def read_basis_set_file(file_input_basis, nuclei_array):
"""Reads a GAMESS-UK formatted gaussian basis set file using a list of nuclei objects.
Parameters
----------
file_input_basis : str
nuclei_array : List[Nuclei]
Returns
-------
basis_array : List[Basis]
See Also
--------
expand_basis_set : function for expanding L, P, D and higher functions
"""
file_input_basis = os.path.join('../../', 'basissets/' + file_input_basis)
basis_array = []
for a in range(len(nuclei_array)):
file = open(file_input_basis, 'r')
lines = file.read().replace('\n', ':')
file.close()
regex = nuclei_array[a].element + '.*?#' # e.g. regex = CARBON.*?#
lines = ' '.join(lines.split()) + '#' # remove whitespace and add '#' for last element
lines = re.search(regex, lines).group(0) # return string from regex
lines = re.split(':', lines.replace(': ', ':')) # create list from colon separated string
lines = lines[1:len(lines) - 2]
i = 0
input1 = input2 = []
for line in lines:
if any(letter in line for letter in ('S', 'L', 'P', 'D')):
if i == 1:
input1.append(input2)
input2 = [line[0]]
else:
i = 1
input2 = [line[0]]
else:
input2.append([float(b) for b in line.split()])
input1.append(input2)
# basis set file data is now in a more convenient form for expand_basis_set to process
basis_array_from_fact = expand_basis_set(input1, nuclei_array[a].coordinates)
basis_array += basis_array_from_fact
return basis_array
def test_expand_basis_returns_a_array_of_coefficients_for_a_s_type_gaussian(self):
array = expand_basis_set([['S', [0.15432897, 3.42525091]]], (0, 0, 0.7316))
self.assertEquals(array[0].integral_exponents, (0, 0, 0))
self.assertEquals(array[0].coordinates, (0, 0, 0.7316))
self.assertEquals(array[0].primitive_gaussian_array[0].contraction, 0.15432897)
self.assertEquals(array[0].primitive_gaussian_array[0].exponent, 3.42525091)