ms2: A molecular simulation tool for thermodynamic properties

This work presents the molecular simulation programms2 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’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 straightf orward 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 PCclusters and vector computers to high-end parallel machines. The standard Message Passing Interface (MPI) is used for parallelization and ms2 is therefore easily portable onto a broad range of computing platforms. Auxiliary feature tools facilitate the interaction with the code and t he interpretation of input and output files. The accuracy and reliability of ms2 has been shown for a large variety of fluids in preceding work.

[1]  J. D. Olson,et al.  The second industrial fluid properties simulation challenge , 2005 .

[2]  A. Amerio,et al.  Physikalische Zeitschrift , 1900 .

[3]  Alexander P. Lyubartsev,et al.  Free energy calculations for Lennard-Jones systems and water using the expanded ensemble method A Monte Carlo and molecular dynamics simulation study , 1994 .

[4]  L. F. Rull,et al.  Computer simulation of vapor–liquid equilibria of linear quadrupolar fluids. Departures from the principle of corresponding states , 1994 .

[5]  Hans Hasse,et al.  On the application of force fields for predicting a wide variety of properties: Ethylene oxide as an example , 2008 .

[6]  Berend Smit,et al.  Understanding molecular simulation: from algorithms to applications , 1996 .

[7]  E. M.,et al.  Statistical Mechanics , 2021, Manual for Theoretical Chemistry.

[8]  M. Mezei,et al.  Computer simulation study of liquid CH2F2 with a new effective pair potential model , 1999 .

[9]  H. Hasse,et al.  An optimised molecular model for ammonia , 2008, 0904.4618.

[10]  H. Berendsen,et al.  A systematic study of water models for molecular simulation: Derivation of water models optimized for use with a reaction field , 1998 .

[11]  Journal of Chemical Physics , 1932, Nature.

[12]  Bruna Donatelli.  Comptes rendues hebdomadaires des séances de l'Académie des Sciences , 1982 .

[13]  J. I. Siepmann,et al.  Development of the TraPPE-UA force field for ethylene oxide , 2008 .

[14]  Michael M. Resch,et al.  High performance computing in science and engineering , 2005, 17th International Symposium on Computer Architecture and High Performance Computing (SBAC-PAD'05).

[15]  emontmej,et al.  High Performance Computing , 2003, Lecture Notes in Computer Science.

[16]  Per Linse,et al.  Ewald summation and reaction field methods for potentials with atomic charges, dipoles, and polarizabilities , 2000 .

[17]  Sugata P. Tan,et al.  Recent Advances and Applications of Statistical Associating Fluid Theory , 2008 .

[18]  H. G. Petersen,et al.  Error estimates on averages of correlated data , 1989 .

[19]  D. D. Yue,et al.  Theory of Electric Polarization , 1974 .

[20]  Rolf Lustig,et al.  Angle-average for the powers of the distance between two separated vectors , 1988 .

[21]  Proceedings of the Physical Society , 1948, Nature.

[22]  V. Vacek,et al.  Vapour-liquid equilibria for dipolar two-centre Lennard-Jones fluids by Gibbs-Duhem integration , 1997 .

[23]  Othmar Steinhauser,et al.  Reaction field simulation of water , 1982 .

[24]  Donald R Paul,et al.  Industrial & Engineering Chemistry Research: Looking Back , 2013 .

[25]  C. F. Curtiss,et al.  Molecular Theory Of Gases And Liquids , 1954 .

[26]  J. W.,et al.  The Journal of Physical Chemistry , 1900, Nature.

[27]  Melville S. Green,et al.  Markoff Random Processes and the Statistical Mechanics of Time‐Dependent Phenomena. II. Irreversible Processes in Fluids , 1954 .

[28]  A. Penzkofer,et al.  CHEMICAL PHYSICS LETTERS , 1976 .

[29]  A. Klamt,et al.  COSMO-RS: a novel and efficient method for the a priori prediction of thermophysical data of liquids , 2000 .

[30]  Alexander P. Lyubartsev,et al.  M.DynaMix – a scalable portable parallel MD simulation package for arbitrary molecular mixtures , 2000 .

[31]  Rajamani Krishna,et al.  The Darken Relation for Multicomponent Diffusion in Liquid Mixtures of Linear Alkanes: An Investigation Using Molecular Dynamics (MD) Simulations , 2005 .

[32]  Message Passing Interface Forum.  MPI: A message - passing interface standard , 1994 .

[33]  J. D. Olson,et al.  Industrial Needs in Physical Properties , 2003 .

[34]  H. Hasse,et al.  Prediction of ternary vapor–liquid equilibria for 33 systems by molecular simulation , 2009, 0906.3170.

[35]  B. Widom,et al.  Some Topics in the Theory of Fluids , 1963 .

[36]  Keith E. Gubbins,et al.  Theory of molecular fluids , 1984 .

[37]  R. Kubo.  Statistical-Mechanical Theory of Irreversible Processes : I. General Theory and Simple Applications to Magnetic and Conduction Problems , 1957 .

[38]  Hans Hasse,et al.  Molekulare Modellierung und Simulation für das Prozessdesign , 2008 .

[39]  C. Hoheisel.  Transport properties of molecular liquids , 1994 .

[40]  G. G. Stokes.  "J." , 1890, The New Yale Book of Quotations.

[42]  Berend Smit,et al.  Understanding Molecular Simulation , 2001 .

[43]  H. Hasse,et al.  Chemical potential of quadrupolar two-centre Lennard-Jones fluids by gradual insertion , 2002, 0904.4771.

[44]  D. C. Rapaport,et al.  The Art of Molecular Dynamics Simulation , 1997 .

[45]  Steve Plimpton,et al.  Fast parallel algorithms for short-range molecular dynamics , 1993 .

[46]  W. Stockmayer.  Liquids and Liquid Mixtures. , 1961 .

[47]  N. Metropolis,et al.  Equation of State Calculations by Fast Computing Machines , 1953, Resonance.

[48]  B. Rumpf,et al.  A simple effective pair potential for the molecular simulation of the thermodynamic properties of ammonia , 1999 .

[49]  A. Lyubartsev,et al.  New approach to Monte Carlo calculation of the free energy: Method of expanded ensembles , 1992 .

[50]  P. Lugol.  Annalen der Physik , 1906 .

[51]  K. Shing,et al.  Henry constants in non-ideal fluid mixtures , 1988 .

[52]  Howard J. M. Hanley,et al.  Transport phenomena in fluids , 1969 .

[53]  Carsten Kutzner,et al.  GROMACS 4:  Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation. , 2008, Journal of chemical theory and computation.

[54]  小谷 正雄.  日本物理学会誌及びJournal of the Physical Society of Japanの月刊について , 1955 .

[55]  J. Banavar,et al.  Computer Simulation of Liquids , 1988 .

[56]  J. S. Marshall,et al.  Molecular Theory of Gases , 1967 .

[57]  P. Cummings,et al.  Fluid phase equilibria , 2005 .

[58]  J. Calais.  Theory of molecular fluids. Volume 1: Fundamentals. By C. G. Gray and K. E. Gubbins, The Clarendon Press, Oxford University Press, New York, 1984 , 1990 .

[59]  J. J. Freire,et al.  DETERMINATION OF THE POTENTIAL PARAMETERS OF A SITE MODEL FROM CALCULATIONS OF SECOND VIRIAL COEFFICIENTS OF LINEAR AND BRANCHED ALKANES , 1997 .

[60]  Hans Hasse,et al.  Hydrogen bonding of methanol in supercritical CO2: comparison between 1H NMR spectroscopic data and molecular simulation results. , 2007, The journal of physical chemistry. B.

[61]  John B. Shoven,et al.  I , Edinburgh Medical and Surgical Journal.

[62]  H. Hasse,et al.  Prediction of transport properties by molecular simulation: methanol and ethanol and their mixture. , 2008, The journal of physical chemistry. B.

[63]  H. Hasse,et al.  Grand Equilibrium: vapour-liquid equilibria by a new molecular simulation method , 2002, 0905.0612.

[64]  Ivo Nezbeda,et al.  A New Version of the Insertion Particle Method for Determining the Chemical Potential by Monte Carlo Simulation , 1991 .

[65]  A. Klamt.  Conductor-like Screening Model for Real Solvents: A New Approach to the Quantitative Calculation of Solvation Phenomena , 1995 .

[66]  P. P. Ewald.  Die Berechnung optischer und elektrostatischer Gitterpotentiale , 1921 .

[67]  M. Lísal,et al.  Accurate vapour–liquid equilibrium calculations for complex systems using the reaction Gibbs ensemble Monte Carlo simulation method , 2001 .

[68]  J. Haile,et al.  The influence of unlike molecule interaction parameters on liquid mixture excess properties , 1989 .

[69]  Michael M. Resch,et al.  High Performance Computing in Science and Engineering '08 - Transactions of the High Performance Computing Center, Stuttgart (HLRS) 2008 , 2008, High Performance Computing in Science and Engineering.

[70]  Hans Hasse,et al.  Molecular models for 267 binary mixtures validated by vapor–liquid equilibria: A systematic approach , 2009 .

[71]  H. A. Lorentz.  Ueber die Anwendung des Satzes vom Virial in der kinetischen Theorie der Gase , 1881 .

[72]  E. Ungureanu,et al.  Molecular Physics , 2008, Nature.

[73]  M.G.B. Drew,et al.  The art of molecular dynamics simulation , 1996 .

[74]  A. Barton.  The dynamic liquid state , 1974 .

[75]  Philippe Ungerer,et al.  New optimization method for intermolecular potentials: Optimization of a new anisotropic united atoms potential for olefins: Prediction of equilibrium properties , 2003 .