Related papers: A portable code for dissipative particle dynamics …
Quantum dynamics simulations (QDSs) are one of the most highly anticipated applications of quantum computing. Quantum circuit depth for implementing Hamiltonian simulation algorithms is commonly time dependent so that long time dynamics…
We present a Fortran 95 code for simulating the evolution of astrophysical systems using particles to represent the underlying fluid flow. The code is designed to be versatile, flexible and extensible, with modular options that can be…
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…
We developed a 6D multi-particle tracking program CETASim in C++ programming language to simulate intensity-dependent effects in electron storage rings. The program can simulate the beam collective effects due to short-range/long-range…
The auto differentiable simulation is a type of simulation that outputs of the simulation include not only the simulation result itself, but also their derivatives with respect to various input parameters. It provides an efficient method to…
The cost of combustion simulations is often dominated by the evaluation of net production rates of chemical species and mixture thermodynamics (thermochemistry). Execution on computing accelerators (XPUs) like graphic processing units…
The development and the implementation of a Particle-in-Cell code written in the Unified Parallel C (UPC) language for plasma simulations with application to astrophysics and fusion nuclear energy machines are presented. A simple one…
Discrete particle simulations are widely used to study large-scale particulate flows in complex geometries where particle-particle and particle-fluid interactions require an adequate representation but the computational cost has to be kept…
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…
The particle contact model is important for powder simulations. Although several contact models have been proposed, their validity has not yet been well established. Therefore, we perform molecular dynamics (MD) simulations to clarify the…
Quasi-N-body simulations, such as FastPM, provide a fast way to simulate cosmological structure formation, but have yet to adequately include the effects of massive neutrinos. We present a method to include neutrino particles in FastPM,…
Parallel code design is a challenging task especially when addressing petascale systems for massive parallel processing (MPP), i.e. parallel computations on several hundreds of thousands of cores. An in-house computational fluid dynamics…
In this paper, a stochastic Hamiltonian formulation (SHF) is proposed and applied to dissipative particle dynamics (DPD) simulations. As an extension of Hamiltonian dynamics to stochastic dissipative systems, the SHF provides necessary…
Decoupling approach presents a novel solution/alternative to the highly time-consuming fluid-thermal-structural simulation procedures when thermal effects and resultant displacements on machine tools are analyzed. Using high dimensional…
The high-performance computing (HPC) community has recently seen a substantial diversification of hardware platforms and their associated programming models. From traditional multicore processors to highly specialized accelerators, vendors…
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…
Molecular dynamics simulations have a prominent role in biophysics and drug discovery due to the atomistic information they provide on the structure, energetics and dynamics of biomolecules. Specialized software packages are required to…
We report on the development of a modular platform for programmable quantum simulation with atomic quantum gases. The platform is centered around exchangeable optical modules with versatile functionalities. The performance of each module is…
The Liquid Argon Time Projection Chamber (LArTPC) technology is widely used in high energy physics experiments, including the upcoming Deep Underground Neutrino Experiment (DUNE). Accurately simulating LArTPC detector responses is essential…
Molecular dynamics (MD) simulations and computer-aided drug design (CADD) have advanced substantially over the past two decades, thanks to continuous computer hardware and software improvements. Given these advancements, MD simulations are…