arXiv subjects

James Vance

Publications and source records attributed to James Vance.

3 recordsLinked to original sources

arXiv2026

ESPResSo++: A Fast and Extensible Molecular Simulation Package for Coarse-Grained Models

ESPResSo++ is an open-source software package for molecular dynamics (MD) simulations with a particular emphasis on coarse-grained (CG) models of soft matter systems. Written in C++ with a flexible Python interface, it is designed for high-performance computing (HPC) environments and supports massively parallel simulations through MPI. The package enables simulations of polymers, membranes, colloids and complex fluids with a wide range of interaction models and advanced algorithms.

cond-mat.soft↗

arXiv2021

Implementation and Parallel Optimization of the Lees-Edwards Boundary Condition in ESPResSo++

The Lees-Edwards boundary condition (LEbc) was first developed by Lees and Edwards in 1970s. The current implementation of LEbc in the ESPResSo++ MD software package provides a new possibility in simulating molecular or coarse grained systems under such non-equilibrium conditions, namely by introducing a shear flow which has potential applications in high-speed fluids, thermoplastic and other non-equilibrium processes etc. Using the LEbc code, shear flow simulations were carried out in model systems such as the Lennard-Jones fluids and the Kremer-Grest polymer melts. Some important physical properties and phenomena, including the linear profiles of shear velocities, non-layered density distribution and shear thinning, are successfully reproduced or captured. Results also show in good agreement with those from the previous literature even with unphysical simulation conditions, which on the other side gives a solid validation to our implementation of LEbc. Regarding the high performance computing (HPC) environments, we considered in depth and paid efforts on the parallelization of the LEbc code in ESPResSo++. By this, a modified scheme for data communication has been introduced within the framework of the domain decomposition. The benchmarks show a linear and good scaling for simulations which are parallelized up to 1024 processors in supercomputer systems.

physics.comp-ph↗

arXiv2021

Code modernization strategies for short-range non-bonded molecular dynamics simulations

Modern HPC systems are increasingly relying on greater core counts and wider vector registers. Thus, applications need to be adapted to fully utilize these hardware capabilities. One class of applications that can benefit from this increase in parallelism are molecular dynamics simulations. In this paper, we describe our efforts at modernizing the ESPResSo++ molecular dynamics simulation package by restructuring its particle data layout for efficient memory accesses and applying vectorization techniques to benefit the calculation of short-range non-bonded forces, which results in an overall three times speedup and serves as a baseline for further optimizations. We also implement fine-grained parallelism for multi-core CPUs through HPX, a C++ runtime system which uses lightweight threads and an asynchronous many-task approach to maximize concurrency. Our goal is to evaluate the performance of an HPX-based approach compared to the bulk-synchronous MPI-based implementation. This requires the introduction of an additional layer to the domain decomposition scheme that defines the task granularity. On spatially inhomogeneous systems, which impose a corresponding load-imbalance in traditional MPI-based approaches, we demonstrate that by choosing an optimal task size, the efficient work-stealing mechanisms of HPX can overcome the overhead of communication resulting in an overall 1.4 times speedup compared to the baseline MPI version.

cs.DC↗