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DOE OSTI2021

Importance of resistivity on edge-localized mode onset in spherical tokamaks

In this work, we explore the impact of realistic plasma resistivity on the linear stability of peeling-ballooning (PB) modes in tokamak discharges with low-aspect ratio. For this study we consider discharges that are subject to edge-localized modes (ELMs) in the National Spherical Torus Experiment (NSTX). Employing the state of the art extended-magnetohydrodynamic (MHD) code M3D-C1 it is demonstrated that non-ideal effects can significantly affect PB stability thresholds in NSTX discharges. In particular, robust resistive PB modes are found to exist well before the ideal PB stability threshold is met. These novel results can explain why ideal-MHD theory often does not accurately describe ELM onset in spherical torus configurations, and also present a valuable basis for the development of a predictive model for ELMs in low-aspect ratio tokamaks.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2025

Modeling betatron radiation using particle-in-cell codes for plasma wakefield accelerator diagnostics

The analysis of plasma wakefield acceleration experimental measurements, particularly in the characterization of photons emitted through the betatron radiation mechanism, requires the development of accurate numerical models. These computational models are crucial for supporting modern instrumentation designed to measure the single-shot, double-differential angular-energy radiation spectra resulting from interactions between beams and plasmas. Motivated by the needs of such applications, this paper presents detailed numerical models of betatron radiation generated in beam-plasma acceleration experiments. These models are based on the integration of the Liénard-Wiechert (LW) potentials, applied to computed particle trajectories. The particle trajectories are generated using three distinct methods: first, by tracking particles through idealized fields in the blowout regime of PWFA; second, by obtaining trajectories using the fast quasistatic particle-in-cell (PIC) code quickpic; and third, obtaining trajectories from the fully self-consistent PIC code osiris. To ensure the accuracy and reliability of these models, the paper includes various benchmark tests using analytical expressions, as well as employing the PIC code epoch, which takes an alternative approach by using a Monte Carlo quantum electrodynamics (QED)-based radiation model. Additionally, the paper presents simulations of the expected experimental betatron radiation spectra, taking into account parameters relevant to PWFA and plasma photocathode experiments at the SLAC FACET-II facility.

Yadav, M. [University of California, Los Angeles, ↗

DOE OSTI2021

Implementation of a self-consistent slab model of bilayer structure in the SasView suite

Slab models are simple and useful structural descriptions which have long been used to describe lyotropic lamellar phases, such as lipid bilayers. Typically, slab models assume a midline symmetry and break a bilayer structure into three pieces, a central solvent-free core and two symmetric outer layers composed of the soluble portion of the amphiphile and associated solvent. This breakdown matches reasonably well to the distribution of neutron scattering length density and therefore is a convenient and common approach for the treatment of small-angle scattering data. Here, an implementation of this model within the SasView software suite is reported. The implementation is intended to provide physical consistency through the area per amphiphile molecule and number of solvent molecules included within the solvent-exposed outer layer. The proper use of this model requires knowledge of (or good estimates for) the amphiphile and solvent molecule volume and atomic composition, ultimately providing a self-consistent data treatment with only two free parameters: the lateral area per amphiphile molecule and the number of solvent molecules included in the outer region per amphiphile molecule. Here, the use of this code is demonstrated in the fitting of standard lipid bilayer data sets, obtaining structural parameters consistent with prior literature and illustrating the typical and ideal cases of fitting for neutron scattering data obtained using single or multiple contrast conditions. While demonstrated here for lipid bilayers, this model is intended for general application to block copolymers, surfactants, and other lyotropic lamellar phase structures for which a slab model is able to reasonably estimate the neutron scattering length density/electron-density profile of inner and outer layers of the lamellae.

36 MATERIALS SCIENCE↗

DOE OSTI2024

Self‐consistent transport simulation of boron dust particle injection in the peripheral plasma in Large Helical Device

Abstract The trajectories and the ablation positions of boron dust particles dropped from an impurity powder dropper in the peripheral plasma in the Large Helical Device (LHD) were calculated using a three‐dimensional edge plasma simulation code (EMC3‐EIRENE) and a dust transport simulation code (DUSTT). The simulation shows that the trajectory of the boron dust particles is deflected at the upper divertor leg due to the effect of the hydrogen plasma flow, and the ablation positions of the dust particles in an ergodic layer change toward the outboard side of the torus for higher plasma densities. The effect of the boron ion flow in the divertor leg on the deflection is investigated by coupling the two codes self‐consistently. The simulation predicts that the boron ions in the divertor leg, which are produced by sputtering on the divertor plates, which do not affect the change in the ablation positions. It also shows that the ablation positions move toward the inboard side and approach the Last Closed Flux Surface (LCFS) in case of increased boron dust drop rates, which is caused by the lowered plasma flow in the upper divertor leg due to the lowered electron temperature by radiation cooling by the dropped dust particles.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2021

Methods for a blind analysis of isobar data collected by the STAR collaboration

In 2018, the STAR collaboration collected data from $_{44}^{96}{\mathrm{Ru}}+_{44}^{96}{\mathrm{Ru}}$ and $_{40}^{96}{\mathrm{Zr}}+_{40}^{96}{\mathrm{Zr}}$ at $\sqrt{s_\text {NN}}=200$ GeV to search for the presence of the chiral magnetic effect in collisions of nuclei. The isobar collision species alternated frequently between $_{44}^{96}{\mathrm{Ru}}+_{44}^{96}{\mathrm{Ru}}$ and $_{40}^{96}{\mathrm{Zr}}+_{40}^{96}{\mathrm{Zr}}$ . In order to conduct blind analyses of studies related to the chiral magnetic effect in these isobar data, STAR developed a three-step blind analysis procedure. Analysts are initially provided a “reference sample” of data, comprised of a mix of events from the two species, the order of which respects time-dependent changes in run conditions. After tuning analysis codes and performing time-dependent quality assurance on the reference sample, analysts are provided a species-blind sample suitable for calculating efficiencies and corrections for individual $\approx 30$-min data-taking runs. For this sample, species-specific information is disguised, but individual output files contain data from a single isobar species. Only run-by-run corrections and code alteration subsequent to these corrections are allowed at this stage. Following these modifications, the “frozen” code is passed over the fully un-blind data, completing the blind analysis. As a check of the feasibility of the blind analysis procedure, analysts completed a “mock data challenge,” analyzing data from Au + Au collisions at $\sqrt{s_\text {NN}}=27$ GeV, collected in 2018. The Au + Au data were prepared in the same manner intended for the isobar blind data. Finally, the details of the blind analysis procedure and results from the mock data challenge are presented.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2023

UQpy v4.1: Uncertainty quantification with Python

This paper presents the latest improvements introduced in Version 4 of the UQpy, Uncertainty Quantification with Python, library. In the latest version, the code was restructured to conform with the latest Python coding conventions, refactored to simplify previous tightly coupled features, and improve its extensibility and modularity. To improve the robustness of UQpy, software engineering best practices were adopted. A new software development workflow significantly improved collaboration between team members, and continuous integration and automated testing ensured the robustness and reliability of software performance. Continuous deployment of UQpy allowed its automated packaging and distribution in system agnostic format via multiple channels, while a Docker image enables the use of the toolbox regardless of operating system limitations.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2022

Design study of an edge current density diagnostic using new high-performance single-channel beam emission spectrometers at DIII-D

A novel Motional Stark Effect spectroscopy system has been designed for application at the DIII-D tokamak. The system is optimized for studies of the poloidal and toroidal magnetic field in the plasma pedestal region with frame rates of up to 10 kHz. Further, light from an existing high-photon-throughput collection lens is analyzed using four single-channel f/2.8 Czerny–Turner spectrometers that use custom-made lens systems instead of mirrors. Each spectrometer has two separate outgoing legs and is operated in a positive grating order, which allows for simultaneous observations of D-alpha and D-beta spectra. Forward modeling using the code FIDASIM shows a radial resolution of the system close to 0.6 cm and sufficiently good spectral resolution when masking the high throughput light collection lens in the horizontal direction to avoid overly strong Doppler broadening of beam emission lines. Moreover, a detailed sensitivity study considering realistic levels of readout and photon noise shows that the poloidal and toroidal magnetic field strengths can be inferred with an uncertainty of less than 1%, which will allow the inference of changes of the plasma current during transient events.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2024

Unveiling the microbial realm with VEBA 2.0: a modular bioinformatics suite for end-to-end genome-resolved prokaryotic, (micro)eukaryotic and viral multi-omics from either short- or long-read sequencing

Abstract The microbiome is a complex community of microorganisms, encompassing prokaryotic (bacterial and archaeal), eukaryotic, and viral entities. This microbial ensemble plays a pivotal role in influencing the health and productivity of diverse ecosystems while shaping the web of life. However, many software suites developed to study microbiomes analyze only the prokaryotic community and provide limited to no support for viruses and microeukaryotes. Previously, we introduced the Viral Eukaryotic Bacterial Archaeal (VEBA) open-source software suite to address this critical gap in microbiome research by extending genome-resolved analysis beyond prokaryotes to encompass the understudied realms of eukaryotes and viruses. Here we present VEBA 2.0 with key updates including a comprehensive clustered microeukaryotic protein database, rapid genome/protein-level clustering, bioprospecting, non-coding/organelle gene modeling, genome-resolved taxonomic/pathway profiling, long-read support, and containerization. We demonstrate VEBA’s versatile application through the analysis of diverse case studies including marine water, Siberian permafrost, and white-tailed deer lung tissues with the latter showcasing how to identify integrated viruses. VEBA represents a crucial advancement in microbiome research, offering a powerful and accessible software suite that bridges the gap between genomics and biotechnological solutions.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

FAST-1.0.1 User Installation and Verification Guide

The purpose of this document is to provide the user information about the installation of FAST-1.0.1 on their computers or servers. General information about the code and supported operating systems is described in Section 1.0.1. Self-service oriented FAST-1.0.1 software licensing steps are described in Section 2.0. An installation verification test suite is provided with FAST-1.0.1 and described in Section 3.0. A convenience script for converting FRAPCON to FAST inputs is discussed in Section 4.0. FAST-1.0.1 was developed and released under a software quality assurance program based upon NQA-1-2017. FAST-1.0.1 is the latest baseline code and the result of a bug fixes to FAST-1.0 with other software and methodology developments. The installation verification test suite contains both steady state and transient Anticipated Operation Occurrences (AOOs). Capability to model accident conditions, such as Reactivity Initiated Accidents (RIAs) and Loss Of Coolant Accidents (LOCAs), are targeted for a later release of FAST. FRAPTRAN-2.0 will continue to be used for accident conditions until the release of FAST with accident condition modeling capabilities.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

DOE OSTI2023

Modeling of the cold electron plasma density for radiation belt physics

This review focusses strictly on existing plasma density models, including ionospheric source models, empirical density models, physics-based and machine-learning density models. This review is framed in the context of radiation belt physics and space weather codes. The review is limited to the most commonly used models or to models recently developed and promising. A great variety of conditions is considered such as the magnetic local time variation, geomagnetic conditions, ionospheric source regions, radial and latitudinal dependence, and collisional vs. collisionless conditions. These models can serve to complement satellite observations of the electron plasma density when data are lacking, are for most of them commonly used in radiation belt physics simulations and can improve our understanding of the plasmasphere dynamics.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2024

Early experiences on the OLCF Frontier system with AthenaPK and Parthenon–Hydro

The Oak Ridge Leadership Computing Facility (OLCF) has been preparing the nation's first exascale system, Frontier, for production and end users. Frontier is based on HPE Cray's new EX architecture and Slingshot interconnect and features 74 cabinets of optimized 3rd Gen AMD EPYC CPUs for HPC and AI and AMD Instinct 250X accelerators. As a part of this preparation, “real-world” user codes have been selected to help assess the functionality, performance, and usability of the system. This article describes early experiences using the system in collaboration with the Hamburg Observatory for two selected codes, which have since been adopted in the OLCF test harness. Experiences discussed include efforts to resolve performance variability and per-cycle slowdowns. Results are shown for a performance portable astrophysical magnetohydronamics code, AthenaPK, and a mini-application stressing the core functionality of a performance portable block-structured adaptive mesh refinement framework, Parthenon-Hydro. Here, these results show good scaling characteristics to the full system. At the largest scale, the Parthenon-Hydro miniapp reaches a total of $1.7$ $\times$ $10^{13}$ zone-cycles/s on 9216 nodes (73,728 logical GPUs) at ≈92% weak scaling parallel efficiency (starting from a single node using a second-order, finite-volume method).

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2025

On the role of ion temperature gradient turbulence in driving ion thermal transport in neutral beam injection-heated L-mode plasmas in a superconducting tokamak

In this paper, we report a detailed experimental study of the role of ion-temperature-gradient driven turbulence in driving ion thermal transport in neutral beam injection (NBI)-heated L-mode plasmas in Experimental Advanced Superconducting Tokamak (EAST) (Wan et al 2000 Nucl. Fusion 40 1057) coupled with linear and nonlinear gyrokinetic simulations. Significant ion-scale turbulence k ⟂ < cm −1 (k ⟂ < 1.5, where k ⟂ where is the perpendicular wavenumber and ρ s is the ion gyroradius calculated using local electron temperature T e ), measured with a microwave reflectometer, is observed in the plasma core at for r/a ≈ 0.265 and 0.5 (where r is half the diameter of the closed flux surface at a given radial position, and a is half the diameter of the last closed flux surface). Local linear stability analysis with experimental equilibrium quantities at these two radial locations using the GS2 gyrokinetic code shows that the most unstable ion-scale micro-instability is the ion temperature gradient (ITG) mode. Since the computed maximum ion-scale linear growth rates are larger than the local Waltz-Miller E × B shearing rate (Waltz and Miller 1999 Phys. Plasmas 6 4265), the E × B shear is unable to suppress ion-scale turbulence, consistent with the experimental observation of ion-scale turbulence. Experimental ion and electron thermal transports, calculated with power balance analysis, are both anomalous with ion thermal transport being the dominant channel. Nonlinear gyrokinetic simulations using the electrostatic global particle-in-cell gyrokinetic tokamak simulation (GTS) code (Weixing Wang et al 2010 Phys. Plasmas 17 072511) show good quantitative agreement between predicted ion thermal transport and that from the power balance analysis. These results demonstrate for the first time the important role of ITG turbulence in driving thermal transport in NBI-heated L-mode plasmas in EAST, showing the effectiveness of GTS code in simulating electrostatic turbulence in EAST and the need of suppressing ITG turbulence to improve energy confinement in EAST.

Sun, P. J. [Chinese Academy of Sciences (CAS), Hef↗

DOE OSTI2020

Direct numerical simulations of turbulent reacting flows with shock waves and stiff chemistry using many-core/GPU acceleration

Compressible reacting flows may display sharp spatial variation related to shocks, contact discontinuities or reactive zones embedded within relatively smooth regions. The presence of such phenomena emphasizes the relevance of shock-capturing schemes such as the weighted essentially non-oscillatory (WENO) scheme as an essential ingredient of the numerical solver. However, these schemes are complex and have more computational cost than the simple high-order compact or non-compact schemes. In this paper, we present the implementation of a seventh-order, minimally-dissipative mapped WENO (WENO7M) scheme in a newly developed direct numerical simulation (DNS) code called KAUST Adaptive Reactive Flows Solver (KARFS). In order to make efficient use of the computer resources and reduce the solution time, without compromising the resolution requirement, the WENO routines are accelerated via graphics processing unit (GPU) computation. The performance characteristics and scalability of the code are studied using different grid sizes and block decomposition. Furthermore, the performance portability of KARFS is demonstrated on a variety of architectures including NVIDIA Tesla P100 GPUs and NVIDIA Kepler K20X GPUs. In addition, the capability and potential of the newly implemented WENO7M scheme in KARFS to perform DNS of compressible flows is also demonstrated with model problems involving shocks, isotropic turbulence, detonations and flame propagation into a stratified mixture with complex chemical kinetics.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2025

Enhanced Collisional Losses from a Magnetic Mirror Using the Lenard-Bernstein Collision Operator

Collisions are crucial in governing particle and energy transport in plasmas confined in a magnetic mirror trap. Modern gyrokinetic codes model transport in magnetic mirrors, but some utilize approximate model collision operators. This study focuses on a Pastukhov-style method of images calculation of particle and energy confinement times using a Lenard-Bernstein model collision operator. Prior work on parallel particle and energy balances used a different Fokker-Planck plasma collision operator. The method must be extended in non-trivial ways to study the Lenard-Bernstein operator. To assess the effectiveness of our approach, we compare our results with a modern finite element solver. Our findings reveal that the particle confinement time scales like a exp( a 2 ) using the Lenard-Bernstein operator, in contrast to the more accurate scaling that the Coulomb collision operator would yield a 2 exp( a 2 ), where a 2 is approximately proportional to the ambipolar potential. We propose that codes solving for collisional losses in magnetic mirrors utilizing the Lenard-Bernstein or Dougherty collision operator scale their collision frequency of any electrostatically confined species. This study illuminates the collision operator’s intricate role in the Pastukhov-style method of images calculation of collisional confinement.

fusion plasma↗

DOE OSTI2023

Star formation rate and stellar mass calibrations based on infrared photometry and their dependence on stellar population age and extinction

The stellar mass (M $\star$ ) and the star formation rate (SFR) are among the most important features that characterize galaxies. Measuring these fundamental properties accurately is critical for understanding the present state of galaxies, their history, and future evolution. Infrared (IR) photometry is widely used to measure the M $\star$ and SFR of galaxies because the near-IR traces the continuum emission of the majority of their stellar populations (SPs), and the mid/far-IR traces the dust emission powered by star-forming activity. This work explores the dependence of the IR emission of galaxies on their extinction, and the age of their SPs. It aims to provide accurate and precise IR-photometry SFR and M $\star$ calibrations that account for SP age and extinction while providing quantification of their scatter. We used the CIGALE spectral energy distribution (SED) fitting code to create model SEDs of galaxies with a wide range of star formation histories, dust content, and interstellar medium properties. We fit the relations between M $\star$ and SFR with IR and optical photometry of the model-galaxy SEDs with the Markov chain Monte Carlo (MCMC) method. As an independent confirmation of the MCMC fitting method, we performed a machine-learning random forest (RF) analysis on the same data set. The RF model yields similar results to the MCMC fits, thus validating the latter. This work provides calibrations for the SFR using a combination of the WISE bands 1 and 3, or the JWST NIR-F200W and MIRI-F2100W. It also provides mass-to-light ratio calibrations based on the WISE band-1, the JWST NIR-F200W, and the optical u - r or g - r colors. These calibrations account for the biases attributed to the SP age, while they are given in the form of extinction-dependent and extinction-independent relations. The proposed calibrations show robust estimations while minimizing the scatter and biases throughout a wide range of SFRs and stellar masses. The SFR calibration offers better results, especially in dust-free or passive galaxies where the contributions of old SPs or biases from the lack of dust are significant. Similarly, the M $\star$ calibration yields significantly better results for dusty and high-SFR galaxies where dust emission can otherwise bias the estimations.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2024

Isotope impact on Alfvén eigenmodes and fast ion transport in DIII-D

Abstract Measurements of beam driven Alfvén Eigenmode (AE) activity in matched deuterium (D) and hydrogen (H) DIII-D plasmas show a dramatic difference in unstable mode activity and fast ion transport for a given injected beam power. The dependence of the unstable AE spectrum in reversed magnetic shear plasmas on beam and thermal species is investigated in the current ramp by varying beam power in a sequence of discharges for fixed thermal and beam species at fixed density. In general, a spectrum of Reversed Shear Alfvén Eigenmodes (RSAEs) and Toroidal Alfvén Eigenmodes (TAEs) are driven unstable with sub-Alfvénic D beam injection while primarily only RSAEs are driven unstable for the H beam cases investigated. Further, for a given beam power, the driven AE amplitude is always reduced with H beams relative to D and for H thermal plasma relative to pure D or mixed D/H plasmas. Estimates of the fast ion stored energy combined with modeling using the hybrid kinetic-MHD code MEGA indicate that the dominant mechanism contributing to the difference between H and D beam drive is the faster classical slowing down of H beam ions relative to D and the resultant lower beam ion pressure. Calculations of the AE induced stored energy deficits using the reduced critical gradient model TGLFEP show quantitative agreement with the observed dependencies on injected power, isotope and minimum safety factor.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2026

Dark Energy Survey: DESI-independent angular BAO measurement

In this work, we present a measurement of the angular baryon acoustic oscillation (BAO) scale from the completed Dark Energy Survey (DES) dataset excluding the area of overlap with the Dark Energy Spectroscopic Instrument (DESI). We follow the same methodology and validation process as in the DES Y6 BAO analysis. We interpret the impact of this measurement in the context of the statistical preference for 𝑤 0 ⁢𝑤 𝑎 cold dark matter (CDM) over Λ⁢CDM when combined with DES Y5 Type Ia supernovae (SN), Planck CMB, and DESI BAO. Based on our previous work, using the full Y6 DES BAO sample, in combination with SN, CMB and DESI data release 1 (DR1) BAO, added 0.3⁢𝜎 in this preference (from 3.7⁢𝜎 to 4.0⁢𝜎), but this ignored possible correlations between datasets. Using our new DESI-independent DES BAO likelihood instead, we find a smaller increase in the statistical preference for 𝑤 0 ⁢𝑤 𝑎 ⁢CDM, from 3.7⁢𝜎 to 3.8⁢𝜎 when using DESI DR1 BAO, and from 4.0⁢𝜎 to 4.1⁢𝜎 when updating to the more recent DESI data release 2 (DR2) BAO. These significances reduce to 3.1⁢𝜎 when using the new calibrated DES SN-Dovekie. Alongside this work, we publicly release baofit_wtheta, the BAO fitting code for the angular correlation function used in the DES Y6 BAO analysis.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2025

Eucalyptus – An Analysis Suite for Fault Trees with Uncertainty Quantification

Eucalyptus is a novel code developed at Lawrence Livermore National Laboratory to incorporate uncertainty quantification into Fault Tree Analysis (FTA). This tool addresses the challenge of imperfect knowledge in “grey-box” systems by allowing analysts to incorporate and propagate uncertainty from component-level assessments to system-level effects. Eucalyptus facilitates a consistent evaluation of the impact of subject matter expert judgment and knowledge gaps on overall system response by Monte Carlo generation of possible system fault trees, sampling probabilities of the existence of subsystems and components. Here, the code supports the specification of fault trees through text and allows export to various formats, including auto-generated images, easing analysis and reducing errors. It has undergone extensive verification testing, demonstrating its reliability and readiness for deployment, and leverages on-node parallelism for rapid analysis. Example analyses are shown that include the identification of system failure paths and quantification of the value of further information about system components.

Fault Tree Analysis↗