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)
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, basis, method, processes, symmetry=False):
np.set_printoptions(linewidth=100000, threshold=np.inf)
start_time = time.clock()
electron_energy = correlation = 0.0
nuclei_array, electrons, multiplicity = read_mol_file(mol)
if symmetry:
molecule = MoleculeFactory().point_group(nuclei_array)
else:
molecule = Molecule(nuclei_array, PointGroup([], [], [], [], 'C_{1}'))
basis_set_array = read_basis_set_file(basis, molecule.nuclei_array)
symmetry_object = Symmetry(molecule.point_group, basis_set_array)
coulomb_law_matrix = coulomb_matrix(nuclei_array)
nuclear_repulsion = coulomb_law_matrix.sum() / 2
print('\n*************************************************************************************************')
print('\nA BASIC QUANTUM CHEMICAL PROGRAM IN PYTHON\n\n\n{}'.format([x.element for x in nuclei_array]))
print('\nNUCLEAR REPULSION ARRAY\n{}'.format(coulomb_law_matrix))
if method == 'RHF':
electron_energy = RestrictedHF(molecule.nuclei_array, basis_set_array, electrons, symmetry_object,
processes).begin_scf()[0]
if method == 'UHF':
electron_energy = UnrestrictedHF(molecule.nuclei_array, basis_set_array, electrons, multiplicity,
symmetry_object, processes).begin_scf()[0]
if method == 'GUHF':
electron_energy = BlockedHartreeFock(molecule.nuclei_array, basis_set_array, electrons, multiplicity,
symmetry_object, processes).begin_scf()[0]
if method == 'MP2':
mp2 = MoellerPlesset(
RestrictedHF(molecule.nuclei_array, basis_set_array, electrons, symmetry_object, processes))
electron_energy = mp2.hartree_fock_energy
correlation = mp2.second_order()
if method == 'TDHF':
electron_energy = TimeDependentHartreeFock(
RestrictedHF(molecule.nuclei_array, basis_set_array, electrons, symmetry_object, processes)
).calculate(tda=False)
if method == 'CIS':
electron_energy = TimeDependentHartreeFock(
RestrictedHF(molecule.nuclei_array, basis_set_array, electrons, symmetry_object, processes)
).calculate(tda=True)
if method[0] == 'DFT':
electron_energy = RestrictedKohnSham(molecule.nuclei_array, basis_set_array, electrons,
symmetry_object, processes, method[1], method[2]).begin_scf()[0]
if method == 'CCSD':
ccsd = CoupledClusterSinglesDoubles(
RestrictedHF(molecule.nuclei_array, basis_set_array, electrons, symmetry_object, processes))
electron_energy = ccsd.hartree_fock_energy
correlation = ccsd.calculate_singles_doubles()[0]
if method == 'CCSD(T)':
ccsd = CoupledClusterPerturbativeTriples(
RestrictedHF(molecule.nuclei_array, basis_set_array, electrons, symmetry_object, processes))
electron_energy = ccsd.hartree_fock_energy
correlation = ccsd.calculate_perturbative_triples()
total_energy = electron_energy + nuclear_repulsion + correlation
print('NUCLEAR REPULSION ENERGY: ' + str(nuclear_repulsion) + ' a.u.')
print('SCF ENERGY: ' + str(electron_energy) + ' a.u.')
print('CORRELATION ENERGY: ' + str(correlation) + ' a.u.')
print('TOTAL ENERGY: ' + str(total_energy) + ' a.u.')
print('\n*************************************************************************************************')
print('\nTIME TAKEN: ' + str(time.clock() - start_time) + 's')
print("\nWhat I cannot create I cannot understand - Richard Feynman\n")
return total_energy
