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Treecode-accelerated Green iteration for Kohn-Sham density functional theory. (English) Zbl 07506532

Summary: We present a real-space computational method called treecode-accelerated Green Iteration (TAGI) for all-electron Kohn-Sham Density Functional Theory. TAGI is based on a reformulation of the Kohn-Sham equations in which the eigenvalue problem in differential form is converted into a fixed-point problem in integral form by convolution with the modified Helmholtz Green’s function. In each self-consistent field (SCF) iteration, the fixed-points are computed by Green Iteration, where the discrete convolution sums are efficiently evaluated by a GPU-accelerated barycentric Lagrange treecode. Other techniques used in TAGI include a-priori adaptive mesh refinement, Fejér quadrature, singularity subtraction, gradient-free eigenvalue update, and Anderson mixing to accelerate convergence of the SCF and Green Iterations. Ground state energy computations of several atoms (Li, Be, O) and small molecules (\(\mathrm{H}_2\), CO, \(\mathrm{C_6H}_6\)) demonstrate TAGI’s ability to efficiently achieve chemical accuracy.

MSC:

65Nxx Numerical methods for partial differential equations, boundary value problems
65Dxx Numerical approximation and computational geometry (primarily algorithms)
78Axx General topics in optics and electromagnetic theory

References:

[1] Challacombe, M.; Schwegler, E.; Almlöf, J., Fast assembly of the Coulomb matrix: a quantum chemical tree code, J. Chem. Phys., 104, 4685-4698 (1996)
[2] Challacombe, M.; Schwegler, E., Linear scaling computation of the Fock matrix, J. Chem. Phys., 106, 5526-5536 (1997)
[3] Chew, W. C.; Michielssen, E.; Song, J. M.; Jin, J. M., Fast and Efficient Algorithms in Computational Electromagnetics (2001), Artech House
[4] Cohen, O.; Kronik, L.; Brandt, A., Locally refined multigrid solution of the all-electron Kohn-Sham equation, J. Chem. Theory Comput., 9, 4744-4760 (2013)
[5] Natan, A.; Benjamini, A.; Naveh, D.; Kronik, L.; Tiago, M. L.; Beckman, S. P.; Chelikowsky, J. R., Real-space pseudopotential method for first principles calculations of general periodic and partially periodic systems, Phys. Rev. B, 78, Article 075109 pp. (2008)
[6] Hohenberg, P.; Kohn, W., Inhomogeneous electron gas, Phys. Rev., 136, 3B, B864-B871 (1964)
[7] Kohn, W.; Sham, L. J., Self-consistent equations including exchange and correlation effects, Phys. Rev., 140, 4A, A1133-A1138 (1965)
[8] Burke, K., Perspective on density functional theory, J. Chem. Phys., 136, 15, Article 150901 pp. (2012)
[9] Jones, R. O., Density functional theory: its origins, rise to prominence, and future, Rev. Mod. Phys., 87, 897-923 (2015)
[10] Mardirossian, N.; Head-Gordon, M., Thirty years of density functional theory in computational chemistry: an overview and extensive assessment of 200 density functionals, Mol. Phys., 115, 19, 2315-2372 (2017)
[11] Lin, L.; Lu, J.; Ying, L., Numerical methods for Kohn-Sham density functional theory, Acta Numer., 28, 405-539 (2019) · Zbl 07099162
[12] Kresse, G.; Furthmüller, J., Efficient iterative schemes for ab initio total-energy calculations using a plane-wave basis set, Phys. Rev. B, 54, 16, 11169-11186 (1996)
[13] Gonze, X.; Beuken, J.-M.; Caracas, R.; Detraux, F.; Fuchs, M.; Rignanese, G.-M.; Sindic, L.; Verstraete, M.; Zerah, G.; Jollet, F.; Torrent, M.; Roy, A.; Mikami, M.; Ghosez, P.; Raty, J.-Y.; Allan, D., First-principles computation of material properties: the ABINIT software project, Comput. Mater. Sci., 25, 3, 478-492 (2002)
[14] Segall, M. D.; Lindan, P. J.D.; Probert, M. J.; Pickard, C. J.; Hasnip, P. J.; Clark, S. J.; Payne, M. C., First-principles simulation: ideas, illustrations and the CASTEP code, J. Phys. Condens. Matter, 14, 11, 2717-2744 (2002)
[15] Giannozzi, P.; Baroni, S.; Bonini, N.; Calandra, M.; Car, R.; Cavazzoni, C.; Ceresoli, D.; Chiarotti, G. L.; Cococcioni, M.; Dabo, I.; Dal Corso, A.; de Gironcoli, S.; Fabris, S.; Fratesi, G.; Gebauer, R.; Gerstmann, U.; Gougoussis, C.; Kokalj, A.; Lazzeri, M.; Martin-Samos, L.; Marzari, N.; Mauri, F.; Mazzarello, R.; Paolini, S.; Pasquarello, A.; Paulatto, L.; Sbraccia, C.; Scandolo, S.; Sclauzero, G.; Seitsonen, A. P.; Smogunov, A.; Umari, P.; Wentzcovitch, R. M., Quantum ESPRESSO: a modular and open-source software project for quantum simulations of materials, J. Phys. Condens. Matter, 21, 39, Article 395502 pp. (2009)
[16] Giannozzi, P.; Andreussi, O.; Brumme, T.; Bunau, O.; Buongiorno Nardelli, M.; Calandra, M.; Car, R.; Cavazzoni, C.; Ceresoli, D.; Cococcioni, M.; Colonna, N.; Carnimeo, I.; Dal Corso, A.; de Gironcoli, S.; Delugas, P.; DiStasio, R. A.; Ferretti, A.; Floris, A.; Fratesi, G.; Fugallo, G.; Gebauer, R.; Gerstmann, U.; Giustino, F.; Gorni, T.; Jia, J.; Kawamura, M.; Ko, H.-Y.; Kokalj, A.; Küçükbenli, E.; Lazzeri, M.; Marsili, M.; Marzari, N.; Mauri, F.; Nguyen, N. L.; Nguyen, H.-V.; Otero-de-la Roza, A.; Paulatto, L.; Poncé, S.; Rocca, D.; Sabatini, R.; Santra, B.; Schlipf, M.; Seitsonen, A. P.; Smogunov, A.; Timrov, I.; Thonhauser, T.; Umari, P.; Vast, N.; Wu, X.; Baroni, S., Advanced capabilities for materials modelling with quantum ESPRESSO, J. Phys. Condens. Matter, 29, 46, Article 465901 pp. (2017)
[17] Loucks, T.; Slater, J. C., Augmented plane wave method: a guide to performing electronic structure calculations, (Phys. Today, vol. 20 (1967)), 92-93
[18] Andersen, O. K., Linear methods in band theory, Phys. Rev. B, 12, 8, 3060-3083 (1975)
[19] Wimmer, E.; Krakauer, H.; Weinert, M.; Freeman, A. J., Full-potential self-consistent linearized-augmented-plane-wave method for calculating the electronic structure of molecules and surfaces: \( \operatorname{O}_2\) molecule, Phys. Rev. B, 24, 2, 864-875 (1981)
[20] Weinert, M.; Wimmer, E.; Freeman, A. J., Total-energy all-electron density functional method for bulk solids and surfaces, Phys. Rev. B, 26, 8, 4571-4578 (1982)
[21] Sjöstedt, E.; Nordström, L.; Singh, D., An alternative way of linearizing the augmented plane-wave method, Solid State Commun., 114, 1, 15-20 (2000)
[22] Madsen, G. K.H.; Blaha, P.; Schwarz, K.; Sjöstedt, E.; Nordström, L., Efficient linearization of the augmented plane-wave method, Phys. Rev. B, 64, 19, Article 195134 pp. (2001)
[23] Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R.; Scalmani, G.; Barone, V.; Petersson, G. A.; Nakatsuji, H.; Li, X.; Caricato, M.; Marenich, A. V.; Bloino, J.; Janesko, B. G.; Gomperts, R.; Mennucci, B.; Hratchian, H. P.; Ortiz, J. V.; Izmaylov, A. F.; Sonnenberg, J. L.; Williams-Young, D.; Ding, F.; Lipparini, F.; Egidi, F.; Goings, J.; Peng, B.; Petrone, A.; Henderson, T.; Ranasinghe, D.; Zakrzewski, V. G.; Gao, J.; Rega, N.; Zheng, G.; Liang, W.; Hada, M.; Ehara, M.; Toyota, K.; Fukuda, R.; Hasegawa, J.; Ishida, M.; Nakajima, T.; Honda, Y.; Kitao, O.; Nakai, H.; Vreven, T.; Throssell, K.; Montgomery, J. A.; Peralta, J. E.; Ogliaro, F.; Bearpark, M. J.; Heyd, J. J.; Brothers, E. N.; Kudin, K. N.; Staroverov, V. N.; Keith, T. A.; Kobayashi, R.; Normand, J.; Raghavachari, K.; Rendell, A. P.; Burant, J. C.; Iyengar, S. S.; Tomasi, J.; Cossi, M.; Millam, J. M.; Klene, M.; Adamo, C.; Cammi, R.; Ochterski, J. W.; Martin, R. L.; Morokuma, K.; Farkas, O.; Foresman, J. B.; Fox, D. J. (2016), Gaussian 16 Revision B.01, Gaussian Inc. Wallingford CT
[24] Valiev, M.; Bylaska, E.; Govind, N.; Kowalski, K.; Straatsma, T.; Van Dam, H.; Wang, D.; Nieplocha, J.; Apra, E.; Windus, T.; de Jong, W., NWChem: a comprehensive and scalable open-source solution for large scale molecular simulations, Comput. Phys. Commun., 181, 9, 1477-1489 (2010) · Zbl 1216.81179
[25] Tsuchida, E.; Tsukada, M., Large-scale electronic-structure calculations based on the adaptive finite-element method, J. Phys. Soc. Jpn., 67, 11, 3844-3858 (1998)
[26] Pask, J. E.; Klein, B. M.; Fong, C. Y.; Sterne, P. A., Real-space local polynomial basis for solid-state electronic-structure calculations: a finite-element approach, Phys. Rev. B, 59, 19, 12352-12358 (1999)
[27] Lehtovaara, L.; Havu, V.; Puska, M., All-electron density functional theory and time-dependent density functional theory with high-order finite elements, J. Chem. Phys., 131, 5, 1-10 (2009)
[28] Motamarri, P.; Nowak, M.; Leiter, K.; Knap, J.; Gavini, V., Higher-order adaptive finite-element methods for Kohn-Sham density functional theory, J. Comput. Phys., 253, 308-343 (2013) · Zbl 1349.74331
[29] Motamarri, P.; Gavini, V., Subquadratic-scaling subspace projection method for large-scale Kohn-Sham density functional theory calculations using spectral finite-element discretization, Phys. Rev. B, 90, 11, Article 115127 pp. (2014)
[30] Kanungo, B.; Gavini, V., Large-scale all-electron density functional theory calculations using an enriched finite-element basis, Phys. Rev. B, 95, 3, Article 035112 pp. (2017)
[31] Motamarri, P.; Das, S.; Rudraraju, S.; Ghosh, K.; Davydov, D.; Gavini, V., DFT-FE - a massively parallel adaptive finite-element code for large-scale density functional theory calculations, Comput. Phys. Commun., 246, Article 106853 pp. (2020) · Zbl 07678420
[32] Das, S.; Motamarri, P.; Gavini, V.; Turcksin, B.; Li, Y. W.; Leback, B., Fast, scalable and accurate finite-element based ab initio calculations using mixed precision computing: 46 PFLOPS simulation of a metallic dislocation system, (Int. Conf. High Perform. Comput. Networking, Storage Anal. SC (2019), IEEE Computer Society: IEEE Computer Society New York, NY, USA), 1-11
[33] Rokhlin, V., Rapid solution of integral equations of scattering theory in two dimensions, J. Comput. Phys., 86, 2, 414-439 (1990) · Zbl 0686.65079
[34] Jorgenson, R.; Mittra, R., Efficient calculation of the free-space periodic Green’s function, IEEE Trans. Antennas Propag., 38, 5, 633-642 (1990) · Zbl 0947.78526
[35] Coifman, R.; Rokhlin, V.; Wandzura, S., The fast multipole method for the wave equation: a pedestrian prescription, IEEE Antennas Propag. Mag., 35, 3, 7-12 (1993)
[36] Medgyesi-Mitschang, L. N.; Putnam, J. M.; Gedera, M. B., Generalized method of moments for three-dimensional penetrable scatterers, J. Opt. Soc. Am. A, 11, 4, 1383 (1994)
[37] Bleszynski, E.; Bleszynski, M.; Jaroszewicz, T., AIM: adaptive integral method for solving large-scale electromagnetic scattering and radiation problems, Radio Sci., 31, 5, 1225-1251 (1996)
[38] Volakis, J. L.; Sertel, K., Integral Equation Methods for Electromagnetics (2011), Scitech
[39] Botha, M. M., Solving the volume integral equations of electromagnetic scattering, J. Comput. Phys., 218, 1, 141-158 (2006) · Zbl 1111.78012
[40] Faddeyev, L. D.; Seckler, B., The inverse problem in the quantum theory of scattering, J. Math. Phys., 4, 1, 72-104 (1963) · Zbl 0112.45101
[41] Johnson, B. R.; Secrest, D., The solution of the nonrelativistic quantum scattering problem without exchange, J. Math. Phys., 7, 12, 2187-2195 (1966)
[42] Alt, E.; Grassberger, P.; Sandhas, W., Reduction of the three-particle collision problem to multi-channel two-particle Lippmann-Schwinger equations, Nucl. Phys. B, 2, 2, 167-180 (1967)
[43] Masel, R. I.; Merrill, R. P.; Miller, W. H., Quantum scattering from a sinusoidal hard wall: atomic diffraction from solid surfaces, Phys. Rev. B, 12, 12, 5545-5551 (1975)
[44] Adhikari, S. K., Quantum scattering in two dimensions, Am. J. Phys., 54, 4, 362-367 (1986)
[45] Hecht, K. T., Operator form of scattering Green’s function and the integral equation for the scattering problem, (Scattering (2000), Springer New York: Springer New York New York, NY), 477-480
[46] Kalos, M. H.; Carlo, Monte, Calculations of the ground state of three- and four-body nuclei, Phys. Rev., 128, 4, 1791-1795 (1962)
[47] Zhao, Z.; Kovvali, N.; Lin, W.; Ahn, C.-H.; Couchman, L.; Carin, L., Volumetric fast multipole method for modeling Schrödinger’s equation, J. Comput. Phys., 224, 2, 941-955 (2007) · Zbl 1114.65361
[48] Harrison, R. J.; Fann, G. I.; Yanai, T.; Gan, Z.; Beylkin, G., Multiresolution quantum chemistry: basic theory and initial applications, J. Chem. Phys., 121, 23, 11587-11598 (2004)
[49] Harrison, R. J.; Beylkin, G.; Bischoff, F. A.; Calvin, J. A.; Fann, G. I.; Fosso-Tande, J.; Galindo, D.; Hammond, J. R.; Hartman-Baker, R.; Hill, J. C.; Jia, J.; Kottmann, J. S.; Ou, M. J.; Pei, J.; Ratcliff, L. E.; Reuter, M. G.; Richie-Halford, A. C.; Romero, N. A.; Sekino, H.; Shelton, W. A.; Sundahl, B. E.; Thornton, W. S.; Valeev, E. F.; Vázquez-Mayagoitia, Á.; Vence, N.; Yanai, T.; Yokoi, Y., Madness: A Multiresolution, Adaptive Numerical Environment for Scientific Simulation, SIAM J. Sci. Comput., vol. 38, S123-S142 (2016), Society for Industrial and Applied Mathematics Publications · Zbl 1365.65327
[50] Mohlenkamp, M. J.; Young, T., Convergence of Green iterations for Schrödinger equations, Recent Adv. Comput. Sci., 201-208 (2008) · Zbl 1157.65507
[51] Mohlenkamp, M. J., Function space requirements for the single-electron functions within the multiparticle Schrödinger equation, J. Math. Phys., 54, 6, Article 062105 pp. (2013)
[52] Khoromskij, B. N., On tensor approximation of Green iterations for Kohn-Sham equations, Comput. Vis. Sci., 11, 4-6, 259-271 (2008) · Zbl 1522.65249
[53] Rakhuba, M. V.; Oseledets, I. V., Fast multidimensional convolution in low-rank tensor formats via cross approximation, SIAM J. Sci. Comput., 37, 2, A565-A582 (2015) · Zbl 1320.65197
[54] Rakhuba, M. V.; Oseledets, I. V., Grid-based electronic structure calculations: the tensor decomposition approach, J. Comput. Phys., 312, 19-30 (2016) · Zbl 1351.82040
[55] Fejér, L., Mechanische Quadraturen mit positiven Cotesschen Zahlen, Math. Z., 37, 1, 287-309 (1933) · JFM 59.0261.03
[56] Trefethen, L. N., Is Gauss quadrature better than Clenshaw-Curtis?, SIAM Rev., 50, 1, 67-87 (2008) · Zbl 1141.65018
[57] Rabinowitz, P., Approximate methods of higher analysis. L.V. Kantorovich and V.I. Krylov, Science, 134, 3487, 1358 (1961), translated from the third Russian edition by Curtis D. Benster. Interscience, New York, 1959
[58] Anselone, P. M., Singularity subtraction in the numerical solution of integral equations, J. Aust. Math. Soc. Ser. B, Appl. Math., 22, 4, 408-418 (1981) · Zbl 0477.65095
[59] Wang, L.; Krasny, R.; Tlupova, S., A kernel-independent treecode based on barycentric Lagrange interpolation, Commun. Comput. Phys., 28, 1415-1436 (2020) · Zbl 1473.65025
[60] Vaughn, N.; Wilson, L.; Krasny, R., A GPU-accelerated Barycentric Lagrange Treecode, (2020 IEEE International Parallel and Distributed Processing Symposium Workshops. 2020 IEEE International Parallel and Distributed Processing Symposium Workshops, IPDPSW, New Orleans, LA, USA (2020)), 701-710
[61] Goedecker, S., Linear scaling electronic structure methods, Rev. Mod. Phys., 71, 4, 1085-1123 (1999)
[62] Anderson, D. G., Iterative procedures for nonlinear integral equations, J. ACM, 12, 4, 547-560 (1965) · Zbl 0149.11503
[63] Ceperley, D. M.; Alder, B. J., Ground state of the electron gas by a stochastic method, Phys. Rev. Lett., 45, 7, 566-569 (1980)
[64] Perdew, J. P.; Zunger, A., Self-interaction correction to density-functional approximations for many-electron systems, Phys. Rev. B, 23, 10, 5048-5079 (1981)
[65] Marques, M. A.L.; Oliveira, M. J.T.; Burnus, T., Libxc: a library of exchange and correlation functionals for density functional theory, Comput. Phys. Commun., 183, 10, 2272-2281 (2012)
[66] Lehtola, S.; Steigemann, C.; Oliveira, M. J.; Marques, M. A., Recent developments in libxc — a comprehensive library of functionals for density functional theory, SoftwareX, 7, 1-5 (2018)
[67] Chelikowsky, J. R.; Troullier, N.; Saad, Y., Finite-difference-pseudopotential method: electronic structure calculations without a basis, Phys. Rev. Lett., 72, 8, 1240-1243 (1994)
[68] Bernholc, J.; Hodak, M.; Lu, W., Recent developments and applications of the real-space multigrid method, J. Phys. Condens. Matter, 20, 29, Article 294205 pp. (2008)
[69] Saad, Y.; Chelikowsky, J. R.; Shontz, S. M., Numerical methods for electronic structure calculations of materials, SIAM Rev., 52, 1, 3-54 (2010) · Zbl 1185.82004
[70] Chen, H.; Dai, X.; Gong, X.; He, L.; Zhou, A., Adaptive finite element approximations for Kohn-Sham models, Multiscale Model. Simul., 12, 4, 1828-1869 (2014) · Zbl 1316.35260
[71] Trefethen, L. N., Spectral Methods in MATLAB (2008), SIAM
[72] Trefethen, L. N.; Bau, D. I., Numerical Linear Algebra (2000), SIAM Society for Industrial and Applied Mathematics · Zbl 0984.65019
[73] Barnes, J.; Hut, P., A hierarchical O(N log N) force-calculation algorithm, Nature, 324, 6096, 446-449 (1986)
[74] Greengard, L.; Rokhlin, V., A fast algorithm for particle simulations, J. Comput. Phys., 73, 2, 325-348 (1987) · Zbl 0629.65005
[75] Berrut, J.-P.; Trefethen, L. N., Barycentric Lagrange interpolation, SIAM Rev., 46, 3, 501-517 (2004) · Zbl 1061.65006
[76] Li, P.; Johnston, H.; Krasny, R., A Cartesian treecode for screened Coulomb interactions, J. Comput. Phys., 228, 10, 3858-3868 (2009) · Zbl 1165.78304
[77] Salzer, H. E., Lagrangian interpolation at the Chebyshev points \(x_{n , \nu} \equiv \cos(\nu \pi / n), \nu = 0(1) n\); some unnoted advantages, Comput. J., 15, 156-159 (1972) · Zbl 0242.65007
[78] Buck, I., Reaching the summit: accelerated computing powering world’s fastest supercomputer (2018)
[79] Tsuchida, E.; Tsukada, M., Adaptive finite-element method for electronic-structure calculations, Phys. Rev. B, 54, 7602-7605 (1996)
[80] Tsuchida, E.; Tsukada, M., Large-scale electronic-structure calculations based on the adaptive finite-element method, J. Phys. Soc. Jpn., 67, 11, 3844-3858 (1998)
[81] Zhou, Y.; Saad, Y.; Tiago, M. L.; Chelikowsky, J. R., Self-consistent-field calculations using Chebyshev-filtered subspace iteration, J. Comput. Phys., 219, 1, 172-184 (2006) · Zbl 1105.65111
[82] Zhou, Y.; Saad, Y.; Tiago, M. L.; Chelikowsky, J. R., Parallel self-consistent-field calculations via Chebyshev-filtered subspace acceleration, Phys. Rev. E, 74, Article 066704 pp. (2006)
[83] Zhou, Y.; Chelikowsky, J. R.; Saad, Y., Chebyshev-filtered subspace iteration method free of sparse diagonalization for solving the Kohn-Sham equation, J. Comput. Phys., 274, 770-782 (2014) · Zbl 1351.82098
[84] Krasny, R.; Wang, L., A treecode based on barycentric Hermite interpolation for electrostatic particle interactions, Comput. Math. Biophys., 7, 73-84 (2019) · Zbl 1439.78003
[85] Duan, Z.-H.; Krasny, R., A treecode algorithm for computing Ewald summation of dipolar systems, (Proceedings of the 2003 ACM Symposium on Applied Computing. Proceedings of the 2003 ACM Symposium on Applied Computing, SAC ’03 (2003), Association for Computing Machinery: Association for Computing Machinery New York, NY, USA), 172-177
[86] Boateng, H. A., Periodic Coulomb tree method: an alternative to parallel particle mesh Ewald, J. Chem. Theory Comput., 16, 1, 7-17 (2020)
[87] Vaughn, N., GPU Accelerated Barycentric Treecodes and their Application to Kohn-Sham Density Functional Theory (2020), University of Michigan, Ph.D. thesis
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