def setUp(self):
carbon_1 = MagicMock(element='CARBON',
charge=6,
mass=12,
coordinates=(-0.98781, 0.41551, 0.00000))
hydrogen_1 = MagicMock(element='HYDROGEN',
charge=1,
mass=1,
coordinates=(0.08219, 0.41551, 0.00000))
hydrogen_2 = MagicMock(element='HYDROGEN',
charge=1,
mass=1,
coordinates=(-1.34447, 0.70319, -0.96692))
hydrogen_3 = MagicMock(element='HYDROGEN',
charge=1,
mass=1,
coordinates=(-1.34448, 1.10904, 0.73260))
hydrogen_4 = MagicMock(element='HYDROGEN',
charge=1,
mass=1,
coordinates=(-1.34448, -0.56571, 0.23432))
self.nuclei_array_ch4 = [
carbon_1, hydrogen_1, hydrogen_2, hydrogen_3, hydrogen_4
]
self.molecule_factory = MoleculeFactory(symmetry=True)
self.symmetry_factory = SymmetryFactory()
def setUp(self):
carbon_1 = MagicMock(element='CARBON', charge=6, mass=12, coordinates=(-0.5297, 0.0100, -0.5606))
carbon_2 = MagicMock(element='CARBON', charge=6, mass=12, coordinates=(0.5297, -0.0100, 0.5606))
hydrogen_1 = MagicMock(element='HYDROGEN', charge=1, mass=1, coordinates=(-0.1452, 0.5058, -1.4448))
hydrogen_2 = MagicMock(element='HYDROGEN', charge=1, mass=1, coordinates=(-1.4207, 0.5374, -0.2390))
hydrogen_3 = MagicMock(element='HYDROGEN', charge=1, mass=1, coordinates=(-0.8163, -0.9984, -0.8374))
hydrogen_4 = MagicMock(element='HYDROGEN', charge=1, mass=1, coordinates=(0.1452, -0.5058, 1.4448))
hydrogen_5 = MagicMock(element='HYDROGEN', charge=1, mass=1, coordinates=(0.8163, 0.9984, 0.8374))
hydrogen_6 = MagicMock(element='HYDROGEN', charge=1, mass=1, coordinates=(1.4207, -0.5374, 0.2390))
self.nuclei_array_c2h6 = [
carbon_1, carbon_2, hydrogen_1, hydrogen_2, hydrogen_3, hydrogen_4, hydrogen_5, hydrogen_6
]
self.molecule_factory = MoleculeFactory(symmetry=True)
self.symmetry_factory = SymmetryFactory()
def setUp(self):
nitrogen_1 = MagicMock(element='NITROGEN',
charge=7,
mass=14,
coordinates=(0.0000000000, 0.0000000000,
1.0399092291))
nitrogen_2 = MagicMock(element='NITROGEN',
charge=7,
mass=14,
coordinates=(0.0000000000, 0.0000000000,
-1.0399092291))
self.nuclei_array_n2 = [nitrogen_1, nitrogen_2]
self.molecule_factory = MoleculeFactory(symmetry=True)
self.symmetry_factory = SymmetryFactory()
def setUp(self):
particle_1 = MagicMock(element='HYDROGEN',
charge=1,
mass=1,
coordinates=(0.4391356726, 0.1106588251,
-0.4635601962))
particle_2 = MagicMock(element='HYDROGEN',
charge=1,
mass=1,
coordinates=(-0.5185079933, 0.3850176090,
0.0537084789))
particle_3 = MagicMock(element='HYDROGEN',
charge=1,
mass=1,
coordinates=(0.0793723207, -0.4956764341,
0.4098517173))
self.nuclei_array = [particle_1, particle_2, particle_3]
self.molecule_factory = MoleculeFactory(symmetry=True)
self.symmetry_factory = SymmetryFactory()
def setUp(self):
nitrogen_1 = MagicMock(element='NITROGEN',
charge=7,
mass=14,
coordinates=(0.0000000000, 0.0000000000,
-2.2684205883))
nitrogen_2 = MagicMock(element='NITROGEN',
charge=7,
mass=14,
coordinates=(0.0000000000, 0.0000000000,
-0.1349300877))
oxygen_1 = MagicMock(element='OXYGEN',
charge=8,
mass=16,
coordinates=(0.0000000000, 0.0000000000,
2.1042369647))
self.nuclei_array_n2o = [nitrogen_1, nitrogen_2, oxygen_1]
self.molecule_factory = MoleculeFactory(symmetry=True)
self.symmetry_factory = SymmetryFactory()
def setUp(self):
oxygen_1 = MagicMock(element='OXYGEN',
charge=8,
mass=16,
coordinates=(-1.4186923158, 0.1090030362,
0.0000000000))
hydrogen_1 = MagicMock(element='HYDROGEN',
charge=1,
mass=1,
coordinates=(-1.7313653816, -1.6895740638,
0.0000000000))
fluorine_1 = MagicMock(element='FLUORINE',
charge=9,
mass=19,
coordinates=(1.2899273141, 0.0031592817,
0.0000000000))
self.nuclei_array_hof = [oxygen_1, hydrogen_1, fluorine_1]
self.molecule_factory = MoleculeFactory(symmetry=True)
self.symmetry_factory = SymmetryFactory()
def setUp(self):
oxygen_1 = MagicMock(element='OXYGEN',
charge=8,
mass=16,
coordinates=(0.0000000000, 0.0000000000,
-0.1363928482))
hydrogen_1 = MagicMock(element='HYDROGEN',
charge=1,
mass=1,
coordinates=(0.0000000000, 1.4236595095,
0.9813433754))
hydrogen_2 = MagicMock(element='HYDROGEN',
charge=1,
mass=1,
coordinates=(0.0000000000, -1.4236595095,
0.9813433754))
self.nuclei_array_h2o = [oxygen_1, hydrogen_1, hydrogen_2]
self.molecule_factory = MoleculeFactory(symmetry=True)
self.symmetry_factory = SymmetryFactory()
def setUp(self):
carbon_1 = MagicMock(element='CARBON',
charge=6,
mass=12,
coordinates=(0.7516, -0.0225, -0.0209))
carbon_2 = MagicMock(element='CARBON',
charge=6,
mass=12,
coordinates=(-0.7516, 0.0225, 0.0209))
hydrogen_1 = MagicMock(element='HYDROGEN',
charge=1,
mass=1,
coordinates=(1.1851, -0.0039, 0.9875))
hydrogen_2 = MagicMock(element='HYDROGEN',
charge=1,
mass=1,
coordinates=(1.1669, 0.8330, -0.5693))
hydrogen_3 = MagicMock(element='HYDROGEN',
charge=1,
mass=1,
coordinates=(1.1155, -0.9329, -0.5145))
hydrogen_4 = MagicMock(element='HYDROGEN',
charge=1,
mass=1,
coordinates=(-1.1669, -0.8334, 0.5687))
hydrogen_5 = MagicMock(element='HYDROGEN',
charge=1,
mass=1,
coordinates=(-1.1157, 0.9326, 0.5151))
hydrogen_6 = MagicMock(element='HYDROGEN',
charge=1,
mass=1,
coordinates=(-1.1850, 0.0044, -0.9875))
self.nuclei_array_c2h6 = [
carbon_1, carbon_2, hydrogen_1, hydrogen_2, hydrogen_3, hydrogen_4,
hydrogen_5, hydrogen_6
]
self.molecule_factory = MoleculeFactory(symmetry=True)
self.symmetry_factory = SymmetryFactory()
def setUp(self):
carbon_1 = MagicMock(element='CARBON',
charge=6,
mass=12,
coordinates=(0.0000000000, 1.2594652672,
0.0000000000))
carbon_2 = MagicMock(element='CARBON',
charge=6,
mass=12,
coordinates=(0.0000000000, -1.2594652672,
0.0000000000))
hydrogen_1 = MagicMock(element='HYDROGEN',
charge=1,
mass=1,
coordinates=(1.7400646600, 2.3216269636,
0.0000000000))
hydrogen_2 = MagicMock(element='HYDROGEN',
charge=1,
mass=1,
coordinates=(-1.7400646600, 2.3216269636,
0.0000000000))
hydrogen_3 = MagicMock(element='HYDROGEN',
charge=1,
mass=1,
coordinates=(1.7400646600, -2.3216269636,
0.0000000000))
hydrogen_4 = MagicMock(element='HYDROGEN',
charge=1,
mass=1,
coordinates=(-1.7400646600, -2.3216269636,
0.0000000000))
self.nuclei_array_c2h4 = [
carbon_1, carbon_2, hydrogen_1, hydrogen_2, hydrogen_3, hydrogen_4
]
self.molecule_factory = MoleculeFactory(symmetry=True)
self.symmetry_factory = SymmetryFactory()
def setUp(self):
carbon_1 = MagicMock(element='CARBON',
charge=6,
mass=12,
coordinates=(1.2455, 0.5367, -0.0729))
carbon_2 = MagicMock(element='CARBON',
charge=6,
mass=12,
coordinates=(0.9239, -0.9952, 0.0237))
carbon_3 = MagicMock(element='CARBON',
charge=6,
mass=12,
coordinates=(-0.1226, -0.7041, 1.1548))
carbon_4 = MagicMock(element='CARBON',
charge=6,
mass=12,
coordinates=(0.1989, 0.8277, 1.0582))
carbon_5 = MagicMock(element='CARBON',
charge=6,
mass=12,
coordinates=(0.1226, 0.7042, -1.1548))
carbon_6 = MagicMock(element='CARBON',
charge=6,
mass=12,
coordinates=(-0.9239, 0.9952, -0.0237))
carbon_7 = MagicMock(element='CARBON',
charge=6,
mass=12,
coordinates=(-1.2454, -0.5367, 0.0729))
carbon_8 = MagicMock(element='CARBON',
charge=6,
mass=12,
coordinates=(-0.1989, -0.8277, -1.0582))
hydrogen_1 = MagicMock(element='HYDROGEN',
charge=1,
mass=1,
coordinates=(2.2431, 0.9666, -0.1313))
hydrogen_2 = MagicMock(element='HYDROGEN',
charge=1,
mass=1,
coordinates=(1.6638, -1.7924, 0.0426))
hydrogen_3 = MagicMock(element='HYDROGEN',
charge=1,
mass=1,
coordinates=(-0.2209, -1.2683, 2.0797))
hydrogen_4 = MagicMock(element='HYDROGEN',
charge=1,
mass=1,
coordinates=(0.3583, 1.4907, 1.9059))
hydrogen_5 = MagicMock(element='HYDROGEN',
charge=1,
mass=1,
coordinates=(0.2208, 1.2681, -2.0799))
hydrogen_6 = MagicMock(element='HYDROGEN',
charge=1,
mass=1,
coordinates=(-1.6640, 1.7922, -0.0427))
hydrogen_7 = MagicMock(element='HYDROGEN',
charge=1,
mass=1,
coordinates=(-2.2430, -0.9665, 0.1313))
hydrogen_8 = MagicMock(element='HYDROGEN',
charge=1,
mass=1,
coordinates=(-0.3583, -1.4906, -1.9058))
self.nuclei_array_c8h8 = [
carbon_1, carbon_2, carbon_3, carbon_4, carbon_5, carbon_6,
carbon_7, carbon_8, hydrogen_1, hydrogen_2, hydrogen_3, hydrogen_4,
hydrogen_5, hydrogen_6, hydrogen_7, hydrogen_8
]
self.molecule_factory = MoleculeFactory(symmetry=True)
self.symmetry_factory = SymmetryFactory()
self.inversion_symmetry = InversionSymmetry()
def __init__(self, symmetry=False, error=1e-3):
self.symmetry = symmetry
self.error = error
self.symmetry_factory = SymmetryFactory(error)