An object oriented Python interface for atomistic simulations

T. Hynninen*, L. Himanen, V. Parkkinen, T. Musso, J. Corander, A. S. Foster

*Tämän työn vastaava kirjoittaja

Tutkimustuotos: LehtiartikkeliArticleScientificvertaisarvioitu

2 Sitaatiot (Scopus)


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:

Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland.

Licensing provisions: Standard CPC licence,

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: 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.

JulkaisuComputer Physics Communications
DOI - pysyväislinkit
TilaJulkaistu - tammikuuta 2016
OKM-julkaisutyyppiA1 Julkaistu artikkeli, soviteltu

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