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The octet rule in chemical space: generating virtual molecules

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arXiv 2017年

作者： Hamaekers, Rafel Maaß, Astrid Hamaekers, Jan Fraunhofer Institute Algorithms and Scientific Computing SCAI Schloss Birlinghoven Sankt AugustinD-53754 Germany

We present a generator of virtual molecules that selects valid chem- istry on the basis of the octet rule. Also, we introduce a mesomer group key that allows a fast detection of duplicates in the generated *** to existing approaches, our model is simpler and faster, generates new chemistry and avoids invalid chemistry. Its versatility is illustrated by the correct generation of molecules containing third-row elements and a surprisingly adept handling of complex boron chem- *** any empirical parameters, our model is designed to be valid also in unexplored regions of chemical space. One first unex- pected finding is the high prevalence of dipolar structures among gen- erated molecules. Copyright © 2017, The Authors. All rights reserved.

关键词： Molecules

DARE: A Reflective Platform Designed to Enable Agile Data-Driven Research on the Cloud

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DARE: A Reflective Platform Designed to Enable Agile Data-Dr...

IEEE International Conference on e-Science and Grid computing

作者： Iraklis Klampanos Athanasios Davvetas André Gemünd Malcolm Atkinson Antonios Koukourikos Rosa Filgueira Amrey Krause Alessandro Spinuso Angelos Charalambidis Federica Magnoni Emanuele Casarotti Christian Pagé Mike Lindner Andreas Ikonomopoulos Vangelis Karkaletsis Institute of Informatics and Telecommunications NCSR "Demokritos" Greece Fraunhofer Institute for Algorithms and Scientific Computing School of Informatics The University of Edinburgh UK NCSR "Demokritos" EPCC The University of Edinburgh UK Koninklijk Nederlands Meteorologisch Instituut (KNMI) The Netherlands Istituto Nazionale Geofisica e Vulcanologia (INGV) Italy Centre Européen de Recherche et de Formation Avancée en Calcul Scientifique Karlsruher Institut f??r Technologie (KIT) Germany Institute of Nuclear & Radiological Sciences and Technology Energy & Safety NCSR "Demokritos" Greece

ISBN: (数字)9781728124513

ISBN: (纸本)9781728124520

The DARE platform has been designed to help research developers deliver user-facing applications and solutions over diverse underlying e-infrastructures, data and computational contexts. The platform is Cloud-ready, and relies on the exposure of APIs, which are suitable for raising the abstraction level and hiding complexity. At its core, the platform implements the cataloguing and execution of fine-grained and Python-based dispel4py workflows as services. Reflection is achieved via a logical knowledge base, comprising multiple internal catalogues, registries and semantics, while it supports persistent and pervasive data provenance. This paper presents design and implementation aspects of the DARE platform, as well as it provides directions for future development.

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Kernel-based stochastic collocation for the random two-phase navier-stokes equations

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arXiv 2018年

作者： Griebel, M. Rieger, C. Zaspel, P. Institute for Numerical Simulation Bonn University Endenicher Allee 19b BonnD-53115 Fraunhofer Institute for Algorithms and Scientific Computing Scai Schloss Birlinghoven Sankt AugustinD-53754 Department of Mathematics Rwth Aachen University Schinkelstr. 2 AachenD-52062 Department of Mathematics and Computer Science University of Basel Spiegelgasse 1 Basel4051

In this work, we apply stochastic collocation methods with radial kernel basis functions for an uncertainty quantification of the random incompressible two-phase Navier-Stokes equations. Our approach is non-intrusive and we use the existing fluid dynamics solver NaSt3DGPF to solve the incompressible two-phase Navier-Stokes equation for each given realization. We are able to empirically show that the resulting kernel-based stochastic collocation is highly competitive in this setting and even outperforms some other standard methods. Copyright © 2018, The Authors. All rights reserved.

关键词： Viscous flow

Sparse Grids and Applications - Munich 2012

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2016年

作者： Jochen Garcke Dirk Pflger

ISBN: (纸本)9783319381534

Sparse grids have gained increasing interest in recent years for the numerical treatment of high-dimensional problems. Whereas classical numerical discretization schemes fail in more than three or four dimensions, sparse grids make it possible to overcome the curse of dimensionality to some degree, extending the number of dimensions that can be dealt with. This volume of LNCSE collects the papers from the proceedings of the second workshop on sparse grids and applications, demonstrating once again the importance of this numerical discretization scheme. The selected articles present recent advances on the numerical analysis of sparse grids as well as efficient data structures, and the range of applications extends to uncertainty quantification settings and clustering, to name but a few examples.

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Orbital-enriched flat-top partition of unity method for the Schrödinger eigenproblem

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arXiv 2018年

作者： Albrecht, Clelia Klaar, Constanze Pask, John Ernest Schweitzer, Marc Alexander Sukumar, N. Ziegenhagel, Albert Fraunhofer Institute for Algorithms and Scientific Computing SCAI Schloss Birlinghoven Sankt Augustin53757 Germany Physics Division Lawrence Livermore National Laboratory 7000 East Avenue LivermoreCA94550 United States Institute for Numerical Simulation Rheinische Friedrich-Wilhelms-Universität Wegelerstr. 6 Bonn53115 Germany Department of Civil and Environmental Engineering University of California DavisCA95616 United States

Quantum mechanical calculations require the repeated solution of a Schrödinger equation for the wavefunctions of the system, from which materials properties follow. Recent work has shown the effectiveness of enriched finite element type Galerkin methods at significantly reducing the degrees of freedom required to obtain accurate solutions. However, time to solution has been adversely affected by the need to solve a generalized rather than standard eigenvalue problem and the ill-conditioning of associated systems matrices. In this work, we address both issues by proposing a stable and efficient orbital-enriched partition of unity method to solve the Schrödinger boundary-value problem in a parallelepiped unit cell subject to Bloch-periodic boundary conditions. In the proposed partition of unity method, the three-dimensional domain is covered by overlapping patches, with a compactly-supported weight function associated with each patch. A key ingredient in our approach is the use of non-negative weight functions that possess the flat-top property, i.e., each weight function is identically equal to unity over some finite subset of its support. This flattop property provides a pathway to devise a stable approximation over the whole domain. On each patch, we use p-th degree orthogonal (Legendre) polynomials that ensure p-th order completeness, and in addition include eigenfunctions of the radial Schrödinger equation. Furthermore, we adopt a variational lumping approach to construct a (block-)diagonal overlap matrix that yields a standard eigenvalue problem for which there exist efficient eigensolvers. The accuracy, stability, and efficiency of the proposed method is demonstrated for the Schrödinger equation with a harmonic potential as well as a localized Gaussian potential. We show that the proposed approach delivers optimal rates of convergence in the energy, and the use of orbital enrichment significantly reduces the number of degrees of freedom for a given desired accu

关键词： Eigenvalues and eigenfunctions

ATK-ForceField: A new generation molecular dynamics software package

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arXiv 2017年

作者： Schneider, Julian Hamaekers, Jan Chill, Samuel T. Smidstrup, Søren Bulin, Johannes Thesen, Ralph Blom, Anders Stokbro, Kurt QuantumWise A/S Fruebjergvej 3 CopenhagenDK-2100 Denmark Fraunhofer Institute for Algorithms and Scientific Computing SCAI Schloss Birlinghoven Sankt Augustin53754 Germany

ATK-ForceField is a software package for atomistic simulations using classical interatomic potentials. It is implemented as a part of the Atomistix ToolKit (ATK), which is a Python programming environment that makes it easy to create and analyze both standard and highly customized simulations. This paper will focus on the atomic interaction potentials, molecular dynamics, and geometry optimization features of the software, however, many more advanced modeling features are available. The implementation details of these algorithms and their computational performance will be shown. We present three illustrative examples of the types of calculations that are possible with ATK-ForceField: modeling thermal transport properties in a silicon germanium crystal, vapor deposition of selenium molecules on a selenium surface, and a simulation of creep in a copper polycrystal. Copyright © 2017, The Authors. All rights reserved.

关键词： Software packages

A representer theorem for deep kernel learning

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arXiv 2017年

作者： Bohn, Bastian Griebel, Michael Rieger, Christian 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 paper we provide a finite-sample and an infinite-sample representer theorem for the concatenation of (linear combinations of) kernel functions of reproducing kernel Hilbert spaces. These results serve as mathematical foundation for the analysis of machine learning algorithms based on compositions of functions. As a direct consequence in the finite-sample case, the corresponding infinite-dimensional minimization problems can be recast into (nonlinear) finite-dimensional minimization problems, which can be tackled with nonlinear optimization algorithms. Moreover, we show how concatenated machine learning problems can be reformulated as neural networks and how our representer theorem applies to a broad class of state-of-the-art deep learning methods. Copyright © 2017, The Authors. All rights reserved.

关键词： Sampling

Benchmark gas distribution network for cross-sectoral applications

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Benchmark gas distribution network for cross-sectoral applic...

International Energy and Sustainability Conference (IESC)

作者： Christian Brosig Silvan Fassbender Eberhard Waffenschmidt Sebastian Janocha Bernhard Klaassen Cologne Institute of Renewable Energy (ClRE) Cologne University of Applied Sciences Cologne Germany Rheinische NETZGesellschaft mbH (RNG) Cologne Germany Fraunhofer Institute for Algorithms and Scientific Computing SCAI Sankt Augustin Germany

Cross-sectoral coupling of energy systems could provide the necessary flexibility for future energy systems with a high share of renewable energies. The gas grid implies large storage capacities and thus promises an economically attractive balance for fluctuating energy sources. A benchmark gas distribution network, coupled to the CIGRE benchmark network for electricity is presented within this paper, to universally investigate the impacts on gas grid infrastructure. The network includes interconnected meshed and radial topologies for both low and medium pressure gas networks. They have been synthesized from existing real networks in cooperation with the Rheinische NETZGesellschaft mbH. Applications range from analyzing network impacts of widespread CHP or fuel cell implementation, over comparing the cost-effectiveness of different future pathways between expansion and decommissioning of the gas grid network, to analyzing the impacts of distributed injection of renewable gas. The overall aim is to build a complete network benchmark for an integral cross-sectoral energy system including also heat.

关键词： Steel Benchmark testing Fuel cells Hydrogen Cogeneration Regulators Couplings

Static spherically symmetric solutions of Einstein field equations with radial dark matter

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arXiv 2017年

作者： Nikitin, Igor Department of High Performance Analytics Fraunhofer Institute for Algorithms and Scientific Computing Schloss Birlinghoven Sankt Augustin53757 Germany

We study a static spherically symmetric problem with a black hole and radially directed geodesic flows of dark matter. The obtained solutions have the following properties. At large distances, the gravitational field produces constant velocities of circular motion, i.e., flat rotation curves. At smaller distances, the field switches to Newtonian regime, then to Schwarzschild regime. Deviations from Schwarzschild regime start below the gravitational radius. The dark matter prevents the creation of event horizon, instead, a spherical region possessing extremely large redshift is created. The structure of space-time for the obtained solutions is investigated and the implications for the models of the galaxies are discussed. Copyright © 2017, The Authors. All rights reserved.

关键词： Gravitation