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At least 1,603 records · Page 89

SU-D-206-02: Evaluation of Partial Storage of the System Matrix for Cone Beam Computed Tomography Using a GPU Platform

Purpose: Iterative reconstruction algorithms in computed tomography (CT) require a fast method for computing the intersections between the photons’ trajectories and the object, also called ray-tracing or system matrix computation. This work evaluates different ways to store the system matrix, aiming to reconstruct dense image grids in reasonable time. Methods: We propose an optimized implementation of the Siddon’s algorithm using graphics processing units (GPUs) with a novel data storage scheme. The algorithm computes a part of the system matrix on demand, typically, for one projection angle. The proposed method was enhanced with accelerating options: storage of larger subsets of the system matrix, systematic reuse of data via geometric symmetries, an arithmetic-rich parallel code and code configuration via machine learning. It was tested on geometries mimicking a cone beam CT acquisition of a human head. To realistically assess the execution time, the ray-tracing routines were integrated into a regularized Poisson-based reconstruction algorithm. The proposed scheme was also compared to a different approach, where the system matrix is fully pre-computed and loaded at reconstruction time. Results: Fast ray-tracing of realistic acquisition geometries, which often lack spatial symmetry properties, was enabled via the proposed method. Ray-tracing interleaved with projection and backprojection operations required significant additional time. In most cases, ray-tracing was shown to use about 66 % of the total reconstruction time. In absolute terms, tracing times varied from 3.6 s to 7.5 min, depending on the problem size. The presence of geometrical symmetries allowed for non-negligible ray-tracing and reconstruction time reduction. Arithmetic-rich parallel code and machine learning permitted a modest reconstruction time reduction, in the order of 1 %. Conclusion: Partial system matrix storage permitted the reconstruction of higher 3D image grid sizes and larger projection datasets at the cost of additional time, when compared to the fully pre-computed approach. This work was supported in part by the Fonds de recherche du Quebec - Nature et technologies (FRQ-NT). The authors acknowledge partial support by the CREATE Medical Physics Research Training Network grant of the Natural Sciences and Engineering Research Council of Canada (Grant No. 432290).

60 APPLIED LIFE SCIENCES↗

Comparison of calculated and measured velocities near the tip of a model rotor blade at transonic speeds

The ability of the ROT22 code to predict accurately the transonic flow field in the crucial region around and beyond the tip of a high speed rotor blade was assessed. The computations were compared with extensive laser velocimetry measurements made at zero advance ratio and tip Mach numbers of 0.85, 0.88, 0.90, and 0.95. The comparison between theory and experiment was made using 300 scans for the three orthogonal velocity components covering a volume having a height of over one blade chord, a width of nearly two chords, and a length ranging from about 1 to 1.6 chords, depending on the tip speeds. The good agreement between the calculated and measured velocities established the ability of the code to predict the off blade flow field at high tip speeds. This supplements previous comparisons where surface pressures were shown to be well predicted on two different tips at advance ratios to 0.45, especially at the critical 90 deg azimuth blade position. These results demonstrate that the ROT22 code can be used with confidence to predict the important tip region flow field including the occurrence, strength, and location of shock waves causing high drag and noise.

Tauber, M. E.↗

Development of Three-Dimensional Flow Code Package to Predict Performance and Stability of Aircraft with Leading Edge Ice Contamination

In the work reported herein, a simplified, uncoupled, zonal procedure is utilized to assess the capability of numerically simulating icing effects on a Boeing 727-200 aircraft. The computational approach combines potential flow plus boundary layer simulations by VSAERO for the un-iced aircraft forces and moments with Navier-Stokes simulations by NPARC for the incremental forces and moments due to iced components. These are compared with wind tunnel force and moment data, supplied by the Boeing Company, examining longitudinal flight characteristics. Grid refinement improved the local flow features over previously reported work with no appreciable difference in the incremental ice effect. The computed lift curve slope with and without empennage ice matches the experimental value to within 1%, and the zero lift angle agrees to within 0.2 of a degree. The computed slope of the un-iced and iced aircraft longitudinal stability curve is within about 2% of the test data. This work demonstrates the feasibility of a zonal method for the icing analysis of complete aircraft or isolated components within the linear angle of attack range. In fact, this zonal technique has allowed for the viscous analysis of a complete aircraft with ice which is currently not otherwise considered tractable.

Aircraft icing↗

Reproducibility of fixed-node diffusion Monte Carlo across diverse community codes: The case of water–methane dimer

Fixed-node diffusion quantum Monte Carlo (FN-DMC) is a widely trusted many-body method for solving the Schrödinger equation, known for its reliable predictions of material and molecular properties. Furthermore, its excellent scalability with system complexity and near-perfect utilization of computational power make FN-DMC ideally positioned to leverage new advances in computing to address increasingly complex scientific problems. Even though the method is widely used as a computational gold standard, reproducibility across the numerous FN-DMC code implementations has yet to be demonstrated. This difficulty stems from the diverse array of DMC algorithms and trial wave functions, compounded by the method’s inherent stochastic nature. Here, this study represents a community-wide effort to assess the reproducibility of the method, affirming that yes, FN-DMC is reproducible (when handled with care). Using the water–methane dimer as the canonical test case, we compare results from eleven different FN-DMC codes and show that the approximations to treat the non-locality of pseudopotentials are the primary source of the discrepancies between them. In particular, we demonstrate that, for the same choice of determinantal component in the trial wave function, reliable and reproducible predictions can be achieved by employing the T-move, the determinant locality approximation, or the determinant T-move schemes, while the older locality approximation leads to considerable variability in results. These findings demonstrate that, with appropriate choices of algorithmic details, fixed-node DMC is reproducible across diverse community codes—highlighting the maturity and robustness of the method as a tool for open and reliable computational science.

Della Pia, Flaviano [Univ. of Cambridge (United Ki↗

A Process for Assessing NASA's Capability in Aircraft Noise Prediction Technology

An acoustic assessment is being conducted by NASA that has been designed to assess the current state of the art in NASA s capability to predict aircraft related noise and to establish baselines for gauging future progress in the field. The process for determining NASA s current capabilities includes quantifying the differences between noise predictions and measurements of noise from experimental tests. The computed noise predictions are being obtained from semi-empirical, analytical, statistical, and numerical codes. In addition, errors and uncertainties are being identified and quantified both in the predictions and in the measured data to further enhance the credibility of the assessment. The content of this paper contains preliminary results, since the assessment project has not been fully completed, based on the contributions of many researchers and shows a select sample of the types of results obtained regarding the prediction of aircraft noise at both the system and component levels. The system level results are for engines and aircraft. The component level results are for fan broadband noise, for jet noise from a variety of nozzles, and for airframe noise from flaps and landing gear parts. There are also sample results for sound attenuation in lined ducts with flow and the behavior of acoustic lining in ducts.

Dahl, Milo D.↗

A Monte Carlo volumetric-ray-casting estimator for global fluence tallies on GPUs

A Monte Carlo fluence estimator has been designed to take advantage of the computational power of graphical processing units (GPUs). This new estimator, termed the volumetric-ray-casting estimator, is an extension of the expectation estimator. It can be used as a replacement of the track-length estimator for the estimation of global fluence. Calculations for this estimator are performed on the GPU while the Monte Carlo random walk is performed on the central processing unit (CPU). This method lowers the implementation cost for GPU acceleration of existing Monte Carlo particle transport codes as there is little modification of the particle history logic flow. Three test problems have been evaluated to assess the performance of the volumetric-ray-casting estimator for neutron transport on GPU hardware in comparison to the standard track-length estimator on CPU hardware. Evaluation of neutron transport through air in a criticality accident scenario showed that the volumetric-ray-casting estimator achieved 23 times the performance of the track-length estimator using a single core CPU paired with a GPU and 15 times the performance of the track-length estimator using an eight core CPU paired with a GPU. Finally, simulation of a pressurized water reactor fuel assembly showed that the performance improvement was 6 times within the fuel and 7 times within the control rods using an eight core CPU paired with a single GPU.

74 ATOMIC AND MOLECULAR PHYSICS↗

A model for trapping and re-solution regarding intra-granular bubbles in UO 2 , linked to atomic-scale simulations

In the literature, a clear definition of the irradiation re-solution frequency of gas from bubbles in the UO 2 fuel is absent. Moreover, for intra-granular bubbles, a detailed calculation of the cumulated displaced gas quantities in function of the distance from the radius of the bubble after a re-solution event has never been published. The assessment of these two elements is very useful if we want to increase the adherence of fission gas release codes to our present knowledge of the behavior of fission gases. Hence, we suggest to link the definition of the re-solution frequency to atomic-scale simulations. Furthermore, we present the cumulated displaced gas quantities obtained from Molecular Dynamics calculations, from which we have derived a re-solution profile that can be exploited to better consider the irradiation re-solution phenomenon inside Fission Gas Release codes. On top of that, we have built a new trapping/re-solution model for intra-granular bubbles linked to Molecular Dynamics simulations that can be easily incorporated into Fission Gas Release codes. In conclusion, we also check that the model is properly built through the comparison of the new model against a reference.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Historical perspectives of BEPU research in US

Civilian nuclear energy started in earnest in the 1950s and experienced rapid growth in 1960-80s with increasingly larger reactors. These reactors were initially regulated based on the experience from the smaller reactors, but this could not be applied to the larger power reactors. Therefore, in 1974 the US Nuclear Regulatory Commission set up safety requirements based on defense in depth in 10 CFR 50.46, and set of guidance in 10 CFR 50 presented in Appendix K, for models and simulations of reactor safety analyses, to ensure conservatism in predicted safety parameters. These methods resulted in both conservative safety margins as well as economic and operational penalties. In the late 1970s and early 1980s, a large number of experiential programs provided data that allowed for the creation of best estimate models. These best estimate models showed the conservatism in Appendix K models. In 1988-89, USNRC modified the regulations and allowed the use of best estimate models provided they were coupled to a reliable and defensible measure of uncertainty in the prediction of safety parameters. This change in regulation strongly encouraged global activity for the development of best estimate codes and methods. To aide in this development, the USNRC provided one acceptable approach, the Code Scaling, Acceptability and Uncertainty Evaluation Methodology (CSAU). This approach was later refined in the Evaluation Model Development and Assessment Process (EMDAP).

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

Radiation characterization summary for the WSMR fast burst reactor environment at the 6-inch location

The characterization of the neutron, prompt gamma-ray, and delayed gamma-ray radiation fields for the White Sands Missile Range (WSMR) Fast Burst Reactor, also known as molybdenum-alloy Godiva (Molly-G) has been assessed at the 6-inch irradiation location. The neutron energy spectra, uncertainties, and common radiation metrics are presented. Code-dependent recommended constants are given to facilitate the conversion of various dosimetry readings into radiation metrics desired by experimenters. The Molly-G core was designed and configured similarly to Godiva II, as an unreflected, unmoderated, cylindrical annulus of uranium-molybdenum-alloy fuel with molybdenum loading of 10%. At the 6-inch position, the axial fluence maximum is about 2.4×10 13 n/cm 2 per MJ of reactor energy; about 0.1% of the neutron fluence is below 1 keV and 96% is above 100 keV. The 1-MeV Damage-Equivalent Silicon (DES) fluence is estimated at 2.2×10 13 n/cm 2 per MJ of reactor energy. The prompt gamma-ray dose is roughly 2.5E+03 rad(Si) per MJ and the delayed gamma-ray dose is about 1.3E+03 rad(Si) per MJ.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

Evaluation of PBR Spent Fuel Criticality and Dose Rate Compliance for Storage and Transportation

Spent tri-structural isotropic (TRISO)–based fuels have a strong track record in storage and transportation without documented incidents. This work seeks to reduce uncertainty to aid in more informed spent fuel management of TRISO-based fuels by modeling both fresh and spent pebble bed reactor (PBR) fuel and comparing the results to the regulatory standards from 10 CFR 71. SCALE was used for all modeling due to it having fast and accurate methods for handling PBR fuel modeling, as well as having an efficient method for shielding calculations in monaco with automated variance reduction using importance calculations (MAVRIC), which utilizes the consistent adjoint-driven importance sampling (CADIS) and the forward-weighted consistent adjoint-driven importance sampling (FW-CADIS) methods. KENO-VI was used for all criticality calculations, TSUNAMI was used for uncertainty quantification on k-effective, TRITON and the Oak Ridge isotope generation code (ORIGEN) were both used for depletion of the fuel, and MAVRIC was used for shielding calculations. For criticality assessments, this study focused on the requirement that the value of the neutron multiplication factor, k-effective (k-eff), would not exceed a peak value of 0.95, including uncertainty, with 95% confidence. Criticality was initially examined by modeling fresh fuel from three different designs—HTR-10 fuel, PBMR-400 fuel, and demonstration fuel representative of a TRISO-fueled modern high-temperature gas reactor (HTGR) design, henceforth referred to as Demo HTGR—and placing them into various sized containers with conditions described in 10 CFR 71 to quantify the peak k-eff state. When the peak value of 0.95 k-eff was exceeded, mitigation methods were examined in those scenarios. Burnup credit, pebble displacement in areas of strong neutron multiplication, and random pebble replacement using pebbles of various compositions and replacement fractions were examined. In summary, the criticality of PBR fuels can be well accounted for by restricting container size, taking credit for burnup, or by displacing/replacing pebbles. Uncertainty of the k-eff due to nuclear data uncertainties was recorded at ~0.6644%Δk/k, or roughly 664% mil (pcm). The nuclear data–induced uncertainty was relatively small and should not require significant modification in the design to be accounted for. Revisions to the evaluated nuclear data file values have been shown to have a larger impact than nuclear data–induced uncertainty. For dose rate aspects, U.S. Nuclear Regulatory Commission regulations require a maximum dose rate of 10 millirem per hour (mrem/h) at 2 meters. In examining the dose rate behavior of spent PBR fuel, the representative Demo HTGR fuel was modeled exclusively due to it possessing the highest target burnup of the examined fuels. Equilibrium cycle modeling methods were used to produce a higher-fidelity discharge isotopic composition than simple assumptions, such as reflected pebbles. The discharge composition was used as a source term in the fixed-source transport shielding calculations, and dose rates were calculated at 2 m for the shortest possible cooling time. The low concentration of fuel material led to dose rates that were in line with regulatory limits, despite the high burnup when compared to traditional light water reactor fuels. In conclusion, the methods employed in this study would require more work to further verify and validate and are limited to the criticality and dose rate analyses performed.

11 - NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

SU-G-201-13: Investigation of Dose Variation Induced by HDR Ir-192 Source Global Shift Within the Varian Ring Applicator Using Monte Carlo Methods

Purpose: The Varian tandem and ring applicators are used to deliver HDR Ir-192 brachytherapy for cervical cancer. The source path within the ring is hard to predict due to the larger interior ring lumen. Some studies showed the source could be several millimeters different from planned positions, while other studies demonstrated minimal dosimetric impact. A global shift can be applied to limit the effect of positioning offsets. The purpose of this study was to assess the necessities of implementing a global source shift using Monte Carlo (MC) simulations. Methods: The MCNP5 radiation transport code was used for all MC simulations. To accommodate TG-186 guidelines and eliminate inter-source attenuation, a BrachyVision plan with 10 dwell positions (0.5cm step sizes) was simulated as the summation of 10 individual sources with equal dwell times for simplification. To simplify the study, the tandem was also excluded from the MC model. Global shifts of ±0.1, ±0.3, ±0.5 cm were then simulated as distal and proximal from the reference positions. Dose was scored in water for all MC simulations and was normalized to 100% at the normalization point 0.5 cm from the cap in the ring plane. For dose comparison, Point A was 2 cm caudal from the buildup cap and 2 cm lateral on either side of the ring axis. With seventy simulations, 108 photon histories gave a statistical uncertainties (k=1) <2% for (0.1 cm)3 voxels. Results: Compared to no global shift, average Point A doses were 0.0%, 0.4%, and 2.2% higher for distal global shifts, and 0.4%, 2.8%, and 5.1% higher for proximal global shifts, respectively. The MC Point A doses differed by < 1% when compared to BrachyVision. Conclusion: Dose variations were not substantial for ±0.3 cm global shifts, which is common in clinical practice.

60 APPLIED LIFE SCIENCES↗

Multi-choice Viromics Pipeline (MVP) v1

MVP stands for Multi-choice Viromics Pipeline. It is a pipeline that utilizes a suite of state-of-art tools: geNomad to identify viruses, proviruses, and plasmids in sequencing data, CheckV to assess the quality, and completeness of identified viral genomes, including identification of host contamination for integrated proviruses, A custom code for a rapid genome clustering based on pairwise ANI, Bowtie2, Samtools, and CoverM to calculate coverage of individual viral genomes by read mapping, A custom code to create a vOTU table of abundance, MMseqs2 to compare viral proteins to multiple databases. It provides a quick, and intuitive pipeline to get viral sequences and corresponding properties that can be used for downstream analyses.

Roux, Simon↗

Five key aspects of metaproteomics as a tool to understand functional interactions in host-associated microbiomes

Host-associated microbial communities (microbiomes) play critical roles in human, animal, and plant health and development. However, interactions between the host, members of the microbiome, and invading pathogens are in most cases still poorly understood. Such interactions are multidimensional and can alter the taxonomic composition and/or the functional metabolic activities of the microbiome in response to disease or treatment conditions. For example, after 2 days of antibiotic treatment, the mouse gut microbiome is altered and more susceptible to invasion by the pathogen Clostridioides difficile. Studies of these multidimensional interactions have been fueled by the ability to use high-throughput sequencing of phylogenetic marker genes to profile microbial community composition and shotgun metagenomics to profile functional potential. However, many protein-coding genes predicted from metagenomes are not necessarily expressed under a given condition, and thus, it is difficult to assess the activities and functional interactions in microbial communities based on DNA sequencing data alone. The physiological and pathological processes expressed in these communities under specific conditions are better reflected by the abundances of transcripts or proteins. In this Pearl, we provide a brief introduction to metaproteomics, which is a tool for the large-scale analysis of proteins in microbiomes that allows researchers to address a diversity of questions related to functions and interactions in microbiomes. The term “metaproteomics” was first used in 2004 for “the large-scale characterization of the entire protein complement of environmental microbiota at a given point in time”, and since then, a large array of metaproteomics approaches have been developed. Our objective in this Pearl is to highlight what we feel are 5 essential elements to be considered for a metaproteomics research campaign and to introduce nonexpert readers to the topic without going into too much technical detail.

59 BASIC BIOLOGICAL SCIENCES↗

ASC Tri-lab Co-design Level 2 Milestone Report 2015

In 2015, the three Department of Energy (DOE) National Laboratories that make up the Advanced Sci- enti c Computing (ASC) Program (Sandia, Lawrence Livermore, and Los Alamos) collaboratively explored performance portability programming environments in the context of several ASC co-design proxy applica- tions as part of a tri-lab L2 milestone executed by the co-design teams at each laboratory. The programming environments that were studied included Kokkos (developed at Sandia), RAJA (LLNL), and Legion (Stan- ford University). The proxy apps studied included: miniAero, LULESH, CoMD, Kripke, and SNAP. These programming models and proxy-apps are described herein. Each lab focused on a particular combination of abstractions and proxy apps, with the goal of assessing performance portability using those. Performance portability was determined by: a) the ability to run a single application source code on multiple advanced architectures, b) comparing runtime performance between \native" and \portable" implementations, and c) the degree to which these abstractions can improve programmer productivity by allowing non-portable implementation details to be hidden from the application developer. This report captures the work that was completed for this milestone, and outlines future co-design work to be performed by application developers, programming environment developers, compiler writers, and hardware vendors.

97 MATHEMATICS AND COMPUTING↗

PFLOTRAN-RepoTREND Source Term Comparison Summary.

Code inter-comparison studies are useful exercises to verify and benchmark independently developed software to ensure proper function, especially when the software is used to model high-consequence systems which cannot be physically tested in a fully representative environment. This summary describes the results of the first portion of the code inter-comparison between PFLOTRAN and RepoTREND, which compares the radionuclide source term used in a typical performance assessment.

97 MATHEMATICS AND COMPUTING↗

Summary of LANL FY19 Technical Interface Coordination with SHINE

In FY19, Los Alamos National Laboratory (LANL) provided technical support for SHINE emergent needs and technical interface coordination including coordination of SHINE CFD and thermal hydraulics conference calls, Mo-99 meetings and reviews, national laboratory conference calls, and program management activities such as reporting and tracking requirements for current FY19 activities. LANL has also provided general technology consultation support for emerging issues. LANL has participated in the bi-weekly conference calls with SHINE and other national laboratories regarding LANL’s current activities. Activities discussed include FY18 carryover items including the ANSYS Fluent-Nek5000 comparison study (for assessment of Nek5000 for coupled calculations), Supo 3-D CFD model geometry validation, and releasing CFD-MCNP coupled codes for the generic solution vessel simulations. Also, additional mid-year funded activities discussed during these conference calls include the ANL bubble experiment #2 collaboration. SHINE had a general technology consultation request in FY19. SHINE inquired about LANL’s capability to measure enrichment percentage of uranium samples, however, additional information is needed to continue. The meeting minutes for these activities are shown in Appendix A. LANL has also been providing monthly updates on the laboratory SharePoint site (managed by Pacific Northwest National Laboratory) regarding current FY19 activities. Monthly updates include current activity milestone and deliverable status, completion date updates and variances if applicable, and actual cost at the task dependent activity level. LANL attended several Mo-99 meetings and reviews in FY19. LANL attended the FY19 Mo-99 Laboratory Mid-Year Program and Financial Review at Argonne National Laboratory (ANL) on March 20-21, 2019, as well as the FY19 Mo-99 Program Meeting and Mid-Year Financial Review in Chicago, IL on April 29-30, 2019. LANL also attended the FY20 Laboratory Work Package Planning Meeting at ANL on June 4-6, 2019.

43 PARTICLE ACCELERATORS↗

SURF Model Resolution in xRage Code

A key issue for detonation wave simulations with a reactive burn model is the resolution needed for the reaction zone. The reaction-zone width is a physical length scale. For plastic-bonded explosives, it is small (on the order of 100 microns) but affects important detonation properties such as the detonation speed. Even with adaptive mesh refinement, a well resolved reaction zone is computationally expensive. Here we consider the trade-off between computational expense and accuracy when the resolution of the reaction zone is varied for simulations with the xRage code of PBX 9501 with the SURF burn model and of PBX 9502 with the SURFplus burn model. For assessing shock initiation, the numerical Pop plot is simulated, and for assessing propagating detonation waves, the cylinder test is used as a test problem. The reaction-zone resolution is varied from a cell size of 6.25 to 200 microns, and key properties of the solutions are compared. With 6 micron resolution, the numerical solution is near mesh converged and can be used to judge the accuracy of the coarser resolution simulations. For the propagating detonation wave in the cylinder test, at 200 microns the detonation speed is low by a couple of per cent. In terms of cpu-hours, the finest resolution is about a factor of 100 more expensive than the coarsest resolution.

45 MILITARY TECHNOLOGY, WEAPONRY, AND NATIONAL DEF↗

Verification and Validation of High Explosive Reactive Burn Models Implemented in LANL's EAP and LAP Code Base (FY2020 L2 Milestone MRT 7129) [Slides]

Advanced reactive burn models enable phenomena to be modeled that aren’t possible with programmed burn. Programmed burn propagates a burn front at a prescribed speed from a prescribed initiation point. Reactive burn uses the hydro variables (pressure, temperature, etc.) to determine when, how rapidly, and to what extent a zone detonates. This enables a completely new set of problems to be simulated. Our goal in this milestone has been to improve the usability of reactive burn modes. Thus, the closure criteria are: 1. Perform code and solution verification of the reactive burn models using appropriate solutions and simplified HE setups. 2. Perform validation assessments using small-scale experiments. 3. Evaluate sensitivities and quantify uncertainties due to model form variations and mesh dependencies.

45 MILITARY TECHNOLOGY, WEAPONRY, AND NATIONAL DEF↗