019665	1✔
412	assert data["solvent_data"]["cmirs"]["max_pos_field_e"] == 0.0178177740	1✔
413
414	def test_cmirs_dielst10(self):	1✔
415	data = QCOutput(	1✔
416	os.path.join(PymatgenTest.TEST_FILES_DIR, "molecules", "new_qchem_files", "cmirs_dielst10_single.qcout")
417	).data
418	assert data["solvent_method"] == "ISOSVP"	1✔
419	assert data["solvent_data"]["isosvp"]["isosvp_dielectric"] == 10	1✔
420	assert data["solvent_data"]["cmirs"]["CMIRS_enabled"] is True	1✔
421	assert data["solvent_data"]["cmirs"]["dispersion_e"] == 0.6955550107	1✔
422	assert data["solvent_data"]["cmirs"]["exchange_e"] == 0.2652679507	1✔
423	assert data["solvent_data"]["cmirs"]["min_neg_field_e"] == 0.0005235850	1✔
424	assert data["solvent_data"]["cmirs"]["max_pos_field_e"] == 0.0179866718	1✔
425
426	def test_cmirs_water(self):	1✔
427	data = QCOutput(	1✔
428	os.path.join(PymatgenTest.TEST_FILES_DIR, "molecules", "new_qchem_files", "cmirs_water_single.qcout")
429	).data
430	assert data["solvent_method"] == "ISOSVP"	1✔
431
432	# ISOSVP parameters
433	assert data["solvent_data"]["isosvp"]["isosvp_dielectric"] == 78.39	1✔
434	assert data["solvent_data"]["isosvp"]["final_soln_phase_e"] == -40.4752415075	1✔
435	assert data["solvent_data"]["isosvp"]["solute_internal_e"] == -40.4748535587	1✔
436	assert data["solvent_data"]["isosvp"]["change_solute_internal_e"] == 0.0000122982	1✔
437	assert data["solvent_data"]["isosvp"]["reaction_field_free_e"] == -0.0003879488	1✔
438	assert data["solvent_data"]["isosvp"]["total_solvation_free_e"] == 0.0037602703	1✔
439
440	# CMIRS parameters
441	assert data["solvent_data"]["cmirs"]["CMIRS_enabled"] is True	1✔
442	assert data["solvent_data"]["cmirs"]["dispersion_e"] == 0.6722278965	1✔
443	assert data["solvent_data"]["cmirs"]["exchange_e"] == 0.2652032616	1✔
444	assert data["solvent_data"]["cmirs"]["min_neg_field_e"] == 0.0004967767	1✔
445	assert data["solvent_data"]["cmirs"]["max_pos_field_e"] == 0.0180445935	1✔
446
447	def test_NBO_hyperbonds(self):	1✔
448	data = QCOutput(os.path.join(PymatgenTest.TEST_FILES_DIR, "molecules", "new_qchem_files", "hyper.qout")).data	1✔
449	assert len(data["nbo_data"]["hyperbonds"][0]["hyperbond index"].keys()) == 2	1✔
450	assert data["nbo_data"]["hyperbonds"][0]["BD(A-B)"][1] == 106	1✔
451	assert data["nbo_data"]["hyperbonds"][0]["bond atom 2 symbol"][0] == "C"	1✔
452	assert data["nbo_data"]["hyperbonds"][0]["occ"][1] == 3.0802	1✔
453
454	def test_NBO_3C(self):	1✔
455	data = QCOutput(os.path.join(PymatgenTest.TEST_FILES_DIR, "molecules", "new_qchem_files", "3C.qout")).data	1✔
456	assert len(data["nbo_data"]["hybridization_character"]) == 3	1✔
457	assert data["nbo_data"]["hybridization_character"][2]["type"][0] == "3C"	1✔
458	assert data["nbo_data"]["hybridization_character"][2]["type"][10] == "3Cn"	1✔
459	assert data["nbo_data"]["hybridization_character"][2]["type"][20] == "3C*"	1✔
460	assert data["nbo_data"]["hybridization_character"][2]["atom 3 pol coeff"][15] == "0.3643"	1✔
461	assert data["nbo_data"]["hybridization_character"][2]["atom 3 polarization"][8] == "56.72"	1✔
462	assert data["nbo_data"]["hybridization_character"][2]["atom 3 symbol"][3] == "B"	1✔
463	assert data["nbo_data"]["perturbation_energy"][0]["donor atom 2 number"][2592] == 36	1✔
464	assert data["nbo_data"]["perturbation_energy"][0]["donor atom 2 symbol"][2125] == "B12"	1✔
465	assert data["nbo_data"]["perturbation_energy"][0]["donor atom 2 number"][2593] == "info_is_from_3C"	1✔
466	assert data["nbo_data"]["perturbation_energy"][0]["acceptor type"][723] == "3C*"	1✔
467	assert data["nbo_data"]["perturbation_energy"][0]["perturbation energy"][3209] == 3.94	1✔
468
469
470	if __name__ == "__main__":	1✔
471	unittest.main()	×

materialsproject / pymatgen / 4075885785

Source File Press 'n' to go to next uncovered line, 'b' for previous

Source File
Press 'n' to go to next uncovered line, 'b' for previous