An object oriented Python interface for atomistic simulations

T. Hynninen; L. Himanen; Ville Parkkinen; T. Musso; J. Corander; A. S. Foster

doi:10.1016/j.cpc.2015.09.010

An object oriented Python interface for atomistic simulations

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

^*Corresponding author for this work

University of Turku
University of Helsinki

Research output: Contribution to journal › Article › Scientific › peer-review

2 Citations (Scopus)

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 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/

Original language	English
Pages (from-to)	230-237
Number of pages	8
Journal	Computer Physics Communications
Volume	198
DOIs	https://doi.org/10.1016/j.cpc.2015.09.010
Publication status	Published - Jan 2016
MoE publication type	A1 Journal article-refereed

Funding

We acknowledge financial support from the Academy of Finland through its Centres of Excellence Programme (Project No. 251748), EU projects MORDRED (Contract No. 261868) and PAMS (Contract No. 610446). T.M. was supported by the Finnish Academy of Science and Letters and Vilho, Yrjo, Kalle Vaisala Foundation. We acknowledge use of the Finnish CSC-IT Center for Sciences supercomputing resources.

Keywords

Atomistic simulations
Classical potential
Object oriented
Python
Fortran
ENERGY

Access to Document

10.1016/j.cpc.2015.09.010

Cite this

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title = "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/similar to 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.githublo/pysic/Running time: Depends on the size of system. (C) 2015 Elsevier B.V. All rights reserved.",

keywords = "Atomistic simulations, Classical potential, Object oriented, Python, Fortran, ENERGY",

author = "T. Hynninen and L. Himanen and Ville Parkkinen and T. Musso and J. Corander and Foster, \{A. S.\}",

note = "| openaire: EC/FP7/610446/EU//PAMS | openaire: EC/FP7/261868/EU//MORDRED",

year = "2016",

month = jan,

doi = "10.1016/j.cpc.2015.09.010",

language = "English",

volume = "198",

pages = "230--237",

journal = "Computer Physics Communications",

issn = "0010-4655",

publisher = "Elsevier",

}

TY - JOUR

T1 - An object oriented Python interface for atomistic simulations

AU - Hynninen, T.

AU - Himanen, L.

AU - Parkkinen, Ville

AU - Musso, T.

AU - Corander, J.

AU - Foster, A. S.

N1 - | openaire: EC/FP7/610446/EU//PAMS | openaire: EC/FP7/261868/EU//MORDRED

PY - 2016/1

Y1 - 2016/1

N2 - 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/similar to 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.githublo/pysic/Running time: Depends on the size of system. (C) 2015 Elsevier B.V. All rights reserved.

AB - 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/similar to 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.githublo/pysic/Running time: Depends on the size of system. (C) 2015 Elsevier B.V. All rights reserved.

KW - Atomistic simulations

KW - Classical potential

KW - Object oriented

KW - Python

KW - Fortran

KW - ENERGY

U2 - 10.1016/j.cpc.2015.09.010

DO - 10.1016/j.cpc.2015.09.010

M3 - Article

SN - 0010-4655

VL - 198

SP - 230

EP - 237

JO - Computer Physics Communications

JF - Computer Physics Communications

ER -

An object oriented Python interface for atomistic simulations

Abstract

Funding

Keywords

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