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_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))
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))
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)
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)
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))
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))
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))
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