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_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)