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  • 101.
    Holm, Marcus
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Tillenius, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Black-Schaffer, David
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computer Systems.
    A simple model for tuning tasks2011In: Proc. 4th Swedish Workshop on Multi-Core Computing, Linköping, Sweden: Linköping University , 2011, p. 45-49Conference paper (Other academic)
  • 102. Horuk, Christopher B.
    et al.
    Douglas, Geoffrey
    Gupta, Anand
    Krintz, Chandra
    Bales, Ben
    Bellesia, Giovanni
    Drawert, Brian
    Wolski, Rich
    Petzold, Linda
    Hellander, Andreas
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Automatic and portable cloud deployment for scientific simulations2014In: Proc. 12th International Conference on High Performance Computing and Simulation, Piscataway, NJ: IEEE , 2014, p. 374-381Conference paper (Refereed)
  • 103.
    Höök, Lars Josef
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Numerical Analysis.
    Eckerdal, Anna
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    On the bimodality in an introductory programming course: An analysis of student performance factors2015In: Proc. 3rd International Conference on Learning and Teaching in Computing and Engineering, Los Alamitos, CA: IEEE Computer Society, 2015, p. 79-86Conference paper (Refereed)
  • 104. Jallow, Alieu
    et al.
    Hellander, Andreas
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Toor, Salman
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Cost-aware application development and management using CLOUD-METRIC2017In: Proc. 7th International Conference on Cloud Computing and Services Science, Setúbal, Portugal: SciTePress, 2017, p. 515-522Conference paper (Refereed)
  • 105.
    Jayawardena, Mahen
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    An e-Science Approach to Genetic Analysis of Quantitative Traits2010Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Many important traits in plants, animals and humans are quantitative, and most such traits are generally believed to be affected by multiple genetic loci. Standard computational tools for mapping of quantitative traits (i.e. for finding Quantitative Trait Loci, QTL, in the genome) use linear regression models for relating the observed phenotypes to the genetic composition of individuals in an experimental population. Using these tools to simultaneously search for multiple QTL is computationally demanding. The main reason for this is the complex optimization landscape for the multidimensional global optimization problems that must be solved. This thesis describes parallel algorithms, implementations and tools for simultaneous mapping of several QTL. These new computational tools enable genetic analysis exploiting new classes of multidimensional statistical models, potentially resulting in interesting results in genetics.

    We first describe how the standard, brute-force algorithm for global optimization in QTL analysis is parallelized and implemented on a grid system. Then, we also present a parallelized version of the more elaborate global optimization algorithm DIRECT and show how this can be efficiently deployed and used on grid systems and other loosely-coupled architectures. The parallel DIRECT scheme is further developed to exploit both coarse-grained parallelism in grid systems or clusters as well as fine-grained, tightly-coupled parallelism in multi-core nodes. The results show that excellent speedup and performance can be archived on grid systems and clusters, even when using a tightly-coupled algorithm such as DIRECT. Finally, we provide two distinctly different front-ends for our code. One is a grid portal providing a graphical front-end suitable for novice users and standard forms of QTL analysis. The other is a prototype of an R-based grid-enabled problem solving environment. Both of these front-ends can, after some further refinement, be utilized by geneticists for performing multidimensional genetic analysis of quantitative traits on a regular basis.

    List of papers
    1. Using parallel computing and grid systems for genetic mapping of quantitative traits
    Open this publication in new window or tab >>Using parallel computing and grid systems for genetic mapping of quantitative traits
    2007 (English)In: Applied Parallel Computing: State of the Art in Scientific Computing, Berlin: Springer-Verlag , 2007, p. 627-636Conference paper, Published paper (Refereed)
    Place, publisher, year, edition, pages
    Berlin: Springer-Verlag, 2007
    Series
    Lecture Notes in Computer Science ; 4699
    National Category
    Bioinformatics (Computational Biology)
    Identifiers
    urn:nbn:se:uu:diva-11546 (URN)10.1007/978-3-540-75755-9_76 (DOI)000250904900076 ()978-3-540-75754-2 (ISBN)
    Available from: 2007-09-26 Created: 2007-09-26 Last updated: 2018-01-12Bibliographically approved
    2. Grid-enabling an efficient algorithm for demanding global optimization problems in genetic analysis
    Open this publication in new window or tab >>Grid-enabling an efficient algorithm for demanding global optimization problems in genetic analysis
    2007 (English)In: Proc. 3rd International Conference on e-Science and Grid Computing, Los Alamitos, CA: IEEE Computer Society, 2007, p. 205-212Conference paper, Published paper (Refereed)
    Place, publisher, year, edition, pages
    Los Alamitos, CA: IEEE Computer Society, 2007
    National Category
    Computer Sciences Computational Mathematics
    Identifiers
    urn:nbn:se:uu:diva-12617 (URN)10.1109/E-SCIENCE.2007.40 (DOI)000253614600025 ()978-0-7695-3064-2 (ISBN)
    Available from: 2008-01-08 Created: 2008-01-08 Last updated: 2018-01-12Bibliographically approved
    3. Efficient optimization algorithms and implementations for genetic analysis of complex traits on a grid system with multicore nodes
    Open this publication in new window or tab >>Efficient optimization algorithms and implementations for genetic analysis of complex traits on a grid system with multicore nodes
    2008 (English)Conference paper, Published paper (Refereed)
    Place, publisher, year, edition, pages
    Trondheim, Norway: Norwegian University of Science and Technology, 2008
    National Category
    Computer Sciences Computational Mathematics
    Identifiers
    urn:nbn:se:uu:diva-111590 (URN)
    Conference
    PARA 2008: State of the Art in Scientific and Parallel Computing
    Projects
    UPMARC
    Available from: 2010-01-12 Created: 2009-12-17 Last updated: 2018-01-12Bibliographically approved
    4. Computational and visualization tools for genetic analysis of complex traits
    Open this publication in new window or tab >>Computational and visualization tools for genetic analysis of complex traits
    2010 (English)Report (Other academic)
    Series
    Technical report / Department of Information Technology, Uppsala University, ISSN 1404-3203 ; 2010-001
    National Category
    Software Engineering Computational Mathematics
    Identifiers
    urn:nbn:se:uu:diva-111593 (URN)
    Projects
    eSSENCE
    Available from: 2010-01-12 Created: 2009-12-17 Last updated: 2018-01-12Bibliographically approved
    5. A Grid-Enabled Problem Solving Environment for QTL Analysis in R
    Open this publication in new window or tab >>A Grid-Enabled Problem Solving Environment for QTL Analysis in R
    Show others...
    2010 (English)In: Proc. 2nd International Conference on Bioinformatics and Computational Biology, Cary, NC: ISCA , 2010, p. 202-209Conference paper, Published paper (Refereed)
    Place, publisher, year, edition, pages
    Cary, NC: ISCA, 2010
    National Category
    Software Engineering Genetics
    Identifiers
    urn:nbn:se:uu:diva-111594 (URN)978-1-880843-76-5 (ISBN)
    Projects
    eSSENCE
    Available from: 2010-01-12 Created: 2009-12-17 Last updated: 2018-01-12Bibliographically approved
  • 106.
    Jayawardena, Mahen
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Parallel algorithms and implementations for genetic analysis of quantitative traits2007Licentiate thesis, comprehensive summary (Other academic)
    Abstract [en]

    Many important traits in plants, animals and humans are quantitative, and most such traits are generally believed to be regulated by multiple genetic loci. Standard computational tools for analysis of quantitative traits use linear regression models for relating the observed phenotypes to the genetic composition of individuals in a population. However, using these tools to simultaneously search for multiple genetic loci is very computationally demanding. The main reason for this is the complex nature of the optimization landscape for the multidimensional global optimization problems that must be solved. This thesis describes parallel algorithms and implementation techniques for such optimization problems. The new computational tools will eventually enable genetic analysis exploiting new classes of multidimensional statistical models, potentially resulting in interesting results in genetics.

    We first describe how the algorithm used for global optimization in the standard, serial software is parallelized and implemented on a grid system. Then, we also describe a parallelized version of the more elaborate global optimization algorithm DIRECT and show how this can be deployed on grid systems and other loosely-coupled architectures. The parallel DIRECT scheme is further developed to exploit both coarse-grained parallelism in grid or clusters as well as fine-grained, tightly-coupled parallelism in multi-core nodes. The results show that excellent speedup and performance can be archived on grid systems and clusters, even when using a tightly-coupled algorithms such as DIRECT. Finally, a pilot implementation of a grid portal providing a graphical front-end for our code is implemented. After some further development, this portal can be utilized by geneticists for performing multidimensional genetic analysis of quantitative traits on a regular basis.

  • 107.
    Jayawardena, Mahen
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Holmgren, Sverker
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Grid-enabling an efficient algorithm for demanding global optimization problems in genetic analysis2007In: Proc. 3rd International Conference on e-Science and Grid Computing, Los Alamitos, CA: IEEE Computer Society, 2007, p. 205-212Conference paper (Refereed)
  • 108.
    Jayawardena, Mahen
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Ljungberg, Kajsa
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Holmgren, Sverker
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Using parallel computing and grid systems for genetic mapping of quantitative traits2007In: Applied Parallel Computing: State of the Art in Scientific Computing, Berlin: Springer-Verlag , 2007, p. 627-636Conference paper (Refereed)
  • 109.
    Jayawardena, Mahen
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Löf, Henrik
    Holmgren, Sverker
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Efficient optimization algorithms and implementations for genetic analysis of complex traits on a grid system with multicore nodes2008Conference paper (Refereed)
  • 110.
    Jayawardena, Mahen
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Nettelblad, Carl
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Toor, Salman
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Östberg, Per-Olov
    Elmroth, Erik
    Holmgren, Sverker
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    A Grid-Enabled Problem Solving Environment for QTL Analysis in R2010In: Proc. 2nd International Conference on Bioinformatics and Computational Biology, Cary, NC: ISCA , 2010, p. 202-209Conference paper (Refereed)
  • 111.
    Jayawardena, Mahen
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Toor, Salman
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Holmgren, Sverker
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    A grid portal for genetic analysis of complex traits2009In: Proc. 32nd International Convention on Information and Communication Technology, Electronics and Microelectronics: Volume I, Rijeka, Croatia: MIPRO , 2009, p. 281-284Conference paper (Refereed)
  • 112.
    Jayawardena, Mahen
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Toor, Salman
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Holmgren, Sverker
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Computational and visualization tools for genetic analysis of complex traits2010Report (Other academic)
  • 113. John, Aji
    et al.
    Ausmees, Kristiina
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Muenzen, Kathleen
    Kuhn, Catherine
    Tan, Amanda
    SWEEP: Accelerating scientific research through scalable serverless workflows2019In: Companion Proc. 12th International Conference on Utility and Cloud Computing, New York: ACM Press, 2019, p. 43-50Conference paper (Refereed)
  • 114. Kaucka, Marketa
    et al.
    Ivashkin, Evgeny
    Gyllborg, Daniel
    Zikmund, Tomas
    Tesarova, Marketa
    Kaiser, Jozef
    Xie, Meng
    Petersen, Julian
    Pachnis, Vassilis
    Nicolis, Silvia K.
    Yu, Tian
    Sharpe, Paul
    Arenas, Ernest
    Brismar, Hjalmar
    Blom, Hans
    Clevers, Hans
    Suter, Ueli
    Chagin, Andrei S.
    Fried, Kaj
    Hellander, Andreas
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Adameyko, Igor
    Analysis of neural crest-derived clones reveals novel aspects of facial development2016In: Science Advances, ISSN 2375-2548, Vol. 2, no 8, p. e1600060:1-16, article id e1600060Article in journal (Refereed)
  • 115. Kaucka, Marketa
    et al.
    Zikmund, Tomas
    Tesarova, Marketa
    Gyllborg, Daniel
    Hellander, Andreas
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Jaros, Josef
    Kaiser, Jozef
    Petersen, Julian
    Szarowska, Bara
    Newton, Phillip T.
    Dyachuk, Vyacheslav
    Li, Lei
    Qian, Hong
    Johansson, Anne-Sofie
    Mishina, Yuji
    Currie, Josh
    Tanaka, Elly M.
    Erickson, Alek
    Dudley, Andrew
    Brismar, Hjalmar
    Southam, Paul
    Coen, Enrico
    Chen, Min
    Weinstein, Lee S.
    Hampl, Ales
    Arenas, Ernest
    Chagin, Andrei S.
    Fried, Kaj
    Adameyko, Igor
    Oriented clonal cell dynamics enables accurate growth and shaping of vertebrate cartilage2017In: eLIFE, E-ISSN 2050-084X, Vol. 6, article id e25902Article in journal (Refereed)
  • 116.
    Kieri, Emil
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Accelerated convergence for Schrödinger equations with non-smooth potentials2013Report (Other academic)
  • 117.
    Kieri, Emil
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Accelerated convergence for Schrödinger equations with non-smooth potentials2014In: BIT Numerical Mathematics, ISSN 0006-3835, E-ISSN 1572-9125, Vol. 54, p. 729-748Article in journal (Refereed)
  • 118.
    Kieri, Emil
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Numerical Methods for Wave Propagation: Analysis and Applications in Quantum Dynamics2016Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    We study numerical methods for time-dependent partial differential equations describing wave propagation, primarily applied to problems in quantum dynamics governed by the time-dependent Schrödinger equation (TDSE). We consider both methods for spatial approximation and for time stepping. In most settings, numerical solution of the TDSE is more challenging than solving a hyperbolic wave equation. This is mainly because the dispersion relation of the TDSE makes it very sensitive to dispersion error, and infers a stringent time step restriction for standard explicit time stepping schemes. The TDSE is also often posed in high dimensions, where standard methods are intractable.

    The sensitivity to dispersion error makes spectral methods advantageous for the TDSE. We use spectral or pseudospectral methods in all except one of the included papers. In Paper III we improve and analyse the accuracy of the Fourier pseudospectral method applied to a problem with limited regularity, and in Paper V we construct a matrix-free spectral method for problems with non-trivial boundary conditions. Due to its stiffness, the TDSE is most often solved using exponential time integration. In this thesis we use exponential operator splitting and Krylov subspace methods. We rigorously prove convergence for force-gradient operator splitting methods in Paper IV. One way of making high-dimensional problems computationally tractable is low-rank approximation. In Paper VI we prove that a splitting method for dynamical low-rank approximation is robust to singular values in the approximation approaching zero, a situation which is difficult to handle since it implies strong curvature of the approximation space.

    List of papers
    1. An adaptive pseudospectral method for wave packet dynamics
    Open this publication in new window or tab >>An adaptive pseudospectral method for wave packet dynamics
    2012 (English)In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 137, p. 044111:1-12Article in journal (Refereed) Published
    National Category
    Computational Mathematics
    Identifiers
    urn:nbn:se:uu:diva-179058 (URN)10.1063/1.4737893 (DOI)000307611500012 ()
    Projects
    eSSENCE
    Available from: 2012-07-26 Created: 2012-08-06 Last updated: 2017-12-07Bibliographically approved
    2. Coupling of Gaussian beam and finite difference solvers for semiclassical Schrödinger equations
    Open this publication in new window or tab >>Coupling of Gaussian beam and finite difference solvers for semiclassical Schrödinger equations
    2015 (English)In: Advances in Applied Mathematics and Mechanics, ISSN 2070-0733, E-ISSN 2075-1354, Vol. 7, p. 687-714Article in journal (Refereed) Published
    National Category
    Computational Mathematics
    Identifiers
    urn:nbn:se:uu:diva-262240 (URN)10.4208/aamm.2013.m411 (DOI)000361055400001 ()
    Projects
    eSSENCE
    Available from: 2015-09-09 Created: 2015-09-10 Last updated: 2017-12-04Bibliographically approved
    3. Accelerated convergence for Schrödinger equations with non-smooth potentials
    Open this publication in new window or tab >>Accelerated convergence for Schrödinger equations with non-smooth potentials
    2014 (English)In: BIT Numerical Mathematics, ISSN 0006-3835, E-ISSN 1572-9125, Vol. 54, p. 729-748Article in journal (Refereed) Published
    National Category
    Computational Mathematics
    Identifiers
    urn:nbn:se:uu:diva-214685 (URN)10.1007/s10543-013-0465-x (DOI)000342210300009 ()
    Projects
    eSSENCE
    Available from: 2014-01-01 Created: 2014-01-09 Last updated: 2017-12-06Bibliographically approved
    4. Stiff convergence of force-gradient operator splitting methods
    Open this publication in new window or tab >>Stiff convergence of force-gradient operator splitting methods
    2015 (English)In: Applied Numerical Mathematics, ISSN 0168-9274, E-ISSN 1873-5460, Vol. 94, p. 33-45Article in journal (Refereed) Published
    National Category
    Computational Mathematics
    Identifiers
    urn:nbn:se:uu:diva-248024 (URN)10.1016/j.apnum.2015.03.005 (DOI)000355498600003 ()
    Projects
    eSSENCE
    Available from: 2015-03-18 Created: 2015-03-26 Last updated: 2017-12-04Bibliographically approved
    5. A matrix-free Legendre spectral method for initial–boundary value problems
    Open this publication in new window or tab >>A matrix-free Legendre spectral method for initial–boundary value problems
    2016 (English)In: Electronic Transactions on Numerical Analysis, ISSN 1068-9613, E-ISSN 1068-9613, Vol. 45, p. 283-304Article in journal (Refereed) Published
    National Category
    Computational Mathematics
    Identifiers
    urn:nbn:se:uu:diva-267728 (URN)000393415700015 ()
    Projects
    eSSENCE
    Available from: 2016-07-29 Created: 2015-11-25 Last updated: 2017-12-01Bibliographically approved
    6. Discretized dynamical low-rank approximation in the presence of small singular values
    Open this publication in new window or tab >>Discretized dynamical low-rank approximation in the presence of small singular values
    2016 (English)In: SIAM Journal on Numerical Analysis, ISSN 0036-1429, E-ISSN 1095-7170, Vol. 54, p. 1020-1038Article in journal (Refereed) Published
    National Category
    Computational Mathematics
    Identifiers
    urn:nbn:se:uu:diva-267729 (URN)10.1137/15M1026791 (DOI)000375488100021 ()
    Projects
    eSSENCE
    Available from: 2016-04-05 Created: 2015-11-25 Last updated: 2017-12-01Bibliographically approved
  • 119.
    Kieri, Emil
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Numerical Quantum Dynamics2013Licentiate thesis, comprehensive summary (Other academic)
    Abstract [en]

    We consider computational methods for simulating the dynamics of molecular systems governed by the time-dependent Schrödinger equation. Solving the Schrödinger equation numerically poses a challenge due to its often highly oscillatory solutions, and to the exponential growth of work and memory with the number of particles in the system.

    Two different classes of problems are studied: the dynamics of the nuclei in a molecule and the dynamics of an electron in orbit around a nucleus. For the first class of problems we present new computational methods which exploit the relation between quantum and classical dynamics in order to make the computations more efficient. For the second class of problems, the lack of regularity in the solution poses a computational challenge. Using knowledge of the non-smooth features of the solution we construct a new method with two orders higher accuracy than what is achieved by direct application of a difference stencil.

    List of papers
    1. An adaptive pseudospectral method for wave packet dynamics
    Open this publication in new window or tab >>An adaptive pseudospectral method for wave packet dynamics
    2012 (English)In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 137, p. 044111:1-12Article in journal (Refereed) Published
    National Category
    Computational Mathematics
    Identifiers
    urn:nbn:se:uu:diva-179058 (URN)10.1063/1.4737893 (DOI)000307611500012 ()
    Projects
    eSSENCE
    Available from: 2012-07-26 Created: 2012-08-06 Last updated: 2017-12-07Bibliographically approved
    2. Coupling of Gaussian beam and finite difference solvers for semiclassical Schrödinger equations
    Open this publication in new window or tab >>Coupling of Gaussian beam and finite difference solvers for semiclassical Schrödinger equations
    2013 (English)Report (Other academic)
    Series
    Technical report / Department of Information Technology, Uppsala University, ISSN 1404-3203 ; 2013-019
    National Category
    Computational Mathematics
    Identifiers
    urn:nbn:se:uu:diva-208501 (URN)
    Projects
    eSSENCE
    Available from: 2013-09-29 Created: 2013-10-01 Last updated: 2013-10-08Bibliographically approved
    3. Accelerated convergence for Schrödinger equations with non-smooth potentials
    Open this publication in new window or tab >>Accelerated convergence for Schrödinger equations with non-smooth potentials
    2013 (English)Report (Other academic)
    Series
    Technical report / Department of Information Technology, Uppsala University, ISSN 1404-3203 ; 2013-007
    National Category
    Computational Mathematics
    Identifiers
    urn:nbn:se:uu:diva-198253 (URN)
    Projects
    eSSENCE
    Available from: 2013-04-10 Created: 2013-04-10 Last updated: 2013-10-08Bibliographically approved
  • 120.
    Kieri, Emil
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Stiff convergence of force-gradient operator splitting methods2014Report (Other academic)
  • 121.
    Kieri, Emil
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Stiff convergence of force-gradient operator splitting methods2015In: Applied Numerical Mathematics, ISSN 0168-9274, E-ISSN 1873-5460, Vol. 94, p. 33-45Article in journal (Refereed)
  • 122.
    Kieri, Emil
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Holmgren, Sverker
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Karlsson, Hans O.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    An adaptive pseudospectral method for wave packet dynamics2012In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 137, p. 044111:1-12Article in journal (Refereed)
  • 123.
    Kieri, Emil
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Kreiss, Gunilla
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Numerical Analysis.
    Runborg, Olof
    Coupling of Gaussian beam and finite difference solvers for semiclassical Schrödinger equations2013Report (Other academic)
  • 124.
    Kieri, Emil
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Kreiss, Gunilla
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Numerical Analysis.
    Runborg, Olof
    Coupling of Gaussian beam and finite difference solvers for semiclassical Schrödinger equations2015In: Advances in Applied Mathematics and Mechanics, ISSN 2070-0733, E-ISSN 2075-1354, Vol. 7, p. 687-714Article in journal (Refereed)
  • 125.
    Kieri, Emil
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Lubich, Christian
    Walach, Hanna
    Discretised dynamical low-rank approximation in the presence of small singular values2015In: Mathematical Methods in Quantum Molecular Dynamics, Zürich, Switzerland: EMS Publishing House , 2015, p. 1516-1517Conference paper (Other academic)
  • 126.
    Kieri, Emil
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Lubich, Christian
    Walach, Hanna
    Discretized dynamical low-rank approximation in the presence of small singular values2016In: SIAM Journal on Numerical Analysis, ISSN 0036-1429, E-ISSN 1095-7170, Vol. 54, p. 1020-1038Article in journal (Refereed)
  • 127.
    Kormann, Katharina
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    A time–space adaptive method for the Schrödinger equation2012Report (Other academic)
  • 128.
    Kormann, Katharina
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Efficient and Reliable Simulation of Quantum Molecular Dynamics2012Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    The time-dependent Schrödinger equation (TDSE) models the quantum nature of molecular processes.  Numerical simulations based on the TDSE help in understanding and predicting the outcome of chemical reactions. This thesis is dedicated to the derivation and analysis of efficient and reliable simulation tools for the TDSE, with a particular focus on models for the interaction of molecules with time-dependent electromagnetic fields.

    Various time propagators are compared for this setting and an efficient fourth-order commutator-free Magnus-Lanczos propagator is derived. For the Lanczos method, several communication-reducing variants are studied for an implementation on clusters of multi-core processors. Global error estimation for the Magnus propagator is devised using a posteriori error estimation theory. In doing so, the self-adjointness of the linear Schrödinger equation is exploited to avoid solving an adjoint equation. Efficiency and effectiveness of the estimate are demonstrated for both bounded and unbounded states. The temporal approximation is combined with adaptive spectral elements in space. Lagrange elements based on Gauss-Lobatto nodes are employed to avoid nondiagonal mass matrices and ill-conditioning at high order. A matrix-free implementation for the evaluation of the spectral element operators is presented. The framework uses hybrid parallelism and enables significant computational speed-up as well as the solution of larger problems compared to traditional implementations relying on sparse matrices.

    As an alternative to grid-based methods, radial basis functions in a Galerkin setting are proposed and analyzed. It is found that considerably higher accuracy can be obtained with the same number of basis functions compared to the Fourier method. Another direction of research presented in this thesis is a new algorithm for quantum optimal control: The field is optimized in the frequency domain where the dimensionality of the optimization problem can drastically be reduced. In this way, it becomes feasible to use a quasi-Newton method to solve the problem.

    List of papers
    1. Accurate time propagation for the Schrödinger equation with an explicitly time-dependent Hamiltonian
    Open this publication in new window or tab >>Accurate time propagation for the Schrödinger equation with an explicitly time-dependent Hamiltonian
    2008 (English)In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 128, p. 184101:1-11Article in journal (Refereed) Published
    National Category
    Computational Mathematics Computer Sciences
    Identifiers
    urn:nbn:se:uu:diva-16180 (URN)10.1063/1.2916581 (DOI)000255983500008 ()
    Available from: 2008-05-10 Created: 2008-05-10 Last updated: 2018-01-12Bibliographically approved
    2. Global error control of the time-propagation for the Schrödinger equation with a time-dependent Hamiltonian
    Open this publication in new window or tab >>Global error control of the time-propagation for the Schrödinger equation with a time-dependent Hamiltonian
    2011 (English)In: Journal of Computational Science, ISSN 1877-7503, E-ISSN 1877-7511, Vol. 2, p. 178-187Article in journal (Refereed) Published
    National Category
    Computational Mathematics
    Identifiers
    urn:nbn:se:uu:diva-156538 (URN)10.1016/j.jocs.2011.02.003 (DOI)000208808200011 ()
    Projects
    eSSENCE
    Available from: 2011-02-18 Created: 2011-07-31 Last updated: 2017-12-08Bibliographically approved
    3. A time–space adaptive method for the Schrödinger equation
    Open this publication in new window or tab >>A time–space adaptive method for the Schrödinger equation
    2012 (English)Report (Other academic)
    Series
    Technical report / Department of Information Technology, Uppsala University, ISSN 1404-3203 ; 2012-023
    National Category
    Computational Mathematics
    Identifiers
    urn:nbn:se:uu:diva-180182 (URN)
    Projects
    eSSENCE
    Available from: 2012-08-31 Created: 2012-08-31 Last updated: 2012-09-27Bibliographically approved
    4. Error control for simulations of a dissociative quantum system
    Open this publication in new window or tab >>Error control for simulations of a dissociative quantum system
    2010 (English)In: Numerical Mathematics and Advanced Applications: 2009, Berlin: Springer-Verlag , 2010, p. 523-531Conference paper, Published paper (Refereed)
    Place, publisher, year, edition, pages
    Berlin: Springer-Verlag, 2010
    National Category
    Computational Mathematics Computer Sciences
    Identifiers
    urn:nbn:se:uu:diva-132929 (URN)10.1007/978-3-642-11795-4_56 (DOI)000395207900056 ()978-3-642-11794-7 (ISBN)
    Projects
    eSSENCE
    Available from: 2010-10-29 Created: 2010-10-29 Last updated: 2018-06-16Bibliographically approved
    5. Communication-efficient algorithms for numerical quantum dynamics
    Open this publication in new window or tab >>Communication-efficient algorithms for numerical quantum dynamics
    2012 (English)In: Applied Parallel and Scientific Computing: Part II, Berlin: Springer-Verlag , 2012, p. 368-378Conference paper, Published paper (Refereed)
    Place, publisher, year, edition, pages
    Berlin: Springer-Verlag, 2012
    Series
    Lecture Notes in Computer Science ; 7134
    National Category
    Computer Sciences Computational Mathematics
    Identifiers
    urn:nbn:se:uu:diva-135980 (URN)10.1007/978-3-642-28145-7_36 (DOI)000309716000036 ()978-3-642-28144-0 (ISBN)
    Conference
    PARA 2010: State of the Art in Scientific and Parallel Computing
    Projects
    eSSENCEUPMARC
    Available from: 2012-02-16 Created: 2010-12-09 Last updated: 2018-01-12Bibliographically approved
    6. Parallel finite element operator application: Graph partitioning and coloring
    Open this publication in new window or tab >>Parallel finite element operator application: Graph partitioning and coloring
    2011 (English)In: Proc. 7th International Conference on e-Science, Los Alamitos, CA: IEEE Computer Society, 2011, p. 332-339Conference paper, Published paper (Refereed)
    Place, publisher, year, edition, pages
    Los Alamitos, CA: IEEE Computer Society, 2011
    National Category
    Computer Sciences Computational Mathematics
    Identifiers
    urn:nbn:se:uu:diva-166267 (URN)10.1109/eScience.2011.53 (DOI)978-1-4577-2163-2 (ISBN)
    Projects
    eSSENCE
    Available from: 2012-01-09 Created: 2012-01-11 Last updated: 2018-01-12Bibliographically approved
    7. An RBF–Galerkin approach to the time-dependent Schrödinger equation
    Open this publication in new window or tab >>An RBF–Galerkin approach to the time-dependent Schrödinger equation
    2012 (English)Report (Other academic)
    Series
    Technical report / Department of Information Technology, Uppsala University, ISSN 1404-3203 ; 2012-024
    National Category
    Computational Mathematics
    Identifiers
    urn:nbn:se:uu:diva-180388 (URN)
    Projects
    eSSENCE
    Available from: 2012-09-05 Created: 2012-09-05 Last updated: 2012-09-27Bibliographically approved
    8. A Fourier-coefficient based solution of an optimal control problem in quantum chemistry
    Open this publication in new window or tab >>A Fourier-coefficient based solution of an optimal control problem in quantum chemistry
    2010 (English)In: Journal of Optimization Theory and Applications, ISSN 0022-3239, E-ISSN 1573-2878, Vol. 147, p. 491-506Article in journal (Refereed) Published
    National Category
    Computational Mathematics Computer Sciences
    Identifiers
    urn:nbn:se:uu:diva-128817 (URN)10.1007/s10957-010-9735-9 (DOI)000283509600006 ()
    Projects
    eSSENCE
    Available from: 2010-07-21 Created: 2010-07-25 Last updated: 2018-01-12Bibliographically approved
  • 129.
    Kormann, Katharina
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Numerical methods for quantum molecular dynamics2009Licentiate thesis, comprehensive summary (Other academic)
    Abstract [en]

    The time-dependent Schrödinger equation models the quantum nature of molecular processes. Numerical simulations of these models help in understanding and predicting the outcome of chemical reactions.

    In this thesis, several numerical algorithms for evolving the Schrödinger equation with an explicitly time-dependent Hamiltonian are studied and their performance is compared for the example of a pump-probe and an interference experiment for the rubidium diatom. For the important application of interaction dynamics between a molecule and a time-dependent field, an efficient fourth order Magnus-Lanczos propagator is derived. Error growth in the equation is analyzed by means of a posteriori error estimation theory and the self-adjointness of the Hamiltonian is exploited to yield a low-cost global error estimate for numerical time evolution. Based on this theory, an h,p-adaptive Magnus-Lanczos propagator is developed that is capable to control the global error. Numerical experiments for various model systems (including a three dimensional model and a dissociative configuration) show that the error estimate is effective and the number of time steps needed to meet a certain accuracy is reduced due to adaptivity.

    Moreover, the thesis proposes an efficient numerical optimization framework for the design of femtosecond laser pulses with the aim of manipulating chemical reactions. This task can be formulated as an optimal control problem with the electric field of the laser being the control variable. In the algorithm described here, the electric field is Fourier transformed and it is optimized over the Fourier coefficients. Then, the frequency band is narrowed which facilitates the application of a quasi-Newton method. Furthermore, the restrictions on the frequency band make sure that the optimized pulse can be realized by the experimental equipment. A numerical comparison shows that the new method can outperform the Krotov method, which is a standard scheme in this field.

    List of papers
    1. Accurate time propagation for the Schrödinger equation with an explicitly time-dependent Hamiltonian
    Open this publication in new window or tab >>Accurate time propagation for the Schrödinger equation with an explicitly time-dependent Hamiltonian
    2008 (English)In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 128, p. 184101:1-11Article in journal (Refereed) Published
    National Category
    Computational Mathematics Computer Sciences
    Identifiers
    urn:nbn:se:uu:diva-16180 (URN)10.1063/1.2916581 (DOI)000255983500008 ()
    Available from: 2008-05-10 Created: 2008-05-10 Last updated: 2018-01-12Bibliographically approved
    2. Global error control of the time-propagation for the Schrödinger equation with a time-dependent Hamiltonian
    Open this publication in new window or tab >>Global error control of the time-propagation for the Schrödinger equation with a time-dependent Hamiltonian
    2009 (English)Report (Other academic)
    Series
    Technical report / Department of Information Technology, Uppsala University, ISSN 1404-3203 ; 2009-021
    National Category
    Computational Mathematics
    Identifiers
    urn:nbn:se:uu:diva-108364 (URN)
    Available from: 2009-09-16 Created: 2009-09-16 Last updated: 2011-11-18Bibliographically approved
    3. A Fourier-coefficient based solution of an optimal control problem in quantum chemistry
    Open this publication in new window or tab >>A Fourier-coefficient based solution of an optimal control problem in quantum chemistry
    2009 (English)Report (Other academic)
    Series
    Technical report / Department of Information Technology, Uppsala University, ISSN 1404-3203 ; 2009-022
    National Category
    Computational Mathematics Computer Sciences
    Identifiers
    urn:nbn:se:uu:diva-108365 (URN)
    Available from: 2009-09-16 Created: 2009-09-16 Last updated: 2018-01-13Bibliographically approved
  • 130.
    Kormann, Katharina
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Holmgren, Sverker
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Karlsson, Hans O.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical and Analytical Chemistry, Quantum Chemistry.
    A Fourier-coefficient based solution of an optimal control problem in quantum chemistry2010In: Journal of Optimization Theory and Applications, ISSN 0022-3239, E-ISSN 1573-2878, Vol. 147, p. 491-506Article in journal (Refereed)
  • 131.
    Kormann, Katharina
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Holmgren, Sverker
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Karlsson, Hans O.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical and Analytical Chemistry, Quantum Chemistry.
    A Fourier-coefficient based solution of an optimal control problem in quantum chemistry2009Report (Other academic)
  • 132.
    Kormann, Katharina
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Holmgren, Sverker
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Karlsson, Hans O.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical and Analytical Chemistry, Quantum Chemistry.
    Accurate time propagation for the Schrödinger equation with an explicitly time-dependent Hamiltonian2008In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 128, p. 184101:1-11Article in journal (Refereed)
  • 133.
    Kormann, Katharina
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Holmgren, Sverker
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Karlsson, Hans O.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical and Analytical Chemistry, Quantum Chemistry.
    Global error control of the time-propagation for the Schrödinger equation with a time-dependent Hamiltonian2009Report (Other academic)
  • 134.
    Kormann, Katharina
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Holmgren, Sverker
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Karlsson, Hans O.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical and Analytical Chemistry, Quantum Chemistry.
    Global error control of the time-propagation for the Schrödinger equation with a time-dependent Hamiltonian2011In: Journal of Computational Science, ISSN 1877-7503, E-ISSN 1877-7511, Vol. 2, p. 178-187Article in journal (Refereed)
  • 135.
    Kormann, Katharina
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Kronbichler, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Numerical Analysis.
    Parallel finite element operator application: Graph partitioning and coloring2011In: Proc. 7th International Conference on e-Science, Los Alamitos, CA: IEEE Computer Society, 2011, p. 332-339Conference paper (Refereed)
  • 136.
    Kormann, Katharina
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Kronbichler, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Numerical Analysis.
    Müller, Bernhard
    Derivation of strictly stable high order difference approximations for variable-coefficient PDE2012In: Journal of Scientific Computing, ISSN 0885-7474, E-ISSN 1573-7691, Vol. 50, p. 167-197Article in journal (Refereed)
  • 137.
    Kormann, Katharina
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Larsson, Elisabeth
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Numerical Analysis.
    A Galerkin radial basis function method for the Schrödinger equation2013In: SIAM Journal on Scientific Computing, ISSN 1064-8275, E-ISSN 1095-7197, Vol. 35, p. A2832-A2855Article in journal (Refereed)
  • 138.
    Kormann, Katharina
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Larsson, Elisabeth
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Numerical Analysis.
    An RBF–Galerkin approach to the time-dependent Schrödinger equation2012Report (Other academic)
  • 139.
    Kormann, Katharina
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Larsson, Elisabeth
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Numerical Analysis.
    Radial basis functions for the time-dependent Schrödinger equation2011In: Numerical Analysis and Applied Mathematics: ICNAAM 2011, Melville, NY: American Institute of Physics (AIP), 2011, p. 1323-1326Conference paper (Refereed)
  • 140.
    Kormann, Katharina
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Nissen, Anna
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Numerical Analysis.
    Error control for simulations of a dissociative quantum system2010In: Numerical Mathematics and Advanced Applications: 2009, Berlin: Springer-Verlag , 2010, p. 523-531Conference paper (Refereed)
  • 141.
    Kowalewski, Markus
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Kahra, Steffen
    Leschhorn, Günther
    Schätz, Tobias
    de Vivie-Riedle, Regina
    Femtosecond pump-probe spectroscopy for single trapped molecular ions2013In: Proc. 18th International Conference on Ultrafast Phenomena, EDP Sciences, 2013, p. 02028:1-3Conference paper (Refereed)
  • 142.
    Kowalewski, Markus
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Larsson, Elisabeth
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Numerical Analysis.
    Heryudono, Alfa
    An adaptive interpolation scheme for molecular potential energy surfaces2016In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 145, p. 084104:1-10, article id 084104Article in journal (Refereed)
  • 143.
    Kowalewski, Markus
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Mikosch, Jochen
    Wester, Roland
    de Vivie-Riedle, Regina
    Nucleophilic substitution dynamics: Comparing wave packet calculations with experiment2014In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 118, p. 4661-4669Article in journal (Refereed)
  • 144.
    Kreiss, Gunilla
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Numerical Analysis.
    Lötstedt, PerUppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Numerical Analysis.Målqvist, AxelUppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Numerical Analysis.Neytcheva, MayaUppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Numerical Mathematics and Advanced Applications: 20092010Conference proceedings (editor) (Refereed)
  • 145.
    Kronbichler, Martin
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Numerical Analysis.
    Kormann, Katharina
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    A generic interface for parallel cell-based finite element operator application2011Report (Other academic)
  • 146.
    Kronbichler, Martin
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Numerical Analysis.
    Kormann, Katharina
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    A generic interface for parallel cell-based finite element operator application2012In: Computers & Fluids, ISSN 0045-7930, E-ISSN 1879-0747, Vol. 63, p. 135-147Article in journal (Refereed)
  • 147. Kronbichler, Martin
    et al.
    Ljungkvist, Karl
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Multigrid for matrix-free high-order finite element computations on graphics processors2019In: ACM Transactions on Parallel Computing, ISSN 2329-4949, Vol. 6, no 1, p. 2:1-32, article id 2Article in journal (Refereed)
  • 148.
    Kruchinina, Anastasia
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Efficient Density Matrix Methods for Large Scale Electronic Structure Calculations2019Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Efficient and accurate methods for computing the density matrix are necessary to be able to perform large scale electronic structure calculations. For sufficiently sparse matrices, the computational cost of recursive polynomial expansions to construct the density matrix scales linearly with increasing system size. In this work, parameterless stopping criteria for recursive polynomial expansions are developed. The proposed stopping criteria automatically adapt to a change in the requested accuracy, perform at almost no additional cost and do not require any user-defined tolerances.

    Compared to the traditional diagonalization approach, in linear scaling methods molecular orbitals are not readily available. In this work, the interior eigenvalue problem for the Fock/Kohn-Sham matrix is coupled to the recursive polynomial expansions. The idea is to view the polynomial, obtained in the recursive expansion, as an eigenvalue filter, giving large separation between eigenvalues of interest. An efficient method for computation of homo and lumo eigenvectors is developed. Moreover, a method for computation of multiple eigenvectors around the homo-lumo gap is implemented and evaluated.

    An original method for inverse factorization of Hermitian positive definite matrices is developed in this work. Novel theoretical tools for analysis of the decay properties of matrix element magnitude in electronic structure calculations are proposed. Of particular interest is an inverse factor of the basis set overlap matrix required for the density matrix construction. It is shown that the proposed inverse factorization algorithm drastically reduces the communication cost compared to state-of-the-art methods.

    To perform large scale numerical tests, most of the proposed methods are implemented in the quantum chemistry program Ergo, also presented in this thesis. The recursive polynomial expansion in Ergo is parallelized using the Chunks and Tasks matrix library. It is shown that the communication cost per process of the recursive polynomial expansion implementation tends to a constant in a weak scaling setting.

    List of papers
    1. Parameterless stopping criteria for recursive density matrix expansions
    Open this publication in new window or tab >>Parameterless stopping criteria for recursive density matrix expansions
    2016 (English)In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 12, p. 5788-5802Article in journal (Refereed) Published
    National Category
    Computational Mathematics
    Identifiers
    urn:nbn:se:uu:diva-310710 (URN)10.1021/acs.jctc.6b00626 (DOI)000389866500011 ()
    Projects
    eSSENCE
    Available from: 2016-10-26 Created: 2016-12-19 Last updated: 2019-09-20Bibliographically approved
    2. On-the-fly computation of frontal orbitals in density matrix expansions
    Open this publication in new window or tab >>On-the-fly computation of frontal orbitals in density matrix expansions
    2018 (English)In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 14, p. 139-153Article in journal (Refereed) Published
    National Category
    Computational Mathematics
    Identifiers
    urn:nbn:se:uu:diva-338750 (URN)10.1021/acs.jctc.7b00968 (DOI)000419998300013 ()29193971 (PubMedID)
    Projects
    eSSENCE
    Available from: 2017-12-01 Created: 2018-01-12 Last updated: 2019-09-20Bibliographically approved
    3. Ergo: An open-source program for linear-scaling electronic structure calculations
    Open this publication in new window or tab >>Ergo: An open-source program for linear-scaling electronic structure calculations
    2018 (English)In: SoftwareX, E-ISSN 2352-7110, Vol. 7, p. 107-111Article in journal (Refereed) Published
    National Category
    Software Engineering
    Identifiers
    urn:nbn:se:uu:diva-348090 (URN)10.1016/j.softx.2018.03.005 (DOI)000457139300020 ()
    Projects
    eSSENCE
    Available from: 2018-04-05 Created: 2018-04-10 Last updated: 2019-09-20Bibliographically approved
    4. Localized inverse factorization
    Open this publication in new window or tab >>Localized inverse factorization
    2018 (English)In: Computing Research Repository, no 1812.04919Article in journal (Other academic) Submitted
    National Category
    Computational Mathematics
    Identifiers
    urn:nbn:se:uu:diva-381327 (URN)
    Projects
    eSSENCE
    Available from: 2018-12-12 Created: 2019-04-08 Last updated: 2019-09-20Bibliographically approved
    5. Efficient computation of the density matrix with error control on distributed computer systems
    Open this publication in new window or tab >>Efficient computation of the density matrix with error control on distributed computer systems
    2019 (English)In: Computing Research Repository, no 1909.12533Article in journal (Other academic) Submitted
    National Category
    Computational Mathematics Computer Sciences
    Identifiers
    urn:nbn:se:uu:diva-393386 (URN)
    Projects
    eSSENCE
    Available from: 2019-09-27 Created: 2019-09-20 Last updated: 2019-09-30Bibliographically approved
    6. Multiple eigenvectors around the homo–lumo gap as a cheap by-product in linear scaling electronic structure calculations
    Open this publication in new window or tab >>Multiple eigenvectors around the homo–lumo gap as a cheap by-product in linear scaling electronic structure calculations
    2019 (English)In: Computing Research Repository, no 1909.11662Article in journal (Other academic) Submitted
    National Category
    Computational Mathematics
    Identifiers
    urn:nbn:se:uu:diva-393385 (URN)
    Projects
    eSSENCE
    Available from: 2019-09-25 Created: 2019-09-20 Last updated: 2019-09-30Bibliographically approved
  • 149.
    Kruchinina, Anastasia
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Multiple eigenvectors around the homo–lumo gap as a cheap by-product in linear scaling electronic structure calculations2019In: Computing Research Repository, no 1909.11662Article in journal (Other academic)
  • 150.
    Kruchinina, Anastasia
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Rudberg, Elias
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Rubensson, Emanuel H.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Efficient computation of the density matrix with error control on distributed computer systems2019In: Computing Research Repository, no 1909.12533Article in journal (Other academic)
1234567 101 - 150 of 328
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