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At least 1,513 records · Page 84

Working with Workflows: Highlights from 5 years Building Scientific Workflows

In 2006, the SciDAC Scientific Data Management (SDM) Center proposed to continue its work deploying leading edge data management and analysis capabilities to scientific applications. One of three thrust areas within the proposed center was focused on Scientific Process Automation (SPA) using workflow technology. As a founding member of the Kepler consortium [LAB+09], the SDM Center team was well positioned to begin deploying workflows immediately. We were also keenly aware of some of the deficiencies in Kepler when applied to high performance computing workflows, which allowed us to focus our research and development efforts on critical new capabilities which were ultimately integrated into the Kepler open source distribution, benefiting the entire community. Significant work was required to ensure Kepler was capable of supporting large-scale production runs for SciDAC applications. Our work on generic actors and templates have improved the portability of workflows across machines and provided a higher level of abstraction for workflow developers. Fault tolerance and provenance tracking were obvious areas for improvement within Kepler given the longevity and complexity of our target workflows. To monitor workflow execution, we developed and deployed a web-based dashboard. We then generalized this interface and released it so it could be deployed at other locations. Outreach has always been a primary focus of our work and we had many successful deployments across a number of scientific domains while continually publishing and presenting our work. This short paper describes our most significant accomplishments over the past 5 years. Additional information about the SDM Center can be found in the companion paper: The Scientific Data Management Center: Available Technologies and Highlights.

99 GENERAL AND MISCELLANEOUS↗

Localized Evaluation for Constructing Discrete Vector Fields

Topological abstractions offer a method to summarize the behavior of vector fields, but computing them robustly can be challenging due to numerical precision issues. One alternative is to represent the vector field using a discrete approach, which constructs a collection of pairs of simplices in the input mesh that satisfies criteria introduced by Forman's discrete Morse theory. While numerous approaches exist to compute pairs in the restricted case of the gradient of a scalar field, state-of-the-art algorithms for the general case of vector fields require expensive optimization procedures. This paper introduces a fast, novel approach for pairing simplices of two-dimensional, triangulated vector fields that do not vary in time. The key insight of our approach is that we can employ a local evaluation, inspired by the approach used to construct a discrete gradient field, where every simplex in a mesh is considered by no more than one of its vertices. Specifically, we observe that for any edge in the input mesh, we can uniquely assign an outward direction of flow. We can further expand this consistent notion of outward flow at each vertex, which corresponds to the concept of a downhill flow in the case of scalar fields. Working with outward flow enables a linear-time algorithm that processes the (outward) neighborhoods of each vertex one-by-one, similar to the approach used for scalar fields. Here, we couple our approach to constructing discrete vector fields with a method to extract, simplify, and visualize topological features. Empirical results on analytic and simulation data demonstrate drastic improvements in running time, produce features similar to the current state-of-the-art, and show the application of simplification to large, complex flows.

97 MATHEMATICS AND COMPUTING↗

Constructing compact and effective graphs for recommender systems via node and edge aggregations

Exploiting graphs for recommender systems has great potential to flexibly incorporate heterogeneous information for producing better recommendation results. As our baseline approach, we first introduce a naive graph-based recommendation method, which operates with a heterogeneous log-metadata graph constructed from user log and content metadata databases. Although the na ve graph-based recommendation method is simple, it allows us to take advantages of heterogeneous information and shows promising flexibility and recommendation accuracy. However, it often leads to extensive processing time due to the sheer size of the graphs constructed from entire user log and content metadata databases. In this paper, we propose node and edge aggregation approaches to constructing compact and e ective graphs called Factor-Item bipartite graphs by aggregating nodes and edges of a log-metadata graph. Furthermore, experimental results using real world datasets indicate that our approach can significantly reduce the size of graphs exploited for recommender systems without sacrificing the recommendation quality.

97 MATHEMATICS AND COMPUTING↗

Limits on Mode Coherence in Pulsating DA White Dwarfs Due to a Nonstatic Convection Zone

The standard theory of pulsations deals with the frequencies and growth rates of infinitesimal perturbations in a stellar model. Modes which are calculated to be linearly driven should increase their amplitudes exponentially with time; the fact that nearly constant amplitudes are usually observed is evidence that nonlinear mechanisms inhibit the growth of finite amplitude pulsations. Models predict that the mass of convection zones in pulsating hydrogen-atmosphere (DAV) white dwarfs is very sensitive to temperature (i.e., M CZ α T –90 eff ), leading to the possibility that even low-amplitude pulsators may experience significant nonlinear effects. In particular, the outer turning point of finite-amplitude g-mode pulsations can vary with the local surface temperature, producing a reflected wave that is out of phase with what is required for a standing wave. This can lead to a lack of coherence of the mode and a reduction in its global amplitude. In this paper we show that: (1) whether a mode is calculated to propagate to the base of the convection zone is an accurate predictor of its width in the Fourier spectrum, (2) the phase shifts produced by reflection from the outer turning point are large enough to produce significant damping, and (3) amplitudes and periods are predicted to increase from the blue edge to the middle of the instability strip, and subsequently decrease as the red edge is approached. Furthermore, this amplitude decrease is in agreement with the observational data while the period decrease has not yet been systematically studied.

79 ASTRONOMY AND ASTROPHYSICS↗

Molecular Dynamics Simulation and Analysis of Interfacial Water at Selected Sulfide Mineral Surfaces under Anaerobic Conditions

In this paper, we report on a molecular dynamics simulation (MDS) study of the behavior of interfacial water at selected sulfide mineral surfaces under anaerobic conditions. The study revealed the interfacial water structure and wetting characteristics of the pyrite (100) surface, galena (100) surface, chalcopyrite (012) surface, sphalerite (110) surface, and molybdenite surfaces (i.e., the face, armchair-edge, and zigzag-edge surfaces), including simulated contact angles, relative number density profiles, water dipole orientations, hydrogen-bonding, and residence times. For force fields of the metal and sulfur atoms in selected sulfide minerals used in the MDS, we used the universal force field (UFF) and another set of force fields optimized by quantum chemical calculations for interactions with interfacial water molecules at selected sulfide mineral surfaces. Simulation results for the structural and dynamic properties of interfacial water molecules indicate the natural hydrophobic character for the selected sulfide mineral surfaces under anaerobic conditions as well as the relatively weak hydrophobicity for the sphalerite (110) surface and two molybdenite edge surfaces. Part of the financial support for this study was provided by the U.S. Department of Energy (DOE) under Basic Science Grant No. DE-FG-03-93ER14315. The Division of Chemical Sciences, Geosciences, and Biosciences, Office of Basic Energy Sciences (BES), of the DOE, funded work performed by Liem X. Dang. Battelle operates Pacific Northwest National Laboratory for DOE. The calculations were carried out using computer resources provided by BES. The authors are grateful to Professor Tsun-Mei Chang for valuable discussions.

Jin, Jiaqi↗

How Does Metal Spin State Affect Electronic Communication in Mixed-Valence Dimers? Insights from Ultrafast Near-Infrared and Soft X-ray Transient Absorption Spectroscopy

Recent advancements in photocatalysis, photovoltaics, and quantum information science take advantage of electron spin, and determining how spin multiplicity affects electron transfer is key to understanding these phenomena. Here, in this study, we examine how metal spin state affects electronic communication in an organometallic mixed-valence dimer, ferrocenyl cobaltocenium ([Fe II Cp 2 Co III Cp 2 ] + ). This complex can be photoexcited from its low-spin singlet Fe II ground state to form intermediate-spin triplet Fe II and high-spin quintet Fe II excited states. Using femtosecond optical transient absorption (OTA) spectroscopy with visible (vis), near-infrared (NIR), and short-wave IR (SWIR) probes, supported by time-dependent density functional theory (TD-DFT) calculations, we measure Fe II Co III →Fe III Co II intervalence charge transfer (IVCT) bands in each of the Fe II spin states. Mulliken–Hush analysis of the excited-state IVCT bands was used to compute the electronic coupling between the metal centers in all three spin states, which increased as quintet < triplet < singlet. Meanwhile, the peak energy of the bands, and thus the ΔG of the IVCT transition, increased as triplet < quintet < singlet. Then, to directly probe the electronic structure at each metal center, we employed picosecond soft X-ray transient absorption (XTA) spectroscopy at the Fe and Co L 3 edges. Our results show that the low-spin and high-spin states of [Fe II Cp 2 Co III Cp 2 ] + are valence-localized, while the intermediate-spin state is partially delocalized. The differences in charge delocalization are attributed to differences in orbital occupation and geometry that affect the free energy and superexchange coupling.

Burke, John H. [Univ. of Illinois at Urbana-Champa↗

Li-Ion Localization and Energetics as a Function of Anode Structure

Here in this work, we study the effect of carbon composite anode structure on the localization and energetics of Li-ions. A computational molecular dynamics study is combined with experimental results from neutron scattering experiments to understand the effect of composite density, crystallite size, volume fraction of crystalline carbon, and ion loading on the nature of ion storage in novel, lignin-derived composite materials. In a recent work, we demonstrated that these carbon composites display a fundamentally different mechanism for Li-ion storage than traditional graphitic anodes. The edges of the crystalline and amorphous fragments of aromatic carbon that exist in these composites are terminated by hydrogen atoms, which play a crucial role in adsorption. In this work, we demonstrate how differences in composite structure due to changes in the processing conditions alter the type and extent of the interface between the amorphous and crystalline domains, thus impacting the nature of Li-ion storage. The effects of structural properties are evaluated using a suite of pair distribution functions as well as an original technique to extract archetypal structures, in the form of three-dimensional atomic density distributions, from highly disordered systems. The energetics of Li-ion binding are understood by relating changes in the energy and charge distributions to changes in structural properties. The distribution of Li-ion energies reveals that some structures lead to greater chemisorption, while others have greater physisorption. Carbon composites with a high volume fraction of small crystallites demonstrate the highest ion storage capacity because of the high interfacial area between the crystalline and amorphous domains. Finally, at these interfaces, stable H atoms, terminating the graphitic crystallites, provide favorable sites for reversible Li adsorption.

25 ENERGY STORAGE↗

Quantitative modeling of ICRF antennas with integrated time domain RF sheath and plasma physics

Significant efforts have been made to quantitatively benchmark the sheath sub-grid model used in our time-domain simulations of plasma-immersed antenna near fields, which includes highly detailed three-dimensional geometry, the presence of the slow wave, and the non-linear evolution of the sheath potential. We present both our quantitative benchmarking strategy, and results for the ITER antenna configuration, including detailed maps of electric field, and sheath potential along the entire antenna structure. Our method is based upon a time-domain linear plasma model, using the finite-difference electromagnetic Vorpal/Vsim software. This model has been augmented with a non-linear rf-sheath sub-grid model, which provides a self-consistent boundary condition for plasma current where it exists in proximity to metallic surfaces. Very early, this algorithm was designed and demonstrated to work on very complicated three-dimensional geometry, derived from CAD or other complex description of actual hardware, including ITER antennas. Initial work with the simulation model has also provided a confirmation of the existence of propagating slow waves in the low density edge region, which can significantly impact the strength of the rf-sheath potential, which is thought to contribute to impurity generation. Our sheath algorithm is based upon per-point lumped-circuit parameters for which we have estimates and general understanding, but which allow for some tuning and fitting. We are now engaged in a careful benchmarking of the algorithm against known analytic models and existing computational techniques to insure that the predictions of rf-sheath voltage are quantitatively consistent and believable, especially where slow waves share in the field with the fast wave. Currently in progress, an addition to the plasma force response accounting for the sheath potential, should enable the modeling of sheath plasma waves, a predicted additional root to the dispersion, existing at the plasma-metal interface. Our model is presently restricted to plasma in the vicinity of metallic (highly conducting) surfaces, however we report on a new effort to include thin and thick dielectric (poorly conducting) surfaces, which are of interest to both fusion devices and to industrial plasmas, where dielectric, or dielectric-coated vessels and geometry are heavily used.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Validating Intra-Plate Power Distributions in the Advanced Test Reactor

We report that the neutronics software, HELIOS, was validated in 2015 for performing core reload design and safety analysis of the Advanced Test Reactor. However, when HELIOS was benchmarked against historic fission-wire measurements (i.e., zero-power full-core measurements) a statistically resolved calculation-to-measurement bias was discovered. The azimuthal power along each fuel plate computed by HELIOS has consistently shown to under-predict measurements made by fission-wires in historic zero-power tests near the fuel element side-plates. It was hypothesized during the HELIOS software validation work, that this bias is attributable to local moderation in coolant vents in the side-plates axially just above and below the fission-wires on the fuel-plate edges. This work used detailed MCNP and MC21 models of the side-plate vents to test this hypothesis. By comparing the average azimuthal biases between HELIOS, and 2D and 3D MCNP models, and a 3D MC21 model, it was found that the HELIOS azimuthal bias is not due to the measurement.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

Spectral Equivalence of Low-Order Discretizations for High-Order H(curl) and H(div) Spaces

In this paper, we present spectral equivalence results for high-order tensor product edge- and face-based finite elements for the H(curl) and H(div) function spaces. Specifically, we show for certain choices of shape functions that the mass and stiffness matrices of the high-order elements are spectrally equivalent to those for an assembly of low-order elements on the associated Gauss--Lobatto--Legendre mesh. Based on this equivalence, efficient preconditioners can be designed with favorable computational complexity. Numerical results are presented which confirm the theory and demonstrate the benefits of the equivalence results for overlapping Schwarz preconditioners.

97 MATHEMATICS AND COMPUTING↗

2013 Gordon Research Conference, Inorganic reaction mechanisms, Galveston, TX, March 3-8 2013

The 2013 Gordon Conference on Inorganic Reaction Mechanisms will present cutting-edge research on the molecular aspects of inorganic reactions involving elements from throughout the periodic table and state-of-the art techniques that are used in the elucidation of reaction mechanisms. The Conference will feature a wide range of topics, such as homogeneous and heterogeneous catalysis, metallobiochemistry, electron-transfer in energy reactions, polymerization, nitrogen fixation, green chemistry, oxidation, solar conversion, alkane functionalization, organotransition metal chemistry, and computational chemistry. The talks will cover themes of current interest including energy, materials, and bioinorganic chemistry. Sections cover: Electron-Transfer in Energy Reactions; Catalytic Polymerization and Oxidation Chemistry; Kinetics and Spectroscopy of Heterogeneous Catalysts; Metal-Organic Chemistry and its Application in Synthesis; Green Energy Conversion;Organometallic Chemistry and Activation of Small Molecules; Advances in Kinetics Modeling and Green Chemistry; Metals in Biology and Disease; Frontiers in Catalytic Bond Activation and Cleavage.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Bismuth zinc vanadate, BiZn{sub 2}VO{sub 6}: New crystal structure type and electronic structure

We report a combined experimental and computational study of the crystal structure and electronic properties of bismuth zinc vanadate, BiZn{sub 2}VO{sub 6}, known for its visible light photocatalytic activity. The crystal structure has been solved from laboratory powder X-ray diffraction data using the repeated minimisations from random starting values method. BiZn{sub 2}VO{sub 6} adopts a new structure type, based on the following building blocks: corner- and edge-sharing ZnO{sub 4} tetrahedra, ZnO{sub 6} octahedra and VO{sub 4} tetrahedra, and Bi{sub 2}O{sub 12} dimers. It is the only known member of the BiM{sub 2}AO{sub 6} (M=Pb, Ca, Cd, Mn, Zn, Mg, Cu; A=V, P, As) family which does not appear to be structurally closely related to others. The electronic structure of BiZn{sub 2}VO{sub 6}, calculated by DFT methods, shows that it is an indirect gap semiconductor with a calculated band gap of 1.6 eV, which compares favourably to the experimentally measured value of 2.4 eV. - Graphical abstract: The crystal structure of BiZn{sub 2}VO{sub 6}, a new structure type in the BiM{sub 2}AO{sub 6} (M=Mg, Ca, Cd, Cu, Pb, Mn, Zn; A=V, P, As) family. - Highlights: • Structure solution from PXRD data by repeated minimisations from random starting values. • New structure type in the BiM{sub 2}AO{sub 6} (M=Pb, Ca, Cd, Mn, Zn, Mg, Cu; A=V, P, As) family. • Electronic structure calculation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Theoretical Perspective on Operando Spectroscopy of Fluxional Nanocatalysts

Improvements in operando spectroscopy have enabled the catalysis community to investigate the dynamic nature of catalysts under operating conditions with increasing detail. Still, the highly dynamic nature of some catalysts, such as fluxional supported subnano clusters, presents a formidable challenge even for the most state-of-the-art techniques. Here, the reason is that such fluxional catalytic interfaces contain a variety of thermally accessible states. Operando spectroscopies used in catalysis generally fall into two categories: ensemble-based techniques, which provide spectra containing the signals of the entire ensemble of states of the catalyst and are not necessarily dominated by the most active species, and localized techniques, which provide atomistic-level information about the dynamics of active sites in a very small area, which might not include the most active species. Combining many different kinds of techniques can provide detailed insight; however, we propose that effective utilization of specific computational techniques and approaches within the fluxionality paradigm can fill the gap and enable atomistic characterization of the most relevant catalytic sites.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Potential design problems for ITER fusion device

The international thermonuclear experimental reactor (ITER) is a worldwide project currently being built in France for the demonstration of the feasibility of thermonuclear technologies for future realization of successful commercial fusion energy. ITER is of the tokamak based design using strong magnetic fields to confine the very hot plasma needed to induce the fusion reaction. Tokamak devices are currently the front leading designs. Building a successful magnetic fusion device for energy production is of great challenge. A key obstacle to such design is the performance during abnormal events including plasma disruptions and so-called edge-localized modes (ELMs). In these events, a massive and sudden release of energy occurs quickly, due to loss of full or partial plasma confinement, leading to very high transient power loads on the reactor surface boundaries. A successful reactor design should tolerate several of these transient events without serious damages such as melting and vaporization of the structure. This paper highlights, through comprehensive state-of-the-art computer simulation of the entire ITER interior design during such transient events, e.g., ELMs occurring at normal operation and disruptions during abnormal operation, potential serious problems with current plasma facing components (PFCs) design. The HEIGHTS computer package is used in these simulations. The ITER reactor design was simulated in full and exact 3D geometry including all known relevant physical processes involved during these transient events. The current ITER divertor design may not work properly and may requires significant modifications or new innovative design to prevent serious damage and to ensure successful operation.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Explicit formulae for Chern-Simons invariants of the twist-knot orbifolds and edge polynomials of twist knots

We calculate the Chern-Simons invariants of twist-knot orbifolds using the Schläfli formula for the generalized Chern-Simons function on the family of twist knot cone-manifold structures. Following the general instruction of Hilden, Lozano, and Montesinos-Amilibia, we here present concrete formulae and calculations. We use the Pythagorean Theorem, which was used by Ham, Mednykh and Petrov, to relate the complex length of the longitude and the complex distance between the two axes fixed by two generators. As an application, we calculate the Chern-Simons invariants of cyclic coverings of the hyperbolic twist-knot orbifolds. We also derive some interesting results. The explicit formulae of the A-polynomials of twist knots are obtained from the complex distance polynomials. Hence the edge polynomials corresponding to the edges of the Newton polygons of the A-polynomials of twist knots can be obtained. In particular, the number of boundary components of every incompressible surface corresponding to slope −4n+2 turns out to be 2. Bibliography: 39 titles. (paper)

97 MATHEMATICS AND COMPUTING↗

Numerical error analysis of SOLPS-ITER simulations of EAST

Abstract Plasma edge simulations with codes like SOLPS-ITER are widely employed to interpret fusion experiments. However, numerical errors appearing in such simulations are rarely investigated, despite their potential large impact on simulation results. These errors consist of the statistical error and the bias, both resulting from the finite number of employed EIRENE Monte Carlo particles and incomplete convergence, and the discretization error due to the finite resolution of the computational grids. In this contribution, the resulting numerical errors on simulations of pure deuterium and neon seeded H-mode EAST discharges are examined. The statistical error can be kept small compared to other numerical error contributions by averaging the plasma profiles. This allows investigating the bias and discretization errors using Richardson extrapolation. It is shown that grid refinement and the number of employed Monte Carlo particles have the largest influence on the result, in agreement with similar studies of an ITER deuterium case. For the first time, numerical error bars on the entire simulated target profiles are determined showing that the largest numerical error is 17.9%, mainly due to the plasma grid discretization. On top, also numerical errors on simulated neutral pressures are investigated in detail, for which the statistical error is dominant. The analysis demonstrates which setup is needed to keep numerical errors limited: the SOLPS-ITER averaging procedure should be employed including enough EIRENE particles, and the involved grids should be sufficiently refined to reduce discretization errors.

Boeyaert, Dieter (ORCID:0000000309208660)↗

Calibrating Bayesian generative machine learning for Bayesiamplification

Recently, combinations of generative and Bayesian deep learning have been introduced in particle physics for both fast detector simulation and inference tasks. These neural networks aim to quantify the uncertainty on the generated distribution originating from limited training statistics. The interpretation of a distribution-wide uncertainty however remains ill-defined. We show a clear scheme for quantifying the calibration of Bayesian generative machine learning models. For a Continuous Normalizing Flow applied to a low-dimensional toy example, we evaluate the calibration of Bayesian uncertainties from either a mean-field Gaussian weight posterior, or Monte Carlo sampling network weights, to gauge their behaviour on unsteady distribution edges. Well calibrated uncertainties can then be used to roughly estimate the number of uncorrelated truth samples that are equivalent to the generated sample and clearly indicate data amplification for smooth features of the distribution.

97 MATHEMATICS AND COMPUTING↗

Convex Relaxations of the Network Flow Problem Under Cycle Constraints

In this paper, we consider the problem of optimizing the flows in a lossless flow network with additional nonconvex cycle constraints on nodal variables; such constraints appear in several applications, including electric power, water distribution, and natural gas networks. This problem is a nonconvex version of the minimum-cost network flow problem (NFP), and to solve it, we propose three different approaches. One approach is based on solving a convex approximation of the problem, obtained by augmenting the cost function with an entropy-like term to relax the nonconvex constraints. We show that the approximation error, for which we give an upper bound, can be made small enough for practical use. An alternative approach is to solve the classical NFP, that is, without the cycle constraints, and solve a separate optimization problem afterwards in order to recover the actual flows satisfying the cycle constraints; the solution of this separate problem maximizes the individual entropies of the cycles. The third approach is based on replacing the nonconvex constraint set with a convex inner approximation, which yields a suboptimal solution for the cyclic networks with each edge belonging to at most two cycles. We validate the practical usefulness of the theoretical results through numerical examples, in which we study the standard test systems for water and electric power distribution networks.

42 ENGINEERING↗