README.md

PAFI Examples

Test Systems

• systems/EAM-SIA-Fe : Dumbell SIA with Marinica07 EAM Fe
• systems/EAM-VAC-W : Vacancy with Marinica04 EAM W

Test scripts

• XML files can be used to overwrite default parameters, or they can be set in python

• configuration_files/*_TEST.xml are for quick testing- DO NOT USE THESE FOR SCIENCE!

• configurations_files/*_REAL.xml have realistic sampling values.

• All run with e.g. export NPROCS=4;mpirun -np ${NPROCS} python input_python.py

• Example XML usage in input_xml.py:

    from mpi4py import MPI
    from pafi import PAFIManager
    config = "./configuration_files/PartialConfiguration_TEST.xml"
    manager = PAFIManager(MPI.COMM_WORLD,config)
    manager.run()
    manager.close()

• Example python usage in input_python.py:

    from mpi4py import MPI
    from pafi import PAFIManager
    # Overwrite parameters within python script
    parameters = PAFIParser()
    parameters.set_pathway("systems/EAM-SIA-Fe/image_*.dat")
    parameters.set_potential("systems/EAM-SIA-Fe/Fe.eam.fs")

    # TEST VALUES
    parameters.axes["Temperature"] = [100.]
    parameters.set("nRepeats",2)
    parameters.set("SampleSteps",10)
    parameters.set("ThermSteps",10)
    parameters.set("ThermWindow",10)

    manager = PAFIManager(MPI.COMM_WORLD,parameters=parameters)
    manager.run()
    manager.close()

Post processing

• Can print integration results with python post_processing.py

• See also jupyter notebook PlottingExamples.ipynb