Update 0.2 to “pysimm: A python package for simulation of molecular systems”

Alexander G. Demidov; Michael E. Fortunato; Coray M. Colina

SoftwareX (Jan 2018)

Update 0.2 to “pysimm: A python package for simulation of molecular systems”

Alexander G. Demidov,
Michael E. Fortunato,
Coray M. Colina

Affiliations

Alexander G. Demidov: Department of Chemistry, University of Florida, Gainesville FL 32611, United States
Michael E. Fortunato: Department of Chemistry, University of Florida, Gainesville FL 32611, United States
Coray M. Colina: Department of Chemistry, University of Florida, Gainesville FL 32611, United States; Department of Materials Science and Engineering and Nuclear Engineering, University of Florida, Gainesville, FL 32611, United States; Corresponding author at: Department of Chemistry, University of Florida, Gainesville, FL 32611, USA.

Journal volume & issue: Vol. 7
pp. 70 – 73

Abstract

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An update to the pysimm Python molecular simulation API is presented. A major part of the update is the implementation of a new interface with CASSANDRA — a modern, versatile Monte Carlo molecular simulation program. Several significant improvements in the LAMMPS communication module that allow better and more versatile simulation setup are reported as well. An example of an application implementing iterative CASSANDRA–LAMMPS interaction is illustrated. Keywords: Amorphous polymers, Molecular dynamics simulations, Monte Carlo simulations

Published in SoftwareX

ISSN: 2352-7110 (Online)
Publisher: Elsevier
Country of publisher: Netherlands
LCC subjects: Science: Mathematics: Instruments and machines: Electronic computers. Computer science: Computer software
Website: http://www.journals.elsevier.com/softwarex/

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