Related papers: HOOMD-blue: A Python package for high-performance …

We describe a highly optimized implementation of MPI domain decomposition in a GPU-enabled, general-purpose molecular dynamics code, HOOMD-blue (Anderson and Glotzer, arXiv:1308.5587). Our approach is inspired by a traditional CPU-based…

RUMD is a general purpose, high-performance molecular dynamics (MD) simulation package running on graphical processing units (GPU's). RUMD addresses the challenge of utilizing the many-core nature of modern GPU hardware when simulating…

The freud Python package is a powerful library for analyzing simulation data. Written with modern simulation and data analysis workflows in mind, freud provides a Python interface to fast, parallelized C++ routines that run efficiently on…

PLUMED is an open-source software package that is widely used for analyzing and enhancing molecular dynamics simulations that works in conjunction with most available molecular dynamics softwares. While the computational cost of PLUMED…

We design and implement HPMC, a scalable hard particle Monte Carlo simulation toolkit, and release it open source as part of HOOMD-blue. HPMC runs in parallel on many CPUs and many GPUs using domain decomposition. We employ BVH trees…

The RMPCDMD software package performs hybrid Molecular Dynamics simulations, coupling Multiparticle Collision Dynamics to model the solvent and Molecular Dynamics to model suspended colloids, including hydrodynamics, thermal fluctuations,…

We present the CALVADOS package for performing simulations of biomolecules using OpenMM and the coarse-grained CALVADOS model. The package makes it easy to run simulations using the family of CALVADOS models of biomolecules including…

PySDM is an open-source Python package for simulating the dynamics of particles undergoing condensational and collisional growth, interacting with a fluid flow and subject to chemical composition changes. It is intended to serve as a…

We present an open source Python 3 library aimed at practitioners of molecular simulation, especially Monte Carlo simulation. The aims of the library are to facilitate the generation of simulation data for a wide range of problems; and to…

HIPSTER (Heavily Ionising Particle Standard Toolkit for Event Recognition) is an open source Python package designed to facilitate the use of TensorFlow in a high energy physics analysis context. The core functionality of the software is…

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,…

QC Lab is an open-source Python package for QC dynamics simulations aimed to promote the development of QC algorithms, and their application to a wide variety of relevant model problems. It follows a modular design that facilitates…

Molecular dynamics is widely used to study various phenomena, such as diffusion, shock wave propagation, and plasma dynamics. A wide range of software packages supports the expanding scope of molecular dynamics applications. However, the…

Enhancing sampling and analyzing simulations are central issues in molecular simulation. Recently, we introduced PLUMED, an open-source plug-in that provides some of the most popular molecular dynamics (MD) codes with implementations of a…

The HANDE quantum Monte Carlo project offers accessible stochastic algorithms for general use for scientists in the field of quantum chemistry. HANDE is an ambitious and general high-performance code developed by a geographically-dispersed…

We present HTMPC, a Heavily Templated C++ library for large-scale simulations implementing multi-particle collision dynamics (MPC), a particle-based mesoscale hydrodynamic simulation method. The implementation is plugin-based, and designed…

Polyhedral nanocrystals are building blocks for nanostructured materials that find applications in catalysis and plasmonics. Synthesis efforts and self-assembly experiments have been assisted by computer simulations that predict phase…

Particle-Mesh (PM) codes are still very useful tools for testing predictions of cosmological models in cases when extra high resolution is not very important. We release for public use a cosmological PM N-body code. We provide a complete…

We introduce the cosmological HYPER code based on an innovative hydro-particle-mesh (HPM) algorithm for efficient and rapid simulations of gas and dark matter. For the HPM algorithm, we update the approach of Gnedin & Hui (1998) to expand…

A Python package for post-processing of plane two-dimensional data from computational fluid dynamics simulations is presented. The package, called turbulucid, provides means for scripted, reproducible analysis of large simulation campaigns…