Related papers: A portable code for dissipative particle dynamics …
The rapid development of quantum computers has enabled demonstrations of quantum advantages on various tasks. However, real quantum systems are always dissipative due to their inevitable interaction with the environment, and the resulting…
This work introduces ParAMS -- a versatile Python package that aims to make parameterization workflows in computational chemistry and physics more accessible, transparent and reproducible. We demonstrate how ParAMS facilitates the parameter…
We present DiffXPBD, a novel and efficient analytical formulation for the differentiable position-based simulation of compliant constrained dynamics (XPBD). Our proposed method allows computation of gradients of numerous parameters with…
Dissipative particle dynamics (DPD) is a well-established mesoscale simulation method. However, there have been long-standing ambiguities regarding the dependence of its (purely repulsive) force field parameter on temperature as well as the…
We propose an efficient simulation algorithm based on the dissipative particle dynamics (DPD) method for studying electrohydrodynamic phenomena in electrolyte fluids. The fluid flow is mimicked with DPD particles while the evolution of the…
A new open source tool for fluid simulation of multi-component plasmas is presented, based on a flexible software design that is applicable to scientific simulations in a wide range of fields. This design enables the same code to be…
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…
We have investigated plasma-surface interactions with molecular dynamics (MD) simulations. It, however, is high cost computation and is limited to simulations for materials of nanometer order. In order to overcome the limitation, a…
Modeling plasma accelerators is a computationally challenging task and the quasi-static particle-in-cell algorithm is a method of choice in a wide range of situations. In this work, we present the first performance-portable, quasi-static,…
Molecular dynamics facilitates the simulation of a complex system to be analyzed at molecular and atomic levels. Simulations can last a long period of time, even months. Due to this cause the graphics processing units (GPUs) and multi-core…
Bosonic exchange symmetry leads to fascinating quantum phenomena, from exciton condensation in quantum materials to the superfluidity of liquid Helium-4. Unfortunately, path integral molecular dynamics (PIMD) simulations of bosons are…
This article describes a new, fully adaptive Particle-Multiple-Mesh numerical simulation code developed primarily for simulations of small regions (such as a group of galaxies) in a cosmological context. It integrates the equations of…
We provide a two dimensional deformation model to describe how soft squishy circular particles respond to external forces and collisions. This model involves formulating mathematical equations and algorithms for the shape of a deformed…
A large number of powerful, high-quality, and open-source simulation packages exist to efficiently perform molecular dynamics simulations, and their prevalence has greatly accelerated discoveries across a wide range of scientific domains.…
This master thesis introduces the idea of dynamic cutoffs in molecular dynamics simulations, based on the distance between particles and the interface, and presents a solution for detecting interfaces in real-time. Our dynamic cutoff method…
Dissipative particle dynamics (DPD) is an effective mesoscopic particle model with a lower computational cost than molecular dynamics because of the soft potentials that it employs. However, the soft potential is not strong enough to…
Molecular dynamics simulations are one of the methods in scientific computing that benefit from GPU acceleration. For those devices, SYCL is a promising API for writing portable codes. In this paper, we present the case study of "HAL's MD…
We use molecular dynamics computer simulations to investigate the local motion of the particles in a supercooled simple liquid. Using the concept of the distance matrix we find that the alpha-relaxation corresponds to a small number of…
Event-driven molecular dynamics is a valuable tool in condensed and soft matter physics when particles can be modeled as hard objects or more generally if their interaction potential can be modeled in a stepwise fashion. Hard spheres model…
The supercomputing platforms available for high performance computing based research evolve at a great rate. However, this rapid development of novel technologies requires constant adaptations and optimizations of the existing codes for…