Gábor Rutkai

ms2: 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 summary Program title: m s 2 Catalogue identifier: AEJF_v2_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEJF_v2_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.: 50375 No. of bytes in distributed program, including test data, etc.: 345786 Distribution format: tar.gz Programming language: Fortran90. Computer: The simulation program m s 2 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: m s 2 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_0 Journal reference of previous version: Comput. Phys. Comm. 182 (2011) 2350 Does 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 formalism Reasons 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 m s 2 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 m s 2 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.

Equation of State for the Lennard-Jones Fluid

An empirical equation of state correlation is proposed for the Lennard-Jones model fluid. The equation in terms of the Helmholtz energy is based on a large molecular simulation data set and thermal virial coefficients. The underlying data set consists of directly simulated residual Helmholtz energy derivatives with respect to temperature and density in the canonical ensemble. Using these data introduces a new methodology for developing equations of state from molecular simulation. The correlation is valid for temperatures 0.5 < T/Tc < 7 and pressures up to p/pc = 500. Extensive comparisons to simulation data from the literature are made. The accuracy and extrapolation behavior are better than for existing equations of state.

Communication: Fundamental equation of state correlation with hybrid data sets

A strategy is proposed for empirical fundamental equation of state correlations for pure fluids on the basis of hybrid data sets, composed of experimental and molecular simulation data. Argon and hydrogen chloride are used as examples.

Long-range correction for multi-site Lennard-Jones models and planar interfaces

A slab-based long-range correction (LRC) approach for multi-site Lennard-Jones models is presented for systems with a planar film geometry that is based on the work by Janeček [J. Phys. Chem. B 110: 6264 (2006)]. It is efficient because it relies on a centre-of-mass cut-off scheme and scales in terms of numerics almost perfectly with the molecule number. For validation, a series of simulations with the two-centre Lennard-Jones model fluid, carbon dioxide and cyclohexane is carried out. The results of the present approach, a site-based LRC and simulations without any LRC are compared with respect to the saturated liquid density and the surface tension. The present simulation results exhibit only a weak dependence on the cut-off radius, indicating a high accuracy of the implemented LRC.

Comparative study of the Grüneisen parameter for 28 pure fluids

The Grüneisen parameter γG is widely used for studying thermal properties of solids at high pressure and also has received increasing interest in different applications of non-ideal fluid dynamics. Because there is a lack of systematic studies of the Grüneisen parameter in the entire fluid region, this study aims to fill this gap. Grüneisen parameter data from molecular modelling and simulation are reported for 28 pure fluids and are compared with results calculated from fundamental equations of state that are based on extensive experimental data sets. We show that the Grüneisen parameter follows a general density-temperature trend and characterize the fluid systems by specifying a span of minimum and maximum values of γG. Exceptions to this trend can be found for water.

Thermodynamic correlation of molecular simulation data

Strategies to fit molecular simulation data-sets to low parameter fundamental equation of state correlations are reported. The Lennard-Jones model system truncated and shifted at interatomic distance rc/σ = 2.5 is used as an example. Homogeneous fluid states, vapour–liquid equilibrium including estimation of the critical point, and the Joule–Thomson inversion curve are investigated. The results suggest that small molecular simulation data-sets at homogeneous states are sufficient to provide consistent thermodynamic information over large portions of the fluid state.

How well does the Lennard-Jones potential represent the thermodynamic properties of noble gases?

ABSTRACT The Lennard-Jones potential as well as its truncated and shifted (rc = 2.5σ) variant are applied to the noble gases neon, argon, krypton, and xenon. These models are comprehensively compared with the currently available experimental knowledge in terms of vapour pressure, saturated liquid density, as well as thermodynamic properties from the single phase fluid regions including density, speed of sound, and isobaric heat capacity data. The expectation that these potentials exhibit a more modest performance for neon as compared to argon, krypton, and xenon due to increasing quantum effects does not seem to hold for the investigated properties. On the other hand, the assumption that the truncated and shifted (rc = 2.5σ) variant of the Lennard-Jones potential may have shortcomings because the long range interactions are entirely neglected beyond the cut-off radius rc, are supported by the present findings for the properties from the single phase fluid regions. For vapour pressure and saturated liquid density such a clear assessment cannot be made.

Assessing the accuracy of improved force-matched water models derived from Ab initio molecular dynamics simulations.

The accuracy of water models derived from ab initio molecular dynamics simulations by means on an improved force‐matching scheme is assessed for various thermodynamic, transport, and structural properties. It is found that although the resulting force‐matched water models are typically less accurate than fully empirical force fields in predicting thermodynamic properties, they are nevertheless much more accurate than generally appreciated in reproducing the structure of liquid water and in fact superseding most of the commonly used empirical water models. This development demonstrates the feasibility to routinely parametrize computationally efficient yet predictive potential energy functions based on accurate ab initio molecular dynamics simulations for a large variety of different systems.

Surface Tension, Large Scale Thermodynamic Data Generation and Vapor-Liquid Equilibria of Real Compounds

The surface tension of oxygen and nitrogen was calculated using molecular dynamics simulation. Due to the inhomogeneity of the system, the long range correction approach of Janecek [1] was used. The results regarding the temperature dependence of the surface tension were compared to simulation data by Neyt et al. [2] and experimental data.

Equation of state for 1,2-dichloroethane based on a hybrid data set

ABSTRACT A fundamental equation of state in terms of the Helmholtz energy is presented for 1,2-dichloroethane. Due to a narrow experimental database, not only laboratory measurements but also molecular simulation data are applied to the fitting procedure. The present equation of state is valid from the triple point up to 560 K for pressures of up to 100 MPa. The accuracy of the equation is assessed in detail. Furthermore, a reasonable extrapolation behaviour is verified.