1
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Weike N, Fritsch F, Eisfeld W. Compensation States Approach in the Hybrid Diabatization Scheme: Extension to Multidimensional Data and Properties. J Phys Chem A 2024; 128:4353-4368. [PMID: 38748493 DOI: 10.1021/acs.jpca.4c01134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2024]
Abstract
The diabatization of reactive systems for more than just a couple of states is a very demanding problem and generally requires advanced diabatization techniques. Especially for dissociative processes, the drastic changes in the adiabatic wave functions often would require large diabatic state bases, which quickly become impractical. Recently, we addressed this problem by the compensation states approach developed in the context of our hybrid diabatization scheme. This scheme utilizes wave function as well as energy data in combination with a diabatic potential model. In regions where the initial diabatic state basis becomes insufficient for an appropriate representation of the adiabatic states, new model states are generated. The new model states compensate for the state space not spanned by the initial diabatic basis. Such a compensation state is obtained by projecting the initial diabatic state space out of the adiabatic wave function. This yields a very efficient basis representation of the electronic Hamiltonian. The present work presents two new aspects. First, it is shown how other operators like the spin-orbit operator in the framework of the Effective Relativistic Coupling by Asymptotic Representation (ERCAR) can be evaluated in this compact model state space without losing the correct wave function information and accuracy. Second, the extension of the approach to multidimensional potential energy surface models is presented for methyl iodide including the C-I dissociation coordinate and the angular H3C-I bending coordinates.
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Affiliation(s)
- Nicole Weike
- Theoretische Chemie, Universität Bielefeld, Postfach 100131, D-33501 Bielefeld, Germany
| | - Fabian Fritsch
- Theoretische Chemie, Universität Bielefeld, Postfach 100131, D-33501 Bielefeld, Germany
| | - Wolfgang Eisfeld
- Theoretische Chemie, Universität Bielefeld, Postfach 100131, D-33501 Bielefeld, Germany
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2
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Weike N, Eisfeld W. The effective relativistic coupling by asymptotic representation approach for molecules with multiple relativistic atoms. J Chem Phys 2024; 160:064104. [PMID: 38341788 DOI: 10.1063/5.0191529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 01/18/2024] [Indexed: 02/13/2024] Open
Abstract
The Effective Relativistic Coupling by Asymptotic Representation (ERCAR) approach is a method to generate fully coupled diabatic potential energy surfaces (PESs) including relativistic effects, especially spin-orbit coupling. The spin-orbit coupling of a full molecule is determined only by the atomic states of selected relativistically treated atoms. The full molecular coupling effect is obtained by a diabatization with respect to asymptotic states, resulting in the correct geometry dependence of the spin-orbit effect. The ERCAR approach has been developed over the last decade and initially only for molecules with a single relativistic atom. This work presents its extension to molecules with more than a single relativistic atom using the iodine molecule as a proof-of-principle example. The theory for the general multiple atomic ERCAR approach is given. In this case, the diabatic basis is defined at the asymptote where all relativistic atoms are separated from the remaining molecular fragment. The effective spin-orbit operator is then a sum of spin-orbit operators acting on isolated relativistic atoms. PESs for the iodine molecule are developed within the new approach and it is shown that the resulting fine structure states are in good agreement with spin-orbit ab initio calculations.
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Affiliation(s)
- Nicole Weike
- Theoretische Chemie, Universität Bielefeld, Postfach 100131, D-33501 Bielefeld, Germany
| | - Wolfgang Eisfeld
- Theoretische Chemie, Universität Bielefeld, Postfach 100131, D-33501 Bielefeld, Germany
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3
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Manzhos S, Ihara M, Carrington T. Using Collocation to Solve the Schrödinger Equation. J Chem Theory Comput 2023; 19:1641-1656. [PMID: 36974479 DOI: 10.1021/acs.jctc.2c01232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/10/2023]
Abstract
We review the collocation approach to the solution of the Schrödinger equation and its uses in applications. Interrelations between collocation and other methods are highlighted. We also stress advantages and disadvantages of the rectangular collocation formulation. Using collocation makes it possible to use any, e.g. optimized, coordinates and basis functions, including nonintegrable basis functions, and provides a straightforward way of dealing with singularities in the potential. In addition, we stress that using collocation facilitates tuning the shape of basis functions and the placement of points, both of which can be done with machine-learning methods. Applications to electronic and vibrational problems are reviewed focusing on calculations for molecules on surfaces for which there are few variational calculations. Collocation has advantages when potential energy surfaces are unavailable, in particular, for molecule-surface systems, and for systems for which standard direct product quadrature grids, often used with variational methods, are costly.
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Affiliation(s)
- Sergei Manzhos
- School of Materials and Chemical Technology, Tokyo Institute of Technology, Ookayama 2-12-1, Meguro-ku, Tokyo 152-8552, Japan
| | - Manabu Ihara
- School of Materials and Chemical Technology, Tokyo Institute of Technology, Ookayama 2-12-1, Meguro-ku, Tokyo 152-8552, Japan
| | - Tucker Carrington
- Department of Chemistry, Queen’s University, 90 Bader Lane, Kingston, Ontario K7L 3N6, Canada
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4
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Mátyus E, Martín Santa Daría A, Avila G. Exact quantum dynamics developments for floppy molecular systems and complexes. Chem Commun (Camb) 2023; 59:366-381. [PMID: 36519578 DOI: 10.1039/d2cc05123k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Molecular rotation, vibration, internal rotation, isomerization, tunneling, intermolecular dynamics of weakly and strongly interacting systems, intra-to-inter-molecular energy transfer, hindered rotation and hindered translation over surfaces are important types of molecular motions. Their fundamentally correct and detailed description can be obtained by solving the nuclear Schrödinger equation on a potential energy surface. Many of the chemically interesting processes involve quantum nuclear motions which are 'delocalized' over multiple potential energy wells. These 'large-amplitude' motions in addition to the high dimensionality of the vibrational problem represent challenges to the current (ro)vibrational methodology. A review of the quantum nuclear motion methodology is provided, current bottlenecks of solving the nuclear Schrödinger equation are identified, and solution strategies are reviewed. Technical details, computational results, and analysis of these results in terms of limiting models and spectroscopically relevant concepts are highlighted for selected numerical examples.
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Affiliation(s)
- Edit Mátyus
- ELTE, Eötvös Loránd University, Institute of Chemistry, Pázmány Péter sétány 1/A, 1117 Budapest, Hungary.
| | - Alberto Martín Santa Daría
- ELTE, Eötvös Loránd University, Institute of Chemistry, Pázmány Péter sétány 1/A, 1117 Budapest, Hungary.
| | - Gustavo Avila
- ELTE, Eötvös Loránd University, Institute of Chemistry, Pázmány Péter sétány 1/A, 1117 Budapest, Hungary.
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5
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Shanavas Rasheeda D, Martín Santa Daría A, Schröder B, Mátyus E, Behler J. High-dimensional neural network potentials for accurate vibrational frequencies: the formic acid dimer benchmark. Phys Chem Chem Phys 2022; 24:29381-29392. [PMID: 36459127 DOI: 10.1039/d2cp03893e] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
In recent years, machine learning potentials (MLP) for atomistic simulations have attracted a lot of attention in chemistry and materials science. Many new approaches have been developed with the primary aim to transfer the accuracy of electronic structure calculations to large condensed systems containing thousands of atoms. In spite of these advances, the reliability of modern MLPs in reproducing the subtle details of the multi-dimensional potential-energy surface is still difficult to assess for such systems. On the other hand, moderately sized systems enabling the application of tools for thorough and systematic quality-control are nowadays rarely investigated. In this work we use benchmark-quality harmonic and anharmonic vibrational frequencies as a sensitive probe for the validation of high-dimensional neural network potentials. For the case of the formic acid dimer, a frequently studied model system for which stringent spectroscopic data became recently available, we show that high-quality frequencies can be obtained from state-of-the-art calculations in excellent agreement with coupled cluster theory and experimental data.
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Affiliation(s)
- Dilshana Shanavas Rasheeda
- Universität Göttingen, Institut für Physikalische Chemie, Theoretische Chemie, Tammannstraβe 6, 37077 Göttingen, Germany.
| | - Alberto Martín Santa Daría
- ELTE, Eötvös Loránd University, Institute of Chemistry, Pázmány Péter sétány 1/A, 1117 Budapest, Hungary
| | - Benjamin Schröder
- Universität Göttingen, Institut für Physikalische Chemie, Tammannstraβe 6, 37077 Göttingen, Germany
| | - Edit Mátyus
- ELTE, Eötvös Loránd University, Institute of Chemistry, Pázmány Péter sétány 1/A, 1117 Budapest, Hungary
| | - Jörg Behler
- Universität Göttingen, Institut für Physikalische Chemie, Theoretische Chemie, Tammannstraβe 6, 37077 Göttingen, Germany.
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6
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Abstract
In the past two decades, machine learning potentials (MLPs) have reached a level of maturity that now enables applications to large-scale atomistic simulations of a wide range of systems in chemistry, physics, and materials science. Different machine learning algorithms have been used with great success in the construction of these MLPs. In this review, we discuss an important group of MLPs relying on artificial neural networks to establish a mapping from the atomic structure to the potential energy. In spite of this common feature, there are important conceptual differences among MLPs, which concern the dimensionality of the systems, the inclusion of long-range electrostatic interactions, global phenomena like nonlocal charge transfer, and the type of descriptor used to represent the atomic structure, which can be either predefined or learnable. A concise overview is given along with a discussion of the open challenges in the field. Expected final online publication date for the Annual Review of Physical Chemistry, Volume 73 is April 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Emir Kocer
- Institut für Physikalische Chemie, Theoretische Chemie, Universität Göttingen, Göttingen, Germany;, ,
| | - Tsz Wai Ko
- Institut für Physikalische Chemie, Theoretische Chemie, Universität Göttingen, Göttingen, Germany;, ,
| | - Jörg Behler
- Institut für Physikalische Chemie, Theoretische Chemie, Universität Göttingen, Göttingen, Germany;, ,
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7
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Omodemi O, Sprouse S, Herbert D, Kaledin M, Kaledin AL. On the Cartesian Representation of the Molecular Polarizability Tensor Surface by Polynomial Fitting to Ab Initio Data. J Chem Theory Comput 2021; 18:37-45. [PMID: 34958587 DOI: 10.1021/acs.jctc.1c01015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We describe an approach to constructing an analytic Cartesian representation of the molecular dipole polarizability tensor surface in terms of polynomials in interatomic distances with a training set of ab initio data points obtained from a molecular dynamics (MD) simulation or by any other available means. The proposed formulation is based on a perturbation treatment of the unmodified point dipole polarizability model of Applequist [ J. Am. Chem. Soc. 1972, 94, 2952] and is shown here to be, by construction (i) free of short-range or other singularities or discontinuities, (ii) symmetric and translationally invariant, and (iii) nonreliant on a body-fixed coordinate system. Permutational invariance of like nuclei is demonstrated to be readily applicable, making this approach useful for highly fluxional and reactive systems. Derivation of the method is described in detail, adding brief didactic numerical examples of H2 and H2O and concluding with an MD simulation of the Raman spectrum of H5O2+ at 300 K with the polarizability tensor fitted to CCSD(T)/aug-cc-pVTZ data obtained using the HBB-4B potential [ J. Chem. Phys. 2005, 122, 044308].
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Affiliation(s)
- Oluwaseun Omodemi
- Department of Chemistry & Biochemistry, Kennesaw State University, 370 Paulding Avenue NW, Box # 1203, Kennesaw, Georgia 30144, United States
| | - Sarah Sprouse
- Department of Chemistry & Biochemistry, Kennesaw State University, 370 Paulding Avenue NW, Box # 1203, Kennesaw, Georgia 30144, United States
| | - Destyni Herbert
- Department of Chemistry & Biochemistry, Kennesaw State University, 370 Paulding Avenue NW, Box # 1203, Kennesaw, Georgia 30144, United States
| | - Martina Kaledin
- Department of Chemistry & Biochemistry, Kennesaw State University, 370 Paulding Avenue NW, Box # 1203, Kennesaw, Georgia 30144, United States
| | - Alexey L Kaledin
- Cherry L. Emerson Center for Scientific Computation, Emory University, 1515 Dickey Drive, Atlanta, Georgia 30322, United States
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8
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Unke O, Chmiela S, Sauceda HE, Gastegger M, Poltavsky I, Schütt KT, Tkatchenko A, Müller KR. Machine Learning Force Fields. Chem Rev 2021; 121:10142-10186. [PMID: 33705118 PMCID: PMC8391964 DOI: 10.1021/acs.chemrev.0c01111] [Citation(s) in RCA: 360] [Impact Index Per Article: 120.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Indexed: 12/27/2022]
Abstract
In recent years, the use of machine learning (ML) in computational chemistry has enabled numerous advances previously out of reach due to the computational complexity of traditional electronic-structure methods. One of the most promising applications is the construction of ML-based force fields (FFs), with the aim to narrow the gap between the accuracy of ab initio methods and the efficiency of classical FFs. The key idea is to learn the statistical relation between chemical structure and potential energy without relying on a preconceived notion of fixed chemical bonds or knowledge about the relevant interactions. Such universal ML approximations are in principle only limited by the quality and quantity of the reference data used to train them. This review gives an overview of applications of ML-FFs and the chemical insights that can be obtained from them. The core concepts underlying ML-FFs are described in detail, and a step-by-step guide for constructing and testing them from scratch is given. The text concludes with a discussion of the challenges that remain to be overcome by the next generation of ML-FFs.
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Affiliation(s)
- Oliver
T. Unke
- Machine
Learning Group, Technische Universität
Berlin, 10587 Berlin, Germany
- DFG
Cluster of Excellence “Unifying Systems in Catalysis”
(UniSysCat), Technische Universität Berlin, 10623 Berlin, Germany
| | - Stefan Chmiela
- Machine
Learning Group, Technische Universität
Berlin, 10587 Berlin, Germany
| | - Huziel E. Sauceda
- Machine
Learning Group, Technische Universität
Berlin, 10587 Berlin, Germany
- BASLEARN,
BASF-TU Joint Lab, Technische Universität
Berlin, 10587 Berlin, Germany
| | - Michael Gastegger
- Machine
Learning Group, Technische Universität
Berlin, 10587 Berlin, Germany
- DFG
Cluster of Excellence “Unifying Systems in Catalysis”
(UniSysCat), Technische Universität Berlin, 10623 Berlin, Germany
- BASLEARN,
BASF-TU Joint Lab, Technische Universität
Berlin, 10587 Berlin, Germany
| | - Igor Poltavsky
- Department
of Physics and Materials Science, University
of Luxembourg, L-1511 Luxembourg City, Luxembourg
| | - Kristof T. Schütt
- Machine
Learning Group, Technische Universität
Berlin, 10587 Berlin, Germany
| | - Alexandre Tkatchenko
- Department
of Physics and Materials Science, University
of Luxembourg, L-1511 Luxembourg City, Luxembourg
| | - Klaus-Robert Müller
- Machine
Learning Group, Technische Universität
Berlin, 10587 Berlin, Germany
- BIFOLD−Berlin
Institute for the Foundations of Learning and Data, Berlin, Germany
- Department
of Artificial Intelligence, Korea University, Anam-dong, Seongbuk-gu, Seoul 02841, Korea
- Max Planck
Institute for Informatics, Stuhlsatzenhausweg, 66123 Saarbrücken, Germany
- Google
Research, Brain Team, Berlin, Germany
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9
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Affiliation(s)
- Jörg Behler
- Universität Göttingen, Institut für Physikalische Chemie, Theoretische Chemie, Tammannstraße 6, 37077 Göttingen, Germany
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10
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Abstract
We introduce new and robust decompositions of mean-field Hartree-Fock and Kohn-Sham density functional theory relying on the use of localized molecular orbitals and physically sound charge population protocols. The new lossless property decompositions, which allow for partitioning one-electron reduced density matrices into either bond-wise or atomic contributions, are compared to alternatives from the literature with regard to both molecular energies and dipole moments. Besides commenting on possible applications as an interpretative tool in the rationalization of certain electronic phenomena, we demonstrate how decomposed mean-field theory makes it possible to expose and amplify compositional features in the context of machine-learned quantum chemistry. This is made possible by improving upon the granularity of the underlying data. On the basis of our preliminary proof-of-concept results, we conjecture that many of the structure-property inferences in existence today may be further refined by efficiently leveraging an increase in dataset complexity and richness.
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Affiliation(s)
- Janus J Eriksen
- School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, United Kingdom
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11
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Manzhos S, Carrington T. Neural Network Potential Energy Surfaces for Small Molecules and Reactions. Chem Rev 2020; 121:10187-10217. [PMID: 33021368 DOI: 10.1021/acs.chemrev.0c00665] [Citation(s) in RCA: 110] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
We review progress in neural network (NN)-based methods for the construction of interatomic potentials from discrete samples (such as ab initio energies) for applications in classical and quantum dynamics including reaction dynamics and computational spectroscopy. The main focus is on methods for building molecular potential energy surfaces (PES) in internal coordinates that explicitly include all many-body contributions, even though some of the methods we review limit the degree of coupling, due either to a desire to limit computational cost or to limited data. Explicit and direct treatment of all many-body contributions is only practical for sufficiently small molecules, which are therefore our primary focus. This includes small molecules on surfaces. We consider direct, single NN PES fitting as well as more complex methods that impose structure (such as a multibody representation) on the PES function, either through the architecture of one NN or by using multiple NNs. We show how NNs are effective in building representations with low-dimensional functions including dimensionality reduction. We consider NN-based approaches to build PESs in the sums-of-product form important for quantum dynamics, ways to treat symmetry, and issues related to sampling data distributions and the relation between PES errors and errors in observables. We highlight combinations of NNs with other ideas such as permutationally invariant polynomials or sums of environment-dependent atomic contributions, which have recently emerged as powerful tools for building highly accurate PESs for relatively large molecular and reactive systems.
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Affiliation(s)
- Sergei Manzhos
- Centre Énergie Matériaux Télécommunications, Institut National de la Recherche Scientifique, 1650, Boulevard Lionel-Boulet, Varennes, Québec City, Québec J3X 1S2, Canada
| | - Tucker Carrington
- Chemistry Department, Queen's University, Kingston Ontario K7L 3N6, Canada
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12
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Boussaidi MA, Ren O, Voytsekhovsky D, Manzhos S. Random Sampling High Dimensional Model Representation Gaussian Process Regression (RS-HDMR-GPR) for Multivariate Function Representation: Application to Molecular Potential Energy Surfaces. J Phys Chem A 2020; 124:7598-7607. [DOI: 10.1021/acs.jpca.0c05935] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Mohamed Ali Boussaidi
- Centre Énergie Matériaux Télécommunications, Institut National de la Recherche Scientifique, 1650 boulevard Lionel-Boulet, Varennes QC J3X 1S2, Canada
- Ecole Nationale d’Ingénieurs de Tunis, Rue Béchir Salem Belkhiria Campus universitaire, BP 37, 1002, Le Bélvédère, Tunis, Tunisia
| | - Owen Ren
- Centre Énergie Matériaux Télécommunications, Institut National de la Recherche Scientifique, 1650 boulevard Lionel-Boulet, Varennes QC J3X 1S2, Canada
- Purefacts Inc., 48 Yonge Street, Suite 400, Toronto, ON M5E 1G6, Canada
| | | | - Sergei Manzhos
- Centre Énergie Matériaux Télécommunications, Institut National de la Recherche Scientifique, 1650 boulevard Lionel-Boulet, Varennes QC J3X 1S2, Canada
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13
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Williams DMG, Eisfeld W. Complete Nuclear Permutation Inversion Invariant Artificial Neural Network (CNPI-ANN) Diabatization for the Accurate Treatment of Vibronic Coupling Problems. J Phys Chem A 2020; 124:7608-7621. [DOI: 10.1021/acs.jpca.0c05991] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- David M. G. Williams
- Theoretische Chemie, Universität Bielefeld, Postfach 100131, D-33501 Bielefeld, Germany
| | - Wolfgang Eisfeld
- Theoretische Chemie, Universität Bielefeld, Postfach 100131, D-33501 Bielefeld, Germany
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14
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Wodraszka R, Carrington T. A collocation-based multi-configuration time-dependent Hartree method using mode combination and improved relaxation. J Chem Phys 2020; 152:164117. [DOI: 10.1063/5.0006081] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Robert Wodraszka
- Chemistry Department, Queen’s University, Kingston, Ontario K7L 3N6, Canada
| | - Tucker Carrington
- Chemistry Department, Queen’s University, Kingston, Ontario K7L 3N6, Canada
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15
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Manzhos S. Machine learning for the solution of the Schrödinger equation. MACHINE LEARNING-SCIENCE AND TECHNOLOGY 2020. [DOI: 10.1088/2632-2153/ab7d30] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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16
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Abstract
As the quantum chemistry (QC) community embraces machine learning (ML), the number of new methods and applications based on the combination of QC and ML is surging. In this Perspective, a view of the current state of affairs in this new and exciting research field is offered, challenges of using machine learning in quantum chemistry applications are described, and potential future developments are outlined. Specifically, examples of how machine learning is used to improve the accuracy and accelerate quantum chemical research are shown. Generalization and classification of existing techniques are provided to ease the navigation in the sea of literature and to guide researchers entering the field. The emphasis of this Perspective is on supervised machine learning.
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Affiliation(s)
- Pavlo O Dral
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, Department of Chemistry, and College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
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17
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Unke OT, Koner D, Patra S, Käser S, Meuwly M. High-dimensional potential energy surfaces for molecular simulations: from empiricism to machine learning. MACHINE LEARNING-SCIENCE AND TECHNOLOGY 2020. [DOI: 10.1088/2632-2153/ab5922] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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18
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Williams DMG, Viel A, Eisfeld W. Diabatic neural network potentials for accurate vibronic quantum dynamics—The test case of planar NO3. J Chem Phys 2019; 151:164118. [DOI: 10.1063/1.5125851] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- David M. G. Williams
- Theoretische Chemie, Universität Bielefeld, Postfach 100131, D-33501 Bielefeld, Germany
| | - Alexandra Viel
- Univ Rennes, CNRS, IPR (Institut de Physique de Rennes) - UMR 6251, F-35000 Rennes, France
| | - Wolfgang Eisfeld
- Theoretische Chemie, Universität Bielefeld, Postfach 100131, D-33501 Bielefeld, Germany
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19
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Unke OT, Meuwly M. PhysNet: A Neural Network for Predicting Energies, Forces, Dipole Moments, and Partial Charges. J Chem Theory Comput 2019; 15:3678-3693. [DOI: 10.1021/acs.jctc.9b00181] [Citation(s) in RCA: 285] [Impact Index Per Article: 57.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Oliver T. Unke
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
| | - Markus Meuwly
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
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20
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Wodraszka R, Carrington T. A pruned collocation-based multiconfiguration time-dependent Hartree approach using a Smolyak grid for solving the Schrödinger equation with a general potential energy surface. J Chem Phys 2019; 150:154108. [DOI: 10.1063/1.5093317] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Robert Wodraszka
- Chemistry Department, Queen’s University, Kingston, Ontario K7L 3N6, Canada
| | - Tucker Carrington
- Chemistry Department, Queen’s University, Kingston, Ontario K7L 3N6, Canada
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21
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Williams DMG, Eisfeld W. Neural network diabatization: A new ansatz for accurate high-dimensional coupled potential energy surfaces. J Chem Phys 2018; 149:204106. [DOI: 10.1063/1.5053664] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- David M. G. Williams
- Theoretische Chemie, Universität Bielefeld, Postfach 100131, D-33501 Bielefeld, Germany
| | - Wolfgang Eisfeld
- Theoretische Chemie, Universität Bielefeld, Postfach 100131, D-33501 Bielefeld, Germany
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22
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Meuwly M. Reactive molecular dynamics: From small molecules to proteins. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2018. [DOI: 10.1002/wcms.1386] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Markus Meuwly
- Department of Chemistry University of Basel Basel Switzerland
- Department of Chemistry Brown University Providence Rhode Island
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23
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Unke OT, Meuwly M. A reactive, scalable, and transferable model for molecular energies from a neural network approach based on local information. J Chem Phys 2018; 148:241708. [PMID: 29960298 DOI: 10.1063/1.5017898] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Despite the ever-increasing computer power, accurate ab initio calculations for large systems (thousands to millions of atoms) remain infeasible. Instead, approximate empirical energy functions are used. Most current approaches are either transferable between different chemical systems, but not particularly accurate, or they are fine-tuned to a specific application. In this work, a data-driven method to construct a potential energy surface based on neural networks is presented. Since the total energy is decomposed into local atomic contributions, the evaluation is easily parallelizable and scales linearly with system size. With prediction errors below 0.5 kcal mol-1 for both unknown molecules and configurations, the method is accurate across chemical and configurational space, which is demonstrated by applying it to datasets from nonreactive and reactive molecular dynamics simulations and a diverse database of equilibrium structures. The possibility to use small molecules as reference data to predict larger structures is also explored. Since the descriptor only uses local information, high-level ab initio methods, which are computationally too expensive for large molecules, become feasible for generating the necessary reference data used to train the neural network.
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Affiliation(s)
- Oliver T Unke
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
| | - Markus Meuwly
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
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Kamath A, Vargas-Hernández RA, Krems RV, Carrington T, Manzhos S. Neural networks vs Gaussian process regression for representing potential energy surfaces: A comparative study of fit quality and vibrational spectrum accuracy. J Chem Phys 2018; 148:241702. [DOI: 10.1063/1.5003074] [Citation(s) in RCA: 108] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Aditya Kamath
- Department of Mechanical Engineering, National University of Singapore, Block EA, #07-08, 9 Engineering Drive 1, Singapore 117576
| | | | - Roman V. Krems
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada
| | - Tucker Carrington
- Department of Chemistry, Queen’s University, Chernoff Hall, 90 Bader Lane, Kingston, Ontario K7L 3N6, Canada
| | - Sergei Manzhos
- Department of Mechanical Engineering, National University of Singapore, Block EA, #07-08, 9 Engineering Drive 1, Singapore 117576
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25
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Klinting EL, Thomsen B, Godtliebsen IH, Christiansen O. Employing general fit-bases for construction of potential energy surfaces with an adaptive density-guided approach. J Chem Phys 2018; 148:064113. [DOI: 10.1063/1.5016259] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
| | - Bo Thomsen
- Department of Chemistry, Aarhus University, DK-8000 Aarhus C, Denmark
| | | | - Ove Christiansen
- Department of Chemistry, Aarhus University, DK-8000 Aarhus C, Denmark
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26
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Wodraszka R, Carrington T. A new collocation-based multi-configuration time-dependent Hartree (MCTDH) approach for solving the Schrödinger equation with a general potential energy surface. J Chem Phys 2018; 148:044115. [DOI: 10.1063/1.5018793] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Robert Wodraszka
- Department of Chemistry, Queen’s University, Kingston, Ontario K7L 3N6, Canada
| | - Tucker Carrington
- Department of Chemistry, Queen’s University, Kingston, Ontario K7L 3N6, Canada
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28
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Genetic algorithm approach to global optimization of the full-dimensional potential energy surface for hydrogen atom at fcc-metal surfaces. Chem Phys Lett 2017. [DOI: 10.1016/j.cplett.2017.03.086] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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29
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Brown A, Pradhan E. Fitting potential energy surfaces to sum-of-products form with neural networks using exponential neurons. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2017. [DOI: 10.1142/s0219633617300014] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
In this paper, the use of the neural network (NN) method with exponential neurons for directly fitting ab initio data to generate potential energy surfaces (PESs) in sum-of-product form will be discussed. The utility of the approach will be highlighted using fits of CS2, HFCO, and HONO ground state PESs based upon high-level ab initio data. Using a generic interface between the neural network PES fitting, which is performed in MATLAB, and the Heidelberg multi-configuration time-dependent Hartree (MCTDH) software package, the PESs have been tested via comparison of vibrational energies to experimental measurements. The review demonstrates the potential of the PES fitting method, combined with MCTDH, to tackle high-dimensional quantum dynamics problems.
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Affiliation(s)
- Alex Brown
- Department of Chemistry, University of Alberta, Edmonton, AB, T6G 2G2, Canada
| | - E. Pradhan
- Department of Chemistry, University of Alberta, Edmonton, AB, T6G 2G2, Canada
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30
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Manzhos S, Carrington T. Using an internal coordinate Gaussian basis and a space-fixed Cartesian coordinate kinetic energy operator to compute a vibrational spectrum with rectangular collocation. J Chem Phys 2016; 145:224110. [DOI: 10.1063/1.4971295] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Sergei Manzhos
- Department of Mechanical Engineering, National University of Singapore, Block EA #07-08, 9 Engineering Drive 1, 117576 Singapore
| | - Tucker Carrington
- Chemistry Department, Queen’s University, Kingston, Ontario K7L 3N6, Canada
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31
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Wittenbrink N, Venghaus F, Williams D, Eisfeld W. A new approach for the development of diabatic potential energy surfaces: Hybrid block-diagonalization and diabatization by ansatz. J Chem Phys 2016; 145:184108. [DOI: 10.1063/1.4967258] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Nils Wittenbrink
- Theoretische Chemie, Universität Bielefeld, Postfach 100131, D-33501 Bielefeld, Germany
| | - Florian Venghaus
- Theoretische Chemie, Universität Bielefeld, Postfach 100131, D-33501 Bielefeld, Germany
| | - David Williams
- Theoretische Chemie, Universität Bielefeld, Postfach 100131, D-33501 Bielefeld, Germany
| | - Wolfgang Eisfeld
- Theoretische Chemie, Universität Bielefeld, Postfach 100131, D-33501 Bielefeld, Germany
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32
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Wodraszka R, Carrington T. Using a pruned, nondirect product basis in conjunction with the multi-configuration time-dependent Hartree (MCTDH) method. J Chem Phys 2016; 145:044110. [DOI: 10.1063/1.4959228] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Robert Wodraszka
- Department of Chemistry, Queen’s University, Kingston, Ontario K7L 3N6, Canada
| | - Tucker Carrington
- Department of Chemistry, Queen’s University, Kingston, Ontario K7L 3N6, Canada
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33
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Venghaus F, Eisfeld W. Block-diagonalization as a tool for the robust diabatization of high-dimensional potential energy surfaces. J Chem Phys 2016; 144:114110. [DOI: 10.1063/1.4943869] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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34
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Ndengué S, Dawes R, Wang XG, Carrington T, Sun Z, Guo H. Calculated vibrational states of ozone up to dissociation. J Chem Phys 2016; 144:074302. [DOI: 10.1063/1.4941559] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Steve Ndengué
- Department of Chemistry, Missouri University of Science and Technology, Rolla, Missouri 65409, USA
| | - Richard Dawes
- Department of Chemistry, Missouri University of Science and Technology, Rolla, Missouri 65409, USA
| | - Xiao-Gang Wang
- Chemistry Department, Queen’s University, Kingston, Ontario K7L 3N6, Canada
| | - Tucker Carrington
- Chemistry Department, Queen’s University, Kingston, Ontario K7L 3N6, Canada
| | - Zhigang Sun
- State Key Laboratory of Molecular Reaction Dynamics and Center for Theoretical and Computational Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China and Center for Advanced Chemical Physics and 2011 Frontier Center for Quantum Science and Technology, University of Science and Technology of China, 96 Jinzhai Road, Hefei 230026, China
| | - Hua Guo
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131, USA
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35
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Avila G, Carrington T. A multi-dimensional Smolyak collocation method in curvilinear coordinates for computing vibrational spectra. J Chem Phys 2015; 143:214108. [DOI: 10.1063/1.4936294] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Gustavo Avila
- Chemistry Department, Queen’s University, Kingston, Ontario K7L 3N6, Canada
| | - Tucker Carrington
- Chemistry Department, Queen’s University, Kingston, Ontario K7L 3N6, Canada
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36
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Manzhos S, Carrington T, Laverdure L, Mosey N. Computing the Anharmonic Vibrational Spectrum of UF6 in 15 Dimensions with an Optimized Basis Set and Rectangular Collocation. J Phys Chem A 2015; 119:9557-67. [DOI: 10.1021/acs.jpca.5b07627] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Sergei Manzhos
- Department
of Mechanical Engineering, National University of Singapore, Block EA
#07-08, 9 Engineering Drive 1, Singapore 117576
| | - Tucker Carrington
- Department of Chemistry, Queen’s University, Chernoff Hall, 90 Bader Lane, Kingston, ON, Canada K7L 3N6
| | - Laura Laverdure
- Department of Chemistry, Queen’s University, Chernoff Hall, 90 Bader Lane, Kingston, ON, Canada K7L 3N6
| | - Nicholas Mosey
- Department of Chemistry, Queen’s University, Chernoff Hall, 90 Bader Lane, Kingston, ON, Canada K7L 3N6
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37
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Avila G, Carrington T. Using multi-dimensional Smolyak interpolation to make a sum-of-products potential. J Chem Phys 2015; 143:044106. [DOI: 10.1063/1.4926651] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Gustavo Avila
- Chemistry Department, Queen’s University, Kingston, Ontario K7L 3N6, Canada
| | - Tucker Carrington
- Chemistry Department, Queen’s University, Kingston, Ontario K7L 3N6, Canada
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38
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Brown J, Carrington T. Using an iterative eigensolver to compute vibrational energies with phase-spaced localized basis functions. J Chem Phys 2015; 143:044104. [DOI: 10.1063/1.4926805] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- James Brown
- Chemistry Department, Queen’s University, Kingston, Ontario K7L 3N6, Canada
| | - Tucker Carrington
- Chemistry Department, Queen’s University, Kingston, Ontario K7L 3N6, Canada
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39
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Abstract
I review two new ideas for coping with the size of large product basis sets and large product grids when one computes vibrational energy levels. The first is based on a tensor reduction scheme. It exploits advantages of a sum-of-products potential. The key idea is to use a basis each of whose function is a sum of optimized products and to compress the number of terms in each basis function. When the potential does not have the sum-of-products form, it is usually necessary to use quadrature. The second idea uses a nondirect product grid that has structure and is therefore compatible with efficient matrix–vector products.
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Affiliation(s)
- Tucker Carrington
- Chemistry Department, Queen’s University, Kingston, ON K7L 3N6, Canada
- Chemistry Department, Queen’s University, Kingston, ON K7L 3N6, Canada
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40
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Majumder M, Hegger SE, Dawes R, Manzhos S, Wang XG, Tucker C, Li J, Guo H. Explicitly correlated MRCI-F12 potential energy surfaces for methane fit with several permutation invariant schemes and full-dimensional vibrational calculations. Mol Phys 2015. [DOI: 10.1080/00268976.2015.1015642] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Moumita Majumder
- Department of Chemistry, Missouri University of Science and Technology, Rolla, MO, USA
| | - Samuel E. Hegger
- Department of Chemistry, Missouri University of Science and Technology, Rolla, MO, USA
| | - Richard Dawes
- Department of Chemistry, Missouri University of Science and Technology, Rolla, MO, USA
| | - Sergei Manzhos
- Department of Mechanical Engineering, National University of Singapore, Singapore
| | - Xiao-Gang Wang
- Chemistry Department, Queen's University, Kingston, Canada
| | | | - Jun Li
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, NM, USA
| | - Hua Guo
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, NM, USA
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41
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Wang XG, Carrington T. Using experimental data and a contracted basis Lanczos method to determine an accurate methane potential energy surface from a least squares optimization. J Chem Phys 2014; 141:154106. [DOI: 10.1063/1.4896569] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Xiao-Gang Wang
- Chemistry Department, Queen's University, Kingston, Ontario K7L 3N6, Canada
| | - Tucker Carrington
- Chemistry Department, Queen's University, Kingston, Ontario K7L 3N6, Canada
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42
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Füchsel G, Tremblay JC, Saalfrank P. A six-dimensional potential energy surface for Ru(0001)(2×2):CO. J Chem Phys 2014; 141:094704. [DOI: 10.1063/1.4894083] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Gernot Füchsel
- Institut für Chemie, Universität Potsdam, Karl-Liebknecht-Straße 24-25, D-14476 Potsdam-Golm, Germany
| | - Jean Christophe Tremblay
- Institut für Chemie und Biochemie - Physikalische und Theoretische Chemie, Freie Universität Berlin, Takustr. 3, 14195 Berlin, Germany
| | - Peter Saalfrank
- Institut für Chemie, Universität Potsdam, Karl-Liebknecht-Straße 24-25, D-14476 Potsdam-Golm, Germany
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43
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Leclerc A, Carrington T. Calculating vibrational spectra with sum of product basis functions without storing full-dimensional vectors or matrices. J Chem Phys 2014; 140:174111. [DOI: 10.1063/1.4871981] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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44
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Behler J. Representing potential energy surfaces by high-dimensional neural network potentials. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2014; 26:183001. [PMID: 24758952 DOI: 10.1088/0953-8984/26/18/183001] [Citation(s) in RCA: 158] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The development of interatomic potentials employing artificial neural networks has seen tremendous progress in recent years. While until recently the applicability of neural network potentials (NNPs) has been restricted to low-dimensional systems, this limitation has now been overcome and high-dimensional NNPs can be used in large-scale molecular dynamics simulations of thousands of atoms. NNPs are constructed by adjusting a set of parameters using data from electronic structure calculations, and in many cases energies and forces can be obtained with very high accuracy. Therefore, NNP-based simulation results are often very close to those gained by a direct application of first-principles methods. In this review, the basic methodology of high-dimensional NNPs will be presented with a special focus on the scope and the remaining limitations of this approach. The development of NNPs requires substantial computational effort as typically thousands of reference calculations are required. Still, if the problem to be studied involves very large systems or long simulation times this overhead is regained quickly. Further, the method is still limited to systems containing about three or four chemical elements due to the rapidly increasing complexity of the configuration space, although many atoms of each species can be present. Due to the ability of NNPs to describe even extremely complex atomic configurations with excellent accuracy irrespective of the nature of the atomic interactions, they represent a general and therefore widely applicable technique, e.g. for addressing problems in materials science, for investigating properties of interfaces, and for studying solvation processes.
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Affiliation(s)
- J Behler
- Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, D-44780 Bochum, Germany
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45
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Brown J, Wang XG, Carrington T, Grubbs GS, Dawes R. Computational study of the rovibrational spectrum of CO2–CS2. J Chem Phys 2014; 140:114303. [DOI: 10.1063/1.4867792] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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46
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Roy TK, Gerber RB. Vibrational self-consistent field calculations for spectroscopy of biological molecules: new algorithmic developments and applications. Phys Chem Chem Phys 2013; 15:9468-92. [DOI: 10.1039/c3cp50739d] [Citation(s) in RCA: 141] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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47
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Chan M, Carrington T, Manzhos S. Anharmonic vibrations of the carboxyl group in acetic acid on TiO2: implications for adsorption mode assignment in dye-sensitized solar cells. Phys Chem Chem Phys 2013; 15:10028-34. [DOI: 10.1039/c3cp00065f] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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48
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Jose KVJ, Artrith N, Behler J. Construction of high-dimensional neural network potentials using environment-dependent atom pairs. J Chem Phys 2012; 136:194111. [PMID: 22612084 DOI: 10.1063/1.4712397] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
An accurate determination of the potential energy is the crucial step in computer simulations of chemical processes, but using electronic structure methods on-the-fly in molecular dynamics (MD) is computationally too demanding for many systems. Constructing more efficient interatomic potentials becomes intricate with increasing dimensionality of the potential-energy surface (PES), and for numerous systems the accuracy that can be achieved is still not satisfying and far from the reliability of first-principles calculations. Feed-forward neural networks (NNs) have a very flexible functional form, and in recent years they have been shown to be an accurate tool to construct efficient PESs. High-dimensional NN potentials based on environment-dependent atomic energy contributions have been presented for a number of materials. Still, these potentials may be improved by a more detailed structural description, e.g., in form of atom pairs, which directly reflect the atomic interactions and take the chemical environment into account. We present an implementation of an NN method based on atom pairs, and its accuracy and performance are compared to the atom-based NN approach using two very different systems, the methanol molecule and metallic copper. We find that both types of NN potentials provide an excellent description of both PESs, with the pair-based method yielding a slightly higher accuracy making it a competitive alternative for addressing complex systems in MD simulations.
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Affiliation(s)
- K V Jovan Jose
- Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, D-44780 Bochum, Germany
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49
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Richter F, Carbonniere P, Dargelos A, Pouchan C. An adaptive potential energy surface generation method using curvilinear valence coordinates. J Chem Phys 2012; 136:224105. [DOI: 10.1063/1.4724305] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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50
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Szalay V, Lengyel K, Kovács L, Timón V, Hernández-Laguna A. Vibrations of H+(D+) in stoichiometric LiNbO3 single crystal. J Chem Phys 2011; 135:124501. [PMID: 21974529 DOI: 10.1063/1.3626839] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
A first principles quantum mechanical calculation of the vibrational energy levels and transition frequencies associated with protons in stoichiometric LiNbO(3) single crystal has been carried out. The hydrogen contaminated crystal has been approximated by a model one obtains by translating a supercell, i.e., a cluster of LiNbO(3) unit cells containing a single H(+) and a Li(+) vacancy. Based on the supercell model an approximate Hamiltonian operator describing vibrations of the proton sublattice embedded in the host crystal has been derived. It is further simplified to a sum of uncoupled Hamiltonian operators corresponding to different wave vectors (ks) and each describing vibrations of a quasi-particle (quasi-proton). The three dimensional (3D) Hamiltonian operator of k=0 has been employed to calculate vibrational levels and transition frequencies. The potential energy surface (PES) entering this Hamiltonian operator has been calculated point wise on a large set of grid points by using density functional theory, and an analytical approximation to the PES has been constructed by non-parametric approximation. Then, the nuclear motion Schrödinger equation has been solved by employing the method of discrete variable representation. It has been found that the (quasi-)H(+) vibrates in a strongly anharmonic PES. Its vibrations can be described approximately as a stretching, and two orthogonal bending vibrations. The theoretically calculated transition frequencies agree within 1% with those experimentally determined, and they have allowed the assignment of one of the hitherto unassigned bands as a combination of the stretching and the bending of lower fundamental frequency.
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Affiliation(s)
- Viktor Szalay
- Research Institute for Solid State Physics and Optics, Hungarian Academy of Sciences, P. O. Box 49, H-1525 Budapest, Hungary.
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