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DOE OSTI2024

A hybrid-kinetic simulation tool for non-thermal warm x-ray z-pinch sources, with gas-puff and wire array exemplars

Increasing the fluence of z-pinch x-ray radiation sources above ∼ 10 keV has been a long-standing goal for scientists at Sandia National Laboratories’ Z Machine. Optimizing sources for non-thermal “cold Kα” emission in higher atomic-number materials appears to be a promising path to increase warm x-ray yield. However, this emission is generated by supra-thermal electrons, which are not treated in the magnetohydrodynamic (MHD) codes that are typically used in z-pinch source development. MHD codes do not allow for charge separation or space-charge-generated electric fields, and constrain particle kinematics to Maxwellian distributions. The kinetic codes which do accommodate discrete, non-thermal energy distributions are computationally prohibitive when modeling plasmas near solid density and when modeling/tracking higher ionization states. Thus, modeling non-thermal z-pinch sources requires a new simulation tool. In this report, we present a new hybrid modeling capability that uses the fast features of MHD-type particles to the greatest extent possible, then transitions to the slower but more complete kinetic particle treatment to correctly capture the particle energy spectra that generate non-thermal emission. This capability is founded on the fully-relativistic particle-in-cell code Chicago, which already includes fluid particle treatments. The governing equations and hybrid methodology presented here are applied in simulations of an argon gas-puff and a molybdenum wire-array to provide preliminary code validation. The argon simulation is compared to measured implosion times and yields from Jones et al., Phys. Plasmas 22, 020706 (2015). The simulated x-ray yield is within 25% of measurements and the implosion times agree within a few percent. The molybdenum wire array simulation captures the implosion timing reported in Hansen et al., Phys. Plasmas 21, 031202 (2014), but work is needed to verify the available EOS table. These exemplar simulations represents the type of non-thermal sources that will be developed using the hybrid code capability going forward.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2021

NEMA-Phase Compliant Traffic Signal Controller Module in SUMO

The controller modules in SUMO use a stage-based control structure. A phase is defined as a stage of all allowed movements at a time instance. However, traffic signal controllers used in North America widely use National Electrical Manufacturers Association (NEMA) phase definition. A NEMA phase is defined by a certain flow movement at an intersection. At one time, more than one NEMA phase could happen together as long as they do not conflict with each other. We can visualize the NEMA phases and timings in Ring-and-Barrier structured NEMA diagrams. For one controller, only one phase from a ring can be activated at a time. Phases from different rings could be activated together as long as they are not from the different sides of a barrier. When a controller is operated in fixed-time control mode, we can model the NEMA phase timing as a corresponding stage-based control timing without any issues. When introducing actuation into the signal control, a Ring-and-Barrier structured traffic signal controller can be more flexible than stage-based controller by allowing different possible phase combinations. We made two efforts in modeling Ring-and-Barrier structured controllers in SUMO. One is to translate a NEMA phases timing into SUMO-readable phases and timings as an additional file for SUMO. This translation worked well for fixed-time control. To model actuated control and coordinated actuated control, we augmented the SUMO source code by adding a Ring-and-Barrier structured controller module. This module could implement traffic signal timing from controllers using NEMA phases. We also augmented TraCI to be able to set new NEMA phase timings during simulations. We examined the Ring-and-Barrier structured traffic signal controller module by both visually observing the simulation animations and the simulation records. The developed control module can model the generalized Ring-and-Barrier structured traffic signal timing that is used in North America. SEE: https://github.com/eclipse/sumo/blob/main/src/microsim/traffic_lights/NEMAController.cpp

Wang, Qichao↗

DOE OSTI2022

Modernization efforts for the R -Matrix code SAMMY [Abstract]

The R-Matrix code SAMMY is a widely used nuclear data evaluation code focused on the resolved range, which includes corrections for experimental effects. The code is still mostly written in Fortran 77, and uses a memory management system suitable for the time of its initial writing (1984). A modernization effort is under way to bring the code in-line with modern software development practices. A continuous-integration testing framework was added, automating the large existing set of test cases. It is run on every commit. The memory management was updated to current standard practices suitable for modern software analysis tools. The code can be obtained from https://code.ornl.gov/RNSD/SAMMY. The resonance parameters and covariance information are now stored in C++ objects shared by SAMMY and AMPX, the processing code that generates nuclear data libraries for SCALE. This allows for easier maintenance and access to the resonance parameters inside and outside of SAMMY. This feature is already used by accessing and changing parameters in memory in the Bayesian Monte Carlo Evaluation Framework for Cross Sections Nuclear Data and Integral Benchmark Experiments project, Further plans include the switch to the ENDF reading and writing routines in AMPX, as these routines are more robust, easier to maintain, and support more features. Of note here is support for the new GNDS format. Previously it wasn’t easy to share the full covariance matrix for evaluations containing more than one isotope due to limitations on the ENDF format; this is now supported in GNDS. The data are currently available in a binary SAMMY format and can be exported to GNDS to make them more widely available and sharable. The next step will be to use the same resonance processing code at 0K in AMPX and SAMMY as one of the available Reich-Moore R-Matrix formalism. The first step toward this goal is to isolate the reconstruction into a module that takes resonance parameters as its input and does not depend on SAMMY global parameters. This goal has been achieved and it should now be possible to more easily change the resonance formalism and add enhancements as the Phenomenological R-Matrix parameterization of direct, doorway, and compound nuclear reactions discussed elsewhere on this conference. This concerted modernization and enhancement effort provides multiple advantages to the nuclear data community. It will allow parameter optimization using enhanced formalisms, including experimental effects, that better match complex experimental data. Then those evaluated parameters can immediately be passed off to AMPX to be reconstructed with the exact same cross section model and be put into a data library for subsequent testing using SCALE and the Valid Benchmark suite or other suitable benchmark suites.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2022

Stochastic Modeling in a Multimaterial Continuum Mixture Shock Physics Code

Stochastic modelling approaches are presented to capture random effects at multiple time and length scales. Random processes that occur at the microscale produce nondeterministic effects at the macroscale. Here we present three stochastic modeling approaches that describe random processes at microscopic length scales and map these processes to the macroscopic length scale. The first stochastic modeling approach is based upon a particle based numerical technique to solve a Stochastic Differential Equation (SDE) using an arbitrary diffusion process to capture random processes at the microstructural level. The second approach prescribes a Probability Density Function (PDF) for the drift and diffusion of the random variable derived using the forward and backward Kolmogorov equations. This method requires mean and drift evolution PDF transport equations. The third approach is the coupling of multiple random variables which are dependent on each other. The relationship of the PDFs and a coupling function, known as a copula, produces a Joint Probability Density Function (JPDF). These stochastic modeling approaches are implemented into a Multiple Component (MC) shock physics computational code and used to model statistical fracture and reactive flow applications.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2025

Lepton flavor asymmetries: from the early Universe to BBN

Large primordial lepton flavor asymmetries with almost vanishing total baryon-minus-lepton number can evade the usual BBN and CMB constraints if neutrino oscillations lead to perfect flavor equilibration. Solving the momentum averaged quantum kinetic equations (QKEs) describing neutrino oscillations and interactions, we perform the first systematic investigation of this scenario, uncovering a rich flavor structure in stark contradiction to the assumption of simple flavor equilibration. We find (i) a particular direction in flavor space, ∆ne ≃ – 2/3 (– 1)∆n μ for normal (inverted) neutrino mass hierarchy, in which the flavor equilibration is efficient and primordial asymmetries are essentially unconstrained, (ii) a minimal washout factor, ∆$n_{e}^{2}$| BBN ≤ 0.03 (0.016) ∑ α ∆$n_{α}^{2}$| ini yielding a conservative estimate for the allowed primordial asymmetries in a generic flavor direction, and (iii) particularly strong or weak washout if one of the initial flavor asymmetries vanishes due to non-adiabatic muon- or electron-driven MSW transitions. These results open up the possibility of a first-order QCD phase transition facilitated by large lepton asymmetries as well as baryogenesis from large and compensated ∆n e = ∆n μ asymmetries. Our systematic approach of deriving momentum averaged QKEs includes collision terms beyond the damping approximation, energy transfer between the neutrino and electron-photon plasma, and provides a fast and reliable way to investigate the impact of primordial lepton asymmetries at the time of BBN. We publicly release the Mathematica code COFLASY-M on https://github.com/mariofnavarro/COFLASY which solves the QKEs numerically.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2020

Validation and application of a multiphase CFD model for hydrodynamics, temperature field and RTD simulation in a pilot-scale biomass pyrolysis vapor phase upgrading reactor

Accurate prediction of transport phenomena is critical for VPU reactor design, optimization, and scale-up. The current study focused on the validation and application of a multiphase CFD model within an open-source code MFiX for hydrodynamics, temperature field, and residence time distribution (RTD) simulation in a non-reacting circulating fluidized bed riser for biomass pyrolysis vapor phase upgrading (VPU). First, an Eulerian-Eulerian approach three-dimensional CFD model was employed to simulate the pilot-scale VPU riser on the supercomputer Joule. Excellent quantitative agreement between experimental and simulated results was achieved for pressure drops and temperature field in a range of operating conditions. Then the validated multiphase CFD model was applied to predict gas and solid residence time distributions (RTDs) since prediction and analysis of RTD is an important tool to study the complex multiphase flow behavior and mixing inside chemical reactors. The predictions show that solid mean residence time is 3.5 times the gas residence time; the solid RTD is more sensitive to the process gas flow rate than the solids circulation rate.

09 BIOMASS FUELS↗

DOE OSTI2023

Hermes-3: Multi-component plasma simulations with BOUT++

A new open source tool for fluid simulation of multi-component plasmas is presented, based on a flexible software design that is applicable to scientific simulations in a wide range of fields. Hermes-3 is built on plasma simulation framework BOUT++, consolidating earlier SD1D and Hermes models into a single code that can be configured at run-time to solve plasma models in 1D, 2D or 3D, either for transport (steady-state) or turbulent (time-evolving) problems, with an arbitrary number of ion and neutral species. Here, we describe the improved numerical algorithms and software design that have been implemented in Hermes-3. To demonstrate the capabilities of this tool, applications relevant to the boundary of tokamak plasmas are presented: 1D simulations of diveror plasmas evolving equations for all charge states of neon and deuterium; 2D transport simulations of tokamak equilibria in single-null X-point geometry with plasma ion and neutral atom species; and simulations of the time-dependent propagation of plasma filaments (blobs). Hermes-3 is publicly available on Github under the GPL-3 open source license. The repository includes documentation and a suite of unit, integrated and convergence tests.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2025

Development of a River Dynamical Core for E3SM to simulate compound flooding on Exascale-class heterogeneous supercomputers

Flooding events pose significant risk to human life, property, and infrastructure. Physically-consistent quantification of altered flood risks in global models requires hyper-resolution (~1 km) or fine flood simulations using two-dimensional (2D) physics schemes, both of which are unavailable in the current generation Earth System Models. Here, in this work, we have developed the River Dynamical Core (RDycore), which is an open-source, 2D shallow water equation (SWE) library for the U.S. Department of Energy's Energy Exascale Earth System Model (E3SM). RDycore uses PETSc and libCEED libraries that allows it to run efficiently on CPUs and GPUs, as well as select a time-integration algorithm at runtime without requiring any code modifications. RDycore achieves spatial error convergence rates for problems with analytical and manufactured solutions similar to those reported previously in the literature, or consistent with the implemented first-order spatial discretization scheme. RDycore's accuracy in predicting flooding for a well-studied dam break problem is comparable to existing SWE models. For a problem with 471 million grid cells, RDycore achieves a speedup of 6.6x and 7.6x on GPUs compared to CPUs when using 320 compute nodes on DOE's Perlmutter and Frontier supercomputers, respectively. The one-way coupling of the RDycore library within E3SM is demonstrated by performing multiple 5-day flooding simulations during Hurricane Harvey driven by five precipitation datasets. The E3SM--RDycore simulations at 30 m spatial resolution accurately simulate maximum water height during the hurricane when benchmarked against a previously published study and achieve a speedup of 15x (Perlmutter) and 21x (Frontier) on GPUs relative to CPUs. The work presented here is the foundational step in providing hardware and algorithmic portability framework for simulating kilometer-scale river dynamics within E3SM.

Flood Simulation↗

DOE OSTI2023

Typologies of actionable climate information and its use

Developing actionable climate information and integrating it into decision-making are two crucial elements for promoting effective societal responses to climate change. However, what constitutes actionable climate information, and how it is used, varies based on the actors, systems, and scales that are relevant to specific decisions. Yet, the terms ‘actionable climate information’ or ‘use of climate information’ are used abstractly. There is a lack of holistic understanding of the various types of information that can be deemed as usable by different users, and the different ways in which they may be used in decision-making. Typologies or generalizable categorizations can help both knowledge producers and users to better envision the entire landscape of climate information and its uses and can help to reduce the time and cost of actionable knowledge production. Through systematic coding and analysis of ~ 4 years of co-production engagements between climate scientists and resource managers, this paper presents empirically derived typologies of actionable climate information and its use, and explores whether certain uses are better informed by specific types of climate information. These typologies provide a valuable starting point for climate information producers, users, and boundary spanners working on climate-informed resource management, to reduce some of the time-intensive elements of the process.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2021

Neural network model of the multi-mode anomalous transport module for accelerated transport simulations

Here, a neural network version of the Multi-Mode Anomalous Transport Module, known as MMMnet, has been developed to calculate plasma turbulent diffusivities in DIII-D with a calculation time suitable for control applications. MMMnet uses a simple artificial neural network structure to predict the ion thermal, electron thermal, and toroidal momentum diffusivities while reproducing Multi-Mode Model (MMM) data with good accuracy and keeping the calculation time as a fraction of that associated with MMM. Model-based control techniques require models with fast calculation times, making many existing physics-oriented predictive codes unsuitable. The control-oriented predictive code COTSIM (Control Oriented Transport SIMulator) calculates the most significant plasma dynamics in response to the different actuators while running at a speed useful for control design. In order to achieve this calculation speed, COTSIM often relies on scaling laws and control-level models. Replacing some of these scaling laws and control-level models with neural network versions of more complex physics-level models has the potential of increasing the range of validity and the level of accuracy of COTSIM without compromising its computational speed. In this work, MMMnet is integrated into COTSIM to improve the turbulent diffusivity predictions, which will in turn improve the prediction accuracy associated with the dynamics of many plasma properties.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2024

Emergency department visits in California associated with wildfire PM 2.5 : differing risk across individuals and communities

The threats to human health from wildfires and wildfire smoke (WFS) in the United States (US) are increasing due to continued climate change. A growing body of literature has documented important adverse health effects of WFS exposure, but there is insufficient evidence regarding how risk related to WFS exposure varies across individual or community level characteristics. To address this evidence gap, we utilized a large nationwide database of healthcare utilization claims for emergency department (ED) visits in California across multiple wildfire seasons (May through November, 2012–2019) and quantified the health impacts of fine particulate matter <2.5 μm (PM 2.5 ) air pollution attributable to WFS, overall and among subgroups of the population. We aggregated daily counts of ED visits to the level of the Zip Code Tabulation Area (ZCTA) and used a time-stratified case-crossover design and distributed lag non-linear models to estimate the association between WFS and relative risk of ED visits. We further assessed how the association with WFS varied across subgroups defined by age, race, social vulnerability, and residential air conditioning (AC) prevalence. Over a 7 day period, PM 2.5 from WFS was associated with elevated risk of ED visits for all causes (1.04% (0.32%, 1.71%)), non-accidental causes (2.93% (2.16%, 3.70%)), and respiratory disease (15.17% (12.86%, 17.52%)), but not with ED visits for cardiovascular diseases (1.06% (–1.88%, 4.08%)). Analysis across subgroups revealed potential differences in susceptibility by age, race, and AC prevalence, but not across subgroups defined by ZCTA-level Social Vulnerability Index scores. These results suggest that PM 2.5 from WFS is associated with higher rates of all cause, non-accidental, and respiratory ED visits with important heterogeneity across certain subgroups. Notably, lower availability of residential AC was associated with higher health risks related to wildfire activity.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2025

The impact of varying inhomogeneous reionization histories on metrics of Ly α opacity

The epoch of hydrogen reionization is complete by z = 5⁠, but its progression at higher redshifts is uncertain. Measurements of Ly α forest opacity show large scatter at z < 6⁠, suggestive of spatial fluctuations in neutral fraction, temperature, or ionizing background, either individually or in combination. However, there are degeneracies in the impact of such fluctuations, necessitating careful modelling. We develop a framework for modelling the reionization history and associated temperature fluctuations, with the intention of incorporating ionizing background fluctuations at a later time. We generate several reionization histories using seminumerical code AMBER, and implement them in the Nyx cosmological hydrodynamics code to examine the impact on the evolution of gas within the simulation and the associated metrics of the Ly α forest opacity. We find that the pressure smoothing scale within the intergalactic medium is strongly correlated with the adiabatic index of the temperature–density relation. We find that while models with 20 000 K photoheating at reionization are better able to reproduce the shape of the observed z = 5 1D flux power spectrum than colder ones, they fail to match the highest wavenumbers. The simulated autocorrelation function and optical depth distributions are systematically low and narrow, respectively, compared to the observed values, but are in better agreement when the reionization history is longer in duration, more symmetric in its distribution of reionization redshifts, or if there are remaining neutral regions at z < 6.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2024

Benefits and Limits of Phasing Alleles for Network Inference of Allopolyploid Complexes

Abstract Accurately reconstructing the reticulate histories of polyploids remains a central challenge for understanding plant evolution. Although phylogenetic networks can provide insights into relationships among polyploid lineages, inferring networks may be hindered by the complexities of homology determination in polyploid taxa. We use simulations to show that phasing alleles from allopolyploid individuals can improve phylogenetic network inference under the multispecies coalescent by obtaining the true network with fewer loci compared with haplotype consensus sequences or sequences with heterozygous bases represented as ambiguity codes. Phased allelic data can also improve divergence time estimates for networks, which is helpful for evaluating allopolyploid speciation hypotheses and proposing mechanisms of speciation. To achieve these outcomes in empirical data, we present a novel pipeline that leverages a recently developed phasing algorithm to reliably phase alleles from polyploids. This pipeline is especially appropriate for target enrichment data, where the depth of coverage is typically high enough to phase entire loci. We provide an empirical example in the North American Dryopteris fern complex that demonstrates insights from phased data as well as the challenges of network inference. We establish that our pipeline (PATÉ: Phased Alleles from Target Enrichment data) is capable of recovering a high proportion of phased loci from both diploids and polyploids. These data may improve network estimates compared with using haplotype consensus assemblies by accurately inferring the direction of gene flow, but statistical nonidentifiability of phylogenetic networks poses a barrier to inferring the evolutionary history of reticulate complexes.

Evolutionary Biology↗

DOE OSTI2026

Toward Energy-Efficient HPC: Insights from Power Profiling a Cloud-Resolving Earth System Model

Power is a fundamental constraint as supercomputing advances to exascale. Efficient operation within strict power budgets requires application-aware power management based on a detailed understanding of application-level power behavior. This work analyzes the Energy Exascale Earth System Model (E3SM) atmosphere component, SCREAM, on Perlmutter (NERSC) and Frontier (OLCF). We characterize power variation across inputs, concurrency levels, and power caps, evaluate the energy impact of code optimizations, and attribute energy within the code using a newly developed GPU energy model. Results show that SCREAM’s peak power remains stable during its core execution phase and decreases gradually as concurrency increases. Power capping experiments reveal a performance–energy "sweet spot". On Perlmutter, limiting GPU power to 50% of thermal design power (TDP) achieves up to 15% energy savings with a 7% performance penalty. On Frontier, a 40% TDP cap yields up to 10% energy savings with less than 10% performance loss. Code optimizations reduce SCREAM energy by shortening run time without increasing power. Modeling reveals a critical insight: data movement accounts for approximately 70% of SCREAM’s GPU energy. This fundamentally shifts the optimization focus from FLOPS to data transfer reduction for this class of applications, offering the most impactful strategy for improving energy efficiency. This work establishes a foundation for practical, application-aware power management at exascale.

Zhao, Zhengji [Lawrence Berkeley National Laborato↗

DOE OSTI2022

gismo-cloud-deployment

Tools for executing time-consuming tasks with developer-defined custom code blocks in parallel on the AWS EKS platform.

Leu, Jimmy↗

DOE OSTI2023

cyquandyn

CyQuanDyn is a collection of codes developed for modelling the phonon-induced carrier pumping in ZrTe5 system. Codes in the collection include 1) TLS: time-dependent two-orbital spinless fermion Bogoliubov-de Gennes Hamiltonian simulation, 2) TDSE: ab initio time-dependent Schrödinger equation simulation of the ZrTe5 system under the periodic modulation of A1g Raman mode. Associated publication is T. Jiang, P. P. Orth, L. Luo, L.-L. Wang, F. Zhang, C.-Z. Wang, J. Zhao, K.-M. Ho, J. Wang, and Y.-X. Yao, Ab-Initio Simulations of Coherent Phonon-Induced Pumping of Carriers in ZrTe5. [arXiv:2304.08449 (2023).](https://arxiv.org/abs/2304.08449)

Yao, Yongxin↗

DOE OSTI2024

Improved Earthquake Source Parameters with 3D Wavespeed Models in California and Nevada

Seismic tomography harnesses earthquake data to explore the inaccessible structure of the Earth. Adjoint waveform tomography (AWT), a method of seismic tomography, updates the tomographic model by optimizing the fit between observed earthquake data and synthetic waveforms. The synthetic data are calculated by solving the wave equation through a given 3D model. An important requirement to calculating synthetics is the source information (location, centroid time, depth, and moment tensor). Errors in source information affect the quality of the synthetics produced, which in turn can limit how structure can be inferred in the AWT workflow. Here, to test the effect of updating source information, we used MTTime (Chiang, 2020), a time-domain full-waveform moment tensor inversion code, to calculate the moment tensors and depths of 118 earthquakes that occurred in California and Nevada over a 20-yr period. We calculated 3D Green’s functions using a 3D seismic wavespeed model of California and Nevada (Doody et al., 2023b). We show that the inverted solutions provide better waveform fits than the Global Centroid Moment Tensor catalog and increase usable, well-correlated data by up to 7%. Therefore, we argue that recalculating source parameters should be considered in AWT workflows, particularly for smaller magnitude events (⁠M w > 5.0).

58 GEOSCIENCES↗

DOE OSTI2021

Simulating Magnetized Electron Cooling for EIC with JSPEC

We present a possible electron cooling configuration for the proposed Electron Ion Collider (EIC) facility, developed using a Nelder-Mead Simplex optimization procedure built into JSPEC, an electron cooling code developed at Jefferson Lab. We show the time evolution of the emittance of the ion beam in the presence of this cooler evaluated assuming the ion distribution remains Gaussian. We also show that bi-gaussian distributions emerge in simulations of ion macro-particles. We show how intra-beam scattering can be treated with a core-tail model in simulations of ion macro-particles. The Sirepo/JSPEC* and Sirepo/Jupyter** apps will be presented, with instructions enabling the community to reproduce our simulations.

Coleman, S. J.↗