Related papers: A portable code for dissipative particle dynamics …
A proper treatment of electrostatic interactions is crucial for the accurate calculation of forces in computer simulations. Electrostatic interactions are typically modeled using Ewald based methods, which have become one of the…
We develop a computational method based on Dissipative Particle Dynamics (DPD) that introduces solvent hydrodynamic interactions to coarse-grained models of solutes, such as ions, molecules, or polymers. DPD-solvent (DPDS) is a fully…
Discrete time crystals (DTCs) are nonequilibrium phases of matter with exotic observable dynamics. Among their remarkable features is their response to a periodic drive at a fraction of its frequency. Current successful experiments are…
XMDS2 is a cross-platform, GPL-licensed, open source package for numerically integrating initial value problems that range from a single ordinary differential equation up to systems of coupled stochastic partial differential equations. The…
We present our recent code modernizations of the of the ab initio molecular dynamics program CPMD (www.cpmd.org) with a special focus on the ultra-soft pseudopotential (USPP) code path. Following the internal instrumentation of CPMD, all…
Phase diagrams (PDs) illustrate the relative stability of competing phases under varying conditions, serving as critical tools for synthesizing complex materials. Reliable phase diagrams rely on precise free energy calculations, which are…
Particle methods are less computationally efficient than grid based numerical solution of the Navier Stokes equation. However, they have important advantages including rigorous mass conservation, momentum conservation and isotropy. In…
Particle tracking simulations with space charge effects are very important for high-intensity proton rings. Since they include not only Hamilton mechanics of a single particle but constructing charge densities and solving Poisson equations…
A template-based generic programming approach was presented in a previous paper that separates the development effort of programming a physical model from that of computing additional quantities, such as derivatives, needed for embedded…
Many-body dispersion (MBD) is a powerful framework to treat van der Waals (vdW) dispersion interactions in density-functional theory and related atomistic modeling methods. Several independent implementations of MBD with varying degree of…
The Pencil Code is a highly modular physics-oriented simulation code that can be adapted to a wide range of applications. It is primarily designed to solve partial differential equations (PDEs) of compressible hydrodynamics and has lots of…
We introduce two improvements in the numerical scheme to simulate collision and slow shearing of irregular particles. First, we propose an alternative approach based on simple relations to compute the frictional contact forces. The approach…
This paper introduces open-source computational fluid dynamics software named open computational fluid dynamic code for scientific computation with graphics processing unit (GPU) system (OpenCFD-SCU), developed by the authors for direct…
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…
We present a first-principles computer code package (ABACUS) that is based on density functional theory and numerical atomic basis sets. Theoretical foundations and numerical techniques used in the code are described, with focus on the…
High precision atomic data is indispensable for experiments involving studies of fundamental interactions, astrophysics, atomic clocks, plasma science, and others. We develop new parallel atomic structure codes and explore the difficulties…
In this dissertation, a fully object-oriented, fully relativistic, multi-dimensional Particle-In-Cell code was developed and applied to answer key questions in plasma-based accelerator research. The simulations increase the understanding of…
Near-term large quantum computers are not able to operate as a single processing unit. It is therefore required to partition a quantum circuit into smaller parts, and then each part is executed on a small unit. This approach is known as…
The dissipative particle dynamics (DPD) simulation method has been shown to be a promising tool to study self-assembly of soft matter systems. In particular, it has been used to study block copolymer (BCP) self-assembly. However, previous…
We examine the performance of various commonly used integration schemes in dissipative particle dynamics simulations. We consider this issue using three different model systems, which characterize a variety of different conditions often…