Overview

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Birmingham Parallel Genetic Algorithm (BPGA).

Installation

To download the BPGA you need Git installed on your computer. If Git is installed use the following command to download the BPGA:

git clone https://bitbucket.org/JBADavis/bpga.git

then add the following line to your ~/.bashrc file:

export PYTHONPATH=$PYTHONPATH:~/bpga

Serial Jobs

Calculations must be run in separate directories, each of which must contain the following files:

INCAR
KPOINTS
POTCAR 
Run.py

Where the Run.py file is the BPGA's input script. An example calculation directorycan be found in:

~/bpga/Examples/Au2Ir2 

To run a calculation on a different HPC change the subString variable in Run.py to the required command for a parallel VASP run:

subString = "aprun -n 24 vasp5.gamma" 

Selection

Selection is currently only through roulette wheel selection. Tournament will be added again soon!

Crossover

Crossover is performed once an initial pool of random structure has been generated and assessed.

Deaven and Ho 1pt crossover can be performed with either a random or weighted cutting plane:

cross = "random"
cross = "weighted"

The weighted plane is determined by fitness of the two clusters selected for crossover.

Mutation

Mutation is performed according the mutation rate set in Run.py. The available mutation methods available are:

mutType = "random"
mutType = "move"
mutType = "homotop"
mutType = "rotate"  

Random

A new random cluster geometry is generated and minimised.

Move

A cluster is selected from the pool and 20% of the geometry is displaced by up to 1 angstrom.

homotop

(Only for bimetallic clusters)

A cluster is selected from the pool and two atoms have their atom types swapped.

Rotate

(Surface global optimisation only)

A low energy cluster is selected from the pool and a random rotation is performed.