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Nishimura R, Yoshikawa T, Sakata K, Nakai H. Excitation configuration analysis for divide-and-conquer excited-state calculation method using dynamical polarizability. J Chem Phys 2024; 160:244103. [PMID: 38913842 DOI: 10.1063/5.0207935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Accepted: 05/23/2024] [Indexed: 06/26/2024] Open
Abstract
The authors previously developed a divide-and-conquer (DC)-based non-local excited-state calculation method for large systems using dynamical polarizability [Nakai and Yoshikawa, J. Chem. Phys. 146, 124123 (2017)]. This method evaluates the excitation energies and oscillator strengths using information on the dynamical polarizability poles. This article proposes a novel analysis of the previously developed method to obtain further configuration information on excited states, including excitation and de-excitation coefficients of each excitation configuration. Numerical applications to simple molecules, such as ethylene, hydrogen molecule, ammonia, and pyridazine, confirmed that the proposed analysis could accurately reproduce the excitation and de-excitation coefficients. The combination with the DC scheme enables both the local and non-local excited states of large systems with an excited nature to be treated.
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Affiliation(s)
- Ryusei Nishimura
- Department of Chemistry and Biochemistry, School of Advanced Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku, Tokyo 169-8555, Japan
| | - Takeshi Yoshikawa
- Faculty of Pharmaceutical Sciences, Toho University, 2-2-1 Miyama, Funabashi, Chiba 274-8510, Japan
- Waseda Research Institute for Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku, Tokyo 169-8555, Japan
| | - Ken Sakata
- Faculty of Pharmaceutical Sciences, Toho University, 2-2-1 Miyama, Funabashi, Chiba 274-8510, Japan
| | - Hiromi Nakai
- Department of Chemistry and Biochemistry, School of Advanced Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku, Tokyo 169-8555, Japan
- Waseda Research Institute for Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku, Tokyo 169-8555, Japan
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2
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Nakai H, Kobayashi M, Yoshikawa T, Seino J, Ikabata Y, Nishimura Y. Divide-and-Conquer Linear-Scaling Quantum Chemical Computations. J Phys Chem A 2023; 127:589-618. [PMID: 36630608 DOI: 10.1021/acs.jpca.2c06965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Fragmentation and embedding schemes are of great importance when applying quantum-chemical calculations to more complex and attractive targets. The divide-and-conquer (DC)-based quantum-chemical model is a fragmentation scheme that can be connected to embedding schemes. This feature article explains several DC-based schemes developed by the authors over the last two decades, which was inspired by the pioneering study of DC self-consistent field (SCF) method by Yang and Lee (J. Chem. Phys. 1995, 103, 5674-5678). First, the theoretical aspects of the DC-based SCF, electron correlation, excited-state, and nuclear orbital methods are described, followed by the two-component relativistic theory, quantum-mechanical molecular dynamics simulation, and the introduction of three programs, including DC-based schemes. Illustrative applications confirmed the accuracy and feasibility of the DC-based schemes.
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Affiliation(s)
- Hiromi Nakai
- Department of Chemistry and Biochemistry, School of Advanced Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku, Tokyo169-8555, Japan.,Waseda Research Institute for Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku, Tokyo169-8555, Japan
| | - Masato Kobayashi
- Department of Chemistry, Faculty of Science, Hokkaido University, Kita 10 Nishi 8, Kita-ku, Sapporo, Hokkaido060-0810, Japan.,Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Kita 21 Nishi 10, Kita-ku, Sapporo, Hokkaido001-0021, Japan
| | - Takeshi Yoshikawa
- Faculty of Pharmaceutical Sciences, Toho University, 2-2-1 Miyama, Funabashi, Chiba274-8510, Japan
| | - Junji Seino
- Department of Chemistry and Biochemistry, School of Advanced Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku, Tokyo169-8555, Japan.,Waseda Research Institute for Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku, Tokyo169-8555, Japan
| | - Yasuhiro Ikabata
- Information and Media Center, Toyohashi University of Technology, 1-1 Hibarigaoka, Tempaku-cho, Toyohashi, Aichi441-8580, Japan.,Department of Computer Science and Engineering, Toyohashi University of Technology, 1-1 Hibarigaoka, Tempaku-cho, Toyohashi, Aichi441-8580, Japan
| | - Yoshifumi Nishimura
- Waseda Research Institute for Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku, Tokyo169-8555, Japan
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3
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Yoshikawa T, Takanashi T, Nakai H. Quantum Algorithm of the Divide-and-Conquer Unitary Coupled Cluster Method with a Variational Quantum Eigensolver. J Chem Theory Comput 2022; 18:5360-5373. [PMID: 35926142 DOI: 10.1021/acs.jctc.2c00602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The variational quantum eigensolver (VQE) with shallow or constant-depth quantum circuits is one of the most pursued approaches in the noisy intermediate-scale quantum (NISQ) devices with incoherent errors. In this study, the divide-and-conquer (DC) linear scaling technique, which divides the entire system into several fragments, is applied to the VQE algorithm based on the unitary coupled cluster (UCC) method, denoted as DC-qUCC/VQE, to reduce the number of required qubits. The unitarity of the UCC ansatz that enables the evaluation of the total energy as well as various molecular properties as expectation values can be easily implemented on quantum devices because the quantum gates are unitary operators themselves. Based on this feature, the present DC-qUCC/VQE algorithm is designed to conserve the total number of electrons in the entire system using the density matrix evaluated on a quantum computer. Numerical assessments clarified that the energy errors of the DC-qUCC/VQE calculations decrease by using the constraint of the total number of electrons. Furthermore, the DC-qUCC/VQE algorithm could reduce the number of quantum gates and shows the possibility of decreasing incoherent errors.
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Affiliation(s)
- Takeshi Yoshikawa
- Faculty of Pharmaceutical Sciences, Toho University, 2-2-1 Miyama, Funabashi, Chiba 274-8510, Japan.,Waseda Research Institute for Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, Japan
| | - Tomoya Takanashi
- 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 Biochemistry, School of Advanced Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, Japan.,Elements Strategy Initiative for Catalysts and Batteries (ESICB), Kyoto University, Katsura, Kyoto 615-8520, Japan
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4
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Nakai H. Development of Linear-Scaling Relativistic Quantum Chemistry Covering the Periodic Table. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2021. [DOI: 10.1246/bcsj.20210091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Hiromi Nakai
- Department of Chemistry and Biochemistry, School of Advanced Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, Japan
- Waseda Research Institute for Science and Engineering (WISE), Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, Japan
- Elements Strategy Initiative for Catalysts and Batteries (ESICB), Kyoto University, Katsura, Kyoto 615-8520, Japan
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5
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Yoshikawa T, Yoshihara J, Nakai H. Large-scale excited-state calculation using dynamical polarizability evaluated by divide-and-conquer based coupled cluster linear response method. J Chem Phys 2020; 152:024102. [PMID: 31941302 DOI: 10.1063/1.5124909] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
This study attempted to propose an efficient scheme at the coupled cluster linear response (CCLR) level to perform large-scale excited-state calculations of not only local excitations but also nonlocal ones such as charge transfers and transitions between delocalized orbitals. Although standard applications of fragmentation techniques to the excited-state calculations brought about the limitations that could only deal with local excitations, this study solved the problem by evaluating the excited states as the poles of dynamical polarizability. Because such an approach previously succeeded at the time-dependent density functional theory level [H. Nakai and T. Yoshikawa, J. Chem. Phys. 146, 124123 (2017)], this study was considered as an extension to the CCLR level. To evaluate the dynamical polarizability at the CCLR level, we revisited three equivalent formulas, namely, coupled-perturbed self-consistent field (CPSCF), random phase approximation (RPA), and Green's function (GF). We further extended these formulas to the linear-scaling methods based on the divide-and-conquer (DC) technique. We implemented the CCLR with singles and doubles (CCSDLR) program for the six schemes, i.e., the standard and DC-type CPSCF, RPA, and GF. Illustrative applications of the present methods demonstrated the accuracy and efficiency. Although the standard three treatments could exactly reproduced the conventional frequency-domain CCSDLR results, their computational costs were commonly higher than that of the conventional ones due to large amount of computations for individual frequencies of the external electric field. The DC-type treatments, which approximately reproduced the conventional results, could achieve quasilinear scaling computational costs. Among them, DC-GF was found to exhibit the best performance.
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Affiliation(s)
- Takeshi Yoshikawa
- Waseda Research Institute for Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, Japan
| | - Jyunya Yoshihara
- Department of Chemistry and Biochemistry, School of Advanced 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
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6
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Yoshikawa T, Komoto N, Nishimura Y, Nakai H. GPU-Accelerated Large-Scale Excited-State Simulation Based on Divide-and-Conquer Time-Dependent Density-Functional Tight-Binding. J Comput Chem 2019; 40:2778-2786. [PMID: 31441083 DOI: 10.1002/jcc.26053] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 08/04/2019] [Accepted: 08/07/2019] [Indexed: 01/09/2023]
Abstract
The present study implemented the divide-and-conquer time-dependent density-functional tight-binding (DC-TDDFTB) code on a graphical processing unit (GPU). The DC method, which is a linear-scaling scheme, divides a total system into several fragments. By separately solving local equations in individual fragments, the DC method could reduce slow central processing unit (CPU)-GPU memory access, as well as computational cost, and avoid shortfalls of GPU memory. Numerical applications confirmed that the present code on GPU significantly accelerated the TDDFTB calculations, while maintaining accuracy. Furthermore, the DC-TDDFTB simulation of 2-acetylindan-1,3-dione displays excited-state intramolecular proton transfer and provides reasonable absorption and fluorescence energies with the corresponding experimental values. © 2019 Wiley Periodicals, Inc.
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Affiliation(s)
- Takeshi Yoshikawa
- Waseda Research Institute for Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo, 169-8555, Japan
| | - Nana Komoto
- Department of Chemistry and Biochemistry, School of Advanced Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo, 169-8555, Japan
| | - 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 Biochemistry, School of Advanced Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo, 169-8555, Japan.,Elements Strategy Initiative for Catalysts and Batteries (ESICB), Kyoto University, Katsura, Kyoto, 615-8520, Japan
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7
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Nakai H, Yoshikawa T. Development of an excited-state calculation method for large systems using dynamical polarizability: A divide-and-conquer approach at the time-dependent density functional level. J Chem Phys 2017; 146:124123. [DOI: 10.1063/1.4978952] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Affiliation(s)
- Hiromi Nakai
- Department of Chemistry and Biochemistry, School of Advanced Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, Japan
- Research Institute for Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, Japan
- CREST, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
- Elements Strategy Initiative for Catalysts and Batteries (ESICB), Kyoto University, Katsura, Kyoto 615-8520, Japan
| | - Takeshi Yoshikawa
- Department of Chemistry and Biochemistry, School of Advanced Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, Japan
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8
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Nakai H, Yoshikawa T, Nonaka Y. Efficient pole-search algorithm for dynamic polarizability: Toward alternative excited-state calculation for large systems. J Comput Chem 2017; 38:7-14. [PMID: 27706818 DOI: 10.1002/jcc.24507] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Revised: 09/17/2016] [Accepted: 09/19/2016] [Indexed: 11/10/2022]
Abstract
This study presents an efficient algorithm to search for the poles of dynamic polarizability to obtain excited states of large systems with nonlocal excitation nature. The present algorithm adopts a homogeneous search with a constant frequency interval and a bisection search to achieve high accuracy. Furthermore, the subtraction process of the information about the detected poles from the total dynamic polarizability is used to extract the undetected pole contributions. Numerical assessments confirmed the accuracy and efficiency of the present algorithm in obtaining the excitation energies and oscillator strengths of all dipole-allowed excited states. A combination of the present pole-search algorithm and divide-and-conquer-based dynamic polarizability calculations was found to be promising to treat nonlocal excitations of large systems. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Hiromi Nakai
- Department of Chemistry and Biochemistry, School of Advanced Science and Engineering, Waseda University, Tokyo, 169-8555, Japan.,Research Institute for Science and Engineering, Waseda University, Tokyo, 169-8555, Japan.,CREST, Japan Science and Technology Agency, Saitama, 332-0012, Japan.,ESICB, Kyoto University, Kyoto, 615-8520, Japan
| | - Takeshi Yoshikawa
- Department of Chemistry and Biochemistry, School of Advanced Science and Engineering, Waseda University, Tokyo, 169-8555, Japan
| | - Yutaro Nonaka
- Department of Chemistry and Biochemistry, School of Advanced Science and Engineering, Waseda University, Tokyo, 169-8555, Japan
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9
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Furche F, Krull BT, Nguyen BD, Kwon J. Accelerating molecular property calculations with nonorthonormal Krylov space methods. J Chem Phys 2016; 144:174105. [DOI: 10.1063/1.4947245] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Affiliation(s)
- Filipp Furche
- Department of Chemistry, University of California, Irvine, 1102 Natural Sciences II, Irvine, California 92697-2025, USA
| | - Brandon T. Krull
- Department of Chemistry, University of California, Irvine, 1102 Natural Sciences II, Irvine, California 92697-2025, USA
| | - Brian D. Nguyen
- Department of Chemistry, University of California, Irvine, 1102 Natural Sciences II, Irvine, California 92697-2025, USA
| | - Jake Kwon
- Department of Chemistry, University of California, Irvine, 1102 Natural Sciences II, Irvine, California 92697-2025, USA
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10
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Wang LW. Divide-and-conquer quantum mechanical material simulations with exascale supercomputers. Natl Sci Rev 2014. [DOI: 10.1093/nsr/nwu060] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Abstract
Recent developments in large-scale materials science simulations, especially under the divide-and-conquer method, are reviewed. The pros and cons of the divide-and-conquer method are discussed. It is argued that the divide-and-conquer method, such as the linear-scaling 3D fragment method, is an ideal approach to take advantage of the heterogeneous architectures of modern-day supercomputers despite their relatively large prefactors among linear-scaling methods. Some developments in graphics processing unit (GPU) electronic structure calculations are also reviewed. The accelerators like GPU could be an essential part for the future exascale supercomputing.
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Affiliation(s)
- Lin-Wang Wang
- Materials Sciences Division, Lawrence Berkeley National Laboratory, One Cyclotron Road, Mail Stop 66, Berkeley, CA 94720, USA
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11
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Nakata H, Schmidt MW, Fedorov DG, Kitaura K, Nakamura S, Gordon MS. Efficient Molecular Dynamics Simulations of Multiple Radical Center Systems Based on the Fragment Molecular Orbital Method. J Phys Chem A 2014; 118:9762-71. [DOI: 10.1021/jp507726m] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Hiroya Nakata
- Department
of Biomolecular Engineering, Tokyo Institute of Technology, 4259 Nagatsutacho, Midori-ku, Yokohama, Kanagawa 226-8501, Japan
- Research Cluster
for Innovation, Nakamura Lab, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
- Kojimachi Business
Center Building, Japan Society for the Promotion of Science, 5-3-1 Kojimachi, Chiyoda-ku, Tokyo 102-0083, Japan
| | - Michael W. Schmidt
- Department
of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011, United States
| | - Dmitri G. Fedorov
- NRI, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Umezono, Tsukuba, Ibaraki 305-8568, Japan
| | - Kazuo Kitaura
- Graduate
School of System Informatics, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe 657-8501, Japan
| | - Shinichiro Nakamura
- Research Cluster
for Innovation, Nakamura Lab, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Mark S. Gordon
- Department
of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011, United States
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12
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Nakata H, Fedorov DG, Yokojima S, Kitaura K, Sakurai M, Nakamura S. Unrestricted density functional theory based on the fragment molecular orbital method for the ground and excited state calculations of large systems. J Chem Phys 2014; 140:144101. [DOI: 10.1063/1.4870261] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
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13
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Yoshikawa T, Kobayashi M, Fujii A, Nakai H. Novel Approach to Excited-State Calculations of Large Molecules Based on Divide-and-Conquer Method: Application to Photoactive Yellow Protein. J Phys Chem B 2013; 117:5565-73. [DOI: 10.1021/jp401819d] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | - Masato Kobayashi
- Waseda Institute for Advanced Study, Waseda University, Tokyo 169-8050, Japan
| | | | - Hiromi Nakai
- CREST, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama
332-0012, Japan
- ESICB, Kyoto University, Kyotodaigaku-Katsura, Nishigyoku,
Kyoto 615-8520, Japan
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14
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Kobayashi M, Nakai H. An effective energy gradient expression for divide-and-conquer second-order Møller–Plesset perturbation theory. J Chem Phys 2013; 138:044102. [DOI: 10.1063/1.4776228] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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15
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Kobayashi M, Touma T, Nakai H. Dynamic hyperpolarizability calculations of large systems: The linear-scaling divide-and-conquer approach. J Chem Phys 2012; 136:084108. [DOI: 10.1063/1.3687341] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
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16
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NAKAI H. Discovery of Chemical Principles:Symmetry Rules for Degenerate Excitations. JOURNAL OF COMPUTER CHEMISTRY-JAPAN 2012. [DOI: 10.2477/jccj.2012-0004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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17
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Yam C, Zhang Q, Wang F, Chen G. Linear-scaling quantum mechanical methods for excited states. Chem Soc Rev 2012; 41:3821-38. [DOI: 10.1039/c2cs15259b] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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18
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Kobayashi M, Nakai H. How does it become possible to treat delocalized and/or open-shell systems in fragmentation-based linear-scaling electronic structure calculations? The case of the divide-and-conquer method. Phys Chem Chem Phys 2012; 14:7629-39. [DOI: 10.1039/c2cp40153c] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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19
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Gordon MS, Fedorov DG, Pruitt SR, Slipchenko LV. Fragmentation Methods: A Route to Accurate Calculations on Large Systems. Chem Rev 2011; 112:632-72. [DOI: 10.1021/cr200093j] [Citation(s) in RCA: 836] [Impact Index Per Article: 64.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Mark S. Gordon
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames Iowa 50011, United States
| | - Dmitri G. Fedorov
- Nanosystem Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Umezono, Tsukuba, Ibaraki 305-8568, Japan
| | - Spencer R. Pruitt
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames Iowa 50011, United States
| | - Lyudmila V. Slipchenko
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
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20
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Yoshikawa T, Kobayashi M, Nakai H. Linear-scaling divide-and-conquer second-order Møller–Plesset perturbation calculation for open-shell systems: implementation and application. Theor Chem Acc 2011. [DOI: 10.1007/s00214-011-1008-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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21
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Katouda M, Kobayashi M, Nakai H, Nagase S. Two‐level hierarchical parallelization of second‐order Møller–plesset perturbation calculations in divide‐and‐conquer method. J Comput Chem 2011; 32:2756-64. [DOI: 10.1002/jcc.21855] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2011] [Revised: 03/30/2011] [Accepted: 05/13/2011] [Indexed: 11/11/2022]
Affiliation(s)
- Michio Katouda
- Department of Theoretical and Computational Molecular Science, Institute for Molecular Science, Okazaki 444‐8585, Japan
| | - Masato Kobayashi
- Department of Theoretical and Computational Molecular Science, Institute for Molecular Science, Okazaki 444‐8585, Japan
- Department of Chemistry and Biochemistry, School of Advanced Science and Engineering, Waseda University, Tokyo 169‐8555, Japan
| | - Hiromi Nakai
- Department of Theoretical and Computational Molecular Science, Institute for Molecular Science, Okazaki 444‐8585, Japan
- Department of Chemistry and Biochemistry, School of Advanced Science and Engineering, Waseda University, Tokyo 169‐8555, Japan
- Research Institute for Science and Engineering, Waseda University, Tokyo 169‐8555, Japan
- CREST, Japan Science and Technology Agency, Tokyo 102‐0075, Japan
| | - Shigeru Nagase
- Department of Theoretical and Computational Molecular Science, Institute for Molecular Science, Okazaki 444‐8585, Japan
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22
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Touma T, Kobayashi M, Nakai H. Finite-field evaluation of static (hyper)polarizabilities based on the linear-scaling divide-and-conquer method. Theor Chem Acc 2011. [DOI: 10.1007/s00214-011-0964-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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23
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24
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Brorsen K, Fedorov DG. Fully analytic energy gradient in the fragment molecular orbital method. J Chem Phys 2011; 134:124115. [DOI: 10.1063/1.3568010] [Citation(s) in RCA: 88] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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25
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Fedorov DG. A combined effective fragment potential–fragment molecular orbital method. II. Analytic gradient and application to the geometry optimization of solvated tetraglycine and chignolin. J Chem Phys 2011; 134:034110. [DOI: 10.1063/1.3517110] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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26
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Kobayashi M, Kunisada T, Akama T, Sakura D, Nakai H. Reconsidering an analytical gradient expression within a divide-and-conquer self-consistent field approach: Exact formula and its approximate treatment. J Chem Phys 2011; 134:034105. [DOI: 10.1063/1.3524337] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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Linear-scaling electronic structure calculation program based on divide-and-conquer method. ACTA ACUST UNITED AC 2011. [DOI: 10.1016/j.procs.2011.04.122] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Divide-and-Conquer Approaches to Quantum Chemistry: Theory and Implementation. CHALLENGES AND ADVANCES IN COMPUTATIONAL CHEMISTRY AND PHYSICS 2011. [DOI: 10.1007/978-90-481-2853-2_5] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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Sawada T, Fedorov DG, Kitaura K. Binding of Influenza A Virus Hemagglutinin to the Sialoside Receptor Is Not Controlled by the Homotropic Allosteric Effect. J Phys Chem B 2010; 114:15700-5. [DOI: 10.1021/jp1068895] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Toshihiko Sawada
- Nanosystem Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Umezono, Tsukuba, Ibaraki 305-8568, Japan, Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan, and Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Dmitri G. Fedorov
- Nanosystem Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Umezono, Tsukuba, Ibaraki 305-8568, Japan, Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan, and Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Kazuo Kitaura
- Nanosystem Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Umezono, Tsukuba, Ibaraki 305-8568, Japan, Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan, and Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
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Kobayashi M, Yoshikawa T, Nakai H. Divide-and-conquer self-consistent field calculation for open-shell systems: Implementation and application. Chem Phys Lett 2010. [DOI: 10.1016/j.cplett.2010.10.005] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Nagata T, Fedorov DG, Kitaura K. Importance of the hybrid orbital operator derivative term for the energy gradient in the fragment molecular orbital method. Chem Phys Lett 2010. [DOI: 10.1016/j.cplett.2010.04.043] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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