Morse-Smale Analysis of Ion Diffusion in Ab Initio Battery Materials Simulations

Gyulassy, Attila; Knoll, Aaron; Lau, Kah Chun; Wang, Bei; Bremer, Peer-Timo; Papka, Michael; Curtiss, Larry A; Pascucci, Valerio

doi:10.1007/978-3-319-44684-4_8

Title: Morse-Smale Analysis of Ion Diffusion in Ab Initio Battery Materials Simulations

Journal Article · Sat Jun 03 00:00:00 EDT 2017 · Topological Methods in Data Analysis and Visualization IV. TopoInVis 2015. Mathematics and Visualization

DOI:https://doi.org/10.1007/978-3-319-44684-4_8· OSTI ID:1370671

Gyulassy, Attila ^[1]; Knoll, Aaron ^[1]; Lau, Kah Chun ^[2]; Wang, Bei ^[1]; Bremer, Peer-Timo ^[3]; Papka, Michael ^[2]; Curtiss, Larry A ^[2]; Pascucci, Valerio ^[1]

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)

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 Morse-Smale complex is a proven, versatile tool for topological analysis of scalar fields. In this paper, we apply the discrete Morse-Smale complex to analysis of first-principles battery materials simulations. We consider a carbon nanosphere structure used in battery materials research, and employ Morse-Smale 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 1-skeleton of the Morse-Smale complex to reconstruct our diffusion paths. Furthermore, it is the first application where specific motifs in the graph structure of the complete 1-skeleton 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.

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Research Organization:: Energy Frontier Research Centers (EFRC) (United States). Center for Electrical Energy Storage (CEES)

Sponsoring Organization:: USDOE Office of Science (SC), Basic Energy Sciences (BES)

DOE Contract Number:: AC02-06CH11357

OSTI ID:: 1370671

Journal Information:: Topological Methods in Data Analysis and Visualization IV. TopoInVis 2015. Mathematics and Visualization, Related Information: CEES partners with Argonne National Laboratory (lead); University of Illinois, Urbana-Champaign; Northwest University

Publisher:: Springer, Cham; Carr H., Garth C., Weinkauf T. (eds)

Country of Publication:: United States

Language:: English

References (23)

Generalized Gradient Approximation Made Simple Perdew, John P.; Burke, Kieron; Ernzerhof, Matthias Physical Review Letters, Vol. 77, Issue 18, p. 3865-3868 https://doi.org/10.1103/PhysRevLett.77.3865	journal	October 1996
MOLE: A Voronoi Diagram-Based Explorer of Molecular Channels, Pores, and Tunnels Petřek, Martin; Košinová, Pavlína; Koča, Jaroslav Structure, Vol. 15, Issue 11 https://doi.org/10.1016/j.str.2007.10.007	journal	November 2007
Three-dimensional beta-shapes and beta-complexes via quasi-triangulation Kim, Deok-Soo; Cho, Youngsong; Sugihara, Kokichi Computer-Aided Design, Vol. 42, Issue 10 https://doi.org/10.1016/j.cad.2010.06.004	journal	October 2010
Ab Initio Investigations of Lithium Diffusion in Carbon Nanotube Systems Meunier, Vincent; Kephart, Jeremy; Roland, Christopher Physical Review Letters, Vol. 88, Issue 7 https://doi.org/10.1103/PhysRevLett.88.075506	journal	February 2002
Energetics and Kinetics of Li Intercalation in Irradiated Graphene Scaffolds Song, J.; Ouyang, B.; Medhekar, N. V. ACS Applied Materials & Interfaces, Vol. 5, Issue 24 https://doi.org/10.1021/am403685w	journal	December 2013
Characterizing Molecular Interactions in Chemical Systems Gunther, David; Boto, Roberto A.; Contreras-Garcia, Juila IEEE Transactions on Visualization and Computer Graphics, Vol. 20, Issue 12 https://doi.org/10.1109/TVCG.2014.2346403	journal	December 2014
Probing the evolution and morphology of hard carbon spheres Pol, Vilas G.; Wen, Jianguo; Lau, Kah Chun Carbon, Vol. 68 https://doi.org/10.1016/j.carbon.2013.10.059	journal	March 2014
Efficiency of ab-initio total energy calculations for metals and semiconductors using a plane-wave basis set Kresse, G.; Furthmüller, J. Computational Materials Science, Vol. 6, Issue 1, p. 15-50 https://doi.org/10.1016/0927-0256(96)00008-0	journal	July 1996
A Practical Approach to Morse-Smale Complex Computation: Scalability and Generality Gyulassy, A.; Bremer, P. -T.; Hamann, B. IEEE Transactions on Visualization and Computer Graphics, Vol. 14, Issue 6 https://doi.org/10.1109/TVCG.2008.110	journal	November 2008
Tunnels and Voids in Molecules via Voronoi Diagram Kim, Deok-Soo; Sugihara, Kokichi 2012 Ninth International Symposium on Voronoi Diagrams in Science and Engineering (ISVD) https://doi.org/10.1109/ISVD.2012.25	conference	June 2012
MolAxis: Efficient and accurate identification of channels in macromolecules Yaffe, Eitan; Fishelovitch, Dan; Wolfson, Haim J. Proteins: Structure, Function, and Bioinformatics, Vol. 73, Issue 1 https://doi.org/10.1002/prot.22052	journal	April 2008
Computing Morse-Smale Complexes with Accurate Geometry Gyulassy, A.; Bremer, P.; Pascucci, V. IEEE Transactions on Visualization and Computer Graphics, Vol. 18, Issue 12 https://doi.org/10.1109/TVCG.2012.209	journal	December 2012
CASTp: computed atlas of surface topography of proteins with structural and topographical mapping of functionally annotated residues Dundas, J.; Ouyang, Z.; Tseng, J. Nucleic Acids Research, Vol. 34, Issue Web Server https://doi.org/10.1093/nar/gkl282	journal	July 2006
Diffusion Mechanism of Lithium Ion through Basal Plane of Layered Graphene Yao, Fei; Güneş, Fethullah; Ta, Huy Quang Journal of the American Chemical Society, Vol. 134, Issue 20 https://doi.org/10.1021/ja301586m	journal	May 2012
Direct Feature Visualization Using Morse-Smale Complexes Gyulassy, A.; Kotava, N.; Kim, M. IEEE Transactions on Visualization and Computer Graphics, Vol. 18, Issue 9 https://doi.org/10.1109/TVCG.2011.272	journal	September 2012
Segmenting molecular surfaces Natarajan, Vijay; Wang, Yusu; Bremer, Peer-Timo Computer Aided Geometric Design, Vol. 23, Issue 6 https://doi.org/10.1016/j.cagd.2006.02.003	journal	August 2006
Topological Spines: A Structure-preserving Visual Representation of Scalar Fields Correa, C.; Lindstrom, P.; Bremer, Peer-Timo IEEE Transactions on Visualization and Computer Graphics, Vol. 17, Issue 12 https://doi.org/10.1109/TVCG.2011.244	journal	December 2011
Molecular shape analysis based upon the morse-smale complex and the connolly function Cazals, F.; Chazal, F.; Lewiner, T. Proceedings of the nineteenth conference on Computational geometry - SCG '03 https://doi.org/10.1145/777792.777845	conference	January 2003
Voronoi-Based Extraction and Visualization of Molecular Paths Lindow, N.; Baum, D.; Hege, H-C IEEE Transactions on Visualization and Computer Graphics, Vol. 17, Issue 12 https://doi.org/10.1109/TVCG.2011.259	journal	December 2011
Topology Based Selection and Curation of Level Sets Bajaj, Chandrajit; Gillette, Andrew; Goswami, Samrat Topology-Based Methods in Visualization II https://doi.org/10.1007/978-3-540-88606-8_4	book	January 2009
Anatomy of protein pockets and cavities: Measurement of binding site geometry and implications for ligand design Liang, Jie; Woodward, Clare; Edelsbrunner, Herbert Protein Science, Vol. 7, Issue 9 https://doi.org/10.1002/pro.5560070905	journal	September 1998
Three-dimensional alpha shapes Edelsbrunner, Herbert; Mücke, Ernst P. ACM Transactions on Graphics, Vol. 13, Issue 1 https://doi.org/10.1145/174462.156635	journal	January 1994
Investigation of the Decomposition Mechanism of Lithium Bis(oxalate)borate (LiBOB) Salt in the Electrolyte of an Aprotic Li-O ₂ Battery Lau, Kah Chun; Lu, Jun; Low, John Energy Technology, Vol. 2, Issue 4 https://doi.org/10.1002/ente.201300164	journal	March 2014

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