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A third-order discrete unified gas kinetic scheme for continuum and rarefied flows: Low-speed isothermal case

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arXiv 2017年

作者： Wu, Chen Shu, Chang Shi, Baochang Chen, Zhen State Key Laboratory of Coal Combustion Huazhong University of Science and Technology Wuhan430074 China Department of Mechanical Engineering National University of Singapore 10 Kent Ridge Crescent Singapore119260 Singapore School of Mathematics and Statistics Huazhong University of Science and Technology Wuhan430074 China Hubei Key Laboratory of Engineering Modeling and Scientific Computing Huazhong University of Science and Technology Wuhan430074 China

An efficient third-order discrete unified gas kinetic scheme (DUGKS) with efficiency is presented in this work for simulating continuum and rarefied flows. By employing two-stage time-stepping scheme and the high-order DUGKS flux reconstruction strategy, third-order of accuracy in both time and space can be achieved in the present method. It is also analytically proven that the second-order DUGKS is a special case of the present method. Compared with the high-order lattice Boltzmann equation LBE based methods, the present method is capable to deal with the rarefied flows by adopting the Newton-Cotes quadrature to approximate the integrals of moments. Instead of being constrained by the second-order (or lower-order) of accuracy in time splitting scheme as in the conventional high-order Runge-Kutta (RK) based kinetic methods, the present method solves the original BE, which overcomes the limitation in time accuracy. Typical benchmark tests are carried out for comprehensive evaluation of the present method. It is observed in the tests that the present method is advantageous over the original DUGKS in accuracy and capturing delicate flow structures. Moreover, the efficiency of the present third-order method is also shown in simulating rarefied flows. Copyright © 2017, The Authors. All rights reserved.

关键词： Boltzmann equation

A parallel thermal reservoir simulator on distributed-memory supercomputers

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A parallel thermal reservoir simulator on distributed-memory...

SPE Asia Pacific Oil and Gas Conference and Exhibition 2016

作者： Zhong, He Liu, Hui Cui, Tao Wang, Kun Yang, Bo Yang, Min Chen, Zhangxin Dept. of Chemical and Petroleum Engineering University of Calgary 2500 University Drive NW CalgaryAB Canada State Key Laboratory of Scientific and Engineering Computing Academy of Mathematics and Systems Science Chinese Academy of Sciences China

ISBN: (纸本)9781510835849

This paper describes the algorithms and implementation of a parallel thermal reservoir simulator designed for heavy oil simulation using distributed-memory supercomputers that can solve prohibitive problems efficiently. The thermal simulator inherits the features of a sequential thermal simulator. The performance of supercomputers is proportional to the number of CPUs. As a result, thermal problems can be solved thousands of times faster using supercomputers. This parallel simulator is based on our in-house platform, which provides grid management, data management, linear solvers and a visualization module. The exchange of information between CPUs is achieved by using the message passing interface standard, MPI. Results indicate that this simulator exhibits excellent scalability on the IBM Blue Gene/Q system and is thousands of times faster than serial simulators on a workstation. The simulator is also capable of simulating models with billions of grid blocks and fine resolution results can be obtained. © 2016 Society of Petroleum Engineers. All rights reserved.

关键词： Simulators

Uniqueness and traveling waves in a cell motility model

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arXiv 2017年

作者： Mizuhara, Matthew S. Zhang, Peng Department of Mathematics Pennsylvania State University University ParkPA16802 United States Institute of Natural Sciences Department of Mathematics Shanghai Jiao Tong University Key Laboratory of Scientific and Engineering Computing Shanghai Jiao Tong University Ministry of Education 800 Dongchuan Road Shanghai200240 China

We study a non-linear and non-local evolution equation for curves obtained as the sharp interface limit of a phase-field model for crawling motion of eukaryotic cells on a substrate. We establish uniqueness of solutions to the sharp interface limit equation in the so-called subcritical parameter regime. The proof relies on a Grönwall estimate for a specially chosen weighted L2 norm. Next, as persistent motion of crawling cells is of central interest to biologists we study the existence of traveling wave solutions. We prove that traveling wave solutions exist in the supercritical parameter regime provided the non-linear term of the sharp interface limit equation possesses certain asymmetry (related, e.g., to myosin contractility). Finally, we numerically investigate traveling wave solutions and simulate their dynamics. Due to non-uniqueness of solutions of the sharp interface limit equation we simulate a related, singularly perturbed PDE system which is uniquely solvable. Our simulations predict instability of traveling wave solutions and capture both bipedal wandering cell motion as well as rotating cell motion;these behaviors qualitatively agree with recent experimental and theoretical *** Codes 35Q92, 35K55, 65-04 Copyright © 2017, The Authors. All rights reserved.

关键词： Cytology

DASHMM accelerated adaptive fast multipole poisson-boltzmann solver on distributed memory architecture

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arXiv 2017年

作者： Zhang, B. DeBuhr, J. Niedzielski, D. Mayolo, S. Lu, B. Sterling, T. Center for Research in Extreme Scale Technologies School of Informatics Computing and Engineering Indiana University BloomingtonIN47404 United States Department of Physics Rensselaer Polytechnic Institute TroyNY12180 United States Department of Computer Science Tennessee Technological University CookevilleTN38505 United States State Key Laboratory of Scientific/Engineering Computing Academy of Mathematics and Systems Science Chinese Academy of Sciences Beijing100190

We present an updated version of the AFMPB package for fast calculation of molecular solvation-free energy. The main feature of the new version is the successful adoption of the DASHMM library, which enables AFMPB to operate on distributed memory computers. As a result, the new version can easily handle larger molecules or situations with higher accuracy requirements. To demonstrate the updated code, we applied the new version to a dengue virus system with more than one million atoms and a mesh with approximately 20 million triangles, and were able to reduce the time-to-solution from 10 hours reported in the previous release on a shared memory computer to less than 30 seconds on a Cray XC30 cluster using 12, 288 cores. Copyright © 2017, The Authors. All rights reserved.

关键词： Boundary element method

Erratum to: Search for single top-quark production via flavour-changing neutral currents at 8 TeV with the ATLAS detector

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The European Physical Journal C 2022年第1期82卷 1-15页

作者： Aad, G. Abbott, B. Abdallah, J. Abdinov, O. Aben, R. Abolins, M. AbouZeid, O. S. Abramowicz, H. Abreu, H. Abreu, R. Abulaiti, Y. Acharya, B. S. Adamczyk, L. Adams, D. L. Adelman, J. Adomeit, S. Adye, T. Affolder, A. A. Agatonovic-Jovin, T. Agricola, J. Aguilar-Saavedra, J. A. Ahlen, S. P. Ahmadov, F. Aielli, G. Akerstedt, H. Åkesson, T. P. A. Akimov, A. V. Alberghi, G. L. Albert, J. Albrand, S. Alconada Verzini, M. J. Aleksa, M. Aleksandrov, I. N. Alexa, C. Alexander, G. Alexopoulos, T. Alhroob, M. Alimonti, G. Alio, L. Alison, J. Alkire, S. P. Allbrooke, B. M. M. Allport, P. P. Aloisio, A. Alonso, A. Alonso, F. Alpigiani, C. Altheimer, A. Alvarez Gonzalez, B. Álvarez Piqueras, D. Alviggi, M. G. Amadio, B. T. Amako, K. Amaral Coutinho, Y. Amelung, C. Amidei, D. Amor Dos Santos, S. P. Amorim, A. Amoroso, S. Amram, N. Amundsen, G. Anastopoulos, C. Ancu, L. S. Andari, N. Andeen, T. Anders, C. F. Anders, G. Anders, J. K. Anderson, K. J. Andreazza, A. Andrei, V. Angelidakis, S. Angelozzi, I. Anger, P. Angerami, A. Anghinolfi, F. Anisenkov, A. V. Anjos, N. Annovi, A. Antonelli, M. Antonov, A. Antos, J. Anulli, F. Aoki, M. Aperio Bella, L. Arabidze, G. Arai, Y. Araque, J. P. Arce, A. T. H. Arduh, F. A. Arguin, J-F. Argyropoulos, S. Arik, M. Armbruster, A. J. Arnaez, O. Arnal, V. Arnold, H. Arratia, M. Arslan, O. Artamonov, A. Artoni, G. Asai, S. Asbah, N. Ashkenazi, A. Åsman, B. Asquith, L. Assamagan, K. Astalos, R. Atkinson, M. Atlay, N. B. Augsten, K. Aurousseau, M. Avolio, G. Axen, B. Ayoub, M. K. Azuelos, G. Baak, M. A. Baas, A. E. Baca, M. J. Bacci, C. Bachacou, H. Bachas, K. Backes, M. Backhaus, M. Bagiacchi, P. Bagnaia, P. Bai, Y. Bain, T. Baines, J. T. Baker, O. K. Baldin, E. M. Balek, P. Balestri, T. Balli, F. Banas, E. Banerjee, Sw. Bannoura, A. A. E. Bansil, H. S. Barak, L. Barberio, E. L. Barberis, D. Barbero, M. Barillari, T. Barisonzi, M. Barklow, T. Barlow, N. Barnes, S. L. Barnett, B. M. Barnett, R. M. Barnovska, Z. Baroncelli, A. Barone, G. Barr, A. J. Barreiro, F. Barreiro Guimarães da Costa, J. Bartol CPPM Aix-Marseille Université and CNRS/IN2P3 Marseille France Homer L. Dodge Department of Physics and Astronomy University of Oklahoma Norman USA Institute of Physics Academia Sinica Taipei Taiwan Institute of Physics Azerbaijan Academy of Sciences Baku Azerbaijan Nikhef National Institute for Subatomic Physics and University of Amsterdam Amsterdam The Netherlands Department of Physics and Astronomy Michigan State University East Lansing USA Department of Physics University of Toronto Toronto Canada Raymond and Beverly Sackler School of Physics and Astronomy Tel Aviv University Tel Aviv Israel Department of Physics Technion: Israel Institute of Technology Haifa Israel Center for High Energy Physics University of Oregon Eugene USA Department of Physics Stockholm University Stockholm Sweden The Oskar Klein Centre Stockholm Sweden INFN Gruppo Collegato di Udine Sezione di Trieste Udine Italy ICTP Trieste Italy Department of Physics King’s College London London UK AGH University of Science and Technology Faculty of Physics and Applied Computer Science Kraków Poland Physics Department Brookhaven National Laboratory Upton USA Department of Physics Northern Illinois University De Kalb USA Fakultät für Physik Ludwig-Maximilians-Universität München Munich Germany Particle Physics Department Rutherford Appleton Laboratory Didcot UK Oliver Lodge Laboratory University of Liverpool Liverpool UK Institute of Physics University of Belgrade Belgrade Serbia II Physikalisches Institut Georg-August-Universität Göttingen Germany Laboratório de Instrumentação e Física Experimental de Partículas-LIP Lisbon Portugal Departamento de Fisica Teorica y del Cosmos and CAFPE Universidad de Granada Granada Spain Department of Physics Boston University Boston USA Joint Institute for Nuclear Research JINR Dubna Dubna Russia INFN Sezione di Roma Tor Vergata Rome Italy Dipartimento di Fisica Università di Roma Tor Vergata Rome Italy Fysiska institutionen Lunds uni

Author Correction: BigNeuron: a resource to benchmark and predict performance of algorithms for automated tracing of neurons in light microscopy datasets

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Nature methods 2024年第10期21卷 1959页

作者： Linus Manubens-Gil Zhi Zhou Hanbo Chen Arvind Ramanathan Xiaoxiao Liu Yufeng Liu Alessandro Bria Todd Gillette Zongcai Ruan Jian Yang Miroslav Radojević Ting Zhao Li Cheng Lei Qu Siqi Liu Kristofer E Bouchard Lin Gu Weidong Cai Shuiwang Ji Badrinath Roysam Ching-Wei Wang Hongchuan Yu Amos Sironi Daniel Maxim Iascone Jie Zhou Erhan Bas Eduardo Conde-Sousa Paulo Aguiar Xiang Li Yujie Li Sumit Nanda Yuan Wang Leila Muresan Pascal Fua Bing Ye Hai-Yan He Jochen F Staiger Manuel Peter Daniel N Cox Michel Simonneau Marcel Oberlaender Gregory Jefferis Kei Ito Paloma Gonzalez-Bellido Jinhyun Kim Edwin Rubel Hollis T Cline Hongkui Zeng Aljoscha Nern Ann-Shyn Chiang Jianhua Yao Jane Roskams Rick Livesey Janine Stevens Tianming Liu Chinh Dang Yike Guo Ning Zhong Georgia Tourassi Sean Hill Michael Hawrylycz Christof Koch Erik Meijering Giorgio A Ascoli Hanchuan Peng Institute for Brain and Intelligence Southeast University Nanjing China. Microsoft Corporation Redmond WA USA. Tencent AI Lab Bellevue WA USA. Computing Environment and Life Sciences Directorate Argonne National Laboratory Lemont IL USA. Kaya Medical Seattle WA USA. University of Cassino and Southern Lazio Cassino Italy. Center for Neural Informatics Structures and Plasticity Krasnow Institute for Advanced Study George Mason University Fairfax VA USA. Faculty of Information Technology Beijing University of Technology Beijing China. Beijing International Collaboration Base on Brain Informatics and Wisdom Services Beijing China. Nuctech Netherlands Rotterdam the Netherlands. Janelia Research Campus Howard Hughes Medical Institute Ashburn VA USA. Department of Electrical and Computer Engineering University of Alberta Edmonton Alberta Canada. Ministry of Education Key Laboratory of Intelligent Computation and Signal Processing Anhui University Hefei China. Paige AI New York NY USA. Scientific Data Division and Biological Systems and Engineering Division Lawrence Berkeley National Lab Berkeley CA USA. Helen Wills Neuroscience Institute and Redwood Center for Theoretical Neuroscience UC Berkeley Berkeley CA USA. RIKEN AIP Tokyo Japan. Research Center for Advanced Science and Technology (RCAST) The University of Tokyo Tokyo Japan. School of Computer Science University of Sydney Sydney New South Wales Australia. Texas A&M University College Station TX USA. Cullen College of Engineering University of Houston Houston TX USA. Graduate Institute of Biomedical Engineering National Taiwan University of Science and Technology Taipei Taiwan. National Centre for Computer Animation Bournemouth University Poole UK. PROPHESEE Paris France. Department of Neuroscience Columbia University New York NY USA. Mortimer B. Zuckerman Mind Brain Behavior Institute Columbia University New York NY USA. Department of Computer Science Northern Illinois Universit

Recent developments in the PySCF program package

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arXiv 2020年

作者： Sun, Qiming Zhang, Xing Banerjee, Samragni Bao, Peng Barbry, Marc Blunt, Nick S. Bogdanov, Nikolay A. Booth, George H. Chen, Jia Cui, Zhi-Hao Eriksen, Janus Juul Gao, Yang Guo, Sheng Hermann, Jan Hermes, Matthew R. Koh, Kevin Koval, Peter Lehtola, Susi Li, Zhendong Liu, Junzi Mardirossian, Narbe McClain, James D. Motta, Mario Mussard, Bastien Pham, Hung Q. Pulkin, Artem Purwanto, Wirawan Robinson, Paul J. Ronca, Enrico Sayfutyarova, Elvira Scheurer, Maximilian Schurkus, Henry F. Smith, James E.T. Sun, Chong Sun, Shi-Ning Upadhyay, Shiv Wagner, Lucas K. Wang, Xiao White, Alec Whitfield, James Daniel Williamson, Mark J. Wouters, Sebastian Yang, Jun Yu, Jason M. Zhu, Tianyu Berkelbach, Timothy C. Sharma, Sandeep Sokolov, Alexander Yu. Chan, Garnet Kin-Lic AxiomQuant Investment Management LLC Shanghai200120 China Division of Chemistry and Chemical Engineering California Institute of Technology PasadenaCA91125 United States Department of Chemistry and Biochemistry The Ohio State University ColumbusOH43210 United States Beijing National Laboratory for Molecular Sciences State Key Laboratory for Structural Chemistry of Unstable and Stable Species Institute of Chemistry Chinese Academy of Sciences Beijing100190 China Simbeyond B.V. P.O. Box 513 EindhovenNL-5600 MB Netherlands Department of Chemistry Lensfield Road CambridgeCB2 1EW United Kingdom Max Planck Institute for Solid State Research Heisenbergstraße 1 Stuttgart70569 Germany Department of Physics King's College London Strand LondonWC2R 2LS United Kingdom Department of Physics University of Florida GainesvilleFL32611 United States Quantum Theory Project University of Florida GainesvilleFL32611 United States School of Chemistry University of Bristol Cantock's Close BristolBS8 1TS United Kingdom Division of Engineering and Applied Science California Institute of Technology PasadenaCA91125 United States Google Inc. Mountain ViewCA94043 United States FU Berlin Department of Mathematics and Computer Science Arnimallee 6 Berlin14195 Germany TU Berlin Machine Learning Group Marchstr. 23 Berlin10587 Germany Department of Chemistry Chemical Theory Center Supercomputing Institute University of Minnesota 207 Pleasant Street SE MinneapolisMN55455 United States Department of Chemistry and Biochemistry The University of Notre Dame du Lac 251 Nieuwland Science Hall Notre DameIN46556 United States Simune Atomistics S.L. Avenida Tolosa 76 Donostia-San Sebastian Spain HelsinkiFI-00014 Finland Key Laboratory of Theoretical and Computational Photochemistry Ministry of Education College of Chemistry Beijing Normal University Beijing100875 China Department of Chemistry The Johns Hopkins University BaltimoreMD21218 United States AMGEN

PYSCF is a Python-based general-purpose electronic structure platform that both supports first-principles simulations of molecules and solids, as well as accelerates the development of new methodology and complex computational workflows. The present paper explains the design and philosophy behind PYSCF that enables it to meet these twin objectives. With several case studies, we show how users can easily implement their own methods using PYSCF as a development environment. We then summarize the capabilities of PYSCF for molecular and solid-state simulations. Finally, we describe the growing ecosystem of projects that use PYSCF across the domains of quantum chemistry, materials science, machine learning and quantum information science. Copyright © 2020, The Authors. All rights reserved.

关键词： Python

Correction to: Multivariate statistical and trend analyses of surface water quality in the central Indian River Lagoon area, Florida

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Environmental Earth Sciences 2018年第5期77卷 1-1页

作者： Sayem Zaman Ming Ye Fan Zhang Mingming Zhu Department of Scientific Computing Florida State University Tallahassee USA Draper Aden Associates Richmond USA School of Computer Science and Software Engineering Tianjin Polytechnic University Tianjin China Department of Earth Ocean and Atmospheric Science Florida State University Tallahassee USA Key Laboratory of Tibetan Environmental Changes and Land Surface Processes Institute of Tibetan Plateau Research Chinese Academy of Sciences Beijing China Center of Hydraulic Engineering Regulation and Management Jinzhou Waterwork Office Jinzhou China

Unfortunately, the online version of the original article has an error in authors’ names.

关键词：

A discontinuous galerkin method by patch reconstruction for biharmonic problem

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arXiv 2017年

作者： Li, Ruo Ming, Pingbing Sun, Zhiyuan Yang, Fanyi Yang, Zhijian CAPT LMAM and School of Mathematical Sciences Peking University Beijing100871 China State Key Laboratory of Scientific and Engineering Computing Academy of Mathematics and Systems Science Chinese Academy of Sciences No.55 Zhong-Guan-Cun East Road Beijing100190 China School of Mathematical Sciences University of Chinese Academy of Sciences No. 19A Yu-Quan Road Beijing100049 China School of Mathematical Sciences Peking University Beijing100871 China School of Mathematics and Statistics Wuhan University Wuhan430072 China

We propose a new discontinuous Galerkin method based on the least-squares patch reconstruction for the biharmonic problem. We prove the optimal error estimate of the proposed method. The two-dimensional and three-dimensional numerical examples are presented to confirm the accuracy and efficiency of the method with several boundary conditions and several types of polygon meshes and polyhedral meshes.49N45, 65N21 Copyright © 2017, The Authors. All rights reserved.

关键词： Galerkin methods