Types_Of_Mutations.py

This class is designed

Organisms.GA.Types_Of_Mutations.homotopMutate(cluster_to_mutate)

This definition is designed to swap the positions of two elementally different atoms in a cluster

Parameters:

cluster_to_mutate (GA.Cluster) – The cluster to move the atoms in the cluster.

:returns The newly created mutated cluster :rtypes GA.Cluster

Organisms.GA.Types_Of_Mutations.moveMutate(cluster_to_mutate, dist_to_move)

This method randomly displaces all the atoms within the structure cluster_to_mutate from its original position. This def depends on the value of the maximum bond length of the cluster, self.r_ij. The def will cause all atoms in the cluster to move randomly by up to a 1/2 of self.r_ij from their original position.

Parameters:

  • cluster_to_mutate (GA.Cluster) – The cluster to move the atoms in the cluster.

  • dist_to_move (float) – The fistnace to move clusters by

:returns The newly created mutated cluster :rtypes GA.Cluster

Organisms.GA.Types_Of_Mutations.randomMutate(boxtoplaceinlength, vacuumAdd, cluster_makeup=None, cluster_to_mutate=None, percentage_of_cluster_to_randomise=None)

This definition provides the random method for the mutation procedure. In this method, a cluster is designed by randomly placing the designed atoms of elements into a predefined unit cell.

Parameters:

  • boxtoplaceinlength (float) – This is the length of the box you would like to place atoms in to make a randomly constructed cluster.

  • vacuumAdd (float) – The length of vacuum added around the cluster. Written in A.

  • cluster_makeup ({'Element': int(number of that 'element' in this cluster),...}) – check this

  • cluster_to_mutate (ASE.Atoms) – If the user desired, they can tell this definition what cluster they want to mutate. Default: None.

  • percentage_of_cluster_to_randomise (float) – This is the percentage of the number of atoms in the cluster to randomise

Returns mutant:

The description of the mutant cluster.

Rtypes:

ase.Atoms or GA.Cluster