class TestNuclearAttractionMatrixHeHCation(TestCase):
def setUp(self):
hydrogen_basis_1 = MagicMock(contraction=0.15432897, exponent=3.42525091, coordinates=(0, 0, -0.7316), integral_exponents=(0, 0, 0), normalisation = 1.794441832218435)
hydrogen_basis_2 = MagicMock(contraction=0.53532814, exponent=0.62391373, coordinates=(0, 0, -0.7316), integral_exponents=(0, 0, 0), normalisation = 0.5003264923314032)
hydrogen_basis_3 = MagicMock(contraction=0.44463454, exponent=0.16885540, coordinates=(0, 0, -0.7316), integral_exponents=(0, 0, 0), normalisation = 0.18773545851092535)
helium_basis_1 = MagicMock(contraction=0.15432897, exponent=9.75393461, coordinates=(0, 0, 0.7316), integral_exponents=(0, 0, 0), normalisation = 3.9336432656254527)
helium_basis_2 = MagicMock(contraction=0.53532814, exponent=1.77669115, coordinates=(0, 0, 0.7316), integral_exponents=(0, 0, 0), normalisation = 1.0967787981767012)
helium_basis_3 = MagicMock(contraction=0.44463454, exponent=0.48084429, coordinates=(0, 0, 0.7316), integral_exponents=(0, 0, 0), normalisation = 0.41154131374122654)
helium_basis = MagicMock(primitive_gaussian_array=[helium_basis_1, helium_basis_2, helium_basis_3], coordinates=(0, 0, -0.7316), integral_exponents=(0, 0, 0))
hydrogen_basis = MagicMock(primitive_gaussian_array=[hydrogen_basis_1, hydrogen_basis_2, hydrogen_basis_3], coordinates=(0, 0, 0.7316), integral_exponents=(0, 0, 0))
basis_set_array = [helium_basis, hydrogen_basis]
helium_nuclei = MagicMock(element='HELIUM', charge=2, mass=4, coordinates=(0.000000, 0.000000, 0.7316))
hydrogen_nuclei = MagicMock(element='HYDROGEN', charge=1, mass=1, coordinates=(0.000000, 0.000000, -0.7316))
nuclei_array = [helium_nuclei, hydrogen_nuclei]
self.kinetic_energy_integral = NuclearAttractionMatrix(basis_set_array, nuclei_array)
def test_method_calculate_returns_the_nuclear_attraction_energy_of_helium_1s(self):
kinetic_energy = self.kinetic_energy_integral.calculate(0, 0)
testing.assert_approx_equal(kinetic_energy, -4.817, 5)
def test_method_calculate_returns_the_nuclear_attraction_energy_of_quantum_mechanical_off_diagonal_parts(self):
kinetic_energy = self.kinetic_energy_integral.calculate(0, 1)
testing.assert_approx_equal(kinetic_energy, -1.5142, 3)
def test_method_calculate_returns_the_nuclear_attraction_energy_of_hydrogen_1s(self):
kinetic_energy = self.kinetic_energy_integral.calculate(1, 1)
testing.assert_approx_equal(kinetic_energy, -2.4912, 4)
class TestNuclearAttractionMatrixHydrogen(TestCase):
def setUp(self):
hydrogen_basis_1 = MagicMock(contraction=0.15432897, exponent=3.42525091, coordinates=(0, 0, 0.7000), integral_exponents=(0, 0, 0), normalisation = 1.794441832218435)
hydrogen_basis_2 = MagicMock(contraction=0.53532814, exponent=0.62391373, coordinates=(0, 0, 0.7000), integral_exponents=(0, 0, 0), normalisation = 0.5003264923314032)
hydrogen_basis_3 = MagicMock(contraction=0.44463454, exponent=0.16885540, coordinates=(0, 0, 0.7000), integral_exponents=(0, 0, 0), normalisation = 0.18773545851092535)
hydrogen_basis_4 = MagicMock(contraction=0.15432897, exponent=3.42525091, coordinates=(0, 0, -0.7000), integral_exponents=(0, 0, 0), normalisation = 1.794441832218435)
hydrogen_basis_5 = MagicMock(contraction=0.53532814, exponent=0.62391373, coordinates=(0, 0, -0.7000), integral_exponents=(0, 0, 0), normalisation = 0.5003264923314032)
hydrogen_basis_6 = MagicMock(contraction=0.44463454, exponent=0.16885540, coordinates=(0, 0, -0.7000), integral_exponents=(0, 0, 0), normalisation = 0.18773545851092535)
hydrogen_1_basis = MagicMock(primitive_gaussian_array=[hydrogen_basis_1, hydrogen_basis_2, hydrogen_basis_3], coordinates=(0, 0, -0.7000), integral_exponents=(0, 0, 0))
hydrogen_2_basis = MagicMock(primitive_gaussian_array=[hydrogen_basis_4, hydrogen_basis_5, hydrogen_basis_6], coordinates=(0, 0, 0.7000), integral_exponents=(0, 0, 0))
basis_set_array = [hydrogen_1_basis, hydrogen_2_basis]
hydrogen_1_nuclei = MagicMock(element='HYDROGEN', charge=1, mass=1, coordinates=(0.000000, 0.000000, 0.7000))
hydrogen_2_nuclei = MagicMock(element='HYDROGEN', charge=1, mass=1, coordinates=(0.000000, 0.000000, -0.7000))
nuclei_array = [hydrogen_1_nuclei, hydrogen_2_nuclei]
self.kinetic_energy_integral = NuclearAttractionMatrix(basis_set_array, nuclei_array)
def test_method_calculate_returns_the_nuclear_attraction_energy_of_hydrogen_1s(self):
kinetic_energy = self.kinetic_energy_integral.calculate(0, 0)
testing.assert_approx_equal(kinetic_energy, -1.8804, 4)
def test_method_calculate_returns_the_nuclear_attraction_energy_of_quantum_mechanical_off_diagonal_parts(self):
kinetic_energy = self.kinetic_energy_integral.calculate(0, 1)
testing.assert_approx_equal(kinetic_energy, -1.1948, 4)
class HartreeFock:
def __init__(self, nuclei_array, basis_set_array, electrons, scf_method):
self.nuclei_array = nuclei_array
self.basis_set_array = basis_set_array
self.electrons = electrons
self.scf_method = scf_method
self.orbital_overlap_matrix = OrbitalOverlapMatrix(basis_set_array)
self.kinetic_energy_matrix = KineticEnergyMatrix(basis_set_array)
self.nuclear_attraction_matrix = NuclearAttractionMatrix(basis_set_array, nuclei_array)
# self.repulsion_elements = TwoElectronRepulsionElementCook(basis_set_array)
self.repulsion_elements = TwoElectronRepulsionElementOS(basis_set_array)
# self.repulsion_elements = TwoElectronRepulsionElementHGP(basis_set_array)
self.linear_algebra = LinearAlgebra
self.core_hamiltonian = np.matrix([])
self.repulsion = np.matrix([])
def start(self):
print('\n*****************************************************************************************************')
orbital_overlap = self.orbital_overlap_matrix.create()
kinetic_energy = self.kinetic_energy_matrix.create()
nuclear_potential = self.nuclear_attraction_matrix.create()
self.linear_algebra = self.linear_algebra(orbital_overlap)
self.core_hamiltonian = kinetic_energy + nuclear_potential
print('\nMATRICES\n')
print('\nORBITAL OVERLAP MATRIX')
print(orbital_overlap)
print('\nKINETIC ENERGY MATRIX')
print(kinetic_energy)
print('\nNUCLEAR POTENTIAL ENERGY MATRIX')
print(nuclear_potential)
print('\nCORE HAMILTONIAN MATRIX')
print(self.core_hamiltonian)
print('\n*****************************************************************************************************')
print('\nINITIAL GUESS\n')
initial_orbital_energies, initial_orbital_coefficients = self.linear_algebra.diagonalize(self.core_hamiltonian)
print('\nORBITAL ENERGY EIGENVALUES')
print(initial_orbital_energies)
print('\nORBITAL COEFFICIENTS')
print(initial_orbital_coefficients)
print('\n*****************************************************************************************************')
print('\nBEGIN TWO ELECTRON REPULSION CALCULATION')
start_repulsion = time.clock()
self.repulsion = self.repulsion_elements.store_parallel(4)
print('TIME TAKEN: ' + str(time.clock() - start_repulsion) + 's\n')
return initial_orbital_coefficients
def __init__(self, nuclei_array, basis_set_array, electrons, scf_method):
self.nuclei_array = nuclei_array
self.basis_set_array = basis_set_array
self.electrons = electrons
self.scf_method = scf_method
self.orbital_overlap_matrix = OrbitalOverlapMatrix(basis_set_array)
self.kinetic_energy_matrix = KineticEnergyMatrix(basis_set_array)
self.nuclear_attraction_matrix = NuclearAttractionMatrix(basis_set_array, nuclei_array)
# self.repulsion_elements = TwoElectronRepulsionElementCook(basis_set_array)
self.repulsion_elements = TwoElectronRepulsionElementOS(basis_set_array)
# self.repulsion_elements = TwoElectronRepulsionElementHGP(basis_set_array)
self.linear_algebra = LinearAlgebra
self.core_hamiltonian = np.matrix([])
self.repulsion = np.matrix([])
def setUp(self):
hydrogen_basis_1 = MagicMock(contraction=0.15432897, exponent=3.42525091, coordinates=(0, 0, -0.7316), integral_exponents=(0, 0, 0), normalisation = 1.794441832218435)
hydrogen_basis_2 = MagicMock(contraction=0.53532814, exponent=0.62391373, coordinates=(0, 0, -0.7316), integral_exponents=(0, 0, 0), normalisation = 0.5003264923314032)
hydrogen_basis_3 = MagicMock(contraction=0.44463454, exponent=0.16885540, coordinates=(0, 0, -0.7316), integral_exponents=(0, 0, 0), normalisation = 0.18773545851092535)
helium_basis_1 = MagicMock(contraction=0.15432897, exponent=9.75393461, coordinates=(0, 0, 0.7316), integral_exponents=(0, 0, 0), normalisation = 3.9336432656254527)
helium_basis_2 = MagicMock(contraction=0.53532814, exponent=1.77669115, coordinates=(0, 0, 0.7316), integral_exponents=(0, 0, 0), normalisation = 1.0967787981767012)
helium_basis_3 = MagicMock(contraction=0.44463454, exponent=0.48084429, coordinates=(0, 0, 0.7316), integral_exponents=(0, 0, 0), normalisation = 0.41154131374122654)
helium_basis = MagicMock(primitive_gaussian_array=[helium_basis_1, helium_basis_2, helium_basis_3], coordinates=(0, 0, -0.7316), integral_exponents=(0, 0, 0))
hydrogen_basis = MagicMock(primitive_gaussian_array=[hydrogen_basis_1, hydrogen_basis_2, hydrogen_basis_3], coordinates=(0, 0, 0.7316), integral_exponents=(0, 0, 0))
basis_set_array = [helium_basis, hydrogen_basis]
helium_nuclei = MagicMock(element='HELIUM', charge=2, mass=4, coordinates=(0.000000, 0.000000, 0.7316))
hydrogen_nuclei = MagicMock(element='HYDROGEN', charge=1, mass=1, coordinates=(0.000000, 0.000000, -0.7316))
nuclei_array = [helium_nuclei, hydrogen_nuclei]
self.kinetic_energy_integral = NuclearAttractionMatrix(basis_set_array, nuclei_array)
def setUp(self):
hydrogen_basis_1 = MagicMock(contraction=0.15432897, exponent=3.42525091, coordinates=(0, 0, 0.7000), integral_exponents=(0, 0, 0), normalisation = 1.794441832218435)
hydrogen_basis_2 = MagicMock(contraction=0.53532814, exponent=0.62391373, coordinates=(0, 0, 0.7000), integral_exponents=(0, 0, 0), normalisation = 0.5003264923314032)
hydrogen_basis_3 = MagicMock(contraction=0.44463454, exponent=0.16885540, coordinates=(0, 0, 0.7000), integral_exponents=(0, 0, 0), normalisation = 0.18773545851092535)
hydrogen_basis_4 = MagicMock(contraction=0.15432897, exponent=3.42525091, coordinates=(0, 0, -0.7000), integral_exponents=(0, 0, 0), normalisation = 1.794441832218435)
hydrogen_basis_5 = MagicMock(contraction=0.53532814, exponent=0.62391373, coordinates=(0, 0, -0.7000), integral_exponents=(0, 0, 0), normalisation = 0.5003264923314032)
hydrogen_basis_6 = MagicMock(contraction=0.44463454, exponent=0.16885540, coordinates=(0, 0, -0.7000), integral_exponents=(0, 0, 0), normalisation = 0.18773545851092535)
hydrogen_1_basis = MagicMock(primitive_gaussian_array=[hydrogen_basis_1, hydrogen_basis_2, hydrogen_basis_3], coordinates=(0, 0, -0.7000), integral_exponents=(0, 0, 0))
hydrogen_2_basis = MagicMock(primitive_gaussian_array=[hydrogen_basis_4, hydrogen_basis_5, hydrogen_basis_6], coordinates=(0, 0, 0.7000), integral_exponents=(0, 0, 0))
basis_set_array = [hydrogen_1_basis, hydrogen_2_basis]
hydrogen_1_nuclei = MagicMock(element='HYDROGEN', charge=1, mass=1, coordinates=(0.000000, 0.000000, 0.7000))
hydrogen_2_nuclei = MagicMock(element='HYDROGEN', charge=1, mass=1, coordinates=(0.000000, 0.000000, -0.7000))
nuclei_array = [hydrogen_1_nuclei, hydrogen_2_nuclei]
self.kinetic_energy_integral = NuclearAttractionMatrix(basis_set_array, nuclei_array)