Organisms: A Genetic Algorithm for Nanoclusters
latest
How the Organisms Program Works
Installation: Setting Up the Organisms Program and Pre-Requisites Packages
How To Use The Organisms Program
Run.py
- Running the Genetic Algorithm
Files Made During the Genetic Algorithm
Examples of Running the Organisms Program with
Run.py
RunMinimisation.py
- Writing a Local Minimisation Function for the Genetic Algorithm
MakeTrials.py
- Creating Multiple, Repeated Genetic Algorithm Trials
Safely Finishing the Genetic Algorithm Midway through the Algorithm
Restarting the Genetic Algorithm
Common Issues of the Genetic Algorithm and Ways to Solve Them
Helpful Programs to Create and Run the Genetic Algorithm
Helpful Programs for Gathering data and Post-processing Data
Information about using the
make_energy_vs_similarity_results.py
script
Other Helpful Programs for Gathering data and Post-processing Data
Initialising a New Population
Using Predation Operators with the Genetic Algorithm
Using Fitness Operators with the Genetic Algorithm
The Structural Comparison Method (SCM)
Using the Memory Operator
Using Epoch Methods
Recording Clusters From The Genetic Algorithm
Using Databases with the Genetic Algorithm
Adding Surfaces
The Genetic Algorithm Python Files
Index
Python Module Index
Organisms: A Genetic Algorithm for Nanoclusters
Index
Edit on GitHub
Index
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A
add() (Organisms.GA.Collection.Collection method)
(Organisms.GA.GA_Recording_System.GA_Recording_Database method)
(Organisms.GA.Predation_Operators.IDCM_Predation_Operator_Scripts.LoD_Comparison_Database.LoD_Comparison_Database method)
(Organisms.GA.SCM_Scripts.CNA_Database.CNA_Database method)
add_clusters_into_RAM() (Organisms.GA.Collection.Collection method)
(Organisms.GA.GA_Recording_System.GA_Recording_Database method)
add_collection() (Organisms.GA.EnergyProfile.EnergyProfile method)
(Organisms.GA.GA_Recording_System.GA_Recording_System method)
add_collection_to_database() (Organisms.GA.GA_Recording_System.GA_Recording_Database method)
add_epoch_note() (Organisms.GA.EnergyProfile.EnergyProfile method)
add_epoch_note_due_to_population_energy_convergence() (Organisms.GA.EnergyProfile.EnergyProfile method)
add_found_LES_note() (Organisms.GA.EnergyProfile.EnergyProfile method)
add_metadata() (in module Organisms.GA.GA_Initiate)
(Organisms.GA.Collection.Collection method)
(Organisms.GA.GA_Recording_System.GA_Recording_System method)
add_to() (Organisms.GA.EnergyProfile.EnergyProfile method)
add_to_database() (Organisms.GA.Collection.Collection method)
(Organisms.GA.Fitness_Operators.Energy_Fitness_Operator.Energy_Fitness_Operator method)
(Organisms.GA.Fitness_Operators.SCM_and_Energy_Fitness_Operator.SCM_and_Energy_Fitness_Operator method)
(Organisms.GA.Predation_Operators.Energy_Predation_Operator.Energy_Predation_Operator method)
(Organisms.GA.Predation_Operators.IDCM_Predation_Operator.IDCM_Predation_Operator method)
(Organisms.GA.Predation_Operators.No_Predation_Operator.No_Predation_Operator method)
(Organisms.GA.Predation_Operators.Predation_Operator.Predation_Operator method)
(Organisms.GA.Predation_Operators.SCM_Predation_Operator.SCM_Predation_Operator method)
add_to_history_file() (Organisms.GA.Collection.Collection method)
are_all_entries_false() (Organisms.GA.Predation_Operators.IDCM_Predation_Operator_Scripts.LoD_Comparison_Database.LoD_Comparison_Database method)
assess_clusters_in_database() (Organisms.GA.Collection.Collection method)
assess_for_violations() (in module Organisms.GA.Predation_Operators.Energy_Predation_Operator_Scripts.Simple_Energy_Predation_Operator)
(Organisms.GA.Predation_Operators.Energy_Predation_Operator.Energy_Predation_Operator method)
(Organisms.GA.Predation_Operators.IDCM_Predation_Operator.IDCM_Predation_Operator method)
(Organisms.GA.Predation_Operators.No_Predation_Operator.No_Predation_Operator method)
(Organisms.GA.Predation_Operators.Predation_Operator.Predation_Operator method)
(Organisms.GA.Predation_Operators.SCM_Predation_Operator.SCM_Predation_Operator method)
assess_for_violations_force_replacement() (in module Organisms.GA.Predation_Operators.Energy_Predation_Operator_Scripts.Comprehensive_Energy_Predation_Operator_energy)
(in module Organisms.GA.Predation_Operators.Energy_Predation_Operator_Scripts.Comprehensive_Energy_Predation_Operator_fitness)
(Organisms.GA.Predation_Operators.IDCM_Predation_Operator.IDCM_Predation_Operator method)
(Organisms.GA.Predation_Operators.SCM_Predation_Operator.SCM_Predation_Operator method)
assess_for_violations_message() (Organisms.GA.Predation_Operators.IDCM_Predation_Operator.IDCM_Predation_Operator method)
(Organisms.GA.Predation_Operators.SCM_Predation_Operator.SCM_Predation_Operator method)
assess_for_violations_no_force_replacement() (in module Organisms.GA.Predation_Operators.Energy_Predation_Operator_Scripts.Comprehensive_Energy_Predation_Operator_energy)
(in module Organisms.GA.Predation_Operators.Energy_Predation_Operator_Scripts.Comprehensive_Energy_Predation_Operator_fitness)
(Organisms.GA.Predation_Operators.IDCM_Predation_Operator.IDCM_Predation_Operator method)
(Organisms.GA.Predation_Operators.SCM_Predation_Operator.SCM_Predation_Operator method)
assign_all_fitnesses_after_assessing_against_predation_operator() (Organisms.GA.Fitness_Operators.Energy_Fitness_Operator.Energy_Fitness_Operator method)
(Organisms.GA.Fitness_Operators.Fitness_Operator.Fitness_Operator method)
(Organisms.GA.Fitness_Operators.SCM_and_Energy_Fitness_Operator.SCM_and_Energy_Fitness_Operator method)
assign_all_fitnesses_after_natural_selection() (Organisms.GA.Fitness_Operators.Energy_Fitness_Operator.Energy_Fitness_Operator method)
(Organisms.GA.Fitness_Operators.Fitness_Operator.Fitness_Operator method)
(Organisms.GA.Fitness_Operators.SCM_and_Energy_Fitness_Operator.SCM_and_Energy_Fitness_Operator method)
assign_all_fitnesses_before_assessing_against_predation_operator() (Organisms.GA.Fitness_Operators.Energy_Fitness_Operator.Energy_Fitness_Operator method)
(Organisms.GA.Fitness_Operators.Fitness_Operator.Fitness_Operator method)
(Organisms.GA.Fitness_Operators.SCM_and_Energy_Fitness_Operator.SCM_and_Energy_Fitness_Operator method)
assign_initial_population_fitnesses() (Organisms.GA.Fitness_Operators.Energy_Fitness_Operator.Energy_Fitness_Operator method)
(Organisms.GA.Fitness_Operators.Fitness_Operator.Fitness_Operator method)
(Organisms.GA.Fitness_Operators.SCM_and_Energy_Fitness_Operator.SCM_and_Energy_Fitness_Operator method)
assign_resumed_population_fitnesses() (Organisms.GA.Fitness_Operators.Energy_Fitness_Operator.Energy_Fitness_Operator method)
(Organisms.GA.Fitness_Operators.Fitness_Operator.Fitness_Operator method)
(Organisms.GA.Fitness_Operators.SCM_and_Energy_Fitness_Operator.SCM_and_Energy_Fitness_Operator method)
AtomInClusterPosition() (in module Organisms.GA.ExternalDefinitions)
B
backup() (Organisms.GA.Epoch.Epoch method)
backup_database() (Organisms.GA.Collection.Collection method)
backup_files() (Organisms.GA.Population.Population method)
backup_state_file() (Organisms.GA.Population.Population method)
C
centre_cluster_at_centre_of_cell() (Organisms.GA.Cluster.Cluster method)
centre_offspring_at_centre_of_cell() (Organisms.GA.Crossover.Crossover method)
centre_parents_about_origin() (Organisms.GA.Crossover.Crossover method)
change_fitness_function() (Organisms.GA.Epoch.Epoch method)
change_mutation_chances() (Organisms.GA.Mutation.Mutation method)
check() (Organisms.GA.EnergyProfile.EnergyProfile method)
(Organisms.GA.Fitness_Operators.Fitness_Operator.Fitness_Operator method)
(Organisms.GA.Mutation.Mutation method)
(Organisms.GA.Predation_Operators.Predation_Operator.Predation_Operator method)
check_asap3_version() (in module Organisms.GA.Get_Predation_and_Fitness_Operators)
check_clusters_in_database() (Organisms.GA.Collection.Collection method)
(Organisms.GA.GA_Recording_System.GA_Recording_Database method)
(Organisms.GA.GA_Recording_System.GA_Recording_System method)
check_database() (Organisms.GA.Predation_Operators.IDCM_Predation_Operator.IDCM_Predation_Operator method)
(Organisms.GA.SCM_Scripts.CNA_Database.CNA_Database method)
check_database_and_determine_if_to_use_backup() (Organisms.GA.Collection.Collection method)
check_for_backup() (Organisms.GA.Epoch.Epoch method)
Check_for_Issue_with_Scheme_with_collection() (in module Organisms.GA.Predation_Operators.Energy_Predation_Operator_Scripts.Comprehensive_Energy_Predation_Operator_energy)
(in module Organisms.GA.Predation_Operators.Energy_Predation_Operator_Scripts.Comprehensive_Energy_Predation_Operator_fitness)
(in module Organisms.GA.Predation_Operators.Energy_Predation_Operator_Scripts.Simple_Energy_Predation_Operator)
check_for_issues() (Organisms.GA.Predation_Operators.IDCM_Predation_Operator_Scripts.LoD_Comparison_Database.LoD_Comparison_Database method)
check_historyfile() (Organisms.GA.Collection.Collection method)
check_initial_population() (in module Organisms.GA.Predation_Operators.Energy_Predation_Operator_Scripts.Comprehensive_Energy_Predation_Operator_energy)
(in module Organisms.GA.Predation_Operators.Energy_Predation_Operator_Scripts.Comprehensive_Energy_Predation_Operator_fitness)
(in module Organisms.GA.Predation_Operators.Energy_Predation_Operator_Scripts.Simple_Energy_Predation_Operator)
(Organisms.GA.Predation_Operators.Energy_Predation_Operator.Energy_Predation_Operator method)
(Organisms.GA.Predation_Operators.IDCM_Predation_Operator.IDCM_Predation_Operator method)
(Organisms.GA.Predation_Operators.No_Predation_Operator.No_Predation_Operator method)
(Organisms.GA.Predation_Operators.Predation_Operator.Predation_Operator method)
(Organisms.GA.Predation_Operators.SCM_Predation_Operator.SCM_Predation_Operator method)
check_PoolProfileTXT_exists() (Organisms.GA.Collection.Collection method)
Check_Population_against_predation_operator() (in module Organisms.GA.Initialise_Population)
check_rho_i() (in module Organisms.GA.Fitness_Operators.Energetic_Fitness_Contribution)
clean() (Organisms.GA.Offspring_Pool.Offspring_Pool method)
close() (Organisms.GA.Collection.Collection method)
(Organisms.GA.EnergyProfile.EnergyProfile method)
(Organisms.GA.GA_Program_Details.GA_Program_Details method)
Cluster (class in Organisms.GA.Cluster)
Cluster_Block (class in Organisms.GA.Predation_Operators.Energy_Predation_Operator_Scripts.Comprehensive_Energy_Predation_Operator_energy)
(class in Organisms.GA.Predation_Operators.Energy_Predation_Operator_Scripts.Comprehensive_Energy_Predation_Operator_fitness)
(class in Organisms.GA.Predation_Operators.IDCM_Predation_Operator)
(class in Organisms.GA.Predation_Operators.SCM_Predation_Operator)
CNA_Database (class in Organisms.GA.SCM_Scripts.CNA_Database)
cna_profile_generator() (in module Organisms.GA.SCM_Scripts.CNA_Database)
Collection (class in Organisms.GA.Collection)
Collections_Iterator (class in Organisms.GA.Collections_Iterator)
convert_population_fitness_to_SCM_fitness_contribution() (Organisms.GA.Fitness_Operators.SCM_and_Energy_Fitness_Operator.SCM_and_Energy_Fitness_Operator method)
convert_to_bytes() (in module Organisms.GA.GA_Recording_System)
create() (Organisms.GA.EnergyProfile.EnergyProfile method)
(Organisms.GA.GA_Program_Details.GA_Program_Details method)
create_a_cluster() (in module Organisms.GA.Initialise_Population)
Create_An_Offspring() (in module Organisms.GA.Get_Offspring)
Create_An_Unoptimised_Offspring() (in module Organisms.GA.Get_Offspring)
create_collection_history() (Organisms.GA.Collection.Collection method)
Crossover (class in Organisms.GA.Crossover)
current_state_file() (Organisms.GA.Population.Population method)
custom_verify_cluster() (Organisms.GA.Cluster.Cluster method)
Cut_and_Splice_Devon_and_Ho() (Organisms.GA.Crossover.Crossover method)
D
daemon (Organisms.GA.SCM_Scripts.MyPool.NoDaemonProcess property)
deepcopy() (Organisms.GA.Cluster.Cluster method)
deepcopy_skeleton() (Organisms.GA.Cluster.Cluster method)
delete_collection_database() (Organisms.GA.Collection.Collection method)
did_get_data_from_backup() (Organisms.GA.Epoch.Epoch method)
direct_function() (Organisms.GA.Fitness_Operators.Fitness_Function.Fitness_Function method)
displacement_of_plane() (Organisms.GA.Crossover.Crossover method)
does_backup_exist() (Organisms.GA.Epoch.Epoch method)
does_contain_database() (Organisms.GA.Collection.Collection method)
does_epoch_data_exist_on_disk() (Organisms.GA.Epoch.Epoch method)
E
end_clock() (Organisms.GA.GA_Program_Details.GA_Program_Details method)
ending_details() (Organisms.GA.GA_Program_Details.GA_Program_Details method)
Energy_Fitness_Operator (class in Organisms.GA.Fitness_Operators.Energy_Fitness_Operator)
energy_fitness_options() (Organisms.GA.Fitness_Operators.Energy_Fitness_Operator.Energy_Fitness_Operator method)
Energy_Predation_Operator (class in Organisms.GA.Predation_Operators.Energy_Predation_Operator)
Energy_Predation_Operators_Options() (Organisms.GA.Predation_Operators.Energy_Predation_Operator.Energy_Predation_Operator method)
EnergyProfile (class in Organisms.GA.EnergyProfile)
Epoch (class in Organisms.GA.Epoch)
epoch_end_clock() (Organisms.GA.GA_Program_Details.GA_Program_Details method)
epoch_start_clock() (Organisms.GA.GA_Program_Details.GA_Program_Details method)
Exploded() (in module Organisms.GA.ExternalDefinitions)
exponential_function() (Organisms.GA.Fitness_Operators.Fitness_Function.Fitness_Function method)
F
Fitness_Function (class in Organisms.GA.Fitness_Operators.Fitness_Function)
Fitness_Operator (class in Organisms.GA.Fitness_Operators.Fitness_Operator)
G
GA_Initiate() (in module Organisms.GA.GA_Initiate)
GA_Program (class in Organisms.GA.GA_Program)
GA_Program_Details (class in Organisms.GA.GA_Program_Details)
GA_Program_Logo_coloured() (in module Organisms.GA.GA_Introducing_Remarks)
GA_Recording_Database (class in Organisms.GA.GA_Recording_System)
GA_Recording_System (class in Organisms.GA.GA_Recording_System)
GA_Setup() (in module Organisms.GA.GA_Setup)
GA_Starts() (Organisms.GA.EnergyProfile.EnergyProfile method)
get_all_averages_for_a_cluster() (Organisms.GA.SCM_Scripts.CNA_Database.CNA_Database method)
get_average() (Organisms.GA.SCM_Scripts.Similarity_Profile.Similarity_Profile method)
get_cluster_distance_list() (in module Organisms.GA.Predation_Operators.IDCM_Predation_Operator_Scripts.IDCM_Methods)
get_cluster_energies() (Organisms.GA.Collection.Collection method)
get_cluster_from_name() (Organisms.GA.Collection.Collection method)
get_cluster_names() (Organisms.GA.Collection.Collection method)
(Organisms.GA.GA_Recording_System.GA_Recording_Database method)
(Organisms.GA.Predation_Operators.IDCM_Predation_Operator_Scripts.LoD_Comparison_Database.LoD_Comparison_Database method)
get_clusters() (Organisms.GA.Collection.Collection method)
get_CNA_fitness_contribution() (in module Organisms.GA.Fitness_Operators.CNA_Fitness_Contribution)
get_CNA_fitness_contribution_normalised() (in module Organisms.GA.Fitness_Operators.CNA_Fitness_Contribution)
get_CNA_fitness_parameter() (in module Organisms.GA.Fitness_Operators.CNA_Fitness_Contribution)
get_CNA_fitness_parameter_normalised() (in module Organisms.GA.Fitness_Operators.CNA_Fitness_Contribution)
get_CNA_similarities() (in module Organisms.GA.SCM_Scripts.A_SCM_Methods)
(in module Organisms.GA.SCM_Scripts.T_SCM_Methods)
get_CNA_similarity() (in module Organisms.GA.SCM_Scripts.A_SCM_Methods)
(in module Organisms.GA.SCM_Scripts.T_SCM_Methods)
get_comparison() (in module Organisms.GA.SCM_Scripts.Similarity_Profile)
(Organisms.GA.SCM_Scripts.Similarity_Profile.Similarity_Profile method)
get_current_generation_and_last_cluster_generated_from_EnergyProfile() (Organisms.GA.EnergyProfile.EnergyProfile method)
get_current_generation_from_state_file() (Organisms.GA.Population.Population method)
get_data_from_current_state_file() (Organisms.GA.Population.Population method)
get_details() (Organisms.GA.Population.Population method)
(Organisms.GA.SCM_Scripts.CNA_Database.CNA_Database method)
get_distance() (in module Organisms.GA.Predation_Operators.IDCM_Predation_Operator_Scripts.IDCM_Methods)
get_elemental_makeup() (in module Organisms.GA.ExternalDefinitions)
(Organisms.GA.Cluster.Cluster method)
get_energetic_fitness_contribution() (in module Organisms.GA.Fitness_Operators.Energetic_Fitness_Contribution)
get_energy_predation_methods() (Organisms.GA.Predation_Operators.Energy_Predation_Operator.Energy_Predation_Operator method)
get_entry() (Organisms.GA.Predation_Operators.IDCM_Predation_Operator_Scripts.LoD_Comparison_Database.LoD_Comparison_Database method)
get_fitness() (Organisms.GA.Fitness_Operators.Fitness_Function.Fitness_Function method)
get_fitness_operator() (in module Organisms.GA.Get_Predation_and_Fitness_Operators)
get_history_path() (Organisms.GA.Collection.Collection method)
get_identical_structures_initial_population() (Organisms.GA.Predation_Operators.IDCM_Predation_Operator.IDCM_Predation_Operator method)
get_index() (Organisms.GA.Collection.Collection method)
(Organisms.GA.GA_Recording_System.GA_Recording_Database method)
get_lowest_and_highest_energies_from_collections() (in module Organisms.GA.Fitness_Operators.Energetic_Fitness_Contribution)
get_lowest_and_highest_similarities_from_collections() (in module Organisms.GA.Fitness_Operators.CNA_Fitness_Contribution)
get_max_mean_min_energies() (Organisms.GA.Collection.Collection method)
get_max_similarity() (Organisms.GA.SCM_Scripts.CNA_Database.CNA_Database method)
get_mutation_type() (Organisms.GA.Mutation.Mutation method)
get_pool_folder_size() (Organisms.GA.Population.Population method)
get_population_fitness() (Organisms.GA.Fitness_Operators.SCM_and_Energy_Fitness_Operator.SCM_and_Energy_Fitness_Operator method)
get_predation_and_fitness_operators() (in module Organisms.GA.Get_Predation_and_Fitness_Operators)
get_predation_operator() (in module Organisms.GA.Get_Predation_and_Fitness_Operators)
get_rCut_values() (in module Organisms.GA.SCM_Scripts.SCM_initialisation)
get_rCuts() (in module Organisms.GA.SCM_Scripts.SCM_initialisation)
get_results() (Organisms.GA.SCM_Scripts.Similarity_Profile.Similarity_Profile method)
get_resume_from_generation() (in module Organisms.GA.GA_Initiate)
get_resumed_mean_energy_epoch_details() (Organisms.GA.Epoch.Epoch method)
get_resumed_same_population_epoch_details() (Organisms.GA.Epoch.Epoch method)
get_rho_i() (in module Organisms.GA.Fitness_Operators.Energetic_Fitness_Contribution)
get_SCM_methods() (in module Organisms.GA.SCM_Scripts.SCM_initialisation)
get_similar_clusters_in_database() (Organisms.GA.SCM_Scripts.CNA_Database.CNA_Database method)
get_similar_clusters_to_remove() (Organisms.GA.Predation_Operators.SCM_Predation_Operator.SCM_Predation_Operator method)
get_single_atomic_CNA_profile_method() (in module Organisms.GA.SCM_Scripts.A_SCM_Methods)
get_single_total_CNA_profile_method() (in module Organisms.GA.SCM_Scripts.T_SCM_Methods)
get_size() (in module Organisms.GA.GA_Recording_System)
get_tasks() (in module Organisms.GA.Initialise_Population)
(Organisms.GA.GA_Program.GA_Program method)
get_time_now() (Organisms.GA.Timer.Timer method)
get_total_cluster_energy() (Organisms.GA.Cluster.Cluster method)
get_total_length_of_running_time() (Organisms.GA.Timer.Timer method)
H
half_index_custom_method() (Organisms.GA.Crossover.Crossover method)
half_index_half_method() (Organisms.GA.Crossover.Crossover method)
half_index_random_method() (Organisms.GA.Crossover.Crossover method)
half_index_weighted_method() (Organisms.GA.Crossover.Crossover method)
has_elapsed_time() (Organisms.GA.Timer.Timer method)
history_file_name() (Organisms.GA.Collection.Collection method)
homotopMutate() (in module Organisms.GA.Types_Of_Mutations)
I
IDCM_Predation_Operator (class in Organisms.GA.Predation_Operators.IDCM_Predation_Operator)
import_clusters_from_database_to_memory() (Organisms.GA.Collection.Collection method)
import_information_from_database() (Organisms.GA.GA_Recording_System.GA_Recording_Database method)
(Organisms.GA.GA_Recording_System.GA_Recording_System method)
import_surface() (in module Organisms.GA.Cluster)
InclusionboxOfCluster() (in module Organisms.GA.ExternalDefinitions)
InclusionRadiusOfCluster() (in module Organisms.GA.ExternalDefinitions)
information_from_the_same_generation() (Organisms.GA.Epoch.Epoch method)
Initate_New_GAProgram() (in module Organisms.GA.GA_Initiate)
Initial_ProgramChecking() (in module Organisms.GA.GA_Initiate)
initial_similarity_profile_generator() (in module Organisms.GA.SCM_Scripts.CNA_Database)
initialise_mean_energy_epoch_details() (Organisms.GA.Epoch.Epoch method)
Initialise_Population() (in module Organisms.GA.Initialise_Population)
Initialise_Population_with_Randomly_Generated_Clusters() (in module Organisms.GA.Initialise_Population)
initialise_same_population_epoch_details() (Organisms.GA.Epoch.Epoch method)
Introducing_Remarks() (in module Organisms.GA.GA_Introducing_Remarks)
is_cluster_pair_in_the_database() (Organisms.GA.Predation_Operators.IDCM_Predation_Operator_Scripts.LoD_Comparison_Database.LoD_Comparison_Database method)
is_LES_note_in_EnergyProfile() (Organisms.GA.EnergyProfile.EnergyProfile method)
is_pair_in_the_database() (Organisms.GA.SCM_Scripts.CNA_Database.CNA_Database method)
is_position_already_occupied_by_an_atom_in_Cluster() (in module Organisms.GA.ExternalDefinitions)
is_there_an_energy_range() (Organisms.GA.Collection.Collection method)
is_there_an_similarity_range() (Organisms.GA.Fitness_Operators.SCM_and_Energy_Fitness_Operator.SCM_and_Energy_Fitness_Operator method)
isfloat() (in module Organisms.GA.Mutation)
K
keys() (Organisms.GA.Predation_Operators.IDCM_Predation_Operator_Scripts.LoD_Comparison_Database.LoD_Comparison_Database method)
(Organisms.GA.SCM_Scripts.CNA_Database.CNA_Database method)
L
linear_function() (Organisms.GA.Fitness_Operators.Fitness_Function.Fitness_Function method)
LoD_compare_two_structures() (in module Organisms.GA.Predation_Operators.IDCM_Predation_Operator_Scripts.IDCM_Methods)
LoD_Comparison_Database (class in Organisms.GA.Predation_Operators.IDCM_Predation_Operator_Scripts.LoD_Comparison_Database)
LoD_Similarity_Analysis() (Organisms.GA.Predation_Operators.IDCM_Predation_Operator_Scripts.LoD_Comparison_Database.LoD_Comparison_Database method)
M
make_collection_folder() (Organisms.GA.Collection.Collection method)
make_database_table() (Organisms.GA.Predation_Operators.IDCM_Predation_Operator_Scripts.LoD_Comparison_Database.LoD_Comparison_Database method)
make_folder() (in module Organisms.GA.GA_Recording_System)
make_simple_table() (Organisms.GA.SCM_Scripts.CNA_Database.CNA_Database method)
mate_Cut_and_Splice() (Organisms.GA.Crossover.Crossover method)
mate_Cut_and_Splice_error_checking_1() (Organisms.GA.Crossover.Crossover method)
mate_Cut_and_Splice_error_checking_2() (Organisms.GA.Crossover.Crossover method)
mating() (Organisms.GA.Crossover.Crossover method)
max_energy() (Organisms.GA.Collection.Collection method)
mean_energy() (Organisms.GA.Collection.Collection method)
min_energy() (Organisms.GA.Collection.Collection method)
module
Organisms.GA.Cluster
Organisms.GA.Collection
Organisms.GA.Collections_Iterator
Organisms.GA.Crossover
Organisms.GA.EnergyProfile
Organisms.GA.Epoch
Organisms.GA.ExternalDefinitions
Organisms.GA.Fitness_Operators.CNA_Fitness_Contribution
Organisms.GA.Fitness_Operators.Energetic_Fitness_Contribution
Organisms.GA.Fitness_Operators.Energy_Fitness_Operator
Organisms.GA.Fitness_Operators.Fitness_Function
Organisms.GA.Fitness_Operators.Fitness_Operator
Organisms.GA.Fitness_Operators.SCM_and_Energy_Fitness_Operator
Organisms.GA.GA_Initiate
Organisms.GA.GA_Introducing_Remarks
Organisms.GA.GA_Program
Organisms.GA.GA_Program_Details
Organisms.GA.GA_Recording_System
Organisms.GA.GA_Setup
Organisms.GA.Get_Offspring
Organisms.GA.Get_Predation_and_Fitness_Operators
Organisms.GA.Initialise_Population
Organisms.GA.Memory_Operator
Organisms.GA.Mutation
Organisms.GA.Offspring_Pool
Organisms.GA.Population
Organisms.GA.Predation_Operators.Energy_Predation_Operator
Organisms.GA.Predation_Operators.Energy_Predation_Operator_Scripts.Comprehensive_Energy_Predation_Operator_energy
Organisms.GA.Predation_Operators.Energy_Predation_Operator_Scripts.Comprehensive_Energy_Predation_Operator_fitness
Organisms.GA.Predation_Operators.Energy_Predation_Operator_Scripts.Simple_Energy_Predation_Operator
Organisms.GA.Predation_Operators.IDCM_Predation_Operator
Organisms.GA.Predation_Operators.IDCM_Predation_Operator_Scripts.IDCM_Methods
Organisms.GA.Predation_Operators.IDCM_Predation_Operator_Scripts.LoD_Comparison_Database
Organisms.GA.Predation_Operators.No_Predation_Operator
Organisms.GA.Predation_Operators.Predation_Operator
Organisms.GA.Predation_Operators.SCM_Predation_Operator
Organisms.GA.SCM_Scripts.A_SCM_Methods
Organisms.GA.SCM_Scripts.CNA_Database
Organisms.GA.SCM_Scripts.MyPool
Organisms.GA.SCM_Scripts.SCM_initialisation
Organisms.GA.SCM_Scripts.Similarity_Profile
Organisms.GA.SCM_Scripts.T_SCM_Methods
Organisms.GA.Surface
Organisms.GA.Timer
Organisms.GA.Types_Of_Mutations
move_backup_database_to_normal_backup() (Organisms.GA.Collection.Collection method)
move_backup_to_current_files() (Organisms.GA.Population.Population method)
moveMutate() (in module Organisms.GA.Types_Of_Mutations)
Mutation (class in Organisms.GA.Mutation)
mutation() (Organisms.GA.Mutation.Mutation method)
MyConstraint (class in Organisms.GA.Surface)
MyPool (class in Organisms.GA.SCM_Scripts.MyPool)
N
natural_selection() (Organisms.GA.GA_Program.GA_Program method)
no_epoch() (Organisms.GA.Epoch.Epoch method)
No_Predation_Operator (class in Organisms.GA.Predation_Operators.No_Predation_Operator)
NoDaemonProcess (class in Organisms.GA.SCM_Scripts.MyPool)
O
Offspring_Pool (class in Organisms.GA.Offspring_Pool)
open() (Organisms.GA.Collection.Collection method)
(Organisms.GA.EnergyProfile.EnergyProfile method)
(Organisms.GA.GA_Program_Details.GA_Program_Details method)
Organisms.GA.Cluster
module
Organisms.GA.Collection
module
Organisms.GA.Collections_Iterator
module
Organisms.GA.Crossover
module
Organisms.GA.EnergyProfile
module
Organisms.GA.Epoch
module
Organisms.GA.ExternalDefinitions
module
Organisms.GA.Fitness_Operators.CNA_Fitness_Contribution
module
Organisms.GA.Fitness_Operators.Energetic_Fitness_Contribution
module
Organisms.GA.Fitness_Operators.Energy_Fitness_Operator
module
Organisms.GA.Fitness_Operators.Fitness_Function
module
Organisms.GA.Fitness_Operators.Fitness_Operator
module
Organisms.GA.Fitness_Operators.SCM_and_Energy_Fitness_Operator
module
Organisms.GA.GA_Initiate
module
Organisms.GA.GA_Introducing_Remarks
module
Organisms.GA.GA_Program
module
Organisms.GA.GA_Program_Details
module
Organisms.GA.GA_Recording_System
module
Organisms.GA.GA_Setup
module
Organisms.GA.Get_Offspring
module
Organisms.GA.Get_Predation_and_Fitness_Operators
module
Organisms.GA.Initialise_Population
module
Organisms.GA.Memory_Operator
module
Organisms.GA.Mutation
module
Organisms.GA.Offspring_Pool
module
Organisms.GA.Population
module
Organisms.GA.Predation_Operators.Energy_Predation_Operator
module
Organisms.GA.Predation_Operators.Energy_Predation_Operator_Scripts.Comprehensive_Energy_Predation_Operator_energy
module
Organisms.GA.Predation_Operators.Energy_Predation_Operator_Scripts.Comprehensive_Energy_Predation_Operator_fitness
module
Organisms.GA.Predation_Operators.Energy_Predation_Operator_Scripts.Simple_Energy_Predation_Operator
module
Organisms.GA.Predation_Operators.IDCM_Predation_Operator
module
Organisms.GA.Predation_Operators.IDCM_Predation_Operator_Scripts.IDCM_Methods
module
Organisms.GA.Predation_Operators.IDCM_Predation_Operator_Scripts.LoD_Comparison_Database
module
Organisms.GA.Predation_Operators.No_Predation_Operator
module
Organisms.GA.Predation_Operators.Predation_Operator
module
Organisms.GA.Predation_Operators.SCM_Predation_Operator
module
Organisms.GA.SCM_Scripts.A_SCM_Methods
module
Organisms.GA.SCM_Scripts.CNA_Database
module
Organisms.GA.SCM_Scripts.MyPool
module
Organisms.GA.SCM_Scripts.SCM_initialisation
module
Organisms.GA.SCM_Scripts.Similarity_Profile
module
Organisms.GA.SCM_Scripts.T_SCM_Methods
module
Organisms.GA.Surface
module
Organisms.GA.Timer
module
Organisms.GA.Types_Of_Mutations
module
P
perform_epoch() (Organisms.GA.Epoch.Epoch method)
perform_epoch_mean_energy() (Organisms.GA.Epoch.Epoch method)
perform_epoch_no_epoch() (Organisms.GA.Epoch.Epoch method)
perform_epoch_on_population() (Organisms.GA.GA_Program.GA_Program method)
perform_epoch_same_population() (Organisms.GA.Epoch.Epoch method)
pickClusterFromThePopulation() (Organisms.GA.Mutation.Mutation method)
pickParentsFromThePopulation() (Organisms.GA.Crossover.Crossover method)
Place_Already_Created_Clusters_In_Population() (in module Organisms.GA.Initialise_Population)
pop() (Organisms.GA.Collection.Collection method)
pop_identical_structures() (Organisms.GA.Predation_Operators.IDCM_Predation_Operator.IDCM_Predation_Operator method)
Population (class in Organisms.GA.Population)
Predation_Operator (class in Organisms.GA.Predation_Operators.Predation_Operator)
print_clusters() (Organisms.GA.Population.Population method)
print_cna_database_details() (Organisms.GA.SCM_Scripts.CNA_Database.CNA_Database method)
print_elapsed_time() (Organisms.GA.Timer.Timer method)
print_initial_message() (Organisms.GA.Fitness_Operators.SCM_and_Energy_Fitness_Operator.SCM_and_Energy_Fitness_Operator method)
Process (Organisms.GA.SCM_Scripts.MyPool.MyPool attribute)
R
randomMutate() (in module Organisms.GA.Types_Of_Mutations)
read_collection_database() (Organisms.GA.Collection.Collection method)
record_collection() (Organisms.GA.GA_Recording_System.GA_Recording_System method)
record_initial_populations() (Organisms.GA.GA_Recording_System.GA_Recording_System method)
record_population_at_generation() (Organisms.GA.GA_Recording_System.GA_Recording_System method)
remove() (Organisms.GA.Collection.Collection method)
(Organisms.GA.Predation_Operators.IDCM_Predation_Operator_Scripts.LoD_Comparison_Database.LoD_Comparison_Database method)
(Organisms.GA.SCM_Scripts.CNA_Database.CNA_Database method)
remove_backup() (Organisms.GA.Epoch.Epoch method)
remove_backup_database() (Organisms.GA.Collection.Collection method)
remove_backup_database_if_exists() (Organisms.GA.Collection.Collection method)
remove_backup_files() (Organisms.GA.Population.Population method)
remove_backup_state_file() (Organisms.GA.Population.Population method)
remove_backup_state_file_if_exists() (Organisms.GA.Population.Population method)
remove_calculator() (Organisms.GA.Cluster.Cluster method)
remove_clusters_from_database_that_are_from_unsuccessful_generations() (Organisms.GA.Collection.Collection method)
remove_end_lines_from_text() (in module Organisms.GA.EnergyProfile)
remove_from_database() (Organisms.GA.Fitness_Operators.Energy_Fitness_Operator.Energy_Fitness_Operator method)
(Organisms.GA.Fitness_Operators.SCM_and_Energy_Fitness_Operator.SCM_and_Energy_Fitness_Operator method)
(Organisms.GA.Predation_Operators.Energy_Predation_Operator.Energy_Predation_Operator method)
(Organisms.GA.Predation_Operators.IDCM_Predation_Operator.IDCM_Predation_Operator method)
(Organisms.GA.Predation_Operators.No_Predation_Operator.No_Predation_Operator method)
(Organisms.GA.Predation_Operators.Predation_Operator.Predation_Operator method)
(Organisms.GA.Predation_Operators.SCM_Predation_Operator.SCM_Predation_Operator method)
remove_offspring_and_replace_with_population_that_violate_predation_operator() (Organisms.GA.Predation_Operators.Predation_Operator.Predation_Operator method)
remove_offspring_that_violate_the_predation_operator() (Organisms.GA.Predation_Operators.Predation_Operator.Predation_Operator method)
remove_similar_clusters_in_population() (Organisms.GA.Predation_Operators.IDCM_Predation_Operator.IDCM_Predation_Operator method)
remove_to_database() (Organisms.GA.Collection.Collection method)
(Organisms.GA.GA_Recording_System.GA_Recording_Database method)
repair_current_state_file() (Organisms.GA.Population.Population method)
replace() (Organisms.GA.Collection.Collection method)
replace_population_with_offspring() (Organisms.GA.Predation_Operators.Predation_Operator.Predation_Operator method)
replace_with_backup() (Organisms.GA.Epoch.Epoch method)
reset() (Organisms.GA.Fitness_Operators.Energy_Fitness_Operator.Energy_Fitness_Operator method)
(Organisms.GA.Fitness_Operators.SCM_and_Energy_Fitness_Operator.SCM_and_Energy_Fitness_Operator method)
(Organisms.GA.Predation_Operators.Energy_Predation_Operator.Energy_Predation_Operator method)
(Organisms.GA.Predation_Operators.IDCM_Predation_Operator.IDCM_Predation_Operator method)
(Organisms.GA.Predation_Operators.IDCM_Predation_Operator_Scripts.LoD_Comparison_Database.LoD_Comparison_Database method)
(Organisms.GA.Predation_Operators.No_Predation_Operator.No_Predation_Operator method)
(Organisms.GA.Predation_Operators.Predation_Operator.Predation_Operator method)
(Organisms.GA.Predation_Operators.SCM_Predation_Operator.SCM_Predation_Operator method)
(Organisms.GA.SCM_Scripts.CNA_Database.CNA_Database method)
resume_ga_recording_system_from_current_generation() (Organisms.GA.GA_Recording_System.GA_Recording_System method)
Resume_GAProgram() (in module Organisms.GA.GA_Initiate)
rotate() (Organisms.GA.Crossover.Crossover method)
roulette() (Organisms.GA.Crossover.Crossover method)
run() (Organisms.GA.Crossover.Crossover method)
(Organisms.GA.Mutation.Mutation method)
run_GA() (Organisms.GA.GA_Program.GA_Program method)
S
SCM_and_Energy_Fitness_Operator (class in Organisms.GA.Fitness_Operators.SCM_and_Energy_Fitness_Operator)
SCM_Predation_Operator (class in Organisms.GA.Predation_Operators.SCM_Predation_Operator)
see_tree() (Organisms.GA.SCM_Scripts.CNA_Database.Tree method)
set_settings() (Organisms.GA.Epoch.Epoch method)
setting_up_epoch_to_resume_GA() (Organisms.GA.Epoch.Epoch method)
should_epoch() (Organisms.GA.Epoch.Epoch method)
should_epoch_using_mean_energy_epoch() (Organisms.GA.Epoch.Epoch method)
should_epoch_using_same_population_epoch() (Organisms.GA.Epoch.Epoch method)
Similarity_Profile (class in Organisms.GA.SCM_Scripts.Similarity_Profile)
similarity_profile_generator() (in module Organisms.GA.SCM_Scripts.CNA_Database)
sort_by_energy() (Organisms.GA.Collection.Collection method)
(Organisms.GA.GA_Recording_System.GA_Recording_Database method)
sort_by_fitness() (Organisms.GA.Offspring_Pool.Offspring_Pool method)
sort_by_name() (Organisms.GA.Collection.Collection method)
(Organisms.GA.GA_Recording_System.GA_Recording_Database method)
sortZ() (Organisms.GA.Cluster.Cluster method)
start_clock() (Organisms.GA.GA_Program_Details.GA_Program_Details method)
T
tail() (in module Organisms.GA.EnergyProfile)
tanh_function() (Organisms.GA.Fitness_Operators.Fitness_Function.Fitness_Function method)
Timer (class in Organisms.GA.Timer)
tournament() (Organisms.GA.Crossover.Crossover method)
Tree (class in Organisms.GA.Predation_Operators.IDCM_Predation_Operator_Scripts.LoD_Comparison_Database)
(class in Organisms.GA.SCM_Scripts.CNA_Database)
U
update_cluster_in_database_for_if_in_population() (Organisms.GA.GA_Recording_System.GA_Recording_Database method)
(Organisms.GA.GA_Recording_System.GA_Recording_System method)
update_LoD_database() (Organisms.GA.Predation_Operators.IDCM_Predation_Operator.IDCM_Predation_Operator method)
V
verify_cluster() (Organisms.GA.Cluster.Cluster method)
version_no() (in module Organisms.GA.GA_Introducing_Remarks)
view() (Organisms.GA.Cluster.Cluster method)
view_cluster() (Organisms.GA.Collection.Collection method)
W
which_clusters_in_LoD_comparison_database_are_similar() (Organisms.GA.Predation_Operators.IDCM_Predation_Operator_Scripts.LoD_Comparison_Database.LoD_Comparison_Database method)
Will_Mutation_Occur() (in module Organisms.GA.Get_Offspring)
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