def test_charged_fragment():
mol = Molecule(symbols=["Li", "Li"],
geometry=[0, 0, 0, 0, 0, 5],
fragment_charges=[0.0, 0.0],
fragment_multiplicities=[2, 2],
fragments=[[0], [1]])
assert mol.molecular_multiplicity == 3
assert mol.molecular_charge == 0
f1 = mol.get_fragment(0)
assert f1.molecular_multiplicity == 2
assert f1.fragment_multiplicities == [2]
assert pytest.approx(f1.molecular_charge) == 0
assert pytest.approx(f1.fragment_charges) == [0]
def test_get_fragment(group_fragments, orient):
mol = Molecule(
**{
"fragments": [[0], [1, 2, 3], [4, 5, 6]],
"symbols": ["he", "o", "h", "h", "o", "h", "h"],
# same geom as test_water_orient but with He at origin
"geometry":
np.array([
[0.0, 0.0, 0.0],
[-1.551007, -0.114520, 0.000000],
[-1.934259, 0.762503, 0.000000],
[-0.599677, 0.040712, 0.000000],
[-0.114520, -1.551007, 10.000000],
[0.762503, -1.934259, 10.000000],
[0.040712, -0.599677, 10.000000],
]) / qcel.constants.bohr2angstroms,
})
assert mol.nelectrons() == 22
assert compare_values(32.25894779318589,
mol.nuclear_repulsion_energy(),
atol=1.0e-5)
assert mol.symbols[0] == "He"
monomers_nelectrons = [2, 10, 10]
monomers_nre = [0.0, 9.163830150548483, 9.163830150548483]
monomers = [
mol.get_fragment(ifr, group_fragments=group_fragments, orient=orient)
for ifr in range(3)
]
for fr in range(3):
assert monomers[fr].nelectrons() == monomers_nelectrons[fr]
assert compare_values(monomers[fr].nuclear_repulsion_energy(),
monomers_nre[fr],
"monomer nre",
atol=1.0e-5)
idimers = [(0, 1), (0, 2), (1, 2), (1, 0), (2, 0), (2, 1)]
dimers_nelectrons = [12, 12, 20, 12, 12, 20]
dimers_nre = [
16.8777971, 10.2097206, 23.4990904, 16.8777971, 10.2097206, 23.4990904
]
dimers = [
mol.get_fragment(rl, group_fragments=group_fragments, orient=orient)
for rl in idimers
]
for ifr in range(len(idimers)):
# print('dd', ifr, idimers[ifr], dimers[ifr].nuclear_repulsion_energy(), dimers[ifr].get_hash())
assert dimers[ifr].nelectrons(
) == dimers_nelectrons[ifr], "dimer nelec"
assert compare_values(dimers[ifr].nuclear_repulsion_energy(),
dimers_nre[ifr],
"dimer nre",
atol=1.0e-5)
if group_fragments and orient:
assert dimers[0].get_hash() != dimers[3].get_hash(
) # atoms out of order
assert dimers[1].get_hash() != dimers[4].get_hash(
) # atoms out of order
assert dimers[2].get_hash() == dimers[5].get_hash()
elif not group_fragments and not orient:
assert dimers[0].get_hash() == dimers[3].get_hash()
assert dimers[1].get_hash() == dimers[4].get_hash()
assert dimers[2].get_hash() == dimers[5].get_hash()
else:
assert 0 # lgtm: [py/unreachable-statement]
ghdimers_nelectrons = [2, 2, 10, 10, 10, 10]
ghdimers_nre = [
0.0, 0.0, 9.163830150548483, 9.163830150548483, 9.163830150548483,
9.163830150548483
]
ghdimers = [
mol.get_fragment(rl,
gh,
group_fragments=group_fragments,
orient=orient) for rl, gh in idimers
]
for ifr in range(len(idimers)):
# print('gh', ifr, idimers[ifr], ghdimers[ifr].nuclear_repulsion_energy(), ghdimers[ifr].get_hash())
assert ghdimers[ifr].nelectrons(
) == ghdimers_nelectrons[ifr], "gh dimer nelec"
assert compare_values(ghdimers[ifr].nuclear_repulsion_energy(),
ghdimers_nre[ifr],
"gh dimer nre",
atol=1.0e-5)
if group_fragments and orient:
assert ghdimers[0].get_hash() != ghdimers[3].get_hash(
) # diff atoms ghosted
assert ghdimers[1].get_hash() != ghdimers[4].get_hash(
) # diff atoms ghosted
assert ghdimers[2].get_hash() == ghdimers[5].get_hash()
elif not group_fragments and not orient:
assert ghdimers[0].get_hash() != ghdimers[3].get_hash(
) # diff atoms ghosted
assert ghdimers[1].get_hash() != ghdimers[4].get_hash(
) # diff atoms ghosted
assert ghdimers[2].get_hash() != ghdimers[5].get_hash(
) # real pattern different
assert not np.allclose(ghdimers[2].real, ghdimers[5].real)
else:
assert 0 # lgtm: [py/unreachable-statement]
