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))