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

Huang, Rao; Lo, Li-Ta; Wen, Yuhua; Voter, Arthur F.; Perez, Danny

doi:10.1063/1.4996922

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

Journal Article · Wed Aug 16 00:00:00 EDT 2017 · Journal of Chemical Physics

DOI:https://doi.org/10.1063/1.4996922· OSTI ID:1463546

^[1];

^[2]; Wen, Yuhua ^[3]; Voter, Arthur F. ^[2];

^[2]

Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Xiamen Univ. (China)
Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
Xiamen Univ. (China)

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.

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Research Organization:: Los Alamos National Laboratory (LANL), Los Alamos, NM (United States)

Sponsoring Organization:: USDOE Office of Nuclear Energy (NE)

Grant/Contract Number:: AC52-06NA25396

OSTI ID:: 1463546

Alternate ID(s):: OSTI ID: 1375255

Report Number(s):: LA-UR-17-23766

Journal Information:: Journal of Chemical Physics, Vol. 147, Issue 15; ISSN 0021-9606

Publisher:: American Institute of Physics (AIP)Copyright Statement

Country of Publication:: United States

Language:: English

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Cited by: 6 works

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