arXiv subjects

Jadran Vrabec

Publications and source records attributed to Jadran Vrabec.

At least 19 recordsLinked to original sources

arXiv2025

Cyclic Data Streaming on GPUs for Short Range Stencils Applied to Molecular Dynamics

In the quest for highest performance in scientific computing, we present a novel framework that relies on high-bandwidth communication between GPUs in a compute cluster. The framework offers linear scaling of performance for explicit algorithms that is only limited by the size of the dataset and the number of GPUs. Slices of the dataset propagate in a ring of processes (GPUs) from one GPU, where they are processed, to the next, which results in a parallel-in-time parallelization. The user of the framework has to write GPU kernels that implement the algorithm and provide slices of the dataset. Knowledge about the underlying parallelization strategy is not required because the communication between processes is carried out by the framework. As a case study, molecular dynamics simulation based on the Lennard-Jones potential is implemented to measure the performance for a homogeneous fluid. Single node performance and strong scaling behavior of this framework is compared to LAMMPS, which is outperformed in the strong scaling case.

cs.DC↗

arXiv2024

Scope of physics-based simulation artefacts

Data and metadata documentation requirements for explainable-AI-ready (XAIR) models and data in physics-based simulation technology are discussed by analysing different perspectives from the literature on two core aspects: First, the scope of the simulation; this category is taken to include subject matter, the objective with which the simulation is conducted, and the object of reference, i.e., the simulated physical system or process. Second, the artefacts that need to be documented in order to make data and models XAIR, and modelling and simulation workflows explainable; two CEN workshop agreements, MODA and ModGra, are compared for this purpose. As a result, minimum requirements for an ontologization of the scope of simulation artefacts are formulated, and the object-objective abstractness diagram is proposed as a tool for visualizing the landscape of use cases for physics-based simulation.

physics.comp-ph↗

arXiv2022

Connecting Entropy Scaling and Density Scaling

It is shown that the residual entropy (entropy minus that of the ideal gas at the same temperature and density) is mostly synonymous with the independent variable of density scaling, identifying a direct link between these two approaches. The two-body residual entropy is demonstrated to not be a suitable surrogate for the total residual entropy in the gas phase. The residual entropy and the effective hardness of interaction (itself a derivative at constant residual entropy) are studied for the Lennard-Jones monomer and dimer as well as a range of rigid molecular models for carbon dioxide. It is observed that the density scaling exponent is related to the two-body interactions.

physics.chem-ph↗

arXiv2020

Comparison of Macro- and Microscopic Solutions of the Riemann Problem II. Two-Phase Shock Tube

The Riemann problem is one of the basic building blocks for numerical methods in computational fluid mechanics. Nonetheless, there are still open questions and gaps in theory and modelling for situations with complex thermodynamic behavior. In this series, we compare numerical solutions of the macroscopic flow equations with molecular dynamics simulation data. To enable molecular dynamics for sufficiently large scales in time and space, we selected the truncated and shifted Lennard-Jones potential for which also highly accurate equations of state are available. A comparison of a two-phase Riemann problem is shown, which involves a liquid and a vapor phase, with an undergoing phase transition. The loss of hyperbolicity allows for the occurrence of anomalous wave structures. We successfully compare the molecular dynamics data with two macroscopic numerical solutions obtained by either assuming local phase equilibrium or by imposing a kinetic relation and allowing for metastable states.

physics.comp-ph↗

arXiv2019

Reexamination of Tolman's law and the Gibbs adsorption equation for curved interfaces

In manuscript arXiv:1703.08719 [cond-mat.soft], it was claimed that the well-known deduction of Tolman's law is not rigorous, since Tolman's argument implies that two different definitions of the surface tension, called $γ$ and $\barγ$ in the manuscript, coincide. This claim is retracted as it can be shown by free-energy minimization that $γ= \barγ$ indeed holds for the Laplace radius. Joachim Groß, Philipp Rehner, Carlos Vega, Øivind Wilhelmsen, and the anonymous reviewers of The Journal of Chemical Physics contributed to finding the mistake in the manuscript.

cond-mat.soft↗

arXiv2019

MolMod: An open access database of force fields for molecular simulations of fluids

The MolMod database is presented, which is openly accessible at http://molmod.boltzmann-zuse.de/ and contains presently intermolecular force fields for over 150 pure fluids. It was developed and is maintained by the Boltzmann-Zuse Society for Computational Molecular Engineering (BZS). The set of molecular models in the MolMod database provides a coherent framework for molecular simulations of fluids. The molecular models in the MolMod database consist of Lennard-Jones interaction sites, point charges, and point dipoles and quadrupoles, which can be equivalently represented by multiple point charges. The force fields can be exported as input files for the simulation programs ms2 and ls1 mardyn, Gromacs, and LAMMPS. To characterise the semantics associated with the numerical database content, a force-field nomenclature is introduced that can also be used in other contexts in materials modelling at the atomistic and mesoscopic levels. The models of the pure substances that are included in the data base were generally optimised such as to yield good representations of experimental data of the vapour-liquid equilibrium with a focus on the vapour pressure and the saturated liquid density. In many cases, the models also yield good predictions of caloric, transport, and interfacial properties of the pure fluids. For all models, references to the original works in which they were developed are provided. The models can be used straightforwardly for predictions of properties of fluid mixtures using established combination rules. Input errors are a major source of errors in simulations. The MolMod database contributes to reducing such errors.

physics.comp-ph↗

arXiv2015

ms2: A molecular simulation tool for thermodynamic properties, new version release

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.

cs.CE↗

arXiv2015

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

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

physics.comp-ph↗

arXiv2014

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 which 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, multi-center 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, e.g. for fluids at interfaces, as well as non-equilibrium molecular dynamics simulation of heat and mass transfer.

cs.CE↗

arXiv2013

Computational molecular engineering as an emerging technology in process engineering

The present level of development of molecular force field methods is assessed from the point of view of simulation-based engineering, outlining the immediate perspective for further development and highlighting the newly emerging discipline of Computational Molecular Engineering (CME) which makes basic research in soft matter physics fruitful for industrial applications. Within the coming decade, major breakthroughs can be reached if a research focus is placed on processes at interfaces, combining aspects where an increase in the accessible length and time scales due to massively parallel high-performance computing will lead to particularly significant improvements.

cs.DC↗

arXiv2013

Molecular modelling and simulation of electrolyte solutions, biomolecules, and wetting of component surfaces

Massively-parallel molecular dynamics simulation is applied to systems containing electrolytes, vapour-liquid interfaces, and biomolecules in contact with water-oil interfaces. Novel molecular models of alkali halide salts are presented and employed for the simulation of electrolytes in aqueous solution. The enzymatically catalysed hydroxylation of oleic acid is investigated by molecular dynamics simulation taking the internal degrees of freedom of the macromolecules into account. Thereby, Ewald summation methods are used to compute the long range electrostatic interactions. In systems with a phase boundary, the dispersive interaction, which is modelled by the Lennard-Jones potential here, has a more significant long range contribution than in homogeneous systems. This effect is accounted for by implementing the Janecek cutoff correction scheme. On this basis, the HPC infrastructure at the Steinbuch Centre for Computing was accessed and efficiently used, yielding new insights on the molecular systems under consideration.

cond-mat.soft↗

arXiv2011

Static and dynamic properties of curved vapour-liquid interfaces by massively parallel molecular dynamics simulation

Curved fluid interfaces are investigated on the nanometre length scale by molecular dynamics simulation. Thereby, droplets surrounded by a metastable vapour phase are stabilized in the canonical ensemble. Analogous simulations are conducted for cylindrical menisci separating vapour and liquid phases under confinement in planar nanopores. Regarding the emergence of nanodroplets during nucleation, a non-equilibrium phenomenon, both the non-steady dynamics of condensation processes and stationary quantities related to supersaturated vapours are considered. Results for the truncated and shifted Lennard-Jones fluid and for mixtures of quadrupolar fluids confirm the applicability of the capillarity approximation and the classical nucleation theory.

physics.comp-ph↗

arXiv2011

The 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 that defined with 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 analysed 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-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 sigma. In these simulations, the magnitudes of the excess equimolar radius and the Tolman length are shown to be smaller than sigma/2. Other methodical approaches, from which mutually contradicting findings have been reported, are critically discussed, outlining possible sources of inaccuracy.

cond-mat.soft↗

arXiv2011

Atomistic simulations of electrolyte solutions and hydrogels with explicit solvent models

Two of the most challenging tasks in molecular simulation consist in capturing the properties of systems with long-range interactions (e.g. electrolyte solutions) as well as systems containing large molecules such as hydrogels. For the development and optimization of molecular force fields and models, a large number of simulation runs have to be evaluated to obtain the sensitivity of the target properties with respect to the model parameters. The present work discusses force field development for electrolytes regarding thermodynamic properties of their aqueous solutions. Furthermore, simulations are conducted for the volume transition of hydrogels in the presence of electrolytes. It is shown that the properties of these complex systems can be captured by molecular simulation.

physics.chem-ph↗

arXiv2010

Research on the behavior of liquid fluids atop superhydrophobic gas-bubbled surfaces

Superhydrophobic surfaces play an important role in the development of new product coatings such as cars, but also in mechanical engineering, especially design of turbines and compressors. Thus a vital part of the design of these surfaces is the computational simulation of such with a special interest on variation of shape and size of minor pits grooved into plane surfaces. In the present work, the dependence of the contact angle on the fluid-wall dispersive energy is determined by molecular simulation and static as well as dynamic properties of unpolar fluids in contact with extremely rough surfaces are obtained.

physics.flu-dyn↗

arXiv2010

Molecular simulation of fluid dynamics on the nanoscale

Molecular dynamics simulation is applied to Poiseuille flow of liquid methane in planar graphite channels, covering channel diameters between 3 and 135 nm. On this length scale, a transition is found between the regime where local ordering induced by the wall dominates the entire system and larger channel diameters where the influence of boundary slip is still present, but of a more limited extent. The validity of Darcy's law for pressure-driven flow through porous media is not affected by the transition between these regimes.

cond-mat.mes-hall↗

arXiv2010

Development of models and methods for the molecular simulation of large systems and molecules

The most important factor for quantitative results in molecular dynamics simulation are well developed force fields and models. In the present work, the development of new models and the usage of force fields from the literature in large systems are presented. Both tasks lead to time consuming simulations that require massively parallel high performance computing. In the present work, new models for carbon dioxide and cyclohexanolare discussed and a new method for the model development is introduced. Force fields and models for the simulation of PNIPAAm hydrogel in pure water and sodium chloride solution are tested and verified and applied to the simulation of nucleation processes.

physics.comp-ph↗

arXiv2010

Contact angle dependence on the fluid-wall dispersive energy

Vapor-liquid 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.

cond-mat.mes-hall↗