def test_ric_add_ic(self):
with path("saddle.test.data", "water.xyz") as mol_path:
mol = Utils.load_file(mol_path)
ri_mol = Internal(mol.coordinates, mol.numbers, 0, 1)
ri_mol = ReducedInternal.update_to_reduced_internal(ri_mol)
ri_mol.add_bond(1, 0)
ri_mol.add_bond(1, 2)
ri_mol.add_bond(0, 2)
ri_mol.vspace
ri_mol.add_angle(0, 1, 2)
ri_mol.add_angle(1, 0, 2)
ri_mol.select_key_ic(0, 2)
vp_ref = np.array(
[
[4.40930006e-01, -7.79280781e-01, 6.12072474e-17],
[-5.61408260e-01, -6.12047068e-01, -3.33066907e-16],
[-4.57920570e-01, -3.28254718e-02, -7.16200549e-01],
[-5.22760813e-01, 4.87258745e-02, 5.58315734e-01],
[8.62054537e-02, 1.21112047e-01, -4.18736570e-01],
]
)
for i in range(vp_ref.shape[1]):
assert np.allclose(ri_mol.vspace[:, i], vp_ref[:, i]) or np.allclose(
ri_mol.vspace[:, i], -1 * vp_ref[:, i]
)
ri_mol.set_key_ic_number(1)
assert ri_mol._red_space is None
assert ri_mol._non_red_space is None
def create_ts_state(self, start_with, ratio=0.5, task="ts", flex_sin=True):
"""Create transition state guess structure.
The selection process is based on the linear combination of
internal structure of both reactant and product.
Arguments
---------
start_with : string
The initial structure of transition state to optimize from.
choices:
"reactant" : optimize ts structure from reactant
"product" : optimize ts structure from product
ratio : float, default is 0.5
The ratio of linear combination of ic for reactant and product.
ts = ratio * reactant + (1 - ratio) * product
"""
if start_with == "reactant":
model = self.reactant
elif start_with == "product":
model = self.product
else:
raise InvalidArgumentError(
"The input of start_with is not supported")
if ratio > 1.0 or ratio < 0:
raise InvalidArgumentError("The input of ratio is not supported")
ts_internal = deepcopy(model)
target_ic = (ratio * self.reactant.ic_values +
(1.0 - ratio) * self.product.ic_values)
ts_internal.set_target_ic(target_ic)
# ts_internal.list_ic
ts_internal.converge_to_target_ic(ignore_dihed=False,
flex_sin=flex_sin)
# ts_internal.optimize_to_target_ic(dihed_weight=0, hess_check=False)
# ts_internal.optimize_to_target_ic(method='BFGS')
# dihed_weight=0, hess=True, method="Newton-CG", hess_check=False, max_iter=500
# )
if task == "ts":
ts_internal = ReducedInternal.update_to_reduced_internal(
ts_internal)
elif task == "path":
path_vector = self.product.ic_values - self.reactant.ic_values
ts_internal = PathRI.update_to_path_ri(ts_internal, path_vector)
# change the ts_internal to Class ReducedInternal
self._ts = ts_internal # set _ts attribute
def test_ic_ric_transform(self):
with path("saddle.test.data", "water.xyz") as mol_path:
mol = Utils.load_file(mol_path)
ri_mol = Internal(mol.coordinates, mol.numbers, 0, 1)
ri_mol.add_bond(1, 0)
ri_mol.add_bond(1, 2)
ri_mol.add_bond(0, 2)
ri_mol.add_angle(0, 1, 2)
ri_mol.add_angle(1, 0, 2)
vc_ref = np.array([1.81413724, 1.81413724, 2.96247453, 1.91063401, 0.61547931])
assert np.allclose(ri_mol.ic_values, vc_ref)
ri_mol = ReducedInternal.update_to_reduced_internal(ri_mol)
assert isinstance(ri_mol, ReducedInternal)
ri_mol.set_key_ic_number(2)
ri_mol.select_key_ic(0, 2)
print(ri_mol.vspace)
vp_ref = np.array(
[
[4.40930006e-01, -7.79280781e-01, 6.12072474e-17],
[-5.61408260e-01, -6.12047068e-01, -3.33066907e-16],
[-4.57920570e-01, -3.28254718e-02, -7.16200549e-01],
[-5.22760813e-01, 4.87258745e-02, 5.58315734e-01],
[8.62054537e-02, 1.21112047e-01, -4.18736570e-01],
]
)
for i in range(vp_ref.shape[1]):
assert np.allclose(ri_mol.vspace[:, i], vp_ref[:, i]) or np.allclose(
ri_mol.vspace[:, i], -1 * vp_ref[:, i]
)
ri_mol.set_key_ic_number(1)
assert ri_mol._red_space is None
assert ri_mol._non_red_space is None
ri_mol.set_key_ic_number(2)
for i in range(vp_ref.shape[1]):
assert np.allclose(ri_mol.vspace[:, i], vp_ref[:, i]) or np.allclose(
ri_mol.vspace[:, i], -1 * vp_ref[:, i]
)
new_coor = np.array(
[
[1.40, -0.93019123, -0.0],
[-0.0, 0.11720081, -0.0],
[-1.40, -0.93019123, -0.0],
]
)
ri_mol.set_new_coordinates(new_coor)
ref_ic = [
1.7484364736491811,
2.8,
1.7484364736491811,
1.8569769819,
0.6423078258,
]
assert np.allclose(ri_mol.ic_values, ref_ic)
ri_mol.vspace
assert ri_mol._red_space is not None
assert ri_mol._non_red_space is not None
print(ri_mol._red_space)
ri_mol.add_angle(0, 2, 1)
print(ri_mol._red_space)
assert ri_mol._red_space is None
assert ri_mol._non_red_space is None