def make_default_variations(default_fractions, composition_space):
"""
Creates the variations with default parameter values and the provided
default fractions.
Returns a list containing the variation objects (Mating, StructureMut,
NumAtomsMut and Permutation).
Args:
default_fractions: a dictionary containing the default fractions to use
for each variation
composition_space: the CompositionSpace of the search
"""
variations_list = []
mating = variations.Mating({'fraction': default_fractions['mating']})
structure_mut = variations.StructureMut(
{'fraction': default_fractions['structure_mut']})
num_atoms_mut = variations.NumAtomsMut(
{'fraction': default_fractions['num_atoms_mut']})
permutation = variations.Permutation(
{'fraction': default_fractions['permutation']}, composition_space)
variations_list.append(mating)
variations_list.append(structure_mut)
variations_list.append(num_atoms_mut)
variations_list.append(permutation)
return variations_list
def make_variations(parameters, default_fractions, composition_space):
"""
Creates the variations, using default parameter values if needed.
Returns a list containing the variation objects (Mating, StructureMut,
NumAtomssMut and Permutation).
Args:
parameters: the dictionary produced by calling yaml.load() on the input
file
default_fractions: a dictionary containing the default fractions to use
for each variation
composition_space: the CompositionSpace of the search
"""
if 'Variations' not in parameters:
return make_default_variations(default_fractions, composition_space)
elif parameters['Variations'] in (None, 'default'):
return make_default_variations(default_fractions, composition_space)
else:
variations_list = []
# mating
if 'Mating' not in parameters['Variations']:
pass
elif parameters['Variations']['Mating'] is None:
print('If the "Mating" keyword is used, its "fraction" keyword '
'must also be set.')
print('Quitting...')
quit()
else:
if parameters['Variations']['Mating']['fraction'] in (None,
'default'):
print('The "fraction" kwyword is not optional and must '
'contain a valid entry (between 0 and 1) for the Mating '
'variation.')
print('Quitting...')
quit()
else:
mating = variations.Mating(parameters['Variations']['Mating'])
variations_list.append(mating)
# structure mutation
if 'StructureMut' not in parameters['Variations']:
pass
elif parameters['Variations']['StructureMut'] is None:
print('If the "StructureMut" keyword is used, its "fraction" '
'keyword must also be set.')
print('Quitting...')
quit()
else:
if parameters['Variations']['StructureMut']['fraction'] in (
None, 'default'):
print('The "fraction" keyword is not optional and must '
'contain a valid entry (between 0 and 1) for the '
'StructureMut variation.')
print('Quitting...')
quit()
else:
structure_mut = variations.StructureMut(
parameters['Variations']['StructureMut'])
variations_list.append(structure_mut)
# mutating the number of atoms in the cell
if 'NumAtomsMut' not in parameters['Variations']:
pass
elif parameters['Variations']['NumAtomsMut'] is None:
print('If the "NumAtomsMut" keyword is used, its "fraction" '
'keyword must also be set.')
print('Quitting...')
quit()
else:
if parameters['Variations']['NumAtomsMut']['fraction'] in (
None, 'default'):
print('The "fraction" keyword is not optional and must '
'contain a valid entry (between 0 and 1) for the '
'NumAtomsMut variation.')
print('Quitting...')
quit()
else:
num_atoms_mut = variations.NumAtomsMut(
parameters['Variations']['NumAtomsMut'])
variations_list.append(num_atoms_mut)
# permutation (swapping atoms)
if 'Permutation' not in parameters['Variations']:
pass
elif parameters['Variations']['Permutation'] is None:
print('If the "Permutation" keyword is used, its "fraction" '
'keyword must also be set.')
print('Quitting...')
quit()
else:
if parameters['Variations']['Permutation']['fraction'] in (
None, 'default'):
print('The "fraction" keyword is not optional and must '
'contain a valid entry (between 0 and 1) for the '
'Permutation variation.')
print('Quitting...')
else:
permutation = variations.Permutation(
parameters['Variations']['Permutation'], composition_space)
variations_list.append(permutation)
return variations_list