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arXiv 2023年

作者： Zeng, Jinzhe Zhang, Duo Lu, Denghui Mo, Pinghui Li, Zeyu Chen, Yixiao Rynik, Marián Huang, Li'ang Li, Ziyao Shi, Shaochen Wang, Yingze Ye, Haotian Tuo, Ping Yang, Jiabin Ding, Ye Li, Yifan Tisi, Davide Zeng, Qiyu Bao, Han Xia, Yu Huang, Jiameng Muraoka, Koki Wang, Yibo Chang, Junhan Yuan, Fengbo Bore, Sigbjørn Løland Cai, Chun Lin, Yinnian Wang, Bo Xu, Jiayan Zhu, Jia-Xin Luo, Chenxing Zhang, Yuzhi Goodall, Rhys E.A. Liang, Wenshuo Singh, Anurag Kumar Yao, Sikai Zhang, Jingchao Wentzcovitch, Renata Han, Jiequn Liu, Jie Jia, Weile York, Darrin M. Weinan, E. Car, Roberto Zhang, Linfeng Wang, Han Laboratory for Biomolecular Simulation Research Institute for Quantitative Biomedicine Department of Chemistry and Chemical Biology Rutgers University PiscatawayNJ08854 United States AI for Science Institute Beijing100080 China DP Technology Beijing100080 China Academy for Advanced Interdisciplinary Studies Peking University Beijing100871 China HEDPS CAPT College of Engineering Peking University Beijing100871 China College of Electrical and Information Engineering Hunan University Changsha China Yuanpei College Peking University Beijing100871 China Program in Applied and Computational Mathematics Princeton University PrincetonNJ08540 United States Department of Experimental Physics Comenius University Mlynská Dolina F2 Bratislava842 48 Slovakia Center for Quantum Information Institute for Interdisciplinary Information Sciences Tsinghua University Beijing100084 China Center for Data Science Peking University Beijing100871 China ByteDance Research Zhonghang Plaza No. 43 North 3rd Ring West Road Haidian District Beijing China College of Chemistry and Molecular Engineering Peking University Beijing100871 China Baidu Inc. Beijing China Key Laboratory of Structural Biology of Zhejiang Province School of Life Sciences Westlake University Zhejiang Hangzhou China Westlake AI Therapeutics Lab Westlake Laboratory of Life Sciences and Biomedicine Zhejiang Hangzhou China Department of Chemistry Princeton University PrincetonNJ08544 United States SISSA Scuola Internazionale Superiore di Studi Avanzati Trieste34136 Italy Laboratory of Computational Science and Modeling Institute of Materials École Polytechnique Fédérale de Lausanne Lausanne1015 Switzerland Department of Physics National University of Defense Technology Hunan Changsha410073 China State Key Lab of Processors Institute of Computing Technology Chinese Academy of Sciences Beijing China University of Chinese Academy of Sciences Beijing China School of Electronics Engineerin

DeePMD-kit is a powerful open-source software package that facilitates molecular dynamics simulations using machine learning potentials (MLP) known as Deep Potential (DP) models. This package, which was released in 2017, has been widely used in the fields of physics, chemistry, biology, and material science for studying atomistic systems. The current version of DeePMD-kit offers numerous advanced features such as DeepPot-SE, attention-based and hybrid descriptors, the ability to fit tensile properties, type embedding, model deviation, Deep Potential - Range Correction (DPRc), Deep Potential Long Range (DPLR), GPU support for customized operators, model compression, non-von Neumann molecular dynamics (NVNMD), and improved usability, including documentation, compiled binary packages, graphical user interfaces (GUI), and application programming interfaces (API). This article presents an overview of the current major version of the DeePMD-kit package, highlighting its features and technical details. Additionally, the article benchmarks the accuracy and efficiency of different models and discusses ongoing developments. © 2023, CC BY-NC-ND.

关键词： Molecular dynamics

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Fully Discrete Galerkin Finite Element Method for the Cubic Nonlinear Schr(o)dinger Equation

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高等学校计算数学学报（英文版） 2017年第3期10卷 671-688页

作者： Jianyun Wang Yunqing Huang School of Science Hunan University of Technology Zhuzhou 412007 China Hunan Key Laboratory for Computation and Simulation in Science and Engineering School of Mathematics and Computational Science Xiangtan University Xiangtan 411105 China

This paper is concemed with numerical method for a two-dimensional timedependent cubic nonlinear Schr(o)dinger *** approximations are obtained by the Galerkin finite element method in space in conjunction with the backward Euler method and the Crank-Nicolson method in time,*** prove optimal L2 error estimates for two fully discrete schemes by using elliptic projection ***,a numerical example is provided to verify our theoretical results.

关键词： Finite element method nonlinear Schr(o)dinger equations backward Euler scheme Crank-Nicolson scheme

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A finite element method of the self-consistent field theory on general curved surfaces

arXiv

引用

arXiv 2018年

作者： Wei, Huayi Xu, Ming Si, Wei Jiang, Kai School of Mathematics and Computational Science Xiangtan University Xiangtan Hunan411105 China Hunan Key Laboratory for Computation and Simulation in Science and Engineering

Block copolymers provide a wonderful platform in studying the soft condensed matter systems. Many fascinating ordered structures have been discovered in bulk and confined systems. Among various theories, the self-consistent field theory (SCFT) has been proven to be a powerful tool for studying the equilibrium ordered structures. Many numerical methods have been developed to solve the SCFT model. However, most of these focus on the bulk systems, and little work on the confined systems, especially on general curved surfaces. In this work, we developed a linear surface finite element method, which has a rigorous mathematical theory to guarantee numerical precsion, to study the self-assembled phases of block copolymers on general curved surfaces based on the SCFT. Furthermore, to capture the consistent surface for a given self-assembled pattern, an adaptive approach to optimize the size of the general curved surface has been proposed. To demonstrate the power of this approach, we investigate the self-assembled patterns of diblock copolymers on several distinct curved surfaces, including five closed surfaces and an unclosed surface. Numerical results illustrate the efficiency of the proposed method. The obtained ordered structures are consistent with the previous results on standard surfaces, such as sphere and torus. Certainly, the proposed numerical framework has the capability of studying the phase behaviors on general surfaces precisely. Copyright © 2018, The Authors. All rights reserved.

关键词： Mean field theory

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High-order energy stable schemes of incommensurate phase-field crystal model

arXiv

引用

arXiv 2018年

作者： Jiang, Kai Si, Wei School of Mathematics and Computational Science Hunan Key Laboratory for Computation and Simulation in Science and Engineering Xiangtan University Xiangtan Hunan411105 China

This article focuses on the development of high-order energy stable schemes for the multi-length-scale incommensurate phase-field crystal model which is able to study the phase behavior of aperiodic structures. These high-order schemes based on the scalar auxiliary variable (SAV) and spectral deferred correction (SDC) approaches are suitable for the L2 gradient flow equation, i.e., the Allen-Cahn dynamic equation. Concretely, we propose a second-order Crank-Nicolson (CN) scheme of the SAV system, prove the energy dissipation law, and give the error estimate in the almost periodic function sense. Moreover, we use the SDC method to improve the computational accuracy of the SAV/CN scheme. Numerical results demonstrate the advantages of high-order numerical methods in numerical computations and show the influence of length-scales on the formation of ordered structures. Copyright © 2018, The Authors. All rights reserved.

关键词： Numerical methods

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Recovery based finite element method for biharmonic equation in two dimensional

arXiv

引用

arXiv 2018年

作者： Huang, Yunqing Wei, Huayi Yang, Wei Yi, Nianyu Hunan Key Laboratory for Computation and Simulation in Science and Engineering School of Mathematics and Computational Science Xiangtan University Xiangtan411105 China

We design and numerically validate a recovery based linear finite element method for solving the biharmonic equation. The main idea is to replace the gradient operator ∇ on linear finite element space by G(∇) in the weak formulation of the biharmonic equation, where G is the recovery operator which recovers the piecewise constant function into the linear finite element space. By operator G, Laplace operator ∆ is replaced by ∇ · G(∇). Furthermore the boundary condition on normal derivative ∇u · n is treated by the boundary penalty method. The explicit matrix expression of the proposed method is also introduced. Numerical examples on uniform and adaptive meshes are presented to illustrate the correctness and effectiveness of the proposed *** Codes 65N30 Copyright © 2018, The Authors. All rights reserved.

关键词： Finite element method

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Corrigendum to "Recycling of LiFePO4 cathode materials from spent lithium-ion batteries through ultrasound-assisted Fenton reaction and lithium compensation" [Waste Manage. 136 (2021) 67-75]

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Waste management (New York, N.Y.) 2022年 137卷 168页

作者： Xiangping Chen Shuzhen Li Yi Wang Youzhou Jiang Xiao Tan Weijiang Han Shubin Wang School of Environmental Science and Engineering Shaanxi University of Science & Technology Xi'an Shaanxi Province 710021 PR China. Electronic address: chenxiangping@***. School of Environmental Science and Engineering Shaanxi University of Science & Technology Xi'an Shaanxi Province 710021 PR China. College of Chemistry and Chemical Engineering Central South University Changsha Hunan Province 410083 PR China. State Environmental Protection Key Laboratory of Urban Ecological Environment Simulation and Protection South China Institute of Environmental Sciences Ministry of Ecology and Environment (MEE) Guangzhou Guangdong Province 510655 PR China. State Environmental Protection Key Laboratory of Urban Ecological Environment Simulation and Protection South China Institute of Environmental Sciences Ministry of Ecology and Environment (MEE) Guangzhou Guangdong Province 510655 PR China. Electronic address: wang.s.bean@***.

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Spin-dependent electron transport along hairpinlike DNA molecules

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Physical Review B 2020年第19期102卷 195406-195406页

作者： Pei-Jia Hu Si-Xian Wang Xiao-Hui Gao Yan-Yang Zhang Tie-Feng Fang Ai-Min Guo Qing-Feng Sun Hunan Key Laboratory for Super-microstructure and Ultrafast Process School of Physics and Electronics Central South University Changsha 410083 China School of Physics and Electronic Engineering Guangzhou University Guangzhou 510006 China School of Physical Science and Technology Lanzhou University Lanzhou 730000 China International Center for Quantum Materials School of Physics Peking University Beijing 100871 China Collaborative Innovation Center of Quantum Matter Beijing 100871 China CAS Center for Excellence in Topological Quantum Computation University of Chinese Academy of Sciences Beijing 100190 China

The chirality-induced spin selectivity (CISS), demonstrated in diverse chiral molecules by numerous experimental and theoretical groups, has been attracting extensive and ongoing interest in recent years. As the secondary structure of DNA, the charge transfer along DNA hairpins has been widely studied for more than two decades, finding that DNA hairpins exhibit spin-related effects as reported in recent experiments. Here, we propose a setup to demonstrate directly the CISS effect in DNA hairpins contacted by two nonmagnetic leads at both ends of the stem. Our results indicate that DNA hairpins present a pronounced CISS effect and the spin polarization could be enhanced by using conducting molecules as the loop. In particular, DNA hairpins exhibit several intriguing features. First, the local spin currents can flow circularly and assemble into a number of vortex clusters when the electron energy locates in the left/right electronic band of the stem. The chirality of vortex clusters in each band is the same and will be reversed by switching the electron energy from the left band to the right one, inducing the sign reversal of the spin polarization. Interestingly, the local spin currents can be greater than the corresponding spin component of the source-drain current. Second, both the conductance and the spin polarization can increase with molecular length as well as dephasing strength, contrary to the physical intuition that the transmission ability of molecular wires should be poorer when suffering from stronger scattering. Third, we unveil the optimal contact configuration of efficient electron transport and that of the CISS effect, which are distinct from each other and can be controlled by dephasing strength. The experimental realization of these results is discussed and the underlying physical mechanism is illustrated.

关键词： Quantum transport Spin filtering DNA Nonequilibrium Green's function

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An Improved Third-order CWENO-Z Scheme at critical points

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IOP Conference Series: Materials science and engineering 2019年第3期569卷

作者： Shujiang Tang Mingjun Li Shuang Han School of mathematics and computational science Xiangtan University Xiangtan Hunan 411105 China Hunan Key Laboratory for Computation and Simulation in Science and Engineering Xiangtan Hunan 411105 China

In this paper, by modifying the smoothness factor of the third-order CWENO scheme, we present the two-parameter CWENO-NZ3 scheme to improve accuracy at critical points. We selected some classical examples for numerical simulation, such as one-dimensional Sod shock tube, Shock-entropy wave interaction, Riemann problem with strong discontinuity and Rayleigh-Taylor instability problem. Numerically comparing with the classical third-order CWENO schemes, it is found that the improved schemes not only improve accuracy and resolution at the extreme points, but also reduce dissipation.

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A spatial sixth-order CCD-TVD method for solving multidimensional coupled Burgers' equation

arXiv

引用

arXiv 2018年

作者： Pan, Kejia Wu, Xiaoxin Yue, Xiaoqiang Ni, Runxin School of Mathematics and Statistics Central South University Changsha Hunan410083 China School of Mathematics and Computational Science Hunan Key Laboratory for Computation and Simulation in Science and Engineering Xiangtan University Hunan411105 China

In this paper, an efficient and high-order accuracy finite difference method is proposed for solving multidimensional nonlinear Burgers' equation. The third-order three stage Runge-Kutta total variation diminishing (TVD) scheme is employed for the time discretization, and the three-point combined compact difference (CCD) scheme is used for spatial discretization. Our method is third-order accurate in time and sixth-order accurate in space. The CCD-TVD method treats the nonlinear term explicitly thus it is very efficient and easy to implement. In addition, we prove the unique solvability of the CCD system under non-periodic boundary conditions. Numerical experiments including both two-dimensional and three-dimensional problems have been conducted to demonstrate the high efficiency and accuracy of the proposed method. Copyright © 2018, The Authors. All rights reserved.

关键词： Runge Kutta methods

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Multifractal temporally weighted detrended cross-correlation analysis of multivariate time series

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Chaos (Woodbury, N.Y.) 2020年第2期30卷 023134页

作者： Shan Jiang Bao-Gen Li Zu-Guo Yu Fang Wang Vo Anh Yu Zhou Hunan Key Laboratory for Computation and Simulation in Science and Engineering and Key Laboratory of Intelligent Computing and Information Processing of Ministry of Education Xiangtan University Xiangtan Hunan 411105 China. College of Information and Science Technology Hunan Agricultural University Changsha Hunan 410128 China. Faculty of Science Engineering and Technology Swinburne University of Technology PO Box 218 Hawthorn Victoria 3122 Australia. Institute of Future Cities and Department of Geography and Resource Management The Chinese University of Hong Kong Shatin Hong Kong China.

Fractal and multifractal properties of various systems have been studied extensively. In this paper, first, the multivariate multifractal detrend cross-correlation analysis (MMXDFA) is proposed to investigate the multifractal features in multivariate time series. MMXDFA may produce oscillations in the fluctuation function and spurious cross correlations. In order to overcome these problems, we then propose the multivariate multifractal temporally weighted detrended cross-correlation analysis (MMTWXDFA). In relation to the multivariate detrended cross-correlation analysis and multifractal temporally weighted detrended cross-correlation analysis, an innovation of MMTWXDFA is the application of the signed Manhattan distance to calculate the local detrended covariance function. To evaluate the performance of the MMXDFA and MMTWXDFA methods, we apply them on some artificially generated multivariate series. Several numerical tests demonstrate that both methods can identify their fractality, but MMTWXDFA can detect long-range cross correlations and simultaneously quantify the levels of cross correlation between two multivariate series more accurately.

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