Related papers: A portable code for dissipative particle dynamics …
We present the implementation of two advanced capillary bridge approximations within the Discrete Element Method (DEM) framework of the open-source code MercuryDPM. While MercuryDPM already includes a simplified version of the Willett…
Recent results on supercomputers show that beyond 65K cores, the efficiency of molecular dynamics simulations of interfacial systems decreases significantly. In this paper, we introduce a dynamic cutoff method (DCM) for interfacial systems…
A massively parallel simulation code, called \textit{dHybrid}, has been developed to perform global scale studies of space plasma interactions. This code is based on an explicit hybrid model; the numerical stability and parallel scalability…
We present the Fortran code SIMLA, which is designed for the study of charged particle dynamics in laser and other background fields. This can be done classically via the Landau-Lifshitz equation, or alternatively, via the simulation of…
ParticLS (\emph{Partic}le \emph{L}evel \emph{S}ets) is a software library that implements the discrete element method (DEM) and meshfree methods. ParticLS tracks the interaction between individual particles whose geometries are defined by…
Dissipative particle dynamics (DPD) belongs to a class of models and computational algorithms developed to address mesoscale problems in complex fluids and soft matter in general. It is based on the notion of particles that represent…
In this talk I discuss the general question of the portability of Molecular Dynamics codes for diffusive systems on parallel computers of the APE family. The intrinsic single precision arithmetics of the today available APE platforms does…
Recent developments in many-body potential energy representation via deep learning have brought new hopes to addressing the accuracy-versus-efficiency dilemma in molecular simulations. Here we describe DeePMD-kit, a package written in…
Molecular dynamics (MD) simulation is a powerful computational tool to study the behavior of macromolecular systems. But many simulations of this field are limited in spatial or temporal scale by the available computational resource. In…
The complexity of combustion simulations demands the latest high-performance computing tools to accelerate its time-to-solution results. A current trend on HPC systems is the utilization of CPUs with SIMD or vector extensions to exploit…
Dynamic programming (DP) is a fundamental and powerful algorithmic paradigm taught in most undergraduate (and many graduate) algorithms classes. DP problems are challenging for many computer science students because they require identifying…
Warm dense matter systems created in the laboratory are highly dynamical. In such cases electron dynamics is often needed to accurately simulate the evolution and properties of the system. Large systems force one to make simple…
We present a new scalable algorithm for short-range molecular dynamics simulations on distributed memory MIMD multicomputer based on a message-passing multi-cell approach. We have implemented the algorithm on the Connection Machine 5 (CM-5)…
We develop a Python-based open-source package to analyze the results stemming from ab initio molecular-dynamics simulations of fluids. The package is best suited for applications on natural systems, like silicate and oxide melts,…
The formation of the large-scale structure, the evolution and distribution of galaxies, quasars, and dark matter on cosmological scales, requires numerical simulations. Differentiable simulations provide gradients of the cosmological…
We present the first open-source, GPU-based code for complex plasmas. The code, OpenDust, aims to provide researchers both experimenters and theorists user-friendly and high-performance tool for self-consistent calculation forces, acting on…
Multi-scale computer simulations combine the computationally efficient classical algorithms with more expensive but also more accurate ab-initio quantum mechanical algorithms. This work describes one implementation of multi-scale…
There exist methods for determining effective conservative interactions in coarse grained particle based mesoscopic simulations. The resulting models can be used to capture thermal equilibrium behavior, but in the model system we study do…
Dissipative Particle Dynamics (DPD) is a popular simulation model for investigating hydrodynamic behavior of systems with non-negligible equilibrium thermal fluctuations. DPD employs soft core repulsive interactions between the system…
MuSim is a new user-friendly program designed to interface to many different particle simulation codes, regardless of their data formats or geometry descriptions. It presents the user with a compelling graphical user interface that includes…