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Title: Cluster analysis of accelerated molecular dynamics simulations: A case study of the decahedron to icosahedron transition in Pt nanoparticles

Abstract

Modern molecular-dynamics-based techniques are extremely powerful to investigate the dynamical evolution of materials. With the increase in sophistication of the simulation techniques and the ubiquity of massively parallel computing platforms, atomistic simulations now generate very large amounts of data, which has to be carefully analyzed in order to reveal key features of the underlying trajectories, including the nature and characteristics of the relevant reaction pathways. We show that clustering algorithms, such as the Perron Cluster Cluster Analysis, can provide reduced representations that greatly facilitate the interpretation of complex trajectories. To illustrate this point, clustering tools are used to identify the key kinetic steps in complex Accelerated Molecular Dynamics trajectories exhibiting shape uctuations in Pt nanoclusters. This analysis provides an easily-interpretable coarse representation of the reaction pathways in terms of a handful of clusters, in contrast to the raw trajectory that contains thousands of unique states and tens of thousands of transitions.

Authors:
ORCiD logo [1]; ORCiD logo [2];  [3];  [2]; ORCiD logo [2]
  1. Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Xiamen Univ. (China)
  2. Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
  3. Xiamen Univ. (China)
Publication Date:
Research Org.:
Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
Sponsoring Org.:
USDOE Office of Nuclear Energy (NE)
OSTI Identifier:
1463546
Alternate Identifier(s):
OSTI ID: 1375255
Report Number(s):
LA-UR-17-23766
Journal ID: ISSN 0021-9606
Grant/Contract Number:  
AC52-06NA25396
Resource Type:
Accepted Manuscript
Journal Name:
Journal of Chemical Physics
Additional Journal Information:
Journal Volume: 147; Journal Issue: 15; Journal ID: ISSN 0021-9606
Publisher:
American Institute of Physics (AIP)
Country of Publication:
United States
Language:
English
Subject:
74 ATOMIC AND MOLECULAR PHYSICS; Material Science

Citation Formats

Huang, Rao, Lo, Li-Ta, Wen, Yuhua, Voter, Arthur F., and Perez, Danny. Cluster analysis of accelerated molecular dynamics simulations: A case study of the decahedron to icosahedron transition in Pt nanoparticles. United States: N. p., 2017. Web. https://doi.org/10.1063/1.4996922.
Huang, Rao, Lo, Li-Ta, Wen, Yuhua, Voter, Arthur F., & Perez, Danny. Cluster analysis of accelerated molecular dynamics simulations: A case study of the decahedron to icosahedron transition in Pt nanoparticles. United States. https://doi.org/10.1063/1.4996922
Huang, Rao, Lo, Li-Ta, Wen, Yuhua, Voter, Arthur F., and Perez, Danny. Wed . "Cluster analysis of accelerated molecular dynamics simulations: A case study of the decahedron to icosahedron transition in Pt nanoparticles". United States. https://doi.org/10.1063/1.4996922. https://www.osti.gov/servlets/purl/1463546.
@article{osti_1463546,
title = {Cluster analysis of accelerated molecular dynamics simulations: A case study of the decahedron to icosahedron transition in Pt nanoparticles},
author = {Huang, Rao and Lo, Li-Ta and Wen, Yuhua and Voter, Arthur F. and Perez, Danny},
abstractNote = {Modern molecular-dynamics-based techniques are extremely powerful to investigate the dynamical evolution of materials. With the increase in sophistication of the simulation techniques and the ubiquity of massively parallel computing platforms, atomistic simulations now generate very large amounts of data, which has to be carefully analyzed in order to reveal key features of the underlying trajectories, including the nature and characteristics of the relevant reaction pathways. We show that clustering algorithms, such as the Perron Cluster Cluster Analysis, can provide reduced representations that greatly facilitate the interpretation of complex trajectories. To illustrate this point, clustering tools are used to identify the key kinetic steps in complex Accelerated Molecular Dynamics trajectories exhibiting shape uctuations in Pt nanoclusters. This analysis provides an easily-interpretable coarse representation of the reaction pathways in terms of a handful of clusters, in contrast to the raw trajectory that contains thousands of unique states and tens of thousands of transitions.},
doi = {10.1063/1.4996922},
journal = {Journal of Chemical Physics},
number = 15,
volume = 147,
place = {United States},
year = {2017},
month = {8}
}

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    Works referencing / citing this record:

    Long-time molecular dynamics simulations on massively parallel platforms: A comparison of parallel replica dynamics and parallel trajectory splicing
    journal, December 2017

    • Perez, Danny; Huang, Rao; Voter, Arthur F.
    • Journal of Materials Research, Vol. 33, Issue 7
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