Sassena — X-ray and neutron scattering calculated from molecular dynamics trajectories using massively parallel computers

2012 ◽  
Vol 183 (7) ◽  
pp. 1491-1501 ◽  
Author(s):  
Benjamin Lindner ◽  
Jeremy C. Smith
Keyword(s):  
Molecular Dynamics ◽  
Neutron Scattering ◽  
Parallel Computers ◽  
Massively Parallel ◽  
X Ray ◽  
Massively Parallel Computers

IMD: A Software Package for Molecular Dynamics Studies on Parallel Computers

1997 ◽  
Vol 08 (05) ◽  
pp. 1131-1140 ◽  
Author(s):  
J. Stadler ◽  
R. Mikulla ◽  
H.-R. Trebin
Keyword(s):  
Molecular Dynamics ◽  
Software Package ◽  
Large Scale ◽  
Md Simulation ◽  
Parallel Computers ◽  
Massively Parallel ◽  
Massively Parallel Computers ◽  
Communication Scheme ◽  
And Performance ◽  
Dynamics Simulations

We report on implementation and performance of the program IMD, designed for short range molecular dynamics simulations on massively parallel computers. After a short explanation of the cell-based algorithm, its extension to parallel computers as well as two variants of the communication scheme are discussed. We provide performance numbers for simulations of different sizes and compare them with values found in the literature. Finally we describe two applications, namely a very large scale simulation with more than 1.23×109 atoms, to our knowledge the largest published MD simulation up to this day and a simulation of a crack propagating in a two-dimensional quasicrystal.

Molecular dynamics for very large systems on massively parallel computers: The MPSim program

1997 ◽  
Vol 18 (4) ◽  
pp. 501-521 ◽  
Author(s):  
Kian-Tat Lim ◽  
Sharon Brunett ◽  
Mihail Iotov ◽  
Richard B. McClurg ◽  
Nagarajan Vaidehi ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Parallel Computers ◽  
Massively Parallel ◽  
Massively Parallel Computers ◽  
Large Systems

scholarly journals The DL_POLY molecular dynamics package

2005 ◽  
Vol 220 (5/6) ◽  
Author(s):  
William Smith ◽  
Ilian T. Todorov ◽  
Maurice Leslie
Keyword(s):  
Molecular Dynamics ◽  
Parallel Computers ◽  
Massively Parallel ◽  
Small Systems ◽  
Molecular Systems ◽  
Classical Molecular Dynamics ◽  
Massively Parallel Computers ◽  
Wide Range ◽  
Single Processor

AbstractThe DL_POLY package provides a set of classical molecular dynamics programs that have application over a wide range of atomic and molecular systems. Written for parallel computers they offer capabilities stretching from small systems consisting of a few hundred atoms running on a single processor, up to systems of several million atoms running on massively parallel computers with thousands of processors. In this article we describe the structure of the programs and some applications.

The Fast Multipole Method in Canonical Ensemble Dynamics on Massively Parallel Computers

1992 ◽  
Vol 278 ◽  
Author(s):  
Steven R. Lustig ◽  
J.J. Cristy ◽  
D.A. Pensak
Keyword(s):  
Canonical Ensemble ◽  
Yukawa Potential ◽  
Direct Method ◽  
Fast Multipole Method ◽  
Parallel Computers ◽  
Massively Parallel ◽  
Fast Multipole ◽  
Massively Parallel Computers ◽  
Multipole Method ◽  
Execution Times

AbstractThe fast multipole method (FMM) is implemented in canonical ensemble particle simulations to compute non-bonded interactions efficiently with explicit error control. Multipole and local expansions have been derived to implement the FMM efficiently in Cartesian coordinates for soft-sphere (inverse power law), Lennard- Jones, Morse and Yukawa potential functions. Significant reductions in execution times have been achieved with respect to the direct method. For a given number, N, of particles the execution times of the direct method scale asO(N2). The FMM execution times scale asO(N) on sequential workstations and vector processors and asymptotically0(logN) on massively parallel computers. Connection Machine CM-2 and WAVETRACER-DTC parallel FMM implementations execute faster than the Cray-YMP vectorized FMM for ensemble sizes larger than 28k and 35k, respectively. For 256k particle ensembles the CM-2 parallel FMM is 12 times faster than the Cray-YMP vectorized direct method and 2.2 times faster than the vectorized FMM. For 256k particle ensembles the WAVETRACER-DTC parallel FMM is 33 times faster than the Cray-YMP vectorized direct method.

Sign in / Sign up

Export Citation Format

Share Document