Related papers: On the hierarchical parallelization of ab initio s…
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…
Discovering atom-level phenomena requires molecular dynamics (MD) simulations with ab initio accuracy. Machine learning interatomic potentials (MLIPs) enable stable, high-accuracy MD simulations, and their models exhibit scaling-law trends…
We present a method to sample reactive pathways via biased molecular dynamics simulations in trajectory space. We show that the use of enhanced sampling techniques enables unconstrained exploration of multiple reaction routes. Time…
Accelerated molecular dynamics (MD) simulations are implemented to model the sliding process of AFM experiments at speeds close to those found in experiment. In this study the hyperdynamics method, originally devised to extend MD time…
New hybrid Molecular Dynamics-Monte Carlo methods are proposed to increase the efficiency of constant-pressure simulations. Two variations of the isobaric Molecular Dynamics component of the algorithms are considered. In the first, we use…
Disordered molecular systems such as amorphous catalysts, organic thin films, electrolyte solutions, and water are at the cutting edge of computational exploration today. Traditional simulations of such systems at length-scales relevant to…
The introduction of accelerator devices such as graphics processing units (GPUs) has had profound impact on molecular dynamics simulations and has enabled order-of-magnitude performance advances using commodity hardware. To fully reap these…
Engineering simulations are usually based on complex, grid-based, or mesh-free methods for solving partial differential equations. The results of these methods cover large fields of physical quantities at very many discrete spatial…
Force-matched water models provide a practical route from first-principles reference data to long classical and path-integral molecular simulations. Previous flexible four-site potentials in the spirit of q-TIP4P/F showed that fitting…
This paper describes `Ludwig', a versatile code for the simulation of Lattice-Boltzmann (LB) models in 3-D on cubic lattices. In fact `Ludwig' is not a single code, but a set of codes that share certain common routines, such as I/O and…
Aiming to accelerate the training of large deep neural networks (DNN) in an energy-efficient way, analog in-memory computing (AIMC) emerges as a solution with immense potential. AIMC accelerator keeps model weights in memory without moving…
Training large deep learning models at scale is very challenging. This paper proposes Chimera, a novel pipeline parallelism scheme which combines bidirectional pipelines for efficiently training large-scale models. Chimera is a synchronous…
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…
A fully parallel version of the contact dynamics (CD) method is presented in this paper. For large enough systems, 100% efficiency has been demonstrated for up to 256 processors using a hierarchical domain decomposition with dynamic load…
The numerical simulation of multiphase flows involving dispersed components with large scale disparities, such as the collisions between millimeter-sized bubbles and micron-sized mineral particles in flotation, poses a significant…
We present a multiscale simulation approach for hydroxide transport in aqueous solutions of potassium hydroxide, combining ab initio molecular dynamics (AIMD) simulations with force field ensemble averaging and lattice Monte Carlo…
We present in this work a new reconstruction scheme, so-called MUSCL-THINC-BVD scheme, to solve the five-equation model for interfacial two phase flows. This scheme employs the traditional shock capturing MUSCL (Monotone Upstream-centered…
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…
Recent advances in random-walk particle-tracking have enabled direct simulation of mixing and reactions on particles by allowing the particles to interact with each other using a multi-point mass transfer scheme. The mass transfer scheme…
We describe a new implementation of a parallel Tree-SPH code with the aim to simulate Galaxy Formation and Evolution. The code has been parallelized using SHMEM, a Cray proprietary library to handle communications between the 256 processors…