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_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_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_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_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_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_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_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_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_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_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_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_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_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
