An object oriented Python interface for atomistic simulations

Abstract

Programmable simulation environments allow one to monitor and control calculations efficiently and automatically before, during, and after runtime. Environments directly accessible in a programming environment can be interfaced with powerful external analysis tools and extensions to enhance the functionality of the core program, and by incorporating a flexible object based structure, the environments make building and analysing computational setups intuitive. In this work, we present a classical atomistic force field with an interface written in Python language. The program is an extension for an existing object based atomistic simulation environment. Program summaryProgram title: PysicCatalogue identifier: AEYE_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEYE_v1_0.htmlProgram obtainable from: CPC Program Library, Queen’s University, Belfast, N. Ireland.Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.htmlNo. of lines in distributed program, including test data, etc.: 74.743.No. of bytes in distributed program, including test data, etc.: 758.903.Distribution format: tar.gzProgramming language: Python, Fortran 90.Computer: Program has been tested on Linux and OS X workstations, and a Cray supercomputer.Operating system: Linux, Unix, OS X, Windows.RAM: Depends on the size of system.Classification: 7.7, 16.9, 4.14.External routines: Atomic Simulation Environment, NumPy necessary. Scipy, Matplotlib, HDF5, h5py recommended. The random number generator, Mersenne Twister, is included from the source: http://www.math.sci.hiroshima-u.ac.jp/~m-mat/MT/VERSIONS/FORTRAN/mt95.f90Nature of problem: Automated simulation control, interaction tuning and an intuitive interface for running atomistic simulations.Solution method: Object oriented interface to a flexible classical potential.Additional comments:User guide:http://thynnine.github.io/pysic/Running time: Depends on the size of system.