Related papers: Long-range interactions & parallel scalability in …
Molecular dynamics simulations are a central computational methodology in materials design for relating atomic composition to mechanical properties. However, simulating materials with atomic-level resolution on a macroscopic scale is…
Scaling long-context ability is essential for Large Language Models (LLMs). To amortize the memory consumption across multiple devices in long-context training, inter-data partitioning (a.k.a. Data Parallelism) and intra-data partitioning…
The solution for non-linear, complex partial differential Equations (PDEs) is achieved through numerical approximations, which yield a linear system of equations. This approach is prevalent in Computational Fluid Dynamics (CFD), but it…
Euler-Lagrange (EL) simulations provide a direct and robust framework for modeling disperse multiphase flows. However, they are computationally expensive. While various approaches have attempted to leverage heterogeneous computing…
We present a technique designed for parallelizing large rigid body simulations, capable of exploiting multiple CPU cores within a computer and across a network. Our approach can be applied to simulate both unilateral and bilateral…
To minimise systematic errors in Monte Carlo simulations of charged particles, long range electrostatic interactions have to be calculated accurately and efficiently. Standard approaches, such as Ewald summation or the naive application of…
Molecular dynamics (MD) simulations are a central tool in science and engineering enabling the study of dynamical behavior and the link between microscopic structure and macroscopic function. Their high computational cost, however, has…
We construct a coarse-grained (CG) model for dipalmitoylphosphatidylcholine (DPPC)/cholesterol bilayers and apply it to large-scale simulation studies of lipid membranes. Our CG model is a two-dimensional representation of the membrane,…
The numerical simulation of cardiac electrophysiology is a highly challenging problem in scientific computing. The Bidomain system is the most complete mathematical model of cardiac bioelectrical activity. It consists of an elliptic and a…
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…
Large-scale molecular dynamics simulations with high accuracy have been increasingly popular for their capability to bridge the gap between atomistic modeling and mesoscale phenomena. Both machine learning potentials and enhanced sampling…
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…
To address the computational challenges of ab initio molecular dynamics and the accuracy limitations of empirical force fields, the introduction of machine learning force fields has proven effective in various systems including metals and…
We review a scalable two- and three-dimensional computer code for low-temperature plasma simulations in multi-material complex geometries. Our approach is based on embedded boundary (EB) finite volume discretizations of the minimal…
High precision atomic data is indispensable for experiments involving studies of fundamental interactions, astrophysics, atomic clocks, plasma science, and others. We develop new parallel atomic structure codes and explore the difficulties…
We test the performances of two different approaches to the computation of forces for molecular dynamics simulations on Graphics Processing Units. A "vertex-based" approach, where a computing thread is started per particle, is compared to a…
A crucial aspect in the simulation of electrochemical interfaces consists in treating the distribution of electronic charge of electrode materials that are put in contact with an electrolyte solution. Recently, it has been shown how a…
We present a parallel implementation of cellular automata to simulate chemical reactions on surfaces. The scaling of the computer time with the number of processors for this parallel implementation is quite close to the ideal T/P, where T…
We show how quantum-inspired 2d tensor networks can be used to efficiently and accurately simulate the largest quantum processors from IBM, namely Eagle (127 qubits), Osprey (433 qubits) and Condor (1121 qubits). We simulate the dynamics of…
Path integral Monte Carlo (PIMC) and path integral molecular dynamics (PIMD) provide the golden standard for the ab initio simulations of identical particles. In this work, we achieved significant GPU acceleration based on PIMD, which is…