def test_water_minima_data():
# Give it a name
mol_dict = water_dimer_minima.dict()
mol_dict["name"] = "water dimer"
mol = Molecule(orient=True, **mol_dict)
assert len(mol.pretty_print()) == 661
assert len(mol.to_string("psi4")) == 479
assert sum(x == y for x, y in zip(
mol.symbols, ["O", "H", "H", "O", "H", "H"])) == mol.geometry.shape[0]
assert mol.name == "water dimer"
assert mol.molecular_charge == 0
assert mol.molecular_multiplicity == 1
assert np.sum(mol.real) == mol.geometry.shape[0]
assert np.allclose(mol.fragments, [[0, 1, 2], [3, 4, 5]])
assert np.allclose(mol.fragment_charges, [0, 0])
assert np.allclose(mol.fragment_multiplicities, [1, 1])
assert hasattr(mol, "provenance")
assert np.allclose(
mol.geometry,
[
[2.81211080, 0.1255717, 0.0],
[3.48216664, -1.55439981, 0.0],
[1.00578203, -0.1092573, 0.0],
[-2.6821528, -0.12325075, 0.0],
[-3.27523824, 0.81341093, 1.43347255],
[-3.27523824, 0.81341093, -1.43347255],
],
)
assert mol.get_hash() == "3c4b98f515d64d1adc1648fe1fe1d6789e978d34"
def test_water_minima_data():
# Give it a name
mol_dict = water_dimer_minima.dict()
mol_dict['name'] = "water dimer"
mol = Molecule(orient=True, **mol_dict)
assert len(str(mol)) == 662
assert len(mol.to_string()) == 442
assert sum(x == y for x, y in zip(
mol.symbols, ['O', 'H', 'H', 'O', 'H', 'H'])) == mol.geometry.shape[0]
assert mol.name == "water dimer"
assert mol.molecular_charge == 0
assert mol.molecular_multiplicity == 1
assert np.sum(mol.real) == mol.geometry.shape[0]
assert np.allclose(mol.fragments, [[0, 1, 2], [3, 4, 5]])
assert np.allclose(mol.fragment_charges, [0, 0])
assert np.allclose(mol.fragment_multiplicities, [1, 1])
assert hasattr(mol, "provenance")
assert np.allclose(
mol.geometry,
[[2.81211080, 0.1255717, 0.], [3.48216664, -1.55439981, 0.],
[1.00578203, -0.1092573, 0.], [-2.6821528, -0.12325075, 0.],
[-3.27523824, 0.81341093, 1.43347255],
[-3.27523824, 0.81341093, -1.43347255]])
assert mol.get_hash() == "b41f1e38bc4be5482fcd1d4dd53ca7c65146ab91"
def test_molecule_repeated_hashing():
mol = Molecule(**{
'symbols': ['H', 'O', 'O', 'H'],
'geometry': [
1.7317, 1.2909, 1.037100000000001,
1.3156, -0.0074, -0.2807,
-1.3143, 0.0084, -0.2741,
-1.7241, -1.3079, 1.0277
]
}) # yapf: disable
h1 = mol.get_hash()
assert mol.get_molecular_formula() == "H2O2"
mol2 = Molecule(orient=False, **mol.dict())
assert h1 == mol2.get_hash()
mol3 = Molecule(orient=False, **mol2.dict())
assert h1 == mol3.get_hash()
def test_molecule_repeated_hashing():
mol = Molecule(
**{
"symbols": ["H", "O", "O", "H"],
"geometry": [
[1.7317, 1.2909, 1.037100000000001],
[1.3156, -0.0074, -0.2807],
[-1.3143, 0.0084, -0.2741],
[-1.7241, -1.3079, 1.0277],
],
})
h1 = mol.get_hash()
assert mol.get_molecular_formula() == "H2O2"
mol2 = Molecule(orient=False, **mol.dict())
assert h1 == mol2.get_hash()
mol3 = Molecule(orient=False, **mol2.dict())
assert h1 == mol3.get_hash()
