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_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_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