Related papers: The MOLDY short-range molecular dynamics package

Molecular dynamics (MD) is an important research tool extensively applied in materials science. Running MD on a graphics processing unit (GPU) is an attractive new approach for accelerating MD simulations. Currently, GPU implementations of…

We develop an algorithm suitable for parallel molecular dynamics simulations in $d$ spatial dimensions and describe its implementation in C++. All routines work in arbitrary $d$; the maximum simulated $d$ is limited only by available…

Extended Lagrangian molecular dynamics (XLMD) is a general method for performing molecular dynamics simulations using quantum and classical many-body potentials. Recently several new XLMD schemes have been proposed and tested on several…

We present recent developments in the parallelization scheme of ECHO-3DHPC, an efficient astrophysical code used in the modelling of relativistic plasmas. With the help of the Intel Software Development Tools, like Fortran compiler and…

We present a plane-wave ultrasoft pseudopotential implementation of first-principle molecular dynamics, which is well suited to model large molecular systems containing transition metal centers. We describe an efficient strategy for…

We present a new set of QCD codes in both message passing and data parallel versions. The message passing package used is PARMACS, although other packages may be used. Data parallel software is written in High Performance fortran, an…

Molecular dynamics simulations play an increasingly important role in the rational design of (nano)-materials and in the study of biomacromolecules. However, generating input files and realistic starting coordinates for these simulations is…

Targeting simulations on parallel hardware architectures, this paper presents computational kernels for efficient computations in mortar finite element methods. Mortar methods enable a variationally consistent imposition of coupling…

This article presents the parallel implementation of the coupled harmonic oscillator. From the analytical solution of the coupled harmonic oscillator, the design parameters are obtained. After that, a numerical integration of the system…

Matrix Distributed Processing (MDP) is a C++ library for fast development of efficient parallel algorithms. It constitues the core of FermiQCD. MDP enables programmers to focus on algorithms, while parallelization is dealt with…

DL_POLY Quantum 2.1 is introduced here as a highly modular, sustainable, and scalable general-purpose molecular dynamics (MD) simulation software for large-scale long-time MD simulations of condensed phase and interfacial systems with the…

Machine learning potentials (MLPs) have advanced rapidly and show great promise to transform molecular dynamics (MD) simulations. However, most existing software tools are tied to specific MLP architectures, lack integration with standard…

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)…

OpenCL is a standard for parallel programming of heterogeneous systems. The benefits of a common programming standard are clear; multiple vendors can provide support for application descriptions written according to the standard, thus…

We present an $R$-matrix Fortran package to solve coupled-channel problems in nuclear physics. The basis functions are chosen as Lagrange functions, which permits simple calculations of the matrix elements. The main input are the coupling…

Gyrokinetic codes in plasma physics need outstanding computational resources to solve increasingly complex problems, requiring the effective exploitation of cutting-edge HPC architectures. This paper focuses on the enabling of ORB5, a…

It is well known that modern functional programming languages are naturally amenable to parallel programming. Achieving efficient parallelism using functional languages, however, remains difficult. Perhaps the most important reason for this…

The force field by Lenosky and coworkers is the latest force field for silicon which is one of the most studied materials. It has turned out to be highly accurate in a large range of test cases. The optimization and parallelization of this…

Efficient implementations of the classical molecular dynamics (MD) method for Lennard-Jones particle systems are considered. Not only general algorithms but also techniques that are efficient for some specific CPU architectures are also…

An increasingly large number of HPC systems rely on heterogeneous architectures combining traditional multi-core CPUs with power efficient accelerators. Designing efficient applications for these systems has been troublesome in the past as…