MOLECULAR DYNAMICS SIMULATIONS OF GRANULAR MATERIALS ON THE INTEL iPSC/860

In this paper we present an efficient algorithm to perform Molecular Dynamics simulations on a distributed memory parallel computer, the Intel iPSC/860. The proposed model describes the flow properties of granular materials in two dimensions. The specific implementation on a 32 node iPSC/860, especially the message passing and load balancing algorithms, are discussed in detail. Performance data are shown for different computers and varying node numbers of the iPSC/860. As a physical example we calculate some properties of the outflow behavior from a two-dimensional hopper and we discuss possible extensions of our model to three dimensions. Our simulations show that Molecular Dynamics simulations can be implemented quite efficiently on a distributed memory parallel computer if one assures load balancing and optimizes the internode communications.

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Fracture of Nanophase Ceramics: A Molecular-Dynamics Study

MRS Proceedings ◽

10.1557/proc-457-187 ◽

1996 ◽

Vol 457 ◽

Author(s):

Aiichiro Nakano ◽

Rajiv K. Kalia ◽

Andrey Omeltchenko ◽

Kenji Tsuruta ◽

Priya Vashishta

Keyword(s):

Molecular Dynamics ◽

Silicon Nitride ◽

Load Balancing ◽

Molecular Dynamics Simulations ◽

Dynamic Fracture ◽

Parallel Computers ◽

Fracture Surfaces ◽

Affine Structures ◽

Dynamics Simulations ◽

Multiscale Algorithms

ABSTRACTNew multiscale algorithms and a load-balancing scheme are combined for molecular-dynamics simulations of nanocluster-assembled ceramics on parallel computers. Million-atom simulations of the dynamic fracture in nanophase silicon nitride reveal anisotropie self-affine structures and crossover phenomena associated with fracture surfaces.

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Adaptive Load-Balancing for Force-Decomposition Based 3-Body Molecular Dynamics Simulations in A Heterogeneous Distributed Environment with Variable Number of Processors

2007 International Conference on Parallel Processing (ICPP 2007) ◽

10.1109/icpp.2007.11 ◽

2007 ◽

Cited By ~ 1

Author(s):

J.V. Sumanth ◽

David R. Swanson ◽

Hong Jiang

Keyword(s):

Molecular Dynamics ◽

Load Balancing ◽

Molecular Dynamics Simulations ◽

Variable Number ◽

Distributed Environment ◽

Dynamics Simulations ◽

Force Decomposition

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Distributed load balancing for molecular dynamics simulations

Proceedings 16th Annual International Symposium on High Performance Computing Systems and Applications ◽

10.1109/hpcsa.2002.1019172 ◽

2003 ◽

Cited By ~ 3

Author(s):

A. Di Serio ◽

M.B. Ibanez

Keyword(s):

Molecular Dynamics ◽

Load Balancing ◽

Molecular Dynamics Simulations ◽

Distributed Load ◽

Dynamics Simulations

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Molecular Dynamics Simulations of Granular Materials

The Physics of Granular Media ◽

10.1002/352760362x.ch13 ◽

2004 ◽

pp. 297-324 ◽

Cited By ~ 18

Author(s):

Stefan Luding

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Granular Materials ◽

Dynamics Simulations

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Performance optimization of reactive molecular dynamics simulations with dynamic charge distribution models on distributed memory platforms

Proceedings of the ACM International Conference on Supercomputing - ICS '19 ◽

10.1145/3330345.3330359 ◽

2019 ◽

Cited By ~ 1

Author(s):

Kurt A. O'Hearn ◽

Abdullah Alperen ◽

Hasan Metin Aktulga

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Charge Distribution ◽

Performance Optimization ◽

Distributed Memory ◽

Distribution Models ◽

Reactive Molecular Dynamics ◽

Dynamic Charge ◽

Dynamics Simulations

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Ab-Initio Molecular Dynamics of Organic Compounds on a Massively Parallel Computer

MRS Proceedings ◽

10.1557/proc-408-131 ◽

1995 ◽

Vol 408 ◽

Author(s):

François Gygi

Keyword(s):

Experimental Data ◽

Molecular Dynamics ◽

Ab Initio ◽

Molecular Dynamics Simulations ◽

Organic Compounds ◽

Organic Molecules ◽

Curvilinear Coordinates ◽

Parallel Computer ◽

Massively Parallel ◽

Dynamics Simulations

AbstractWe present results of ab-initio electronic structure calculations and molecular dynamics simulations of organic molecules carried out using adaptive curvilinear coordinates, within the local density approximation of density functional theory. This approach allows for an accurate treatment of first-row elements, which makes it particularly suitable for investigations of organic compounds. A recent formulation of this method relies on a real-space approach which combines the advantages of finite-difference methods with the accuracy of adaptive coordinates, and is well suited for implementation on massively parallel computers. We used molecular dynamics simulations to obtain the fully relaxed structures of nitrosyl fluoride (FNO), and of the aromatic heterocycles furan and pyrrole. The equilibrium geometries obtained show excellent agreement with experimental data. The harmonic vibrational frequencies of furan and pyrrole were calculated by diagonalization of their dynamical matrix and are found to agree with experimental data within an rms error of 25 cm-1 and 28 cm-1 for furan and pyrrole respectively. This accuracy is comparable to that attained for smaller organic molecules using elaborate quantum chemistry methods.

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