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_class(self):
with path("saddle.test.data", "methanol.xyz") as file_path:
mol = Utils.load_file(file_path)
self.molecule = mol
with path("saddle.test.data", "h2o2.xyz") as file_path2:
mol2 = Utils.load_file(file_path2)
self.h2o2 = mol2
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 save_to(self, filename, mode="w"):
"""Save current coordinates of molecule into a .xzy file.
Parameters
----------
filename : str
File name of the saved file
mode : str, optional
I/O mode of file
"""
Utils.save_file(filename, self, mode=mode)
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_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_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 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 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_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_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_create_input_file(self):
self.gwob.title = "test_untitled"
input_file = self.gwob._create_input_file(0, 1)
filepath = WORK_DIR / (input_file + ".com")
mol = Utils.load_file(filepath)
self.file_list.append(filepath)
assert np.allclose(self.gwob.molecule.coordinates, mol.coordinates)
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_create_input_gjf(self):
self.gwob.create_gauss_input(
0, 1, spe_title="test_2nd_gauss", path=self.test_path, postfix=".gjf"
)
filepath = self.test_path / "test_2nd_gauss.gjf"
self.file_list.append(filepath)
mol = Utils.load_file(filepath)
assert np.allclose(self.gwob.molecule.coordinates, mol.coordinates)
def ts_to_file(self, filename=""):
"""Save the ts structure to xyz file.
Parameters
----------
filename : str, optional
filename of stored file
Raises
------
InvalidArgumentError
the input filename is not valid.
"""
if filename:
Utils.save_file(filename, self.ts)
else:
raise InvalidArgumentError("Invalid empty filename")
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 test_save_xyz(self):
with path("saddle.test.data", "water.xyz") as file_path:
water_mol = Utils.load_file(file_path)
with path("saddle.test.data", "") as file_path:
new_file_name = file_path / "test_base_mole_test_file"
Utils.save_file(new_file_name, water_mol)
new_add_file = new_file_name.parent / (new_file_name.name + ".xyz")
TestUtils.file_list.append(new_add_file)
with path("saddle.test.data",
"test_base_mole_test_file.xyz") as file_path:
mol = Utils.load_file(file_path)
ref_coor = np.array([
[1.481237149, -0.93019116, 0.0],
[0.0, 0.11720080, 0],
[-1.481237149, -0.93019116, 0.0],
])
assert np.allclose(mol.coordinates, ref_coor)
assert np.allclose(mol.numbers, [1, 8, 1])
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_load_xyz(self):
with path("saddle.test.data", "water.xyz") as file_path:
nums, coors, title = Utils._load_xyz(file_path)
assert np.allclose(nums, np.array([1, 8, 1]))
ref_coor = np.array([
[1.481237149, -0.93019116, 0.0],
[0.0, 0.11720080, 0],
[-1.481237149, -0.93019116, 0.0],
])
assert np.allclose(coors, ref_coor)
assert title == "water"
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_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_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 from_file(
cls, filename: str, charge: int = 0, multi: int = 1, title=""
) -> "Cartesian":
"""Create an Cartesian instance from file .xyz, .com, .gjf or .fchk.
Arguments
---------
filename : str
the path of the file
charge : int, default is 0
the charge of the given molecule(system)
multi : int, dufault is 1
the multiplicity of the given molecule(system)
Return
------
new Cartesian instance : Cartesian
"""
mol = Utils.load_file(filename)
return cls(mol.coordinates, mol.numbers, charge, multi, title=title)
def test_main_function(self):
"""Test the main function and use case for procrustes."""
# file_path = resource_filename(
# Requirement.parse('saddle'), 'data/water.xyz')
with path("saddle.procrustes.test.data", "water.xyz") as file_path:
water = Utils.load_file(file_path)
water.coordinates = np.array([[0, 1, 0], [1, 0, 0], [-1, -1, 1]])
water_2 = deepcopy(water)
water_2.coordinates = np.array([[-1, 0, 0], [0, 1, 0], [1, -1, 0]])
water_2.coordinates += 1
water_3 = deepcopy(water)
water_3.coordinates = np.array([[1, 0, 0], [0, -1, 0], [-1, 1, 0]])
water_3.coordinates -= 1
pcs = Procrustes(water, water_2, water_3)
final_xyz = pcs.rotate_mols()
assert isinstance(final_xyz, Iterable)
assert len(list(final_xyz)) == 2
for i in final_xyz:
assert np.allclose(i, water.coordinates)
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 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)