EMPIRE User Manual
This is the user manual for EMPIRE, a simulation code for electromagnetics and plasma physics.
70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.
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EMPIRE-PIC: A Performance Portable Unstructured Particle-in-Cell Code
In this study we introduce EMPIRE-PIC, a finite element method particle-in-cell (FEM-PIC) application developed at Sandia National Laboratories. The code has been developed in C++ using the Trilinos library and the Kokkos Performance Portability Framework to enable running on multiple modern compute architectures while only requiring maintenance of a single codebase. EMPIRE-PIC is capable of solving both electrostatic and electromagnetic problems in two- and three-dimensions to second-order accuracy in space and time. In this paper we validate the code against three benchmark problems — a simple electron orbit, an electrostatic Langmuir wave, and a transverse electromagnetic wave propagating through a plasma. We demonstrate the performance of EMPIRE-PIC on four different architectures: Intel Haswell CPUs, Intel's Xeon Phi Knights Landing, ARM Thunder-X2 CPUs, and NVIDIA Tesla V100 GPUs attached to IBM POWER9 processors. This analysis demonstrates scalability of the code up to more than two thousand GPUs, and greater than one hundred thousand CPUs.
97 MATHEMATICS AND COMPUTING↗
3D full wave fast wave modeling with realistic antenna geometry and SOL plasma
This paper reports the significant advancement of our ability to model and to understand how RF waves interact with the SOL plasma, by simulating the full torus 3D SOL plasma together with the antenna and core plasma. We introduce and use a recently developed and open source code, Petra-M, which was constructed on the scalable MFEM C++ finite element library, and performed 3D full wave simulations in the HHFW regime for both NSTX-U and LAPD plasmas. A first full wave simulation for a full 3D torus including a realistic antenna geometry and SOL plasma region for NSTX-U is presented. A scan of the antenna phasing shows a strong interaction between FWs and the SOL plasma for lower antenna phasing, which is consistent with previous NSTX HHFW observations. The effect of the 3D wave field on the fast ion population from NBI beams in NSTX-U is also discussed by using the 3D field obtained from the Petra-M simulations in the full-orbit following particle SPIRAL code. On LAPD, 3D full wave simulations of a new HHFW 4-strap antenna recently installed by TAE Technologies on LAPD are performed showing a qualitative agreement with experimental data.
Bertelli, Nicola↗
Sensitivity and uncertainty analysis of PWR spent fuel observables to operational and model parameters
Sensitivity and uncertainty analyses of spent nuclear fuel (SNF) observables - decay heat, neutron and γ-ray emission rate - to operational and model parameters have been performed. A 2D model representing a typical PWR 17x17 UO{sub 2} fuel assembly has been taken as reference. The Serpent code and ENDF/B-VII.1 evaluated nuclear data library have been used for the analyses. Relative uncertainty of decay heat, neutron and γ-ray emission rates due to Monte Carlo counting statistics, as well as the number of fuel pin radial regions required for an accurate characterization of SNF neutron emission, have been estimated. A parametric study has been carried out to investigate the impact of the homogenization to an average value of the fuel and moderator temperature, boron concentration power and burnup on the prediction of the selected observables. In addition, linear sensitivity coefficients have been calculated. (authors)
11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
AlphaZero Reimplementation with Zoning Game and Associated Materials [SWR-26-016]
Here, we present a de novo, extensible, modular, research-oriented, single-player reimplementation of the "AlphaZero" class of algorithms originally described in [1]. We also present a novel task called the Zoning Game, designed as a toy problem to test the applicability of various AlphaZero-based paradigms to infrastructure planning problems, along with several other games. We implement specializations of AlphaZero to play several games. We also include code that serves as a starting point to explore language generation with AlphaZero, as well as documentation and other related materials. [1] Silver, D., Schrittwieser, J., Simonyan, K., Antonoglou, I., Huang, A., Guez, A., Hubert, T., Baker, L., Lai, M., Bolton, A., Chen, Y., Lillicrap, T., Hui, F., Sifre, L., van den Driessche, G., Graepel, T., & Hassabis, D. (2017). Mastering the game of Go without human knowledge. Nature, 550(7676), 354–359. https://doi.org/10.1038/nature24270
Konar-Steenberg, Gabriel [National Laboratory of t↗
Surrogate modeling of Monte Carlo radiation transport with convolutional neural networks for shielding optimization
Here, we present a machine learning (ML)-based surrogate model using convolutional neural networks (CNN) designed to emulate the attenuation of neutron fields as they pass through various shielding materials. This model can compute the outgoing neutron flux almost instantaneously and achieves reasonable accuracy compared to traditional Monte Carlo (MC)-based codes, which are computationally intensive. This emulator alleviates the complexity of neutron radiation transport through shielding materials by reducing the dimensionality and enables shielding optimization for a known radiation environment. This optimization process, which would have taken an unrealistic timeline due to several complex radiation transport simulations, can now be achieved in minutes, thus increasing computational capabilities in radiation shielding assessment. We demonstrate the applications of this emulator in computing effective dose rates and optimizing shielding solutions for a heavy-ion accelerator facility, such as the Facility for Rare Isotope Beams, where secondary neutrons produced via beam interactions dominate the radiation environment.
accelerator shielding↗
Simulation of multi-shell fullerenes using Machine-Learning Gaussian Approximation Potential
Multi-shell fullerenes ”buckyonions ” were simulated, starting from initially random configurations, using a density-functional-theory (DFT)-trained machine-learning carbon potential within the Gaussian Approximation Potential (GAP) Framework [Volker L. Deringer and Gábor Csányi, Phys. Rev. B 95, 094203 (2017)]. Fullerenes formed from seven different system sizes, ranging from 60 ~ 3774 atoms, were considered. The buckyonions are formed by clustering and layering starting from the outermost shell and proceeding inward. Inter-shell cohesion is partly due to interaction between delocalized π electrons protruding into the gallery. The energies of the models were validated ex post facto using density functional codes, VASP and SIESTA , revealing an energy difference within the range of 0.02 - 0.08 eV/atom after conjugate gradient energy convergence of the models was achieved with both methods.
74 ATOMIC AND MOLECULAR PHYSICS↗
Accurately simulating nine-dimensional phase space of relativistic particles in strong fields
Next-generation high-power laser systems that can be focused to ultra-high intensities exceeding 10 23 W/cm 2 are enabling new physics regimes and applications. The physics of how these lasers interact with matter is highly nonlinear, relativistic, and can involve lowest-order quantum effects. The current tool of choice for modeling these interactions is the particle-in-cell (PIC) method. In the presence of strong electromagnetic fields, the motion of charged particles and their spin is affected by radiation reaction (either the semi-classical or the quantum limit). Standard (PIC) codes usually use Boris or similar operator-splitting methods to advance the particles in standard phase space. These methods have been shown to require very small time steps in the strong-field regime in order to obtain accurate results. In addition, some problems require tracking the spin of particles, which creates a nine-dimensional (9D) particle phase space, i.e., (x, u, s). Therefore, numerical algorithms that enable high-fidelity modeling of the 9D phase space in the strong-field regime (where both the spin and momentum evolution are affected by radiation reaction) are desired. Here we present a new particle pusher that works in 9D and 6D phase space (i.e., with and without spin) based on analytical rather than leapfrog solutions to the momentum and spin advance from the Lorentz force, together with the semi-classical form of radiation reaction in the Landau-Lifshitz equation and spin evolution given by the Bargmann-Michel-Telegdi equation. Analytical solutions for the position advance are also obtained, but these are not amenable to the staggering of space and time in standard PIC codes. These analytical solutions are obtained by assuming a locally uniform and constant electromagnetic field during a time step. The solutions provide the 9D phase space advance in terms of a particle's proper time, and a mapping is used to determine the proper time step duration for each particle as a function of the lab frame time step. Due to the analytical integration of particle trajectory and spin orbit, the constraint on the time step needed to resolve trajectories in ultra-high fields can be greatly reduced. The time step required in a PIC code for accurately advancing the fields may provide additional constraints. We present single-particle simulations to show that the proposed particle pusher can greatly improve the accuracy of particle trajectories in 6D or 9D phase space for given laser fields. We have implemented the new pusher into the PIC code Osiris. Example simulations show that the proposed pusher provides improvement for a given time step. A discussion on the numerical efficiency of the proposed pusher is also provided.
72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
Beam impedance and heating analysis of the diagnostic stripline
In this work the heat transfer analysis has been performed for the stripline kicker, design of which is used at many accelerator facilities as a part of the transverse bunch-by-bunch feed-back system, including NSLS-II. The experimental data of the electrode temperature have been collected from a special diagnostic stripline designed with six infrared view ports. The temperature analysis is based on the power loss calculations and the loss factor computed by the 3-D electromagnetic simulation code GdfidL. To estimate the power loss, we analyze the real part of the longitudinal impedance and the loss factor for two different regimes. We use the ANSYS finite element code to correlate the temperature with the power loss. Lambertson and Shafer formalisms of the longitudinal and transverse beam impedances are discussed for the simplified stripline geometries. The required characteristic impedances and the geometric factors are determined analytically for the simplified geometries and compared with the results for the designed stripline geometry using the 2-D POISSON code by solving the Laplace’s equation in two dimensions. Lambertson’s equations are compared with numerical results. We introduce the frequency range, within which we can apply the analytical approach.
43 PARTICLE ACCELERATORS↗
Laser-heated capillary discharge waveguides as tunable structures for laser-plasma acceleration
Laser-heated capillary discharge waveguides are novel, low plasma density guiding structures able to guide intense laser pulses over many diffraction lengths and have recently enabled the acceleration of electrons to 7.8 GeV by using a laser-plasma accelerator (LPA). These devices represent an improvement over conventional capillary discharge waveguides, as the channel matched spot size and plasma density can be tuned independently of the capillary radius. This has allowed the guiding of petawatt-scale pulses focused to small spot sizes within large diameter capillaries, preventing laser damage of the capillary structure. High performance channel-guided LPAs require control of matched spot size and density, which experiments and simulations reported here show can be tuned over a wide range via initial discharge and laser parameters. In this paper, measurements of the matched spot size and plasma density in laser-heated capillary discharges are presented, which are found to be in excellent agreement with simulations performed using the MHD code MARPLE. Strategies for optimizing accelerator performance are identified based on these results.
70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
Estimates of global recycling coefficients for LTX- β discharges
We report the first observation of global recycling coefficient R near 0.5 in the Lithium Tokamak eXperiment-β (LTX-β), significantly below the minimum R previously reported in other devices. In a series of experiments with varied Li wall conditioning, estimates of the recycling coefficient have been made using a Lyman-α array and DEGAS2 modeling. A progressive reduction in Lyman-α emission with increased lithium and an increase in edge electron temperature are observed. It is also observed that with increasing Li coating thickness, the effective particle confinement time τp* is reduced and approaches TRANSP calculated energy confinement time (τE), with τp* near τE,TRANSP for the lowest recycling coefficients. Edge temperatures approaching core plasma temperatures, first reported in LTX, can now be directly connected to estimates of the recycling coefficient and qualitatively agree with previous UEDGE simulations. The particle flux to the limiting surfaces appears to be significantly reduced in comparison with fluid scrape-off layer (SOL) models, indicating that a large fraction of the SOL ions are mirror trapped. SOL collisionality drops more than an order of magnitude below the banana regime boundary, indicating the importance of kinetic effects. Full-f 1x2v gyrokinetic simulations of SOL field lines with the GKEYLL code indicate that the fraction of ions trapped along field lines increases as collisionality drops, as a result of increased lithium evaporation.
70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
Heritable, multinucleotide deletions in plants using viral delivery of a repair exonuclease and guide RNAs
Abstract CRISPR/Cas9-mediated mutagenesis typically results in short insertion/deletion mutations, which are often too small to disrupt the function of cis-acting regulatory elements. Here, we describe a highly efficient in planta gene editing approach called VirTREX2-HLDel that achieves heritable multinucleotide deletions in both protein-coding genes and noncoding DNA regulatory elements. VirTREX2-HLDel uses RNA viruses to deliver both the 3 prime repair exonuclease 2 (TREX2) and single-guide RNAs. Our method enables recovery of multiplexed heritable deletions and increases the heritable gene editing frequency at poorly edited sites. We identified functional conservation and divergence of MICRORNA164 (miR164) in Nicotiana benthamiana and tomato (Solanum lycopersicum) using VirTREX2-HLDel and observed previously uncharacterized phenotypes in plants with large deletions at this locus. Our viral delivery method reduces the need for tissue culture and will accelerate the understanding of protein-coding and regulatory regions in plants.
59 BASIC BIOLOGICAL SCIENCES↗
Addition of tabulated equation of state and neutrino leakage support to illinoisgrmhd
Here we have added support for realistic, microphysical, finite-temperature equations of state (EOS) and neutrino physics via a leakage scheme to illinoisgrmhd, an open-source GRMHD code for dynamical spacetimes in the einstein toolkit. These new features are provided by two new, nrpy+-based codes: nrpyeos, which performs highly efficient EOS table lookups and interpolations, and nrpyleakage, which implements a new, adaptive mesh refinement (AMR)-capable neutrino leakage scheme in the einstein toolkit. We have performed a series of strenuous validation tests that demonstrate the robustness of these new codes, particularly on the Cartesian AMR grids provided by carpet. Furthermore, we show results from fully dynamical GRMHD simulations of single unmagnetized neutron stars, and magnetized binary neutron star mergers. This new version of illinoisgrmhd, as well as nrpyeos and nrpyleakage, is pedagogically documented in jupyter notebooks and fully open source. The codes will be proposed for inclusion in an upcoming version of the einstein toolkit.
79 ASTRONOMY AND ASTROPHYSICS↗
Inverse bremsstrahlung absorption rate for super-Gaussian electron distribution functions including plasma screening
Here we provide analytic expressions for the effective Coulomb logarithm for inverse bremsstrahlung absorption which predict significant corrections to the Langdon effect and overall absorption rate compared to previous estimates. The calculation of the collisional absorption rate of laser energy in a plasma by the inverse bremsstrahlung mechanism usually makes the approximation of a constant Coulomb logarithm. We dispense with this approximation and instead take into account the velocity dependence of the Coulomb logarithm, leading to a more accurate expression for the absorption rate valid in both classical and quantum conditions. In contrast to previous work, the laser intensity enters into the Coulomb logarithm. In most laser-plasma interactions the electron distribution function is super-Gaussian [Langdon, Phys. Rev. Lett. 44, 575 (1980)], and we find the absorption rate under these conditions is increased by as much as ≈ 30% compared to previous estimates at low density. In many cases of interest the correction to Langdon's predicted reduction in absorption is large; for example at Z = 6 and Te = 400 eV the Langdon prediction for the absorption is in error by a factor of ≈ 2. However, we also account for the additional effect of plasma screening, which predicts a reduction in absorption by a similar amount (up to ≈ 30%). These two effects compete to determine the overall absorption, which may be increased or decreased, depending on the conditions. The corrections can be incorporated into radiation-hydrodynamics simulation codes by replacing the familiar Coulomb logarithm with an analytic expression which depends on the super-Gaussian order “M” and the screening length.
70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
RESONANT MATCHING SECTION FOR CEBAF ENERGY UPGRADE
In order to prevent emittance growth during long stores of the proton beam at the future Electron-Ion Collider (EIC), we need to have some mechanism to provide fast cooling of the dense proton beams. One promising method is coherent electron cooling (CeC), which uses an electron beam to both ?measure? the positions of protons within the bunch and then apply energy kicks which tend to reduce their longitudinal and transverse actions. In this work, we discuss the under- lying physics of this process. We then discuss simulations which constrain the electrons to move only longitudinally in order to perform fast optimizations and long-term track- ing of the bunch evolution, and benchmark these results against fully 3D codes. Additionally, we discuss practical challenges, including the necessity of a high-quality elec- tron beam and sub-micron alignment of the electrons and protons.
Deitrick, K.↗
FY20 SAM Code Developments and Validations for Transient Safety Analysis of Advanced non-LWRs
The System Analysis Module (SAM) is under development at Argonne National Laboratory as a modern system-level modeling and simulation tool for advanced non-light water reactor safety analyses. It utilizes the object-oriented application framework MOOSE to leverage the modern software environment and advanced numerical methods. The capabilities of SAM are being extended to enable the transient modeling, analysis, and design of various advanced nuclear reactor systems. This report summarizes major progress in SAM code development, capability enhancements, demonstration, and validation to support transient safety analysis of advanced non-LWRs. Rapid developments continued in fiscal year 2020 (FY20) to support various needs of the advanced reactor community, especially the NRC and industry on the licensing safety analysis of advanced reactor designs. Significant code changes were made to provide various capability enhancements, bug fixes, and user friendliness improvements. Major code updates are summarized in Section 1, while four important enhancements are detailed in Sections 2-5, including a multi-dimension flow model; reactivity feedback and decay heat models; control and trip system modeling, and additional fluid and solid thermophysical property models. Code validation activities in FY20 include using test data from the Fast Flux Test Facility (FFTF), the High Temperature Test Facility (HTTF), and several separate effects test facilities for pebble-bed modeling.
21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗
Differential Gene Expression in Host Ubiquitination Processes in Childhood Malarial Anemia
Background: Malaria remains one of the leading global causes of childhood morbidity and mortality. In holoendemic Plasmodium falciparum transmission regions, such as western Kenya, severe malarial anemia [SMA, hemoglobin (Hb) < 6.0 g/dl] is the primary form of severe disease. Ubiquitination is essential for regulating intracellular processes involved in innate and adaptive immunity. Although dysregulation in ubiquitin molecular processes is central to the pathogenesis of multiple human diseases, the expression patterns of ubiquitination genes in SMA remain unexplored. Methods: To examine the role of the ubiquitination processes in pathogenesis of SMA, differential gene expression profiles were determined in Kenyan children ( n = 44, aged <48 mos) with either mild malarial anemia (M l MA; Hb ≥9.0 g/dl; n = 23) or SMA (Hb <6.0 g/dl; n = 21) using the Qiagen Human Ubiquitination Pathway RT 2 Profiler PCR Array containing a set of 84 human ubiquitination genes. Results: In children with SMA, 10 genes were down-regulated ( BRCC3 , FBXO3 , MARCH5 , RFWD2 , SMURF2 , UBA6 , UBE2A , UBE2D1 , UBE2L3 , UBR1 ), and five genes were up-regulated ( MDM2 , PARK2 , STUB1 , UBE2E3 , UBE2M ). Enrichment analyses revealed Ubiquitin-Proteasomal Proteolysis as the top disrupted process, along with altered sub-networks involved in proteasomal, protein, and ubiquitin-dependent catabolic processes. Conclusion: Collectively, these novel results show that protein coding genes of the ubiquitination processes are involved in the pathogenesis of SMA.
60 APPLIED LIFE SCIENCES↗