Related papers: The MOLDY short-range molecular dynamics package
From the point of view of statistical mechanics, a full characterisation of a molecular system requires the experimental determination of its possible states, their populations and the respective interconversion rates. Well-established…
Multivariate partial fractioning is a powerful tool for simplifying rational function coefficients in scattering amplitude computations. Since current research problems lead to large sets of complicated rational functions, performance of…
The trend towards highly parallel multi-processing is ubiquitous in all modern computer architectures, ranging from handheld devices to large-scale HPC systems; yet many applications are struggling to fully utilise the multiple levels of…
One of the barriers to the adoption of parallel computing is the inherent complexity of its programming. The Open Multi-Processing (OpenMP) Application Programming Interface (API) facilitates such implementations, providing high abstraction…
Hybrid particle-field molecular dynamics combines standard molecular potentials with density-field models into a computationally efficient methodology that is well-adapted for the study of mesoscale soft matter systems. Here, we introduce a…
We developed a portable code for dissipative particle dynamics (DPD) simulations. This Fortran program named CAMUS has a couple of notable features. One is the omission of constructing the so-called neighboring particles list, providing a…
Parallel jobs are different from sequential jobs and require a different type of process management. We present here a process management system for parallel programs such as those written using MPI. A primary goal of the system, which we…
With the slowing of Moore's Law, heterogeneous computing platforms such as Field Programmable Gate Arrays (FPGAs) have gained increasing interest for accelerating HPC workloads. In this work we present, to the best of our knowledge, the…
This report discusses the implementation of two parallel algorithms on a distributed memory system for studying vortex dynamics in type-II superconductors. These algorithms are the same as that implemented for classical molecular dynamics…
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…
We present an alternative GPU acceleration for plane waves pseudopotentials electronic structure codes designed for systems that have small unit cells but require a large number of k points to sample the Brillouin zone as happens, for…
We present the Glasgow Parallel Reduction Machine (GPRM), a novel, flexible framework for parallel task-composition based many-core programming. We allow the programmer to structure programs into task code, written as C++ classes, and…
We present a new approach for the two-temperature molecular dynamics (MD) model for coupled simulations of electronic and phonon heat conduction in nanoscale systems. The proposed method uses a master equation to perform heat conduction of…
A fundamental objective of materials modeling is identifying atomic structures that align with experimental observables. Conventional approaches for disordered materials involve sampling from thermodynamic ensembles and hoping for an…
Simulations of biological macromolecules play an important role in understanding the physical basis of a number of complex processes such as protein folding. Even with increasing computational power and evolution of specialized…
We discuss the possibility of implementing asynchronous replica-exchange (or parallel tempering) molecular dynamics. In our scheme, the exchange attempts are driven by asynchronous messages sent by one of the computing nodes, so that…
OpenMP is a cross-platform API that extends C, C++ and Fortran and provides shared-memory parallelism platform for those languages. The use of many cores and HPC technologies for scientific computing has been spread since the 1990s, and now…
Polarons are crucial for charge transport in semiconductors, significantly impacting material properties and device performance. The dynamics of small polarons can be investigated using first-principles molecular dynamics (FPMD). However,…
Python demonstrates lower performance in comparison to traditional high performance computing (HPC) languages such as C, C++, and Fortran. This performance gap is largely due to Python's interpreted nature and the Global Interpreter Lock…
The time domain analysis of eddy current problems often requires the simulation of long time intervals, e.g. until a steady state is reached. Fast-switching excitations e.g. in pulsedwidth modulated signals require in addition very small…