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.

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.

Molecular dynamics simulation of the crystallization of liquid GaAs nanoparticles

2019 ◽  
Vol 33 (31) ◽  
pp. 1950392
Author(s):  
Qian Chen ◽  
Yao Zhou ◽  
Zean Tian ◽  
Tinghong Gao ◽  
Ting Xiao ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Coordination Number ◽  
Large Scale ◽  
Crystallization Process ◽  
Surface Effect ◽  
Dynamics Simulation ◽  
Massively Parallel ◽  
Zinc Blende ◽  
Zinc Blende Structure ◽  
Number Form

The GaAs nanoparticles crystallization process was simulated with the molecular dynamics package large-scale atomic/molecular massively parallel simulator (LAMMPS). The results show that due to the surface effect, GaAs nanoparticles have a low melting temperature and poor order, and that their atomic thermal vibration at high temperatures is more severe than that of GaAs crystals. The crystallization process of GaAs nanoparticles begins at 970 K and generally completes at 920 K. Atoms with coordination number 3 or 4 form honeycomb-like defective (111) faces of zinc-blende structure on the surface; and atoms with a higher coordination number form two-dimensional dense structures at the subsurface.

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.

scholarly journals Molecular Dynamics Simulation of Tolman Length and Interfacial Tension of Symmetric Binary Lennard–Jones Liquid

Symmetry ◽  
2021 ◽  
Vol 13 (8) ◽  
pp. 1376
Author(s):  
Hideki Kanda ◽  
Wahyudiono ◽  
Motonobu Goto
Keyword(s):  
Molecular Dynamics ◽  
Interfacial Tension ◽  
Large Scale ◽  
Interfacial Area ◽  
Dynamics Simulation ◽  
Continuum Approximation ◽  
Lennard Jones ◽  
Partially Miscible ◽  
Tolman Length ◽  
Dividing Surface

The Tolman length and interfacial tension of partially miscible symmetric binary Lennard–Jones (LJ) fluids (A, B) was revealed by performing a large-scale molecular dynamics (MD) simulation with a sufficient interfacial area and cutting distance. A unique phenomenon was observed in symmetric binary LJ fluids, where two surfaces of tension existed on both sides of an equimolar dividing surface. The range of interaction εAB between the different liquids and the temperature in which the two LJ fluids partially mixed was clarified, and the Tolman length exceeded 3 σ when εAB was strong at higher temperatures. The results show that as the temperature or εAB increases, the Tolman length increases and the interfacial tension decreases. This very long Tolman length indicates that one should be very careful when applying the concept of the liquid–liquid interface in the usual continuum approximation to nanoscale droplets and capillary phase separation in nanopores.

Analysis of a one-billion atom simulation of work-hardening in ductile materials

2004 ◽  
Vol 821 ◽  
Author(s):  
Markus J. Buehler ◽  
Alexander Hartmaier ◽  
Mark Duchaineau ◽  
Farid F. Abraham ◽  
Huajian Gao
Keyword(s):  
Molecular Dynamics ◽  
Work Hardening ◽  
Large Scale ◽  
Pair Potential ◽  
Model Material ◽  
Dynamics Simulation ◽  
Ductile Materials ◽  
Lennard Jones ◽  
Cutting Processes ◽  
First Time

AbstractWe analyze a large-scale molecular dynamics simulation of work hardening in a ductile model material comprising of 500 million atoms interacting with a Lennard-Jones pair potential within a classical molecular dynamics scheme. With tensile loading, we observe emission of thousands of dislocations from two sharp cracks. The dislocations interact in a complex way, revealing three fundamental mechanisms of work-hardening. These are (1) dislocation cutting processes, jog formation and generation of point defects; (2) activation of secondary slip systems by cross-slip; and (3) formation of sessile Lomer-Cottrell locks. The dislocations self-organize into a complex sessile defect topology. Our analysis illustrates mechanisms formerly only known from textbooks and observed indirectly in experiment. It is the first time that such a rich set of fundamental phenomena has been seen in a single computer simulation.

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.

Multicanonical Molecular Dynamics Simulation Study of the Liquid-Solid and Solid-Solid Transitions in Lennard-Jones Clusters

2011 ◽  
Author(s):  
Toshihiro Kaneko ◽  
Kenji Yasuoka ◽  
Ayori Mitsutake ◽  
Xiao Cheng Zeng
Keyword(s):  
Molecular Dynamics ◽  
Heat Capacity ◽  
Transition Temperature ◽  
Peak Position ◽  
Temperature Curve ◽  
Dynamics Simulation ◽  
Lennard Jones ◽  
Dynamics Simulations ◽  
First Time ◽  
Good Agreement

Multicanonical molecular dynamics simulations are applied, for the first time, to study the liquid-solid and solid-solid transitions in Lennard-Jones (LJ) clusters. The transition temperatures are estimated based on the peak position in the heat capacity versus temperature curve. For LJ31, LJ58 and LJ98, our results on the solid-solid transition temperature are in good agreement with previous ones. For LJ309, the predicted liquid-solid transition temperature is also in agreement with previous result.

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