Related papers: fix pimd/langevin: An Efficient Implementation of …
We introduce a scheme for molecular simulations, the Deep Potential Molecular Dynamics (DeePMD) method, based on a many-body potential and interatomic forces generated by a carefully crafted deep neural network trained with ab initio data.…
Modern computing systems suffer from the dichotomy between computation on one side, which is performed only in the processor (and accelerators), and data storage/movement on the other, which all other parts of the system are dedicated to.…
We develop an algorithm suitable for parallel molecular dynamics simulations in $d$ spatial dimensions and describe its implementation in C++. All routines work in arbitrary $d$; the maximum simulated $d$ is limited only by available…
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…
A hierarchical parallelization has been implemented in a new unified code PIMD-SMASH for ab initio simulation where the replicas and the Born-Oppenheimer forces are parallelized. It is demonstrated that ab initio path integral molecular…
Processing-in-memory (PIM) architectures have demonstrated great potential in accelerating numerous deep learning tasks. Particularly, resistive random-access memory (RRAM) devices provide a promising hardware substrate to build PIM…
A multilevel approach to sample the potential energy surface in a path integral formalism is proposed. The purpose is to reduce the required number of ab initio evaluations of energy and forces in ab initio path integral molecular dynamics…
We present our recent code modernizations of the of the ab initio molecular dynamics program CPMD (www.cpmd.org) with a special focus on the ultra-soft pseudopotential (USPP) code path. Following the internal instrumentation of CPMD, all…
Chemical potential of species in solution is essential for understanding various chemical processes at interfaces. Molecular dynamics (MD) simulations, constrained by fixed compositions, cannot satisfy a constant chemical potential…
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…
Efficient simulation of Laser Powder Bed Fusion (LPBF) is crucial for process prediction due to the lasting issue of high computational cost associated with traditional numerical methods such as finite element analysis (FEA). While a…
Towards the efficient simulation of near-term quantum devices using tensor network states, we introduce an improved real-space parallelizable matrix-product state (MPS) compression method. This method enables efficient compression of all…
Medical imaging and multi-modal clinical settings often face the challange of missing modality in their diagnostic pipelines. Existing imputation methods either lack representational capacity or are computationally expensive. We propose…
Large language models (LLMs) are widely used for natural language understanding and text generation. An LLM model relies on a time-consuming step called LLM decoding to generate output tokens. Several prior works focus on improving the…
Graph Neural Networks (GNNs) are emerging ML models to analyze graph-structure data. Graph Neural Network (GNN) execution involves both compute-intensive and memory-intensive kernels, the latter dominates the total time, being significantly…
Ring polymer molecular dynamics (RPMD) has proven to be an accurate approach for calculating thermal rate coefficients of various chemical reactions. For wider application of this methodology, efficient ways to generate the underlying…
We discuss the computational bottlenecks in molecular dynamics (MD) and describe the challenges in parallelizing the computation intensive tasks. We present a hybrid algorithm using MPI (Message Passing Interface) with OpenMP threads for…
We report a novel hybrid method of simultaneous atomistic simulation of solids in critical regions (contacts surfaces, cracks areas, etc.), along with continuum modeling of other parts. The continuum is treated in terms of quasi-atoms of…
Most recently, path integral molecular dynamics (PIMD) has been successfully applied to perform simulations of identical bosons and fermions by B. Hirshberg et al.. In this work, we demonstrate that PIMD can be developed to calculate…
Reactive molecular dynamics simulations are computationally demanding. Reaching spatial and temporal scales where interesting scientific phenomena can be observed requires efficient and scalable implementations on modern hardware. In this…