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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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2
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Hutama AS, Marlina LA, Chou CP, Irle S, Hofer TS. Development of Density-Functional Tight-Binding Parameters for the Molecular Dynamics Simulation of Zirconia, Yttria, and Yttria-Stabilized Zirconia. ACS OMEGA 2021; 6:20530-20548. [PMID: 34395999 PMCID: PMC8359130 DOI: 10.1021/acsomega.1c02411] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 07/15/2021] [Indexed: 06/13/2023]
Abstract
In this work, a set of density-functional tight-binding (DFTB) parameters for the Zr-Zr, Zr-O, Y-Y, Y-O, and Zr-Y interactions was developed for bulk and surface simulations of ZrO2 (zirconia), Y2O3 (yttria), and yttria-stabilized zirconia (YSZ) materials. The parameterization lays the ground work for realistic simulations of zirconia-, yttria-, and YSZ-based electrolytes in solid oxide fuel cells and YSZ-based catalysts on long timescales and relevant size scales. The parameterization was validated for the zirconia and yttria polymorphs observed under standard conditions based on density functional theory calculations and experimental data. Additionally, we performed DFTB-based molecular dynamics (MD) simulations to compute structural and vibrational properties of these materials. The results show that the parameters can give a qualitatively correct phase ordering of zirconia, where the tetragonal phase is more stable than the cubic phase at a lower temperature. The lattice parameters are only slightly overestimated by 0.05-0.1 Å (2% error), still within the typical accuracy of first-principles methods. Additionally, the MD results confirm that zirconia and yttria phases are stable against transformations under standard conditions. The parameterization also predicts that vibrational spectra are within the range of 100-1000 cm-1 for zirconia and 100-800 cm-1 for yttria, which is in good agreement with predictions both from full quantum mechanics and a recently developed classical force field. To further demonstrate the advantage of the developed DFTB parameters in terms of computational resources, we conducted DFTB/MD simulations of the YSZ4 and YS12 models containing approximately 750 atoms.
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Affiliation(s)
- Aulia Sukma Hutama
- Department
of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Gadjah Mada, Yogyakarta 55281, Indonesia
| | - Lala Adetia Marlina
- Department
of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Gadjah Mada, Yogyakarta 55281, Indonesia
| | - Chien-Pin Chou
- Department
of Applied Chemistry, National Chiao Tung
University, Hsinchu 30010, Taiwan
| | - Stephan Irle
- Computational
Sciences and Engineering Division & Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, United States
| | - Thomas S. Hofer
- Theoretical
Chemistry Division, Institute of General, Inorganic and Theoretical
Chemistry, Center for Chemistry and Biomedicine, University of Innsbruck, Innsbruck A-6020, Austria
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3
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Hutama AS, Chou CP, Nishimura Y, Witek HA, Irle S. Density-Functional Tight-Binding Parameters for Bulk Zirconium: A Case Study for Repulsive Potentials. J Phys Chem A 2021; 125:2184-2196. [PMID: 33645988 DOI: 10.1021/acs.jpca.0c11178] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Density-functional tight-binding (DFTB) parameters are presented for the simulation of the bulk phases of zirconium. Electronic parameters were obtained using a band structure fitting strategy, while two-center repulsive potentials were created by particle swarm optimization. As objective functions for the repulsive potential fitting, we employed the Birch-Murnaghan equations of state for hexagonal close-packed (HCP), body-centered cubic (BCC) and ω phases of Zr from density-functional theory (DFT). When fractional atomic coordinates are not allowed to change in the generation of the equation-of-state curves, long-range repulsive DFTB potentials are able to almost perfectly reproduce equilibrium structures, relative DFT energies of the bulk phases, and bulk moduli. However, the same potentials lead to artifacts in the DFTB potential energy surfaces when atom positions in the unit cell are allowed to fully relax during the change of unit cell parameters. Conventional short-range repulsive DFTB potentials, while inferior in their ability to reproduce DFT bulk energetics, are able to correctly reproduce the qualitative shape of the DFT potential energy surfaces, including the location of global minima, and can therefore be considered more transferable.
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Affiliation(s)
- Aulia Sukma Hutama
- Department of Chemistry, Nagoya University, Nagoya 464-8601, Japan.,Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Gadjah Mada, Yogyakarta 55281, Indonesia
| | - Chien-Pin Chou
- Department of Applied Chemistry, National Chiao Tung University, Hsinchu 30010, Taiwan
| | - Yoshifumi Nishimura
- Waseda Research Institute for Science and Engineering, Waseda University, Tokyo 169-8555, Japan
| | - Henryk A Witek
- Department of Applied Chemistry, National Chiao Tung University, Hsinchu 30010, Taiwan.,Institute of Molecular Science, National Chiao Tung University, Hsinchu 30010, Taiwan.,Center for Emergent Functional Matter Science, National Chiao Tung University, Hsinchu 30010, Taiwan
| | - Stephan Irle
- Computational Sciences and Engineering Division & Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, United States
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4
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Peels M, Knizia G. Fast Evaluation of Two-Center Integrals over Gaussian Charge Distributions and Gaussian Orbitals with General Interaction Kernels. J Chem Theory Comput 2020; 16:2570-2583. [PMID: 32040326 DOI: 10.1021/acs.jctc.9b01296] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
We present efficient algorithms for computing two-center integrals and integral derivatives, with general interaction kernels K(r12), over Gaussian charge distributions of general angular momenta l. While formulated in terms of traditional ab initio integration techniques, full derivations and required secondary information, as well as a reference implementation, are provided to make the content accessible to other fields. Concretely, the presented algorithms are based on an adaption of the McMurchie-Davidson Recurrence Relation (MDRR) combined with analytical properties of the solid harmonic transformation; this obviates all intermediate recurrences except the adapted MDRR itself, and allows it to be applied to fully contracted auxiliary kernel integrals. The technique is particularly well-suited for semiempirical molecular orbital methods, where it can serve as a more general and efficient replacement of Slater-Koster tables, and for first-principles quantum chemistry methods employing density fitting. But the formalism's high efficiency and ability of handling general interaction kernels K(r12) and multipolar Gaussian charge distributions may also be of interest for modeling electrostatic interactions and short-range exchange and charge penetration effects in classical force fields and model potentials. With the presented technique, a 4894 × 4894 univ-JKFIT Coulomb matrix JAB = (A|1/r12|B) (183 MiB) can be computed in 50 ms on a Q2'2018 notebook CPU, without any screening or approximations.
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Affiliation(s)
- Mieke Peels
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Gerald Knizia
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
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Podeszwa R, Jankiewicz W, Krzuś M, Witek HA. Correcting long-range electrostatics in DFTB. J Chem Phys 2019; 150:234110. [DOI: 10.1063/1.5099694] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Rafał Podeszwa
- Institute of Chemistry, University of Silesia, Szkolna 9, 41-006 Katowice, Poland
| | - Wojciech Jankiewicz
- Institute of Chemistry, University of Silesia, Szkolna 9, 41-006 Katowice, Poland
| | - Magdalena Krzuś
- Institute of Chemistry, University of Silesia, Szkolna 9, 41-006 Katowice, Poland
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Kraków, Poland
| | - Henryk A. Witek
- Department of Applied Chemistry and Institute of Molecular Science, National Chiao Tung University, 1001 University Rd., Hsinchu 30010, Taiwan
- Center for Emergent Functional Matter Science, National Chiao Tung University, 1001 University Rd., Hsinchu 30010, Taiwan
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6
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Chou CP, Sakti AW, Nishimura Y, Nakai H. Development of Divide-and-Conquer Density-Functional Tight-Binding Method for Theoretical Research on Li-Ion Battery. CHEM REC 2019; 19:746-757. [PMID: 30462370 DOI: 10.1002/tcr.201800141] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 10/25/2018] [Accepted: 10/26/2018] [Indexed: 01/24/2023]
Abstract
The density-functional tight-binding (DFTB) method is one of the useful quantum chemical methods, which provides a good balance between accuracy and computational efficiency. In this account, we reviewed the basis of the DFTB method, the linear-scaling divide-and-conquer (DC) technique, as well as the parameterization process. We also provide some refinement, modifications, and extension of the existing parameters that can be applicable for lithium-ion battery systems. The diffusion constants of common electrolyte molecules and LiTFSA salt in solution have been estimated using DC-DFTB molecular dynamics simulation with our new parameters. The resulting diffusion constants have good agreement to the experimental diffusion constants.
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Affiliation(s)
- Chien-Pin Chou
- Waseda Research Institute for Science and Engineering (WISE), Waseda University, Tokyo, 169-8555, Japan
| | - Aditya Wibawa Sakti
- Element Strategy Initiative for Catalysts and Batteries (ESICB), Kyoto University, Kyotodaigaku-Katsura, Kyoto, 615-8520, Japan
| | - Yoshifumi Nishimura
- Waseda Research Institute for Science and Engineering (WISE), Waseda University, Tokyo, 169-8555, Japan
| | - Hiromi Nakai
- Waseda Research Institute for Science and Engineering (WISE), Waseda University, Tokyo, 169-8555, Japan.,Element Strategy Initiative for Catalysts and Batteries (ESICB), Kyoto University, Kyotodaigaku-Katsura, Kyoto, 615-8520, Japan.,Department of Chemistry and Biochemistry, School of Advanced Science and Enigineering, Waseda University, Tokyo, 169-8555, Japan
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Giese TJ, York DM. Quantum mechanical force fields for condensed phase molecular simulations. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2017; 29:383002. [PMID: 28817382 PMCID: PMC5821073 DOI: 10.1088/1361-648x/aa7c5c] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Molecular simulations are powerful tools for providing atomic-level details into complex chemical and physical processes that occur in the condensed phase. For strongly interacting systems where quantum many-body effects are known to play an important role, density-functional methods are often used to provide the model with the potential energy used to drive dynamics. These methods, however, suffer from two major drawbacks. First, they are often too computationally intensive to practically apply to large systems over long time scales, limiting their scope of application. Second, there remain challenges for these models to obtain the necessary level of accuracy for weak non-bonded interactions to obtain quantitative accuracy for a wide range of condensed phase properties. Quantum mechanical force fields (QMFFs) provide a potential solution to both of these limitations. In this review, we address recent advances in the development of QMFFs for condensed phase simulations. In particular, we examine the development of QMFF models using both approximate and ab initio density-functional models, the treatment of short-ranged non-bonded and long-ranged electrostatic interactions, and stability issues in molecular dynamics calculations. Example calculations are provided for crystalline systems, liquid water, and ionic liquids. We conclude with a perspective for emerging challenges and future research directions.
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Bandura AV, Lukyanov SI, Evarestov RA. Atom–atom force field for simulation of zirconia bulk, nanosheets and nanotubes. MOLECULAR SIMULATION 2017. [DOI: 10.1080/08927022.2017.1303685] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Andrei V. Bandura
- Institute of Chemistry, St. Petersburg State University, St. Petersburg, Russia
| | - Sergey I. Lukyanov
- Institute of Chemistry, St. Petersburg State University, St. Petersburg, Russia
| | - Robert A. Evarestov
- Institute of Chemistry, St. Petersburg State University, St. Petersburg, Russia
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9
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Chou CP, Nishimura Y, Fan CC, Mazur G, Irle S, Witek HA. Automatized Parameterization of DFTB Using Particle Swarm Optimization. J Chem Theory Comput 2015; 12:53-64. [DOI: 10.1021/acs.jctc.5b00673] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Chien-Pin Chou
- Department
of Applied Chemistry and Institute of Molecular Science, National Chiao Tung University, Hsinchu 30010, Taiwan
| | - Yoshifumi Nishimura
- Department
of Applied Chemistry and Institute of Molecular Science, National Chiao Tung University, Hsinchu 30010, Taiwan
| | - Chin-Chai Fan
- Department
of Applied Chemistry and Institute of Molecular Science, National Chiao Tung University, Hsinchu 30010, Taiwan
| | - Grzegorz Mazur
- K. Gumiński
Department of Theoretical Chemistry, Jagiellonian University, Ingardena
3, 30-060 Cracow, Poland
| | | | - Henryk A. Witek
- Department
of Applied Chemistry and Institute of Molecular Science, National Chiao Tung University, Hsinchu 30010, Taiwan
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