def test_to_from_file_complex(tmp_path, dtype):
p = tmp_path / ("water." + dtype)
water_dimer_minima.to_file(p)
mol = Molecule.from_file(p)
assert mol == water_dimer_minima
def test_from_file_json(tmp_path):
p = tmp_path / "water.json"
p.write_text(water_dimer_minima.json())
mol = Molecule.from_file(p)
assert mol.compare(water_dimer_minima)
def test_from_file_string(tmp_path):
p = tmp_path / "water.psimol"
p.write_text(water_dimer_minima.to_string("psi4"))
mol = Molecule.from_file(p)
assert mol.compare(water_dimer_minima)
assert mol.compare(water_dimer_minima.dict())
def test_from_file_numpy(tmp_path):
ele = np.array(water_molecule.atomic_numbers).reshape(-1, 1)
npwater = np.hstack((ele, water_molecule.geometry))
# Try npy
p = tmp_path / "water.npy"
np.save(p, npwater)
mol = Molecule.from_file(p)
assert mol.compare(water_molecule)
def test_to_from_file_simple(tmp_path, dtype, filext):
benchmol = Molecule.from_data("""
O 0 0 0
H 0 1.5 0
H 0 0 1.5
""")
p = tmp_path / ("water." + filext)
benchmol.to_file(p)
mol = Molecule.from_file(p)
assert mol == benchmol
def test_to_from_file_charge_spin(tmp_path, dtype, filext):
benchmol = Molecule.from_data("""
1 2
O 0 0 0
H 0 1.5 0
H 0 0 1.5
""")
p = tmp_path / ("water." + filext)
benchmol.to_file(p, dtype=dtype)
mol = Molecule.from_file(p, dtype=dtype)
assert mol.molecular_charge == 1
assert mol.molecular_multiplicity == 2
assert mol.fragment_charges[0] == 1
assert mol.fragment_multiplicities[0] == 2
assert mol == benchmol
