def test_displace_hooh_cart(self):
mol = Molecule("""
H -0.8026739226 -0.8820752737 0.4535861764
O -0.0110284705 -0.7248476524 -0.0721631764
O 0.0110284705 0.7248476524 -0.0721631764
H 0.8026739226 0.8820752737 0.4535861764
"""
)
mol.convert_units(Bohr)
mol.internal_representation = rep = InternalRepresentation(mol, """
bond 2 1
bond 3 2
bend 3 2 1
bond 4 3
bend 4 3 2
tors 4 3 2 1
"""
)
d = Displacement.from_increments((0,-1,0,0,0,0), rep,
Vector([0.1*Angstrom, 0.1*Angstrom, 0.2*Degrees, 0.1*Angstrom, 0.2*Degrees, 0.2*Degrees])
)
deg_to_def = Degrees.to(AngularUnit.default)
self.assertAlmostEqual(
rep[1].in_units(Angstrom) - 0.1*Angstrom,
d.displaced_representation[1].in_units(Angstrom)
)
def test_displace_all_hooh(self):
mol = Molecule.from_z_matrix("""
H
O 1 0.963242
O 2 1.449863 1 100.120071
H 3 0.963242 2 100.120071 1 -67.344079
""",
create_representation=True)
rep = mol.internal_representation
deg_to_def = Degrees.to(AngularUnit.default)
self.assertAlmostEqual(rep[5].value, -67.344079 * deg_to_def)
d = Displacement.from_increments(Vector(0, -1, 0, 0, 0, 0), rep,
Vector([0.1] * 6))
self.assertAlmostEqual(0.963242, d.displaced_representation[0].value)
self.assertAlmostEqual(1.349863, d.displaced_representation[1].value)
self.assertAlmostEqual(
100.120071 * deg_to_def,
d.displaced_representation[2].value_with_units.in_units(
AngularUnit.default))
self.assertAlmostEqual(0.963242, d.displaced_representation[3].value)
self.assertAlmostEqual(
100.120071 * deg_to_def,
d.displaced_representation[4].value_with_units.in_units(
AngularUnit.default))
self.assertAlmostEqual(
-67.344079 * deg_to_def,
d.displaced_representation[5].value_with_units.in_units(
AngularUnit.default))
def test_displace_hooh_cart(self):
mol = Molecule("""
H -0.8026739226 -0.8820752737 0.4535861764
O -0.0110284705 -0.7248476524 -0.0721631764
O 0.0110284705 0.7248476524 -0.0721631764
H 0.8026739226 0.8820752737 0.4535861764
""")
mol.convert_units(Bohr)
mol.internal_representation = rep = InternalRepresentation(
mol, """
bond 2 1
bond 3 2
bend 3 2 1
bond 4 3
bend 4 3 2
tors 4 3 2 1
""")
d = Displacement.from_increments(
(0, -1, 0, 0, 0, 0), rep,
Vector([
0.1 * Angstrom, 0.1 * Angstrom, 0.2 * Degrees, 0.1 * Angstrom,
0.2 * Degrees, 0.2 * Degrees
]))
deg_to_def = Degrees.to(AngularUnit.default)
self.assertAlmostEqual(
rep[1].in_units(Angstrom) - 0.1 * Angstrom,
d.displaced_representation[1].in_units(Angstrom))
def test_displace_bond_length(self):
mol = Molecule.from_z_matrix("""
H
O 1 1.0
""", create_representation=True
)
rep = mol.internal_representation
d = Displacement.from_increments(Vector(1), rep, Vector(0.1))
self.assertAlmostEqual(d.displaced_representation[0].value, 1.1)
def test_displace_bond_length(self):
mol = Molecule.from_z_matrix("""
H
O 1 1.0
""",
create_representation=True)
rep = mol.internal_representation
d = Displacement.from_increments(Vector(1), rep, Vector(0.1))
self.assertAlmostEqual(d.displaced_representation[0].value, 1.1)
def test_displace_torsion(self):
mol = Molecule.from_z_matrix("""
H
O 1 1.0
O 2 1.0 1 90
H 3 1.0 2 90 1 90
""", create_representation=True
)
rep = mol.internal_representation
d = Displacement.from_increments(Vector(0,0,0,0,0,1), rep, Vector(0,0,0,0,0,0.1))
deg_to_def = Degrees.to(AngularUnit.default)
self.assertAlmostEqual(d.displaced_representation[0].value, 1.0)
self.assertAlmostEqual(d.displaced_representation[5].value, 90.1 * deg_to_def)
def test_displace_bond_angle(self):
deg_to_def = Degrees.to(AngularUnit.default)
mol = Molecule.from_z_matrix("""
H
O 1 1.0
H 2 1.0 1 90
""", create_representation=True
)
rep = mol.internal_representation
d = Displacement.from_increments(Vector(1, 0, 0), rep, Vector([0.1]*3))
self.assertAlmostEqual(d.displaced_representation[0].value, 1.1)
self.assertAlmostEqual(d.displaced_representation[2].value, 90.*deg_to_def)
def test_displace_torsion(self):
mol = Molecule.from_z_matrix("""
H
O 1 1.0
O 2 1.0 1 90
H 3 1.0 2 90 1 90
""",
create_representation=True)
rep = mol.internal_representation
d = Displacement.from_increments(Vector(0, 0, 0, 0, 0, 1), rep,
Vector(0, 0, 0, 0, 0, 0.1))
deg_to_def = Degrees.to(AngularUnit.default)
self.assertAlmostEqual(d.displaced_representation[0].value, 1.0)
self.assertAlmostEqual(d.displaced_representation[5].value,
90.1 * deg_to_def)
def test_displace_bond_angle(self):
deg_to_def = Degrees.to(AngularUnit.default)
mol = Molecule.from_z_matrix("""
H
O 1 1.0
H 2 1.0 1 90
""",
create_representation=True)
rep = mol.internal_representation
d = Displacement.from_increments(Vector(1, 0, 0), rep,
Vector([0.1] * 3))
self.assertAlmostEqual(d.displaced_representation[0].value, 1.1)
self.assertAlmostEqual(d.displaced_representation[2].value,
90. * deg_to_def)
def test_displace_all_zmat(self):
mol = Molecule.from_z_matrix("""
H
O 1 1.0
O 2 1.0 1 90
H 3 1.0 2 90 1 -90
""", create_representation=True
)
rep = mol.internal_representation
d = Displacement.from_increments(Vector(1,-1,1,-1,1,-1), rep, Vector([0.1]*6))
deg_to_def = Degrees.to(AngularUnit.default)
self.assertAlmostEqual(d.displaced_representation[0].value, 1.1)
self.assertAlmostEqual(d.displaced_representation[1].value, 0.9)
self.assertAlmostEqual(d.displaced_representation[2].value, 90.1 * deg_to_def)
self.assertAlmostEqual(d.displaced_representation[3].value, 0.9)
self.assertAlmostEqual(d.displaced_representation[4].value, 90.1 * deg_to_def)
self.assertAlmostEqual(d.displaced_representation[5].value, -90.1 * deg_to_def)
def test_displace_all_hooh(self):
mol = Molecule.from_z_matrix("""
H
O 1 0.963242
O 2 1.449863 1 100.120071
H 3 0.963242 2 100.120071 1 -67.344079
""", create_representation=True
)
rep = mol.internal_representation
deg_to_def = Degrees.to(AngularUnit.default)
self.assertAlmostEqual(rep[5].value, -67.344079 * deg_to_def)
d = Displacement.from_increments(Vector(0,-1,0,0,0,0), rep, Vector([0.1]*6))
self.assertAlmostEqual(0.963242, d.displaced_representation[0].value)
self.assertAlmostEqual(1.349863, d.displaced_representation[1].value)
self.assertAlmostEqual(100.120071 * deg_to_def, d.displaced_representation[2].value_with_units.in_units(AngularUnit.default))
self.assertAlmostEqual(0.963242, d.displaced_representation[3].value)
self.assertAlmostEqual(100.120071 * deg_to_def, d.displaced_representation[4].value_with_units.in_units(AngularUnit.default))
self.assertAlmostEqual(-67.344079 * deg_to_def, d.displaced_representation[5].value_with_units.in_units(AngularUnit.default))
def test_displace_all_zmat(self):
mol = Molecule.from_z_matrix("""
H
O 1 1.0
O 2 1.0 1 90
H 3 1.0 2 90 1 -90
""",
create_representation=True)
rep = mol.internal_representation
d = Displacement.from_increments(Vector(1, -1, 1, -1, 1, -1), rep,
Vector([0.1] * 6))
deg_to_def = Degrees.to(AngularUnit.default)
self.assertAlmostEqual(d.displaced_representation[0].value, 1.1)
self.assertAlmostEqual(d.displaced_representation[1].value, 0.9)
self.assertAlmostEqual(d.displaced_representation[2].value,
90.1 * deg_to_def)
self.assertAlmostEqual(d.displaced_representation[3].value, 0.9)
self.assertAlmostEqual(d.displaced_representation[4].value,
90.1 * deg_to_def)
self.assertAlmostEqual(d.displaced_representation[5].value,
-90.1 * deg_to_def)
