Related papers: Parallel-in-time method for calculation of long-ra…
Parallel-in-time methods are developed to accelerate the direct-adjoint looping procedure. Particularly, we utilize the Paraexp algorithm, previously developed to integrate equations forward in time, to accelerate the direct-adjoint looping…
Particle tracking in large-scale numerical simulations of turbulent flows presents one of the major bottlenecks in parallel performance and scaling efficiency. Here, we describe a particle tracking algorithm for large-scale parallel…
Typical biomolecular systems such as cellular membranes, DNA, and protein complexes are highly charged. Thus, efficient and accurate treatment of electrostatic interactions is of great importance in computational modelling of such systems.…
The present paper deals with the problem of improving the efficiency of large scale turbulent flow simulations. The high-fidelity methods for modelling turbulent flows become available for a wider range of applications thanks to the…
This paper proposes a general formulation for temporal parallelisation of dynamic programming for optimal control problems. We derive the elements and associative operators to be able to use parallel scans to solve these problems with…
In this article we introduce a novel coupled algorithm for massively parallel direct numerical simulations of electrophoresis in microfluidic flows. This multiphysics algorithm employs an Eulerian description of fluid and ions, combined…
As compute power increases with time, more involved and larger simulations become possible. However, it gets increasingly difficult to efficiently use the provided computational resources. Especially in particle-based simulations with a…
Massively parallel computer architectures create new opportunities for the performance of long-timescale molecular dynamics (MD) simulations. Here, we introduce the path-accelerated molecular dynamics (PAMD) method that takes advantage of…
We have extended the multilevel summation (MLS) method, originally developed to evaluate long-range Coulombic interactions in molecular dynamics (MD) simulations [Skeel et al., J. Comput. Chem., 23, 673 (2002)], to handle dispersion…
In this paper, we propose, analyze and implement efficient time parallel methods for the Cahn-Hilliard (CH) equation. It is of great importance to develop efficient numerical methods for the CH equation, given the range of applicability of…
In this work, we have developed a multiscale computational algorithm to couple finite element method with an open source molecular dynamics code --- the Large scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) --- to perform…
Machine learning potentials have achieved great success in accelerating atomistic simulations. Many of them relying on atom-centered local descriptors are natural for parallelization. More recent message passing neural network (MPNN) models…
A weighted version of the parareal method for parallel-in-time computation of time dependent problems is presented. Linear stability analysis for a scalar weighing strategy shows that the new scheme may enjoy favorable stability properties…
In view of the existing limitations of sequential computing, parallelization has emerged as an alternative in order to improve the speedup of numerical simulations. In the framework of evolutionary problems, space-time parallel methods…
Coulomb interaction, following an inverse-square force-law, quantifies the amount of force between two stationary and electrically charged particles. The long-range nature of Coulomb interactions poses a major challenge to molecular…
We present a parallel implementation of cellular automata to simulate chemical reactions on surfaces. The scaling of the computer time with the number of processors for this parallel implementation is quite close to the ideal T/P, where T…
The athermal quasistatic deformation method provides an elegant solution to overcome the limitation of short time spans in molecular simulations. It provides overdamped conditions, allowing for the extraction of purely structural responses…
The effectiveness of a new algorithm, parallel tempering, is studied for numerical simulations of biological molecules. These molecules suffer from a rough energy landscape. The resulting slowing down in numerical simulations is overcome by…
This report discusses the implementation of two parallel algorithms on a distributed memory system for studying vortex dynamics in type-II superconductors. These algorithms are the same as that implemented for classical molecular dynamics…
In this contribution the usage of the Parareal method is proposed for the time-parallel solution of the eddy current problem. The method is adapted to the particular challenges of the problem that are related to the differential algebraic…