Related papers: The MOLDY short-range molecular dynamics package
While fast multipole methods (FMMs) are in widespread use for the rapid evaluation of potential fields governed by the Laplace, Helmholtz, Maxwell or Stokes equations, their coupling to high-order quadratures for evaluating layer potentials…
With recent advancements in machine learning for interatomic potentials, Python has become the go-to programming language for exploring new ideas. While machine-learning potentials are often developed in Python-based frameworks, existing…
Manual parallelization of code remains a significant challenge due to the complexities of modern software systems and the widespread adoption of multi-core architectures. This paper introduces OMPar, an AI-driven tool designed to automate…
In this work, we present a general purpose deep neural network package for representing energies, forces, dipole moments, and polarizabilities of atomistic systems. This so-called recursively embedded atom neural network model takes both…
The TREE method has been widely used for long-range interaction {\it N}-body problems. We have developed a parallel TREE code for two-component classical plasmas with open boundary conditions and highly non-uniform charge distributions. The…
We investigate theoretically the possibility to observe dynamical mode locking, in the form of Shapiro steps, when a time-periodic potential or force modulation is applied to a two-dimensional (2D) lattice of colloidal particles that are…
Polyhedral compilers perform optimizations such as tiling and parallelization; when doing both, they usually generate code that executes "barrier-synchronized wavefronts" of tiles. We present a system to express and generate code for hybrid…
For the parallel-in-time integration method Parareal, pipelining can be used to hide some of the cost of the serial correction step and improve its efficiency. The paper introduces a basic OpenMP implementation of pipelined Parareal and…
VSIPL and OpenMP are two open standards for portable high performance computing. VSIPL delivers optimized single processor performance while OpenMP provides a low overhead mechanism for executing thread based parallelism on shared memory…
Traditional heterogeneous parallel algorithms, designed for heterogeneous clusters of workstations, are based on the assumption that the absolute speed of the processors does not depend on the size of the computational task. This assumption…
PLUMED is an open-source software package that is widely used for analyzing and enhancing molecular dynamics simulations that works in conjunction with most available molecular dynamics softwares. While the computational cost of PLUMED…
We present new version of previously published Fortran and C programs for solving the Gross-Pitaevskii equation for a Bose-Einstein condensate with contact interaction in one, two and three spatial dimensions in imaginary and real time,…
We introduce mapping-variable ring polymer molecular dynamics (MV-RPMD), a model dynamics for the direct simulation of multi-electron processes. An extension of the RPMD idea, this method is based on an exact, imaginary time path-integral…
MLMOD is a software package for incorporating machine learning approaches and models into simulations of microscale mechanics and molecular dynamics in LAMMPS. Recent machine learning approaches provide promising data-driven approaches for…
The recent evolution of software and hardware technologies is leading to a renewed computational interest in Particle-In-Cell (PIC) methods such as the Material Point Method (MPM). Indeed, provided some critical aspects are properly…
Multimodal models often experience a significant performance drop when one or more modalities are missing during inference. To address this challenge, we propose a simple yet effective approach that enhances robustness to missing modalities…
High-rate quantum LDPC (qLDPC) codes reduce memory overhead by densely packing many logical qubits into a single block of physical qubits. Here we extend this concept to high-rate computation by constructing \emph{batched} fault-tolerant…
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…
Faced with physical and energy density limitations on clock speed, contemporary microprocessor designers have increasingly turned to on-chip parallelism for performance gains. Algorithms should accordingly be designed with ample amounts of…
We present an accelerated ``on-the-fly'' coupled-cluster path-integral molecular dynamics (PIMD) method for finite-temperature simulations in which electron correlation and nuclear quantum effects are treated simultaneously. The approach is…