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Communication-efficient algorithms for numerical quantum dynamics
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.
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.
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.
2012 (English)In: Applied Parallel and Scientific Computing: Part II, Berlin: Springer-Verlag , 2012, 368-378 p.Conference paper, Published paper (Refereed)
Place, publisher, year, edition, pages
Berlin: Springer-Verlag , 2012. 368-378 p.
Series
Lecture Notes in Computer Science, 7134
National Category
Computer Science Computational Mathematics
Identifiers
URN: urn:nbn:se:uu:diva-135980DOI: 10.1007/978-3-642-28145-7_36ISI: 000309716000036ISBN: 978-3-642-28144-0 (print)OAI: oai:DiVA.org:uu-135980DiVA: diva2:375913
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: 2014-11-21Bibliographically approved
In thesis
1. Towards an adaptive solver for high-dimensional PDE problems on clusters of multicore processors
Open this publication in new window or tab >>Towards an adaptive solver for high-dimensional PDE problems on clusters of multicore processors
2012 (English)Licentiate thesis, comprehensive summary (Other academic)
Abstract [en]

Accurate numerical simulation of time-dependent phenomena in many spatial dimensions is a challenging computational task apparent in a vast range of application areas, for instance quantum dynamics, financial mathematics, systems biology and plasma physics. Particularly problematic is that the number of unknowns in the governing equations (the number of grid points) grows exponentially with the number of spatial dimensions introduced, often referred to as the curse of dimensionality. This limits the range of problems that we can solve, since the computational effort and requirements on memory storage directly depend on the number of unknowns for which to solve the equations.

In order to push the limit of tractable problems, we are developing an implementation framework, HAParaNDA, for high-dimensional PDE-problems. By using high-order accurate schemes and adaptive mesh refinement (AMR) in space, we aim at reducing the number of grid points used in the discretization, thereby enabling the solution of larger and higher-dimensional problems. Within the framework, we use structured grids for spatial discretization and a block-decomposition of the spatial domain for parallelization and load balancing. For integration in time, we use exponential integration, although the framework allows the flexibility of other integrators to be implemented as well. Exponential integrators using the Lanzcos or the Arnoldi algorithm has proven a succesful and efficient approach for large problems. Using a truncation of the Magnus expansion, we can attain high levels of accuracy in the solution.

As an example application, we have implemented a solver for the time-dependent Schrödinger equation using this framework. We provide scaling results for small and medium sized clusters of multicore nodes, and show that the solver fulfills the expected rate of convergence.

Place, publisher, year, edition, pages
Uppsala University, 2012
Series
Information technology licentiate theses: Licentiate theses from the Department of Information Technology, ISSN 1404-5117 ; 2012-003
National Category
Computer Science Computational Mathematics
Research subject
Scientific Computing
Identifiers
urn:nbn:se:uu:diva-169259 (URN)
Supervisors
Projects
eSSENCE
Available from: 2012-03-09 Created: 2012-02-25 Last updated: 2017-08-31Bibliographically approved
2. Efficient and Reliable Simulation of Quantum Molecular Dynamics
Open this publication in new window or tab >>Efficient and Reliable Simulation of Quantum Molecular Dynamics
2012 (English)Doctoral 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.

Place, publisher, year, edition, pages
Uppsala: Acta Universitatis Upsaliensis, 2012. 52 p.
Series
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology, ISSN 1651-6214 ; 970
Keyword
time-dependent Schrödinger equation, quantum optimal control, exponential integrators, spectral elements, radial basis functions, global error control and adaptivity, high-performance computing implementation
National Category
Computational Mathematics
Research subject
Scientific Computing with specialization in Numerical Analysis
Identifiers
urn:nbn:se:uu:diva-180251 (URN)978-91-554-8466-8 (ISBN)
Public defence
2012-10-19, Room 2446, Polacksbacken, Lägerhyddsvägen 2D, Uppsala, 10:00 (English)
Opponent
Supervisors
Projects
eSSENCE
Funder
eSSENCE - An eScience Collaboration
Available from: 2012-09-27 Created: 2012-09-01 Last updated: 2013-01-23Bibliographically approved
3. Adaptive Solvers for High-Dimensional PDE Problems on Clusters of Multicore Processors
Open this publication in new window or tab >>Adaptive Solvers for High-Dimensional PDE Problems on Clusters of Multicore Processors
2014 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Accurate numerical solution of time-dependent, high-dimensional partial differential equations (PDEs) usually requires efficient numerical techniques and massive-scale parallel computing. In this thesis, we implement and evaluate discretization schemes suited for PDEs of higher dimensionality, focusing on high order of accuracy and low computational cost.

Spatial discretization is particularly challenging in higher dimensions. The memory requirements for uniform grids quickly grow out of reach even on large-scale parallel computers. We utilize high-order discretization schemes and implement adaptive mesh refinement on structured hyperrectangular domains in order to reduce the required number of grid points and computational work. We allow for anisotropic (non-uniform) refinement by recursive bisection and show how to construct, manage and load balance such grids efficiently. In our numerical examples, we use finite difference schemes to discretize the PDEs. In the adaptive case we show how a stable discretization can be constructed using SBP-SAT operators. However, our adaptive mesh framework is general and other methods of discretization are viable.

For integration in time, we implement exponential integrators based on the Lanczos/Arnoldi iterative schemes for eigenvalue approximations. Using adaptive time stepping and a truncated Magnus expansion, we attain high levels of accuracy in the solution at low computational cost. We further investigate alternative implementations of the Lanczos algorithm with reduced communication costs.

As an example application problem, we have considered the time-dependent Schrödinger equation (TDSE). We present solvers and results for the solution of the TDSE on equidistant as well as adaptively refined Cartesian grids.

Place, publisher, year, edition, pages
Uppsala: Acta Universitatis Upsaliensis, 2014. 34 p.
Series
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology, ISSN 1651-6214 ; 1199
Keyword
adaptive mesh refinement, anisotropic refinement, exponential integrators, Lanczos' algorithm, hybrid parallelization, time-dependent Schrödinger equation
National Category
Computational Mathematics
Research subject
Scientific Computing
Identifiers
urn:nbn:se:uu:diva-234984 (URN)978-91-554-9095-9 (ISBN)
Public defence
2014-12-12, Room 2446, Polacksbacken, Lägerhyddsvägen 2, Uppsala, 10:15 (English)
Opponent
Supervisors
Projects
eSSENCE
Available from: 2014-11-21 Created: 2014-10-27 Last updated: 2015-02-03Bibliographically approved

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Gustafsson, MagnusKormann, KatharinaHolmgren, Sverker

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