Related papers: The Multiple Time-Stepping Method for 3-Body Inter…
Parallel computing is a standard approach to achieving high-performance computing (HPC). Three commonly used methods to implement parallel computing include: 1) applying multithreading technology on single-core or multi-core CPUs; 2)…
We present our recent code modernizations of the of the ab initio molecular dynamics program CPMD (www.cpmd.org) with a special focus on the ultra-soft pseudopotential (USPP) code path. Following the internal instrumentation of CPMD, all…
In this paper we consider the problem of identifying intersections between two sets of d-dimensional axis-parallel rectangles. This is a common problem that arises in many agent-based simulation studies, and is of central importance in the…
The problem of counting collisions or interactions is common in areas as computer graphics and scientific simulations. Since it is a major bottleneck in applications of these areas, a lot of research has been carried out on such subject,…
In molecular dynamics (MD), systems are molecules made up of atoms, and the aim is to determine their evolution over time. MD is based on a numerical resolution algorithm, whose role is to apply the forces generated by the various…
Molecular Dynamics (MD) codes predict the fundamental properties of matter by following the trajectories of a collection of interacting model particles. To exploit diverse modern manycore hardware, efficient codes must use all available…
Molecular dynamics simulates the~movements of atoms. Due to its high cost, many methods have been developed to "push the~simulation forward". One of them, metadynamics, can hasten the~molecular dynamics with the~help of variables describing…
This paper introduces a random-batch molecular dynamics (RBMD) package for fast simulations of particle systems at the nano/micro scale. Different from existing packages, the RBMD uses random batch methods for nonbonded interactions of…
We present non-convex maximal dissipation principle (NMDP), a time integration scheme for articulated bodies with simultaneous contacts. Our scheme resolves contact forces via the maximal dissipation principle (MDP). Prior MDP solvers…
The linked cell list algorithm is an essential part of molecular simulation software, both molecular dynamics and Monte Carlo. Though it scales linearly with the number of particles, there has been a constant interest in increasing its…
The Multilevel Monte Carlo (MLMC) method has proven to be an effective variance-reduction statistical method for Uncertainty Quantification (UQ) in Partial Differential Equation (PDE) models, combining model computations at different levels…
GROMACS is one of the most widely used HPC software packages using the Molecular Dynamics (MD) simulation technique. In this work, we quantify GROMACS parallel performance using different configurations, HPC systems, and FFT libraries…
Multicasting is an efficient technique for simultaneously transmitting common messages from the base station (BS) to multiple mobile users (MUs). Multicast scheduling over multiple channels, which aims to jointly minimize the energy…
Based on the particle-in-cell (PIC) plasma simulation method, the speed-limited PIC (SLPIC) method delivers faster kinetic plasma simulation in cases where the particle distributions evolve slowly compared with the maximum stable PIC…
Molecular dynamics simulations have emerged as a fundamental instrument for studying biomolecules. At the same time, it is desirable to perform simulations of a collection of particles under various conditions in which the molecules can…
Multimodal chatbots have become one of the major topics for dialogue systems in both research community and industry. Recently, researchers have shed light on the multimodality of responses as well as dialogue contexts. This work explores…
We report a novel hybrid method of simultaneous atomistic simulation of solids in critical regions (contacts surfaces, cracks areas, etc.), along with continuum modeling of other parts. The continuum is treated in terms of quasi-atoms of…
The definition of heat current operator for systems for non-pairwise additive interactions and its impact on related lattice thermal conductivity ($\kappa_{L}$) via molecular dynamics simulation (MD) are ambiguous and controversial when…
Computer simulation is an important tool for scientific progress, especially when lab experiments are either extremely costly and difficult or lack the required resolution. However, all of the simulation methods come with limitations. In…
Molecular dynamics (MD) simulations present a data-mining challenge, given that they can generate a considerable amount of data but often rely on limited or biased human interpretation to examine their information content. By not asking the…