MorseSmale Analysis of Ion Diffusion in Ab Initio Battery Materials Simulations
Abstract
Ab initio molecular dynamics (AIMD) simulations are increasingly useful in modeling, optimizing and synthesizing materials in energy sciences. In solving Schrödinger’s equation, they generate the electronic structure of the simulated atoms as a scalar field. However, methods for analyzing these volume data are not yet common in molecular visualization. The MorseSmale complex is a proven, versatile tool for topological analysis of scalar fields. In this paper, we apply the discrete MorseSmale complex to analysis of firstprinciples battery materials simulations. We consider a carbon nanosphere structure used in battery materials research, and employ MorseSmale decomposition to determine the possible lithium ion diffusion paths within that structure. Our approach is novel in that it uses the wavefunction itself as opposed distance fields, and that we analyze the 1skeleton of the MorseSmale complex to reconstruct our diffusion paths. Furthermore, it is the first application where specific motifs in the graph structure of the complete 1skeleton define features, namely carbon rings with specific valence. We compare our analysis of DFT data with that of a distance field approximation, and discuss implications on larger classical molecular dynamics simulations.
 Authors:

 Univ. of Utah, Salt Lake City, UT (United States)
 Argonne National Lab. (ANL), Argonne, IL (United States)
 Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)
 Publication Date:
 Research Org.:
 Energy Frontier Research Centers (EFRC) (United States). Center for Electrical Energy Storage (CEES)
 Sponsoring Org.:
 USDOE Office of Science (SC), Basic Energy Sciences (BES) (SC22)
 OSTI Identifier:
 1370671
 DOE Contract Number:
 AC0206CH11357
 Resource Type:
 Journal Article
 Journal Name:
 Topological Methods in Data Analysis and Visualization IV. TopoInVis 2015. Mathematics and Visualization
 Additional Journal Information:
 Related Information: CEES partners with Argonne National Laboratory (lead); University of Illinois, UrbanaChampaign; Northwest University
 Publisher:
 Springer, Cham; Carr H., Garth C., Weinkauf T. (eds)
 Country of Publication:
 United States
 Language:
 English
 Subject:
 36 MATERIALS SCIENCE; 25 ENERGY STORAGE
Citation Formats
Gyulassy, Attila, Knoll, Aaron, Lau, Kah Chun, Wang, Bei, Bremer, PeerTimo, Papka, Michael, Curtiss, Larry A, and Pascucci, Valerio. MorseSmale Analysis of Ion Diffusion in Ab Initio Battery Materials Simulations. United States: N. p., 2017.
Web. doi:10.1007/9783319446844_8.
Gyulassy, Attila, Knoll, Aaron, Lau, Kah Chun, Wang, Bei, Bremer, PeerTimo, Papka, Michael, Curtiss, Larry A, & Pascucci, Valerio. MorseSmale Analysis of Ion Diffusion in Ab Initio Battery Materials Simulations. United States. doi:10.1007/9783319446844_8.
Gyulassy, Attila, Knoll, Aaron, Lau, Kah Chun, Wang, Bei, Bremer, PeerTimo, Papka, Michael, Curtiss, Larry A, and Pascucci, Valerio. Sat .
"MorseSmale Analysis of Ion Diffusion in Ab Initio Battery Materials Simulations". United States. doi:10.1007/9783319446844_8.
@article{osti_1370671,
title = {MorseSmale Analysis of Ion Diffusion in Ab Initio Battery Materials Simulations},
author = {Gyulassy, Attila and Knoll, Aaron and Lau, Kah Chun and Wang, Bei and Bremer, PeerTimo and Papka, Michael and Curtiss, Larry A and Pascucci, Valerio},
abstractNote = {Ab initio molecular dynamics (AIMD) simulations are increasingly useful in modeling, optimizing and synthesizing materials in energy sciences. In solving Schrödinger’s equation, they generate the electronic structure of the simulated atoms as a scalar field. However, methods for analyzing these volume data are not yet common in molecular visualization. The MorseSmale complex is a proven, versatile tool for topological analysis of scalar fields. In this paper, we apply the discrete MorseSmale complex to analysis of firstprinciples battery materials simulations. We consider a carbon nanosphere structure used in battery materials research, and employ MorseSmale decomposition to determine the possible lithium ion diffusion paths within that structure. Our approach is novel in that it uses the wavefunction itself as opposed distance fields, and that we analyze the 1skeleton of the MorseSmale complex to reconstruct our diffusion paths. Furthermore, it is the first application where specific motifs in the graph structure of the complete 1skeleton define features, namely carbon rings with specific valence. We compare our analysis of DFT data with that of a distance field approximation, and discuss implications on larger classical molecular dynamics simulations.},
doi = {10.1007/9783319446844_8},
journal = {Topological Methods in Data Analysis and Visualization IV. TopoInVis 2015. Mathematics and Visualization},
number = ,
volume = ,
place = {United States},
year = {2017},
month = {6}
}
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