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At least 271 records · Page 15

An extension to V ORO ++ for multithreaded computation of Voronoi cells

V ORO ++ is a software library written in C++ for computing the Voronoi tessellation, a technique in computational geometry that is widely used for analyzing systems of particles. V ORO ++ was released in 2009 and is based on computing the Voronoi cell for each particle individually. Here, we take advantage of modern computer hardware, and extend the original serial version to allow for multithreaded computation of Voronoi cells via the OpenMP application programming interface. We test the performance of the code, and demonstrate that it can achieve parallel efficiencies greater than 95% in many cases. Further, the multithreaded extension follows standard OpenMP programming paradigms, allowing it to be incorporated into other programs. We provide an example of this using the VoroTop software library, performing a multithreaded Voronoi cell topology analysis of up to 102.4 million particles.

97 MATHEMATICS AND COMPUTING↗

Bayesian Learning of Adatom Interactions from Atomically Resolved Imaging Data

Atomic structures and adatom geometries of surfaces encode information about the thermodynamics and kinetics of the processes that lead to their formation, and which can be captured by a generative physical model. In this work, we develop a workflow based on a machine-learning-based analysis of scanning tunneling microscopy images to reconstruct the atomic and adatom positions, and a Bayesian optimization procedure to minimize statistical distance between the chosen physical models and experimental observations. We optimize the parameters of a 2- and 3-parameter Ising model describing surface ordering and use the derived generative model to make predictions across the parameter space. For concentration dependence, we compare the predicted morphologies at different adatom concentrations with the dissimilar regions on the sample surfaces that serendipitously had different adatom concentrations. The proposed workflow can be used to reconstruct the thermodynamic models and associated uncertainties from the experimental observations of materials microstructures. The code used in the manuscript is available at https://github.com/saimani5/Adatom_interactions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Code-to-code comparison between FLASH and HYDRA in gas-puff Z-pinch modeling

The numerical modeling of gas-puff Z pinches involves the nonlinear coupling of a broad range of complex, multi-physics phenomena that makes such simulations challenging. The challenge is further compounded by nonlinear instabilities that can impact the dynamics of imploding gas-puff Z pinches, such as the magneto Rayleigh–Taylor instability (MRTI). If the growth rate and amplitude of the latter is comparable to the relevant timescales and properties of the imploding plasma, the MRTI can dramatically alter implosion dynamics, dictate pinch stability, and govern the plasma properties achievable in pulsed-power-driven laboratory experiments. National Laboratories and academic teams have developed numerical tools that can accurately model Z-pinch configurations and provide reliable design capabilities that can guide experimental choices and assist in interpreting experimental results. Most such tools, however, are not broadly available. Here, we present newly developed Z-pinch simulation capabilities of the publicly available FLASH code, applied in the study of MRTI growth and dynamical effects in gas-puff implosions. To verify the new implementations, we perform a comparison of FLASH gas-puff implosion simulations with previously published calculations with the HYDRA code from Lawrence Livermore National Laboratory, which have been validated with experimental data from the CESZAR pulsed-power driver at the University of California, San Diego. The experiments involved double- and triple-nozzle configurations, in an experimental attempt to stabilize the pinch to the MRTI. The code-to-code comparison shows similar results between the FLASH and HYDRA simulations, supporting the use of FLASH in the modeling of future gas-puff Z-pinch experiments at CESZAR.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

FAST-1.2 User Installation and Verification Guide: Developed Under NQA-1-2017

The purpose of this document is to provide the user information about the installation of Fuel Analysis for Steady state and Transient (FAST)-1.2 on their computers or servers. General information about the code and supported operating systems is described in Section 1.0. Self-service oriented FAST-1.2 software licensing steps are described in Section 2.0. An installation verification test suite is provided with FAST-1.2 and described in Section 3.0. A convenience script for converting Fuel Rod Analysis Program – Constant (FRAPCON) to FAST inputs is discussed in Section 4.0. FAST-1.2 was developed and released under a software quality assurance program based upon NQA-1-2017 at Pacific Northwest National Laboratory (PNNL). FAST-1.2 is the latest baseline code. The installation verification test suite contains both steady state and transient Anticipated Operation Occurrences (AOOs), accident conditions, such as Reactivity Initiated Accidents (RIAs) and Loss of Coolant Accidents (LOCAs).

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Thermal Aging Effects on the Yield and Tensile Strength of 9Cr-1Mo-V (Grade 91)

The long-term exposure of 9Cr-1Mo-V (Grade 91) steel to elevated temperature can have a significant effect on reducing its yield and tensile strength. The yield and tensile strength changes, in turn, have potential implications to the assurance of the integrity of components constructed with this material over their design or intended lifetime. The ASME Boiler & Pressure Vessel Code (BPVC), Section III, Division 5 (III-5, high temperature reactors) provides tabulated reduction factors for Grade 91 yield and tensile strength as a function of exposure temperature and time up to 300,000 h. ASME BPVC III-5 s intent to extend these factors to an exposure duration of 500,000 h, the lack of available historic information to support the existing factors, and the recent development of a physics-based prediction model for ASME BPVC application are prime motivation for this study. This work describes results of the conventional time-temperature Hollomon–Jaffe parameter, strength reduction ratio prediction method using an updated, extensive Grade 91 unaged and related aged material strength database. The method, previously used by Oak Ridge National Laboratory in its evaluation of Grade 91 and likely used in development of the existing BPVC III-5 reduction factors, provides strength reduction ratio predictions useful for general component fitness-for-service assessments and for computing BPVC III-5 reduction factors as defined. Specific reduction factors to 500,000 h at 650 °C applicable to ASME BPVC III-5 are computed from the strength reduction ratios.

36 MATERIALS SCIENCE↗

Modulation of Plant and Fungal Gene Expression Upon Cd Exposure and Symbiosis in Ericoid Mycorrhizal Vaccinium myrtillus

The success of Ericaceae in stressful habitats enriched in heavy metals has been ascribed to the distinctive abilities of their mycorrhizal fungal partners to withstand heavy metal stress and to enhance metal tolerance in the host plant. Whereas heavy metal tolerance has been extensively investigated in some ericoid mycorrhizal (ERM) fungi, the molecular and cellular mechanisms that extend tolerance to the host plant are currently unknown. Here, we show a reduced Cd content in Cd-exposed mycorrhizal roots of Vaccinium myrtillus colonized by a metal tolerant isolate of the fungus Oidiodendron maius as compared to non-mycorrhizal roots. To better understand this phenotype, we applied Next Generation Sequencing technologies to analyze gene expression in V. myrtillus and O. maius Zn grown under normal and Cd-stressed conditions, in the free living and in the mycorrhizal status. The results clearly showed that Cd had a stronger impact on plant gene expression than symbiosis, whereas fungal gene expression was mainly regulated by symbiosis. The higher abundance of transcripts coding for stress related proteins in non-mycorrhizal roots may be related to the higher Cd content. Regulated plant metal transporters have been identified that may play a role in reducing Cd content in mycorrhizal roots exposed to this metal.

Cd tolerance, transcriptomics↗

Comparison of Polarized Radiative Transfer Codes Used by the EHT Collaboration

Interpretation of resolved polarized images of black holes by the Event Horizon Telescope (EHT) requires predictions of the polarized emission observable by an Earth-based instrument for a particular model of the black hole accretion system. Such predictions are generated by general relativistic radiative transfer (GRRT) codes, which integrate the equations of polarized radiative transfer in curved spacetime. A selection of ray-tracing GRRT codes used within the EHT Collaboration is evaluated for accuracy and consistency in producing a selection of test images, demonstrating that the various methods and implementations of radiative transfer calculations are highly consistent. When imaging an analytic accretion model, we find that all codes produce images similar within a pixel-wise normalized mean squared error (NMSE) of 0.012 in the worst case. When imaging a snapshot from a cell-based magnetohydrodynamic simulation, we find all test images to be similar within NMSEs of 0.02, 0.04, 0.04, and 0.12 in Stokes I , Q , U , and V , respectively. We additionally find the values of several image metrics relevant to published EHT results to be in agreement to much better precision than measurement uncertainties.

79 ASTRONOMY AND ASTROPHYSICS↗

Xyce Parallel Electronic Simulator Users' Guide (V. 7.3)

This manual describes the use of the Xyce Parallel Electronic Simulator. Xyce has been designed as a SPICE-compatible, high-performance analog circuit simulator, and has been written to support the simulation needs of the Sandia National Laboratories electrical designers. This development has focused on improving capability over the current state-of-the-art in the following areas: Capability to solve extremely large circuit problems by supporting large-scale parallel computing platforms (up to thousands of processors). This includes support for most popular parallel and serial computers; A differential-algebraic-equation (DAE) formulation, which better isolates the device model package from solver algorithms. This allows one to develop new types of analysis without requiring the implementation of analysis-specific device models; Device models that are specifically tailored to meet Sandia's needs, including some radiation-aware devices (for Sandia users only); Object-oriented code design and implementation using modern coding practices. Xyce is a parallel code in the most general sense of the phrase—a message passing parallel implementation—which allows it to run efficiently a wide range of computing platforms. These include serial, shared-memory and distributed-memory parallel platforms. Attention has been paid to the specific nature of circuit-simulation problems to ensure that optimal parallel efficiency is achieved as the number of processors grows.

42 ENGINEERING↗

NWChem: Past, present, and future

Specialized computational chemistry packages have permanently reshaped the landscape of chemical sciences by providing tools to support and guide the experimental effort and for prediction of chemical and materials properties. In this regard, a special role has been played by electronic structure packages where complex chemical and materials processes can be modeled using first-principle-driven methodologies. Over the last few decades, the rapid development of computing technologies and a tremendous increase in computational power has offered a unique chance to study complex chemical transformations using sophisticated and predictive many-body techniques to describe correlated behavior of electrons in molecular and condensed phase systems at different levels of theory. In enabling these simulations, a critical role has been played by novel parallel algorithms capable of taking advantage of computational resources to address polynomial scaling of electronic structure methods. NWChem was among the first electronic structure codes that focused on delivering scalable performance for electronic structure simulations. Herein, we briefly review the NWChem suite of computational codes including its history, design principles, parallel tools, current capabilities, outreach and outlook.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Drift kinetic electrostatic simulations of the edge localized mode heat pulse

In the present work, electrostatic drift kinetic simulations of parallel plasma transport within the tokamak scrape-off layer (SOL) are conducted using the COGENT code. The SOL configuration is represented in one-dimensional slab geometry, incorporating a heat source localized in the midplane. The heat source parameters correspond to those characterizing edge-localized modes observed in the Joint European Torus (JET) tokamak. The numerical model includes kinetic treatment of both ions and electrons, a simplified model for the gyrokinetic Poisson equation that allows one to step over short time scales associated with fast electrostatic shear Alfvèn waves, and the logical sheath boundary condition (LSBC) that enforces global system quasineutrality. A third-order accurate LSBC is derived to be consistent with the third-order accurate upwind advection scheme utilized in the code, and it was shown to noticeably impact the simulation results, especially parallel heat flux at the target plate. The findings of this study are in agreement with results from preceding fluid and kinetic simulations.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

PFPO plasma scenarios for exploration of long pulse operation in ITER

Long Pulse Scenarios (LPS) in ITER foreseen during the Pre-Fusion Power Operation (PFPO) phase of the ITER Research Plan (IRP) are assessed using 1.5D transport simulations within the ASTRA framework. Such assessment is required to predict the operational space for LPS operation in PFPO, as well as to evaluate which physics processes for LPS operation during Fusion Power Operation (FPO) could be studied during PFPO. An important aspect in the development of LPSs in PFPO is to minimize lifetime consumption of the Central Solenoid (CS) for these scenarios. The maximum pulse length achievable for LPSs in PFPO with no consumption of CS lifetime (currents in CS coils $⩽$30 kA per turn) has been assessed for a range of heating schemes and heating mixes, confinement regimes (L-mode and H-mode) and for helium and hydrogen plasmas. The operational space of LPS and pulse length has been explored through density scans with the Heating and Current Drive mix required for the FPO Q $⩾$ 5 steady-state plasma scenario (namely Neutral Beam Injection and Electron Cyclotron Heating) including acceptable shine through losses on the first wall for both helium and hydrogen plasmas. Fast particle physics aspects that are common between FPO plasmas and LPS PFPO H-mode plasmas at low densities are studied including MHD stability analysis with the KINX code and non-perturbative critical gradient model based on high-n Toroidal Alfven Eigenmodes (TAE) stability kinetic ballooning code HINST calculations.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Interpretive modeling of tungsten divertor leakage during experiments with neon gas seeding

Abstract Many existing and future tokamaks with tungsten divertors operate, or will operate, with low- Z impurity seeding, but the direct effect of these seeded impurities on tungsten Scrape-off-Layer (SOL) transport has not been explored in detail. This paper reports on a DIII-D experiment designed to test how tungsten divertor leakage from the Small-Angle Slot V-Shaped, tungsten-coated divertor is impacted by neon seeding at a variety of injection rates and poloidal injection locations. Measurements from the experiment show an inverse relationship between the neon injection rate and the tungsten core penetration factor. Interpretive modeling is performed with a combination of the SOLPS-ITER and DIVIMP codes to assess the underlying tungsten behavior. The modeling results show that the reduction in tungsten divertor leakage is driven by both an increase in the divertor collisionality as well as a reduction in the ion temperature gradient near the divertor target. Collisions between low- Z impurities and tungsten impurities are found to have a significant impact on the tungsten SOL transport, such that ignoring the low- Z impurity collisional effects on the tungsten transport can result in an overestimate of the divertor leakage by an order-of-magnitude. Given the importance of these localized interactions, neon seeding from the closed, slot-like divertor has a clear advantage in being able to reduce tungsten divertor leakage without the high levels of neon core contamination that occur when seeding from other poloidal locations.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Sensitivity study with a $\textit{D}$ and $\textit{B}$ mesons modular simulation code of heavy flavor $R_{AA}$ and azimuthal anisotropies based on beam energy, initial conditions, hadronization, and suppression mechanisms

Heavy flavor probes provide important information about the in-medium properties of the quark-gluon plasma produced in heavy-ion collisions. In this work, we investigate the effects of 2D + 1 event-by-event fluctuating hydrodynamic backgrounds on the nuclear suppression factor and momentum anisotropies of heavy flavor mesons and nonphotonic electrons. Using the state-of-the-art $\textit{D}$ and $\textit{B}$ mesons modular simulation code (called “DAB-MOD”), we perform a systematic comparison of different transport equations in the same background, including a few energy-loss models—with and without energy-loss fluctuations—and a relativistic Langevin model with different drag parametrizations. We present the resulting $\textit{D}$ and $\textit{B}$ mesons $R_{A A}, v_2, v_3,$ and $v_4$ as well as multiparticle cumulants, in AuAu collisions at $\sqrt{s_{NN}}$ = 200 GeV and PbPb collisions at $\sqrt{s_{NN}}$ = 2.76 TeV and $\sqrt{s_{NN}}$ = 5.02 TeV , and compare them to the available experimental data. The $v_2${4}/$v_2${2} ratio, which is known to be a powerful probe of the initial conditions and flow fluctuations in the soft sector, is also studied in the context of heavy flavor. We also investigate the correlations between the transverse anisotropies of heavy mesons and all charged particles to better understand how heavy quarks couple to the hydrodynamically expanding quark-gluon plasma. Finally, we study the influence that different initial conditions and the implementation of heavy-light quark coalescence has on our results.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Start-to-end self-consistent simulation of the UEM beamline

Addressing the preliminary design review report of the ultrafast electron microscope (UEM), start-to-end self-consistent simulations were carried out to explore fundamental aspects affecting the resolution (space-charge effects, energy spread, shot-to-shot energy jitter, contrast formation, etc.). The electron beam energy spread in the single-shot mode and the effective energy spread in the accumulation mode, equivalent to the convolution of the single-shot energy spread and shot-to-shot energy jitter, have been identified as the ultimate limits of the instrument resolution. A full self-consistent simulation from the photocathode to the detector is being performed using the GPT code to find out what resolution can be achieved. Preliminary results of the start-to-end simulations are reported in this note and the plan of further simulations is presented.

43 PARTICLE ACCELERATORS↗

FAST-1.2.2: A Computer Code for Thermal-Mechanical Nuclear Fuel Analysis under Steady-state and Transients

Fuel Analysis under Steady-state and Transients (FAST) is the U.S. Nuclear Regulatory Commission (NRC)’s computer code that calculates the steady-state and transient response of nuclear reactor fuel rods during long-term in-reactor burnup, anticipated operational occurrences (AOOs), design basis accidents (DBAs), and dry storage conditions. The code calculates the temperature, pressure, and deformation of a fuel rod as functions of time-dependent fuel rod power and coolant boundary conditions. The phenomena modeled by the code include heat conduction through the fuel and other materials, heat transfer from the cladding-to-coolant, cladding elastic and plastic deformation (including creep), fuel-cladding mechanical interaction, fission gas release from the fuel, rod internal pressure, void volume, and cladding oxidation. The code contains necessary material and coolant properties, as well as clad-to-coolant heat transfer correlations, for normal operation through postulated accidents and AOOs for today’s U.S.-based light water reactor (LWR) fuel designs. FAST-1.2.2 also contains preliminary materials and models for new LWR fuel concepts, such as accident tolerant fuel (ATF), and non-LWR fuel concepts such as metallic fuels for sodium fast reactors (SFRs). FAST has been developed for use on Windows and Linux operating systems. This document describes FAST-1.2.2 and is one of a series of documents on the code; the other documents detail the material properties used by FAST as well as its integral assessment to experiments and commercial data.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Nek5000 developments in support of industry and the NRC

This year, the Nuclear Energy Advanced Modeling Simulation program (NEAMS) thermal-hydraulics verification and validation (V&V) work has focused in three areas of Nek5000 V&V-driven development. First, in a close collaborative effort with the U. S. Nuclear Regulatory Commission (NRC) staff, we have continued V&V efforts for the HYMERES-2 project using the OECD/NEA sponsored testing in the PSI PANDA facility. This year’s focus of ANL-NRC collaboration involves Nek5000 setups and validation for a range of problems relevant to and including the HYMERES-2 benchmark from PSI. The primary outcome of this year efforts is a more efficient geometry and inlet modeling simplification after a careful sensitivity study of the inlet profiles and pipe geometries. The resulting modeling choice of a short recycling/fully-developed turbulent inlet is within the experimental uncertainty estimate. This finding simplifies the next step of the cross-V&V HYMERES-2 project. In addition, the ANL team continue to provide assistance to the NRC staff in the form of Nek5000 application support in general and on the use of the HPC platforms of ALCF and INL in particular. This supports the NRC’s assessment of Nek5000 for use with the NRC Blue CRAB code suite. Second, we have implemented and tested more robust model of URANS, namely the k – τ model, a variant of the k-ω model, along with other improvements to RANS Nek5000 modeling in general. Because of its demonstrated robustness and stability, the k – τ model is the only RANS model that has been implemented in the new GPU version of the Nek5000 code, nekRS. Lastly, we report the initial implementation of Jacobian-free Newton Krylov approach to the direct Newton method for steady fluid solvers aimed at acceleration of RANS modeling and at IC improvement for LES campaigns. Also leveraging the Exascale Computing Project (ECP) ANL/CEED & SMR team’s software development effort to support NEAMS problems at large scale of the advanced computing architectures, NekRS, a GPU variant of Nek5000, built on top of kernels from libParanumal using OCCA for portability, has been successfully run on the full system of Summit (4608 nodes, 27648 GPUs).

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

Discovering invariant spatial features in electron energy loss spectroscopy images on the mesoscopic and atomic levels

Over the last two decades, Electron Energy Loss Spectroscopy (EELS) imaging with a scanning transmission electron microscope has emerged as a technique of choice for visualizing complex chemical, electronic, plasmonic, and phononic phenomena in complex materials and structures. The availability of the EELS data necessitates the development of methods to analyze multidimensional data sets with complex spatial and energy structures. Traditionally, the analysis of these data sets has been based on analysis of individual spectra, one at a time, whereas the spatial structure and correlations between individual spatial pixels containing the relevant information of the physics of underpinning processes have generally been ignored and analyzed only via the visualization as 2D maps. Here, we develop a machine learning-based approach and workflows for the analysis of spatial structures in 3D EELS data sets using a combination of dimensionality reduction and multichannel rotationally invariant variational autoencoders. This approach is illustrated for the analysis of both the plasmonic phenomena in a system of nanowires and in the core excitations in functional oxides using low loss and core-loss EELS, respectively. The code developed in this manuscript is open sourced and freely available and provided as a Jupyter notebook for the interested reader.

36 MATERIALS SCIENCE↗

Early results in the search for extreme coronal line emitters with the Dark Energy Spectroscopic Instrument

Here, we present the results of our search through the early data release (EDR) of the Dark Energy Spectroscopic Instrument (DESI) for extreme coronal line emitters (ECLEs) – a rare classification of galaxies displaying strong, high-ionization iron coronal emission lines within their spectra. With the requirement of a strong X-ray continuum to generate the coronal emission, ECLEs have been linked to both active galactic nuclei (AGNs) and tidal disruption events (TDEs). We focus our search on identifying TDE-linked ECLEs. We identify three such objects within the EDR sample, highlighting DESI’s effectiveness for discovering new nuclear transients, and determine a galaxy-normalized TDE-linked ECLE rate of RG=5 −3+5×10−6 galaxy−1 yr−1 at a median redshift of z=0.2 – broadly consistent with previous work. Additionally, we identify more than 200 AGNs displaying coronal emission lines, which serve as the primary astrophysical contaminants in searches for TDE-related events. We also include an outline of the custom python code developed for this search.

Clark, Peter [Southampton U.; Portsmouth U., ICG] ↗