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Liu C, Aguirre NF, Cawkwell MJ, Batista ER, Yang P. Efficient Parameterization of Density Functional Tight-Binding for 5 f-Elements: A Th-O Case Study. J Chem Theory Comput 2024. [PMID: 38990696 DOI: 10.1021/acs.jctc.4c00145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/13/2024]
Abstract
Density functional tight binding (DFTB) models for f-element species are challenging to parametrize owing to the large number of adjustable parameters. The explicit optimization of the terms entering the semiempirical DFTB Hamiltonian related to f orbitals is crucial to generating a reliable parametrization for f-block elements, because they play import roles in bonding interactions. However, since the number of parameters grows quadratically with the number of orbitals, the computational cost for parameter optimization is much more expensive for the f-elements than for the main group elements. In this work we present a set of efficient approaches for mitigating the hurdle imposed by the large size of the parameter space. A novel group-by-orbital correction functions for two-center bond integrals was developed. With this approach the number of parameters is reduced, and it grows linearly with the number of elements, maintaining the accuracy and the number of parameters, in the case of f elements, by more than 40%. The parameter optimization step was accelerated by means of the mini-batch BFGS method. This method allows parameter optimizations with much larger training sets than other single batch methods. A stochastic optimizer was employed that helped overcome shallow local minima in the objective function. The proposed algorithm was used to parametrize the DFTB Hamiltonian for the Th-O system, which was subsequently applied to the study of ThO2 nanoparticles. The training set consisted of 6322 unique structures, which is barely feasible with conventional optimization methods. The optimized parameter set, LANL-ThO, displays good agreement with DFT-calculated properties such as energies, forces, and structures for both clusters and bulk ThO2. Benefiting from the fewer number of parameters and lower computational costs for objective function evaluations, this new approach shows its potential applications in DFTB parametrization for elements with high angular momentum, which present a challenge to conventional methods.
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Affiliation(s)
- Chang Liu
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Néstor F Aguirre
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Marc J Cawkwell
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Enrique R Batista
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Ping Yang
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
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2
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Guibourg P, Dontot L, Anglade PM, Gervais B. DFTB Simulation of Charged Clusters Using Machine Learning Charge Inference. J Chem Theory Comput 2024; 20:4007-4018. [PMID: 38690586 DOI: 10.1021/acs.jctc.4c00107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2024]
Abstract
We present a modification to self-consistent charge density functional-based tight binding (SCC-DFTB), which allows computation based on approximate atomic charges. We obtain these charges by means of a machine learning (ML) process that combines a Coulomb model with a neural network. This allows us to avoid the SCC cycles in the SCC-DFTB calculation while maintaining its accuracy. The main input of the model is the atomic positions characterized by a set of atom-centered symmetry functions. The charge inference from our ML algorithm is as close as 10-2 units of charge from the exact SCC solution. Our ML-DFTB approach provides a good approximation of the density matrix and of the energy and forces with only a single diagonalization. This is a significant computational saving with respect to the complete SCC algorithm, which allows us to investigate a bigger ensemble of atoms. We show the quality of our approach in the case of charged silicon carbide (SiC) clusters. The ML-DFTB potential energy surface (PES) mimics the SCC-DFTB PES rather well, despite its simplicity. This allows us to obtain the same geometric structure ordering with respect to energy for small clusters. The dissociation barriers for ion emission are well-reproduced, which opens the way to investigating ion field emission and charged cluster stability. The ML-DFTB approach is obviously not limited to charged clusters or SiC materials. It opens a new route to investigate larger clusters than those investigated by standard SCC-DFTB, as well as surface and solid-state chemistry at the atomic level.
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Affiliation(s)
- Paul Guibourg
- Laboratoire Cimap, UMR6252─Université de Caen Normandie, École Nationale Supérieure d'Ingénieures de Caen, Commissariat à l'Énergie Atomique, Centre National de la Recherche Scientifique, 6 Boulevard Du Maréchal Juin, 14050 Caen Cedex, France
| | - Léo Dontot
- Laboratoire Cimap, UMR6252─Université de Caen Normandie, École Nationale Supérieure d'Ingénieures de Caen, Commissariat à l'Énergie Atomique, Centre National de la Recherche Scientifique, 6 Boulevard Du Maréchal Juin, 14050 Caen Cedex, France
| | - Pierre-Matthieu Anglade
- Laboratoire Cimap, UMR6252─Université de Caen Normandie, École Nationale Supérieure d'Ingénieures de Caen, Commissariat à l'Énergie Atomique, Centre National de la Recherche Scientifique, 6 Boulevard Du Maréchal Juin, 14050 Caen Cedex, France
| | - Benoit Gervais
- Laboratoire Cimap, UMR6252─Université de Caen Normandie, École Nationale Supérieure d'Ingénieures de Caen, Commissariat à l'Énergie Atomique, Centre National de la Recherche Scientifique, 6 Boulevard Du Maréchal Juin, 14050 Caen Cedex, France
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3
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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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4
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Kitheka M, Redington M, Zhang J, Yao Y, Goyal P. BENCHMARKS OF THE DENSITY FUNCTIONAL TIGHT-BINDING METHOD FOR REDOX, PROTONATION AND ELECTRONIC PROPERTIES OF QUINONES. Phys Chem Chem Phys 2022; 24:6742-6756. [DOI: 10.1039/d1cp05333g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Organic materials with controllable molecular design and sustainable resources are promising electrode materials. Crystalline quinones have been investigated in a variety of rechargeable battery chemistries due to their ubiquitous nature,...
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5
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Borlido P, Marques MAL, Botti S. Bishop's hat silicene: a planar square silicon bilayer decorated with adatoms. Phys Chem Chem Phys 2021; 23:16942-16947. [PMID: 34338249 DOI: 10.1039/d1cp01316e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We investigate a family of free-standing quasi-two-dimensional silicon structures based on a planar square bilayer with adatom decorations. When attached to the bilayer, these adatoms form local reconstructions which resemble either a bishop's hat or elongated square bipyramids. We systematically constructed members of this family via exhaustive enumeration and then studied them using tight-binding and density-functional theory. We find that this geometry contributes significantly to the stability of the resulting structures, with some squared bilayers energetically more stable than the honeycomb bilayers. The most interesting phases were then characterized in more detail, and they all turned out metallic. Finally, we propose the [100] surface of ZrO2 as the most suitable substrate for the synthesis of these two-dimensional phases.
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Affiliation(s)
- Pedro Borlido
- Institut für Festkörpertheorie und -optik, Friedrich-Schiller-Universität Jena and European Theoretical Spectroscopy Facility, Max-Wien-Platz 1, 07743 Jena, Germany.
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6
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Sun L, Marques MAL, Botti S. Direct insight into the structure-property relation of interfaces from constrained crystal structure prediction. Nat Commun 2021; 12:811. [PMID: 33547276 PMCID: PMC7864966 DOI: 10.1038/s41467-020-20855-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2019] [Accepted: 12/22/2020] [Indexed: 01/30/2023] Open
Abstract
A major issue that prevents a full understanding of heterogeneous materials is the lack of systematic first-principles methods to consistently predict energetics and electronic properties of reconstructed interfaces. In this work we address this problem with an efficient and accurate computational scheme. We extend the minima-hopping method implementing constraints crafted for two-dimensional atomic relaxation and enabling variations of the atomic density close to the interface. A combination of density-functional and accurate density-functional tight-binding calculations supply energy and forces to structure prediction. We demonstrate the power of this method by applying it to extract structure-property relations for a large and varied family of symmetric and asymmetric tilt boundaries in polycrystalline silicon. We find a rich polymorphism in the interface reconstructions, with recurring bonding patterns that we classify in increasing energetic order. Finally, a clear relation between bonding patterns and electrically active grain boundary states is unveiled and discussed.
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Affiliation(s)
- Lin Sun
- Institut für Festkörpertheorie und -optik, Friedrich-Schiller-Universität Jena, Jena, Germany
| | - Miguel A L Marques
- Institut für Physik, Martin-Luther-Universität Halle-Wittenberg, Halle, Germany
- European Theoretical Spectroscopy Facility
| | - Silvana Botti
- Institut für Festkörpertheorie und -optik, Friedrich-Schiller-Universität Jena, Jena, Germany.
- European Theoretical Spectroscopy Facility, .
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7
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Hourahine B, Aradi B, Blum V, Bonafé F, Buccheri A, Camacho C, Cevallos C, Deshaye MY, Dumitrică T, Dominguez A, Ehlert S, Elstner M, van der Heide T, Hermann J, Irle S, Kranz JJ, Köhler C, Kowalczyk T, Kubař T, Lee IS, Lutsker V, Maurer RJ, Min SK, Mitchell I, Negre C, Niehaus TA, Niklasson AMN, Page AJ, Pecchia A, Penazzi G, Persson MP, Řezáč J, Sánchez CG, Sternberg M, Stöhr M, Stuckenberg F, Tkatchenko A, Yu VWZ, Frauenheim T. DFTB+, a software package for efficient approximate density functional theory based atomistic simulations. J Chem Phys 2020; 152:124101. [PMID: 32241125 DOI: 10.1063/1.5143190] [Citation(s) in RCA: 402] [Impact Index Per Article: 100.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
DFTB+ is a versatile community developed open source software package offering fast and efficient methods for carrying out atomistic quantum mechanical simulations. By implementing various methods approximating density functional theory (DFT), such as the density functional based tight binding (DFTB) and the extended tight binding method, it enables simulations of large systems and long timescales with reasonable accuracy while being considerably faster for typical simulations than the respective ab initio methods. Based on the DFTB framework, it additionally offers approximated versions of various DFT extensions including hybrid functionals, time dependent formalism for treating excited systems, electron transport using non-equilibrium Green's functions, and many more. DFTB+ can be used as a user-friendly standalone application in addition to being embedded into other software packages as a library or acting as a calculation-server accessed by socket communication. We give an overview of the recently developed capabilities of the DFTB+ code, demonstrating with a few use case examples, discuss the strengths and weaknesses of the various features, and also discuss on-going developments and possible future perspectives.
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Affiliation(s)
- B Hourahine
- SUPA, Department of Physics, The University of Strathclyde, Glasgow G4 0NG, United Kingdom
| | - B Aradi
- Bremen Center for Computational Materials Science, University of Bremen, Bremen, Germany
| | - V Blum
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina 27708, USA
| | - F Bonafé
- Max Planck Institute for the Structure and Dynamics of Matter, Hamburg, Germany
| | - A Buccheri
- School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, United Kingdom
| | - C Camacho
- School of Chemistry, University of Costa Rica, San José 11501-2060, Costa Rica
| | - C Cevallos
- School of Chemistry, University of Costa Rica, San José 11501-2060, Costa Rica
| | - M Y Deshaye
- Department of Chemistry and Advanced Materials Science and Engineering Center, Western Washington University, Bellingham, Washington 98225, USA
| | - T Dumitrică
- Department of Mechanical Engineering, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - A Dominguez
- Bremen Center for Computational Materials Science, University of Bremen, Bremen, Germany
| | - S Ehlert
- University of Bonn, Bonn, Germany
| | - M Elstner
- Institute of Physical Chemistry, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - T van der Heide
- Bremen Center for Computational Materials Science, University of Bremen, Bremen, Germany
| | - J Hermann
- Freie Universität Berlin, Berlin, Germany
| | - S Irle
- Computational Sciences and Engineering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - J J Kranz
- Institute of Physical Chemistry, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - C Köhler
- Bremen Center for Computational Materials Science, University of Bremen, Bremen, Germany
| | - T Kowalczyk
- Department of Chemistry and Advanced Materials Science and Engineering Center, Western Washington University, Bellingham, Washington 98225, USA
| | - T Kubař
- Institute of Physical Chemistry, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - I S Lee
- Department of Chemistry, Ulsan National Institute of Science and Technology, Ulsan, South Korea
| | - V Lutsker
- Institut I - Theoretische Physik, University of Regensburg, Regensburg, Germany
| | - R J Maurer
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, United Kingdom
| | - S K Min
- Department of Chemistry, Ulsan National Institute of Science and Technology, Ulsan, South Korea
| | - I Mitchell
- Center for Multidimensional Carbon Materials, Institute for Basic Science (IBS), Ulsan 44919, South Korea
| | - C Negre
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
| | - T A Niehaus
- Université de Lyon, Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière, F-69622 Villeurbanne, France
| | - A M N Niklasson
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
| | - A J Page
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, Australia
| | - A Pecchia
- CNR-ISMN, Via Salaria km 29.300, 00015 Monterotondo Stazione, Rome, Italy
| | - G Penazzi
- Bremen Center for Computational Materials Science, University of Bremen, Bremen, Germany
| | - M P Persson
- Dassault Systemes, Cambridge, United Kingdom
| | - J Řezáč
- Institute of Organic Chemistry and Biochemistry AS CR, Prague, Czech Republic
| | - C G Sánchez
- Instituto Interdisciplinario de Ciencias Básicas, Universidad Nacional de Cuyo, CONICET, Facultad de Ciencias Exactas y Naturales, Mendoza, Argentina
| | - M Sternberg
- Argonne National Laboratory, Lemont, Illinois 60439, USA
| | - M Stöhr
- Department of Physics and Materials Science, University of Luxembourg, L-1511 Luxembourg City, Luxembourg
| | - F Stuckenberg
- Bremen Center for Computational Materials Science, University of Bremen, Bremen, Germany
| | - A Tkatchenko
- Department of Physics and Materials Science, University of Luxembourg, L-1511 Luxembourg City, Luxembourg
| | - V W-Z Yu
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina 27708, USA
| | - T Frauenheim
- Bremen Center for Computational Materials Science, University of Bremen, Bremen, Germany
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8
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Borlido P, Huran AW, Marques MAL, Botti S. Novel two-dimensional silicon-carbon binaries by crystal structure prediction. Phys Chem Chem Phys 2020; 22:8442-8449. [PMID: 32271332 DOI: 10.1039/c9cp06942a] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The semimetallic bandstructure of graphene and silicene limit their use in functional devices. Mixing silicon and carbon offers a rather unexplored pathway to build semiconducting sheets compatible with current Si-based electronics. We present here a complete theoretical study of the phase diagram of two-dimensional silicon-carbon binaries. To scan the composition range, we employ an ab initio global structural prediction method, complemented by exhaustive enumeration of two-dimensional structure prototypes. We find a wealth of two-dimensional low-energy structures, from standard honeycomb single- and double-layers, passing by dumbbell geometries, to carbon nanosheets bridged by Si atoms. Many of these phases depart from planarity, either through buckling, or by germinating three-dimensional networks with a mixture of sp2 and sp3 bonds. We further characterize the most interesting crystal structures, unveiling a large variety of electronic properties, that could be exploited to develop high-performance electronic devices at the nanoscale.
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Affiliation(s)
- Pedro Borlido
- Institut für Festkörpertheorie und -optik, Friedrich-Schiller-Universität Jena and European Theoretical Spectroscopy Facility, Max-Wien-Platz 1, 07743 Jena, Germany.
| | - Ahmad W Huran
- Institut für Physik, Martin-Luther-Universität Halle-Wittenberg, D-06099 Halle, Germany
| | - Miguel A L Marques
- Institut für Physik, Martin-Luther-Universität Halle-Wittenberg, D-06099 Halle, Germany
| | - Silvana Botti
- Institut für Festkörpertheorie und -optik, Friedrich-Schiller-Universität Jena and European Theoretical Spectroscopy Facility, Max-Wien-Platz 1, 07743 Jena, Germany.
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9
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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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10
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Marques MRG, Wolff J, Steigemann C, Marques MAL. Neural network force fields for simple metals and semiconductors: construction and application to the calculation of phonons and melting temperatures. Phys Chem Chem Phys 2019; 21:6506-6516. [PMID: 30843548 DOI: 10.1039/c8cp05771k] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
We present a practical procedure to obtain reliable and unbiased neural network based force fields for solids. Training and test sets are efficiently generated from global structural prediction runs, at the same time assuring the structural variety and importance of sampling the relevant regions of phase space. The neural networks are trained to yield not only good formation energies, but also accurate forces and stresses, which are the quantities of interest for molecular dynamics simulations. Finally, we construct, as an example, several force fields for both semiconducting and metallic elements, and prove their accuracy for a variety of structural and dynamical properties. These are then used to study the melting of bulk copper and gold.
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Affiliation(s)
- Mário R G Marques
- Institut für Physik, Martin-Luther-Universität Halle-Wittenberg, D-06120 Halle (Saale), Germany.
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11
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Van den Bossche M. DFTB-Assisted Global Structure Optimization of 13- and 55-Atom Late Transition Metal Clusters. J Phys Chem A 2019; 123:3038-3045. [DOI: 10.1021/acs.jpca.9b00927] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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12
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Li H, Collins C, Tanha M, Gordon GJ, Yaron DJ. A Density Functional Tight Binding Layer for Deep Learning of Chemical Hamiltonians. J Chem Theory Comput 2018; 14:5764-5776. [PMID: 30351008 DOI: 10.1021/acs.jctc.8b00873] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Current neural networks for predictions of molecular properties use quantum chemistry only as a source of training data. This paper explores models that use quantum chemistry as an integral part of the prediction process. This is done by implementing self-consistent-charge Density-Functional-Tight-Binding (DFTB) theory as a layer for use in deep learning models. The DFTB layer takes, as input, Hamiltonian matrix elements generated from earlier layers and produces, as output, electronic properties from self-consistent field solutions of the corresponding DFTB Hamiltonian. Backpropagation enables efficient training of the model to target electronic properties. Two types of input to the DFTB layer are explored, splines and feed-forward neural networks. Because overfitting can cause models trained on smaller molecules to perform poorly on larger molecules, regularizations are applied that penalize nonmonotonic behavior and deviation of the Hamiltonian matrix elements from those of the published DFTB model used to initialize the model. The approach is evaluated on 15 700 hydrocarbons by comparing the root-mean-square error in energy and dipole moment, on test molecules with eight heavy atoms, to the error from the initial DFTB model. When trained on molecules with up to seven heavy atoms, the spline model reduces the test error in energy by 60% and in dipole moments by 42%. The neural network model performs somewhat better, with error reductions of 67% and 59%, respectively. Training on molecules with up to four heavy atoms reduces performance, with both the spline and neural net models reducing the test error in energy by about 53% and in dipole by about 25%.
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