def make_default_organism_creator(composition_space, constraints):
"""
Returns a list containing a RandomOrganismCreator, or quits.
Args:
composition_space: the CompositionSpace of the search
constraints: the Constraints of the search
"""
if composition_space.objective_function == 'pd':
print('For phase diagram searches, reference structures at each '
'endpoint of the composition space must be provided in the '
'initial population.')
print('Please use the "from_files" keyword in the '
'InitialPopulation block to provide the reference '
'structures.')
print('Quitting...')
quit()
else:
random_organism_creator = organism_creators.RandomOrganismCreator(
'default', composition_space, constraints)
return [random_organism_creator]
def make_organism_creators(parameters, composition_space, constraints):
"""
Returns a list containing organism creator objects.
Args:
parameters: the dictionary produced by calling yaml.load() on the input
file
composition_space: the CompositionSpace of the search
constraints: the Constraints of the search
"""
if 'InitialPopulation' not in parameters:
return make_default_organism_creator(composition_space, constraints)
elif parameters['InitialPopulation'] in (None, 'default'):
return make_default_organism_creator(composition_space, constraints)
# make the specified creators
else:
# check that at least one valid option is used
# TODO: if other organism creators are used, check them here as well
if 'random' not in parameters['InitialPopulation'] and 'from_files' \
not in parameters['InitialPopulation']:
print('At least one valid option for making structures for the '
'initial population must be provided.')
print('Please use the "random" and/or "from_files" keywords in '
'the InitialPopulation block.')
print('Quitting...')
quit()
initial_organism_creators = []
# the random organism creator
if 'random' in parameters['InitialPopulation']:
random_organism_creator = organism_creators.RandomOrganismCreator(
parameters['InitialPopulation']['random'], composition_space,
constraints)
initial_organism_creators.append(random_organism_creator)
# the from files organism creator
if 'from_files' not in parameters['InitialPopulation']:
if composition_space.objective_function == 'pd':
print('For phase diagram searches, reference structures at '
'each endpoint of the composition space must be '
'provided.')
print('Please use the "from_files" keyword in the '
'InitialPopulation block to provide the reference '
'structures.')
print('Quitting...')
quit()
# if nothing is given after the from_files keyword
elif parameters['InitialPopulation']['from_files'] is None:
print('The path to the folder containing the files must be '
'provided. Please use the "path_to_folder" keyword.')
print('Quitting...')
quit()
# if path_to_folder keyword is not given
elif 'path_to_folder' not in parameters['InitialPopulation'][
'from_files']:
print('Incorrect keyword given after "from_files" in the '
'InitialPopulation block. Please use the "path_to_folder" '
'keyword.')
print('Quitting...')
quit()
else:
given_path = parameters['InitialPopulation']['from_files'][
'path_to_folder']
# if no path was given after path_to_folder keyword
if given_path is None:
print('The path to the folder containing the files for the '
'initial population must be provided. Please give the '
'path after the "path_to_folder" keyword.')
print('Quitting...')
quit()
# if the given path does not exist
elif not os.path.exists(given_path):
print('The given folder containing structures for the initial '
'population does not exist.')
print('Quitting...')
quit()
# if the folder exists, check that it contains files
elif len([
f for f in os.listdir(given_path)
if os.path.isfile(os.path.join(given_path, f))
]) == 0:
print('The given folder containing structures for the initial '
'population does not contain any files.')
print('Quitting...')
quit()
else:
files_organism_creator = organism_creators.FileOrganismCreator(
given_path)
# check that the files cover all composition space endpoints
if composition_space.objective_function == 'pd':
cells = files_organism_creator.get_cells()
provided_endpoints = []
for endpoint in composition_space.endpoints:
for cell in cells:
if cell.composition.reduced_composition.almost_equals(
endpoint.reduced_composition) and \
endpoint not in provided_endpoints:
provided_endpoints.append(endpoint)
# check if we got them all
for endpoint in composition_space.endpoints:
if endpoint not in provided_endpoints:
print('Error: valid structure files not provided '
'to the initial population for all '
'endpoints of the composition space.')
print('Quitting...')
quit()
initial_organism_creators.append(files_organism_creator)
# TODO: if other organism creators are used, they should be
# instantiated here
return initial_organism_creators