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

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

Keywords

Atomistic simulations
Classical potential
Object oriented
Python
Fortran
ENERGY

Access to Document

10.1016/j.cpc.2015.09.010

Cite this

@article{7a54f2f222554457b7679844489236a1,

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

Keywords

Access to Document

Fingerprint

Cite this