def create_geometries(self): """ Cut the species in two parts and save the geometries of both parts into new stationary point objects """ # copy the reactant stationary point atom = copy.deepcopy(self.species.atom) geom = copy.deepcopy(self.species.geom) temp = StationaryPoint('temp', self.species.charge, self.species.mult, atom=atom, geom=geom) temp.characterize() # set the bond order of the breaking bond to 0 temp.bond[self.bond[0]][self.bond[1]] = 0 temp.bond[self.bond[1]][self.bond[0]] = 0 self.products, maps = temp.start_multi_molecular()
def create_geometries(self): """ Cut the species in two parts and save the geometries of both parts into new stationary point objects """ # copy the reactant stationary point atom = copy.deepcopy(self.species.atom) geom = copy.deepcopy(self.species.geom) temp = StationaryPoint('temp', self.species.charge, self.species.mult, atom=atom, geom=geom) temp.characterize() # set the bond order of the breaking bond to 0 temp.bond[self.bond[0]][self.bond[1]] = 0 temp.bond[self.bond[1]][self.bond[0]] = 0 self.products, maps = temp.start_multi_molecular()
def testAll(self): with open('multimolecular_data.json') as f: data = json.load(f) for name in data: print(name) par = Parameters() qc = QuantumChemistry(par) structure = data[name]['structure'] mol = StationaryPoint(name,0,1,structure = structure) mol.characterize() mols = mol.start_multi_molecular() calculated = len(mols) expected = data[name]['expected_value'] self.assertEqual(calculated,expected, name + ': expected: {}, calculated: {}'.format(expected,calculated))
def testAll(self): with open('multimolecular_data.json') as f: data = json.load(f) for name in data: print name par = Parameters() qc = QuantumChemistry(par) structure = data[name]['structure'] mol = StationaryPoint(name,0,1,structure = structure) mol.characterize() mols = mol.start_multi_molecular() calculated = len(mols) expected = data[name]['expected_value'] self.assertEqual(calculated,expected, name + ': expected: {}, calculated: {}'.format(expected,calculated))