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Zhou Y, Lu Y, Zhang Z, Zhang DH. An efficient and universal parallel algorithm for high-dimensional quantum dynamics in poly-atomic reactions. J Chem Phys 2024; 160:202502. [PMID: 38785279 DOI: 10.1063/5.0209245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Accepted: 05/06/2024] [Indexed: 05/25/2024] Open
Abstract
This study presents a parallel algorithm for high-dimensional quantum dynamics simulations in poly atomic reactions, integrating distributed- and shared-memory models. The distributions of the wave function and potential energy matrix across message passing interface processes are based on bundled radial and angular dimensions, with implementations featuring either two- or one-sided communication schemes. Using realistic parameters for the H + NH3 reaction, performance assessment reveals linear scalability, exceeding 90% efficiency with up to 600 processors. In addition, owing to the universal and concise structure, the algorithm demonstrates remarkable extensibility to diverse reaction systems, as demonstrated by successes with six-atom and four-atom reactions. This work establishes a robust foundation for high-dimensional dynamics studies, showcasing the algorithm's efficiency, scalability, and adaptability. The algorithm's potential as a valuable tool for unraveling quantum dynamics complexities is underscored, paving the way for future advancements in the field.
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Affiliation(s)
- Yong Zhou
- Anhui Province Key Laboratory for Control and Applications of Optoelectronic Information Materials, Department of Physics, Anhui Normal University, Wuhu 241000, People's Republic of China
- 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, People's Republic of China
| | - Yunpeng Lu
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, Singapore 637371, Singapore
| | - Zhaojun Zhang
- 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, People's Republic of China
| | - Dong H Zhang
- 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, People's Republic of China
- Hefei National Laboratory, Hefei 230088, People's Republic of China
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2
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Mellor TM. Molecular frames for a symmetry-adapted rotational basis set. Mol Phys 2022. [DOI: 10.1080/00268976.2022.2118638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
Affiliation(s)
- Thomas M. Mellor
- Department of Physics and Astronomy, University College London, London, UK
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3
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Yang S, Zhang Z, Zhang DH. A full-dimensional ab initio potential energy and dipole moment surfaces for (NH 3) 2. J Chem Phys 2021; 155:164306. [PMID: 34717358 DOI: 10.1063/5.0072063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
A full-dimensional ab initio potential energy surface (PES) and dipole moment surface (DMS) for the ammonia dimer (NH3)2 are reported. The database of the PES consists of 27 736 ab initio energy points and all of these points were calculated at the UCCSD(T)-F12a/AVTZ level. The PES was fitted by using the fundamental invariant neural network (FI-NN) method that satisfies the permutational symmetry of identical atoms, and the root mean square fitting error for the PES is very small as low as 0.562 meV. The geometries for the (NH3)2 DMS are the same as those used for the PES and are calculated at the XYG3/AVTZ level. This PES can describe a variety of internal floppy motions, including all kinds of vibrational modes no matter intermolecular or intramolecular. The CCSD(T)-PES can dissociate correctly to two NH3 monomers, with De = 1135.55 cm-1 (13.58 kJ/mol) which agrees accurately with the 13.5 ± 0.3 kJ/mol predicted by previous work.
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Affiliation(s)
- Shuo Yang
- 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, People's Republic of China
| | - Zhaojun Zhang
- 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, People's Republic of China
| | - Dong H Zhang
- 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, People's Republic of China
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4
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Zhao B. The symmetric C-D stretching spectator mode in the H + CHD 3 → H 2 + CD 3 reaction and its effect on dynamical modeling. Phys Chem Chem Phys 2021; 23:12105-12114. [PMID: 34027536 DOI: 10.1039/d1cp01614h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The symmetric C-D stretching mode is a spectator mode in the H + CHD3 → H2 + CD3 reaction. Effects of multiple vibrational excitations of the CHD3 reactant are studied with the quantum transition-state (QTS) framework and an eight-dimensional (8D) model Hamiltonian developed by Palma and Clary. By including many thermal flux eigenstates, results have been obtained up to high energies, allowing the study of the symmetric C-D stretching spectator mode. A new concept of a state-specific thermal flux operator is proposed to analyze the C-D stretching spectator mode in detail, providing a new and insightful venue for studying transition-state control of chemical reactions. Furthermore, as a spectator mode, whether the C-D stretching motion can be excluded in a seven-dimensional (7D) model has not been fully interrogated, although the 7D model is a reasonable approximation and has provided accurate theoretical predictions. By comparing with available results of full-dimensional calculations, both the 7D and 8D models predict reasonably accurate results. However, the 7D model underestimates the mixing of two vibrational states that are in Fermi resonance. Despite its spectator nature, the C-D stretch is important in the dynamical modeling of chemical reaction systems affected by state mixing.
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Affiliation(s)
- Bin Zhao
- Theoretische Chemie, Fakultät für Chemie, Universität Bielefeld, Universitätsstraße 25, D-33615 Bielefeld, Germany.
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5
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Quintas-Sánchez E, Dawes R. Spectroscopy and Scattering Studies Using Interpolated Ab Initio Potentials. Annu Rev Phys Chem 2021; 72:399-421. [PMID: 33503385 DOI: 10.1146/annurev-physchem-090519-051837] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The Born-Oppenheimer potential energy surface (PES) has come a long way since its introduction in the 1920s, both conceptually and in predictive power for practical applications. Nevertheless, nearly 100 years later-despite astonishing advances in computational power-the state-of-the-art first-principles prediction of observables related to spectroscopy and scattering dynamics is surprisingly limited. For example, the water dimer, (H2O)2, with only six nuclei and 20 electrons, still presents a formidable challenge for full-dimensional variational calculations of bound states and is considered out of reach for rigorous scattering calculations. The extremely poor scaling of the most rigorous quantum methods is fundamental; however, recent progress in development of approximate methodologies has opened the door to fairly routine high-quality predictions, unthinkable 20 years ago. In this review, in relation to the workflow of spectroscopy and/or scattering studies, we summarize progress and challenges in the component areas of electronic structure calculations, PES fitting, and quantum dynamical calculations.
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Affiliation(s)
- Ernesto Quintas-Sánchez
- 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;
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Zhang Z, Gatti F, Zhang DH. Full-dimensional quantum mechanical calculations of the reaction probability of the H + CH 4 reaction based on a mixed Jacobi and Radau description. J Chem Phys 2020; 152:201101. [PMID: 32486690 DOI: 10.1063/5.0009721] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
A full-dimensional time-dependent wave packet study using mixed polyspherical Jacobi and Radau coordinates for the title reaction has been reported. The non-reactive moiety CH3 has been described using three Radau vectors, whereas two Jacobi vectors have been used for the bond breaking/formation process. A potential-optimized discrete variable representation basis has been employed to describe the vibrational coordinates of the reagent CH4. About one hundred billion basis functions have been necessary to achieve converged results. The reaction probabilities for some initial vibrational states are given. A comparison between the present approach and other methods, including reduced and full-dimensional ones, is also presented.
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Affiliation(s)
- Zhaojun Zhang
- 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, People's Republic of China
| | - Fabien Gatti
- ISMO, Institut des Sciences Moléculaires d'Orsay - UMR 8214 CNRS/Université Paris-Saclay, F-91405 Orsay, France
| | - Dong H Zhang
- 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, People's Republic of China
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Zhang Z, Gatti F, Zhang DH. Full dimensional quantum mechanical calculations of the reaction probability of the H + NH3 collision based on a mixed Jacobi and Radau description. J Chem Phys 2019; 150:204301. [DOI: 10.1063/1.5096047] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Zhaojun Zhang
- 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, People’s Republic of China
| | - Fabien Gatti
- ISMO, Institut des Sciences Moléculaires d’Orsay—UMR 8214 CNRS/Université Paris-Sud, F-91405 Orsay, France
| | - Dong H. Zhang
- 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, People’s Republic of China
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8
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Zhao B, Manthe U. Counter-propagating wave packets in the quantum transition state approach to reactive scattering. J Chem Phys 2019; 150:184103. [DOI: 10.1063/1.5097997] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Bin Zhao
- Theoretische Chemie, Fakultät für Chemie, Universität Bielefeld, Universitätsstr. 25, D-33615 Bielefeld, Germany
| | - Uwe Manthe
- Theoretische Chemie, Fakultät für Chemie, Universität Bielefeld, Universitätsstr. 25, D-33615 Bielefeld, Germany
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9
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Owens A, Yachmenev A, Küpper J, Yurchenko SN, Thiel W. The rotation–vibration spectrum of methyl fluoride from first principles. Phys Chem Chem Phys 2019; 21:3496-3505. [DOI: 10.1039/c8cp01721b] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
State-of-the-art theoretical methods are used to investigate the rotation–vibration spectrum of methyl fluoride.
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Affiliation(s)
- Alec Owens
- Center for Free-Electron Laser Science (CFEL)
- Deutsches Elektronen-Synchrotron DESY
- 22607 Hamburg
- Germany
- The Hamburg Center for Ultrafast Imaging
| | - Andrey Yachmenev
- Center for Free-Electron Laser Science (CFEL)
- Deutsches Elektronen-Synchrotron DESY
- 22607 Hamburg
- Germany
- The Hamburg Center for Ultrafast Imaging
| | - Jochen Küpper
- Center for Free-Electron Laser Science (CFEL)
- Deutsches Elektronen-Synchrotron DESY
- 22607 Hamburg
- Germany
- The Hamburg Center for Ultrafast Imaging
| | - Sergei N. Yurchenko
- Department of Physics and Astronomy
- University College London
- WC1E 6BT London
- UK
| | - Walter Thiel
- Max-Planck-Institut für Kohlenforschung
- 45470 Mülheim an der Ruhr
- Germany
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10
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Dawes R, Quintas‐Sánchez E. THE CONSTRUCTION OF AB INITIO‐BASED POTENTIAL ENERGY SURFACES. REVIEWS IN COMPUTATIONAL CHEMISTRY 2018. [DOI: 10.1002/9781119518068.ch5] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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11
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Zhao Z, Chen J, Zhang Z, Zhang DH, Wang XG, Carrington T, Gatti F. Computing energy levels of CH4, CHD3, CH3D, and CH3F with a direct product basis and coordinates based on the methyl subsystem. J Chem Phys 2018; 148:074113. [DOI: 10.1063/1.5019323] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Zhiqiang Zhao
- 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
| | - Jun Chen
- 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
- Collaborative Innovation Center of Chemistry for Energy Materials (iChEM), College of Chemistry and Chemical Engineering, Xiamen University, Siming South Road 422, 361005 Xiamen, China
| | - Zhaojun Zhang
- 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
| | - Dong H. Zhang
- 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
| | - 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
| | - Fabien Gatti
- ISMO, Institut des Sciences Moléculaires d’Orsay - UMR 8214 CNRS/Université Paris-Sud, F-91405 Orsay, France
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12
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Chen J, Xu X, Liu S, Zhang DH. A neural network potential energy surface for the F + CH4reaction including multiple channels based on coupled cluster theory. Phys Chem Chem Phys 2018; 20:9090-9100. [DOI: 10.1039/c7cp08365c] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
We report here a new global and full dimensional potential energy surface (PES) for the F + CH4reaction.
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Affiliation(s)
- Jun Chen
- State Key Laboratory of Molecular Reaction Dynamics and Center for Theoretical Computational Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences
- Dalian 116023
- China
- Collaborative Innovation Center of Chemistry for Energy Materials (iChEM), College of Chemistry and Chemical Engineering, Xiamen University
- Xiamen 361005
| | - Xin Xu
- State Key Laboratory of Molecular Reaction Dynamics and Center for Theoretical Computational Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences
- Dalian 116023
- China
| | - Shu Liu
- State Key Laboratory of Molecular Reaction Dynamics and Center for Theoretical Computational Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences
- Dalian 116023
- China
| | - Dong H. Zhang
- State Key Laboratory of Molecular Reaction Dynamics and Center for Theoretical Computational Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences
- Dalian 116023
- China
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13
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Wang XG, Carrington T. Using monomer vibrational wavefunctions as contracted basis functions to compute rovibrational levels of an H2O-atom complex in full dimensionality. J Chem Phys 2017; 146:104105. [DOI: 10.1063/1.4977179] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] 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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14
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Shao K, Chen J, Zhao Z, Zhang DH. Communication: Fitting potential energy surfaces with fundamental invariant neural network. J Chem Phys 2016; 145:071101. [DOI: 10.1063/1.4961454] [Citation(s) in RCA: 133] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Kejie Shao
- State Key Laboratory of Molecular Reaction Dynamics and Center for Theoretical Computational Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, People’s Republic of China and University of Chinese Academy of Sciences, Beijing 100049, People’s Republic of China
| | - Jun Chen
- State Key Laboratory of Molecular Reaction Dynamics and Center for Theoretical Computational Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, People’s Republic of China and University of Chinese Academy of Sciences, Beijing 100049, People’s Republic of China
| | - Zhiqiang Zhao
- State Key Laboratory of Molecular Reaction Dynamics and Center for Theoretical Computational Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, People’s Republic of China and University of Chinese Academy of Sciences, Beijing 100049, People’s Republic of China
| | - Dong H. Zhang
- State Key Laboratory of Molecular Reaction Dynamics and Center for Theoretical Computational Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, People’s Republic of China and University of Chinese Academy of Sciences, Beijing 100049, People’s Republic of China
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