The Genetic Algorithm Python Files

Below are all the files that are used by the genetic algorithm to run.

Table of Contents

• GA_Program.py
  • GA_Program
    • GA_Program.get_tasks()
    • GA_Program.natural_selection()
    • GA_Program.perform_epoch_on_population()
    • GA_Program.run_GA()
• GA_Program_Details.py
  • GA_Program_Details
    • GA_Program_Details.close()
    • GA_Program_Details.create()
    • GA_Program_Details.end_clock()
    • GA_Program_Details.ending_details()
    • GA_Program_Details.epoch_end_clock()
    • GA_Program_Details.epoch_start_clock()
    • GA_Program_Details.open()
    • GA_Program_Details.start_clock()
• Cluster.py
  • Cluster
    • Cluster.centre_cluster_at_centre_of_cell()
    • Cluster.custom_verify_cluster()
    • Cluster.deepcopy()
    • Cluster.deepcopy_skeleton()
    • Cluster.get_elemental_makeup()
    • Cluster.get_total_cluster_energy()
    • Cluster.remove_calculator()
    • Cluster.sortZ()
    • Cluster.verify_cluster()
    • Cluster.view()
  • import_surface()
• Surface.py
  • MyConstraint
• Collection.py
  • Collection
    • Collection.add()
    • Collection.add_clusters_into_RAM()
    • Collection.add_metadata()
    • Collection.add_to_database()
    • Collection.add_to_history_file()
    • Collection.assess_clusters_in_database()
    • Collection.backup_database()
    • Collection.check_PoolProfileTXT_exists()
    • Collection.check_clusters_in_database()
    • Collection.check_database_and_determine_if_to_use_backup()
    • Collection.check_historyfile()
    • Collection.close()
    • Collection.create_collection_history()
    • Collection.delete_collection_database()
    • Collection.does_contain_database()
    • Collection.get_cluster_energies()
    • Collection.get_cluster_from_name()
    • Collection.get_cluster_names()
    • Collection.get_clusters()
    • Collection.get_history_path()
    • Collection.get_index()
    • Collection.get_max_mean_min_energies()
    • Collection.history_file_name()
    • Collection.import_clusters_from_database_to_memory()
    • Collection.is_there_an_energy_range()
    • Collection.make_collection_folder()
    • Collection.max_energy()
    • Collection.mean_energy()
    • Collection.min_energy()
    • Collection.move_backup_database_to_normal_backup()
    • Collection.open()
    • Collection.pop()
    • Collection.read_collection_database()
    • Collection.remove()
    • Collection.remove_backup_database()
    • Collection.remove_backup_database_if_exists()
    • Collection.remove_clusters_from_database_that_are_from_unsuccessful_generations()
    • Collection.remove_to_database()
    • Collection.replace()
    • Collection.sort_by_energy()
    • Collection.sort_by_name()
    • Collection.view_cluster()
• Collections_Iterator.py
  • Collections_Iterator
• Population.py
  • Population
    • Population.backup_files()
    • Population.backup_state_file()
    • Population.current_state_file()
    • Population.get_current_generation_from_state_file()
    • Population.get_data_from_current_state_file()
    • Population.get_details()
    • Population.get_pool_folder_size()
    • Population.move_backup_to_current_files()
    • Population.print_clusters()
    • Population.remove_backup_files()
    • Population.remove_backup_state_file()
    • Population.remove_backup_state_file_if_exists()
    • Population.repair_current_state_file()
• EnergyProfile.py
  • EnergyProfile
    • EnergyProfile.GA_Starts()
    • EnergyProfile.add_collection()
    • EnergyProfile.add_epoch_note()
    • EnergyProfile.add_epoch_note_due_to_population_energy_convergence()
    • EnergyProfile.add_found_LES_note()
    • EnergyProfile.add_to()
    • EnergyProfile.check()
    • EnergyProfile.close()
    • EnergyProfile.create()
    • EnergyProfile.get_current_generation_and_last_cluster_generated_from_EnergyProfile()
    • EnergyProfile.is_LES_note_in_EnergyProfile()
    • EnergyProfile.open()
  • remove_end_lines_from_text()
  • tail()
• Offspring_Pool.py
  • Offspring_Pool
    • Offspring_Pool.clean()
    • Offspring_Pool.sort_by_fitness()
• GA_Setup.py
  • GA_Setup()
• GA_Initiate.py
  • GA_Initiate()
  • Initate_New_GAProgram()
  • Initial_ProgramChecking()
  • Resume_GAProgram()
  • add_metadata()
  • get_resume_from_generation()
• GA_Introducing_Remarks.py
  • GA_Program_Logo_coloured()
  • Introducing_Remarks()
  • version_no()
• Initialise_Population.py
  • Check_Population_against_predation_operator()
  • Initialise_Population()
  • Initialise_Population_with_Randomly_Generated_Clusters()
  • Place_Already_Created_Clusters_In_Population()
  • create_a_cluster()
  • get_tasks()
• Get_Offspring.py
  • Create_An_Offspring()
  • Create_An_Unoptimised_Offspring()
  • Will_Mutation_Occur()
• Crossover.py
  • Crossover
    • Crossover.Cut_and_Splice_Devon_and_Ho()
    • Crossover.centre_offspring_at_centre_of_cell()
    • Crossover.centre_parents_about_origin()
    • Crossover.displacement_of_plane()
    • Crossover.half_index_custom_method()
    • Crossover.half_index_half_method()
    • Crossover.half_index_random_method()
    • Crossover.half_index_weighted_method()
    • Crossover.mate_Cut_and_Splice()
    • Crossover.mate_Cut_and_Splice_error_checking_1()
    • Crossover.mate_Cut_and_Splice_error_checking_2()
    • Crossover.mating()
    • Crossover.pickParentsFromThePopulation()
    • Crossover.rotate()
    • Crossover.roulette()
    • Crossover.run()
    • Crossover.tournament()
• Mutation.py
  • Mutation
    • Mutation.change_mutation_chances()
    • Mutation.check()
    • Mutation.get_mutation_type()
    • Mutation.mutation()
    • Mutation.pickClusterFromThePopulation()
    • Mutation.run()
  • isfloat()
• Types_Of_Mutations.py
  • homotopMutate()
  • moveMutate()
  • randomMutate()
• Get_Predation_and_Fitness_Operators.py
  • check_asap3_version()
  • get_fitness_operator()
  • get_predation_and_fitness_operators()
  • get_predation_operator()
• Predation Operators
  • Predation Operator
    • Predation_Operator
  • No_Predation_Operator.py
    • No_Predation_Operator
  • Energy_Predation_Operator.py
    • Energy_Predation_Operator
  • Energy Predation Operator Scripts
    • Simple_Energy_Predation_Operator.py
    • Comprehensive_Energy_Predation_Operator_energy.py
    • Comprehensive_Energy_Predation_Operator_fitness.py
  • IDCM_Predation_Operator.py
    • Cluster_Block
    • IDCM_Predation_Operator
  • IDCM Predation Operator Scripts
    • IDCM_Methods.py
    • LoD_Comparison_Database.py
  • SCM_Predation_Operator.py
    • Cluster_Block
    • SCM_Predation_Operator
• Fitness Operators
  • Fitness_Operator.py
    • Fitness_Operator
  • Energy_Fitness.py
    • Energy_Fitness_Operator
  • Energetic_Fitness_Contribution.py
    • check_rho_i()
    • get_energetic_fitness_contribution()
    • get_lowest_and_highest_energies_from_collections()
    • get_rho_i()
  • SCM_and_Energy_Fitness_Operator.py
    • SCM_and_Energy_Fitness_Operator
  • CNA_Fitness_Contribution.py
    • get_CNA_fitness_contribution()
    • get_CNA_fitness_contribution_normalised()
    • get_CNA_fitness_parameter()
    • get_CNA_fitness_parameter_normalised()
    • get_lowest_and_highest_similarities_from_collections()
  • Fitness_Function.py
    • Fitness_Function
• SCM Scripts
  • SCM_initialisation.py
    • get_SCM_methods()
    • get_rCut_values()
    • get_rCuts()
  • Similarity_Profile.py
    • Similarity_Profile
    • get_comparison()
  • A_SCM_Methods.py
    • get_CNA_similarities()
    • get_CNA_similarity()
    • get_single_atomic_CNA_profile_method()
  • T_SCM_Methods.py
    • get_CNA_similarities()
    • get_CNA_similarity()
    • get_single_total_CNA_profile_method()
  • CNA_Database.py
    • CNA_Database
    • Tree
    • cna_profile_generator()
    • initial_similarity_profile_generator()
    • similarity_profile_generator()
  • MyPool.py
    • MyPool
    • NoDaemonProcess
• Epoch.py
  • Epoch
    • Epoch.backup()
    • Epoch.change_fitness_function()
    • Epoch.check_for_backup()
    • Epoch.did_get_data_from_backup()
    • Epoch.does_backup_exist()
    • Epoch.does_epoch_data_exist_on_disk()
    • Epoch.get_resumed_mean_energy_epoch_details()
    • Epoch.get_resumed_same_population_epoch_details()
    • Epoch.information_from_the_same_generation()
    • Epoch.initialise_mean_energy_epoch_details()
    • Epoch.initialise_same_population_epoch_details()
    • Epoch.no_epoch()
    • Epoch.perform_epoch()
    • Epoch.perform_epoch_mean_energy()
    • Epoch.perform_epoch_no_epoch()
    • Epoch.perform_epoch_same_population()
    • Epoch.remove_backup()
    • Epoch.replace_with_backup()
    • Epoch.set_settings()
    • Epoch.setting_up_epoch_to_resume_GA()
    • Epoch.should_epoch()
    • Epoch.should_epoch_using_mean_energy_epoch()
    • Epoch.should_epoch_using_same_population_epoch()
• Memory_Operator.py
• ExternalDefinitions.py
  • AtomInClusterPosition()
  • Exploded()
  • InclusionRadiusOfCluster()
  • InclusionboxOfCluster()
  • get_elemental_makeup()
  • is_position_already_occupied_by_an_atom_in_Cluster()
• GA_Recording_System.py
  • GA_Recording_Database
    • GA_Recording_Database.add()
    • GA_Recording_Database.add_clusters_into_RAM()
    • GA_Recording_Database.add_collection_to_database()
    • GA_Recording_Database.check_clusters_in_database()
    • GA_Recording_Database.get_cluster_names()
    • GA_Recording_Database.get_index()
    • GA_Recording_Database.import_information_from_database()
    • GA_Recording_Database.remove_to_database()
    • GA_Recording_Database.sort_by_energy()
    • GA_Recording_Database.sort_by_name()
    • GA_Recording_Database.update_cluster_in_database_for_if_in_population()
  • GA_Recording_System
    • GA_Recording_System.add_collection()
    • GA_Recording_System.add_metadata()
    • GA_Recording_System.check_clusters_in_database()
    • GA_Recording_System.import_information_from_database()
    • GA_Recording_System.record_collection()
    • GA_Recording_System.record_initial_populations()
    • GA_Recording_System.record_population_at_generation()
    • GA_Recording_System.resume_ga_recording_system_from_current_generation()
    • GA_Recording_System.update_cluster_in_database_for_if_in_population()
  • convert_to_bytes()
  • get_size()
  • make_folder()
• Timer.py
  • Timer
    • Timer.get_time_now()
    • Timer.get_total_length_of_running_time()
    • Timer.has_elapsed_time()
    • Timer.print_elapsed_time()