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Multilevel B-Spline Repulsive Energy in Nanomodeling of Graphenes

Journal of Surface Engineered Materials and Advanced Technology 2014年第2期4卷 75-86页

作者： Maharavo Randrianarivony Virtual Material Design Fraunhofer Institute for Algorithms and Scientific Computing SCAI Schloss Birlinghoven Sankt Augustin Germany

Quantum energies which are used in applications are usually composed of repulsive and attractive terms. The objective of this study is to use an accurate and efficient fitting of the repulsive energy instead of using standard parametrizations. The investigation is based on Density Functional Theory and Tight Binding simulations. Our objective is not only to capture the values of the repulsive terms but also to efficiently reproduce the elastic properties and the forces. The elasticity values determine the rigidity of a material when some traction or load is applied on it. The pair-potential is based on an exponential term corrected by B-spline terms. In order to accelerate the computations, one uses a hierarchical optimization for the B-splines on different levels. Carbon graphenes constitute the configurations used in the simulations. We report on some results to show the efficiency of the B-splines on different levels.

关键词： Repulsive Potential B-Spline Force Elastic Stress Hierarchy

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On DFT Molecular Simulation for Non-Adaptive Kernel Approximation

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Advances in Materials Physics and Chemistry 2014年第6期4卷 105-115页

作者： Maharavo Randrianarivony Virtual Material Design Fraunhofer Institute for Algorithms and Scientific Computing SCAI Schloss Birlinghoven Sankt Augustin Germany

Using accurate quantum energy computations in nanotechnologic applications is usually very computationally intensive. That makes it difficult to apply in subsequent quantum simulation. In this paper, we present some preliminary results pertaining to stochastic methods for alleviating the numerical expense of quantum estimations. The initial information about the quantum energy originates from the Density Functional Theory. The determination of the parameters is performed by using methods stemming from machine learning. We survey the covariance method using marginal likelihood for the statistical simulation. More emphasis is put at the position of equilibrium where the total atomic energy attains its minimum. The originally intensive data can be reproduced efficiently without losing accuracy. A significant acceleration gain is perceived by using the proposed method.

关键词： DFT Energy Stochastic Covariance Hyperparameter

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VERCE Delivers a Productive E-science Environment for Seismology Research

VERCE Delivers a Productive E-science Environment for Seismo...

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IEEE International Conference on e-Science and Grid computing

作者： Malcolm Atkinson Michele Carpené Emanuele Casarotti Steffen Claus Rosa Filgueira Anton Frank Michelle Galea Tom Garth André Gemünd Heiner Igel Iraklis Klampanos Amrey Krause Lion Krischer Siew Hoon Leong Federica Magnoni Jonas Matser Alberto Michelini Andreas Rietbrock Horst Schwichtenberg Alessandro Spinuso Jean-Pierre Vilotte University of Edinburgh UK Supercomputing Applications and Innovation Department (CINECA) Italy Istituto Nazionale di Geofisica e Vulcanologia (INGV) Italy Fraunhofer Institute for Algorithms and Scientific Computing (SCAI) Germany The University of Edinburgh Edinburgh Edinburgh GB Leibniz Supercomputing Centre Germany University of Liverpool UK Ludwig-Maximilians-University Germany Royal Netherlands Meteorological Institute (KNMI) The Netherlands Institut de Physique du Globe de Paris (IPGP) France

The VERCE project has pioneered an e-Infrastructure to support researchers using established simulation codes on high-performance computers in conjunction with multiple sources of observational data. This is accessed and organised via the VERCE science gateway that makes it convenient for seismologists to use these resources from any location via the Internet. Their data handling is made flexible and scalable by two Python libraries, ObsPy and dispel4py and by data services delivered by ORFEUS and EUDAT. Provenance driven tools enable rapid exploration of results and of the relationships between data, which accelerates understanding and method improvement. These powerful facilities are integrated and draw on many other e-Infrastructures. This paper presents the motivation for building such systems, it reviews how solid-Earth scientists can make significant research progress using them and explains the architecture and mechanisms that make their construction and operation achievable. We conclude with a summary of the achievements to date and identify the crucial steps needed to extend the capabilities for seismologists, for solid-Earth scientists and for similar disciplines.

关键词： Computational modeling Data models Logic gates Context Earthquakes Analytical models Libraries

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A bond order dissection ANOVA approach for efficient electronic structure calculations

Lecture Notes in Computational Science and Engineering

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Lecture Notes in Computational Science and Engineering 2014年 102卷 211-235页

作者： Griebel, Michael Hamaekers, Jan Heber, Frederik Institute for Numerical Simulation University of Bonn Wegelerstr. 6 Bonn53115 Germany Fraunhofer Institute for Algorithms and Scientific Computing SCAI Schloss Birlinghoven Sankt Augustin53754 Germany

In this article, we present a new decomposition approach for the efficient approximate calculation of the electronic structure problem for molecules. It is based on a dimension-wise decomposition of the space the underlying Schrödinger equation lives in, i.e. 3(M+N), where M is the number of nuclei and N is the number of electrons. This decomposition is similar to the ANOVA-approach (analysis of variance) which is well-known in statistics. It represents the energy as a finite sum of contributions which depend on the positions of single nuclei, of pairs of nuclei, of triples of nuclei, and so on. Under the assumption of locality of electronicwave functions, the higher order terms in this expansion decay rapidly and may therefore be omitted. Furthermore, additional terms are eliminated according to the bonding structure of the molecule. This way, only the calculation of the electronic structure of local parts, i.e. small subsystems of the overall system, is necessary to approximate the total ground state energy. To determine the required subsystems, we employ molecular graph theory combined with molecular bonding knowledge. In principle, the local electronic subproblems may be approximately evaluated with whatever technique is appropriate, e.g. HF, CC, CI, or DFT. From these local energies, the total energy of the overall system is then approximately put together in a telescoping sum like fashion. Thus, if the size of the local subproblems is independent of the size of the overall molecular system, linear scaling is directly obtained. We discuss the details of our new approach and apply it to both, various small test systems and interferon alpha as an example of a large biomolecule. © Springer International Publishing Switzerland 2014.

关键词： Analysis of variance (ANOVA)

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Consideration of Process-Related Variations of Spot Welded Joints

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ATZ worldwide 2013年第12期115卷 44-49页

作者： Sommer, Silke Steffes-lai, Daniela Clees, Tanja Fraunhofer Institute for Mechanics of Materials IWM Freiburg Germany Fraunhofer Institute for Algorithms and Scientific Computing SCAI Sankt Augustin Germany

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Using LAMA for efficient AMG on hybrid clusters

Using LAMA for efficient AMG on hybrid clusters

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作者： Kraus, Jiri Förster, Malte Brandes, Thomas Soddemann, Thomas Fraunhofer Institute for Algorithms and Scientific Computing SCAI Schloss Birlinghoven 53754 Sankt Augustin Germany

In this paper, we describe the implementation of an AMG solver for a hybrid cluster that exploits distributed and shared memory parallelization and uses the available GPU accelerators on each node. This solver has been written by using LAMA (Library for Accelerated Math Applications). This library does not only provide an easy-to-use framework for solvers that might run on different devices with different matrix formats, but also comes with features to optimize and hide communication and memory transfers between CPUs and GPUs. These features are explained and their impact on the efficiency of the AMG solver is shown in this paper. The benchmark results show that an efficient use of hybrid clusters is even possible for multi-level methods like AMG where fast solutions are needed on all levels for multiple problem sizes. © 2012 Springer-Verlag.

关键词： Program processors

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Preconditioning for efficiently applying algebraic multigrid in fully implicit reservoir simulations

Preconditioning for efficiently applying algebraic multigrid...

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SPE Reservoir Simulation Symposium 2013

作者： Gries, Sebastian Stüben, Klaus Brown, Geoffrey L. Chen, Dingjun Collins, David A. Fraunhofer Institute for Algorithms and Scientific Computing SCAI Germany Computer Modelling Group Ltd. Canada

ISBN: (纸本)9781627480246

Fully implicit petroleum reservoir simulations result in huge, often very ill-conditioned linear systems of equations to solve for different unknowns, for example, pressure and saturations. It is well known that the full system matrix contains both hyperbolic as well as nearly elliptic sub-systems. Since the solution of the coupled system is mainly determined by the solution of their elliptic (typically pressure) components, (CPR-type) two-stage preconditioning methods still belong to the most popular approaches to tackle such coupled systems. After a suitable extraction and decoupling, the numerically most costly step in such two-stage methods consists in solving these elliptic sub-systems. It is known that algebraic multigrid (AMG) provides a technique to solve elliptic linear equations very efficiently. The main advantage of AMG-based solvers - their numerical scalability - makes them particularly efficient for solving huge linear systems. Depending on the application, the system's properties range from simple to highly indefinite. Unfortunately decoupling pressure and saturation related parts may introduce further difficulties. Consequently, in complex industrial simulations, the application of AMG to elliptic sub-systems might not be straightforward. In fact, an important goal in defining an efficient two-stage preconditioning strategy consists in extracting elliptic sub-systems that are suitable for an efficient AMG solution and, at the same time, ensure a fast overall convergence of the two-stage approach. The importance of this will be demonstrated for several industrial cases. In particular, some of these cases are very hard to solve by AMG if applied in a standard way. Preliminary results for a CPR-type coupling of SAMG to CMG's PARASOL, a variable degree variable ordering ILU preconditioner using FGMRES, are compared to using PARASOL by itself. Alternative preconditioning operators will be presented giving elliptic sub-systems which are not only more suit

关键词： Iterative methods

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Belief - A semiautomatic workflow for BEL network creation 6

Belief - A semiautomatic workflow for BEL network creation

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6th International Symposium on Semantic Mining in Biomedicine, SMBM 2014

作者： Fluck, Juliane Madan, Sumit Ansari, Sam Szostak, Justyna Hoeng, Julia Zimmermann, Marc Hofmann-Apitius, Martin Peitsc, Manuel C. Fraunhofer Institute for Algorithms and Scientific Computing Schloss Birlinghoven Sankt Augustin Germany Philip Morris International R&D Philip Morris Products S.A. Quai Jeanrenaud 5 Neuchâtel2000 Switzerland BonnPAachen International Centre for Information Technology Dahlmannstr. 2 Bonn Germany

In order to build networks for systems biology from the literature an UIMA based extraction workflow using various named entity recognition processes and different relation extraction methods has been composed. The Unstructured Information Management architecture (UIMA) is a Java- based framework that allows assembling complicated workflows from a set of NLP components. The new system is processing scientific articles and is writing the open-access biological expression language (BEL) as output. BEL is a machine and human readable language with defined knowledge statements that can be used for knowledge representation, causal reasoning, and hypothesis generation. In order to curate the automatically derived BEL statements, our workflow integrates a curation interface that provides access to BEL statements generated by text mining and that integrates supporting information to facilitate manual curation. By using the semi-automated curation pipeline, expert time to model relevant causal relationships in BEL could be significantly reduced. In this paper the UIMA workflow and key features of the curation interface are described. © 2014 SMBM 2014 - Proceedings of the 6th International Symposium on Semantic Mining in Biomedicine. All rights reserved.

关键词： Knowledge representation

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Multi-objective optimization and stochastic analysis in focused ultrasonic therapy simulation

Multi-objective optimization and stochastic analysis in focu...

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3rd International Conference on Simulation and Modeling Methodologies, Technologies and Applications, SIMULTECH 2013

作者： Clees, T. Hornung, N. Nikitin, I. Nikitina, L. Steffes-lai, D. Fraunhofer Institute for Algorithms and Scientific Computing Sankt Augustin Germany

ISBN: (纸本)9789898565693

We present new results in stochastic multi-objective optimization applied to focused ultrasonic therapy planning. This type of non-invasive therapy uses focused ultrasound for the destruction of tumor cells and magnetic resonance tomography for identification of tumor volume and healthy organs. During the therapy planning the treatment parameters, such as frequency and intensity of ultrasound, are adjusted to achieve maximal tumor destruction and minimal influence to the healthy organs. For this purpose multi-objective optimization is used. RBF metamodeling is employed for continuous representation of discretely sampled results of numerical simulation and for evaluation of inherent uncertainties. We apply two algorithms for multi-objective optimization capable of non-convex Pareto front detection in the considered problem. Cross-validation procedure and sensitivity analysis are used for estimation of uncertainties. A realistic application case demonstrates the efficiency of the approach.

关键词： Multiobjective optimization

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Efficient quantile estimators for river bed morphodynamics

Efficient quantile estimators for river bed morphodynamics

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3rd International Conference on Simulation and Modeling Methodologies, Technologies and Applications, SIMULTECH 2013

作者： Clees, T. Nikitin, I. Nikitina, L. Pott, S. Fraunhofer Institute for Algorithms and Scientific Computing Sankt Augustin Germany

ISBN: (纸本)9789898565693

The large impact of civil water engineering to nature and society imposes high requirements for the precision of numerical simulations used in planning and evaluation of river engineering concepts. In particular, coupled morphodynamic - hydrodynamic simulation uses models of river bed evolution possessing uncertain parameters. The sources of uncertainty can be the natural variability, the deficient description of the physical processes in the model and the imprecision of the model parameters. The propagation of these uncertainties to the variance of the model result can be quantified with the aid of stochastic analysis. Precise evaluation of stochastic characteristics normally requires a huge amount of samples, which can be provided by surrogate-based modeling of simulation results. In this paper we present our advances in quantile estimation of morphodynamic simulations of river bed evolution. We use metamodeling of bulky simulation results with radial basis functions (RBF), quasi-Monte Carlo sampling (QMC) and efficient quantile estimator (QE). Four different quantile estimators have been tested. A realistic application case is used to demonstrate the efficiency of the approach.

关键词： Monte Carlo methods

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