from pathlib import Path import pytest import numpy as np @pytest.fixture(scope="session") def test_dir(): return Path(__file__).parent.parent.parent.joinpath("test_files").resolve() def assert_schemas_equal(test_schema, valid_schema): """ Recursively test all items in valid_schema are present and equal in test_schema. While test_schema can be a pydantic schema or dictionary, the valid schema must be a (nested) dictionary. This function automatically handles accessing the attributes of classes in the test_schema. Args: test_schema: A pydantic schema or dictionary of the schema. valid_schema: A (nested) dictionary specifying the key and values that must be present in test_schema. This is what the generated test_schema will be tested against """ from pydantic import BaseModel if isinstance(valid_schema, dict): for key, sub_valid_schema in valid_schema.items(): if isinstance(key, str) and hasattr(test_schema, key): sub_test_schema = getattr(test_schema, key) if key == "initial_molecule": sub_test_schema = sub_test_schema.as_dict() elif key == "optimized_molecule": sub_test_schema = ( sub_test_schema.as_dict() if sub_test_schema else {} ) elif not isinstance(test_schema, BaseModel): sub_test_schema = test_schema[key] else: raise ValueError(f"{type(test_schema)} does not have field: {key}") return assert_schemas_equal(sub_test_schema, sub_valid_schema) elif isinstance(valid_schema, list): for i, sub_valid_schema in enumerate(valid_schema): return assert_schemas_equal(test_schema[i], sub_valid_schema) elif isinstance(valid_schema, np.ndarray): assert np.array_equal(test_schema, valid_schema) elif isinstance(valid_schema, float): assert test_schema == pytest.approx(valid_schema) else: assert test_schema == valid_schema class SchemaTestData: """Dummy class to be used to contain all test data information""" class SinglePointTest(SchemaTestData): folder = "qchem_sp_test" task_files = { "standard": { "qcinput_file": "mol.qin.gz", "qcoutput_file": "mol.qout.gz", } } objects = {"standard": []} task_doc = { "calcs_reversed": [ { "output": { "mulliken": [np.array([-0.713178, 0.357278, 0.3559])], "resp": [np.array([-0.872759, 0.436379, 0.436379])], "final_energy": -76.4493700739, }, "input": { "charge": 0, "rem": { "job_type": "sp", "basis": "def2-qzvppd", "max_scf_cycles": "100", "gen_scfman": "true", "xc_grid": "3", "thresh": "14", "s2thresh": "16", "scf_algorithm": "diis", "resp_charges": "true", "symmetry": "false", "sym_ignore": "true", "method": "wb97mv", "solvent_method": "smd", "ideriv": "1", }, "job_type": "sp", }, } ], "input": { "initial_molecule": { "@module": "pymatgen.core.structure", "@class": "Molecule", "charge": 0.0, "spin_multiplicity": 1, "sites": [ { "name": "O", "species": [{"element": "O", "occu": 1}], "xyz": [-0.80595, 2.22952, -0.01914], "properties": {}, "label": "O", }, { "name": "H", "species": [{"element": "H", "occu": 1}], "xyz": [0.18338, 2.20176, 0.01351], "properties": {}, "label": "H", }, { "name": "H", "species": [{"element": "H", "occu": 1}], "xyz": [-1.09531, 1.61602, 0.70231], "properties": {}, "label": "H", }, ], }, "rem": { "job_type": "sp", "basis": "def2-qzvppd", "max_scf_cycles": "100", "gen_scfman": "true", "xc_grid": "3", "thresh": "14", "s2thresh": "16", "scf_algorithm": "diis", "resp_charges": "true", "symmetry": "false", "sym_ignore": "true", "method": "wb97mv", "solvent_method": "smd", "ideriv": "1", }, "level_of_theory": "wB97M-V/def2-QZVPPD/SMD", "task_type": "Single Point", "calc_type": "wB97M-V/def2-QZVPPD/SMD Single Point", "solvation_lot_info": "wB97M-V/def2-QZVPPD/SMD(SOLVENT=WATER)", }, "output": { "mulliken": [np.array([-0.713178, 0.357278, 0.3559])], "resp": [np.array([-0.872759, 0.436379, 0.436379])], "final_energy": -76.4493700739, "dipoles": { "total": 2.4648, "dipole": [np.array([1.4227, -1.3039, 1.5333])], "RESP_total": 2.5411, "RESP_dipole": [np.array([1.4672, -1.3441, 1.5806])], }, }, "custodian": [ { "job": { "@module": "custodian.qchem.jobs", "@class": "QCJob", "@version": "2022.5.26", "qchem_command": ["qchem"], "max_cores": "40", "multimode": "openmp", "input_file": "mol.qin", "output_file": "mol.qout", "qclog_file": "mol.qclog", "suffix": "", "calc_loc": "/tmp", "nboexe": None, "save_scratch": False, "backup": "true", }, "corrections": [], } ], } class OptimizationTest(SchemaTestData): folder = "qchem_opt_test" task_files = { "standard": { "qcinput_file": "mol.qin.gz", "qcoutput_file": "mol.qout.gz", } } objects = {"standard": []} task_doc = { "calcs_reversed": [ { "output": { "optimized_molecule": { "@module": "pymatgen.core.structure", "@class": "Molecule", "charge": 0, "spin_multiplicity": 1, "sites": [ { "name": "O", "species": [{"element": "O", "occu": 1}], "xyz": [-0.8008592596, 2.2248298937, -0.0136245943], "properties": {}, "label": "O", }, { "name": "H", "species": [{"element": "H", "occu": 1}], "xyz": [0.1637955748, 2.1962925542, 0.0199393927], "properties": {}, "label": "H", }, { "name": "H", "species": [{"element": "H", "occu": 1}], "xyz": [-1.0808163152, 1.6261775521, 0.6903652017], "properties": {}, "label": "H", }, ], }, "mulliken": [-0.373491, 0.186964, 0.186527], "resp": [-0.89522, 0.44761, 0.44761], "final_energy": -76.358341626913, }, "input": { "charge": 0, "rem": { "job_type": "sp", "basis": "def2-qzvppd", "max_scf_cycles": "100", "gen_scfman": "true", "xc_grid": "3", "thresh": "14", "s2thresh": "16", "scf_algorithm": "diis", "resp_charges": "true", "symmetry": "false", "sym_ignore": "true", "method": "wb97mv", "solvent_method": "smd", "ideriv": "1", }, "job_type": "sp", }, } ], "input": { "initial_molecule": { "@module": "pymatgen.core.structure", "@class": "Molecule", "charge": 0.0, "spin_multiplicity": 1, "sites": [ { "name": "O", "species": [{"element": "O", "occu": 1}], "xyz": [-0.80595, 2.22952, -0.01914], "properties": {}, "label": "O", }, { "name": "H", "species": [{"element": "H", "occu": 1}], "xyz": [0.18338, 2.20176, 0.01351], "properties": {}, "label": "H", }, { "name": "H", "species": [{"element": "H", "occu": 1}], "xyz": [-1.09531, 1.61602, 0.70231], "properties": {}, "label": "H", }, ], }, "rem": { "job_type": "opt", "basis": "def2-svpd", "max_scf_cycles": "100", "gen_scfman": "true", "xc_grid": "3", "thresh": "14", "s2thresh": "16", "scf_algorithm": "diis", "resp_charges": "true", "symmetry": "false", "sym_ignore": "true", "method": "wb97mv", "solvent_method": "smd", "ideriv": "1", "geom_opt2": "3", }, "level_of_theory": "wB97M-V/def2-SVPD/SMD", "task_type": "Geometry Optimization", "calc_type": "wB97M-V/def2-SVPD/SMD Geometry Optimization", "solvation_lot_info": "wB97M-V/def2-SVPD/SMD(SOLVENT=WATER)", }, "output": { "initial_molecule": { "@module": "pymatgen.core.structure", "@class": "Molecule", "charge": 0.0, "spin_multiplicity": 1, "sites": [ { "name": "O", "species": [{"element": "O", "occu": 1}], "xyz": [-0.80595, 2.22952, -0.01914], "properties": {}, "label": "O", }, { "name": "H", "species": [{"element": "H", "occu": 1}], "xyz": [0.18338, 2.20176, 0.01351], "properties": {}, "label": "H", }, { "name": "H", "species": [{"element": "H", "occu": 1}], "xyz": [-1.09531, 1.61602, 0.70231], "properties": {}, "label": "H", }, ], }, "optimized_molecule": { "@module": "pymatgen.core.structure", "@class": "Molecule", "charge": 0, "spin_multiplicity": 1, "sites": [ { "name": "O", "species": [{"element": "O", "occu": 1}], "xyz": [-0.8008592596, 2.2248298937, -0.0136245943], "properties": {}, "label": "O", }, { "name": "H", "species": [{"element": "H", "occu": 1}], "xyz": [0.1637955748, 2.1962925542, 0.0199393927], "properties": {}, "label": "H", }, { "name": "H", "species": [{"element": "H", "occu": 1}], "xyz": [-1.0808163152, 1.6261775521, 0.6903652017], "properties": {}, "label": "H", }, ], }, "mulliken": [-0.373491, 0.186964, 0.186527], "resp": [-0.89522, 0.44761, 0.44761], "final_energy": -76.358341626913, }, "custodian": [ { "job": { "@module": "custodian.qchem.jobs", "@class": "QCJob", "@version": "2022.5.26", "qchem_command": ["qchem"], "max_cores": "40", "multimode": "openmp", "input_file": "mol.qin", "output_file": "mol.qout", "qclog_file": "mol.qclog", "suffix": "", "calc_loc": "/tmp", "nboexe": "null", "save_scratch": "false", "backup": "true", }, "corrections": [], } ], } objects = {cls.__name__: cls for cls in SchemaTestData.__subclasses__()} def get_test_object(object_name): """Get the schema test data object from the class name.""" return objects[object_name]