Related papers: HSMA: An O(N) electrostatics package implemented i…
We introduce FastPM, a highly-scalable approximated particle mesh N-body solver, which implements the particle mesh (PM) scheme enforcing correct linear displacement (1LPT) evolution via modified kick and drift factors. Employing a…
Machine learning potentials have emerged as a means to enhance the accuracy of biomolecular simulations. However, their application is constrained by the significant computational cost arising from the vast number of parameters compared to…
The constant potential molecular dynamics simulation method proposed by Siepmann and Sprik and reformulated later by Reed (SR-CPM) has been widely employed to investigate the metallic electrolyte/electrode interfaces, especially for…
To minimise systematic errors in Monte Carlo simulations of charged particles, long range electrostatic interactions have to be calculated accurately and efficiently. Standard approaches, such as Ewald summation or the naive application of…
Plasma chemistry of main air components is implemented in a hybrid 2D axisymmetric simulation code to assess the air-breathing concept in an electrodeless plasma thruster. Relevant electron-heavy species collisions for diatomic molecules…
This paper introduces a random-batch molecular dynamics (RBMD) package for fast simulations of particle systems at the nano/micro scale. Different from existing packages, the RBMD uses random batch methods for nonbonded interactions of…
Solvent plays an essential role in a variety of chemical, physical, and biological processes that occur in the solution phase. The reference interaction site model (RISM) and its three-dimensional extension (3D-RISM) serve as powerful…
Efficient simulation of complex plasma dynamics is crucial for advancing fusion energy research. Particle-in-Cell (PIC) Monte Carlo (MC) simulations provide insights into plasma behavior, including turbulence and confinement, which are…
We present a Lagrangian Heterogeneous Multiscale Method (LHMM) for simulating the non-Newtonian rheology of polymer melts in complex two-dimensional flows. The method couples Dissipative Particle Dynamics (DPD) at the microscale with a…
The impressive progress of the kinetic schemes in the solution of gas dynamics problems and the development of effective parallel algorithms for modern high performance parallel computing systems led to the development of advanced methods…
It was recently demonstrated that a simple Monte Carlo (MC) algorithm involving the swap of particle pairs dramatically accelerates the equilibrium sampling of simulated supercooled liquids. We propose two numerical schemes integrating the…
A novel Stochastic Event-Driven Molecular Dynamics (SEDMD) algorithm is developed for the simulation of polymer chains suspended in a solvent. The polymers are represented as chains of hard spheres tethered by square wells and interact with…
We address in this thesis the current need to design new parallel algorithms and tools that ease the development of geodynamic modelling applications that are suited for today's and tomorrow's hardware. We present (1) the MATLAB HPC…
GROMACS is a widely used package for biomolecular simulation, and over the last two decades it has evolved from small-scale efficiency to advanced heterogeneous acceleration and multi-level parallelism targeting some of the largest…
Heterogeneous multiscale methods (HMM) combine molecular accuracy of particle-based simulations with the computational efficiency of continuum descriptions to model flow in soft matter liquids. In these schemes, molecular simulations…
Molecular simulation is a scientific tool dealing with challenges in material science and biology. This is reflected in a permanent development and enhancement of algorithms within scientific simulation packages. Here, we present…
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…
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…
Long ranged electrostatic interactions are time consuming to calculate in molecular dynamics and Monte-Carlo simulations. We introduce an algorithmic framework for simulating charged particles which modifies the dynamics so as to allow…
In this work, we address the question of calculating the local effective Coulomb interaction matrix in materials with strong electronic Coulomb interactions from first principles. To this purpose, we implement the constrained random phase…