Formula omitted]: A molecular simulation tool for thermodynamic properties, new version release

Abstract

A new version release (2.0) of the molecular simulation tool ms2 [S. Deublein et al., Comput. Phys. Commun. 182 (2011) 2350] is presented. Version 2.0 of ms2 features a hybrid parallelization based on MPI and OpenMP for molecular dynamics simulation to achieve higher scalability. Furthermore, the formalism by Lustig [R. Lustig, Mol. Phys. 110 (2012) 3041] is implemented, allowing for a systematic sampling of Massieu potential derivatives in a single simulation run. Moreover, the Green–Kubo formalism is extended for the sampling of the electric conductivity and the residence time. To remove the restriction of the preceding version to electro-neutral molecules, Ewald summation is implemented to consider ionic long range interactions. Finally, the sampling of the radial distribution function is added. Program summaryProgram title:ms2Catalogue identifier: AEJF_v2_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEJF_v2_0.htmlProgram obtainable from: CPC Program Library, Queen’s University, Belfast, N. IrelandLicensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.htmlNo. of lines in distributed program, including test data, etc.: 50375No. of bytes in distributed program, including test data, etc.: 345786Distribution format: tar.gzProgramming language: Fortran90.Computer: The simulation program ms2 is usable on a wide variety of platforms, from single processor machines to modern supercomputers.Operating system: Unix/Linux.Has the code been vectorized or parallelized?: Yes: Message Passing Interface (MPI) protocol and OpenMP Scalability is up to 2000 cores.RAM:ms2 runs on single cores with 512 MB RAM. The memory demand rises with increasing number of cores used per node and increasing number of molecules.Classification: 7.7, 7.9, 12.External routines: Message Passing Interface (MPI)Catalogue identifier of previous version: AEJF_v1_0Journal reference of previous version: Comput. Phys. Comm. 182 (2011) 2350Does the new version supersede the previous version?: Yes.Nature of problem: Calculation of application oriented thermodynamic properties for fluids consisting of rigid molecules: vapor–liquid equilibria of pure fluids and multi-component mixtures, thermal and caloric data as well as transport properties.Solution method: Molecular dynamics, Monte Carlo, various classical ensembles, grand equilibrium method, Green–Kubo formalism, Lustig formalismReasons for new version: The source code was extended to introduce new features.Summary of revisions: The new features of Version 2.0 include: Hybrid parallelization based on MPI and OpenMP for molecular dynamics simulation; Ewald summation for long range interactions; sampling of Massieu potential derivatives; extended Green–Kubo formalism for the sampling of the electric conductivity and the residence time; radial distribution function.Restrictions: None. The system size is user-defined. Typical problems addressed by ms2 can be solved by simulating systems containing typically 1000–4000 molecules.Unusual features: Auxiliary feature tools are available for creating input files, analyzing simulation results and visualizing molecular trajectories.Additional comments: Sample makefiles for multiple operation platforms are provided. Documentation is provided with the installation package and is available at http://www.ms-2.de.Running time: The running time of ms2 depends on the specified problem, the system size and the number of processes used in the simulation. E.g. running four processes on a “Nehalem” processor, simulations calculating vapor–liquid equilibrium data take between two and 12 hours, calculating transport properties between six and 24 hours. Note that the examples given above stand for the total running time as there is no post-processing of any kind involved in property calculations.