scholarly journals Long-time molecular dynamics simulations on massively parallel platforms: A comparison of parallel replica dynamics and parallel trajectory splicing

2017 ◽  
Vol 33 (7) ◽  
pp. 813-822 ◽  
Author(s):  
Danny Perez ◽  
Rao Huang ◽  
Arthur F. Voter
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Massively Parallel ◽  
Long Time ◽  
Dynamics Simulations ◽  
Image Position

Abstract

Investigation of thermal transport properties in pillared-graphene structure using nonequilibrium molecular dynamics simulations

2020 ◽  
Vol 10 (3) ◽  
pp. 506-511 ◽  
Author(s):  
Khaled Almahmoud ◽  
Thiruvillamalai Mahadevan ◽  
Nastaran Barhemmati-Rajab ◽  
Jincheng Du ◽  
Huseyin Bostanci ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Transport Properties ◽  
Thermal Transport ◽  
Nonequilibrium Molecular Dynamics ◽  
Thermal Transport Properties ◽  
Dynamics Simulations ◽  
Image Position

Molecular dynamics simulations of surface oxidation and of surface slip irreversibility under fatigue in oxygen environment

2017 ◽  
Vol 32 (23) ◽  
pp. 4327-4341 ◽  
Author(s):  
Zhengxuan Fan ◽  
Olivier Hardouin Duparc ◽  
Maxime Sauzay ◽  
Boubakar Diawara ◽  
Adri C.T. van Duin
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Surface Oxidation ◽  
Oxygen Environment ◽  
Surface Slip ◽  
Dynamics Simulations ◽  
Image Position

Abstract

scholarly journals ExaViz: a flexible framework to analyse, steer and interact with molecular dynamics simulations

2014 ◽  
Vol 169 ◽  
pp. 119-142 ◽  
Author(s):  
Matthieu Dreher ◽  
Jessica Prevoteau-Jonquet ◽  
Mikael Trellet ◽  
Marc Piuzzi ◽  
Marc Baaden ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Molecular System ◽  
Data Set ◽  
System P ◽  
Alternative Approach ◽  
Long Time ◽  
Flexible Framework ◽  
Sheer Size ◽  
Dynamics Simulations

The amount of data generated by molecular dynamics simulations of large molecular assemblies and the sheer size and complexity of the systems studied call for new ways to analyse, steer and interact with such calculations. Traditionally, the analysis is performed off-line once the huge amount of simulation results have been saved to disks, thereby stressing the supercomputer I/O systems, and making it increasingly difficult to handle post-processing and analysis from the scientist's office. The ExaViz framework is an alternative approach developed to couple the simulation with analysis tools to process the data as close as possible to their source of creation, saving a reduced, more manageable and pre-processed data set to disk. ExaViz supports a large variety of analysis and steering scenarios. Our framework can be used for live sessions (simulations short enough to be fully followed by the user) as well as batch sessions (long-time batch executions). During interactive sessions, at runtime, the user can display plots from analysis, visualise the molecular system and steer the simulation with a haptic device. We also emphasise how a CAVE-like immersive environment could be used to leverage such simulations, offering a large display surface to view and intuitively navigate the molecular system.

A MOLECULAR DYNAMICS RUN WITH 5 180 116 000 PARTICLES

2000 ◽  
Vol 11 (02) ◽  
pp. 317-322 ◽  
Author(s):  
J. ROTH ◽  
F. GÄHLER ◽  
H.-R. TREBIN
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Massively Parallel ◽  
Classical Molecular Dynamics ◽  
Dynamics Simulations ◽  
Parallel Supercomputers

We report on the development of IMD, a scalable program for classical molecular dynamics simulations on massively parallel supercomputers. New features like online-visualization and metacomputing are described.

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