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_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))