Organisms: A Genetic Algorithm for Nanoclusters Logo
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  • 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
    • Table of Contents
      • GA_Program.py
      • GA_Program_Details.py
      • Cluster.py
      • Surface.py
      • Collection.py
      • Collections_Iterator.py
      • Population.py
      • EnergyProfile.py
      • Offspring_Pool.py
      • GA_Setup.py
      • GA_Initiate.py
      • GA_Introducing_Remarks.py
      • Initialise_Population.py
      • Get_Offspring.py
      • Crossover.py
      • Mutation.py
      • Types_Of_Mutations.py
      • Get_Predation_and_Fitness_Operators.py
      • Predation Operators
      • Fitness Operators
      • SCM Scripts
        • SCM_initialisation.py
        • Similarity_Profile.py
        • A_SCM_Methods.py
        • T_SCM_Methods.py
        • CNA_Database.py
        • MyPool.py
      • Epoch.py
      • Memory_Operator.py
      • ExternalDefinitions.py
      • GA_Recording_System.py
      • Timer.py
  • Index
  • Python Module Index
Organisms: A Genetic Algorithm for Nanoclusters
  • The Genetic Algorithm Python Files
  • SCM Scripts
  • Edit on GitHub
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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
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© Copyright 2021, Dr. Geoffrey Weal and Dr. Anna Garden. Revision 2c5229d3.

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