Related papers: On the hierarchical parallelization of ab initio s…
A hybrid-parallel direct-numerical-simulation method with application to turbulent Taylor-Couette flow is presented. The Navier-Stokes equations are discretized in cylindrical coordinates with the spectral Fourier-Galerkin method in the…
An improved implementation of an N-body code for simulating collisionless cosmological dynamics is presented. TPM (Tree-Particle-Mesh) combines the PM method on large scales with a tree code to handle particle-particle interactions at small…
Using the Gaussian-03 for ab initio calculations, we have studied interaction of different acid molecules with a single water molecule. The molecular and supermolecular optimized structures were found with the Becke-3-Lee-Yang-Parr…
We present an improvement of the Gillespie Exact Stochastic Simulation Algorithm, which leverages a bitwise representation of variables to perform independent simulations in parallel. We show that the subsequent gain in computational yield…
We describe a new implementation of a parallel Tree-SPH code with the aim to simulate Galaxy Formation and Evolution. The code has been parallelized using SHMEM, a Cray proprietary library to handle communications between the 256 processors…
Ab initio simulations are capable of providing detailed information of material behavior at the nanoscale. Simulating experimentally relevant situations is, however, often computationally intense. Using hybrid approaches between ab initio…
Furthering our understanding of many of today's interesting problems in plasma physics---including plasma based acceleration and magnetic reconnection with pair production due to quantum electrodynamic effects---requires large-scale kinetic…
We present an efficient parallel algorithm for statistical Molecular Dynamics simulations of ion tracks in solids. The method is based on the Rare Event Enhanced Domain following Molecular Dynamics (REED-MD) algorithm, which has been…
A parallel numerical simulation algorithm is presented for fractional-order systems involving Caputo-type derivatives, based on the Adams-Bashforth-Moulton (ABM) predictor-corrector scheme. The parallel algorithm is implemented using…
Pipeline parallelism (PP) when training neural networks enables larger models to be partitioned spatially, leading to both lower network communication and overall higher hardware utilization. Unfortunately, to preserve the statistical…
We describe a simplified approach to simulating Raman spectra using ab initio molecular dynamics (AIMD) calculations. Our protocol relies on on-the-fly calculations of approximate molecular polarizabilities using a sum over orbitals (as…
A parameterization strategy for molecular models on the basis of force fields is proposed, which allows a rapid development of models for small molecules by using results from quantum mechanical (QM) ab initio calculations and thermodynamic…
The Particle-In-Cell (PIC) method for plasma simulation tracks particle phase space information using particle and grid data structures. High computational costs in 2D and 3D device-scale PIC simulations necessitate parallelization, with…
Since the introduction of the CDC 6600 in 1965 and its `scoreboarding' technique processors have not (necessarily) executed instructions in program order. Programmers of high-level code may sequence independent instructions in arbitrary…
We present simulations of coherent structures in compressible flows near the transition to turbulence using the Dissipative Particle Dynamics (DPD) method. The structures we find are remarkably consistent with experimental observations and…
A path-integral hybrid Monte Carlo approach with enveloping bridging potentials (PIHMC-EBP) is proposed for calculating numerically exact tunneling splittings in molecular systems. The central idea is to construct an approximately…
A mixed basis approach based on density functional theory is extended to one-dimensional(1D) systems. The basis functions here are taken to be the localized B-splines for the two finite non-periodic dimensions and the plane waves for the…
While distributed systems with transfer of processes have become pervasive, methods for reasoning about their behaviour are underdeveloped. In this paper we propose a bisimulation technique for proving behavioural equivalence of such…
The separation between molecular and mesoscopic length and time scales poses a severe limit to molecular simulations of mesoscale phenomena. We describe a hybrid multiscale computational technique which address this problem by keeping the…
In this work we studied polymerization-induced self-assembly by means of computer simulations. Using this model, phase diagrams of the micelle states were constructed depending on the polymer concentration and the asymmetry of the…