An object oriented Python interface for atomistic simulations

T Hynninen and L Himanen and V Parkkinen and T Musso and J Corander and AS Foster, COMPUTER PHYSICS COMMUNICATIONS, 198, 230-237 (2016).

DOI: 10.1016/j.cpc.2015.09.010

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 summary Program title: Pysic Catalogue identifier: AEYE_v1_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEYE_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland. Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. 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.gz Programming 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/similar to m-mat/MT/VERSIONS/FORTRAN/mt95.f90 Nature 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.githublo/pysic/ Running time: Depends on the size of system. (C) 2015 Elsevier B.V. All rights reserved.

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