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Miao Z, Zhang X, Zhang Y, Wang L, Meng Q. Chemistry-Informed Generative Model for Classical Dynamics Simulations. J Phys Chem Lett 2024; 15:532-539. [PMID: 38194494 DOI: 10.1021/acs.jpclett.3c03114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2024]
Abstract
In this work, a chemistry-informed generative model was proposed, leading to the chemistry-informed generative adversarial network (CI-GAN) approach. To easily build the input database for complex molecular systems, an image-input algorithm is also implemented, leading to the capability to directly recognize the molecular image. Extensive test calculations and analysis on typical examples, H + H2, OH + HO2, and H2O/TiO2(110), find that the present CI-GAN approach generates distributions of geometry and energy. Calculations on the above examples show that the present CI-GAN approach is able to generate 50%-80% meaningful results among all of the generated data with chemistry constraints. Thus, it has the potential capability to predict classical dynamics simulations as well as ab initio calculations avoiding expensive calculations. These results and the power of CI-GANs in generating ab initio energies and MD trajectories are deeply discussed.
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Affiliation(s)
- Zekai Miao
- Department of Chemistry, Northwestern Polytechnical University, West Youyi Road 127, 710072 Xi'an, China
| | - Xingyu Zhang
- Department of Chemistry, Northwestern Polytechnical University, West Youyi Road 127, 710072 Xi'an, China
| | - Yuyuan Zhang
- Department of Chemistry, Northwestern Polytechnical University, West Youyi Road 127, 710072 Xi'an, China
| | - Lemei Wang
- Ministry-of-Education Engineering Center for Embedded System Integration, Northwestern Polytechnical University, West Youyi Road 127, 710072 Xi'an, China
| | - Qingyong Meng
- Department of Chemistry, Northwestern Polytechnical University, West Youyi Road 127, 710072 Xi'an, China
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2
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Song Q, Zhang X, Peláez D, Meng Q. Direct Canonical-Polyadic-Decomposition of the Potential Energy Surface from Discrete Data by Decoupled Gaussian Process Regression. J Phys Chem Lett 2022; 13:11128-11135. [PMID: 36442084 DOI: 10.1021/acs.jpclett.2c03080] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
A Gaussian process regression (GPR) approach for directly constructing the canonical polyadic decomposition (CPD) of a multidimensional potential energy surface (PES) by discrete training energies is proposed and denoted by CPD-GPR. The present CPD-GPR method requires the kernel function in a product of a series of one-dimensional functions. To test CPD-GPR, the reactive probabilities of H + H2 as a function of kinetics energy are performed. Comparing the dynamics results computed by the CPD-GPR PES with those by the original PES, a good agreement between these results can be clearly found. Discussions on the previous algorithms for building the decomposed form are also given. We further show that the CPD-GPR method might be the general algorithm for building the decomposed form. However, further development is needed to reduce the CPD rank. Therefore, the present CPD-GPR method might be helpful to inspire ideas for developing new tools in building decomposed potential functions.
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Affiliation(s)
- Qingfei Song
- Department of Chemistry, Northwestern Polytechnical University, West Youyi Road 127, 710072Xi'an, China
- Institut des Sciences Moléculaires d'Orsay, CNRS-UMR 8214, Université Paris-Saclay, Bâtiment 520, F-91405Orsay, France
| | - Xingyu Zhang
- Department of Chemistry, Northwestern Polytechnical University, West Youyi Road 127, 710072Xi'an, China
| | - Daniel Peláez
- Institut des Sciences Moléculaires d'Orsay, CNRS-UMR 8214, Université Paris-Saclay, Bâtiment 520, F-91405Orsay, France
| | - Qingyong Meng
- Department of Chemistry, Northwestern Polytechnical University, West Youyi Road 127, 710072Xi'an, China
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3
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Kasai T, Muthiah B, Po X, Yan C, Lin K, Tanudji J, Diño WA. Pattern analysis of the impact‐parameter dependent trajectories for the H +
H
2
exchange reaction at
T
=
3
and
300 K
: A characteristic propensity for reactive versus nonreactive trajectories found in the time‐dependent interaction potential and a roaming‐like libration motion at cold temperature. J CHIN CHEM SOC-TAIP 2022. [DOI: 10.1002/jccs.202100539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Toshio Kasai
- Department of Chemistry National Taiwan University Taipei Taiwan
- Department of Applied Physics Osaka University Suita Japan
| | | | - Xin‐Hui Po
- Department of Chemistry National Taiwan University Taipei Taiwan
- Department of Statistics National Chengchi University Taipei Taiwan
| | - Chu‐Chun Yan
- Department of Chemistry National Taiwan University Taipei Taiwan
| | - King‐Chuen Lin
- Department of Chemistry National Taiwan University Taipei Taiwan
- Department of Chemistry, Institute of Atomic and Molecular Sciences Academia Sinica Taipei Taiwan
| | | | - Wilson Agerico Diño
- Department of Applied Physics Osaka University Suita Japan
- Center for Atomic and Molecular Technologies Osaka University Suita Japan
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4
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Kwon T, Song HW, Woo SY, Kim J, Sung BJ. The accurate estimation of the third virial coefficients for helium using three‐body neural network potentials. B KOREAN CHEM SOC 2022. [DOI: 10.1002/bkcs.12497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Taejin Kwon
- Department of Chemistry and Research Institute for Basic Science Sogang University Seoul South Korea
| | - Han Wook Song
- Center for Mechanical Metrology Korea Research Institute of Standards and Science (KRISS) Daejeon South Korea
| | - Sam Yong Woo
- Center for Mechanical Metrology Korea Research Institute of Standards and Science (KRISS) Daejeon South Korea
| | - Jong‐Ho Kim
- Center for Mechanical Metrology Korea Research Institute of Standards and Science (KRISS) Daejeon South Korea
| | - Bong June Sung
- Department of Chemistry and Research Institute for Basic Science Sogang University Seoul South Korea
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5
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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: 142] [Impact Index Per Article: 28.4] [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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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: 3.6] [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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7
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Song Q, Zhang Q, Meng Q. Revisiting the Gaussian process regression for fitting high-dimensional potential energy surface and its application to the OH + HO2→O2+ H2O reaction. J Chem Phys 2020; 152:134309. [PMID: 32268765 DOI: 10.1063/1.5143544] [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)
- Qingfei Song
- School of Chemistry and Chemical Engineering, Northwestern Polytechnical University, West Youyi Road 127, 710072 Xi’an, China
- Key Laboratory of Special Functional and Smart Polymer Materials of Ministry of Industry and Information Technology, Northwestern Polytechnical University, West Youyi Road 127, 710072 Xi’an, China
| | - Qiuyu Zhang
- School of Chemistry and Chemical Engineering, Northwestern Polytechnical University, West Youyi Road 127, 710072 Xi’an, China
- Key Laboratory of Special Functional and Smart Polymer Materials of Ministry of Industry and Information Technology, Northwestern Polytechnical University, West Youyi Road 127, 710072 Xi’an, China
| | - Qingyong Meng
- School of Chemistry and Chemical Engineering, Northwestern Polytechnical University, West Youyi Road 127, 710072 Xi’an, China
- Key Laboratory of Special Functional and Smart Polymer Materials of Ministry of Industry and Information Technology, Northwestern Polytechnical University, West Youyi Road 127, 710072 Xi’an, China
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