Martin Horsch

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.

The influence of the liquid slab thickness on the planar vapor–liquid interfacial tension

One of the long standing challenges in molecular simulation is the description of interfaces. On the molecular length scale, finite size effects significantly influence the properties of the interface such as its interfacial tension, which can be reliably investigated by molecular dynamics simulation of planar vapor–liquid interfaces. For the Lennard-Jones fluid, finite size effects are examined here by varying the thickness of the liquid slab. It is found that the surface tension and density in the center of the liquid region decreases significantly for thin slabs. The influence of the slab thickness on both the liquid density and the surface tension is found to scale with 1/S3 in terms of the slab thickness S, and a linear correlation between both effects is obtained. The results corroborate the analysis of A. Malijevský, G. Jackson, J. Phys.: Condens. Matter 24 (2012) 464121, who recently detected an analogous effect for the surface tension of liquid nanodroplets.

Modification of the classical nucleation theory based on molecular simulation data for surface tension, critical nucleus size, and nucleation rate.

Nucleation in supersaturated vapor is investigated with two series of molecular-dynamics simulations in the canonical ensemble. The applied methods are (a) analysis of critical nuclei at moderate supersaturations by simulating equilibria of single droplets with surrounding vapors in small systems; (b) simulation of homogeneous nucleation during condensation with large systems containing 10(5)-10(6) particles for calculating the nucleation rate of vapors at high supersaturations. For the Lennard-Jones fluid, truncated and shifted at 2.5 times the size parameter, it is shown that the classical nucleation theory underestimates both the nucleation rate and the size of the critical nucleus. A surface property corrected modification of this theory is proposed to consistently cover data on the surface tension of the curved interface, the critical nucleus size, and the nucleation rate.

ls1 mardyn: The Massively Parallel Molecular Dynamics Code for Large Systems

The molecular dynamics simulation code ls1 mardyn is presented. It is a highly scalable code, optimized for massively parallel execution on supercomputing architectures and currently holds the world record for the largest molecular simulation with over four trillion particles. It enables the application of pair potentials to length and time scales that were previously out of scope for molecular dynamics simulation. With an efficient dynamic load balancing scheme, it delivers high scalability even for challenging heterogeneous configurations. Presently, multicenter rigid potential models based on Lennard-Jones sites, point charges, and higher-order polarities are supported. Due to its modular design, ls1 mardyn can be extended to new physical models, methods, and algorithms, allowing future users to tailor it to suit their respective needs. Possible applications include scenarios with complex geometries, such as fluids at interfaces, as well as nonequilibrium molecular dynamics simulation of heat and mass transfer.

Transport diffusivities of fluids in nanopores by non-equilibrium molecular dynamics simulation

We present a method to study fluid transport through nanoporous materials using highly efficient non-equilibrium molecular dynamics simulations. A steady flow is induced by applying an external field to the fluid particles within a small slab of the simulation cell. The external field generates a density gradient between both sides of the porous material, which in turn triggers a convective flux through the porous medium. The heat dissipated by the fluid flow is released by a Gaussian thermostat applied to the wall particles. This method is effective for studying diffusivities in a slit pore as well as more natural, complex wall geometries. The dependence of the diffusive flux on the external field sheds light on the transport diffusivities and allows a direct calculation of effective diffusivities. Both pore and fluid particle interactions are represented by coarse-grained molecular models in order to present a proof-of-concept and to retain computational efficiency in the simulations. The application of the method is demonstrated in two different scenarios, namely the effective mass transport through a slit pore and the calculation of the effective self-diffusion through this system. The method allows for a distinction between diffusive and convective contributions of the mass transport.

Contact angle of sessile drops in Lennard-Jones systems.

Molecular dynamics simulations are used for studying the contact angle of nanoscale sessile drops on a planar solid wall in a system interacting via the truncated and shifted Lennard-Jones potential. The entire range between total wetting and dewetting is investigated by varying the solid-fluid dispersive interaction energy. The temperature is varied between the triple point and the critical temperature. A correlation is obtained for the contact angle in dependence of the temperature and the dispersive interaction energy. Size effects are studied by varying the number of fluid particles at otherwise constant conditions, using up to 150,000 particles. For particle numbers below 10,000, a decrease of the contact angle is found. This is attributed to a dependence of the solid-liquid surface tension on the droplet size. A convergence to a constant contact angle is observed for larger system sizes. The influence of the wall model is studied by varying the density of the wall. The effective solid-fluid dispersive interaction energy at a contact angle of θ = 90° is found to be independent of temperature and to decrease linearly with the solid density. A correlation is developed that describes the contact angle as a function of the dispersive interaction, the temperature, and the solid density. The density profile of the sessile drop and the surrounding vapor phase is described by a correlation combining a sigmoidal function and an oscillation term.

Excess equimolar radius of liquid drops.

The curvature dependence of the surface tension is related to the excess equimolar radius of liquid drops, i.e., the deviation of the equimolar radius from the radius defined by the macroscopic capillarity approximation. Based on the Tolman [J. Chem. Phys. 17, 333 (1949)] approach and its interpretation by Nijmeijer et al. [J. Chem. Phys. 96, 565 (1991)], the surface tension of spherical interfaces is analyzed in terms of the pressure difference due to curvature. In the present study, the excess equimolar radius, which can be obtained directly from the density profile, is used instead of the Tolman length. Liquid drops of the truncated and shifted Lennard-Jones fluid are investigated by molecular dynamics simulation in the canonical ensemble, with equimolar radii ranging from 4 to 33 times the Lennard-Jones size parameter σ. In these simulations, the magnitude of the excess equimolar radius is shown to be smaller than σ/2. This suggests that the surface tension of liquid drops at the nanometer length scale is much closer to that of the planar vapor-liquid interface than reported in studies based on the mechanical route.

591 TFLOPS Multi-trillion Particles Simulation on SuperMUC

Anticipating large-scale molecular dynamics simulations (MD) in nano-fluidics, we conduct performance and scalability studies of an optimized version of the code ls1 mardyn. We present our implementation requiring only 32 Bytes per molecule, which allows us to run the, to our knowledge, largest MD simulation to date. Our optimizations tailored to the Intel Sandy Bridge processor are explained, including vectorization as well as shared-memory parallelization to make use of Hyperthreading. Finally we present results for weak and strong scaling experiments on up to 146016 Cores of SuperMUC at the Leibniz Supercomputing Centre, achieving a speed-up of 133k times which corresponds to an absolute performance of 591.2 TFLOPS.

Homogeneous nucleation in supersaturated vapors of methane, ethane, and carbon dioxide predicted by brute force molecular dynamics

Molecular dynamics (MD) simulation is applied to the condensation process of supersaturated vapors of methane, ethane, and carbon dioxide. Simulations of systems with up to a 10(6) particles were conducted with a massively parallel MD program. This leads to reliable statistics and makes nucleation rates down to the order of 10(30) m(-3) s(-1) accessible to the direct simulation approach. Simulation results are compared to the classical nucleation theory (CNT) as well as the modification of Laaksonen, Ford, and Kulmala (LFK) which introduces a size dependence of the specific surface energy. CNT describes the nucleation of ethane and carbon dioxide excellently over the entire studied temperature range, whereas LFK provides a better approach to methane at low temperatures.

Contact Angle Dependence on the Fluid−Wall Dispersive Energy

Menisci of the truncated and shifted Lennard-Jones fluid between parallel planar walls are investigated by molecular dynamics simulation. Thereby, the characteristic energy of the unlike dispersive interaction between fluid molecules and wall atoms is systematically varied to determine its influence on the contact angle. The temperature is varied as well, covering most of the range between the triple-point temperature and the critical temperature of the bulk fluid. The transition between obtuse and acute angles is found to occur at a temperature-independent magnitude of the fluid-wall dispersive interaction energy. On the basis of the present simulation results, fluid-wall interaction potentials can be adjusted to contact angle measurements.