コード例 #1
0
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)
コード例 #2
0
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)
コード例 #3
0
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
コード例 #4
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 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([])
コード例 #5
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    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)
コード例 #6
0
    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)