def test_makease_works_with_openshells(self):
"""Ensure makease works from parsed data for open-shell molecules."""
# make sure we can construct an open shell molecule
data = ccopen("data/ORCA/basicORCA4.2/dvb_sp_un.out").parse()
# Check we have no gradients, as they will be generated by ASE.
with self.assertRaises(AttributeError):
data.grads
dvb_sp_un = cclib2ase.makease(
data.atomcoords[-1],
data.atomnos,
data.atomcharges["mulliken"],
data.atomspins["mulliken"],
data.atommasses,
)
# check whether converting back gives the expected data
ase_data = cclib2ase.makecclib(dvb_sp_un)
assert np.allclose(ase_data.atomcoords, [data.atomcoords[-1]])
assert np.allclose(ase_data.atomnos, data.atomnos)
assert np.allclose(ase_data.atomcharges["mulliken"],
data.atomcharges["mulliken"])
assert np.allclose(ase_data.atomspins["mulliken"],
data.atomspins["mulliken"])
assert np.allclose(ase_data.atommasses, data.atommasses)
assert np.isclose(ase_data.charge, data.charge)
assert np.isclose(ase_data.mult, data.mult)
assert np.isclose(ase_data.natom, len(data.atomnos))
assert np.isclose(ase_data.temperature, 0)
# make sure our object is compatible with ASE API
dvb_sp_un.calc = EMT(label="dvb_sp_un") # not a serious calculator!
# converting back should give updated results
ase_data = cclib2ase.makecclib(dvb_sp_un)
assert np.allclose(ase_data.atomcoords, [data.atomcoords[-1]])
assert np.allclose(ase_data.atomnos, data.atomnos)
assert np.allclose(ase_data.atommasses, data.atommasses)
assert np.allclose(ase_data.atomcharges["mulliken"],
data.atomcharges["mulliken"])
assert np.allclose(
ase_data.atomspins["mulliken"],
0) # spin densities not supported but overwritten by EMT
assert np.isclose(ase_data.charge, data.charge)
assert np.isclose(ase_data.mult, 1)
assert np.isclose(ase_data.natom, len(data.atomnos))
assert np.isclose(ase_data.temperature, 0)
# Both energies and gradients are from the EMT calculation.
assert np.allclose(ase_data.scfenergies, [7.016800805424298])
assert np.shape(ase_data.grads) == (1, ase_data.natom, 3)
def test_makecclib_retrieves_optimization(self):
"""Ensure makecclib works with native ASE Atoms objects."""
h2 = Atoms("H2", positions=[[0, 0, 0], [0, 0, 0.7]])
# Check whether converting back gives the expected data,
data = cclib2ase.makecclib(h2)
assert np.allclose(data.atomcoords, [[[0, 0, 0], [0, 0, 0.7]]])
assert np.allclose(data.atomnos, [1, 1])
assert np.allclose(data.atommasses, [1.008, 1.008])
assert np.isclose(data.natom, 2)
assert np.isclose(data.charge, 0)
assert np.isclose(data.mult, 1)
assert np.isclose(data.temperature, 0)
def test_makease_allows_optimization(self):
"""Ensure makease works from direct input."""
h2 = cclib2ase.makease([[0, 0, 0], [0, 0, 0.7]], [1, 1])
# Check whether converting back gives the expected data,
data = cclib2ase.makecclib(h2)
assert np.allclose(data.atomcoords, [[[0, 0, 0], [0, 0, 0.7]]])
assert np.allclose(data.atomnos, [1, 1])
assert np.allclose(data.atommasses, [1.008, 1.008])
assert np.isclose(data.natom, 2)
assert np.isclose(data.charge, 0)
assert np.isclose(data.mult, 1)
assert np.isclose(data.temperature, 0)
def test_makease_works_with_closedshells(self):
"""Ensure makease works from parsed data for closed-shell molecules."""
# Make sure we can construct a closed shell molecule.
data = ccopen("data/ORCA/basicORCA4.2/dvb_ir.out").parse()
dvb_ir = cclib2ase.makease(
data.atomcoords[-1],
data.atomnos,
data.atomcharges["mulliken"],
None, # no atomspins
data.atommasses,
)
# check whether converting back gives the expected data.
ase_data = cclib2ase.makecclib(dvb_ir)
assert np.allclose(ase_data.atomcoords, [data.atomcoords[-1]])
assert np.allclose(ase_data.atomnos, data.atomnos)
assert np.allclose(ase_data.atomcharges["mulliken"],
data.atomcharges["mulliken"])
assert np.allclose(ase_data.atomspins["mulliken"], 0)
assert np.allclose(ase_data.atommasses, data.atommasses)
assert np.isclose(ase_data.charge, data.charge, atol=1e-5)
assert np.isclose(ase_data.mult, data.mult)
assert np.isclose(ase_data.natom, len(data.atomnos))
assert np.isclose(ase_data.temperature, 0)