%0 Journal Article %1 Deublein20112350 %A Deublein, Stephan %A Eckl, Bernhard %A Stoll, Jürgen %A Lishchuk, Sergey V. %A Guevara-Carrion, Gabriela %A Glass, Colin W. %A Merker, Thorsten %A Bernreuther, Martin %A Hasse, Hans %A Vrabec, Jadran %D 2011 %J Computer Physics Communications %K Carlo Monte chemistry dynamics fortran molecular simulation software %N 11 %P 2350 - 2367 %R 10.1016/j.cpc.2011.04.026 %T ms2: A molecular simulation tool for thermodynamic properties %U http://www.sciencedirect.com/science/article/pii/S0010465511002025 %V 182 %X This work presents the molecular simulation program ms2 that is designed for the calculation of thermodynamic properties of bulk fluids in equilibrium consisting of small electro-neutral molecules. ms2 features the two main molecular simulation techniques, molecular dynamics (MD) and Monte-Carlo. It supports the calculation of vapor-liquid equilibria of pure fluids and multi-component mixtures described by rigid molecular models on the basis of the grand equilibrium method. Furthermore, it is capable of sampling various classical ensembles and yields numerous thermodynamic properties. To evaluate the chemical potential, Widommodifier letter apostrophes test molecule method and gradual insertion are implemented. Transport properties are determined by equilibrium MD simulations following the Green-Kubo formalism. ms2 is designed to meet the requirements of academia and industry, particularly achieving short response times and straightforward handling. It is written in Fortran90 and optimized for a fast execution on a broad range of computer architectures, spanning from single processor PCs over PC-clusters and vector computers to high-end parallel machines. The standard Message Passing Interface (MPI) is used for parallelization and ms2 is therefore easily portable to different computing platforms. Feature tools facilitate the interaction with the code and the interpretation of input and output files. The accuracy and reliability of ms2 has been shown for a large variety of fluids in preceding work.Program summary Program title: ms2 Catalogue identifier: AEJF_v1_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEJF_v1_0.html Program obtainable from: CPC Program Library, Queenmodifier letter apostrophes University, Belfast, N. Ireland Licensing provisions: Special Licence supplied by the authors No. of lines in distributed program, including test data, etc.: 82thin space794 No. of bytes in distributed program, including test data, etc.: 793thin space705 Distribution format: tar.gz Programming language: Fortran90 Computer: The simulation tool ms2 is usable on a wide variety of platforms, from single processor machines over PC-clusters and vector computers to vector-parallel architectures. (Tested with Fortran compilers: gfortran, Intel, PathScale, Portland Group and Sun Studio.) Operating system: Unix/Linux, Windows Has the code been vectorized or parallelized?: Yes. Message Passing Interface (MPI) protocol Scalability. Excellent scalability up to 16 processors for molecular dynamics and >512 processors for Monte-Carlo simulations. RAM: ms2 runs on single processors with 512 MB RAM. The memory demand rises with increasing number of processors used per node and increasing number of molecules. Classification: 7.7, 7.9, 12 External routines: Message Passing Interface (MPI) Nature of problem: Calculation of application oriented thermodynamic properties for rigid electro-neutral molecules: vapor-liquid equilibria, thermal and caloric data as well as transport properties of pure fluids and multi-component mixtures. Solution method: Molecular dynamics, Monte-Carlo, various classical ensembles, grand equilibrium method, Green-Kubo formalism. Restrictions: No. The system size is user-defined. Typical problems addressed by ms2 can be solved by simulating systems containing typically 2000 molecules or less. Unusual features: 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 problem set, the system size and the number of processes used in the simulation. Running four processes on a "Nehalem" processor, simulations calculating VLE data take between two and twelve hours, calculating transport properties between six and 24 hours.

@article{Deublein20112350, abstract = {This work presents the molecular simulation program ms2 that is designed for the calculation of thermodynamic properties of bulk fluids in equilibrium consisting of small electro-neutral molecules. ms2 features the two main molecular simulation techniques, molecular dynamics (MD) and Monte-Carlo. It supports the calculation of vapor-liquid equilibria of pure fluids and multi-component mixtures described by rigid molecular models on the basis of the grand equilibrium method. Furthermore, it is capable of sampling various classical ensembles and yields numerous thermodynamic properties. To evaluate the chemical potential, Widom[modifier letter apostrophe]s test molecule method and gradual insertion are implemented. Transport properties are determined by equilibrium MD simulations following the Green-Kubo formalism. ms2 is designed to meet the requirements of academia and industry, particularly achieving short response times and straightforward handling. It is written in Fortran90 and optimized for a fast execution on a broad range of computer architectures, spanning from single processor PCs over PC-clusters and vector computers to high-end parallel machines. The standard Message Passing Interface (MPI) is used for parallelization and ms2 is therefore easily portable to different computing platforms. Feature tools facilitate the interaction with the code and the interpretation of input and output files. The accuracy and reliability of ms2 has been shown for a large variety of fluids in preceding work.Program summary Program title: ms2 Catalogue identifier: AEJF_v1_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEJF_v1_0.html Program obtainable from: CPC Program Library, Queen[modifier letter apostrophe]s University, Belfast, N. Ireland Licensing provisions: Special Licence supplied by the authors No. of lines in distributed program, including test data, etc.: 82[thin space]794 No. of bytes in distributed program, including test data, etc.: 793[thin space]705 Distribution format: tar.gz Programming language: Fortran90 Computer: The simulation tool ms2 is usable on a wide variety of platforms, from single processor machines over PC-clusters and vector computers to vector-parallel architectures. (Tested with Fortran compilers: gfortran, Intel, PathScale, Portland Group and Sun Studio.) Operating system: Unix/Linux, Windows Has the code been vectorized or parallelized?: Yes. Message Passing Interface (MPI) protocol Scalability. Excellent scalability up to 16 processors for molecular dynamics and >512 processors for Monte-Carlo simulations. RAM: ms2 runs on single processors with 512 MB RAM. The memory demand rises with increasing number of processors used per node and increasing number of molecules. Classification: 7.7, 7.9, 12 External routines: Message Passing Interface (MPI) Nature of problem: Calculation of application oriented thermodynamic properties for rigid electro-neutral molecules: vapor-liquid equilibria, thermal and caloric data as well as transport properties of pure fluids and multi-component mixtures. Solution method: Molecular dynamics, Monte-Carlo, various classical ensembles, grand equilibrium method, Green-Kubo formalism. Restrictions: No. The system size is user-defined. Typical problems addressed by ms2 can be solved by simulating systems containing typically 2000 molecules or less. Unusual features: 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 problem set, the system size and the number of processes used in the simulation. Running four processes on a "Nehalem" processor, simulations calculating VLE data take between two and twelve hours, calculating transport properties between six and 24 hours.}, added-at = {2011-08-03T03:07:53.000+0200}, author = {Deublein, Stephan and Eckl, Bernhard and Stoll, Jürgen and Lishchuk, Sergey V. and Guevara-Carrion, Gabriela and Glass, Colin W. and Merker, Thorsten and Bernreuther, Martin and Hasse, Hans and Vrabec, Jadran}, biburl = {https://www.bibsonomy.org/bibtex/28cddb62047f22e7639f897706e5dfce3/drmatusek}, description = {ScienceDirect - Computer Physics Communications : ms2: A molecular simulation tool for thermodynamic properties}, doi = {10.1016/j.cpc.2011.04.026}, interhash = {f68a47c84ad5736b7fdab5140322363c}, intrahash = {8cddb62047f22e7639f897706e5dfce3}, issn = {0010-4655}, journal = {Computer Physics Communications}, keywords = {Carlo Monte chemistry dynamics fortran molecular simulation software}, month = {November}, number = 11, pages = {2350 - 2367}, timestamp = {2012-10-05T04:51:40.000+0200}, title = {ms2: A molecular simulation tool for thermodynamic properties}, url = {http://www.sciencedirect.com/science/article/pii/S0010465511002025}, volume = 182, year = 2011 }