scholarly journals Parallel Molecular Dynamics with Irregular Domain Decomposition

2011 ◽  
Vol 10 (4) ◽  
pp. 1071-1088 ◽  
Author(s):  
Mauro Bisson ◽  
Massimo Bernaschi ◽  
Simone Melchionna
Keyword(s):  
Molecular Dynamics ◽  
Blood Flow ◽  
Input Parameter ◽  
Complex Geometries ◽  
Irregular Domain ◽  
Irregular Domains ◽  
Additional Input ◽  
Parallel Molecular Dynamics ◽  
Dynamics Simulations ◽  
General Method

AbstractThe spatial domain of Molecular Dynamics simulations is usually a regular box that can be easily divided in subdomains for parallel processing. Recent efforts aimed at simulating complex biological systems, like the blood flow inside arteries, require the execution of Parallel Molecular Dynamics (PMD) in vessels that have, by nature, an irregular shape. In those cases, the geometry of the domain becomes an additional input parameter that directly influences the outcome of the simulation. In this paper we discuss the problems due to the parallelization of MD in complex geometries and show an efficient and general method to perform MD in irregular domains.

Structure, Mechanical Properties, and Thermal Transport in Microporous Silicon Nitride Via Parallel Molecular Dynamics

1995 ◽  
Vol 408 ◽  
Author(s):  
Andrey Omeltchenko ◽  
Aiichiro Nakano ◽  
Rajiv K. Kalia ◽  
Priya Vashishta
Keyword(s):  
Mechanical Properties ◽  
Thermal Conductivity ◽  
Molecular Dynamics ◽  
Silicon Nitride ◽  
Elastic Constants ◽  
Thermal Transport ◽  
Entire System ◽  
Amorphous Silicon Nitride ◽  
Parallel Molecular Dynamics ◽  
Dynamics Simulations

AbstractMolecular dynamics simulations are performed to investigate structure, mechanical properties, and thermal transport in amorphous silicon nitride under uniform dilation. As the density is lowered, we observe the formation of pores below ρ = 2.6 g/cc and at 2.0 g/cc the largest pore percolates through the entire system. Effects of porosity on elastic constants, phonons and thermal conductivity are investigated. Thermal conductivity and Young's modulus are found to scale as ρ1.5 and ρ3.6, respectively.

Parallel Molecular Dynamics Simulations and Immersive Visualization of Thermal Barrier Coating Components: Thermally Growing Oxide and Yttria Stabilized Zirconia

2013 ◽  
Author(s):  
Sanjay Kodiyalam ◽  
Michael Benissan ◽  
Stephen Akwaboa ◽  
Patrick F. Mensah ◽  
Amitava Jana ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Thermal Expansion ◽  
Diffusion Constant ◽  
Yttria Stabilized Zirconia ◽  
Dynamics Simulation ◽  
Heat Current ◽  
Stabilized Zirconia ◽  
Barrier Coating ◽  
Parallel Molecular Dynamics ◽  
Dynamics Simulations

Non-equilibrium parallel molecular dynamics simulation is used to determine the thermal conductivity of Alumina in the [2 1 1 0]direction at 1200 K: When thermal expansion is not allowed it is found to be 3.45 W/mK, while with thermal expansion it is 2.95 W/mK. A short ranged empirical potential for Yttria stabilized Zirconia (YSZ) is developed by fitting to available ab initio and experimentally derived data for Zirconia. With this potential, simulations of YSZ at 2073.16 K, with 4.9–23.1 mol% of Yttria in Zirconia, shows diffusing Oxygen and non-diffusing Zirconium and Yttrium atoms as expected. However, the diffusion constant of oxygen increases with the Yttria content, inconsistent with simulations with long range interactions showing a peak around 10 mol% of Yttria and also inconsistent experiment at 923 K. Visualizing the dynamics of atoms in Alumina, when driven by a heat-current forcing perturbation, shows phonon-like modes indicating the need for smaller perturbation or an alternate method to determine thermal properties.

MASSIVELY DATA-PARALLEL MOLECULAR DYNAMICS

1992 ◽  
Vol 03 (04) ◽  
pp. 709-731
Author(s):  
ERNESTO BONOMI ◽  
MARCO TOMASSINI
Keyword(s):  
Molecular Dynamics ◽  
Heat Bath ◽  
Hard Core ◽  
Parallel Computers ◽  
Particle Systems ◽  
Data Parallel ◽  
Connection Machine ◽  
Large N ◽  
Parallel Molecular Dynamics ◽  
Dynamics Simulations

In light of present day data-parallel computers, an appraisal of molecular dynamics simulations of large N-particle systems, isolated or in contact with a heat-bath, is given. Special attention is focused 011 the Connection Machine CM-2. Particularly the cases of long-range potentials and impulsive hard-core interactions are discussed in detail. Data-parallel strategies including data distribution, communications and computation are presented and compared with well-known sequential approaches. The conclusion offered is that the methods described here are easy to design and offer the possibility of reasonably fast implementations for the reliable simulation of macroscopic samples of matter.

PARALLEL MOLECULAR DYNAMICS SIMULATIONS OF ORGANIC MATERIALS

1994 ◽  
Vol 05 (02) ◽  
pp. 295-298 ◽  
Author(s):  
STEVE PLIMPTON ◽  
BRUCE HENDRICKSON
Keyword(s):  
Molecular Dynamics ◽  
Parallel Algorithms ◽  
Molecular Dynamics Simulations ◽  
Parallel Algorithm ◽  
Communication Cost ◽  
Dynamics Model ◽  
Organic Systems ◽  
Intel Paragon ◽  
Parallel Molecular Dynamics ◽  
Dynamics Simulations

A new parallel algorithm suitable for molecular dynamics simulations of organic systems is presented. It reduces the communication cost and memory requirements of other commonly-used parallel algorithms by a factor of [Formula: see text] where P is the number of processors. The algorithm has been implemented in a CHARMM-like molecular dynamics model and its performance on 1024-processor nCUBE 2 and Intel Paragon machines is discussed.

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