An object oriented Python interface for atomistic simulations

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 func...

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Published in:	Computer physics communications Vol. 198; pp. 230 - 237
Main Authors:	Hynninen, T., Himanen, L., Parkkinen, V., Musso, T., Corander, J., Foster, A.S.
Format:	Journal Article
Language:	English
Published:	Elsevier B.V 01-01-2016
Subjects:	Atomistic simulations Classical potential Computer simulation FORTRAN Mathematical models Object oriented Operating systems Programming languages Python Summaries UNIX (operating system) Windows (computer programs) Atomistic simulations Classical potential Object oriented Python Fortran
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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 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/~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.github.io/pysic/ Running time: Depends on the size of system.
AbstractList	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 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/~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.github.io/pysic/ Running time: Depends on the size of system. 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/~m-mat/MT/VERSIONS/FORTRAN/m t 95.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.github.io/pysic/ Running time: Depends on the size of system.
Author	Himanen, L. Parkkinen, V. Corander, J. Foster, A.S. Musso, T. Hynninen, T.
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