Esempio n. 1
0
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
Esempio n. 2
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 def test_create_basis_set_array_returns_basis_array_with_s_orbital_type_exponents_for_sto_3g(
         self):
     basis_array = read_basis_set_file('STO-3G.gbs', self.nuclei_array)
     testing.assert_array_equal(basis_array[0].integral_exponents,
                                (0, 0, 0))
     testing.assert_array_equal(basis_array[1].integral_exponents,
                                (0, 0, 0))
Esempio n. 3
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 def test_create_basis_set_array_returns_basis_array_with_coordinates_for_sto_3g(
         self):
     basis_array = read_basis_set_file('STO-3G.gbs', self.nuclei_array)
     testing.assert_array_equal(basis_array[0].coordinates,
                                (0.000000, 0.000000, 0.7316))
     testing.assert_array_equal(basis_array[1].coordinates,
                                (0.000000, 0.000000, -0.7316))
Esempio n. 4
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 def test_create_basis_set_array_returns_basis_array_with_exponents_for_sto_3g(self):
     basis_array = read_basis_set_file('STO-3G.gbs', self.nuclei_array)
     self.assertEquals(basis_array[0].primitive_gaussian_array[0].exponent, 6.36242139)
     self.assertEquals(basis_array[0].primitive_gaussian_array[1].exponent, 1.15892300)
     self.assertEquals(basis_array[0].primitive_gaussian_array[2].exponent, 0.31364979)
     self.assertEquals(basis_array[1].primitive_gaussian_array[0].exponent, 3.42525091)
     self.assertEquals(basis_array[1].primitive_gaussian_array[1].exponent, 0.62391373)
     self.assertEquals(basis_array[1].primitive_gaussian_array[2].exponent, 0.16885540)
Esempio n. 5
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 def test_create_basis_set_array_returns_basis_array_with_contraction_coefficients_for_sto_3g(self):
     basis_array = read_basis_set_file('STO-3G.gbs', self.nuclei_array)
     self.assertEquals(basis_array[0].primitive_gaussian_array[0].contraction, 0.15432897)
     self.assertEquals(basis_array[0].primitive_gaussian_array[1].contraction, 0.53532814)
     self.assertEquals(basis_array[0].primitive_gaussian_array[2].contraction, 0.44463454)
     self.assertEquals(basis_array[1].primitive_gaussian_array[0].contraction, 0.15432897)
     self.assertEquals(basis_array[1].primitive_gaussian_array[1].contraction, 0.53532814)
     self.assertEquals(basis_array[1].primitive_gaussian_array[2].contraction, 0.44463454)
Esempio n. 6
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 def test_create_basis_set_array_returns_basis_array_with_primitives_with_s_orbital_type_exponents_for_sto_3g(self):
     basis_array = read_basis_set_file('STO-3G.gbs', self.nuclei_array)
     self.assertEquals(basis_array[0].primitive_gaussian_array[0].integral_exponents, (0, 0, 0))
     self.assertEquals(basis_array[0].primitive_gaussian_array[1].integral_exponents, (0, 0, 0))
     self.assertEquals(basis_array[0].primitive_gaussian_array[2].integral_exponents, (0, 0, 0))
     self.assertEquals(basis_array[1].primitive_gaussian_array[0].integral_exponents, (0, 0, 0))
     self.assertEquals(basis_array[1].primitive_gaussian_array[1].integral_exponents, (0, 0, 0))
     self.assertEquals(basis_array[1].primitive_gaussian_array[2].integral_exponents, (0, 0, 0))
Esempio n. 7
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 def test_create_basis_set_array_returns_basis_array_with_primitives_with_coordinates_for_sto_3g(self):
     basis_array = read_basis_set_file('STO-3G.gbs', self.nuclei_array)
     self.assertEquals(basis_array[0].primitive_gaussian_array[0].coordinates, (0.000000, 0.000000, 0.7316))
     self.assertEquals(basis_array[0].primitive_gaussian_array[1].coordinates, (0.000000, 0.000000, 0.7316))
     self.assertEquals(basis_array[0].primitive_gaussian_array[2].coordinates, (0.000000, 0.000000, 0.7316))
     self.assertEquals(basis_array[1].primitive_gaussian_array[0].coordinates, (0.000000, 0.000000, -0.7316))
     self.assertEquals(basis_array[1].primitive_gaussian_array[1].coordinates, (0.000000, 0.000000, -0.7316))
     self.assertEquals(basis_array[1].primitive_gaussian_array[2].coordinates, (0.000000, 0.000000, -0.7316))
Esempio n. 8
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 def test_create_basis_set_array_returns_basis_array_with_correct_coordinates_for_3_21g(
         self):
     basis_array = read_basis_set_file('3-21G.gbs', self.nuclei_array)
     testing.assert_array_equal(basis_array[0].coordinates,
                                (0.000000, 0.000000, 0.7316))
     testing.assert_array_equal(basis_array[1].coordinates,
                                (0.000000, 0.000000, 0.7316))
     testing.assert_array_equal(basis_array[2].coordinates,
                                (0.000000, 0.000000, -0.7316))
     testing.assert_array_equal(basis_array[3].coordinates,
                                (0.000000, 0.000000, -0.7316))
Esempio n. 9
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    def calculate_energy(self, coordinate_list):

        j = 0
        for i, nuclei in enumerate(self.nuclei_list):
            if i == 0:
                nuclei.coordinates = (0.0, 0.0, coordinate_list.item(j))
                j += 1
            elif i == 1:
                nuclei.coordinates = (0.0, coordinate_list.item(j),
                                      coordinate_list.item(j + 1))
                j += 2
            else:
                nuclei.coordinates = (coordinate_list.item(j),
                                      coordinate_list.item(j + 1),
                                      coordinate_list.item(j + 2))
                j += 3

        with redirect_stdout(open(os.devnull, "w")):
            basis_set = read_basis_set_file(
                self.basis_file, self.first_nuclei + self.nuclei_list)
            energy = self.energy_object.calculate_energy(
                self.first_nuclei + self.nuclei_list, basis_set)

        return energy