Related papers: Coupling Finite Element Method with Large Scale At…
We have developed molecular dynamics codes for a short-range interaction potential that adopt both the flat-MPI and MPI/OpenMP hybrid parallelizations on the basis of a full domain decomposition strategy. Benchmark simulations involving up…
We propose a two-scale finite element method designed for heterogeneous microstructures. Our approach exploits domain diffeomorphisms between the microscopic structures to gain computational efficiency. By using a conveniently constructed…
The study deals with the parallelization of 2D and 3D finite element based Navier-Stokes codes using direct solvers. Development of sparse direct solvers using multifrontal solvers has significantly reduced the computational time of direct…
The paper describes the coupling of the MercuryDPM discrete element method (DEM) code and the implementation of the kernel-independent fast multipole method (KIFMM). The combined simulation framework allows addressing the large class of…
Large molecular dynamics simulations (millions of atoms, tens of microseconds, thousands of processors) hit the strong scalability wall: simulation on twice as many processors does not take half the time. Inspired by large N-body space…
We present a novel convex formulation that weakly couples the Material Point Method (MPM) with rigid body dynamics through frictional contact, optimized for efficient GPU parallelization. Our approach features an asynchronous time-splitting…
Soft materials (e.g., enveloped viruses, liposomes, membranes and supercooled liquids) simultaneously deform or display collective behaviors, while undergoing atomic scale vibrations and collisions. While the multiple space-time character…
Multiscale and inhomogeneous molecular systems are challenging topics in the field of molecular simulation. In particular, modeling biological systems in the context of multiscale simulations and exploring material properties are driving a…
In this paper, we present a finite element method (FEM) framework enhanced by an operator-adapted wavelet decomposition algorithm designed for the efficient analysis of multiscale electromagnetic problems. Usual adaptive FEM approaches,…
Targeting simulations on parallel hardware architectures, this paper presents computational kernels for efficient computations in mortar finite element methods. Mortar methods enable a variationally consistent imposition of coupling…
Immersed boundary-lattice Boltzmann method (IB-LBM) has been widely used for simulation of particle-laden flows recently. However, it was limited to small-scale simulations with no more than O(103) particles. Here, we expand IB-LBM for…
In this paper, we describe a new scalable and modular material point method (MPM) code developed for solving large-scale problems in continuum mechanics. The MPM is a hybrid Eulerian-Lagrangian approach, which uses both moving material…
Scalable and efficient numerical simulations continue to gain importance, as computation is firmly established as the third pillar of discovery, alongside theory and experiment. Meanwhile, the performance of computing hardware grows through…
In this article, a new generic higher-order finite-element framework for massively parallel simulations is presented. The modular software architecture is carefully designed to exploit the resources of modern and future supercomputers.…
We describe a combination of all-atom simulations with CABS, a well-established coarse-grained protein modeling tool, into a single multiscale protocol. The simulation method has been tested on the C-terminal beta hairpin of protein G, a…
Simulating charged many-body systems has been a computational demanding task due to the long-range nature of electrostatic interaction. For the multi-scale model of electrolytes which combines the strengths of atomistic/continuum…
We introduce a particle-based simulation method for granular material in interactive frame rates. We divide the simulation into two decoupled steps. In the first step, a relatively small number of particles is accurately simulated with a…
In this paper, we propose an efficient parallelization strategy for boundary element method (BEM) solvers that perform the electromagnetic analysis of structures with lossy conductors. The proposed solver is accelerated with the adaptive…
The multi-level hp-refinement scheme is a powerful extension of the finite element method that allows local mesh adaptation without the trouble of constraining hanging nodes. This is achieved through hierarchical high-order overlay meshes,…
The availability of open-source molecular simulation software packages allows scientists and engineers to focus on running and analyzing simulations without having to write, parallelize, and validate their own simulation software. While…