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Scientific software is often driven by multiple parameters that affect both accuracy and performance. Since finding the optimal configuration of these parameters is a highly complex task, it extremely common that the software is used…
With the rapid advancement of computational techniques, Molecular Dynamics (MD) simulations have emerged as powerful tools in biomedical research, enabling in-depth investigations of biological systems at the atomic level. Among the diverse…
Molecular dynamics simulations, an indispensable research tool in computational chemistry and materials science, consume a significant portion of the supercomputing cycles around the world. We focus on multi-body potentials and aim at…
LAMMPS is a widely popular classical Molecular Dynamics package. It was designed for materials modeling but it is well prepared for simulations in Soft Matter. The use packages like LAMMPS has advantages and disadvantages. The main…
Since its inception in 1995, LAMMPS has grown to be a world-class molecular dynamics code, with thousands of users, over one million lines of code, and multi-scale simulation capabilities. We discuss how LAMMPS has adapted to the modern…
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…
We present a GPU implementation of LAMMPS, a widely-used parallel molecular dynamics (MD) software package, and show 5x to 13x single node speedups versus the CPU-only version of LAMMPS. This new CUDA package for LAMMPS also enables…
Large language models (LLMs) have demonstrated broad utility across molecular domains, spanning drug discovery and materials design. Analyzing LLMs' latent representations is crucial for elucidating their underlying mechanisms, improving…
Molecular Dynamics (MD) simulation is widely used to analyze the properties of molecules and materials. Most practical applications, such as comparison with experimental measurements, designing drug molecules, or optimizing materials, rely…
Solving constrained nonlinear programs (NLPs) is of great importance in various domains such as power systems, robotics, and wireless communication networks. One widely used approach for addressing NLPs is the interior point method (IPM).…
This paper concerns development of a high-performance implementation of the Particle-in-Cell method for plasma simulation on Intel Xeon Phi coprocessors. We discuss suitability of the method for Xeon Phi architecture and present our…
The Intel Xeon Phi manycore processor is designed to provide high performance matrix computations of the type often performed in data analysis. Common data analysis environments include Matlab, GNU Octave, Julia, Python, and R. Achieving…
Modern HPC systems are increasingly relying on greater core counts and wider vector registers. Thus, applications need to be adapted to fully utilize these hardware capabilities. One class of applications that can benefit from this increase…
Path integral molecular dynamics (PIMD), which maps a quantum particle onto a fictitious classical system of ring polymers and propagates the "beads" of this extended classical system using molecular dynamics, is widely used to capture…
Molecular dynamics models materials by simulating each individual particle's trajectory. Many-body potentials lead to a more accurate trajectory simulation, and are used in materials science and computational chemistry. We present…
Recent results on supercomputers show that beyond 65K cores, the efficiency of molecular dynamics simulations of interfacial systems decreases significantly. In this paper, we introduce a dynamic cutoff method (DCM) for interfacial systems…
We present a Kokkos-accelerated implementation of the Moment Tensor Potential (MTP) for LAMMPS, designed to improve both computational performance and portability across CPUs and GPUs. This package introduces an optimized CPU…
Molecular dynamics simulations are a cornerstone in science, allowing to investigate from the system's thermodynamics to analyse intricate molecular interactions. In general, to create extended molecular trajectories can be a…
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…
For inhomogeneous systems with interfaces, the inclusion of long-range dispersion interactions is necessary to achieve consistency between molecular simulation calculations and experimental results. For accurate and efficient incorporation…