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At least 1,117 records · Page 62

New interpretation of ion cyclotron emission from a tokamak

The tempting interpretation of ion cyclotron emission in terms of compressional Alfvén eigenmodes involving energetic ions is inconsistent with recent TCV experimental observations in some important aspects, such as (i) the perturbed poloidal field is exceeding the parallel perturbed magnetic field significantly, and (ii) the modes are near cyclotron harmonic and exhibit Alfvèn scaling of their frequency. We show that these characteristics can be explained by considering finite Larmor radius effects of thermal ions in shear Alfvén waves that allow such waves to exist well above the ion cyclotron frequency in the form of wave-packets bouncing within the plasma volume.

Plasma waves↗

Electric field and turbulence in global Braginskii simulations across the ASDEX Upgrade edge and scrape-off layer

Turbulence simulations in diverted geometry across the edge and scrape-off layer (SOL) of ASDEX Upgrade are performed with the GRILLIX code (Stegmeir et al 2019 Phys. Plasmas 26 052517). The underlying global (full-f) drift-reduced Braginskii model allows to concurrently study the self-consistent dynamics of the turbulence and the background as well as the evolution of toroidal and zonal flows. Different contributions to the radial electric field are identified. The dominant contribution on closed flux surfaces comes from the ion pressure gradient, due to the diamagnetic drift in the curved magnetic field. Large deviations can be induced, in particular, by the polarization particle flux, leading to zonal flows. The latter are driven by small-scale eddies, but do not exhibit much impact on the overall transport which is driven by ballooning modes at larger scales. Ion viscosity is found to be important in damping poloidal rotation through adjusting of the parallel velocity profile, but not via direct vorticity damping. The zonal flow drive peaks at the separatrix, where a strong shear layer forms due to the sheath-induced counter-propagating SOL flow, allowing for the formation of a transport barrier. The temperature profile across the separatrix is determined by the competition between cross-field transport and outflow in the SOL, the latter being largely controlled by the parallel heat conductivity.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Measuring and unbiasing the BAO shift in the Ly α forest with AbacusSummit

ABSTRACT The Dark Energy Spectroscopic Instrument (DESI) places sub- per cent constraints on measurements of the Baryon Acoustic Oscillation (BAO) scaling parameters from the Ly $\alpha$ forest. However, no systematic error budget stemming from non-linearities in the three-dimensional clustering of the Ly $\alpha$ forest is included in the DESI-Ly $\alpha$ analysis. In this work, we measure the size of the shift of the BAO peak using large Ly $\alpha$ forest mocks produced on the N-body simulation suite AbacusSummit, which adopt the Fluctuating–Gunn–Peterson Approximation (FGPA). Specifically, we measure the Ly $\alpha$ autocorrelation and the Ly $\alpha$-quasar cross-correlation functions. To mitigate the noise, we adopt a linear control variates technique, reducing the error bars by a factor of up to $\sim \sqrt{50}$ on large scales. From the autocorrelation, we detect a small positive shift in radial direction of $\Delta \alpha _{\parallel }= 0.35~{{\ \rm per\ cent}}$ at the 3$\sigma$ level and virtually no shift in the transverse direction, $\alpha _\perp$. From the cross-correlation, we see a similar shift to $\Delta \alpha _\parallel$, albeit with larger error bars, and a small negative shift, $\Delta \alpha _{\perp }=\sim$0.25 per cent, at the 2$\sigma$ level. We also make a connection with the Ly $\alpha$ forest effective field theory (EFT) framework and find that the one-loop EFT power spectrum yields unbiased measurements of the BAO shift parameters in radial and transverse direction for Ly $\alpha$ auto- and the Ly $\alpha$-quasar cross-correlation measurements. When using the one-loop EFT framework, we find that we can recover the BAO parameters without a shift, which has important implications for future Ly $\alpha$ forest analyses based on EFT. This work paves the way for novel full-shape analyses of the currently observing DESI and future surveys such as the PFS, WEAVE-QSO, and 4MOST.

Hadzhiyska, Boryana↗

Scalable Static and Dynamic Community Detection Using Grappolo

Graph clustering, popularly known as community detection, is a fundamental kernel for several applications of relevance to the Defense Advanced Research Projects Agency’s (DARPA) Hierarchical Identify Verify Exploit (HIVE) Pro- gram. Clusters or communities represent natural divisions within a network that are densely connected within a cluster and sparsely connected to the rest of the network. The need to compute clustering on large scale data necessitates the development of efficient algorithms that can exploit modern architectures that are fundamentally parallel in nature. How- ever, due to their irregular and inherently sequential nature, many of the current algorithms for community detection are challenging to parallelize. In response to the HIVE Graph Challenge, we present several parallelization heuristics for fast community detection using the Louvain method as the serial template. We implement all the heuristics in a software library called Grappolo. Using the inputs from the HIVE Challenge, we demonstrate superior performance and high quality solutions based on four parallelization heuristics. We use Grappolo on static graphs as the first step towards community detection on streaming graphs.

Community Detection↗

Efficient Simulation of Nested Hollow Sphere Intersections: for Dynamically Nested Compartmental Models in Cell Biology

In the particle-based simulation of cell-biological systems in continuous space, a key performance bottleneck is the computation of all possible intersections between particles. These typically rely for collision detection on solid sphere approaches. The behavior of cell biological systems is influenced by dynamic hierarchical nesting, such as the forming of, the transport within, and the merging of vesicles. Existing collision detection algorithms are found not to be designed for these types of spatial cell-biological models, because nearly all existing high performance parallel algorithms are focusing on solid sphere interactions. The known algorithms for solid sphere intersections return more intersections than actually occur with nested hollow spheres. Here we define a new problem of computing the intersections among arbitrarily nested hollow spheres of possibly different sizes, thicknesses, positions, and nesting levels. We describe a new algorithm designed to solve this nested hollow sphere intersection problem and implement it for parallel execution on graphical processing units (GPUs). We present first results about the runtime performance and scaling to hundreds of thousands of spheres, and compare the performance with that from a leading solid object intersection package also running on GPUs.

Koester, Till↗

A New Model for Simulating the Imbibition of a Wetting-Phase Fluid in a Matrix-Fracture Dual Connectivity System

The imbibition experiment is an effective approach for measuring petrophysical properties of porous media, with many such experiments performed over the past decade. Quite some empirical, analytical, and numerical models have been developed to simulate spontaneous imbibition of the wetting phase fluid into porous media, but limitations still exist. In previous studies, the imbibition process has been considered to give a piston-like displacement or the porous medium modeled as multiply-sized pores linked with bonds; both approaches fail to yield comprehensive results due to their neglect of the presence of irregular fractures or nonuniform flow paths through the matrix. By building a numerical model for simulating laboratory-scale experimental data, we performed imbibition tests on several fractured Barnett Shale samples having fractures either parallel ( P ) or transverse ( T ) to the bedding plane and used MATLAB to build a new numerical model by combining the imbibition process in fractures and the matrix using concepts from percolation theory. The experimental data show that the rocks with P -direction fractures have a more steady increase of imbibition rates than the case of T -direction one. As the shale matrix with low pore connectivity hampers the upward water movement, the imbibition rate of shales with T -direction fractures will decrease suddenly after the bottom layer in contact with water is saturated during the initial period. This wetting phase movement (WPM) model can simulate 3D porous media with 2D fractures. The rate of imbibition by fractured porous media is associated with physical parameters such as porosity and fracture distribution (e.g., the number and angle of fractures). Using Monte Carlo methods, we examined fracture parameters and predicted elapsed time and cumulative water imbibition, for the Barnett Shale samples. The results show that the rate of imbibed water mass is sensitive to the number of fractures directly connected to water source, and the connectivity between two neighboring grid cells is a key parameter for the wetting-front progression. The findings of this study can help to better understand the imbibition process with multiple influencing processes and factors in fractured-matrix rocks. Although the experiments, data simulation, and prediction results are based only on Barnett Shale samples, the model is readily applicable to imbibition tests of other fractured rocks to show the spatial and temporal behavior during a dynamic imbibition process that are not easily captured experimentally.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

BDEM (Discrete-element-simulator for high-solids granular flows) [SWR-22-72]

BDEM is a discrete element method based simulation tool developed specifically for modeling high-solids granular flows that include polydispersity, heat-transfer, moving boundaries and chemistry. Our solver provides facilities for simulating spherical/non-spherical particles with modified contact and friction models in complex dynamic geometries defined using level-sets or triangulated files. The solver is developed on top of NREL's open-source performance portable library, AMReX, providing parallel execution capabilities on current and upcoming high-performance-computing (HPC) architectures. Simulations at the scale of several millions to billion particles have been performed using this software on large scale computing resources. This software can be applied to non-reacting solids dominant flows in silos, hoppers and screw conveyors as well as in high temperature reacting systems such as screw kilns and auger reactors.

Sitaraman, Hariswaran↗

VTK-m User's Guide (V.1.6)

High-performance computing relies on ever finer threading. Advances in processor technology include ever greater numbers of cores, hyperthreading, accelerators with integrated blocks of cores, and special vectorized instructions, all of which require more software parallelism to achieve peak performance. Traditional visualization solutions cannot support this extreme level of concurrency. Extreme scale systems require a new programming model and a fundamental change in how we design algorithms. To address these issues we created VTK-m: the visualization toolkit for multi-/many-core architectures.

97 MATHEMATICS AND COMPUTING↗

Initial Investigation of Coupled Electron-Photon Transport with SCEPTRE and RAPTURE (Rev.1.1)

The SCEPTRE1 code models coupled photon and electron transport in material media using discrete ordinates methods. The code can use different solvers in 1D and 3D in parallel, promising users the ability to run problems that are significant both in physics and computational scale. One capability that is perhaps unique at this time in the NNSA complex is SCEPTRE’s coupled photon– electron transport physics in a discrete ordinates approach. For example, incident x–rays can generate a significant electron population, whose transport can be simulated within the same code. In this context, fully–coupled means that photons can produce electrons and electrons can produce photons; uncoupled or no–coupling means photons do not produce electrons. Partial–coupling, an intermediate option in which photons can produce electrons but electrons do not produce photons, is not considered in the present work. The MCNP code can treat this physics with a Monte Carlo approach. MCNP should be viewed as complementary to SCEPTRE in both computational method (Monte Carlo versus discrete ordinates) as well as data libraries. SCEPTRE and MCNP should provide important checks on each other, especially from complementary modeling frameworks of a S n (discrete ordinates) mesh based method versus Monte Carlo particle based method. In order to learn more about SCEPTRE, and how it might inform engineering work at the Laboratory, we used it to carry out a set of initial studies. This was a series of 1D simulations of photon beams hitting Aluminum slabs. Our studies mainly used SCEPTRE directly, and made little use of the closely associated RAPTURE code (more on this below). The goals of these studies were first, to familiarize ourselves with operating the code, and second, to begin to assess the importance of coupled electron–photon transport. To support these studies, we began to develop a set of scripts to initialize inputs, run tools, process outputs, and plot results. An initial version of these scripts has been committed to the Lightning workflow repository. This memo relates the results of those studies.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

On Simulating the Formation of Structured, Crystalline Systems via Non-classical Pathways

Observations in crystal growth and assembly from recent in situ methods suggest alternative, non-classical crystallization pathways play an important role in the determination of the micro- and meso- structures in crystalline systems. These processes display parallels that cross-cut multiple disciplines investigating crystallization across four orders of magnitude in size scales and widely differing environments, hinting that alternative crystal growth pathways may be a fundamental scheme in natural crystal formation. Using a system of short-range attractive microbeads, we demonstrate that the addition of a small concentration of sub-species incommensurate with the lattice spacing of the dominant species results in a stark change in crystal size and morphology. These changes are attributed to the presence of fleeting, amorphous-like configurations of beads that ultimately change the melting and growth dynamics in preferred directions. From these real-time observations, we hypothesize the amorphous mineral precursors present in biological mineralized tissues undergo similar non-classical crystallization processes resulting in the complex structures found in biomineralization.

36 MATERIALS SCIENCE↗

Deconvolute individual genomes from metagenome sequences through short read clustering

Metagenome assembly from short next-generation sequencing data is a challenging process due to its large scale and computational complexity. Clustering short reads by species before assembly offers a unique opportunity for parallel downstream assembly of genomes with individualized optimization. However, current read clustering methods suffer either false negative (under-clustering) or false positive (over-clustering) problems. Here we extended our previous read clustering software, SpaRC, by exploiting statistics derived from multiple samples in a dataset to reduce the under-clustering problem. Using synthetic and real-world datasets we demonstrated that this method has the potential to cluster almost all of the short reads from genomes with sufficient sequencing coverage. The improved read clustering in turn leads to improved downstream genome assembly quality.

59 BASIC BIOLOGICAL SCIENCES↗

Parametric instability of a relativistically strong electromagnetic wave.

The stability of a circularly polarized electromagnetic wave that is strong enough to make plasma electrons, but not ions, relativistic is studied. Small perturbations are considered which propagate parallel to the large-amplitude driver. A relativistically strong wave can be unstable on time scales as short as twice its own oscillation period, and decays into a forward-going plasma oscillation and either one or two electromagnetic waves. Ion motion introduces an additional instability which can be important at short perturbation wavelengths, where the driver would otherwise be stable. The unstable ion and electron modes both have potential for producing anomalously large acceleration of relativistic particles, as well as significant amounts of backscattered light. These effects may be important in two applications: (1) the use of intense lasers to heat or compress plasma, and (2) the plasma surrounding a pulsar, if the pulsar is losing energy by radiation of electromagnetic waves at its rotation frequency. Instability persists in the nonrelativistic regime, reducing to stimulated Raman scattering as a special case.

Max, C. E.↗

Characteristics of wake vortex generated by a Boeing 727 jet transport during two-segment and normal ILS approach flight paths

A series of flight tests was conducted to evaluate the vortex wake characteristics of a Boeing 727 (B727-200) aircraft during conventional and two-segment ILS approaches. Twelve flights of the B727, which was equipped with smoke generators for vortex marking, were flown and its vortex wake was intentionally encountered by a Lear Jet model 23 (LR-23) and a Piper Twin Comanche (PA-30). Location of the B727 vortex during landing approach was measured using a system of photo-theodolites. The tests showed that at a given separation distance there were no readily apparent differences in the upsets resulting from deliberate vortex encounters during the two types of approaches. Timed mappings of the position of the landing configuration vortices showed that they tended to descend approximately 91 m(300 ft) below the flight path of the B727. The flaps of the B727 have a dominant effect on the character of the trailed wake vortex. The clean wing produces a strong, concentrated vortex but as the flaps are lowered, the vortex system becomes more diffuse. Pilot opinion and roll acceleration data indicate that 4.5 n.mi. would be a minimum separation distance at which roll control of light aircraft (less than 5,670 kg (12,500 lb) could be maintained during parallel encounters of the B727's landing configuration wake. This minimum separation distance is generally in scale with results determined from previous tests of other aircraft using the small roll control criteria.

Kurkowski, R. L.↗

High-speed computerized tomography

The development of a high-speed reconstruction processor and a channelized architecture to use with a high-resolution tomographic unit is discussed with attention to the convolution reconstruction algorithm. By means of this algorithm, input data and intermediate result precision required throughout the algorithm execution have been studied with computer simulation using profile data derived from mathematically simulated test objects and experimental animal data. A prototype section for a highly parallel all-digital system executes 60 million arithmetic operations per second, and the full-scale version is expected to reconstruct 500 to 1000 cross sections per second.

Swartzlander, E. E., Jr.↗

Application of parallel distributed processing to space based systems

The concept of using Parallel Distributed Processing (PDP) to enhance automated experiment monitoring and control is explored. Recent very large scale integration (VLSI) advances have made such applications an achievable goal. The PDP machine has demonstrated the ability to automatically organize stored information, handle unfamiliar and contradictory input data and perform the actions necessary. The PDP machine has demonstrated that it can perform inference and knowledge operations with greater speed and flexibility and at lower cost than traditional architectures. In applications where the rule set governing an expert system's decisions is difficult to formulate, PDP can be used to extract rules by associating the information an expert receives with the actions taken.

Macdonald, J. R.↗

Prominence formation in a coronal loop

A model is presented which depends on the preferential deposition of heating in the legs of a coronal loop and which produces a stable prominence-scale condensation at the loop top. Dynamic stability is attained by the subsequent adjustment of local parallel gravity by a magnetic inversion at the loop (or arcade) apex. A nonlinear numerical simulation of this process, which includes a deep chromosphere, a heating rate with a fixed dissipation length, and full solar gravity is described.

Mok, Y.↗

Changes in Black Carbon Deposition to Antarctica from Two Ice Core Records, A.D. 1850-2000

Continuous flow analysis was based on a steady sample flow and in-line detection of BC and other chemical substances as described in McConnell et al. (2007). In the cold room, previously cut one meter ice core sticks of 3x3cm, are melted continuously on a heated melter head specifically designed to eliminate contamination from the atmosphere or by the external parts of the ice. The melted ice from the most inner part of the ice stick is continuously pumped by a peristaltic pump and carried to a clean lab by Teflon lines. The recorded signal is continuous, integrating a sample volume of about 0.05 mL, for which the temporal resolution depends on the speed of melting, ice density and snow accumulation rate at the ice core drilling site. For annual accumulation derived from the WAIS and Law Dome ice cores, we assumed ~3.1 cm water equivalent uncertainty in each year's accumulation from short scale spatial variability (glaciological noise) which was determined from several measurements of annual accumulation in multiple parallel ice cores notably from the WAIS Divide ice core site (Banta et al., 2008) and from South Pole site (McConnell et al., 1997; McConnell et al., 2000). Refractory black carbon (rBC) concentrations were determined using the same method as in (Bisiaux et al., 2011) and adapted to continuous flow measurements as described by (McConnell et al., 2007). The technique uses a single particle intracavity laser induced incandescence photometer (SP2, Droplet Measurement Technologies, Boulder, Colorado) coupled to an ultrasonic nebulizer/desolvation (CETAC UT5000) Flow Injection Analysis (FIA). All analyses, sample preparation etc, were performed in a class 100 cleanroom using anti contamination "clean techniques". The samples were not acidified.

Bisiaux, Marion M.↗

Numerical Simulation of Illumination and Thermal Conditions at the Lunar Poles Using LOLA DTMs

We are interested in illumination conditions and the temperature distribution within the upper two meters of regolith near the lunar poles. Here, areas exist receiving almost constant illumination near areas in permanent shadow, which were identified as potential exploration sites for future missions. For our study a numerical simulation of the illumination and thermal environment for lunar near-polar regions is needed. Our study is based on high-resolution, twenty meters per pixel and 400 x 400 km large polar Digital Terrain Models (DTMs), which were derived from Lunar Orbiter Laser Altimeter (LOLA) data. Illumination conditions were simulated by synthetically illuminating the LOLA DTMs using the horizon method considering the Sun as an extended source. We model polar illumination for the central 50 x 50 km subset and use it as an input at each time-step (2 h) to evaluate the heating of the lunar surface and subsequent conduction in the sub-surface. At surface level we balance the incoming insolation with the subsurface conduction and radiation into space, whereas in the sub-surface we consider conduction with an additional constant radiogenic heat source at the bottom of our two-meter layer. Density is modeled as depth-dependent, the specific heat parameter as temperature-dependent and the thermal conductivity as depth- and temperature-dependent. We implemented a fully implicit finite-volume method in space and backward Euler scheme in time to solve the one-dimensional heat equation at each pixel in our 50 x 50 km DTM. Due to the non-linear dependencies of the parameters mentioned above, Newton's method is employed as the non-linear solver together with the Gauss-Seidel method as the iterative linear solver in each Newton iteration. The software is written in OpenCL and runs in parallel on the GPU cores, which allows for fast computation of large areas and long time scales.

Glaser, P.↗