Related papers: The MOLDY short-range molecular dynamics package

Programming embedded systems applications involve writing concurrent, event-driven and timing-aware programs. Traditionally, such programs are written in low-level machine-oriented programming languages like C or Assembly. We present an…

In recent years, machine learning interatomic potentials (MLIPs) have attracted significant attention as a method that enables large-scale, long-time atomistic simulations while maintaining accuracy comparable to electronic structure…

This paper introduces a random-batch molecular dynamics (RBMD) package for fast simulations of particle systems at the nano/micro scale. Different from existing packages, the RBMD uses random batch methods for nonbonded interactions of…

Collective operations are common features of parallel programming models that are frequently used in High-Performance (HPC) and machine/ deep learning (ML/ DL) applications. In strong scaling scenarios, collective operations can negatively…

Although event-driven algorithms have been shown to be far more efficient than time-driven methods such as conventional molecular dynamics, they have not become as popular. The main obstacle seems to be the difficulty of parallelizing…

QCMPI is a quantum computer (QC) simulation package written in Fortran 90 with parallel processing capabilities. It is an accessible research tool that permits rapid evaluation of quantum algorithms for a large number of qubits and for…

High precision atomic data is indispensable for experiments involving studies of fundamental interactions, astrophysics, atomic clocks, plasma science, and others. We develop new parallel atomic structure codes and explore the difficulties…

Recently, there has been growing interest in using standard language constructs (e.g. C++'s Parallel Algorithms and Fortran's do concurrent) for accelerated computing as an alternative to directive-based APIs (e.g. OpenMP and OpenACC).…

This paper introduces algorithms for problems where a decision maker has to control a system composed of several components and has access to only partial information on the state of each component. Such problems are difficult because of…

A new pairwise hybrid machine-learning/molecular mechanics (ML/MM) potential is introduced that is conceived for application to large, heterogeneous condensed-phase systems. The PhysNet ML method describes monomers and short-range dimer…

We discuss the design and implementation of HYDRA_OMP a parallel implementation of the Smoothed Particle Hydrodynamics-Adaptive P3M (SPH-AP3M) code HYDRA. The code is designed primarily for conducting cosmological hydrodynamic simulations…

Multiple time scale molecular dynamics enhances computational efficiency by updating slow motions less frequently than fast motions. However, in practice the largest outer time step possible is limited not by the physical forces but by…

In recent years, molecular dynamics (MD) simulations have emerged as a pivotal tool for understanding the structure, dynamics, and phase behavior in charged soft matter systems. To explore phenomena across greater length and time scales in…

Ferroelectric materials with switchable spontaneous polarization underpin non-volatile memories, transistors, sensors, and emerging neuromorphic chips. Their performance and stability are governed by polarization dynamics and domain…

This article presents a comparison of various implementations of the Lattice Discrete Particle Model (LDPM) for the numerical simulation of concrete and other heterogeneous quasibrittle materials. The comparison involves the use of…

Power density constraints are limiting the performance improvements of modern CPUs. To address this we have seen the introduction of lower-power, multi-core processors such as GPGPU, ARM and Intel MIC. To stay within the power density…

Asymmetric multicore processors (AMPs) couple high-performance big cores and low-power small cores with the same instruction-set architecture but different features, such as clock frequency or microarchitecture. Previous work has shown that…

We modified a MPI-friendly density functional theory (DFT) source code within hybrid parallelization including CUDA. Our objective is to find out how simple conversions within the hybrid parallelization with mid-range GPUs affect DFT code…

Molecular dynamics (MD) simulations play a crucial role in resolving the underlying conformational dynamics of molecular systems. However, their capability to correctly reproduce and predict dynamics in agreement with experiments is limited…

High-energy physics (HEP) experiments have developed millions of lines of code over decades that are optimized to run on traditional x86 CPU systems. However, we are seeing a rapidly increasing fraction of floating point computing power in…