scholarly journals A Linked-Cell Domain Decomposition Method for Molecular Dynamics Simulation on a Scalable Multiprocessor

1992 ◽  
Vol 1 (2) ◽  
pp. 153-161 ◽  
Author(s):  
L.H. Yang ◽  
E.D. Brooks III ◽  
J. Belak
Keyword(s):  
Molecular Dynamics ◽  
Large Scale ◽  
Domain Decomposition Method ◽  
Dynamics Simulation ◽  
Parallel Computer ◽  
Interprocessor Communication ◽  
Programming Paradigm ◽  
C Preprocessor ◽  
Large Scale Simulations ◽  
Cell Data

A molecular dynamics algorithm for performing large-scale simulations using the Parallel C Preprocessor (PCP) programming paradigm on the BBN TC2000, a massively parallel computer, is discussed. The algorithm uses a linked-cell data structure to obtain the near neighbors of each atom as time evoles. Each processor is assigned to a geometric domain containing many subcells and the storage for that domain is private to the processor. Within this scheme, the interdomain (i.e., interprocessor) communication is minimized.

Nano-Indentation Simulation Study Based on Parallel Computing

2012 ◽  
Vol 500 ◽  
pp. 696-701
Author(s):  
Ying Zhu ◽  
Sen Song ◽  
Ling Ling Xie ◽  
Shun He Qi ◽  
Qian Qian Liu
Keyword(s):  
Molecular Dynamics ◽  
Parallel Computing ◽  
Molecular Dynamics Simulation ◽  
Large Scale ◽  
Dynamics Simulation ◽  
Parallel Computer ◽  
Nano Indentation ◽  
Simulation Results ◽  
The Impact ◽  
Simulation Time

This method of parallel computing into nanoindentation molecular dynamics simulation (MDS), the author uses a nine-node parallel computer and takes the single crystal aluminum as the experimental example, to implement the large-scale process simulation of nanoindentation. Compared the simulation results with experimental results is to verify the reliability of the simulation. The method improves the computational efficiency and shortens the simulation time and the expansion of scale simulation can significantly reduce the impact of boundary conditions, effectively improve the accuracy of the molecular dynamics simulation of nanoindentation.

Preparation, Structure, And Electronic Properties Of Amorphous Gaas By Tight-Binding Molecular Dynamics

1993 ◽  
Vol 321 ◽  
Author(s):  
C. Molteni ◽  
L. Colombo ◽  
L. Miglio
Keyword(s):  
Molecular Dynamics ◽  
First Principles ◽  
Large Scale ◽  
Tight Binding ◽  
Computer Experiment ◽  
Dynamics Simulation ◽  
First Principles Calculations ◽  
Amorphous Network ◽  
Large Scale Simulations

ABSTRACTWe investigate the short-range structural properties of a-GaAs as obtained in a computer experiment based on a tight-binding molecular dynamics simulation. The amorphous configuration is obtained by quenching a liquid sample well equilibrated at T=1600 K. A detailed characterization of the topology and defect distribution of the amorphous network is presented and discussed. The electronic structure of our sample is calculated as well. Finally, we discuss the reliability and transferability of the present computational scheme for large-scale simulations of compound semiconductor materials by comparing our results to first-principles calculations.

LARGE-SCALE MOLECULAR-DYNAMICS SIMULATION OF 19 BILLION PARTICLES

2004 ◽  
Vol 15 (01) ◽  
pp. 193-201 ◽  
Author(s):  
KAI KADAU ◽  
TIMOTHY C. GERMANN ◽  
PETER S. LOMDAHL
Keyword(s):  
Molecular Dynamics ◽  
Large Scale ◽  
Dynamics Simulation ◽  
Atomistic Simulations ◽  
Huge Number ◽  
Physical Problems ◽  
Efficient Data ◽  
Dynamics Simulations ◽  
Large Scale Simulations ◽  
Efficient Data Analysis

We have performed parallel large-scale molecular-dynamics simulations on the QSC-machine at Los Alamos. The good scalability of the SPaSM code is demonstrated together with its capability of efficient data analysis for enormous system sizes up to 19 000 416 964 particles. Furthermore, we introduce a newly-developed graphics package that renders in a very efficient parallel way a huge number of spheres necessary for the visualization of atomistic simulations. These abilities pave the way for future atomistic large-scale simulations of physical problems with system sizes on the μ-scale.

scholarly journals HYPER-SYSTOLIC PROCESSING ON APE100/QUADRICS: n2-LOOP COMPUTATIONS

1996 ◽  
Vol 07 (04) ◽  
pp. 485-501 ◽  
Author(s):  
THOMAS LIPPERT ◽  
GERO RITZENHÖFER ◽  
UWE GLAESSNER ◽  
HENNING HOEBER ◽  
ARMIN SEYFRIED ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Body Problem ◽  
Three Dimensional ◽  
Dynamics Simulation ◽  
Parallel Computer ◽  
Massively Parallel ◽  
Interprocessor Communication ◽  
Communication Costs ◽  
N Body Problem ◽  
Performance Gains

We investigate the performance gains from hyper-systolic implementations of n2-loop problems on the massively parallel computer Quadrics, exploiting its three-dimensional interprocessor connectivity. For illustration we study the communication aspects of an exact molecular dynamics simulation of n particles with Coulomb (or gravitational) interactions. We compare the interprocessor communication costs of the standard-systolic and the hyper-systolic approaches for various granularities. We predict gain factors as large as three on the Q4 and eight on the QH4 and measure actual performances on these machine configurations. We conclude that it appears feasible to investigate the thermodynamics of a full gravitating n-body problem with O(16.000) particles using the new method on a QH4 system.

scholarly journals TRILLION-ATOM MOLECULAR DYNAMICS BECOMES A REALITY

2008 ◽  
Vol 19 (09) ◽  
pp. 1315-1319 ◽  
Author(s):  
TIMOTHY C. GERMANN ◽  
KAI KADAU
Keyword(s):  
Molecular Dynamics ◽  
Large Scale ◽  
Shear Instability ◽  
Dynamics Simulation ◽  
Massively Parallel ◽  
Lennard Jones ◽  
Simple Cubic ◽  
Simple Cubic Lattice ◽  
Future Potential ◽  
Large Scale Simulations

By utilizing the molecular dynamics code SPaSM on Livermore's BlueGene/L architecture, consisting of 212 992 IBM PowerPC440 700 MHz processors, a molecular dynamics simulation was run with one trillion atoms. To demonstrate the practicality and future potential of such ultra large-scale simulations, the onset of the mechanical shear instability occurring in a system of Lennard-Jones particles arranged in a simple cubic lattice was simulated. The evolution of the instability was analyzed on-the-fly using the in-house developed massively parallel graphical object-rendering code MD_render.

Large-Scale Molecular Dynamics Investigation of Nanoscale Laser Material Processing

2003 ◽  
Author(s):  
Xinwei Wang ◽  
Hua Zhu
Keyword(s):  
Molecular Dynamics ◽  
Large Scale ◽  
Axial Direction ◽  
Sample Surface ◽  
Dynamics Simulation ◽  
Parallel Computer ◽  
Scanning Tunneling ◽  
Laser Material Processing ◽  
Surface Nanostructures ◽  
Nanoscale Manufacturing

In this work, large-scale molecular dynamics simulation is conducted to explore nanoscale manufacturing with laser-assisted scanning tunneling microscope. Employing a super parallel computer, more than 100 million atoms are modeled to provide substantial details about how the localized thermal and mechanical perturbations result in surface nanostructures. It is found that thermal equilibrium cannot be established due to the small number of atoms. Extremely localized stress accumulation beneath the sample surface results in an explosion of the melted/vaporized material, leaving a nanoscale hole on the sample surface. Normal and shear stress development is observed. Stress propagation in space is strongly influenced by the anisotropic nature of the crystal. The high pressure in the melted/vaporized region pushes the melt adjacent to the solid to move, thereby forming a protrusion at the edge of the hole. More importantly, visible structural destruction is observed in the region close to the bottom of the sample. These destructions are along the direction of 45 degrees with respect to the axial direction, and are attributed to the strong tensile stress. Atomic dislocation is observed in the destructed regions.

Combustion Driven by Fragment-based Ab Initio Molecular Dynamics Simulation

2019 ◽  
Author(s):  
Liqun Cao ◽  
Jinzhe Zeng ◽  
Mingyuan Xu ◽  
Chih-Hao Chin ◽  
Tong Zhu ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Ab Initio ◽  
Large Scale ◽  
Methane Combustion ◽  
Combustion Method ◽  
Dynamics Simulation ◽  
Ab Initio Molecular Dynamics ◽  
Computational Time ◽  
Combustion Mechanism ◽  
Daily Lives

Combustion is a kind of important reaction that affects people's daily lives and the development of aerospace. Exploring the reaction mechanism contributes to the understanding of combustion and the more efficient use of fuels. Ab initio quantum mechanical (QM) calculation is precise but limited by its computational time for large-scale systems. In order to carry out reactive molecular dynamics (MD) simulation for combustion accurately and quickly, we develop the MFCC-combustion method in this study, which calculates the interaction between atoms using QM method at the level of MN15/6-31G(d). Each molecule in systems is treated as a fragment, and when the distance between any two atoms in different molecules is greater than 3.5 Å, a new fragment involved two molecules is produced in order to consider the two-body interaction. The deviations of MFCC-combustion from full system calculations are within a few kcal/mol, and the result clearly shows that the calculated energies of the different systems using MFCC-combustion are close to converging after the distance thresholds are larger than 3.5 Å for the two-body QM interactions. The methane combustion was studied with the MFCC-combustion method to explore the combustion mechanism of the methane-oxygen system.

Sputtering of Graphite by Hydrogen Isotopes in the Fusion Environment: A Molecular Dynamics Simulation Study

2018 ◽  
Vol 4 (4) ◽  
Author(s):  
Qiang Zhao ◽  
Yang Li ◽  
Zheng Zhang ◽  
Xiaoping Ouyang
Keyword(s):  
Molecular Dynamics ◽  
Incident Energy ◽  
Large Scale ◽  
Incident Angle ◽  
Hydrogen Isotopes ◽  
Dynamics Simulation ◽  
Calculation Results ◽  
Sputtering Yield ◽  
Increasing Temperature ◽  
Sputtering Yields

The sputtering of graphite due to the bombardment of hydrogen isotopes is crucial to successfully using graphite in the fusion environment. In this work, we use molecular dynamics to simulate the sputtering using the large-scale atomic/molecular massively parallel simulator (lammps). The calculation results show that the peak values of the sputtering yield are between 25 eV and 50 eV. When the incident energy is greater than the energy corresponding to the peak value, a lower carbon sputtering yield is obtained. The temperature that is most likely to sputter is approximately 800 K for hydrogen, deuterium, and tritium. Below the 800 K, the sputtering yields increase with temperature. By contrast, above the 800 K, the yields decrease with increasing temperature. Under the same temperature and incident energy, the sputtering rate of tritium is greater than that of deuterium, which in turn is greater than that of hydrogen. When the incident energy is 25 eV, the sputtering yield at 300 K increases below an incident angle at 30 deg and remains steady after that.

Crack Growth and Propagation in Metallic Alloys

1995 ◽  
Vol 409 ◽  
Author(s):  
W. C. Morrey ◽  
L. T. Wille
Keyword(s):  
Large Scale ◽  
Critical Strain ◽  
Cleavage Plane ◽  
Crack Tip ◽  
Metallic Alloys ◽  
Propagation Direction ◽  
Dynamics Simulation ◽  
Parallel Computer ◽  
Massively Parallel ◽  
Tip Position

AbstractUsing large-scale molecular dynamics simulation on a massively parallel computer, we have studied the initiation of cracking in a Monel-like alloy of Cu-Ni. In a low temperature 2D sample, fracture from a notch starts at a little beyond 2.5% critical strain when the propagation direction is perpendicular to a cleavage plane. We discuss a method of characterizing crack tip position using a measure of area around the crack tip.

Molecular Dynamics Simulation of a Pullout Test on a Carbon Nanotube in a Polymer Matrix

2014 ◽  
Vol 1700 ◽  
pp. 61-66
Author(s):  
Guttormur Arnar Ingvason ◽  
Virginie Rollin
Keyword(s):  
Molecular Dynamics ◽  
Polymer Matrix ◽  
Large Scale ◽  
Md Simulations ◽  
Dynamics Simulation ◽  
Atomistic Simulations ◽  
Polymer Molecules ◽  
Molecular Potential ◽  
Pull Out ◽  
Walled Carbon Nanotubes

ABSTRACTAdding single walled carbon nanotubes (SWCNT) to a polymer matrix can improve the delamination properties of the composite. Due to the complexity of polymer molecules and the curing process, few 3-D Molecular Dynamics (MD) simulations of a polymer-SWCNT composite have been run. Our model runs on the Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS), with a COMPASS (Condensed phase Optimized Molecular Potential for Atomistic Simulations Studies) potential. This potential includes non-bonded interactions, as well as bonds, angles and dihedrals to create a MD model for a SWCNT and EPON 862/DETDA (Diethyltoluenediamine) polymer matrix. Two simulations were performed in order to test the implementation of the COMPASS parameters. The first one was a tensile test on a SWCNT, leading to a Young’s modulus of 1.4 TPa at 300K. The second one was a pull-out test of a SWCNT from an originally uncured EPON 862/DETDA matrix.

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