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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]
|
