def test_create_representation_bond(self):
with self.assertRaisesRegexp(ValueError, r'atomics.*only representable as.*Cannot create'):
Molecule.from_z_matrix('O', create_representation=True)
mol = Molecule.from_z_matrix('H\nH 1 0.9', create_representation=True)
self.assertEqual(len(mol.internal_representations), 1)
self.assertEqual(len(mol.internal_representations[0]), 1)
def test_zmat(self):
self.assertEqual(
Molecule([Atom("O", [0.0, 0.0, 0.0])]),
Molecule.from_z_matrix("""
O
"""
)
)
self.assertEqual(
Molecule([
Atom("O", [0.0, 0.0, 0.0]),
Atom("O", [0.0, 0.0, 1.0])
]),
Molecule.from_z_matrix("""
O1
O2 O1 1.0
"""
)
)
self.assertEqual(
Molecule([
Atom("O", [0.0, 0.0, 0.0]),
Atom("H", [0.0, 0.0, 1.0]),
Atom("H", [0.0, -1.0, 0.0])
]),
Molecule.from_z_matrix("""
O
H1 O 1.0
H2 O 1.0 H1 90
"""
)
)
def test_future_errors(self):
with self.assertRaisesRegexp(ValueError,
r'Ambiguous atom identifier in z-matrix'):
Molecule.from_z_matrix("""
O
H O 1.0
H H 1.0 O 3.7
""")
def test_create_representation_bond(self):
with self.assertRaisesRegexp(
ValueError, r'atomics.*only representable as.*Cannot create'):
Molecule.from_z_matrix('O', create_representation=True)
mol = Molecule.from_z_matrix('H\nH 1 0.9', create_representation=True)
self.assertEqual(len(mol.internal_representations), 1)
self.assertEqual(len(mol.internal_representations[0]), 1)
def test_errors_18(self):
with self.assertRaisesRegexp(IndexError, r"z-matrix index '0' is out of range"):
Molecule.from_z_matrix('''
O
H 1 0.93
C 2 1.23 1 104.5
B 2 1.35 1 89.5 0 84.3
''', create_representation=True)
def test_errors_19(self):
with self.assertRaisesRegexp(InvalidZMatrixException, r'atom indices in z-matrix line'):
Molecule.from_z_matrix('''
O
H 1 0.93
C 2 1.23 1 104.5
B 2 1.35 1 89.5 1 84.3
''', create_representation=True)
def test_future_errors(self):
with self.assertRaisesRegexp(ValueError, r'Ambiguous atom identifier in z-matrix'):
Molecule.from_z_matrix(
"""
O
H O 1.0
H H 1.0 O 3.7
"""
)
def test_errors_11(self):
with self.assertRaisesRegexp(ValueError,
r'Ambiguous atom identifier in z-matrix'):
Molecule.from_z_matrix("""
O
H O 1.0
H O -1.0 H 37
O2 H 1.5 O 150 H 25
""")
def test_errors_18(self):
with self.assertRaisesRegexp(IndexError,
r"z-matrix index '0' is out of range"):
Molecule.from_z_matrix('''
O
H 1 0.93
C 2 1.23 1 104.5
B 2 1.35 1 89.5 0 84.3
''',
create_representation=True)
def test_errors_11(self):
with self.assertRaisesRegexp(ValueError, r'Ambiguous atom identifier in z-matrix'):
Molecule.from_z_matrix(
"""
O
H O 1.0
H O -1.0 H 37
O2 H 1.5 O 150 H 25
"""
)
def test_errors_19(self):
with self.assertRaisesRegexp(InvalidZMatrixException,
r'atom indices in z-matrix line'):
Molecule.from_z_matrix('''
O
H 1 0.93
C 2 1.23 1 104.5
B 2 1.35 1 89.5 1 84.3
''',
create_representation=True)
def test_misc(self):
# getitem
self.assertEqual(Molecule.from_z_matrix("O")[0].symbol, "O")
# contains
mol = Molecule.from_z_matrix("O")
self.assertIn(mol[0], mol)
self.assertNotIn(Atom("H", 0, 0, 0), mol)
# less than
self.assertLess(mol, Molecule("O 0.0 0.0 1.0"))
def test_misc(self):
# getitem
self.assertEqual(Molecule.from_z_matrix("O")[0].symbol, "O")
# contains
mol = Molecule.from_z_matrix("O")
self.assertIn(mol[0], mol)
self.assertNotIn(Atom("H", 0, 0, 0), mol)
# less than
self.assertLess(mol, Molecule("O 0.0 0.0 1.0"))
def test_displace(self):
mol = Molecule.from_z_matrix('H')
mol.displace(Vector(1., -1., 0.))
self.assertEqual(mol, Molecule("H 1 -1 0"))
mol = Molecule.from_z_matrix('H\nH 1 0.9')
mol.displace(Vector(1., 0., 0., 1., 0., 0.))
self.assertEqual(mol, Molecule("H 1 0 0.0\nH 1 0 0.9 "))
with self.assertRaisesRegexp(ValueError, 'dimension mismatch'):
mol.displace(Vector(1., 0., 0.))
with self.assertRaises(TypeError):
mol.displace(Matrix(1., 0., 0.))
def test_displace(self):
mol = Molecule.from_z_matrix('H')
mol.displace(Vector(1., -1., 0.))
self.assertEqual(mol, Molecule("H 1 -1 0"))
mol = Molecule.from_z_matrix('H\nH 1 0.9')
mol.displace(Vector(1., 0., 0., 1., 0., 0.))
self.assertEqual(mol, Molecule("H 1 0 0.0\nH 1 0 0.9 "))
with self.assertRaisesRegexp(ValueError, 'dimension mismatch'):
mol.displace(Vector(1., 0., 0.))
with self.assertRaises(TypeError):
mol.displace(Matrix(1., 0., 0.))
def test_bond_length_2(self):
mol = Molecule.from_z_matrix('H\nO 1 0.9', create_representation=True)
mol.recenter()
# 'randomize' the position in xyz space to avoid miniscule displacement amounts
mol.rotate(Vector(1,2,1), 32.*Degrees)
coord = mol.internal_representation[0]
assert_has_valid_b_tensor(coord, 2)
def test_bond_length_2(self):
mol = Molecule.from_z_matrix('H\nO 1 0.9', create_representation=True)
mol.recenter()
# 'randomize' the position in xyz space to avoid miniscule displacement amounts
mol.rotate(Vector(1, 2, 1), 32. * Degrees)
coord = mol.internal_representation[0]
assert_has_valid_b_tensor(coord, 2)
def test_2_torsions_4_dry_run(self):
mol = Molecule.from_z_matrix('''
O
H 1 0.93
C 2 1.23 1 104.5
B 3 1.35 2 89.5 1 83.2
O 4 1.25 3 89.5 2 -23.2
''',
create_representation=True)
mol.recenter()
order = 4
coord = mol.internal_representation[5]
natoms = mol.natoms
btens = coord.parent_representation.b_tensor()
analytic_tensor = Tensor(shape=(3 * natoms, ) * order)
for cartcoords in product(coord.variables, repeat=order):
analytic_tensor[tuple(
c.index for c in cartcoords)] = btens[(coord, ) + cartcoords]
coord = mol.internal_representation[8]
natoms = mol.natoms
btens = coord.parent_representation.b_tensor()
analytic_tensor = Tensor(shape=(3 * natoms, ) * order)
for cartcoords in product(coord.variables, repeat=order):
analytic_tensor[tuple(
c.index for c in cartcoords)] = btens[(coord, ) + cartcoords]
def test_create_representation_tors_2(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
)
self.assertEqual(mol.internal_representations[0].coords[5].value_with_units.in_units(AngularUnit.default),
(-90.*Degrees).in_units(AngularUnit.default))
def test_bond_length_7_dry_run(self):
self.setUp()
order = 7
mol = Molecule.from_z_matrix('H\nO 1 0.9', create_representation=True)
mol.recenter()
coord = mol.internal_representation[0]
natoms = mol.natoms
btens = coord.parent_representation.b_tensor()
analytic_tensor = Tensor(shape=(3*natoms,)*order)
for cartcoords in product(coord.variables, repeat=order):
analytic_tensor[tuple(c.index for c in cartcoords)] = btens[(coord,) + cartcoords]
def test_bond_length_7_dry_run(self):
self.setUp()
order = 7
mol = Molecule.from_z_matrix('H\nO 1 0.9', create_representation=True)
mol.recenter()
coord = mol.internal_representation[0]
natoms = mol.natoms
btens = coord.parent_representation.b_tensor()
analytic_tensor = Tensor(shape=(3 * natoms, ) * order)
for cartcoords in product(coord.variables, repeat=order):
analytic_tensor[tuple(
c.index for c in cartcoords)] = btens[(coord, ) + cartcoords]
def test_create_representation_tors_2(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)
self.assertEqual(
mol.internal_representations[0].coords[5].value_with_units.
in_units(AngularUnit.default),
(-90. * Degrees).in_units(AngularUnit.default))
def test_create_rep_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_with_units.in_units(AngularUnit.default),
-67.344079 * deg_to_def)
def test_create_representation_ang(self):
mol = Molecule.from_z_matrix("""
O
H1 O 1.0
H2 O 1.0 H1 90
""", create_representation=True
)
self.assertEqual(len(mol.internal_representations), 1)
self.assertEqual(len(mol.internal_representations[0]), 3)
self.assertEqual(
mol.internal_representations[0].coords[2].value_with_units.in_units(AngularUnit.default),
(90.*Degrees).in_units(AngularUnit.default)
)
def test_create_rep_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_with_units.in_units(AngularUnit.default),
-67.344079 * deg_to_def)
def test_create_representation_ang(self):
mol = Molecule.from_z_matrix("""
O
H1 O 1.0
H2 O 1.0 H1 90
""",
create_representation=True)
self.assertEqual(len(mol.internal_representations), 1)
self.assertEqual(len(mol.internal_representations[0]), 3)
self.assertEqual(
mol.internal_representations[0].coords[2].value_with_units.
in_units(AngularUnit.default),
(90. * Degrees).in_units(AngularUnit.default))
def setUpForValue(self, val, randomize_cartesian_space=True):
self.mol = Molecule.from_z_matrix('''
O
H 1 0.93
C 2 1.23 1 104.5
B 3 1.35 2 89.5 1 ''' + str(val), create_representation=True)
self.mol.recenter()
if randomize_cartesian_space:
# 'randomize' the position in xyz space to avoid miniscule displacement amounts
self.mol.rotate(Vector(0,0,1), 32 * Degrees.to(Radians))
self.mol.rotate(Vector(0,1,0), 32 * Degrees.to(Radians))
self.mol.rotate(Vector(1,0,0), 32 * Degrees.to(Radians))
self.coord = self.mol.internal_representation[5]
def setUpForValue(self, val, randomize_cartesian_space=True):
self.mol = Molecule.from_z_matrix('''
O
H 1 0.93
C 2 1.23 1 104.5
B 3 1.35 2 89.5 1 ''' + str(val),
create_representation=True)
self.mol.recenter()
if randomize_cartesian_space:
# 'randomize' the position in xyz space to avoid miniscule displacement amounts
self.mol.rotate(Vector(0, 0, 1), 32 * Degrees.to(Radians))
self.mol.rotate(Vector(0, 1, 0), 32 * Degrees.to(Radians))
self.mol.rotate(Vector(1, 0, 0), 32 * Degrees.to(Radians))
self.coord = self.mol.internal_representation[5]
def test_zmat(self):
self.assertEqual(
Molecule([Atom("O", [0.0, 0.0, 0.0])]),
Molecule.from_z_matrix("""
O
"""))
self.assertEqual(
Molecule([Atom("O", [0.0, 0.0, 0.0]),
Atom("O", [0.0, 0.0, 1.0])]),
Molecule.from_z_matrix("""
O1
O2 O1 1.0
"""))
self.assertEqual(
Molecule([
Atom("O", [0.0, 0.0, 0.0]),
Atom("H", [0.0, 0.0, 1.0]),
Atom("H", [0.0, -1.0, 0.0])
]),
Molecule.from_z_matrix("""
O
H1 O 1.0
H2 O 1.0 H1 90
"""))
def test_2_torsions_4_dry_run(self):
mol = Molecule.from_z_matrix('''
O
H 1 0.93
C 2 1.23 1 104.5
B 3 1.35 2 89.5 1 83.2
O 4 1.25 3 89.5 2 -23.2
''', create_representation=True)
mol.recenter()
order = 4
coord = mol.internal_representation[5]
natoms = mol.natoms
btens = coord.parent_representation.b_tensor()
analytic_tensor = Tensor(shape=(3*natoms,)*order)
for cartcoords in product(coord.variables, repeat=order):
analytic_tensor[tuple(c.index for c in cartcoords)] = btens[(coord,) + cartcoords]
coord = mol.internal_representation[8]
natoms = mol.natoms
btens = coord.parent_representation.b_tensor()
analytic_tensor = Tensor(shape=(3*natoms,)*order)
for cartcoords in product(coord.variables, repeat=order):
analytic_tensor[tuple(c.index for c in cartcoords)] = btens[(coord,) + cartcoords]
def _generated(self, aval):
mol = Molecule.from_z_matrix('H\nO 1 1.0\nH 2 1.0 1 ' + str(aval), create_representation=True)
coord = mol.internal_representation[2]
self.assertHasValidBVector(coord)
def test_bond_angle(self):
mol = Molecule.from_z_matrix('H\nO 1 1.0\nH 2 1.0 1 90', create_representation=True)
coord = mol.internal_representation[2]
self.assertHasValidBVector(coord)
def test_bond_length(self):
mol = Molecule.from_z_matrix('H\nO 1 1.0', create_representation=True)
coord = mol.internal_representation[0]
self.assertHasValidBVector(coord)
def test_bond_length_6(self):
mol = Molecule.from_z_matrix('H\nO 1 0.9', create_representation=True)
mol.recenter()
coord = mol.internal_representation[0]
assert_has_valid_b_tensor(coord, 6)
def test_bond_length_6(self):
mol = Molecule.from_z_matrix('H\nO 1 0.9', create_representation=True)
mol.recenter()
coord = mol.internal_representation[0]
assert_has_valid_b_tensor(coord, 6)
def _generated(self, aval):
mol = Molecule.from_z_matrix('H\nO 1 1.0\nH 2 1.0 1 ' + str(aval),
create_representation=True)
coord = mol.internal_representation[2]
self.assertHasValidBVector(coord)
def test_bond_angle(self):
mol = Molecule.from_z_matrix('H\nO 1 1.0\nH 2 1.0 1 90',
create_representation=True)
coord = mol.internal_representation[2]
self.assertHasValidBVector(coord)
def test_bond_length(self):
mol = Molecule.from_z_matrix('H\nO 1 1.0', create_representation=True)
coord = mol.internal_representation[0]
self.assertHasValidBVector(coord)
