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)