Mutation.py

This describe a cluster, where the system information is stored in the Genetic Algorithm

class Organisms.GA.Mutation.Mutation(mutation_types, r_ij, vacuum_to_add_length)

This class contains all the information and procedures required to perform a Mutation.

Parameters:

  • mutation_types ([(str, float),...]) – Contains the information about the mutations that the user would like to perform. See Manual for more information about this.

  • r_ij (float) – The maximum distance that should be between atoms to be considered bonded. This value should be as large a possible, to reflected the longest bond possible between atoms in the cluster.

  • vacuum_to_add_length (float) – The amount of vacuum to place around the cluster

change_mutation_chances()

This method will change the format of self.mutation_types into a format that can be used by this Mutation class.

The format of self.mutation_types changes as follows with this example.

[] => []

check(r_ij)

This method will check that the inputs for the mutation_types has been done correctly, without any violating issues.

Parameters:

r_ij (float) – The maximum distance that should be between atoms to be considered bonded. This value should be as large a possible, to reflected the longest bond possible between atoms in the cluster.

get_mutation_type()

This definition will pick the type of mutation.

Returns:

mutation_type

Rtypes:

str.

mutation(mutation_method, cluster_to_mutate, cell_length=None, vacuum_length=None)

This method will perform the mutation and return the mutant.

Inputs:

mutation_method (str.): The type of mutation to use for the mutation cluster_to_mutate (GA>Cluster): This is the cluster that we would like to perform a mutation upon. cell_length (float): This is the cell length of the unit cell. vacuum_length (float): The amount of vacuum to add to the unit cell.

Returns:

mutant

Rtypes:

Atom

pickClusterFromThePopulation(population)

This definition will pick the cluster from the population to mutate.

Inputs:

population (GA.Population): The population to choose the cluster to mutate from.

Returns:

cluster_to_mutate - The list of parents for mating.

Rtypes:

Cluster

run(run_input, cell_length=None, vacuum_length=None)

This definition will run the Mutation Procedure.

Inputs:

run_input (GA.Population/GA.Cluster/ase.Atoms): This is the input data about the cluster to mutate, or the population to take a cluster to mutate. cell_length (float): This is the cell length of the unit cell. vacuum_length (float): The amount of vacuum to add to the unit cell.

Returns:

mutant (GA.Cluster) - The mutated cluster mutation_method (str.) - The type of mutation that was picked to use for this mutation.

Organisms.GA.Mutation.isfloat(element)

Is the input a float.

Parameters:

element (Any) – some input

:returns True if the element can be considered a float, False if not. :rtype ebool.