Crossover.py

This describes the

MatingProcedure.py, 13/04/2017, Geoffrey R. Weal

This program is designed to run the mating procedure of the Genetic Algorithm.

class Organisms.GA.Crossover.Crossover(crossover_type, r_ij, vacuumAdd, size_of_clusters)

This class is designed to perform the mating procedure of the genetic algorithm. This will produce a cluster that is an outcome of the mating procedure.

Parameters:

  • crossover_type (str.) –

    This is the type of mating procedure the user would like to use. There are currently a few options implimented into this mating procedure:

    • ”CAS_weighted”-: Cut and Splice - Deavon and Ho - weighted by fitness of parents (CAS_weighted)

    • ”CAS_random”: Cut and Splice - Deavon and Ho - cut a random percent x% of parent 1 and (100-x)% of parent 2 (CAS_random)

    • ”CAS_half”: Cut and Splice - Deavon and Ho - cut both parents by half (CAS_half)

    • ”CAS_custom_XX”: Cut and Splice - Deavon and Ho - cut a random percent XX% of parent 1 and (100-XXX)% of parent 2. To use this set crossType = CAS_custom_XX, where XX is a float of your choice between 0 and 100.

  • r_ij (float) – the maximum bond distance between atoms in the cluster. This should be the largest value possible for your cluster.

  • vacuumAdd (float) – The vacuum around the cluster

  • size_of_clusters (int) – The number of atoms in the cluster.

Cut_and_Splice_Devon_and_Ho(parents)

This definition is designed to perform the Cut and Splice Method as specified by Devon and Ho to mate the parents to give the offspring. The method works as follows:

  1. Rotate each parent by some random amount in the theta and phi directions.

  2. Sort the assignment of atoms in the cluster from most positive to most negative z value.

  3. Perform a Cut and Splice procedure, where the parents are cut in some way and spliced together to give the offspring.

Parameters:

parents ([Organisms.GA.Cluster, Organisms.GA.Cluster]) – This is the population to choose clusters from to mate together.

Returns:

Returns an offspring that has been created from mating two parent clusters together.

Rtypes:

Organisms.GA.Cluster

centre_offspring_at_centre_of_cell(offspring)

This method will center the offspring as required.

Parameters:

offspring (Organisms.GA.Cluster) – The offspring cluster.

centre_parents_about_origin(parents)

This method will center the parents about the zero point. This is to make sure that their two halfs will allign correctly when they are cut and spliced to form a new offsping

Parameters:

parents ([Organisms.GA.Cluster, Organisms.GA.Cluster]) – This is the population to choose clusters from to mate together.

Returns:

The parents which have been centered about the (0,0,0) point of the unit cell

Rtypes:

[Organisms.GA.Cluster, Organisms.GA.Cluster]

displacement_of_plane(first_half, second_half)

This method will determine the best initial positioning of the plane dividing each half

These two halves will be placed directly on each side of the plane, close enough to eachother that they will fused during optimisation, not too close to eachother that the two halves overlap.

Parameters:

  • first_half (GA.Cluster) – This is the first half of the offspring

  • second_half (GA.Cluster) – This is the second half of the offspring

Returns:

The z offset displacement vector to add to the second_half positions

Return type:

numpy.array

half_index_custom_method(cross_type)

This method will determine how to cut the cluster based on the atom to divide from, where the atoms have been numbered in order of the z axis.

This version of the method divides the parents based on a percentage of atoms to take from parent 1

Here, percentage of parent1 is taken, while 1.0-percentage of parent2 two is taken.

Parameters:

crossover_type (str.) – This is the type of mating procedure the user would like to use. This should be set to “CAS_custom_XX”, where XX is the percentage of parent 1 to be cut.

Returns:

The atom number in the cluster to cut the atom.

Return type:

int

half_index_half_method()

This method will determine how to cut the cluster based on the atom to divide from, where the atoms have been numbered in order of the z axis.

This version of the method divides the parents in half.

Returns:

The atom number in the cluster to cut the atom.

Return type:

int

half_index_random_method()

This method will determine how to cut the cluster based on the atom to divide from, where the atoms have been numbered in order of the z axis.

This version of the method divides the parents at some random atom indice

Returns:

The atom number in the cluster to cut the atom.

Return type:

int

half_index_weighted_method(parents)

This method will determine how to cut the cluster based on the atom to divide from, where the atoms have been numbered in order of the z axis.

This version of the method divides the parents based on their relative fitnesses.

Parameters:

parents ([Organisms.GA.Cluster, Organisms.GA.Cluster]) – This is the population to choose clusters from to mate together.

Returns:

The atom number in the cluster to cut the atom.

Return type:

int

mate_Cut_and_Splice(parents)

This method will perform the mating procedure as specified by the user. This can been designed to be used with multiple parents, however currently it is set up for 2 parents. It has also been developed for mating multi-metallic (multi-elemental) clusters together.

Parameters:

parents ([Organisms.GA.Cluster, Organisms.GA.Cluster]) – This is the population to choose clusters from to mate together.

Returns:

Returns an offspring that has been created from mating two parent clusters together.

Rtypes:

Organisms.GA.Cluster

mate_Cut_and_Splice_error_checking_1(parents)

This is a method for checking if there are any issues with the Cut_and_splice method.

This method is only needed when you are developing or modifying a mating procedure, to help with debugging. Otherwise, you dont need to use this algorithm

Parameters:

parents ([GA.Cluster, GA.Cluster]) – This is the population to choose clusters from to mate together.

Returns:

A list which indicates the types of elements, and the number of those elements, in the cluster

Return type:

{str: int, …}

mate_Cut_and_Splice_error_checking_2(elemental_makeup_of_parents, offspring)

This is a method for checking if there are any issues with the Cut_and_splice method.

This method is only needed when you are developing or modifying a mating procedure, to help with debugging. Otherwise, you dont need to use this algorithm

Parameters:

  • elemental_makeup_of_parents ({str: int, ...}) – A list which indicates the types of elements, and the number of those elements, in the cluster

  • offspring (Organisms.GA.Cluster) – The offspring cluster.

mating(parents)

This definition is designed as a switch to choose the mating method the user wishes to use for the genetic algorithm.

Parameters:

parents ([Organisms.GA.Cluster, Organisms.GA.Cluster]) – This is the population to choose clusters from to mate together.

Returns:

Returns an offspring that has been created from mating two parent clusters together.

Rtypes:

Organisms.GA.Cluster

pickParentsFromThePopulation(population)

This definition will pick the parents for mating.

Parameters:

population (Organisms.GA.Population) – This is the population to choose clusters from to mate together.

Returns:

two clusters from the population that will be mated together to give the offspring.

Rtypes:

(Organisms.GA.Cluster, Organisms.GA.Cluster)

rotate(cluster)

Rotate the cluster by some random angle in the theta and phi directions.

Parameters:

cluster (Organisms.GA.Cluster) – The cluster to be randomly rotated

roulette(population)

Performed the roulette wheel method to obtain the parents for a Mating procedure

Reference: https://pubs.rsc.org/en/content/articlepdf/2003/dt/b305686d

Parameters:

population (Organisms.GA.Population) – This is the population to choose clusters from to mate together.

Returns:

Will return a tuple of two integers that represent the indices of clusters in the population to use as parent to mate together to give a new offspring.

Rtypes:

[int, int]

run(run_input)

Run this the Mating Procedure and gives an offspring.

Parameters:

population (Organisms.GA.Population) – This is the population to choose clusters from to mate together.

Returns:

offspring

Rtypes:

Organisms.GA.Cluster

tournament(population)

Performed the tournament method to obtain the parents for a Mating procedure

Reference: https://pubs.rsc.org/en/content/articlepdf/2003/dt/b305686d

Parameters:

population (Organisms.GA.Population) – This is the population to choose clusters from to mate together.

Returns:

Will return a tuple of two integers that represent the indices of clusters in the population to use as parent to mate together to give a new offspring.

Rtypes:

[int, int]