Related papers: RUMD: A general purpose molecular dynamics package…

Computational Fluid Dynamics (CFD) is the simulation of fluid flow undertaken with the use of computational hardware. The underlying equations are computationally challenging to solve and necessitate high performance computing (HPC) to…

Within the scope of reacting flow simulations, the real-time direct integration (DI) of stiff ordinary differential equations (ODE) for the computation of chemical kinetics stands as the primary demand on computational resources. Meanwhile,…

In this work we present a proof of concept of CUDA-capable, resistive, multi-fluid models of relativistic magnetohydrodynamics (RMHD). Resistive and multi-fluid codes for simulating models of RMHD suffer from stiff source terms, so it is…

This paper presents a computationally efficient implementation of a Hamming code decoder on a graphics processing unit (GPU) to support real-time software-defined radio (SDR), which is a software alternative for realizing wireless…

Development of computer technology in chemistry, bring many application of chemistry. Not only the application to visualize the structure of molecule but also to molecular dynamics simulation. One of them is Gromacs. Gromacs is an example…

We assess costs and efficiency of state-of-the-art high performance cloud computing compared to a traditional on-premises compute cluster. Our use case are atomistic simulations carried out with the GROMACS molecular dynamics (MD) toolkit…

We describe MGARD, a software providing MultiGrid Adaptive Reduction for floating-point scientific data on structured and unstructured grids. With exceptional data compression capability and precise error control, MGARD addresses a wide…

A new molecular simulation toolkit composed of some lately developed force fields and specified models is presented to study the self-assembly, phase transition, and other properties of polymeric systems at mesoscopic scale by utilizing the…

Simulations of standard 1D and 2D quantum walks have been performed within Quantum Computer Simulator (QCS system) environment and with the use of GPU supported by CUDA technology. In particular, simulations of quantum walks may be seen as…

The implementation of Molecular Dynamics (MD) on FPGAs has received substantial attention. Previous work, however, has consisted of either proof-of-concept implementations of components, usually the range-limited force; full systems, but…

LAMMPS is a widely popular classical Molecular Dynamics package. It was designed for materials modeling but it is well prepared for simulations in Soft Matter. The use packages like LAMMPS has advantages and disadvantages. The main…

Chemical potential of species in solution is essential for understanding various chemical processes at interfaces. Molecular dynamics (MD) simulations, constrained by fixed compositions, cannot satisfy a constant chemical potential…

These notes accompany the open-source code published in GitHub which implements a GPU-based line-segment, surface-triangle intersection algorithm in CUDA. It mentions some relevant works and discusses issues specific to this implementation.…

Path-integral molecular dynamics (PIMD) simulations are crucial for accurately capturing nuclear quantum effects in materials. However, their computational intensity and reliance on multiple software packages often limit their applicability…

iPIC3D is a widely used massively parallel Particle-in-Cell code for the simulation of space plasmas. However, its current implementation does not support execution on multiple GPUs. In this paper, we describe the porting of iPIC3D particle…

Open-source process mining provides many algorithms for the analysis of event data which could be used to analyze mainstream processes (e.g., O2C, P2P, CRM). However, compared to commercial tools, they lack the performance and struggle to…

The amount of unstructured text-based data is growing every day. Querying, clustering, and classifying this big data requires similarity computations across large sets of documents. Whereas low-complexity similarity metrics are available,…

The conductor-like polarization model (C-PCM) with switching/Gaussian smooth discretization is a widely used implicit solvation model in chemical simulations. However, its application in quantum mechanical calculations of large-scale…

Tremendous advances in parallel computing and graphics hardware opened up several novel real-time GPU applications in the fields of computer vision, computer graphics as well as augmented reality (AR) and virtual reality (VR). Although…

We present GSPMD, an automatic, compiler-based parallelization system for common machine learning computations. It allows users to write programs in the same way as for a single device, then give hints through a few annotations on how to…