def test_align_separate_v_space(self):
# test for given key_ic_num
random_a = np.random.rand(5, 5)
random_b = np.random.rand(5, 5)
target_v = np.linalg.eigh(np.dot(random_a, random_a.T))[1]
rotate_v = np.linalg.eigh(np.dot(random_b, random_b.T))[1]
new_rot_v = ReducedInternal._align_vspace_separate(target_v, rotate_v, 3)
assert_allclose(target_v, new_rot_v)
# test for 0 key_ic_num
random_a = np.random.rand(5, 5)
random_b = np.random.rand(5, 5)
target_v = np.linalg.eigh(np.dot(random_a, random_a.T))[1]
rotate_v = np.linalg.eigh(np.dot(random_b, random_b.T))[1]
new_rot_v = ReducedInternal._align_vspace_separate(target_v, rotate_v, 0)
assert_allclose(target_v, new_rot_v)
# test for different dimension
random_c = np.random.rand(5, 3)
random_d = np.random.rand(5, 3)
target_v2 = np.linalg.svd(random_c)[0][:, :3]
ref_tar = target_v2.copy()
rotate_v2 = np.linalg.svd(random_d)[0][:, :3]
new_rot_v2 = ReducedInternal._align_vspace_separate(target_v2, rotate_v2, 1)
assert_allclose(target_v2, new_rot_v2)
assert_allclose(ref_tar, new_rot_v2)
assert_allclose(ref_tar, target_v2)
def test_finite_diff_with_water_2(self):
with path("saddle.optimizer.test.data", "water.xyz") as mol_path:
mol = Utils.load_file(mol_path)
red_int = ReducedInternal(mol.coordinates, mol.numbers, 0, 1)
red_int.auto_select_ic()
with path("saddle.optimizer.test.data", "water_old.fchk") as fchk_file:
red_int.energy_from_fchk(fchk_file)
assert red_int.energy - 75.99264142 < 1e-6
red_int.select_key_ic(0)
ref_v = np.array([
[-1.00000000e00, -4.17292908e-16, 0.00000000e00],
[2.10951257e-16, -4.69422035e-01, -8.82973926e-01],
[3.39185671e-16, -8.82973926e-01, 4.69422035e-01],
])
ref_v2 = np.dot(ref_v, ref_v.T)
assert np.allclose(ref_v2, np.dot(red_int.vspace, red_int.vspace.T))
red_int.set_vspace(ref_v)
wt_p1 = PathPoint(red_int=red_int)
step = [-0.001, 0, 0]
wt_p2 = wt_p1.copy()
wt_p2.update_coordinates_with_delta_v(step)
# fchk file is for -0.001
with path("saddle.optimizer.test.data",
"water_new_2.fchk") as fchk_file_new:
wt_p2._instance.energy_from_fchk(fchk_file_new)
wt_p2._instance.align_vspace(wt_p1._instance)
assert np.allclose(wt_p1.vspace, wt_p2.vspace)
result = PathPoint._calculate_finite_diff_h(wt_p1, wt_p2, -0.001)
assert np.allclose(result, wt_p1._instance.v_hessian[:, 0], atol=1e-2)
def setUp(self):
with path("saddle.test.data", "water.xyz") as mol_path:
mol = Utils.load_file(mol_path)
self.red_int = ReducedInternal(mol.coordinates, mol.numbers, 0, 1, "water")
self.red_int.add_bond(1, 0)
self.red_int.add_bond(1, 2)
self.red_int.add_bond(0, 2)
self.red_int.add_angle(0, 1, 2)
self.red_int.add_angle(1, 0, 2)
self.red_int.set_key_ic_number(2)
def test_set_new_vspace(self):
with path("saddle.test.data", "water.xyz") as mol_path:
mol = Utils.load_file(mol_path)
ri_mol = ReducedInternal(mol.coordinates, mol.numbers, 0, 1)
ri_mol.add_bond(1, 0)
ri_mol.add_bond(1, 2)
ri_mol.add_angle(0, 1, 2)
ri_mol.set_key_ic_number(1)
new_vp = np.eye(3)
ri_mol.set_vspace(new_vp)
assert np.allclose(ri_mol.vspace, np.eye(3))
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 setUp(self):
with path("saddle.test.data", "water.xyz") as mol_path:
mol = Utils.load_file(mol_path)
self.old_ob = ReducedInternal(mol.coordinates, mol.numbers, 0, 1)
self.old_ob.add_bond(0, 1)
self.old_ob.add_bond(1, 2)
self.old_ob.add_angle(0, 1, 2)
with path("saddle.optimizer.test.data",
"water_old.fchk") as fchk_file1:
self.old_ob.energy_from_fchk(fchk_file1)
self.new_ob = ReducedInternal(mol.coordinates, mol.numbers, 0, 1)
self.new_ob.add_bond(0, 1)
self.new_ob.add_bond(1, 2)
self.new_ob.add_angle(0, 1, 2)
with path("saddle.optimizer.test.data",
"water_new.fchk") as fchk_file2:
self.new_ob.energy_from_fchk(fchk_file2)
self.new_ob.align_vspace(self.old_ob)
assert_allclose(self.new_ob.vspace, self.old_ob.vspace, atol=1e-6)
self.newp = PathPoint(self.new_ob)
self.oldp = PathPoint(self.old_ob)
def test_finite_different_with_water_3(self):
with path("saddle.optimizer.test.data", "water.xyz") as mol_path:
mol = Utils.load_file(mol_path)
red_int = ReducedInternal(mol.coordinates, mol.numbers, 0, 1)
red_int.auto_select_ic()
red_int.add_bond(0, 2)
with path("saddle.optimizer.test.data", "water_old.fchk") as fchk_file:
red_int.energy_from_fchk(fchk_file)
assert red_int.energy - 75.99264142 < 1e-6
red_int.select_key_ic(0)
wt_p1 = PathPoint(red_int=red_int)
step = [0.001, 0, 0]
wt_p2 = wt_p1.copy()
wt_p2.update_coordinates_with_delta_v(step)
with path("saddle.optimizer.test.data",
"water_new_3.fchk") as fchk_file_new:
wt_p2._instance.energy_from_fchk(fchk_file_new)
wt_p2._instance.align_vspace(wt_p1._instance)
assert np.allclose(wt_p1.vspace, wt_p2.vspace, atol=1e-2)
result = PathPoint._calculate_finite_diff_h(wt_p1, wt_p2, 0.001)
assert np.allclose(result, wt_p1._instance.v_hessian[:, 0], atol=1e-2)
def test_finite_diff_with_water(self):
with path("saddle.optimizer.test.data", "water.xyz") as mol_path:
mol = Utils.load_file(mol_path)
red_int = ReducedInternal(mol.coordinates, mol.numbers, 0, 1)
red_int.auto_select_ic()
with path("saddle.optimizer.test.data", "water_old.fchk") as fchk_file:
red_int.energy_from_fchk(fchk_file)
assert red_int.energy - 75.99264142 < 1e-6
wt_p1 = PathPoint(red_int=red_int)
step = [0.001, 0, 0]
print(wt_p1._instance.vspace)
ref_vspace = np.array([
[0.25801783, -0.66522226, 0.70064694],
[-0.49526649, -0.71373819, -0.49526649],
[-0.82954078, 0.21921937, 0.51361947],
])
# incase different vspace basis error
wt_p1._instance.set_vspace(ref_vspace)
wt_p2 = wt_p1.copy()
wt_p2.update_coordinates_with_delta_v(step)
# wt_p2._instance.create_gauss_input(title='water_new')
with path("saddle.optimizer.test.data",
"water_new.fchk") as fchk_file_new:
wt_p2._instance.energy_from_fchk(fchk_file_new)
wt_p2._instance.align_vspace(wt_p1._instance)
assert np.allclose(wt_p1.vspace, wt_p2.vspace)
result = PathPoint._calculate_finite_diff_h(wt_p1, wt_p2, 0.001)
assert np.allclose(result, wt_p1._instance.v_hessian[:, 0], atol=1e-2)
def setUp(self):
with path("saddle.optimizer.test.data", "water.xyz") as mol_path:
mol = Utils.load_file(mol_path)
red_int = ReducedInternal(mol.coordinates, mol.numbers, 0, 1)
red_int.add_bond(0, 1)
red_int.add_bond(1, 2)
red_int.add_angle(0, 1, 2)
self.mol = red_int
def setUp(self):
with path("saddle.optimizer.test.data", "water.xyz") as mol_path:
mol = Utils.load_file(mol_path)
red_int = ReducedInternal(mol.coordinates, mol.numbers, 0, 1)
red_int.add_bond(1, 0)
red_int.add_bond(1, 2)
red_int.add_bond(0, 2)
red_int.add_angle(0, 1, 2)
red_int.add_angle(1, 0, 2)
red_int.set_key_ic_number(2)
self.ri = red_int
self.pp = PathPoint(red_int)
self.ri._energy = 5.0
np.random.seed(10)
self.ri._energy_gradient = np.random.rand(9)
with self.assertRaises(NotSetError):
self.ri.energy_hessian
assert np.allclose(
self.pp.q_gradient,
np.dot(np.linalg.pinv(self.ri.b_matrix.T), self.pp.x_gradient),
)
with self.assertRaises(NotSetError):
self.pp.v_hessian
self.pp._mod_hessian = np.eye(3)
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
class TestReduceInternal(TestCase):
def setUp(self):
with path("saddle.test.data", "water.xyz") as mol_path:
mol = Utils.load_file(mol_path)
self.red_int = ReducedInternal(mol.coordinates, mol.numbers, 0, 1, "water")
self.red_int.add_bond(1, 0)
self.red_int.add_bond(1, 2)
self.red_int.add_bond(0, 2)
self.red_int.add_angle(0, 1, 2)
self.red_int.add_angle(1, 0, 2)
self.red_int.set_key_ic_number(2)
def test_internal_reset_property(self):
sample_mol = deepcopy(self.red_int)
sample_mol.add_angle(0, 2, 1)
assert len(sample_mol.ic) == 6
assert self.red_int.vspace.shape == (5, 3)
self.red_int.set_new_ics(sample_mol.ic)
assert self.red_int.vspace.shape == (6, 3)
self.red_int.auto_select_ic()
assert self.red_int.vspace.shape == (3, 3)
self.red_int.wipe_ic_info(I_am_sure_i_am_going_to_wipe_all_ic_info=True)
assert self.red_int._vspace is None
assert self.red_int._red_space is None
assert self.red_int._non_red_space is None
self.red_int.add_bond(0, 1)
assert len(self.red_int.ic) == 1
self.red_int.add_bond(2, 1)
self.red_int.add_angle(0, 1, 2)
assert self.red_int.vspace.shape == (3, 3)
assert len(self.red_int.ic) == 3
self.red_int.add_angle(0, 2, 1)
self.red_int.add_angle(1, 0, 2)
assert self.red_int.vspace.shape == (3, 3)
self.red_int.add_bond(0, 2)
self.red_int.delete_ic(0)
assert self.red_int.vspace.shape == (3, 3)
cache_v = self.red_int.vspace.copy()
self.red_int.set_new_coordinates(np.array([[1, 0, 0], [0, 1, 0], [0, 0, 1]]))
assert not np.allclose(cache_v, self.red_int.vspace)
cache_v = self.red_int.vspace
cache_ic = self.red_int.ic_values.copy()
self.red_int.swap_internal_coordinates(0, 1)
assert not np.allclose(cache_v, self.red_int.vspace)
assert cache_ic[0] == self.red_int.ic_values[1]
assert cache_ic[1] == self.red_int.ic_values[0]
# test title
assert self.red_int._title == "water"
def test_property(self):
assert self.red_int.key_ic_number == 2
assert len(self.red_int.ic) == 5
assert isinstance(self.red_int, Internal)
assert self.red_int.df == 3
def test_reduce_coordinates(self):
mole = self.red_int
assert np.allclose(
mole.ic_values, [1.81413724, 1.81413724, 2.96247453, 1.91063401, 0.61547931]
)
mole.select_key_ic(0, 2)
assert np.allclose(
mole.ic_values, [1.81413724, 2.96247453, 1.81413724, 1.91063401, 0.61547931]
)
svd = mole._svd_of_b_matrix()
ref_vectors = np.array(
[
[6.96058989e-01, -3.20802187e-01, -4.62909977e-01],
[-2.70878427e-01, -2.12077861e-01, -7.55929035e-01],
[-2.53716249e-01, 6.67123979e-01, -4.62909977e-01],
[-6.03451079e-01, -4.72457758e-01, 1.97531517e-15],
[1.16625994e-01, 4.28763572e-01, -1.77057094e-15],
]
)
for i in range(svd.shape[1]):
assert np.allclose(svd[:, i], ref_vectors[:, i]) or np.allclose(
svd[:, i], -1 * ref_vectors[:, i]
)
ref_unit = np.array(
[[1.0, 0.0], [0.0, 1.0], [0.0, 0.0], [0.0, 0.0], [0.0, 0.0]]
)
assert np.allclose(mole._reduced_unit_vectors(), ref_unit)
ptrb = mole._reduced_perturbation()
ref_vec = np.dot(mole.b_matrix, np.dot(np.linalg.pinv(mole.b_matrix), ref_unit))
assert np.allclose(ref_vec, ptrb)
ref_red_space = np.array(
[
[0.44093001, -0.77928078], # reduced space
[-0.56140826, -0.61204707],
[-0.45792057, -0.03282547],
[-0.52276081, 0.04872587],
[0.08620545, 0.12111205],
]
)
mole._generate_reduce_space()
assert np.allclose(mole._red_space, ref_red_space)
ref_non_red_space = np.array(
[
[6.12072474e-17], # nonreduced space
[-3.33066907e-16],
[-7.16200549e-01],
[5.58315734e-01],
[-4.18736570e-01],
]
)
mole._generate_nonreduce_space()
assert np.allclose(ref_non_red_space, mole._non_red_space) or np.allclose(
ref_non_red_space, -1 * mole._non_red_space
)
vp_ref = np.hstack((ref_red_space, ref_non_red_space))
mole._reset_v_space()
for i in range(vp_ref.shape[1]):
assert np.allclose(mole.vspace[:, i], vp_ref[:, i]) or np.allclose(
mole.vspace[:, i], -1 * vp_ref[:, i]
)
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
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 test_get_delta_v(self):
with path("saddle.test.data", "water.xyz") as mol_path:
mol = Utils.load_file(mol_path)
ri_mol = ReducedInternal(mol.coordinates, mol.numbers, 0, 1)
ri_mol.add_bond(1, 0)
ri_mol.add_bond(1, 2)
ri_mol.add_angle(0, 1, 2)
ri_mol.set_key_ic_number(1)
vp_ref = np.array(
[
[-1.00000000e00, 1.52461867e-16, -2.25191203e-16],
[-1.57750703e-16, 3.51986473e-01, 9.36005087e-01],
[-1.73472348e-16, -9.36005087e-01, 3.51986473e-01],
]
)
ri_mol.set_vspace(vp_ref)
print(ri_mol.vspace)
assert np.allclose(ri_mol.vspace, vp_ref)
v_change = np.array([-0.2, 0.07039729, 0.18720102])
ic_change = np.dot(ri_mol.vspace, v_change)
assert np.allclose(ic_change, np.array([0.2, 0.2, 0.0]))
ri_mol.update_to_new_structure_with_delta_v(v_change)
assert np.allclose(
ri_mol.ic_values, np.array([2.01413724, 2.01413724, 1.9106340176])
)
def test_set_new_vspace(self):
with path("saddle.test.data", "water.xyz") as mol_path:
mol = Utils.load_file(mol_path)
ri_mol = ReducedInternal(mol.coordinates, mol.numbers, 0, 1)
ri_mol.add_bond(1, 0)
ri_mol.add_bond(1, 2)
ri_mol.add_angle(0, 1, 2)
ri_mol.set_key_ic_number(1)
new_vp = np.eye(3)
ri_mol.set_vspace(new_vp)
assert np.allclose(ri_mol.vspace, np.eye(3))
def test_align_v_space(self):
with path("saddle.test.data", "water.xyz") as mol_path:
mol = Utils.load_file(mol_path)
mol_1 = ReducedInternal(mol.coordinates, mol.numbers, 0, 1)
mol_1.add_bond(1, 0)
mol_1.add_bond(1, 2)
mol_1.add_angle(0, 1, 2)
mol_1.set_key_ic_number(1)
mol_2 = deepcopy(mol_1)
mol_1.set_target_ic([2.0, 2.0, 2.0])
mol_1.converge_to_target_ic()
assert np.allclose(mol_1.ic_values, [2.0, 2.0, 2.0], atol=1e-4)
copy1 = deepcopy(mol_1)
copy2 = deepcopy(mol_2)
copy1.align_vspace(copy2)
assert np.allclose(copy1.vspace, mol_2.vspace)
with path("saddle.test.data", "water_1.fchk") as fchk_path:
# print 'cv2',copy2.vspace
copy2.energy_from_fchk(fchk_path)
# print 'cv2, new',copy2.vspace, copy2.vspace_gradient
ref_ic_gradient = np.dot(copy2.vspace, copy2.vspace_gradient)
# print 'cv2,energy'
copy2.align_vspace(copy1)
# print 'cv2', copy2.vspace, copy2.vspace_gradient
new_ic_gradient = np.dot(copy2.vspace, copy2.vspace_gradient)
assert np.allclose(ref_ic_gradient, new_ic_gradient)
assert np.allclose(copy1.vspace, copy2.vspace)
def test_align_separate_v_space(self):
# test for given key_ic_num
random_a = np.random.rand(5, 5)
random_b = np.random.rand(5, 5)
target_v = np.linalg.eigh(np.dot(random_a, random_a.T))[1]
rotate_v = np.linalg.eigh(np.dot(random_b, random_b.T))[1]
new_rot_v = ReducedInternal._align_vspace_separate(target_v, rotate_v, 3)
assert_allclose(target_v, new_rot_v)
# test for 0 key_ic_num
random_a = np.random.rand(5, 5)
random_b = np.random.rand(5, 5)
target_v = np.linalg.eigh(np.dot(random_a, random_a.T))[1]
rotate_v = np.linalg.eigh(np.dot(random_b, random_b.T))[1]
new_rot_v = ReducedInternal._align_vspace_separate(target_v, rotate_v, 0)
assert_allclose(target_v, new_rot_v)
# test for different dimension
random_c = np.random.rand(5, 3)
random_d = np.random.rand(5, 3)
target_v2 = np.linalg.svd(random_c)[0][:, :3]
ref_tar = target_v2.copy()
rotate_v2 = np.linalg.svd(random_d)[0][:, :3]
new_rot_v2 = ReducedInternal._align_vspace_separate(target_v2, rotate_v2, 1)
assert_allclose(target_v2, new_rot_v2)
assert_allclose(ref_tar, new_rot_v2)
assert_allclose(ref_tar, target_v2)
def test_select_key_ic(self):
with path("saddle.test.data", "water.xyz") as mol_path:
mol = Utils.load_file(mol_path)
mol_1 = ReducedInternal(mol.coordinates, mol.numbers, 0, 1)
mol_1.add_bond(1, 0)
mol_1.add_bond(1, 2)
mol_1.add_angle(0, 1, 2)
mol_1.select_key_ic(0)
assert mol_1.key_ic_number == 1
mol_1.select_key_ic(2)
assert mol_1.key_ic_number == 1
mol_1.select_key_ic(0, 1, 2)
assert mol_1.key_ic_number == 3
def test_select_key_ic(self):
with path("saddle.test.data", "water.xyz") as mol_path:
mol = Utils.load_file(mol_path)
mol_1 = ReducedInternal(mol.coordinates, mol.numbers, 0, 1)
mol_1.add_bond(1, 0)
mol_1.add_bond(1, 2)
mol_1.add_angle(0, 1, 2)
mol_1.select_key_ic(0)
assert mol_1.key_ic_number == 1
mol_1.select_key_ic(2)
assert mol_1.key_ic_number == 1
mol_1.select_key_ic(0, 1, 2)
assert mol_1.key_ic_number == 3
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
def test_align_v_space(self):
with path("saddle.test.data", "water.xyz") as mol_path:
mol = Utils.load_file(mol_path)
mol_1 = ReducedInternal(mol.coordinates, mol.numbers, 0, 1)
mol_1.add_bond(1, 0)
mol_1.add_bond(1, 2)
mol_1.add_angle(0, 1, 2)
mol_1.set_key_ic_number(1)
mol_2 = deepcopy(mol_1)
mol_1.set_target_ic([2.0, 2.0, 2.0])
mol_1.converge_to_target_ic()
assert np.allclose(mol_1.ic_values, [2.0, 2.0, 2.0], atol=1e-4)
copy1 = deepcopy(mol_1)
copy2 = deepcopy(mol_2)
copy1.align_vspace(copy2)
assert np.allclose(copy1.vspace, mol_2.vspace)
with path("saddle.test.data", "water_1.fchk") as fchk_path:
# print 'cv2',copy2.vspace
copy2.energy_from_fchk(fchk_path)
# print 'cv2, new',copy2.vspace, copy2.vspace_gradient
ref_ic_gradient = np.dot(copy2.vspace, copy2.vspace_gradient)
# print 'cv2,energy'
copy2.align_vspace(copy1)
# print 'cv2', copy2.vspace, copy2.vspace_gradient
new_ic_gradient = np.dot(copy2.vspace, copy2.vspace_gradient)
assert np.allclose(ref_ic_gradient, new_ic_gradient)
assert np.allclose(copy1.vspace, copy2.vspace)
class TestSecant(unittest.TestCase):
def setUp(self):
with path("saddle.test.data", "water.xyz") as mol_path:
mol = Utils.load_file(mol_path)
self.old_ob = ReducedInternal(mol.coordinates, mol.numbers, 0, 1)
self.old_ob.add_bond(0, 1)
self.old_ob.add_bond(1, 2)
self.old_ob.add_angle(0, 1, 2)
with path("saddle.optimizer.test.data",
"water_old.fchk") as fchk_file1:
self.old_ob.energy_from_fchk(fchk_file1)
self.new_ob = ReducedInternal(mol.coordinates, mol.numbers, 0, 1)
self.new_ob.add_bond(0, 1)
self.new_ob.add_bond(1, 2)
self.new_ob.add_angle(0, 1, 2)
with path("saddle.optimizer.test.data",
"water_new.fchk") as fchk_file2:
self.new_ob.energy_from_fchk(fchk_file2)
self.new_ob.align_vspace(self.old_ob)
assert_allclose(self.new_ob.vspace, self.old_ob.vspace, atol=1e-6)
self.newp = PathPoint(self.new_ob)
self.oldp = PathPoint(self.old_ob)
def test_secant_condition(self):
result = secant(self.newp, self.oldp)
# separate calculation
part1 = self.newp.v_gradient - self.oldp.v_gradient
part2 = np.dot(self.newp.vspace.T,
np.linalg.pinv(self.newp.b_matrix.T))
part3 = np.dot(
self.newp.b_matrix.T,
np.dot((self.newp.vspace - self.oldp.vspace),
self.newp.v_gradient),
)
part4 = np.dot((self.newp.b_matrix - self.oldp.b_matrix).T,
self.newp.q_gradient)
final = part1 - np.dot(part2, (part3 + part4))
assert np.allclose(result, final, atol=1e-6)
def test_secant_condition_0(self):
d_s = np.dot(self.old_ob.vspace.T,
self.new_ob.ic_values - self.old_ob.ic_values)
ref = np.dot(self.old_ob.v_hessian, d_s)
result = secant(self.newp, self.oldp)
assert_allclose(ref, result, atol=1e-5)
def test_secant_condition_1(self):
d_s = np.dot(self.old_ob.vspace.T,
self.new_ob.ic_values - self.old_ob.ic_values)
ref = np.dot(self.old_ob.v_hessian, d_s)
result = secant_1(self.newp, self.oldp)
assert_allclose(ref, result, atol=1e-5)
def test_secant_condition_2(self):
d_s = np.dot(self.old_ob.vspace.T,
self.new_ob.ic_values - self.old_ob.ic_values)
ref = np.dot(self.old_ob.v_hessian, d_s)
result = secant_2(self.newp, self.oldp)
assert_allclose(ref, result, atol=1e-5)
def test_secant_condition_3(self):
d_s = np.dot(self.old_ob.vspace.T,
self.new_ob.ic_values - self.old_ob.ic_values)
ref = np.dot(self.old_ob.v_hessian, d_s)
result = secant_3(self.newp, self.oldp)
assert_allclose(ref, result, atol=1e-5)
def test_get_delta_v(self):
with path("saddle.test.data", "water.xyz") as mol_path:
mol = Utils.load_file(mol_path)
ri_mol = ReducedInternal(mol.coordinates, mol.numbers, 0, 1)
ri_mol.add_bond(1, 0)
ri_mol.add_bond(1, 2)
ri_mol.add_angle(0, 1, 2)
ri_mol.set_key_ic_number(1)
vp_ref = np.array(
[
[-1.00000000e00, 1.52461867e-16, -2.25191203e-16],
[-1.57750703e-16, 3.51986473e-01, 9.36005087e-01],
[-1.73472348e-16, -9.36005087e-01, 3.51986473e-01],
]
)
ri_mol.set_vspace(vp_ref)
print(ri_mol.vspace)
assert np.allclose(ri_mol.vspace, vp_ref)
v_change = np.array([-0.2, 0.07039729, 0.18720102])
ic_change = np.dot(ri_mol.vspace, v_change)
assert np.allclose(ic_change, np.array([0.2, 0.2, 0.0]))
ri_mol.update_to_new_structure_with_delta_v(v_change)
assert np.allclose(
ri_mol.ic_values, np.array([2.01413724, 2.01413724, 1.9106340176])
)