TopoMS: Comprehensive topological exploration for molecular and condensed-matter systems

Bhatia, Harsh; Gyulassy, Attila G.; Lordi, Vincenzo; Pask, John E.; Pascucci, Valerio; Bremer, Peer‐Timo

doi:10.1002/jcc.25181

TopoMS: Comprehensive topological exploration for molecular and condensed-matter systems

Journal Article · Fri Mar 23 00:00:00 EDT 2018 · Journal of Computational Chemistry

DOI:https://doi.org/10.1002/jcc.25181· OSTI ID:1808752

^[1]; Gyulassy, Attila G. ^[2]; Lordi, Vincenzo ^[3]; Pask, John E. ^[4]; Pascucci, Valerio ^[2]; Bremer, Peer‐Timo ^[5]

Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States). Center for Applied Scientific Computing
Univ. of Utah, Salt Lake City, UT (United States). Scientific Computing and Imaging Institute
Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States). Materials Science Division
Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States). Physics Division
Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States). Center for Applied Scientific Computing; Univ. of Utah, Salt Lake City, UT (United States). Scientific Computing and Imaging Institute

We introduce TopoMS, a computational tool enabling detailed topological analysis of molecular and condensed-matter systems, including the computation of atomic volumes and charges through the quantum theory of atoms in molecules, as well as the complete molecular graph. With roots in techniques from computational topology, and using a shared-memory parallel approach, TopoMS provides scalable, numerically robust, and topologically consistent analysis. TopoMS can be used as a command-line tool or with a GUI (graphical user interface), where the latter also enables an interactive exploration of the molecular graph. This paper presents algorithmic details of TopoMS and compares it with state-of-the-art tools: Bader charge analysis v1.0 (Arnaldsson et al., 01/11/17) and molecular graph extraction using Critic2 (Otero-de-la-Roza et al., Comput. Phys. Commun. 2014, 185, 1007). TopoMS not only combines the functionality of these individual codes but also demonstrates up to 4× performance gain on a standard laptop, faster convergence to fine-grid solution, robustness against lattice bias, and topological consistency. TopoMS is released publicly under BSD License.

View Accepted Manuscript (DOE)

Research Organization:: Lawrence Livermore National Laboratory (LLNL), Livermore, CA (United States)

Sponsoring Organization:: USDOE National Nuclear Security Administration (NNSA)

Grant/Contract Number:: AC52-07NA27344

OSTI ID:: 1808752

Report Number(s):: LLNL-JRNL--740094; 888328

Journal Information:: Journal of Computational Chemistry, Journal Name: Journal of Computational Chemistry Journal Issue: 16 Vol. 39; ISSN 0192-8651

Publisher:: WileyCopyright Statement

Country of Publication:: United States

Language:: English

References (72)

The time-parallel multigrid method Horton, Graham Communications in Applied Numerical Methods, Vol. 8, Issue 9 https://doi.org/10.1002/cnm.1630080906	journal	September 1992
Atomic charges, dipole moments, and Fukui functions using the Hirshfeld partitioning of the electron density De Proft, F.; Van Alsenoy, C.; Peeters, A. Journal of Computational Chemistry, Vol. 23, Issue 12 https://doi.org/10.1002/jcc.10067	journal	June 2002
An improved algorithm to locate critical points in a 3D scalar field as implemented in the program MORPHY Malcolm, Nathaniel O. J.; Popelier, Paul L. A. Journal of Computational Chemistry, Vol. 24, Issue 4 https://doi.org/10.1002/jcc.10203	journal	February 2003
Improved grid-based algorithm for Bader charge allocation Sanville, Edward; Kenny, Steven D.; Smith, Roger Journal of Computational Chemistry, Vol. 28, Issue 5 https://doi.org/10.1002/jcc.20575	journal	January 2007
An efficient grid-based scheme to compute QTAIM atomic properties without explicit calculation of zero-flux surfaces Rodríguez, Juan I.; Köster, Andreas M.; Ayers, Paul W. Journal of Computational Chemistry, Vol. 30, Issue 7 https://doi.org/10.1002/jcc.21134	journal	May 2009
An efficient method for computing the QTAIM topology of a scalar field: The electron density case Rodríguez, Juan I. Journal of Computational Chemistry, Vol. 34, Issue 8 https://doi.org/10.1002/jcc.23180	journal	November 2012
Grid-based algorithm to search critical points, in the electron density, accelerated by graphics processing units Hernández-Esparza, Raymundo; Mejía-Chica, Sol-Milena; Zapata-Escobar, Andy D. Journal of Computational Chemistry, Vol. 35, Issue 31 https://doi.org/10.1002/jcc.23752	journal	October 2014
Calculation of the average properties of atoms in molecules. II: Average Properties of Atoms Biegler-könig, Friedrich W.; Bader, Richard F. W.; Tang, Ting-Hua Journal of Computational Chemistry, Vol. 3, Issue 3 https://doi.org/10.1002/jcc.540030306	journal	September 1982
An efficient approach to calculation of zero-flux atomic surfaces and generation of atomic integration data Stefanov, Boris B.; Cioslowski, Jerzy Journal of Computational Chemistry, Vol. 16, Issue 11 https://doi.org/10.1002/jcc.540161108	journal	November 1995
Morse-Smale Analysis of Ion Diffusion in Ab Initio Battery Materials Simulations Gyulassy, Attila; Knoll, Aaron; Lau, Kah Chun Mathematics and Visualization https://doi.org/10.1007/978-3-319-44684-4_8	book	January 2017
An analytical expression for interatomic surfaces in the theory of atoms in molecules Popelier, P. L. A. Theoretica Chimica Acta, Vol. 87, Issue 6 https://doi.org/10.1007/BF01127809	journal	February 1994
Multi-grid dynamic iteration for parabolic equations Lubich, Ch.; Ostermann, A. BIT, Vol. 27, Issue 2 https://doi.org/10.1007/BF01934186	journal	June 1987
Fourier mode analysis of the multigrid waveform relaxation and time-parallel multigrid methods Vandewalle, S.; Horton, G. Computing, Vol. 54, Issue 4 https://doi.org/10.1007/BF02238230	journal	December 1995
A parallel shooting technique for solving dissipative ODE's Chartier, P.; Philippe, B. Computing, Vol. 51, Issue 3-4 https://doi.org/10.1007/BF02238534	journal	September 1993
A fast algorithm to compute atomic charges based on the topology of the electron density Popelier, P. L. A. Theoretical Chemistry Accounts: Theory, Computation, and Modeling (Theoretica Chimica Acta), Vol. 105, Issue 4-5 https://doi.org/10.1007/s002140000224	journal	April 2001
Topological Persistence and Simplification No authors listed Discrete & Computational Geometry, Vol. 28, Issue 4 https://doi.org/10.1007/s00454-002-2885-2	journal	November 2002
Hierarchical Morse--Smale Complexes for Piecewise Linear 2-Manifolds Edelsbrunner, Herbert; Harer, John; Zomorodian, Afra Discrete and Computational Geometry, Vol. 30, Issue 1 https://doi.org/10.1007/s00454-003-2926-5	journal	May 2003
MORPHY, a program for an automated “atoms in molecules” analysis Popelier, Paul L. A. Computer Physics Communications, Vol. 93, Issue 2-3 https://doi.org/10.1016/0010-4655(95)00113-1	journal	February 1996
A time-parallel multigrid-extrapolation method for parabolic partial differential equations Horton, G.; Knirsch, R. Parallel Computing, Vol. 18, Issue 1 https://doi.org/10.1016/0167-8191(92)90108-J	journal	January 1992
A method to integrate an atom in a molecule without explicit representation of the interatomic surface Popelier, P. L. A. Computer Physics Communications, Vol. 108, Issue 2-3 https://doi.org/10.1016/S0010-4655(97)00121-5	journal	February 1998
Computational tools for the electron localization function topological analysis Noury, Stéphane; Krokidis, Xénophon; Fuster, Franck Computers & Chemistry, Vol. 23, Issue 6 https://doi.org/10.1016/S0097-8485(99)00039-X	journal	November 1999
Résolution d'EDP par un schéma en temps «pararéel » Lions, Jacques-Louis; Maday, Yvon; Turinici, Gabriel Comptes Rendus de l'Académie des Sciences - Series I - Mathematics, Vol. 332, Issue 7 https://doi.org/10.1016/S0764-4442(00)01793-6	journal	April 2001
A fast and robust algorithm for Bader decomposition of charge density Henkelman, Graeme; Arnaldsson, Andri; Jónsson, Hannes Computational Materials Science, Vol. 36, Issue 3 https://doi.org/10.1016/j.commatsci.2005.04.010	journal	June 2006
Critic: a new program for the topological analysis of solid-state electron densities Otero-de-la-Roza, A.; Blanco, M. A.; Pendás, A. Martín Computer Physics Communications, Vol. 180, Issue 1 https://doi.org/10.1016/j.cpc.2008.07.018	journal	January 2009
Critic2: A program for real-space analysis of quantum chemical interactions in solids Otero-de-la-Roza, A.; Johnson, Erin R.; Luaña, Víctor Computer Physics Communications, Vol. 185, Issue 3 https://doi.org/10.1016/j.cpc.2013.10.026	journal	March 2014
A high performance grid-based algorithm for computing QTAIM properties Rodríguez, Juan I.; Bader, Richard F. W.; Ayers, Paul W. Chemical Physics Letters, Vol. 472, Issue 1-3 https://doi.org/10.1016/j.cplett.2009.02.081	journal	April 2009
Parallelization in time through tensor-product space–time solvers Maday, Yvon; Rønquist, Einar M. Comptes Rendus Mathematique, Vol. 346, Issue 1-2 https://doi.org/10.1016/j.crma.2007.09.012	journal	January 2008
Atoms in molecules Bader, R. F. W. Accounts of Chemical Research, Vol. 18, Issue 1 https://doi.org/10.1021/ar00109a003	journal	January 1985
Properties of atoms in molecules: atomic volumes Bader, Richard F. W.; Carroll, Marshall T.; Cheeseman, James R. Journal of the American Chemical Society, Vol. 109, Issue 26 https://doi.org/10.1021/ja00260a006	journal	December 1987
A Numerical Method for the Topological Analysis of the Laplacian of the Electronic Charge Density in Molecules and Solids Aray, Yosslen; Rodríguez, Jesús; López-Boada, Roberto The Journal of Physical Chemistry A, Vol. 101, Issue 11 https://doi.org/10.1021/jp962390a	journal	March 1997
Numerical Determination of the Topological Properties of the Electronic Charge Density in Molecules and Solids Using Density Functional Theory Aray, Yosslen; Rodríguez, Jesús; Rivero, Juan The Journal of Physical Chemistry A, Vol. 101, Issue 37 https://doi.org/10.1021/jp971325d	journal	September 1997
A Bond Path: A Universal Indicator of Bonded Interactions Bader, R. F. W. The Journal of Physical Chemistry A, Vol. 102, Issue 37 https://doi.org/10.1021/jp981794v	journal	September 1998
Laplacian of the Electronic Charge Density and Heat of Adsorption of O ₂ and CO Molecules on 3d Transition Metals Aray, Yosslen; Rodriguez, Jesus; Vega, David The Journal of Physical Chemistry B, Vol. 104, Issue 22 https://doi.org/10.1021/jp9936392	journal	June 2000
Accurate and efficient algorithm for Bader charge integration Yu, Min; Trinkle, Dallas R. The Journal of Chemical Physics, Vol. 134, Issue 6 https://doi.org/10.1063/1.3553716	journal	February 2011
Variational determination of the zero-flux surfaces of atoms in molecules Cioslowski, Jerzy; Stefanov, Boris B. Molecular Physics, Vol. 84, Issue 4 https://doi.org/10.1080/00268979500100481	journal	March 1995
Integration of atoms in molecules: a critical examination Popelier, P. L. A. Molecular Physics, Vol. 87, Issue 5 https://doi.org/10.1080/00268979600100781	journal	April 1996
Calculation of the average properties of atoms in molecules Biegler-Konig, F. W.; Nguyen-Dang, T. Tung; Tal, Y. Journal of Physics B: Atomic and Molecular Physics, Vol. 14, Issue 16 https://doi.org/10.1088/0022-3700/14/16/004	journal	August 1981
A grid-based Bader analysis algorithm without lattice bias Tang, W.; Sanville, E.; Henkelman, G. Journal of Physics: Condensed Matter, Vol. 21, Issue 8 https://doi.org/10.1088/0953-8984/21/8/084204	journal	January 2009
Parallel methods for the numerical integration of ordinary differential equations Miranker, Willard L.; Liniger, Werner Mathematics of Computation, Vol. 21, Issue 99 https://doi.org/10.1090/S0025-5718-1967-0223106-8	journal	September 1967
Multi-level adaptive solutions to boundary-value problems Brandt, Achi Mathematics of Computation, Vol. 31, Issue 138 https://doi.org/10.1090/S0025-5718-1977-0431719-X	journal	May 1977
A parallel method for time discretization of parabolic equations based on Laplace transformation and quadrature Sheen, D. IMA Journal of Numerical Analysis, Vol. 23, Issue 2 https://doi.org/10.1093/imanum/23.2.269	journal	April 2003
Numerical computation of critical properties and atomic basins from three-dimensional grid electron densities Katan, C.; Rabiller, P.; Lecomte, C. Journal of Applied Crystallography, Vol. 36, Issue 1 https://doi.org/10.1107/S0021889802018691	journal	January 2003
EDMA : a computer program for topological analysis of discrete electron densities Palatinus, Lukáš; Prathapa, Siriyara Jagannatha; van Smaalen, Sander Journal of Applied Crystallography, Vol. 45, Issue 3 https://doi.org/10.1107/S0021889812016068	journal	May 2012
Theory and Algorithms for Constructing Discrete Morse Complexes from Grayscale Digital Images Robins, V.; Wood, P. J.; Sheppard, A. P. IEEE Transactions on Pattern Analysis and Machine Intelligence, Vol. 33, Issue 8 https://doi.org/10.1109/TPAMI.2011.95	journal	August 2011
Understanding the Structure of the Turbulent Mixing Layer in Hydrodynamic Instabilities Laney, D.; Bremer, P. -t.; Mascarenhas, A. IEEE Transactions on Visualization and Computer Graphics, Vol. 12, Issue 5 https://doi.org/10.1109/TVCG.2006.186	journal	September 2006
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
Analyzing and Tracking Burning Structures in Lean Premixed Hydrogen Flames Bremer, P. -T.; Weber, G. H.; Pascucci, V. IEEE Transactions on Visualization and Computer Graphics, Vol. 16, Issue 2 https://doi.org/10.1109/TVCG.2009.69	journal	March 2010
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
Parallel Computation of 2D Morse-Smale Complexes Shivashankar, Nithin; M., Senthilnathan; Natarajan, Vijay IEEE Transactions on Visualization and Computer Graphics, Vol. 18, Issue 10 https://doi.org/10.1109/TVCG.2011.284	journal	October 2012
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
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
Conforming Morse-Smale Complexes Gyulassy, Attila; Gunther, David; Levine, Joshua A. IEEE Transactions on Visualization and Computer Graphics, Vol. 20, Issue 12 https://doi.org/10.1109/TVCG.2014.2346434	journal	December 2014
Topological persistence and simplification Edelsbrunner, H.; Letscher, D.; Zomorodian, A. Proceedings 41st Annual Symposium on Foundations of Computer Science https://doi.org/10.1109/sfcs.2000.892133	conference	January 2000
The persistent cosmic web and its filamentary structure - I. Theory and implementation: Persistent cosmic web - I: Theory and implementation Sousbie, T. Monthly Notices of the Royal Astronomical Society, Vol. 414, Issue 1 https://doi.org/10.1111/j.1365-2966.2011.18394.x	journal	April 2011
Analysis of the Parareal Time‐Parallel Time‐Integration Method Gander, Martin J.; Vandewalle, Stefan SIAM Journal on Scientific Computing, Vol. 29, Issue 2 https://doi.org/10.1137/05064607X	journal	January 2007
Multigrid Methods for Variational Problems McCormick, S. F.; Ruge, J. W. SIAM Journal on Numerical Analysis, Vol. 19, Issue 5 https://doi.org/10.1137/0719067	journal	October 1982
Parallel High-Order Integrators Christlieb, Andrew J.; Macdonald, Colin B.; Ong, Benjamin W. SIAM Journal on Scientific Computing, Vol. 32, Issue 2 https://doi.org/10.1137/09075740X	journal	January 2010
Efficient Parallel Algorithms for Solving Initial-Boundary Value and Time-Periodic Parabolic Partial Differential Equations Vandewalle, Stefan; Piessens, Robert SIAM Journal on Scientific and Statistical Computing, Vol. 13, Issue 6 https://doi.org/10.1137/0913075	journal	November 1992
An Algorithm with Polylog Parallel Complexity for Solving Parabolic Partial Differential Equations Horton, G.; Vandewalle, S.; Worley, P. SIAM Journal on Scientific Computing, Vol. 16, Issue 3 https://doi.org/10.1137/0916034	journal	May 1995
A Space-Time Multigrid Method for Parabolic Partial Differential Equations Horton, G.; Vandewalle, S. SIAM Journal on Scientific Computing, Vol. 16, Issue 4 https://doi.org/10.1137/0916050	journal	July 1995
Parallel Time Integration with Multigrid Falgout, R. D.; Friedhoff, S.; Kolev, Tz. V. SIAM Journal on Scientific Computing, Vol. 36, Issue 6 https://doi.org/10.1137/130944230	journal	January 2014
Interweaving PFASST and Parallel Multigrid Minion, M. L.; Speck, R.; Bolten, M. SIAM Journal on Scientific Computing, Vol. 37, Issue 5 https://doi.org/10.1137/14097536X	journal	January 2015
On the $p$-Laplacian and $\infty$-Laplacian on Graphs with Applications in Image and Data Processing Elmoataz, Abderrahim; Toutain, Matthieu; Tenbrinck, Daniel SIAM Journal on Imaging Sciences, Vol. 8, Issue 4 https://doi.org/10.1137/15M1022793	journal	January 2015
Analysis of a New Space-Time Parallel Multigrid Algorithm for Parabolic Problems Gander, Martin J.; Neumüller, Martin SIAM Journal on Scientific Computing, Vol. 38, Issue 4 https://doi.org/10.1137/15M1046605	journal	January 2016
Least-Squares Finite Element Methods and Algebraic Multigrid Solvers for Linear Hyperbolic PDEs De Sterck, H.; Manteuffel, Thomas A.; McCormick, Stephen F. SIAM Journal on Scientific Computing, Vol. 26, Issue 1 https://doi.org/10.1137/S106482750240858X	journal	January 2004
Parallel methods for integrating ordinary differential equations Nievergelt, J. Communications of the ACM, Vol. 7, Issue 12 https://doi.org/10.1145/355588.365137	journal	December 1964
Multidimensional divide-and-conquer Bentley, Jon Louis Communications of the ACM, Vol. 23, Issue 4 https://doi.org/10.1145/358841.358850	journal	April 1980
Simulation of simplicity: a technique to cope with degenerate cases in geometric algorithms Edelsbrunner, H.; Mücke, E. P. Proceedings of the fourth annual symposium on Computational geometry - SCG '88 https://doi.org/10.1145/73393.73406	conference	January 1988
Simulation of simplicity: a technique to cope with degenerate cases in geometric algorithms Edelsbrunner, Herbert; Mücke, Ernst Peter ACM Transactions on Graphics, Vol. 9, Issue 1 https://doi.org/10.1145/77635.77639	journal	January 1990
Toward an efficient parallel in time method for partial differential equations Emmett, Matthew; Minion, Michael Communications in Applied Mathematics and Computational Science, Vol. 7, Issue 1 https://doi.org/10.2140/camcos.2012.7.105	journal	January 2012
Identifying turbulent structures through topological segmentation Bremer, Peer-Timo; Gruber, Andrea; Bennett, Janine Communications in Applied Mathematics and Computational Science, Vol. 11, Issue 1 https://doi.org/10.2140/camcos.2016.11.37	journal	January 2016
New Insights in Atom-Atom Interactions for Future Drug Design Popelier, Paul Current Topics in Medicinal Chemistry, Vol. 12, Issue 17 https://doi.org/10.2174/156802612804547416	journal	September 2012

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