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_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)
class TestSecant(unittest.TestCase):
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)
def test_secant_condition(self):
result = secant(self.newp, self.oldp)
# separate calculation
part1 = self.newp.v_gradient - self.oldp.v_gradient
part2 = np.dot(self.newp.vspace.T,
np.linalg.pinv(self.newp.b_matrix.T))
part3 = np.dot(
self.newp.b_matrix.T,
np.dot((self.newp.vspace - self.oldp.vspace),
self.newp.v_gradient),
)
part4 = np.dot((self.newp.b_matrix - self.oldp.b_matrix).T,
self.newp.q_gradient)
final = part1 - np.dot(part2, (part3 + part4))
assert np.allclose(result, final, atol=1e-6)
def test_secant_condition_0(self):
d_s = np.dot(self.old_ob.vspace.T,
self.new_ob.ic_values - self.old_ob.ic_values)
ref = np.dot(self.old_ob.v_hessian, d_s)
result = secant(self.newp, self.oldp)
assert_allclose(ref, result, atol=1e-5)
def test_secant_condition_1(self):
d_s = np.dot(self.old_ob.vspace.T,
self.new_ob.ic_values - self.old_ob.ic_values)
ref = np.dot(self.old_ob.v_hessian, d_s)
result = secant_1(self.newp, self.oldp)
assert_allclose(ref, result, atol=1e-5)
def test_secant_condition_2(self):
d_s = np.dot(self.old_ob.vspace.T,
self.new_ob.ic_values - self.old_ob.ic_values)
ref = np.dot(self.old_ob.v_hessian, d_s)
result = secant_2(self.newp, self.oldp)
assert_allclose(ref, result, atol=1e-5)
def test_secant_condition_3(self):
d_s = np.dot(self.old_ob.vspace.T,
self.new_ob.ic_values - self.old_ob.ic_values)
ref = np.dot(self.old_ob.v_hessian, d_s)
result = secant_3(self.newp, self.oldp)
assert_allclose(ref, result, atol=1e-5)