def test_create_nuclei_array_returns_array_of_nuclei_with_coordinates(
self):
nuclei_array, electron_count, multiplicity = read_mol_file('HeH+.mol')
testing.assert_array_equal(nuclei_array[0].coordinates,
(0.0, 0.0, 0.487732042))
testing.assert_array_equal(nuclei_array[1].coordinates,
(0.0, 0.0, -0.975464083))
def start(mol_file,
basis_file,
method,
processors,
symmetry=False,
geometry_optimization=None):
np.set_printoptions(linewidth=100000, threshold=np.inf)
start_time = time.clock()
nuclei_list, electrons, multiplicity = read_mol_file(mol_file)
energy_object = Energy(electrons, multiplicity, processors, method)
print(
'\n*************************************************************************************************'
)
print('\nA BASIC QUANTUM CHEMICAL PROGRAM IN PYTHON\n\n\n{}'.format(
[x.element for x in nuclei_list]))
if geometry_optimization is not None:
nelder_mead = NelderMead(basis_file, energy_object, nuclei_list)
energy = nelder_mead.optimize()
else:
nuclei_list, point_group = MoleculeFactory(symmetry).create(
nuclei_list)
basis_set = read_basis_set_file(basis_file, nuclei_list)
energy_object.symmetry_object = Symmetry(point_group, basis_set)
energy = energy_object.calculate_energy(nuclei_list, basis_set)
print(
'\n*************************************************************************************************'
)
print('\nTIME TAKEN: ' + str(time.clock() - start_time) + 's')
print("\nWhat I cannot create I cannot understand - Richard Feynman\n")
return energy
def test_create_nuclei_array_returns_array_of_nuclei_with_names(self):
nuclei_array, electron_count, multiplicity = read_mol_file('HeH+.mol')
self.assertEquals(nuclei_array[0].element, 'HELIUM')
self.assertEquals(nuclei_array[1].element, 'HYDROGEN')
def test_electron_count_return_two(self):
nuclei_array, electron_count, multiplicity = read_mol_file('HeH+.mol')
self.assertEquals(electron_count, 2)
def test_create_nuclei_array_returns_array_of_nuclei_with_mass(self):
nuclei_array, electron_count, multiplicity = read_mol_file('HeH+.mol')
self.assertEquals(nuclei_array[0].mass, 4)
self.assertEquals(nuclei_array[1].mass, 1)