Related papers: A portable code for dissipative particle dynamics …
We discuss the design of state-of-the-art numerical methods for molecular dynamics, focusing on the demands of soft matter simulation, where the purposes include sampling and dynamics calculations both in and out of equilibrium. We discuss…
We present a novel approach of mapping dissipative particle dynamics (DPD) into classical molecular dynamics. By introducing the invariant volume element representing the swarm of atoms we show that the interactions between the emerging…
A new parallel algorithm utilizing partitioned global address space (PGAS) programming model to achieve high scalability is reported for particle tracking in direct numerical simulations of turbulent flow. The work is motivated by the…
Circumstellar discs, from which planetary systems are formed, consist of gas, dust and solids. Simulations of self-consistent dynamics of gas, dust and solids in circumstellar discs is a challenging problem. In the paper we present fast…
Differentiable programming, enabled by automatic differentiation (AD), provides a robust framework for gradient-based optimization in computational plasma physics. While optimization is often only used towards design, we demonstrate that it…
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…
Modern graphics processing units (GPUs) provide impressive computing resources, which can be accessed conveniently through the CUDA programming interface. We describe how GPUs can be used to considerably speed up molecular dynamics (MD)…
In this paper, we introduce our open source implementation of the Coupled Discrete Unified Gas Kinetic Scheme (CDUGKS) of https://journals.aps.org/pre/abstract/10.1103/PhysRevE.98.053310, a phase space scheme capable of handling a wide…
We present Decapodes, a diagrammatic tool for representing, composing, and solving partial differential equations. Decapodes provides an intuitive diagrammatic representation of the relationships between variables in a system of equations,…
While LDPC codes have been demonstrated with desirable error correcting properties, this has come at a cost of diverging from the geometrical constraints of many hardware platforms. Viewing codes as the groundspace of a Hamiltonian, we…
Furthering our understanding of many of today's interesting problems in plasma physics---including plasma based acceleration and magnetic reconnection with pair production due to quantum electrodynamic effects---requires large-scale kinetic…
In this paper, we describe the algorithms we implemented in FDPS to make efficient use of accelerator hardware such as GPGPUs. We have developed FDPS to make it possible for many researchers to develop their own high-performance parallel…
Dissipative particle dynamics (DPD) is now a well-established method for simulating soft matter systems. However, its applicability was recently questioned because some investigations showed an upper coarse-graining limit that would prevent…
We present a novel, fast differentiable simulator for soft-body learning and control applications. Existing differentiable soft-body simulators can be classified into two categories based on their time integration methods: Simulators using…
Charges on the dust grains immersed in a plasma vary in time. We follow the hydrodynamic approach to obtain dispersion relations for some low frequency electrostatic modes, taking into account charge fluctuation on the dust. We have used…
We present a systematic, top-down, thermodynamic parametrization scheme for dissipative particle dynamics (DPD) using water-octanol partition coefficients, supplemented by water-octanol phase equilibria and pure liquid phase density data.…
Graphics processing units have been extensively used to accelerate classical molecular dynamics simulations. However, there is much less progress on the acceleration of force evaluations for many-body potentials compared to pairwise ones.…
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…
Multiparticle collision dynamics (MPCD) is a relatively new algorithm of fluid flow simulations that has been applied mostly to flows around simple objects. One might ask how it behaves in more complex flows. Therefore, we extend MPCD to…
We present an open-source code for the simulation of electron and ion transport for user-defined gas mixtures with static uniform electric and magnetic fields. The program provides microscopic interaction simulation and is interfaced with…