def test_resp_noopt_orient(self, dmso_opt, ref):
charge_options = psiresp.ChargeOptions(equivalent_methyls=True)
orientation_options = psiresp.OrientationOptions(n_reorientations=2)
r = self.cls.from_molecules([dmso_opt],
orientation_options=orientation_options)
charges = r.run(charge_constraint_options=charge_options)
assert_allclose(charges, ref, rtol=0.05, atol=1e-4)
def test_resp_opt(self, ref):
mol = [mol_from_file(self.molfile)]
orientation_options = psiresp.OrientationOptions(n_reorientations=2)
charge_options = psiresp.ChargeOptions(equivalent_methyls=True)
r = self.cls.from_molecules(mol,
optimize_geometry=True,
orientation_options=orientation_options)
charges = r.run(charge_options=charge_options)
assert_allclose(charges, ref, rtol=0.05, atol=1e-3)
def test_resp_noopt(self, ref):
orientation_options = psiresp.OrientationOptions(n_reorientations=2)
opt = [mol_from_file('{}_c1_ATB_opt.xyz'.format(self.molname))]
charge_options = psiresp.ChargeOptions(equivalent_methyls=True)
r = self.cls.from_molecules(opt,
optimize_geometry=False,
orientation_options=orientation_options)
charges = r.run(charge_options=charge_options)
# no idea which point density ATB uses
assert_allclose(charges, ref, rtol=0.05, atol=1e-3)
def nme2ala2(self):
mols = [mol_from_file(f) for f in self.nme2ala2_names]
orient = [(5, 18, 19), (19, 18, 5), (6, 19, 20), (20, 19, 6)]
or_options = psiresp.OrientationOptions(reorientations=orient,
keep_original=False)
chrconstrs = {0: [20, 21, 22, 23, 24, 25], 0.6163: [18], -0.5722: [19]}
chrequivs = [[10, 14], [11, 12, 13, 15, 16, 17]]
ch_options = psiresp.ChargeOptions(charge_equivalences=chrequivs,
charge_constraints=chrconstrs,
equivalent_sp3_hydrogens=False)
resp = psiresp.Resp.from_molecules(
mols,
charge=0,
orientation_options=or_options,
charge_constraint_options=ch_options,
optimize_geometry=self.opt,
name='nme2ala2')
return resp
def methylammonium(self):
mols = [mol_from_file(f) for f in self.methylammonium_names]
orient = [(1, 5, 7), (7, 5, 1)]
or_options = psiresp.OrientationOptions(reorientations=orient,
keep_original=False)
chrconstrs = []
chrequivs = [[6, 7, 8]]
ch_options = psiresp.ChargeOptions(charge_equivalences=chrequivs,
charge_constraints=chrconstrs,
equivalent_sp3_hydrogens=False)
resp = psiresp.Resp.from_molecules(
mols,
charge=1,
multiplicity=1,
orientation_options=or_options,
charge_constraint_options=ch_options,
optimize_geometry=self.opt,
name='methylammonium')
return resp
def test_multi_mol(self, stage_2, a, nme2ala2, methylammonium, redname):
multifit_charges = charges_from_red_file(f"amm_dimethyl_{redname}.dat")
xyz = methylammonium.conformers[0].orientations[0].coordinates
r = psiresp.MultiResp([methylammonium, nme2ala2])
chrconstrs = {
0: [(1, 1), (1, 2), (1, 3), (1, 4), (2, 1), (2, 2), (2, 3), (2, 4),
(2, 5), (2, 6), (2, 7), (2, 8)]
}
ch_options = psiresp.ChargeOptions(charge_constraints=[chrconstrs],
equivalent_sp3_hydrogens=False)
charges = r.run(stage_2=stage_2,
hyp_a1=a,
charge_constraint_options=ch_options)
ref_con = multifit_charges[0][[
0, 1, 2, 3
]].sum() + multifit_charges[1][[0, 1, 2, 3, 4, 5, 6, 7]].sum()
assert_almost_equal(ref_con, 0)
constraint = charges[0][[0, 1, 2, 3]].sum() + charges[1][[
0, 1, 2, 3, 4, 5, 6, 7
]].sum()
assert_almost_equal(constraint, 0)
for charge, ref in zip(charges, multifit_charges):
assert_allclose(charge, ref, rtol=self.rtol, atol=self.atol)
def test_resp_noopt_noorient(self, dmso_orients, ref):
charge_options = psiresp.ChargeOptions(equivalent_methyls=True)
r = self.cls.from_molecules(dmso_orients, charge=0)
charges = r.run(charge_constraint_options=charge_options)
assert_allclose(charges, ref, rtol=0.05, atol=1e-4)