Related papers: fix pimd/langevin: An Efficient Implementation of …
We extend ring-polymer molecular dynamics (RPMD) to allow for the direct simulation of general, electronically non-adiabatic chemical processes. The kinetically constrained (KC) RPMD method uses the imaginary-time path-integral…
Today's computing systems require moving data back-and-forth between computing resources (e.g., CPUs, GPUs, accelerators) and off-chip main memory so that computation can take place on the data. Unfortunately, this data movement is a major…
Time-domain simulations are crucial for ensuring power system stability and avoiding critical scenarios that could lead to blackouts. The next-generation power systems require a significant increase in the computational cost and complexity…
Particle-in-cell codes are the most widely used simulation tools for kinetic studies of ultra-intense laser-plasma interactions. Using the motion of a single electron in a plane electromagnetic wave as a benchmark problem, we show…
Large Language Models (LLMs) have become essential in a variety of applications due to their advanced language understanding and generation capabilities. However, their computational and memory requirements pose significant challenges to…
Protein-ligand (un)binding simulations are a recent focus of biased molecular dynamics simulations. Such binding and unbinding can occur via different pathways in and out of a binding site. We here present a theoretical framework how to…
Today's fast linear algebra and numerical optimization tools have pushed the frontier of model predictive control (MPC) forward, to the efficient control of highly nonlinear and hybrid systems. The field of hybrid MPC has demonstrated that…
Processing-in-memory (PIM) architectures are emerging to reduce data movement in data-intensive applications. These architectures seek to exploit the same physical devices for both information storage and logic, thereby dwarfing the…
The dynamic mode decomposition (DMD) is a simple and powerful data-driven modeling technique that is capable of revealing coherent spatiotemporal patterns from data. The method's linear algebra-based formulation additionally allows for a…
Probabilistic Manifold Decomposition (PMD)\cite{doi:10.1137/25M1738863}, developed in our earlier work, provides a nonlinear model reduction by embedding high-dimensional dynamics onto low-dimensional probabilistic manifolds. The PMD has…
Analog in-memory computing (AIMC) cores offers significant performance and energy benefits for neural network inference with respect to digital logic (e.g., CPUs). AIMCs accelerate matrix-vector multiplications, which dominate these…
The (py)LIon package is a set of tools to simulate the classical trajectories of ensembles of ions in electrodynamic traps. Molecular dynamics simulations are performed using LAMMPS, an efficient and feature-rich program. (py)LIon has been…
This paper discusses recent research that aims to enable computation close to data, an approach we broadly call processing-in-memory (PIM). PIM places computation mechanisms in or near where the data is stored (i.e., inside memory chips or…
The sustainable production of many bulk chemicals relies on heterogeneous catalysis. The rational design or improvement of the required catalysts critically depends on insights into the underlying mechanisms at the atomic scale. In recent…
Molecular sciences address a wide range of problems involving molecules of different types and sizes and their complexes. Recently, geometric deep learning, especially Graph Neural Networks, has shown promising performance in molecular…
The properties of molecules and materials containing light nuclei are affected by their quantum mechanical nature. Modelling these quantum nuclear effects accurately requires computationally demanding path integral techniques. Considerable…
A parallel implementation of coupled spin-lattice dynamics in the LAMMPS molecular dynamics package is presented. The equations of motion for both spin only and coupled spin-lattice dynamics are first reviewed, including a detailed account…
Efficient simulation of complex plasma dynamics is crucial for advancing fusion energy research. Particle-in-Cell (PIC) Monte Carlo (MC) simulations provide insights into plasma behavior, including turbulence and confinement, which are…
Several manufacturers have already started to commercialize near-bank Processing-In-Memory (PIM) architectures. Near-bank PIM architectures place simple cores close to DRAM banks and can yield significant performance and energy improvements…
In this talk I discuss the general question of the portability of Molecular Dynamics codes for diffusive systems on parallel computers of the APE family. The intrinsic single precision arithmetics of the today available APE platforms does…