def test_auto_select_improper_ch3_hf(self):
with path("saddle.test.data", "ch3_hf.xyz") as mol_path:
mol = Utils.load_file(mol_path)
mol = Internal(mol.coordinates, mol.numbers, 0, 1)
mol.auto_select_ic()
ic_ref = np.array([
2.02762919,
2.02769736,
2.02761705,
1.77505755,
4.27707385,
4.87406146,
2.08356856,
2.08391343,
1.64995596,
2.08364916,
1.64984524,
1.64881837,
1.06512165,
0.42765264,
3.14154596,
2.71390135,
0.59485389,
-1.70630517,
1.7061358,
-3.14152957,
2.09455878,
-2.09427619,
-2.87079827,
])
assert_allclose(mol.ic_values, ic_ref)
def setUp(self):
"""Setup function."""
with path("saddle.test.data", "water.xyz") as mol_path:
mol = Utils.load_file(mol_path)
self.mol = Internal(mol.coordinates, mol.numbers, 0, 1)
with path("saddle.test.data", "h2o2.xyz") as mol_path:
mol2 = Utils.load_file(mol_path)
self.h2o2 = Internal(mol2.coordinates, mol2.numbers, 0, 1)
def setUp(self):
with path("saddle.test.data", "ch3_hf.xyz") as rct_path:
self.rct = Utils.load_file(rct_path)
with path("saddle.test.data", "ch3f_h.xyz") as prd_path:
self.prd = Utils.load_file(prd_path)
self.reactant_ic = Internal(self.rct.coordinates, self.rct.numbers, 0,
2)
self.product_ic = Internal(self.prd.coordinates, self.prd.numbers, 0,
2)
def test_auto_dihed_number_ethane(self):
with path("saddle.test.data", "ethane.xyz") as mol_path:
mol = Utils.load_file(mol_path)
mol = Utils.load_file(mol_path)
ethane = Internal(mol.coordinates, mol.numbers, 0, 1)
ethane.auto_select_ic()
counter = 0
for ic in ethane.ic:
if isinstance(ic, DihedralAngle):
counter += 1
assert counter == 5
def test_delete_ic(self):
with path("saddle.test.data", "ethane.xyz") as mol_path:
mol = Utils.load_file(mol_path)
ethane = Internal(mol.coordinates, mol.numbers, 0, 1)
ethane.auto_select_ic()
ethane._delete_ic_index(0)
assert len(ethane.ic) == 23
ethane.auto_select_ic(keep_bond=True)
assert len(ethane.ic) == 12
# print(ethane.ic)
ethane.delete_ic(1, 2, 3)
assert len(ethane.ic) == 9
def test_dihedral_add(self):
"""Test add normal dihedral."""
with path("saddle.test.data", "2h-azirine.xyz") as mol_path:
mol = Utils.load_file(mol_path) # create a water molecule
internal = Internal(mol.coordinates, mol.numbers, 0, 1)
internal.add_bond(0, 1)
internal.add_bond(1, 2)
internal.add_bond(1, 3)
# fake add dihed
internal.add_dihedral(0, 2, 3, 4)
assert len(internal.ic) == 3
internal.add_dihedral(0, 1, 2, 3)
assert len(internal.ic) == 4
assert internal.ic_values[3] == dihed_angle(internal.coordinates[:4])
def test_cost_tfm_dihed(self):
with path("saddle.test.data", "h2o2.xyz") as mol_path:
mol = Internal.from_file(mol_path)
mol.auto_select_ic()
ref_mol = deepcopy(mol)
coor = mol.coordinates.copy()
target_ic = mol.ic_values
# print(mol.ic)
target_ic[0] = 2
target_ic[3] = 2
target_ic[5] = 2
mol.set_target_ic(target_ic)
# print(mol.ic[0].value - mol.ic[0].target)
cost_v = mol._compute_tfm_cost()
cost_g = mol._compute_tfm_gradient()
diff = 1e-4
# assert_allclose(cost_v, (2 - 2.47617635) ** 2)
# finite diff test
mol.list_ic
for i in range(4):
for j in range(3):
coor = ref_mol.coordinates.copy()
coor[i][j] += diff
mol.set_new_coordinates(coor)
cost_v_2 = mol._compute_tfm_cost()
fd = (cost_v_2 - cost_v) / 1e-4
assert_allclose(fd, cost_g[3 * i + j], atol=2e-2)
def test_cost_hessian_angle(self):
with path("saddle.test.data", "h2o2.xyz") as mol_path:
mol = Internal.from_file(mol_path)
mol.add_bond(0, 1)
mol.add_bond(0, 2)
mol.add_angle(1, 0, 2)
# print(mol.b_matrix)
# print(mol.ic)
# assert False
ref_mol = deepcopy(mol)
coor = mol.coordinates.copy()
target_ic = mol.ic_values + 0.5
# print(mol.ic)
mol.set_target_ic(target_ic)
cost_g = mol._compute_tfm_gradient()
cost_h = mol._compute_tfm_hessian()
diff = 1e-4
for j in range(4):
for i in range(3):
coor = ref_mol.coordinates.copy()
coor[j, i] += diff
mol.set_new_coordinates(coor)
cost_g_2 = mol._compute_tfm_gradient()
fd = (cost_g_2 - cost_g) / 1e-4
assert_allclose(fd, cost_h[j * 3 + i], atol=4e-4)
def test_new_dihed_converge(self):
with path("saddle.test.data", "h2o2.xyz") as mol_path:
mol = Utils.load_file(mol_path)
mol = Utils.load_file(mol_path)
h2o2 = Internal(mol.coordinates, mol.numbers, 0, 1)
h2o2.auto_select_ic(dihed_special=True)
assert len(h2o2.ic) == 7
# print(h2o2.ic_values)
target_ic = [2.4, 1.8, 1.8, 1.6, 1.6, 0.8, 0.6]
h2o2.set_target_ic(target_ic)
h2o2.converge_to_target_ic()
# print(h2o2.ic_values)
assert_allclose(h2o2.ic_values, target_ic, atol=1e-2)
def test_h_bond(self):
with path("saddle.test.data", "di_water.xyz") as mol_path:
mol = Internal.from_file(mol_path, charge=0, multi=1)
mol._auto_select_cov_bond() # numbers [8 1 1 8 1 1]
assert np.sum(mol.connectivity[0] == 1) == 2
assert np.sum(mol.connectivity[3] == 1) == 2
assert len(mol.fragments) == 2
# print(mol.connectivity)
mol._auto_select_h_bond()
assert mol.connectivity[2][3] == 2
assert len(mol.fragments) == 2
def test_scipy_opt_tfm_cmpx(self):
with path("saddle.test.data", "ethane.xyz") as mol_path:
mol = Internal.from_file(mol_path)
# conventional dihedral
mol.auto_select_ic()
target_ic = mol.ic_values
target_ic[-1] = -1
mol.set_target_ic(target_ic)
# print(mol.ic_values)
mol.converge_to_target_ic()
x_gradient = mol._compute_tfm_gradient()
assert np.max(np.abs(x_gradient)) < 1e-4
def test_mini_dihed(self):
with path("saddle.test.data", "methanol.xyz") as mol_path:
mol = Internal.from_file(mol_path)
mol._auto_select_cov_bond()
mol._auto_select_h_bond()
mol._auto_select_fragment_bond()
mol._auto_select_angle()
# start real parts
ref = len(mol.ic)
mol._auto_select_minimum_dihed_normal()
assert len(mol.ic) - ref == 1
with path("saddle.test.data", "ethane.xyz") as mol2_path:
mol2 = Internal.from_file(mol2_path)
mol2._auto_select_cov_bond()
mol2._auto_select_h_bond()
mol2._auto_select_fragment_bond()
mol2._auto_select_angle()
# start real parts
ref = len(mol2.ic)
mol2._auto_select_minimum_dihed_normal()
assert len(mol2.ic) - ref == 1
def test_scipy_opt_tfm(self):
with path("saddle.test.data", "h2o2.xyz") as mol_path:
mol = Internal.from_file(mol_path)
mol.auto_select_ic()
target_ic = mol.ic_values
target_ic[0] = 2
target_ic[3] = 2
target_ic[5] = 2
mol.set_target_ic(target_ic)
mol.converge_to_target_ic()
np.allclose(mol.ic_values[0], 2, atol=1e-4)
np.allclose(mol.ic_values[3], 2, atol=1e-4)
np.allclose(mol.ic_values[5], 2, atol=1e-4)
def from_file(cls, rct_file, prd_file, charge=0, multi=1):
"""Create a TSConstruct instance from files for reactant and product.
Arguments
---------
rct_file : str
path to reactant file
prd_file : str
path to product file
charge : int
charge of the given system or molecules as a whole
multi : int
multiplicity of the given system or molecules as a whole
Return
------
new TSConstruct instance : TSConstruct
new instance create from the structure of given reactant and
product
"""
rct_mol = Internal.from_file(rct_file, charge, multi)
prd_mol = Internal.from_file(prd_file, charge, multi)
return cls(rct_mol, prd_mol)
def test_b_matrix_dihed(self):
with path("saddle.test.data", "h2o2.xyz") as mol_path:
mol = Internal.from_file(mol_path)
mol.auto_select_ic()
ref_mol = deepcopy(mol)
for j in range(4):
q1 = mol.ic_values[j]
for i in range(3):
coor = mol.coordinates.copy()
coor[j][i] += 1e-4
ref_mol.set_new_coordinates(coor)
q2 = ref_mol.ic_values[j]
fd = (q2 - q1) / 1e-4
b = mol.b_matrix[j][j * 3 + i]
assert_allclose(fd, b, atol=1e-4)
def test_tfm_hessian_dihed(self):
with path("saddle.test.data", "h2o2.xyz") as mol_path:
mol = Internal.from_file(mol_path)
mol.auto_select_ic()
ref_mol = deepcopy(mol)
qd1 = mol.b_matrix
for j in range(4):
for i in range(3):
coor = mol.coordinates.copy()
coor[j][i] += 1e-4
ref_mol.set_new_coordinates(coor)
qd2 = ref_mol.b_matrix
fd_b = (qd2 - qd1) / 1e-4
analytic_b = mol._cc_to_ic_hessian[:, :, 3 * j + i]
assert_allclose(fd_b, analytic_b, atol=1e-4)
def test_tfm_hessian(self):
with path("saddle.test.data", "h2o2.xyz") as mol_path:
mol = Internal.from_file(mol_path)
mol.add_bond(0, 1)
mol.add_bond(1, 2)
mol.add_angle(0, 1, 2)
ref_mol = deepcopy(mol)
qd1 = mol.b_matrix
for i in range(3):
coor = mol.coordinates.copy()
coor[0][i] += 1e-4
ref_mol.set_new_coordinates(coor)
qd2 = ref_mol.b_matrix
fd_b = (qd2 - qd1) / 1e-4
analytic_b = mol._cc_to_ic_hessian[:, :, i]
assert_allclose(fd_b, analytic_b, atol=1e-4)
def test_bond_type(self):
with path("saddle.test.data", "ch3_hf.xyz") as mol_path:
mol = Internal.from_file(mol_path, charge=0, multi=1)
mol._auto_select_cov_bond() # numbers [6 1 1 1 9 1]
assert np.sum(mol.connectivity[0] == 1) == 3
assert np.sum(mol.connectivity[4] == 1) == 1
mol._auto_select_fragment_bond()
assert np.sum(mol.connectivity[0] == 1) == 3
assert len(np.unique(mol.fragments)) == 1
assert np.sum(mol.connectivity[5] == 3) == 2
mol._regenerate_ic()
assert np.sum(mol.connectivity[0] == 1) == 3
assert len(np.unique(mol.fragments)) == 1
assert np.sum(mol.connectivity[5] == 3) == 2
mol.wipe_ic_info(True)
mol.auto_select_ic()
assert np.sum(mol.connectivity[0] == 1) == 3
assert len(np.unique(mol.fragments)) == 1
assert np.sum(mol.connectivity[5] == 3) == 2
def test_cost_hessian_cmpl(self):
with path("saddle.test.data", "methanol.xyz") as mol_path:
mol = Internal.from_file(mol_path)
mol.auto_select_ic()
ref_mol = deepcopy(mol)
coor = mol.coordinates.copy()
target_ic = mol.ic_values + 0.5
mol.set_target_ic(target_ic)
cost_g = mol._compute_tfm_gradient()
cost_h = mol._compute_tfm_hessian()
diff = 1e-4
for j in range(6):
for i in range(3):
coor = ref_mol.coordinates.copy()
coor[j, i] += diff
mol.set_new_coordinates(coor)
cost_g_2 = mol._compute_tfm_gradient()
fd = (cost_g_2 - cost_g) / 1e-4
assert_allclose(fd, cost_h[j * 3 + i], atol=4e-2)
def test_b_matrix(self):
with path("saddle.test.data", "h2o2.xyz") as mol_path:
mol = Internal.from_file(mol_path)
mol.add_bond(0, 1)
mol.add_bond(1, 2)
mol.add_angle(0, 1, 2)
ref_mol = deepcopy(mol)
q1 = mol.ic_values[0]
for i in range(3):
coor = mol.coordinates.copy()
coor[0][i] += 1e-4
ref_mol.set_new_coordinates(coor)
q2 = ref_mol.ic_values[0]
fd = (q2 - q1) / 1e-4
b = mol.b_matrix[0][i]
assert_allclose(fd, b, atol=1e-4)
q1 = mol.ic_values[1]
for i in range(3):
coor = mol.coordinates.copy()
coor[1][i] += 1e-4
ref_mol.set_new_coordinates(coor)
q2 = ref_mol.ic_values[1]
fd = (q2 - q1) / 1e-4
b = mol.b_matrix[1][3 + i]
assert_allclose(fd, b, atol=1e-4)
q1 = mol.ic_values[2]
for i in range(3):
coor = mol.coordinates.copy()
coor[2][i] += 1e-4
ref_mol.set_new_coordinates(coor)
q2 = ref_mol.ic_values[2]
fd = (q2 - q1) / 1e-4
b = mol.b_matrix[2][6 + i]
assert_allclose(fd, b, atol=1e-4)
def test_auto_ic_select_ethane(self):
with path("saddle.test.data", "ethane.xyz") as mol_path:
mol = Utils.load_file(mol_path)
ethane = Internal(mol.coordinates, mol.numbers, 0, 1)
ethane.auto_select_ic()
assert len(ethane.ic) == 24
def test_fragments_bond_add(self):
with path("saddle.test.data", "ch3_hf.xyz") as mol_path:
mol = Utils.load_file(mol_path)
mol = Internal(mol.coordinates, mol.numbers, 0, 1)
mol._auto_select_fragment_bond()
assert len(mol.ic) == 15
mol.wipe_ic_info(True)
mol.add_bond(0, 1)
mol._auto_select_fragment_bond()
assert len(mol.ic) == 15
mol.wipe_ic_info(True)
mol.add_bond(0, 1)
mol.add_bond(0, 5)
mol.add_bond(0, 3)
mol.add_bond(4, 2)
mol._auto_select_fragment_bond()
assert len(mol.ic) == 6
mol.wipe_ic_info(True)
mol.add_bond(0, 1)
mol.add_bond(2, 3)
mol.add_bond(4, 5)
mol._auto_select_fragment_bond()
assert len(mol.ic) == 9
#
mol.wipe_ic_info(True)
mol.add_bond(0, 1)
mol.add_bond(0, 2)
mol.add_bond(3, 4)
mol.add_bond(4, 5)
mol._auto_select_fragment_bond()
assert_allclose(mol.ic_values[4], 2.02761704779693)
assert mol.ic[4].atoms == (0, 3)
assert_allclose(mol.ic_values[5], 3.501060110109399)
assert mol.ic[5].atoms == (2, 3)
assert len(mol.ic) == 6
class TestInternal(unittest.TestCase):
"""Test internal coordinates transform."""
def setUp(self):
"""Setup function."""
with path("saddle.test.data", "water.xyz") as mol_path:
mol = Utils.load_file(mol_path)
self.mol = Internal(mol.coordinates, mol.numbers, 0, 1)
with path("saddle.test.data", "h2o2.xyz") as mol_path:
mol2 = Utils.load_file(mol_path)
self.h2o2 = Internal(mol2.coordinates, mol2.numbers, 0, 1)
def test_ic_weights(self):
"""Test change internal coordinates weights."""
self.mol.auto_select_ic()
assert_allclose(self.mol.ic_weights, [1, 1, 1])
self.mol.set_ic_weights(np.array([0.5, 0.5, 2]))
assert_allclose(self.mol.ic_weights, [0.5, 0.5, 2])
self.h2o2.auto_select_ic()
self.h2o2.set_dihed_weights(0)
assert self.h2o2.ic[-1].weight == 0
def test_connectivity(self):
"""Test default connectivity."""
assert_allclose(self.mol.connectivity, np.eye(3) * -1)
def test_file_title(self):
"""Test default file title."""
new_mol = Internal(self.mol.coordinates, self.mol.numbers, 0, 1)
assert len(new_mol._title) == 15
def test_add_bond(self):
""""""
init_con = np.eye(3) * -1
assert_allclose(self.mol.connectivity, init_con)
new_con = init_con.copy()
# add a bond connection
self.mol.add_bond(1, 0)
new_con[0, 1] = 1
new_con[1, 0] = 1
# test same connectivity
assert_allclose(self.mol.connectivity, new_con)
assert_allclose(self.mol.ic_values, np.array([1.81413724]))
assert self.mol.ic[0].atoms == (0, 1)
# add dup bond
self.mol.add_bond(0, 1)
ref_hessian = np.array([[
[
0.18374187,
0.25985046,
0.0,
-0.18374187,
-0.25985046,
0.0,
0.0,
0.0,
0.0,
],
[
0.25985046,
0.36748434,
0.0,
-0.25985046,
-0.36748434,
0.0,
0.0,
0.0,
0.0,
],
[0.0, 0.0, 0.55122621, 0.0, 0.0, -0.55122621, 0.0, 0.0, 0.0],
[
-0.18374187,
-0.25985046,
0.0,
0.18374187,
0.25985046,
0.0,
0.0,
0.0,
0.0,
],
[
-0.25985046,
-0.36748434,
0.0,
0.25985046,
0.36748434,
0.0,
0.0,
0.0,
0.0,
],
[0.0, 0.0, -0.55122621, 0.0, 0.0, 0.55122621, 0.0, 0.0, 0.0],
[0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0],
[0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0],
[0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0],
]])
assert_allclose(self.mol._cc_to_ic_hessian, ref_hessian)
assert len(self.mol.ic) == 1
# bond_type 1 == covalent bond
assert_allclose(self.mol.connectivity, new_con)
self.mol.add_bond(2, 1)
assert len(self.mol.ic) == 2
assert self.mol.ic[1].atoms == (1, 2)
assert_allclose(
self.mol._cc_to_ic_gradient,
np.array([
[
0.81649681,
-0.57734995,
0.0,
-0.81649681,
0.57734995,
0.0,
0.0,
0.0,
0.0,
],
[
0.0,
0.0,
0.0,
0.81649681,
0.57734995,
0.0,
-0.81649681,
-0.57734995,
0.0,
],
]),
)
def test_angle_add(self):
"""Test add angle to internal coordinates."""
self.mol.add_angle(0, 1, 2)
assert len(self.mol.ic) == 0
self.mol.add_bond(0, 1)
self.mol.add_bond(1, 2)
connected_index = self.mol.connected_indices(1)
assert_allclose(connected_index, np.array([0, 2]))
self.mol.add_angle(0, 1, 2)
assert len(self.mol.ic) == 3
assert_allclose(self.mol.ic[2].value, 1.9106340153991836)
assert_allclose(
self.mol.b_matrix[2],
np.array([
0.31825043,
0.45007444,
0.0,
0.0,
-0.90014888,
-0.0,
-0.31825043,
0.45007444,
0.0,
]),
)
assert_allclose(
self.mol._cc_to_ic_hessian[2],
np.array([
[
-2.86472766e-01,
-1.01283669e-01,
0.00000000e00,
2.86472766e-01,
1.01283669e-01,
0.00000000e00,
2.08166817e-17,
-6.93889390e-18,
0.00000000e00,
],
[
-1.01283669e-01,
2.86472766e-01,
0.00000000e00,
1.01283669e-01,
-2.86472766e-01,
0.00000000e00,
6.93889390e-18,
4.16333634e-17,
0.00000000e00,
],
[
0.00000000e00,
0.00000000e00,
-1.07427583e-01,
0.00000000e00,
0.00000000e00,
4.29709622e-01,
0.00000000e00,
0.00000000e00,
-3.22282039e-01,
],
[
2.86472766e-01,
1.01283669e-01,
0.00000000e00,
-5.72945532e-01,
0.00000000e00,
0.00000000e00,
2.86472766e-01,
-1.01283669e-01,
0.00000000e00,
],
[
1.01283669e-01,
-2.86472766e-01,
0.00000000e00,
0.00000000e00,
5.72945532e-01,
0.00000000e00,
-1.01283669e-01,
-2.86472766e-01,
0.00000000e00,
],
[
0.00000000e00,
0.00000000e00,
4.29709622e-01,
0.00000000e00,
0.00000000e00,
-8.59419245e-01,
0.00000000e00,
0.00000000e00,
4.29709622e-01,
],
[
2.08166817e-17,
6.93889390e-18,
0.00000000e00,
2.86472766e-01,
-1.01283669e-01,
0.00000000e00,
-2.86472766e-01,
1.01283669e-01,
0.00000000e00,
],
[
-6.93889390e-18,
4.16333634e-17,
0.00000000e00,
-1.01283669e-01,
-2.86472766e-01,
0.00000000e00,
1.01283669e-01,
2.86472766e-01,
0.00000000e00,
],
[
0.00000000e00,
0.00000000e00,
-3.22282039e-01,
0.00000000e00,
0.00000000e00,
4.29709622e-01,
0.00000000e00,
0.00000000e00,
-1.07427583e-01,
],
]),
)
self.mol.set_target_ic((1.6, 1.7, -0.5))
assert_allclose(self.mol.target_ic, np.array([1.6, 1.7, -0.5]))
def test_dihedral_add(self):
"""Test add normal dihedral."""
with path("saddle.test.data", "2h-azirine.xyz") as mol_path:
mol = Utils.load_file(mol_path) # create a water molecule
internal = Internal(mol.coordinates, mol.numbers, 0, 1)
internal.add_bond(0, 1)
internal.add_bond(1, 2)
internal.add_bond(1, 3)
# fake add dihed
internal.add_dihedral(0, 2, 3, 4)
assert len(internal.ic) == 3
internal.add_dihedral(0, 1, 2, 3)
assert len(internal.ic) == 4
assert internal.ic_values[3] == dihed_angle(internal.coordinates[:4])
def test_cost_function(self):
""""""
self.mol.add_bond(0, 1)
self.mol.add_bond(1, 2)
self.mol.add_angle(0, 1, 2)
assert_allclose(
self.mol.ic_values,
[1.8141372422079882, 1.8141372422079882, 1.9106340153991836],
)
self.mol.set_target_ic([1.7, 1.7, 1.5])
self.mol.swap_internal_coordinates(0, 2)
assert_allclose(
self.mol.ic_values,
[1.9106340153991836, 1.8141372422079882, 1.8141372422079882],
)
assert_allclose(self.mol.target_ic, [1.5, 1.7, 1.7])
self.mol.swap_internal_coordinates(0, 2)
assert_allclose(
self.mol.ic_values,
[1.8141372422079882, 1.8141372422079882, 1.9106340153991836],
)
assert_allclose(self.mol.target_ic, [1.7, 1.7, 1.5])
# test cost function in ic
v = self.mol.tf_cost
d = self.mol._cost_q_d
dd = self.mol._cost_q_dd
# calculate ref cost value
ref_cost = (self.mol.ic_values[0] - 1.7)**2 * 2 + (
np.cos(self.mol.ic_values[-1]) - np.cos(1.5))**2
assert_allclose(ref_cost, v)
ref_gradient = np.array(
[0.22827448441597653, 0.22827448441597653, 0.76192388])
assert_allclose(d, ref_gradient)
ref_hessian = np.array([[2.0, 0.0, 0.0], [0.0, 2.0, 0.0],
[0.0, 0.0, 1.5083953582]])
assert_allclose(dd, ref_hessian)
# assert False
new_v, xd, xdd = self.mol.cost_value_in_cc
assert new_v == v
assert_allclose(xd, np.dot(self.mol._cc_to_ic_gradient.T, d))
ref_x_hessian = np.dot(np.dot(self.mol._cc_to_ic_gradient.T, dd),
self.mol._cc_to_ic_gradient)
K = np.tensordot(d, self.mol._cc_to_ic_hessian, 1)
ref_x_hessian += K
assert_allclose(xdd, ref_x_hessian)
new_coor = np.array([
[1.40, -0.93019123, -0.0],
[-0.0, 0.11720081, -0.0],
[-1.40, -0.93019123, -0.0],
])
self.mol.set_new_coordinates(new_coor)
assert_allclose(self.mol.ic_values,
[1.7484364736491811, 1.7484364736491811, 1.85697699])
assert_allclose(
self.mol._cc_to_ic_gradient[0, :6],
np.array(
[0.80071539, -0.59904495, 0.0, -0.80071539, 0.59904495, -0.0]),
)
ref_hessian = np.array([
[0.20524329, 0.27433912, 0.0, -0.20524329, -0.27433912, -0.0],
[0.27433912, 0.36669628, 0.0, -0.27433912, -0.36669628, -0.0],
[0.0, 0.0, 0.57193957, -0.0, -0.0, -0.57193957],
[-0.20524329, -0.27433912, -0.0, 0.20524329, 0.27433912, 0.0],
[-0.27433912, -0.36669628, -0.0, 0.27433912, 0.36669628, 0.0],
[-0.0, -0.0, -0.57193957, 0.0, 0.0, 0.57193957],
])
assert_allclose(self.mol._cc_to_ic_hessian[0, :6, :6], ref_hessian)
def test_transform_function(self):
self.mol.add_bond(0, 1)
self.mol.add_bond(1, 2)
self.mol.add_angle(0, 1, 2)
self.mol.set_target_ic([1.7, 1.7, -0.4])
n_p = self.mol.create_geo_point()
assert isinstance(n_p, Point)
assert n_p.trust_radius == 1.7320508075688772
self.mol.converge_to_target_ic(max_iter=100)
g_array = self.mol.cost_value_in_cc[1]
assert len(g_array[abs(g_array) > 3e-4]) == 0
def test_auto_ic_select_water(self):
self.mol.auto_select_ic()
assert_allclose(
self.mol.ic_values,
[1.8141372422079882, 1.8141372422079882, 1.9106340153991836],
)
def test_auto_ic_select_ethane(self):
with path("saddle.test.data", "ethane.xyz") as mol_path:
mol = Utils.load_file(mol_path)
ethane = Internal(mol.coordinates, mol.numbers, 0, 1)
ethane.auto_select_ic()
assert len(ethane.ic) == 24
def test_auto_dihed_number_ethane(self):
with path("saddle.test.data", "ethane.xyz") as mol_path:
mol = Utils.load_file(mol_path)
mol = Utils.load_file(mol_path)
ethane = Internal(mol.coordinates, mol.numbers, 0, 1)
ethane.auto_select_ic()
counter = 0
for ic in ethane.ic:
if isinstance(ic, DihedralAngle):
counter += 1
assert counter == 5
def test_auto_select_improper_ch3_hf(self):
with path("saddle.test.data", "ch3_hf.xyz") as mol_path:
mol = Utils.load_file(mol_path)
mol = Internal(mol.coordinates, mol.numbers, 0, 1)
mol.auto_select_ic()
ic_ref = np.array([
2.02762919,
2.02769736,
2.02761705,
1.77505755,
4.27707385,
4.87406146,
2.08356856,
2.08391343,
1.64995596,
2.08364916,
1.64984524,
1.64881837,
1.06512165,
0.42765264,
3.14154596,
2.71390135,
0.59485389,
-1.70630517,
1.7061358,
-3.14152957,
2.09455878,
-2.09427619,
-2.87079827,
])
assert_allclose(mol.ic_values, ic_ref)
def test_auto_ic_select_methanol(self):
with path("saddle.test.data", "methanol.xyz") as mol_path:
mol = Utils.load_file(mol_path)
methanol = Internal(mol.coordinates, mol.numbers, 0, 1)
methanol.auto_select_ic()
assert len(methanol.ic) == 15
def test_wipe_ic(self):
self.mol.add_bond(0, 1)
self.mol.add_bond(1, 2)
self.mol.add_bond(0, 2)
assert len(self.mol.ic) == 3
self.mol.wipe_ic_info(False)
assert len(self.mol.ic) == 3
self.mol.wipe_ic_info(True)
assert len(self.mol.ic) == 0
def test_set_new_ic(self):
mol1 = deepcopy(self.mol)
mol2 = deepcopy(self.mol)
mol1.add_bond(0, 1)
mol1.add_bond(0, 2)
mol1.add_angle(1, 0, 2)
mol2.set_new_ics(mol1.ic)
assert_allclose(mol2.ic_values, mol1.ic_values)
mol2.wipe_ic_info(True)
mol2.add_bond(2, 0)
assert len(mol2.ic) == 1
assert not np.allclose(mol2.connectivity, mol1.connectivity)
mol2.set_new_ics(mol1.ic)
assert_allclose(mol1.connectivity, mol2.connectivity)
def test_get_energy_from_fchk(self):
with path("saddle.test.data", "water_1.fchk") as fchk_path:
self.mol.add_bond(0, 1)
self.mol.add_bond(1, 2)
self.mol.add_angle(0, 1, 2)
self.mol.energy_from_fchk(fchk_path)
ref_g = self.mol.internal_gradient.copy()
assert_allclose(self.mol.internal_gradient, ref_g)
ic_ref = deepcopy(self.mol.ic)
self.mol.add_bond(0, 2)
assert not np.allclose(self.mol.internal_gradient.shape, ref_g.shape)
self.mol.set_new_ics(ic_ref)
assert_allclose(self.mol.internal_gradient, ref_g)
self.mol.swap_internal_coordinates(0, 2)
assert_allclose(self.mol.internal_gradient[2], ref_g[0])
assert_allclose(self.mol.internal_gradient[0], ref_g[2])
def test_delete_ic(self):
with path("saddle.test.data", "ethane.xyz") as mol_path:
mol = Utils.load_file(mol_path)
ethane = Internal(mol.coordinates, mol.numbers, 0, 1)
ethane.auto_select_ic()
ethane._delete_ic_index(0)
assert len(ethane.ic) == 23
ethane.auto_select_ic(keep_bond=True)
assert len(ethane.ic) == 12
# print(ethane.ic)
ethane.delete_ic(1, 2, 3)
assert len(ethane.ic) == 9
# print(ethane.ic)
# assert False
def test_fragments_in_mole(self):
with path("saddle.test.data", "ch3_hf.xyz") as mol_path:
mol = Utils.load_file(mol_path)
mol = Internal(mol.coordinates, mol.numbers, 0, 1)
assert len(mol.fragments) == mol.natom
mol.add_bond(0, 1)
mol.add_bond(2, 3)
# print(mol.fragments)
assert len(mol.fragments) == mol.natom - 2
mol.add_bond(0, 2)
assert len(mol.fragments) == mol.natom - 3
mol.add_bond(0, 3)
assert len(mol.fragments) == mol.natom - 3
mol.add_bond(4, 5)
assert len(mol.fragments) == mol.natom - 4
mol.add_bond(0, 5, b_type=3)
assert len(mol.fragments) == 2
def test_fragments_bond_add(self):
with path("saddle.test.data", "ch3_hf.xyz") as mol_path:
mol = Utils.load_file(mol_path)
mol = Internal(mol.coordinates, mol.numbers, 0, 1)
mol._auto_select_fragment_bond()
assert len(mol.ic) == 15
mol.wipe_ic_info(True)
mol.add_bond(0, 1)
mol._auto_select_fragment_bond()
assert len(mol.ic) == 15
mol.wipe_ic_info(True)
mol.add_bond(0, 1)
mol.add_bond(0, 5)
mol.add_bond(0, 3)
mol.add_bond(4, 2)
mol._auto_select_fragment_bond()
assert len(mol.ic) == 6
mol.wipe_ic_info(True)
mol.add_bond(0, 1)
mol.add_bond(2, 3)
mol.add_bond(4, 5)
mol._auto_select_fragment_bond()
assert len(mol.ic) == 9
#
mol.wipe_ic_info(True)
mol.add_bond(0, 1)
mol.add_bond(0, 2)
mol.add_bond(3, 4)
mol.add_bond(4, 5)
mol._auto_select_fragment_bond()
assert_allclose(mol.ic_values[4], 2.02761704779693)
assert mol.ic[4].atoms == (0, 3)
assert_allclose(mol.ic_values[5], 3.501060110109399)
assert mol.ic[5].atoms == (2, 3)
assert len(mol.ic) == 6
def test_dihedral_rotation(self):
with path("saddle.test.data", "h2o2.xyz") as mol_path:
mol = Utils.load_file(mol_path)
h2o2 = Internal(mol.coordinates, mol.numbers, 0, 1)
h2o2.auto_select_ic()
ref_ic = np.array([
2.47617635, 1.85058569, 1.85070922, 1.81937566, 1.81930967,
1.43966113
])
assert_allclose(h2o2.ic_values, ref_ic)
target_ic = [2.4, 1.8, 1.8, 1.6, 1.6, 1.57]
h2o2.set_target_ic(target_ic)
h2o2.converge_to_target_ic()
assert_allclose(h2o2.ic_values, target_ic, atol=1e-3)
target_ic = [2.4, 1.8, 1.8, 1.6, 1.6, 3.14]
h2o2.set_target_ic(target_ic)
h2o2.converge_to_target_ic()
assert_allclose(h2o2.ic_values, target_ic, atol=1e-4)
target_ic = [2.4, 1.8, 1.8, 1.6, 1.6, -1.57]
h2o2.set_target_ic(target_ic)
h2o2.converge_to_target_ic()
assert_allclose(h2o2.ic_values, target_ic, atol=1e-3)
def test_dihedral_repeak(self):
with path("saddle.test.data", "h2o2.xyz") as mol_path:
mol = Utils.load_file(mol_path)
h2o2 = Internal(mol.coordinates, mol.numbers, 0, 1)
h2o2.add_bond(0, 1)
h2o2.add_bond(1, 2)
h2o2.add_bond(2, 3)
h2o2.add_bond(3, 2)
h2o2.add_bond(0, 2)
h2o2.add_bond(1, 3)
assert len(h2o2.ic) == 5
h2o2.add_dihedral(0, 1, 2, 3)
assert len(h2o2.ic) == 6
h2o2.add_dihedral(0, 2, 1, 3)
assert len(h2o2.ic) == 6
def test_new_dihed(self):
with path("saddle.test.data", "h2o2.xyz") as mol_path:
mol = Utils.load_file(mol_path)
h2o2 = Internal(mol.coordinates, mol.numbers, 0, 1)
h2o2.add_bond(0, 1)
h2o2.add_bond(1, 2)
h2o2.add_bond(2, 3)
assert len(h2o2.ic) == 3
h2o2.add_dihedral(0, 1, 2, 3, special=True)
assert len(h2o2.ic) == 5
assert h2o2.b_matrix.shape == (5, 12)
h2o2.add_dihedral(3, 1, 2, 0)
assert len(h2o2.ic) == 5
h2o2.add_dihedral(3, 2, 1, 0, special=True)
assert len(h2o2.ic) == 5
ref_b = h2o2.b_matrix.copy()
h2o2._regenerate_ic()
assert_allclose(h2o2.b_matrix, ref_b)
def test_new_dihed_converge(self):
with path("saddle.test.data", "h2o2.xyz") as mol_path:
mol = Utils.load_file(mol_path)
mol = Utils.load_file(mol_path)
h2o2 = Internal(mol.coordinates, mol.numbers, 0, 1)
h2o2.auto_select_ic(dihed_special=True)
assert len(h2o2.ic) == 7
# print(h2o2.ic_values)
target_ic = [2.4, 1.8, 1.8, 1.6, 1.6, 0.8, 0.6]
h2o2.set_target_ic(target_ic)
h2o2.converge_to_target_ic()
# print(h2o2.ic_values)
assert_allclose(h2o2.ic_values, target_ic, atol=1e-2)
# print(h2o2.ic_values)
def test_bond_type(self):
with path("saddle.test.data", "ch3_hf.xyz") as mol_path:
mol = Internal.from_file(mol_path, charge=0, multi=1)
mol._auto_select_cov_bond() # numbers [6 1 1 1 9 1]
assert np.sum(mol.connectivity[0] == 1) == 3
assert np.sum(mol.connectivity[4] == 1) == 1
mol._auto_select_fragment_bond()
assert np.sum(mol.connectivity[0] == 1) == 3
assert len(np.unique(mol.fragments)) == 1
assert np.sum(mol.connectivity[5] == 3) == 2
mol._regenerate_ic()
assert np.sum(mol.connectivity[0] == 1) == 3
assert len(np.unique(mol.fragments)) == 1
assert np.sum(mol.connectivity[5] == 3) == 2
mol.wipe_ic_info(True)
mol.auto_select_ic()
assert np.sum(mol.connectivity[0] == 1) == 3
assert len(np.unique(mol.fragments)) == 1
assert np.sum(mol.connectivity[5] == 3) == 2
def test_h_bond(self):
with path("saddle.test.data", "di_water.xyz") as mol_path:
mol = Internal.from_file(mol_path, charge=0, multi=1)
mol._auto_select_cov_bond() # numbers [8 1 1 8 1 1]
assert np.sum(mol.connectivity[0] == 1) == 2
assert np.sum(mol.connectivity[3] == 1) == 2
assert len(mol.fragments) == 2
# print(mol.connectivity)
mol._auto_select_h_bond()
assert mol.connectivity[2][3] == 2
assert len(mol.fragments) == 2
def test_mini_dihed(self):
with path("saddle.test.data", "methanol.xyz") as mol_path:
mol = Internal.from_file(mol_path)
mol._auto_select_cov_bond()
mol._auto_select_h_bond()
mol._auto_select_fragment_bond()
mol._auto_select_angle()
# start real parts
ref = len(mol.ic)
mol._auto_select_minimum_dihed_normal()
assert len(mol.ic) - ref == 1
with path("saddle.test.data", "ethane.xyz") as mol2_path:
mol2 = Internal.from_file(mol2_path)
mol2._auto_select_cov_bond()
mol2._auto_select_h_bond()
mol2._auto_select_fragment_bond()
mol2._auto_select_angle()
# start real parts
ref = len(mol2.ic)
mol2._auto_select_minimum_dihed_normal()
assert len(mol2.ic) - ref == 1
def test_b_matrix(self):
with path("saddle.test.data", "h2o2.xyz") as mol_path:
mol = Internal.from_file(mol_path)
mol.add_bond(0, 1)
mol.add_bond(1, 2)
mol.add_angle(0, 1, 2)
ref_mol = deepcopy(mol)
q1 = mol.ic_values[0]
for i in range(3):
coor = mol.coordinates.copy()
coor[0][i] += 1e-4
ref_mol.set_new_coordinates(coor)
q2 = ref_mol.ic_values[0]
fd = (q2 - q1) / 1e-4
b = mol.b_matrix[0][i]
assert_allclose(fd, b, atol=1e-4)
q1 = mol.ic_values[1]
for i in range(3):
coor = mol.coordinates.copy()
coor[1][i] += 1e-4
ref_mol.set_new_coordinates(coor)
q2 = ref_mol.ic_values[1]
fd = (q2 - q1) / 1e-4
b = mol.b_matrix[1][3 + i]
assert_allclose(fd, b, atol=1e-4)
q1 = mol.ic_values[2]
for i in range(3):
coor = mol.coordinates.copy()
coor[2][i] += 1e-4
ref_mol.set_new_coordinates(coor)
q2 = ref_mol.ic_values[2]
fd = (q2 - q1) / 1e-4
b = mol.b_matrix[2][6 + i]
assert_allclose(fd, b, atol=1e-4)
def test_b_matrix_dihed(self):
with path("saddle.test.data", "h2o2.xyz") as mol_path:
mol = Internal.from_file(mol_path)
mol.auto_select_ic()
ref_mol = deepcopy(mol)
for j in range(4):
q1 = mol.ic_values[j]
for i in range(3):
coor = mol.coordinates.copy()
coor[j][i] += 1e-4
ref_mol.set_new_coordinates(coor)
q2 = ref_mol.ic_values[j]
fd = (q2 - q1) / 1e-4
b = mol.b_matrix[j][j * 3 + i]
assert_allclose(fd, b, atol=1e-4)
def test_tfm_hessian(self):
with path("saddle.test.data", "h2o2.xyz") as mol_path:
mol = Internal.from_file(mol_path)
mol.add_bond(0, 1)
mol.add_bond(1, 2)
mol.add_angle(0, 1, 2)
ref_mol = deepcopy(mol)
qd1 = mol.b_matrix
for i in range(3):
coor = mol.coordinates.copy()
coor[0][i] += 1e-4
ref_mol.set_new_coordinates(coor)
qd2 = ref_mol.b_matrix
fd_b = (qd2 - qd1) / 1e-4
analytic_b = mol._cc_to_ic_hessian[:, :, i]
assert_allclose(fd_b, analytic_b, atol=1e-4)
def test_tfm_hessian_dihed(self):
with path("saddle.test.data", "h2o2.xyz") as mol_path:
mol = Internal.from_file(mol_path)
mol.auto_select_ic()
ref_mol = deepcopy(mol)
qd1 = mol.b_matrix
for j in range(4):
for i in range(3):
coor = mol.coordinates.copy()
coor[j][i] += 1e-4
ref_mol.set_new_coordinates(coor)
qd2 = ref_mol.b_matrix
fd_b = (qd2 - qd1) / 1e-4
analytic_b = mol._cc_to_ic_hessian[:, :, 3 * j + i]
assert_allclose(fd_b, analytic_b, atol=1e-4)
def test_cost_tfm_bond(self):
with path("saddle.test.data", "h2o2.xyz") as mol_path:
mol = Internal.from_file(mol_path)
mol.add_bond(0, 1)
ref_mol = deepcopy(mol)
coor = mol.coordinates.copy()
target_ic = mol.ic_values
# print(mol.ic)
target_ic[0] = 2
mol.set_target_ic(target_ic)
# print(mol.ic[0].value - mol.ic[0].target)
cost_v = mol._compute_tfm_cost()
cost_g = mol._compute_tfm_gradient()
diff = 1e-4
assert_allclose(cost_v, (2 - 2.47617635)**2)
# finite diff test
for i in range(4):
for j in range(3):
coor = ref_mol.coordinates.copy()
coor[i][j] += diff
mol.set_new_coordinates(coor)
cost_v_2 = mol._compute_tfm_cost()
fd = (cost_v_2 - cost_v) / 1e-4
print(fd, cost_g[i * 3 + j], i * 3 + j)
assert_allclose(fd, cost_g[3 * i + j], atol=2e-4)
# tests with bond and angle
def test_cost_tfm_angle(self):
with path("saddle.test.data", "h2o2.xyz") as mol_path:
mol = Internal.from_file(mol_path)
mol.add_bond(0, 1)
mol.add_bond(0, 2)
mol.add_angle(1, 0, 2)
ref_mol = deepcopy(mol)
coor = mol.coordinates.copy()
target_ic = mol.ic_values
# print(mol.ic)
target_ic[2] = 2
target_ic[0] = 2
mol.set_target_ic(target_ic)
# print(mol.ic[0].value - mol.ic[0].target)
cost_v = mol._compute_tfm_cost()
cost_g = mol._compute_tfm_gradient()
diff = 1e-4
# assert_allclose(cost_v, (2 - 2.47617635) ** 2)
# finite diff test
for i in range(4):
for j in range(3):
coor = ref_mol.coordinates.copy()
coor[i][j] += diff
mol.set_new_coordinates(coor)
cost_v_2 = mol._compute_tfm_cost()
fd = (cost_v_2 - cost_v) / 1e-4
print(fd, cost_g[i * 3 + j], i * 3 + j)
assert_allclose(fd, cost_g[3 * i + j], atol=2e-4)
def test_cost_tfm_dihed(self):
with path("saddle.test.data", "h2o2.xyz") as mol_path:
mol = Internal.from_file(mol_path)
mol.auto_select_ic()
ref_mol = deepcopy(mol)
coor = mol.coordinates.copy()
target_ic = mol.ic_values
# print(mol.ic)
target_ic[0] = 2
target_ic[3] = 2
target_ic[5] = 2
mol.set_target_ic(target_ic)
# print(mol.ic[0].value - mol.ic[0].target)
cost_v = mol._compute_tfm_cost()
cost_g = mol._compute_tfm_gradient()
diff = 1e-4
# assert_allclose(cost_v, (2 - 2.47617635) ** 2)
# finite diff test
mol.list_ic
for i in range(4):
for j in range(3):
coor = ref_mol.coordinates.copy()
coor[i][j] += diff
mol.set_new_coordinates(coor)
cost_v_2 = mol._compute_tfm_cost()
fd = (cost_v_2 - cost_v) / 1e-4
assert_allclose(fd, cost_g[3 * i + j], atol=2e-2)
def test_cost_tfm_dihed_cmplx(self):
with path("saddle.test.data", "ethane.xyz") as mol_path:
mol = Internal.from_file(mol_path)
mol.auto_select_ic()
ref_mol = deepcopy(mol)
coor = mol.coordinates.copy()
target_ic = mol.ic_values + 0.5
# print(mol.ic)
mol.set_target_ic(target_ic)
# print(mol.ic[0].value - mol.ic[0].target)
cost_v = mol._compute_tfm_cost()
cost_g = mol._compute_tfm_gradient()
diff = 1e-4
# assert_allclose(cost_v, (2 - 2.47617635) ** 2)
# finite diff test
for i in range(8):
for j in range(3):
coor = ref_mol.coordinates.copy()
coor[i][j] += diff
mol.set_new_coordinates(coor)
cost_v_2 = mol._compute_tfm_cost()
fd = (cost_v_2 - cost_v) / 1e-4
assert_allclose(fd, cost_g[3 * i + j], atol=4e-2)
def test_cost_hessian_bond(self):
with path("saddle.test.data", "h2o2.xyz") as mol_path:
mol = Internal.from_file(mol_path)
mol.add_bond(0, 1)
ref_mol = deepcopy(mol)
coor = mol.coordinates.copy()
target_ic = mol.ic_values + 0.5
# print(mol.ic)
mol.set_target_ic(target_ic)
# print(mol.ic[0].value - mol.ic[0].target)
# cost_v = mol._compute_tfm_cost()
cost_g = mol._compute_tfm_gradient()
cost_h = mol._compute_tfm_hessian()
diff = 1e-4
for j in range(4):
for i in range(3):
coor = ref_mol.coordinates.copy()
coor[j, i] += diff
mol.set_new_coordinates(coor)
cost_g_2 = mol._compute_tfm_gradient()
fd = (cost_g_2 - cost_g) / 1e-4
assert_allclose(fd, cost_h[3 * j + i], atol=4e-4)
def test_cost_hessian_angle(self):
with path("saddle.test.data", "h2o2.xyz") as mol_path:
mol = Internal.from_file(mol_path)
mol.add_bond(0, 1)
mol.add_bond(0, 2)
mol.add_angle(1, 0, 2)
# print(mol.b_matrix)
# print(mol.ic)
# assert False
ref_mol = deepcopy(mol)
coor = mol.coordinates.copy()
target_ic = mol.ic_values + 0.5
# print(mol.ic)
mol.set_target_ic(target_ic)
cost_g = mol._compute_tfm_gradient()
cost_h = mol._compute_tfm_hessian()
diff = 1e-4
for j in range(4):
for i in range(3):
coor = ref_mol.coordinates.copy()
coor[j, i] += diff
mol.set_new_coordinates(coor)
cost_g_2 = mol._compute_tfm_gradient()
fd = (cost_g_2 - cost_g) / 1e-4
assert_allclose(fd, cost_h[j * 3 + i], atol=4e-4)
def test_cost_hessian_dihed(self):
with path("saddle.test.data", "h2o2.xyz") as mol_path:
mol = Internal.from_file(mol_path)
mol.auto_select_ic()
ref_mol = deepcopy(mol)
coor = mol.coordinates.copy()
target_ic = mol.ic_values + 0.5
mol.set_target_ic(target_ic)
cost_g = mol._compute_tfm_gradient()
cost_h = mol._compute_tfm_hessian()
diff = 1e-4
for j in range(4):
for i in range(3):
coor = ref_mol.coordinates.copy()
coor[j, i] += diff
mol.set_new_coordinates(coor)
cost_g_2 = mol._compute_tfm_gradient()
fd = (cost_g_2 - cost_g) / 1e-4
assert_allclose(fd, cost_h[j * 3 + i], atol=4e-2)
def test_cost_hessian_cmpl(self):
with path("saddle.test.data", "methanol.xyz") as mol_path:
mol = Internal.from_file(mol_path)
mol.auto_select_ic()
ref_mol = deepcopy(mol)
coor = mol.coordinates.copy()
target_ic = mol.ic_values + 0.5
mol.set_target_ic(target_ic)
cost_g = mol._compute_tfm_gradient()
cost_h = mol._compute_tfm_hessian()
diff = 1e-4
for j in range(6):
for i in range(3):
coor = ref_mol.coordinates.copy()
coor[j, i] += diff
mol.set_new_coordinates(coor)
cost_g_2 = mol._compute_tfm_gradient()
fd = (cost_g_2 - cost_g) / 1e-4
assert_allclose(fd, cost_h[j * 3 + i], atol=4e-2)
def test_scipy_opt_tfm(self):
with path("saddle.test.data", "h2o2.xyz") as mol_path:
mol = Internal.from_file(mol_path)
mol.auto_select_ic()
target_ic = mol.ic_values
target_ic[0] = 2
target_ic[3] = 2
target_ic[5] = 2
mol.set_target_ic(target_ic)
mol.converge_to_target_ic()
np.allclose(mol.ic_values[0], 2, atol=1e-4)
np.allclose(mol.ic_values[3], 2, atol=1e-4)
np.allclose(mol.ic_values[5], 2, atol=1e-4)
def test_scipy_opt_tfm_cmpx(self):
with path("saddle.test.data", "ethane.xyz") as mol_path:
mol = Internal.from_file(mol_path)
# conventional dihedral
mol.auto_select_ic()
target_ic = mol.ic_values
target_ic[-1] = -1
mol.set_target_ic(target_ic)
# print(mol.ic_values)
mol.converge_to_target_ic()
x_gradient = mol._compute_tfm_gradient()
assert np.max(np.abs(x_gradient)) < 1e-4
def test_dihedral_rotation(self):
with path("saddle.test.data", "h2o2.xyz") as mol_path:
mol = Utils.load_file(mol_path)
h2o2 = Internal(mol.coordinates, mol.numbers, 0, 1)
h2o2.auto_select_ic()
ref_ic = np.array([
2.47617635, 1.85058569, 1.85070922, 1.81937566, 1.81930967,
1.43966113
])
assert_allclose(h2o2.ic_values, ref_ic)
target_ic = [2.4, 1.8, 1.8, 1.6, 1.6, 1.57]
h2o2.set_target_ic(target_ic)
h2o2.converge_to_target_ic()
assert_allclose(h2o2.ic_values, target_ic, atol=1e-3)
target_ic = [2.4, 1.8, 1.8, 1.6, 1.6, 3.14]
h2o2.set_target_ic(target_ic)
h2o2.converge_to_target_ic()
assert_allclose(h2o2.ic_values, target_ic, atol=1e-4)
target_ic = [2.4, 1.8, 1.8, 1.6, 1.6, -1.57]
h2o2.set_target_ic(target_ic)
h2o2.converge_to_target_ic()
assert_allclose(h2o2.ic_values, target_ic, atol=1e-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 test_new_dihed(self):
with path("saddle.test.data", "h2o2.xyz") as mol_path:
mol = Utils.load_file(mol_path)
h2o2 = Internal(mol.coordinates, mol.numbers, 0, 1)
h2o2.add_bond(0, 1)
h2o2.add_bond(1, 2)
h2o2.add_bond(2, 3)
assert len(h2o2.ic) == 3
h2o2.add_dihedral(0, 1, 2, 3, special=True)
assert len(h2o2.ic) == 5
assert h2o2.b_matrix.shape == (5, 12)
h2o2.add_dihedral(3, 1, 2, 0)
assert len(h2o2.ic) == 5
h2o2.add_dihedral(3, 2, 1, 0, special=True)
assert len(h2o2.ic) == 5
ref_b = h2o2.b_matrix.copy()
h2o2._regenerate_ic()
assert_allclose(h2o2.b_matrix, ref_b)
def test_fragments_in_mole(self):
with path("saddle.test.data", "ch3_hf.xyz") as mol_path:
mol = Utils.load_file(mol_path)
mol = Internal(mol.coordinates, mol.numbers, 0, 1)
assert len(mol.fragments) == mol.natom
mol.add_bond(0, 1)
mol.add_bond(2, 3)
# print(mol.fragments)
assert len(mol.fragments) == mol.natom - 2
mol.add_bond(0, 2)
assert len(mol.fragments) == mol.natom - 3
mol.add_bond(0, 3)
assert len(mol.fragments) == mol.natom - 3
mol.add_bond(4, 5)
assert len(mol.fragments) == mol.natom - 4
mol.add_bond(0, 5, b_type=3)
assert len(mol.fragments) == 2
def test_file_title(self):
"""Test default file title."""
new_mol = Internal(self.mol.coordinates, self.mol.numbers, 0, 1)
assert len(new_mol._title) == 15
def test_dihedral_repeak(self):
with path("saddle.test.data", "h2o2.xyz") as mol_path:
mol = Utils.load_file(mol_path)
h2o2 = Internal(mol.coordinates, mol.numbers, 0, 1)
h2o2.add_bond(0, 1)
h2o2.add_bond(1, 2)
h2o2.add_bond(2, 3)
h2o2.add_bond(3, 2)
h2o2.add_bond(0, 2)
h2o2.add_bond(1, 3)
assert len(h2o2.ic) == 5
h2o2.add_dihedral(0, 1, 2, 3)
assert len(h2o2.ic) == 6
h2o2.add_dihedral(0, 2, 1, 3)
assert len(h2o2.ic) == 6
def test_auto_ic_select_methanol(self):
with path("saddle.test.data", "methanol.xyz") as mol_path:
mol = Utils.load_file(mol_path)
methanol = Internal(mol.coordinates, mol.numbers, 0, 1)
methanol.auto_select_ic()
assert len(methanol.ic) == 15