Related papers: The MOLDY short-range molecular dynamics package
The sheer sizes of modern datasets are forcing data-structure designers to consider seriously both parallel construction and compactness. To achieve those goals we need to design a parallel algorithm with good scalability and with low…
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…
In this paper, we consider an approach to the parallelizing of the algorithms realizing the modified probability changigng method with adaptation and partial rollback procedure for constrained pseudo-Boolean optimization problems. Existing…
In this work, a new partition-collocation strategy for the parallel execution of CFD--DEM couplings is investigated. Having a good parallel performance is a key issue for an Eulerian-Lagrangian software that aims to be applied to solve…
High-performance computing often relies on parallel programming models such as MPI for distributed-memory systems. While powerful, these models are prone to subtle programming errors, leading to development of multiple correctness checking…
This paper discusses an efficient parallel implementation of the ensemble Kalman filter based on the modified Cholesky decomposition. The proposed implementation starts with decomposing the domain into sub-domains. In each sub-domain a…
An efficient parallelization approach to simulate optical properties of ensembles of quantum emitters in realistic electromagnetic environments is considered. It relies on balancing computing load of utilized processors and is built into…
In order to run Computational Fluid Dynamics (CFD) codes on large scale infrastructures, parallel computing has to be used because of the computational intensive nature of the problems. In this paper we investigate the ADAPT platform where…
The implementation of Molecular Dynamics (MD) on FPGAs has received substantial attention. Previous work, however, has consisted of either proof-of-concept implementations of components, usually the range-limited force; full systems, but…
We propose a modification of the embedded-atom method-type potential aiming at reconciling simulated melting and ground-state properties of metals by means of classical molecular dynamics. Considering titanium, magnesium, gold, and platinum…
Limits on power dissipation have pushed CPUs to grow in parallel processing capabilities rather than clock rate, leading to the rise of "manycore" or GPU-like processors. In order to achieve the best performance, applications must be able…
Present day computational fluid dynamics simulations generate extremely large amounts of data, sometimes on the order of TB/s. Often, a significant fraction of this data is discarded because current storage systems are unable to keep pace.…
The Multilevel Monte Carlo (MLMC) method has proven to be an effective variance-reduction statistical method for Uncertainty Quantification (UQ) in Partial Differential Equation (PDE) models, combining model computations at different levels…
Increasingly volatile electricity prices make simultaneous scheduling optimization desirable for production processes and their energy systems. Simultaneous scheduling needs to account for both process dynamics and binary on/off-decisions…
Parallel task-based programming models, like OpenMP, allow application developers to easily create a parallel version of their sequential codes. The standard OpenMP 4.0 introduced the possibility of describing a set of data dependences per…
Comprehending the performance bottlenecks at the core of the intricate hardware-software interactions exhibited by highly parallel programs on HPC clusters is crucial. This paper sheds light on the issue of automatically asynchronous MPI…
The performance of biomolecular molecular dynamics simulations has steadily increased on modern high performance computing resources but acceleration of the analysis of the output trajectories has lagged behind so that analyzing simulations…
We investigate the coupling of different quantum-embedding approaches with a third molecular-mechanics layer, which can be either polarizable or non-polarizable. In particular, such a coupling is discussed for the multilevel families of…
Molecular simulations of the forced unfolding and refolding of biomolecules or molecular complexes allow to gain important kinetic, structural and thermodynamic information about the folding process and the underlying energy landscape. In…
We present a new method to couple the Direct Simulation Monte Carlo (DSMC) algorithm with molecular dynamics (MD). The coupling approach generalizes prior coupling methods using a cell-based decision. The approach is supported by a lifting…