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Lebedeva IV, García A, Artacho E, Ordejón P. Modular implementation of the linear- and cubic-scaling orbital minimization methods in electronic structure codes using atomic orbitals. ROYAL SOCIETY OPEN SCIENCE 2023; 10:230063. [PMID: 37122948 PMCID: PMC10130719 DOI: 10.1098/rsos.230063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 03/29/2023] [Indexed: 05/03/2023]
Abstract
We present a code modularization approach to design efficient and massively parallel cubic- and linear-scaling solvers for electronic structure calculations using atomic orbitals. The modular implementation of the orbital minimization method, in which linear algebra and parallelization issues are handled via external libraries, is demonstrated in the SIESTA code. The distributed block compressed sparse row (DBCSR) and scalable linear algebra package (ScaLAPACK) libraries are used for algebraic operations with sparse and dense matrices, respectively. The MatrixSwitch and libOMM libraries, recently developed within the Electronic Structure Library, facilitate switching between different matrix formats and implement the energy minimization. We show results comparing the performance of several cubic-scaling algorithms, and also demonstrate the parallel performance of the linear-scaling solvers, and their supremacy over the cubic-scaling solvers for insulating systems with sizes of several hundreds of atoms.
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Affiliation(s)
- Irina V. Lebedeva
- CIC nanoGUNE BRTA, Donostia-San Sebastián 20018, Spain
- Catalan Institute of Nanoscience and Nanotechnology—ICN2 (CSIC and BIST), Campus UAB, Bellaterra 08193, Spain
- Simune Atomistics, Avenida de Tolosa 76, Donostia-San Sebastián 20018, Spain
| | - Alberto García
- Institut de Ciència de Materials de Barcelona (ICMAB-CSIC), Bellaterra 08193, Spain
| | - Emilio Artacho
- CIC nanoGUNE BRTA, Donostia-San Sebastián 20018, Spain
- Donostia International Physics Center DIPC, Donostia-San Sebastián 20018, Spain
- Theory of Condensed Matter, Cavendish Laboratory, University of Cambridge, Cambridge CB3 0HE, UK
- Ikerbasque, Basque Foundation for Science, Bilbao 48011, Spain
| | - Pablo Ordejón
- Catalan Institute of Nanoscience and Nanotechnology—ICN2 (CSIC and BIST), Campus UAB, Bellaterra 08193, Spain
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2
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Stein F, Hutter J. Double-hybrid density functionals for the condensed phase: Gradients, stress tensor, and auxiliary-density matrix method acceleration. J Chem Phys 2022; 156:074107. [DOI: 10.1063/5.0082327] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Frederick Stein
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, Zurich 8057, Switzerland
| | - Jürg Hutter
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, Zurich 8057, Switzerland
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3
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Pauletti M, Rybkin VV, Iannuzzi M. Subsystem Density Functional Theory Augmented by a Delta Learning Approach to Achieve Kohn-Sham Accuracy. J Chem Theory Comput 2021; 17:6423-6431. [PMID: 34505765 DOI: 10.1021/acs.jctc.1c00592] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Simulations based on electronic structure theory naturally include polarization and have no transferability problems. In particular, Kohn-Sham density functional theory (KS-DFT) has become the method of reference for ab initio molecular dynamics simulations of condensed matter systems. However, the high computational cost often poses strict limits on the affordable system size as well as on the extension of sampling (number of configurations). In this work, we propose an improvement to the subsystem density functional theory approach, known as the Kim-Gordon (KG) scheme, thus enabling the sampling of configurations for condensed molecular systems keeping the KS-DFT level accuracy at a fraction of computer time. Our scheme compensates the known KG shortcomings of the electronic kinetic energy term by adding a simple correction and can match KS-DFT accuracy in energies and forces. The computationally cheap correction is determined by means of a machine learning procedure. The proposed KG scheme is applied within a linear scaling self-consistent field formalism and is assessed by a series of molecular dynamics simulations of liquid water under different conditions. Although system-dependent, the correction is transferable between system sizes and temperatures.
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Affiliation(s)
- Michela Pauletti
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, Zurich 8057, Switzerland
| | - Vladimir V Rybkin
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, Zurich 8057, Switzerland
| | - Marcella Iannuzzi
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, Zurich 8057, Switzerland
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4
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Luo Z, Qin X, Wan L, Hu W, Yang J. Parallel Implementation of Large-Scale Linear Scaling Density Functional Theory Calculations With Numerical Atomic Orbitals in HONPAS. Front Chem 2020; 8:589910. [PMID: 33324611 PMCID: PMC7726133 DOI: 10.3389/fchem.2020.589910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 09/08/2020] [Indexed: 11/13/2022] Open
Abstract
Linear-scaling density functional theory (DFT) is an efficient method to describe the electronic structures of molecules, semiconductors, and insulators to avoid the high cubic-scaling cost in conventional DFT calculations. Here, we present a parallel implementation of linear-scaling density matrix trace correcting (TC) purification algorithm to solve the Kohn-Sham (KS) equations with the numerical atomic orbitals in the HONPAS package. Such a linear-scaling density matrix purification algorithm is based on the Kohn's nearsightedness principle, resulting in a sparse Hamiltonian matrix with localized basis sets in the DFT calculations. Therefore, sparse matrix multiplication is the most time-consuming step in the density matrix purification algorithm for linear-scaling DFT calculations. We propose to use the MPI_Allgather function for parallel programming to deal with the sparse matrix multiplication within the compressed sparse row (CSR) format, which can scale up to hundreds of processing cores on modern heterogeneous supercomputers. We demonstrate the computational accuracy and efficiency of this parallel density matrix purification algorithm by performing large-scale DFT calculations on boron nitrogen nanotubes containing tens of thousands of atoms.
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Affiliation(s)
| | - Xinming Qin
- Hefei National Laboratory for Physical Sciences at the Microscale, Department of Chemical Physics, and Synergetic Innovation Center of Quantum Information and Quantum Physics, University of Science and Technology of China, Hefei, China
| | | | - Wei Hu
- Hefei National Laboratory for Physical Sciences at the Microscale, Department of Chemical Physics, and Synergetic Innovation Center of Quantum Information and Quantum Physics, University of Science and Technology of China, Hefei, China
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5
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Oliveira MJT, Papior N, Pouillon Y, Blum V, Artacho E, Caliste D, Corsetti F, de Gironcoli S, Elena AM, García A, García-Suárez VM, Genovese L, Huhn WP, Huhs G, Kokott S, Küçükbenli E, Larsen AH, Lazzaro A, Lebedeva IV, Li Y, López-Durán D, López-Tarifa P, Lüders M, Marques MAL, Minar J, Mohr S, Mostofi AA, O'Cais A, Payne MC, Ruh T, Smith DGA, Soler JM, Strubbe DA, Tancogne-Dejean N, Tildesley D, Torrent M, Yu VWZ. The CECAM electronic structure library and the modular software development paradigm. J Chem Phys 2020; 153:024117. [PMID: 32668924 DOI: 10.1063/5.0012901] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
First-principles electronic structure calculations are now accessible to a very large community of users across many disciplines, thanks to many successful software packages, some of which are described in this special issue. The traditional coding paradigm for such packages is monolithic, i.e., regardless of how modular its internal structure may be, the code is built independently from others, essentially from the compiler up, possibly with the exception of linear-algebra and message-passing libraries. This model has endured and been quite successful for decades. The successful evolution of the electronic structure methodology itself, however, has resulted in an increasing complexity and an ever longer list of features expected within all software packages, which implies a growing amount of replication between different packages, not only in the initial coding but, more importantly, every time a code needs to be re-engineered to adapt to the evolution of computer hardware architecture. The Electronic Structure Library (ESL) was initiated by CECAM (the European Centre for Atomic and Molecular Calculations) to catalyze a paradigm shift away from the monolithic model and promote modularization, with the ambition to extract common tasks from electronic structure codes and redesign them as open-source libraries available to everybody. Such libraries include "heavy-duty" ones that have the potential for a high degree of parallelization and adaptation to novel hardware within them, thereby separating the sophisticated computer science aspects of performance optimization and re-engineering from the computational science done by, e.g., physicists and chemists when implementing new ideas. We envisage that this modular paradigm will improve overall coding efficiency and enable specialists (whether they be computer scientists or computational scientists) to use their skills more effectively and will lead to a more dynamic evolution of software in the community as well as lower barriers to entry for new developers. The model comes with new challenges, though. The building and compilation of a code based on many interdependent libraries (and their versions) is a much more complex task than that of a code delivered in a single self-contained package. Here, we describe the state of the ESL, the different libraries it now contains, the short- and mid-term plans for further libraries, and the way the new challenges are faced. The ESL is a community initiative into which several pre-existing codes and their developers have contributed with their software and efforts, from which several codes are already benefiting, and which remains open to the community.
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Affiliation(s)
- Micael J T Oliveira
- Max Planck Institute for the Structure and Dynamics of Matter, D-22761 Hamburg, Germany
| | - Nick Papior
- DTU Computing Center, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Yann Pouillon
- Departamento CITIMAC, Universidad de Cantabria, Santander, Spain
| | - Volker Blum
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina 27708, USA
| | | | - Damien Caliste
- Department of Physics, IRIG, Univ. Grenoble Alpes and CEA, F-38000 Grenoble, France
| | - Fabiano Corsetti
- Departments of Materials and Physics, and the Thomas Young Centre for Theory and Simulation of Materials, Imperial College London, London SW7 2AZ, United Kingdom
| | | | - Alin M Elena
- Scientific Computing Department, Daresbury Laboratory, Warrington WA4 4AD, United Kingdom
| | - Alberto García
- Institut de Ciència de Materials de Barcelona (ICMAB-CSIC), Bellaterra E-08193, Spain
| | | | - Luigi Genovese
- Department of Physics, IRIG, Univ. Grenoble Alpes and CEA, F-38000 Grenoble, France
| | - William P Huhn
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina 27708, USA
| | - Georg Huhs
- Barcelona Supercomputing Center (BSC), 08034 Barcelona, Spain
| | | | - Emine Küçükbenli
- Scuola Internazionale Superiore di Studi Avanzati, 34136 Trieste, Italy
| | | | - Alfio Lazzaro
- Department of Chemistry, University of Zürich, CH-8057 Zürich, Switzerland
| | | | - Yingzhou Li
- Department of Mathematics, Duke University, Durham, North Carolina 27708-0320, USA
| | | | - Pablo López-Tarifa
- Centro de Física de Materiales, Centro Mixto CSIC-UPV/EHU, 20018 San Sebastián, Spain
| | - Martin Lüders
- Max Planck Institute for the Structure and Dynamics of Matter, D-22761 Hamburg, Germany
| | - Miguel A L Marques
- Institut für Physik, Martin-Luther-Universität Halle-Wittenberg, 06120 Halle (Saale), Germany
| | - Jan Minar
- New Technologies Research Centre, University of West Bohemia, 301 00 Plzen, Czech Republic
| | - Stephan Mohr
- Barcelona Supercomputing Center (BSC), 08034 Barcelona, Spain
| | - Arash A Mostofi
- Departments of Materials and Physics, and the Thomas Young Centre for Theory and Simulation of Materials, Imperial College London, London SW7 2AZ, United Kingdom
| | - Alan O'Cais
- Institute for Advanced Simulation (IAS), Jülich Supercomputing Centre (JSC), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Mike C Payne
- Theory of Condensed Matter, Cavendish Laboratory, University of Cambridge, Cambridge CB3 0HE, United Kingdom
| | - Thomas Ruh
- Institute of Materials Chemistry, TU Wien, 1060 Vienna, Austria
| | - Daniel G A Smith
- Molecular Sciences Software Institute, Blacksburg, Virginia 24060, USA
| | - José M Soler
- Departamento e Instituto de Física de la Materia Condensada (IFIMAC), Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - David A Strubbe
- Department of Physics, University of California, Merced, California 95343, USA
| | | | - Dominic Tildesley
- School of Chemistry, University of Southampton, Southampton SO17 1BJ, United Kingdom
| | | | - Victor Wen-Zhe Yu
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina 27708, USA
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6
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Kühne TD, Iannuzzi M, Del Ben M, Rybkin VV, Seewald P, Stein F, Laino T, Khaliullin RZ, Schütt O, Schiffmann F, Golze D, Wilhelm J, Chulkov S, Bani-Hashemian MH, Weber V, Borštnik U, Taillefumier M, Jakobovits AS, Lazzaro A, Pabst H, Müller T, Schade R, Guidon M, Andermatt S, Holmberg N, Schenter GK, Hehn A, Bussy A, Belleflamme F, Tabacchi G, Glöß A, Lass M, Bethune I, Mundy CJ, Plessl C, Watkins M, VandeVondele J, Krack M, Hutter J. CP2K: An electronic structure and molecular dynamics software package - Quickstep: Efficient and accurate electronic structure calculations. J Chem Phys 2020; 152:194103. [PMID: 33687235 DOI: 10.1063/5.0007045] [Citation(s) in RCA: 839] [Impact Index Per Article: 209.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
CP2K is an open source electronic structure and molecular dynamics software package to perform atomistic simulations of solid-state, liquid, molecular, and biological systems. It is especially aimed at massively parallel and linear-scaling electronic structure methods and state-of-the-art ab initio molecular dynamics simulations. Excellent performance for electronic structure calculations is achieved using novel algorithms implemented for modern high-performance computing systems. This review revisits the main capabilities of CP2K to perform efficient and accurate electronic structure simulations. The emphasis is put on density functional theory and multiple post-Hartree-Fock methods using the Gaussian and plane wave approach and its augmented all-electron extension.
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Affiliation(s)
- Thomas D Kühne
- Dynamics of Condensed Matter and Center for Sustainable Systems Design, Chair of Theoretical Chemistry, Paderborn University, Warburger Str. 100, D-33098 Paderborn, Germany
| | - Marcella Iannuzzi
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Mauro Del Ben
- Computational Research Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Vladimir V Rybkin
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Patrick Seewald
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Frederick Stein
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Teodoro Laino
- IBM Research Europe, CH-8803 Rüschlikon, Switzerland
| | - Rustam Z Khaliullin
- Department of Chemistry, McGill University, CH-801 Sherbrooke St. West, Montreal, Quebec H3A 0B8, Canada
| | - Ole Schütt
- Department of Materials, ETH Zürich, CH-8092 Zürich, Switzerland
| | | | - Dorothea Golze
- Department of Applied Physics, Aalto University, Otakaari 1, FI-02150 Espoo, Finland
| | - Jan Wilhelm
- Institute of Theoretical Physics, University of Regensburg, Universitätsstraße 31, D-93053 Regensburg, Germany
| | - Sergey Chulkov
- School of Mathematics and Physics, University of Lincoln, Brayford Pool, Lincoln, United Kingdom
| | | | - Valéry Weber
- IBM Research Europe, CH-8803 Rüschlikon, Switzerland
| | | | | | | | | | - Hans Pabst
- Intel Extreme Computing, Software and Systems, Zürich, Switzerland
| | - Tiziano Müller
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Robert Schade
- Department of Computer Science and Paderborn Center for Parallel Computing, Paderborn University, Warburger Str. 100, D-33098 Paderborn, Germany
| | - Manuel Guidon
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Samuel Andermatt
- Integrated Systems Laboratory, ETH Zürich, CH-8092 Zürich, Switzerland
| | - Nico Holmberg
- Department of Chemistry and Materials Science, Aalto University, P.O. Box 16100, 00076 Aalto, Finland
| | - Gregory K Schenter
- Physical Science Division, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99352, USA
| | - Anna Hehn
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Augustin Bussy
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Fabian Belleflamme
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Gloria Tabacchi
- Department of Science and High Technology, University of Insubria and INSTM, via Valleggio 9, I-22100 Como, Italy
| | - Andreas Glöß
- BASF SE, Carl-Bosch-Straße 38, D-67056 Ludwigshafen am Rhein, Germany
| | - Michael Lass
- Department of Computer Science and Paderborn Center for Parallel Computing, Paderborn University, Warburger Str. 100, D-33098 Paderborn, Germany
| | - Iain Bethune
- Hartree Centre, Science and Technology Facilities Council, Sci-Tech Daresbury, Warrington WA4 4AD, United Kingdom
| | - Christopher J Mundy
- Physical Science Division, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99352, USA
| | - Christian Plessl
- Department of Computer Science and Paderborn Center for Parallel Computing, Paderborn University, Warburger Str. 100, D-33098 Paderborn, Germany
| | - Matt Watkins
- School of Mathematics and Physics, University of Lincoln, Brayford Pool, Lincoln, United Kingdom
| | - Joost VandeVondele
- Swiss National Supercomputing Centre (CSCS), ETH Zürich, Zürich, Switzerland
| | - Matthias Krack
- Laboratory for Scientific Computing and Modelling, Paul Scherrer Institute, CH-5232 Villigen PSI, Switzerland
| | - Jürg Hutter
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
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7
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Nishimura Y, Nakai H. D
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: Divide‐and‐Conquer Density Functional Tight‐Binding Program for Huge‐System Quantum Mechanical Molecular Dynamics Simulations. J Comput Chem 2019; 40:1538-1549. [DOI: 10.1002/jcc.25804] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 01/31/2019] [Accepted: 02/05/2019] [Indexed: 12/17/2022]
Affiliation(s)
- Yoshifumi Nishimura
- Waseda Research Institute for Science and Engineering, Waseda University 3‐4‐1 Okubo, Shinjuku‐ku, Tokyo 169‐8555 Japan
| | - Hiromi Nakai
- Waseda Research Institute for Science and Engineering, Waseda University 3‐4‐1 Okubo, Shinjuku‐ku, Tokyo 169‐8555 Japan
- Department of Chemistry and BiochemistrySchool of Advanced Science and Engineering, Waseda University 3‐4‐1 Okubo, Shinjuku‐ku, Tokyo 169‐8555 Japan
- ESICB, Kyoto University Kyotodaigaku‐Katsura, Kyoto 615‐8520 Japan
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8
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Manz TA, Chen T. New scaling relations to compute atom-in-material polarizabilities and dispersion coefficients: part 2. Linear-scaling computational algorithms and parallelization. RSC Adv 2019; 9:33310-33336. [PMID: 35529131 PMCID: PMC9073276 DOI: 10.1039/c9ra01983a] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 09/23/2019] [Indexed: 01/24/2023] Open
Abstract
We present two algorithms to compute system-specific polarizabilities and dispersion coefficients such that required memory and computational time scale linearly with increasing number of atoms in the unit cell for large systems. The first algorithm computes the atom-in-material (AIM) static polarizability tensors, force-field polarizabilities, and C6, C8, C9, C10 dispersion coefficients using the MCLF method. The second algorithm computes the AIM polarizability tensors and C6 coefficients using the TS-SCS method. Linear-scaling computational cost is achieved using a dipole interaction cutoff length function combined with iterative methods that avoid large dense matrix multiplies and large matrix inversions. For MCLF, Richardson extrapolation of the screening increments is used. For TS-SCS, a failproof conjugate residual (FCR) algorithm is introduced that solves any linear equation system having Hermitian coefficients matrix. These algorithms have mathematically provable stable convergence that resists round-off errors. We parallelized these methods to provide rapid computation on multi-core computers. Excellent parallelization efficiencies were obtained, and adding parallel processors does not significantly increase memory requirements. This enables system-specific polarizabilities and dispersion coefficients to be readily computed for materials containing millions of atoms in the unit cell. The largest example studied herein is an ice crystal containing >2 million atoms in the unit cell. For this material, the FCR algorithm solved a linear equation system containing >6 million rows, 7.57 billion interacting atom pairs, 45.4 billion stored non-negligible matrix components used in each large matrix-vector multiplication, and ∼19 million unknowns per frequency point (>300 million total unknowns). Linear-scaling algorithms were developed to compute atom-in-material polarizabilities and dispersion coefficients using MCLF and TS-SCS methods.![]()
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Affiliation(s)
- Thomas A. Manz
- Department of Chemical & Materials Engineering
- New Mexico State University
- Las Cruces
- USA
| | - Taoyi Chen
- Department of Chemical & Materials Engineering
- New Mexico State University
- Las Cruces
- USA
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9
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Singh G, Kumar K, Moudgil RK. Alloying-induced spin Seebeck effect and spin figure of merit in Pt-based bimetallic atomic wires of noble metals. Phys Chem Chem Phys 2019; 21:20965-20980. [DOI: 10.1039/c9cp01671f] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
The chemical potential of electrodes can be tuned to generate pure thermal spin voltages in certain bimetallic wires of noble metals.
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Affiliation(s)
- Gurvinder Singh
- Department of Physics
- S. D. College
- Ambala Cantt-133 001
- India
- Department of Physics
| | - Krishan Kumar
- Department of Physics
- S. D. College
- Ambala Cantt-133 001
- India
| | - R. K. Moudgil
- Department of Physics
- Kurukshetra University
- Kurukshetra – 136 119
- India
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10
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Romero-Muñiz C, Nakata A, Pou P, Bowler DR, Miyazaki T, Pérez R. High-accuracy large-scale DFT calculations using localized orbitals in complex electronic systems: the case of graphene-metal interfaces. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2018; 30:505901. [PMID: 30468156 DOI: 10.1088/1361-648x/aaec4c] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Over many years, computational simulations based on density functional theory (DFT) have been used extensively to study many different materials at the atomic scale. However, its application is restricted by system size, leaving a number of interesting systems without a high-accuracy quantum description. In this work, we calculate the electronic and structural properties of a graphene-metal system significantly larger than in previous plane-wave calculations with the same accuracy. For this task we use a localised basis set with the Conquest code, both in their primitive, pseudo-atomic orbital form, and using a recent multi-site approach. This multi-site scheme allows us to maintain accuracy while saving computational time and memory requirements, even in our exemplar complex system of graphene grown on Rh(1 1 1) with and without intercalated atomic oxygen. This system offers a rich scenario that will serve as a benchmark, demonstrating that highly accurate simulations in cells with over 3000 atoms are feasible with modest computational resources.
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Affiliation(s)
- Carlos Romero-Muñiz
- Departamento de Física Teórica de la Materia Condensada, Universidad Autónoma de Madrid, E-28049 Madrid, Spain. First-Principles Simulation Group, Nano-Theory Field, International Center for Materials Nanoarchitectonics (WPI-MANA), National Institute for Materials Science (NIMS), 1-1 Namiki, Tsukuba, Ibaraki 305-0044, Japan
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11
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Keçeli M, Corsetti F, Campos C, Roman JE, Zhang H, Vázquez-Mayagoitia Á, Zapol P, Wagner AF. SIESTA-SIPs: Massively parallel spectrum-slicing eigensolver for an ab initio
molecular dynamics package. J Comput Chem 2018; 39:1806-1814. [DOI: 10.1002/jcc.25350] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2017] [Revised: 03/23/2018] [Accepted: 04/12/2018] [Indexed: 11/06/2022]
Affiliation(s)
- Murat Keçeli
- Chemical Sciences and Engineering Division; Argonne National Laboratory; Argonne Illinois 60439
- Computational Science Division; Argonne National Laboratory; Argonne Illinois 60439
| | - Fabiano Corsetti
- Departments of Materials and Physics and the Thomas Young Centre for Theory and Simulation of Materials; Imperial College London; London SW7 2AZ United Kingdom
| | - Carmen Campos
- D. Sistemes Informàtics i Computació; Universitat Politècnica de València, Camí de Vera s/n; València 46022 Spain
| | - Jose E. Roman
- D. Sistemes Informàtics i Computació; Universitat Politècnica de València, Camí de Vera s/n; València 46022 Spain
| | - Hong Zhang
- Mathematics and Computer Science Division; Argonne National Laboratory; Argonne Illinois 60439
| | - Álvaro Vázquez-Mayagoitia
- Chemical Sciences and Engineering Division; Argonne National Laboratory; Argonne Illinois 60439
- Argonne Leadership Computing Facility; Argonne National Laboratory; Argonne Illinois 60439
| | - Peter Zapol
- Materials Science Division; Argonne National Laboratory; Argonne Illinois 60439
| | - Albert F. Wagner
- Computational Science Division; Argonne National Laboratory; Argonne Illinois 60439
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12
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Scheiber H, Shi Y, Khaliullin RZ. Communication: Compact orbitals enable low-cost linear-scaling ab initio molecular dynamics for weakly-interacting systems. J Chem Phys 2018; 148:231103. [PMID: 29935517 DOI: 10.1063/1.5029939] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Hayden Scheiber
- Department of Chemistry, McGill University, 801 Sherbrooke St. West, Montreal, Québec H3A 0B8, Canada
| | - Yifei Shi
- Department of Chemistry, McGill University, 801 Sherbrooke St. West, Montreal, Québec H3A 0B8, Canada
| | - Rustam Z. Khaliullin
- Department of Chemistry, McGill University, 801 Sherbrooke St. West, Montreal, Québec H3A 0B8, Canada
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13
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Linear scaling DFT calculations for large tungsten systems using an optimized local basis. NUCLEAR MATERIALS AND ENERGY 2018. [DOI: 10.1016/j.nme.2018.01.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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14
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Strak P, Sakowski K, Kempisty P, Krukowski S. Dissipation of the excess energy of the adsorbate-thermalization via electron transfer. Phys Chem Chem Phys 2017; 19:9149-9155. [PMID: 28318002 DOI: 10.1039/c7cp00235a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A new scenario for the thermalization process of adsorbates at solid surfaces is proposed. The scenario is based on the existence of an electric dipole layer in which the electron wavefunctions extend over the positive ions, creating a strong local electric field which drags the electrons into the solid interior and repels the positive ions. During adsorption the electrons tunnel into the solid interior, conveying the excess energy. The positive ions are retarded by the field, losing the excess kinetic energy, and are located smoothly into the adsorption sites. In such a scheme, the excess energy is not dissipated locally, avoiding melting or the creation of defects which is in accordance with experiments. The scenario is supported by ab initio calculation results, including density function theory of the slabs representing the AlN surface and the Schrodinger equation for the time evolution of hydrogen-like atoms at the solid surface.
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Affiliation(s)
- Pawel Strak
- Institute of High Pressure Physics, Polish Academy of Sciences, Sokołowska 29/37, 01-142 Warsaw, Poland.
| | - Konrad Sakowski
- Institute of High Pressure Physics, Polish Academy of Sciences, Sokołowska 29/37, 01-142 Warsaw, Poland.
| | - Pawel Kempisty
- Institute of High Pressure Physics, Polish Academy of Sciences, Sokołowska 29/37, 01-142 Warsaw, Poland. and Center for Integrated Research of Future Electronics (CIRFE), Institute of Materials and Systems for Sustainability (IMaSS), Nagoya University, Nagoya 464-8603, Japan
| | - Stanislaw Krukowski
- Institute of High Pressure Physics, Polish Academy of Sciences, Sokołowska 29/37, 01-142 Warsaw, Poland.
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15
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Desgranges C, Anderson PW, Delhommelle J. Classical and quantum many-body effects on the critical properties and thermodynamic regularities of silicon. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2017; 29:045401. [PMID: 27875329 DOI: 10.1088/1361-648x/29/4/045401] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Using molecular simulation, we determine the critical properties of Si as well as the loci for several remarkable thermodynamic contours spanning the supercritical region of the phase diagram. We consider a classical three-body potential as well as a quantum (tight-binding) many-body model, and determine the loci for the ideality contours, including the Zeno line and the H line of ideal enthalpy. The two strategies (classical or quantum) lead to strongly asymmetric binodals and to critical properties in good agreement with each other. The Zeno and H lines are found to remain linear over a wide temperature interval, despite the changes in electronic structure undergone by the fluid along these contours. We also show that the classical and quantum model yield markedly different results for the parameters defining the H line, the exponents for the power-laws underlying the line of minima for the isothermal enthalpy and for the density required to achieve ideal behavior, most notably for the enthalpy.
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Affiliation(s)
- C Desgranges
- Department of Chemistry, University of North Dakota, 151 Cornell Street Stop 9024, Grand Forks, ND 58202, USA
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16
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Dziedzic J, Mao Y, Shao Y, Ponder J, Head-Gordon T, Head-Gordon M, Skylaris CK. TINKTEP: A fully self-consistent, mutually polarizable QM/MM approach based on the AMOEBA force field. J Chem Phys 2016; 145:124106. [DOI: 10.1063/1.4962909] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Jacek Dziedzic
- School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, United Kingdom
- Faculty of Applied Physics and Mathematics, Gdańsk University of Technology, Gdańsk, Poland
| | - Yuezhi Mao
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Yihan Shao
- Q-Chem Inc., 6601 Owens Drive, Suite 105, Pleasanton, California 94588, USA
| | - Jay Ponder
- Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri 63130, USA
| | - Teresa Head-Gordon
- Department of Chemistry, University of California, Berkeley, California 94720, USA
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, USA
- Department of Bioengineering, University of California, Berkeley, California 94720, USA
| | - Martin Head-Gordon
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Chris-Kriton Skylaris
- School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, United Kingdom
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17
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Desgranges C, Delhommelle J. Evaluation of the grand-canonical partition function using expanded Wang-Landau simulations. IV. Performance of many-body force fields and tight-binding schemes for the fluid phases of silicon. J Chem Phys 2016; 144:124510. [PMID: 27036464 DOI: 10.1063/1.4944619] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We extend Expanded Wang-Landau (EWL) simulations beyond classical systems and develop the EWL method for systems modeled with a tight-binding Hamiltonian. We then apply the method to determine the partition function and thus all thermodynamic properties, including the Gibbs free energy and entropy, of the fluid phases of Si. We compare the results from quantum many-body (QMB) tight binding models, which explicitly calculate the overlap between the atomic orbitals of neighboring atoms, to those obtained with classical many-body (CMB) force fields, which allow to recover the tetrahedral organization in condensed phases of Si through, e.g., a repulsive 3-body term that favors the ideal tetrahedral angle. Along the vapor-liquid coexistence, between 3000 K and 6000 K, the densities for the two coexisting phases are found to vary significantly (by 5 orders of magnitude for the vapor and by up to 25% for the liquid) and to provide a stringent test of the models. Transitions from vapor to liquid are predicted to occur for chemical potentials that are 10%-15% higher for CMB models than for QMB models, and a ranking of the force fields is provided by comparing the predictions for the vapor pressure to the experimental data. QMB models also reveal the formation of a gap in the electronic density of states of the coexisting liquid at high temperatures. Subjecting Si to a nanoscopic confinement has a dramatic effect on the phase diagram with, e.g. at 6000 K, a decrease in liquid densities by about 50% for both CMB and QMB models and an increase in vapor densities between 90% (CMB) and 170% (QMB). The results presented here provide a full picture of the impact of the strategy (CMB or QMB) chosen to model many-body effects on the thermodynamic properties of the fluid phases of Si.
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Affiliation(s)
- Caroline Desgranges
- Department of Chemistry, University of North Dakota, 151 Cornell Street Stop 9024, Grand Forks, North Dakota 58202, USA
| | - Jerome Delhommelle
- Department of Chemistry, University of North Dakota, 151 Cornell Street Stop 9024, Grand Forks, North Dakota 58202, USA
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18
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Hedayatifar L, Irani E, Mazarei M, Rasti S, Azar YT, Rezakhani AT, Mashaghi A, Shayeganfar F, Anvari M, Heydari T, Tabar AR, Nafari N, Vesaghi MA, Asgari R, Rahimi Tabar MR. Optical absorption and electronic spectra of chlorophylls a and b. RSC Adv 2016. [DOI: 10.1039/c6ra20226h] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
We report optical and electronic properties of the two main chlorophylls in green plants, namely, chlorophylls a and b. We estimate the electric moments of these molecules and study absorption spectra of the chlorophylls.
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19
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Akimov AV, Prezhdo OV. Large-Scale Computations in Chemistry: A Bird’s Eye View of a Vibrant Field. Chem Rev 2015; 115:5797-890. [DOI: 10.1021/cr500524c] [Citation(s) in RCA: 159] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Alexey V. Akimov
- Department
of Chemistry, University of South California, Los Angeles, California 90089, United States
| | - Oleg V. Prezhdo
- Department
of Chemistry, University of South California, Los Angeles, California 90089, United States
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20
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Ruiz-Serrano Á, Skylaris CK. Variationally localized search direction method for constrained optimization of non-orthogonal, localized orbitals in electronic structure calculations. J Chem Phys 2013; 139:164110. [DOI: 10.1063/1.4826164] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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21
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Khaliullin RZ, VandeVondele J, Hutter J. Efficient Linear-Scaling Density Functional Theory for Molecular Systems. J Chem Theory Comput 2013; 9:4421-7. [DOI: 10.1021/ct400595k] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Rustam Z. Khaliullin
- Physical
Chemistry Institute, University of Zürich, Winterthurerstrasse 180, 8057 Zürich, Switzerland
- Institute
of Physical Chemistry, Johannes Gutenberg University of Mainz, Staudingerweg
7, 55128 Mainz, Germany
| | - Joost VandeVondele
- Department
of Materials, Swiss Federal Institute of Technology, Wolfgang-Pauli-Strasse
27, 8093 Zürich, Switzerland
| | - Jürg Hutter
- Physical
Chemistry Institute, University of Zürich, Winterthurerstrasse 180, 8057 Zürich, Switzerland
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22
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Ruiz-Serrano Á, Skylaris CK. A variational method for density functional theory calculations on metallic systems with thousands of atoms. J Chem Phys 2013; 139:054107. [DOI: 10.1063/1.4817001] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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23
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Hine NDM, Dziedzic J, Haynes PD, Skylaris CK. Electrostatic interactions in finite systems treated with periodic boundary conditions: application to linear-scaling density functional theory. J Chem Phys 2012; 135:204103. [PMID: 22128924 DOI: 10.1063/1.3662863] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We present a comparison of methods for treating the electrostatic interactions of finite, isolated systems within periodic boundary conditions (PBCs), within density functional theory (DFT), with particular emphasis on linear-scaling (LS) DFT. Often, PBCs are not physically realistic but are an unavoidable consequence of the choice of basis set and the efficacy of using Fourier transforms to compute the Hartree potential. In such cases the effects of PBCs on the calculations need to be avoided, so that the results obtained represent the open rather than the periodic boundary. The very large systems encountered in LS-DFT make the demands of the supercell approximation for isolated systems more difficult to manage, and we show cases where the open boundary (infinite cell) result cannot be obtained from extrapolation of calculations from periodic cells of increasing size. We discuss, implement, and test three very different approaches for overcoming or circumventing the effects of PBCs: truncation of the Coulomb interaction combined with padding of the simulation cell, approaches based on the minimum image convention, and the explicit use of open boundary conditions (OBCs). We have implemented these approaches in the ONETEP LS-DFT program and applied them to a range of systems, including a polar nanorod and a protein. We compare their accuracy, complexity, and rate of convergence with simulation cell size. We demonstrate that corrective approaches within PBCs can achieve the OBC result more efficiently and accurately than pure OBC approaches.
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Affiliation(s)
- Nicholas D M Hine
- Department of Physics, Imperial College London, Exhibition Road, London SW7 2AZ, United Kingdom.
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24
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Ab initio simulation of the effect of the potential of water on the electronic structure of arginine. J Mol Model 2012; 18:859-70. [DOI: 10.1007/s00894-011-1125-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2011] [Accepted: 05/11/2011] [Indexed: 10/18/2022]
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25
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Bowler DR, Miyazaki T. O(N) methods in electronic structure calculations. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2012; 75:036503. [PMID: 22790422 DOI: 10.1088/0034-4885/75/3/036503] [Citation(s) in RCA: 170] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Linear-scaling methods, or O(N) methods, have computational and memory requirements which scale linearly with the number of atoms in the system, N, in contrast to standard approaches which scale with the cube of the number of atoms. These methods, which rely on the short-ranged nature of electronic structure, will allow accurate, ab initio simulations of systems of unprecedented size. The theory behind the locality of electronic structure is described and related to physical properties of systems to be modelled, along with a survey of recent developments in real-space methods which are important for efficient use of high-performance computers. The linear-scaling methods proposed to date can be divided into seven different areas, and the applicability, efficiency and advantages of the methods proposed in these areas are then discussed. The applications of linear-scaling methods, as well as the implementations available as computer programs, are considered. Finally, the prospects for and the challenges facing linear-scaling methods are discussed.
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Affiliation(s)
- D R Bowler
- London Centre for Nanotechnology, UCL, 17-19 Gordon St, London WC1H 0AH, UK.
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26
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27
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Feng S, Cheng X. Theoretical study on electronic properties and pressure-induced phase transition in β-CdP2. COMPUT THEOR CHEM 2011. [DOI: 10.1016/j.comptc.2011.02.028] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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28
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Ordejon P, Artacho E, Soler JM. Mixed Approach to Incorporate Self-Consistency into Order-N LCAO Methods. ACTA ACUST UNITED AC 2011. [DOI: 10.1557/proc-408-85] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
AbstractWe present a method for selfconsistent Density Functional Theory calculations in which the effort required is proportional to the size of the system, thus allowing the aplication to problems with a very large size. The method is based on the LCAO approximation, and uses a mixed approach to obtain the Hamiltonian integrals between atomic orbitals with Order-N effort. We show the performance and the convergence properties of the method in several silicon and carbon systems, and in a DNA periodic chain.
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29
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Density Matrix Methods in Linear Scaling Electronic Structure Theory. CHALLENGES AND ADVANCES IN COMPUTATIONAL CHEMISTRY AND PHYSICS 2011. [DOI: 10.1007/978-90-481-2853-2_16] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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30
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Shang H, Xiang H, Li Z, Yang J. Linear scaling electronic structure calculations with numerical atomic basis set. INT REV PHYS CHEM 2010. [DOI: 10.1080/0144235x.2010.520454] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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31
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Dykeman EC, Sankey OF. Normal mode analysis and applications in biological physics. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2010; 22:423202. [PMID: 21403307 DOI: 10.1088/0953-8984/22/42/423202] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Normal mode analysis has become a popular and often used theoretical tool in the study of functional motions in enzymes, viruses, and large protein assemblies. The use of normal modes in the study of these motions is often extremely fruitful since many of the functional motions of large proteins can be described using just a few normal modes which are intimately related to the overall structure of the protein. In this review, we present a broad overview of several popular methods used in the study of normal modes in biological physics including continuum elastic theory, the elastic network model, and a new all-atom method, recently developed, which is capable of computing a subset of the low frequency vibrational modes exactly. After a review of the various methods, we present several examples of applications of normal modes in the study of functional motions, with an emphasis on viral capsids.
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Affiliation(s)
- Eric C Dykeman
- Department of Physics, Center for Biological Physics, Arizona State University, Tempe, AZ 85287-1504, USA
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32
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Peng M, Zheng H. Equivalent potential of water for the electronic structure of glycine. J Mol Model 2010; 17:111-24. [PMID: 20383651 DOI: 10.1007/s00894-010-0705-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2009] [Accepted: 03/01/2010] [Indexed: 11/26/2022]
Abstract
First-principles, all-electron, ab initio calculations have been performed to construct an equivalent potential of water for the electronic structure of glycine (Gly) in solution. The calculation involved three steps. The first step was to search for the minimum-energy geometric structure of the Gly + nH₂O system. The second step was to calculate the electronic structure of Gly with the potential of water molecules via the self-consistent cluster-embedding method (SCCE), based on the result obtained in the first step. The last step was to calculate the electronic structure of Gly with the potential of dipoles after replacing the water molecules with dipoles. The results show that the occupied molecular orbitals of Gly are raised by about 0.0524 Ry on average due to the effect of water. The effect of water can be simulated well using the dipole potential. The equivalent potential obtained can be applied directly to electronic structure calculations of proteins in solution using the SCCE method.
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Affiliation(s)
- Min Peng
- Physics Department, Tongji University, Shanghai 200092, People's Republic Of China
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33
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Dykeman EC, Twarock R. All-atom normal-mode analysis reveals an RNA-induced allostery in a bacteriophage coat protein. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2010; 81:031908. [PMID: 20365771 DOI: 10.1103/physreve.81.031908] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2009] [Indexed: 05/29/2023]
Abstract
Assembly of the T=3 bacteriophage MS2 is initiated by the binding of a 19 nucleotide RNA stem loop from within the phage genome to a symmetric coat protein dimer. This binding event effects a folding of the FG loop in one of the protein subunits of the dimer and results in the formation of an asymmetric dimer. Since both the symmetric and asymmetric forms of the dimer are needed for the assembly of the protein container, this allosteric switch plays an important role in the life cycle of the phage. We provide here details of an all-atom normal-mode analysis of this allosteric effect. The results suggest that asymmetric contacts between the A -duplex RNA phosphodiester backbone of the stem loop with the EF loop in one coat protein subunit results in an increased dynamic behavior of its FG loop. The four lowest-frequency modes, which encompass motions predominantly on the FG loops, account for over 90% of the increased dynamic behavior due to a localization of the vibrational pattern on a single FG loop. Finally, we show that an analysis of the allosteric effect using an elastic network model fails to predict this localization effect, highlighting the importance of using an all-atom full force field method for this problem.
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Affiliation(s)
- Eric C Dykeman
- Department of Biology, University of York, York YO10 5DD, United Kingdom
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34
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Krukowski S, Kempisty P, Strąk P. Review: GaN growth by ammonia based methods - density functional theory study. CRYSTAL RESEARCH AND TECHNOLOGY 2009. [DOI: 10.1002/crat.200900510] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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35
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Shen X, Gao Y, Zheng H. The equivalent dipole potential of water for the electronic structure of threonine. Mol Phys 2009. [DOI: 10.1080/00268970902905810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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36
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Barraza-Lopez S, Park K, García-Suárez V, Ferrer J. First-principles study of electron transport through the single-molecule magnet Mn12. PHYSICAL REVIEW LETTERS 2009; 102:246801. [PMID: 19659035 DOI: 10.1103/physrevlett.102.246801] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2009] [Indexed: 05/28/2023]
Abstract
We examine electron transport through a single-molecule magnet Mn(12) bridged between Au electrodes using the first-principles method. We find crucial features which were inaccessible in model Hamiltonian studies: spin filtering and a strong dependence of charge distribution on local environments. The spin filtering remains robust with different molecular geometries and interfaces, and strong electron correlations, while the charge distribution over the Mn(12) strongly depends on them. We point out a qualitative difference between locally charged and free-electron-charged Mn(12).
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Affiliation(s)
- Salvador Barraza-Lopez
- Department of Physics, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, USA
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37
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Dykeman EC, Sankey OF. Theory of the low frequency mechanical modes and Raman spectra of the M13 bacteriophage capsid with atomic detail. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2009; 21:035116. [PMID: 21817274 DOI: 10.1088/0953-8984/21/3/035116] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
We present a theoretical study of the low frequency vibrational modes of the M13 bacteriophage using a fully atomistic model. Using ideas from electronic structure theory, the few lowest vibrational modes of the M13 bacteriophage are determined using classical harmonic analysis. The relative Raman intensity is estimated for each of the mechanical modes using a bond polarizability model. Comparison of the atomic mechanical modes calculated here with modes derived from elastic continuum theory shows that a much richer spectrum emerges from an atomistic picture.
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Affiliation(s)
- Eric C Dykeman
- Department of Physics, Center for Biological Physics, Arizona State University, Tempe, AZ 85287-1504, USA
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38
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Krukowski S, Kempisty P, Jalbout AF. Thermodynamic and kinetic approach in density functional theory studies of microscopic structure of GaN(0001) surface in ammonia-rich conditions. J Chem Phys 2008; 129:234705. [DOI: 10.1063/1.3037218] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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39
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Burger SK, Yang W. Linear-scaling quantum calculations using non-orthogonal localized molecular orbitals. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2008; 20:294209. [PMID: 25076813 PMCID: PMC4112540 DOI: 10.1088/0953-8984/20/29/294209] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
An absolute energy minimum variational principle is used for carrying out linear scaling calculations with non-orthogonal localized orbitals. Compared with results based on orthogonal localized molecular orbitals, the method is shown to give significantly more accurate results when the localized molecular orbitals are allowed to be non-orthogonal. This is made possible by introducing a second minimization for approximating the inverse overlap matrix. We also show how an exact line search may be used efficiently with the conjugate gradient method for minimizing the energy functional.
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Affiliation(s)
- Steven K Burger
- Department of Chemistry, McMaster University, 1280 Main St. West, Hamilton, ON, Canada
| | - Weitao Yang
- Department of Chemistry, Duke University, Box 90346, Durham, NC 27708-0346, USA
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40
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Yan S, Zheng H, Zhang T. The equivalent potential of water molecules for electronic structure of alanine. Mol Phys 2008. [DOI: 10.1080/00268970802245184] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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41
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Zhang T, Zheng H, Yan S. The equivalent potential of water for electronic structure of aspartic acid. J Comput Chem 2008; 29:1780-7. [PMID: 18351613 DOI: 10.1002/jcc.20940] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The equivalent potential of water for the electronic structure of aspartic acid (Asp(-)) in solution is constructed by the first-principles, all-electrons, ab initio calculations. Aspartic acid is a hydrophilic amino acid which is negatively charged in neutral water solution. The main process of calculation consists of three steps. Firstly, the geometric structure of the cluster containing Asp(-) and water molecules is calculated by the free cluster calculation. Then, based on the obtained geometric structure, the electronic structure of Asp(-) with the potential of water molecules is calculated using the self-consistent cluster-embedding method. Finally, the electronic structure of Asp(-) with the potential of dipoles is calculated. The results show that the major effect of water on Asp(-)'s electronic structure is lowering the occupied molecular orbitals by about 0.02 Ry on average, and narrowing energy gap by 10.8%. The effect of water on the electronic structure of Asp(-) can be simulated by dipoles potential.
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Affiliation(s)
- Tian Zhang
- Department of Physics, Pohl Institute of Solid State Physics, Tongji University, Shanghai 200092, People's Republic of China.
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42
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Weber V, VandeVondele J, Hutter J, Niklasson AMN. Direct energy functional minimization under orthogonality constraints. J Chem Phys 2008; 128:084113. [DOI: 10.1063/1.2841077] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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43
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Artacho E, Anglada E, Diéguez O, Gale JD, García A, Junquera J, Martin RM, Ordejón P, Pruneda JM, Sánchez-Portal D, Soler JM. The SIESTA method; developments and applicability. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2008; 20:064208. [PMID: 21693870 DOI: 10.1088/0953-8984/14/11/302] [Citation(s) in RCA: 2773] [Impact Index Per Article: 173.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Recent developments in and around the SIESTA method of first-principles simulation of condensed matter are described and reviewed, with emphasis on (i) the applicability of the method for large and varied systems, (ii) efficient basis sets for the standards of accuracy of density-functional methods, (iii) new implementations, and (iv) extensions beyond ground-state calculations.
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Affiliation(s)
- Emilio Artacho
- Department of Chemistry, University of California, Berkeley, CA 94720, USA. Department of Earth Sciences, University of Cambridge, Cambridge CB2 3EQ, UK
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Dykeman EC, Sankey OF. Low frequency mechanical modes of viral capsids: an atomistic approach. PHYSICAL REVIEW LETTERS 2008; 100:028101. [PMID: 18232930 DOI: 10.1103/physrevlett.100.028101] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2007] [Indexed: 05/25/2023]
Abstract
We present a method for the calculation of the low frequency vibrational modes and frequencies of viral capsids, or other large molecules, where the modes are modeled with atomic detail. Extending ideas from electronic structure theory, an energy functional is used to find modes of a classical dynamical matrix below a fixed (pseudo-Fermi) level. The icosahedral satellite tobacco necrosis virus is modeled as an example. We find that atoms around the C5 and C3 axis have small relative displacement while the beta sheet body shows gliding motion.
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Affiliation(s)
- Eric C Dykeman
- Department of Physics, Center for Biological Physics, Arizona State University, Tempe, Arizona 85287-1504, USA
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Krukowski S, Kempisty P, Strąk P, Nowak G, Czernecki R, Leszczynski M, Suski T, Bockowski M, Grzegory I. Modelling the growth of nitrides in ammonia-rich environment. CRYSTAL RESEARCH AND TECHNOLOGY 2007. [DOI: 10.1002/crat.200711019] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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46
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Skylaris CK, Haynes PD. Achieving plane wave accuracy in linear-scaling density functional theory applied to periodic systems: A case study on crystalline silicon. J Chem Phys 2007; 127:164712. [DOI: 10.1063/1.2796168] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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47
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Lee HS, Tuckerman ME. Ab initio molecular dynamics with discrete variable representation basis sets: techniques and application to liquid water. J Phys Chem A 2007; 110:5549-60. [PMID: 16623489 DOI: 10.1021/jp0570770] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Finite temperature ab initio molecular dynamics (AIMD), in which forces are obtained from "on-the-fly" electronic structure calculations, is a widely used technique for studying structural and dynamical properties of chemically active systems. Recently, we introduced an AIMD scheme based on discrete variable representation (DVR) basis sets, which was shown to have improved convergence properties over the conventional plane wave (PW) basis set [Liu,Y.; et al. Phys. Rev. B 2003, 68, 125110]. In the present work, the numerical algorithms for the DVR based AIMD scheme (DVR/AIMD) are provided in detail, and the latest developments of the approach are presented. The accuracy and stability of the current implementation of the DVR/AIMD scheme are tested by performing a simulation of liquid water at ambient conditions. The structural information obtained from the present work is in good agreement with the result of recent AIMD simulations with a PW basis set (PW/AIMD). Advantages of using the DVR/AIMD scheme over the PW/AIMD method are discussed. In particular, it is shown that a DVR/AIMD simulation of liquid water in the complete basis set limit is possible with a relatively small number of grid points.
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Affiliation(s)
- Hee-Seung Lee
- Department of Chemistry, New York University, New York, New York 10003, USA
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Xiang HJ, Yang J, Hou JG, Zhu Q. Linear scaling calculation of band edge states and doped semiconductors. J Chem Phys 2007; 126:244707. [PMID: 17614577 DOI: 10.1063/1.2746322] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Linear scaling methods provide total energy, but no energy levels and canonical wave functions. From the density matrix computed through the density matrix purification methods, we propose an order-N [O(N)] method for calculating both the energies and wave functions of band edge states, which are important for optical properties and chemical reactions. In addition, we also develop an O(N) algorithm to deal with doped semiconductors based on the O(N) method for band edge states calculation. We illustrate the O(N) behavior of the new method by applying it to boron nitride (BN) nanotubes and BN nanotubes with an adsorbed hydrogen atom. The band gap of various BN nanotubes are investigated systematically and the acceptor levels of BN nanotubes with an isolated adsorbed H atom are computed. Our methods are simple, robust, and especially suited for the application in self-consistent field electronic structure theory.
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Affiliation(s)
- H J Xiang
- Hefei National Laboratory for Physical Sciences at Microscale, University of Science and Technology of China, Hefei, Anhui 230026, People's Republic of China
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Seijo L, Barandiarán Z, Soler JM. Order-N and embedded-cluster first-principles DFT calculations using SIESTA/Mosaico. Theor Chem Acc 2007. [DOI: 10.1007/s00214-007-0338-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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50
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Anikin NA, Anisimov VM, Bugaenko VL, Bobrikov VV, Andreyev AM. LocalSCF method for semiempirical quantum-chemical calculation of ultralarge biomolecules. J Chem Phys 2007; 121:1266-70. [PMID: 15260667 DOI: 10.1063/1.1764496] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
A linear-scaling semiempirical method, LocalSCF, has been proposed for the quantum-chemical calculations of ultralarge molecular systems by treating the large-scale molecular task as a variational problem. The method resolves the self-consistent field task through the finite atomic expansion of weakly nonorthogonal localized molecular orbitals. The inverse overlap matrix arising from the nonorthogonality of the localized orbitals is approximated by preserving the first-order perturbation term and applying the second-order correction by means of a penalty function. This allows for the separation of the orbital expansion procedure from the self-consistent field optimization of linear coefficients, thereby maintaining the localized molecular orbital size unchanged during the refinement of linear coefficients. Orbital normalization is preserved analytically by the variation of virtual degrees of freedom, which are orthogonal to the initial orbitals. Optimization of linear coefficients of localized orbitals is performed by a gradient procedure. The computer program running on a commodity personal computer was applied to the GroEL-GroES chaperonin complex containing 119,273 atoms.
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Affiliation(s)
- N A Anikin
- Quantum Biochemistry Group, Konstantina Fedina-3/24, 105215 Moscow, Russian Federation
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