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DOE OSTI2024

HSW-V v1.0: localized injections of interactive volcanic aerosols and their climate impacts in a simple general circulation model

Abstract. A new set of standalone parameterizations is presented for simulating the injection, evolution, and radiative forcing by stratospheric volcanic aerosols against an idealized Held–Suarez–Williamson (HSW) atmospheric background in the Energy Exascale Earth System Model version 2 (E3SMv2). In this model configuration (HSW with enabled volcanism, HSW-V), sulfur dioxide (SO2) and ash are injected into the atmosphere with a specified profile in the vertical, and they proceed to follow a simple exponential decay. The SO2 decay is modeled as a perfect conversion to a long-living sulfate aerosol which persists in the stratosphere. All three species are implemented as tracers in the model framework and are transported by the dynamical core's advection algorithm. The aerosols contribute simultaneously to local heating of the stratosphere and cooling of the surface by a simple plane-parallel Beer–Lambert law applied on two zonally symmetric radiation broadbands in the longwave and shortwave ranges. It is shown that the implementation parameters can be tuned to produce realistic temperature anomaly signatures of large volcanic events. In particular, results are shown for an ensemble of runs that mimic the volcanic eruption of Mt. Pinatubo in 1991. The design requires no coupling to microphysical subgrid-scale parameterizations and thus approaches the computational affordability of prescribed aerosol forcing strategies. The idealized simulations contain a single isolated volcanic event against a statistically uniform climate, where no background aerosols or other sources of externally forced variability are present. HSW-V represents a simpler-to-understand tool for the development of climate source-to-impact attribution methods.

Hollowed, Joseph P. (ORCID:0000000286581672)↗

DOE OSTI2018

Rapid, parallel identification of pathways for catabolism of lignin-derived aromatic compounds in Novosphingobium aromaticivorans

Transposon mutagenesis is a powerful technique in microbial genetics for the identification of genes in uncharacterized pathways. Recently, the throughput of transposon mutagenesis techniques has been dramatically increased through the combination of DNA barcoding and high-throughput sequencing. Here we show that, when applied to catabolic pathways, barcoded transposon libraries can be used to distinguish redundant pathways, decompose complex pathways into substituent modules, discriminate between enzyme homologs, and rapidly identify previously-hypothetical enzymes in an unbiased genome-scale search. We use this technique to identify two genes, which we name desC and desD , are involved in the degradation of the lignin-derived aromatic compound sinapic acid in the non-model bacterium Novosphingobium aromaticivorans . We show that DesC is a methyl-esterase acting on an intermediate formed during sinapic acid catabolism, providing the last enzyme in a proposed catabolic pathway. Here, this approach will be particularly useful in the identification of complete pathways suitable for heterologous expression in metabolic engineering.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2017

The fusion code XGC: Enabling kinetic study of multi-scale edge turbulent transport in ITER [Book Chapter]

The XGC fusion gyrokinetic code combines state-of-the-art, portable computational and algorithmic technologies to enable complicated multiscale simulations of turbulence and transport dynamics in ITER edge plasma on the largest US open-science computer, the CRAY XK7 Titan, at its maximal heterogeneous capability, which have not been possible before due to a factor of over 10 shortage in the time-to-solution for less than 5 days of wall-clock time for one physics case. Frontier techniques such as nested OpenMP parallelism, adaptive parallel I/O, staging I/O and data reduction using dynamic and asynchronous applications interactions, dynamic repartitioning for balancing computational work in pushing particles and in grid related work, scalable and accurate discretization algorithms for non-linear Coulomb collisions, and communication-avoiding subcycling technology for pushing particles on both CPUs and GPUs are also utilized to dramatically improve the scalability and time-to-solution, hence enabling the difficult kinetic ITER edge simulation on a present-day leadership class computer.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2024

Three-wave coupling observed between a shear Alfvén wave and a kink-unstable magnetic flux rope

Results from a laboratory experiment are presented in which, for the first time, a shear Alfvén wave is launched using an antenna in a current-carrying plasma column that is tailored to be either stable or unstable to the kink oscillation. As the plasma is driven kink unstable, the frequency power spectrum of the Alfvén wave evolves from a single peak to a peak with multiple sidebands separated by integer multiples of the kink frequency. The main sidebands (one on either side of the launched wave peak in the power spectrum) are analyzed using azimuthal wavenumber matching, perpendicular and parallel wavenumber decomposition, and bispectral time series analysis. The dispersion relation and three-wave matching conditions are satisfied, given each sideband is a propagating Alfvén wave that results from the interaction of the pump Alfvén wave and the co-propagating component of a half-wavelength, standing kink mode. The interaction is shown to generate smaller perpendicular wavelength Alfvén waves that drive energy transport to scales that will approach the dissipation scale of k⊥ρs=1, with k⊥ being the perpendicular wavenumber and ρs being the ion gyroradius at the electron temperature.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2016

Grover Search and the No-Signaling Principle

Two of the prime properties of quantum physics are the no-signaling principle and the Grover search lower bound. That is, despite admitting stronger-than-classical correlations, quantum mechanics does not imply superluminal signaling, and despite a form of exponential parallelism, quantum mechanics does not imply polynomial-time brute force solution of NP-complete problems. Herein, we investigate the degree to which these two properties are connected. We explore four classes of deviations from quantum mechanics, for which we draw inspiration from the literature on the black hole information paradox. We show that in these models, the physical resources required to send a superluminal signal scale polynomially with the resources needed to speed up Grover’s algorithm. Hence the no-signaling principle is equivalent to the inability to solve NP-hard problems efficiently by brute force within the classes of theories analyzed.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2018

Multiphysics Simulation of DPC Criticality: Scoping Calculations and Coupling Strategy.

Objectives for Multi-Physics Simulations include: Provide a systematic framework for multi-process modeling — Conduct parallel model development efforts that cover the technical areas needed to support criticality consequence screening in performance assessment (PA) and that will be more closely integrated as development proceeds; Investigate separate effects — Allow partitioning of the overall waste package (WP) internal criticality multi-physics modeling effort during development activities, for study of specific processes that can later be coupled if warranted from interpretation of results; Study scaling and bounding approaches — Where possible, represent criticality consequences in PA using simplification of uncertain criticality event frequency and magnitude, bounding of consequences for screening purposes, and scaling of consequences to multiple WPs; and, Integration among participants — Multiple modeling teams (mainly SNL and ORNL, and their collaborators) will work on different parts of the in-package criticality phenomenology. Insights generated this way will be combined for more realistic coupled modeling, and for validation.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

DOE OSTI2019

Chandra Follow-up of the SDSS DR8 Redmapper Catalog Using the MATCha Pipeline

In order to place constraints on cosmology through optical surveys of galaxy clusters, one must first understand the properties of those clusters. To this end, we introduce the Mass Analysis Tool for Chandra (MATCha), a pipeline that uses a parallellized algorithm to analyze archival Chandra data. MATCha simultaneously calculates X-ray temperatures and luminosities and performs centering measurements for hundreds of potential galaxy clusters using archival X-ray exposures. We run MATCha on the redMaPPer SDSS DR8 cluster catalog and use MATCha's output X-ray temperatures and luminosities to analyze the galaxy cluster temperature–richness, luminosity–richness, luminosity–temperature, and temperature–luminosity scaling relations. We detect 447 clusters and determine 246 r 2500 temperatures across all redshifts. Within 0.1 < z < 0.35, we find that r 2500 T X scales with optical richness (λ) as $\mathrm{ln}\left(\tfrac{{k}_{B}{T}_{{\rm{X}}}}{1.0\,\mathrm{keV}}\right)=(0.52\pm 0.05)\mathrm{ln}\left(\tfrac{\lambda }{70}\right)+(1.85\pm 0.03)$ with an intrinsic scatter of $0.27\pm 0.02$ ($1\sigma $). We investigate the distribution of offsets between the X-ray center and redMaPPer center within 0.1 < z < 0.35, finding that 68%.3 ± 6.5% of clusters are well-centered. However, we find a broad tail of large offsets in this distribution, and we explore some of the causes of redMaPPer miscentering.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2022

Versatile soil gas concentration and isotope monitoring: optimization and integration of novel soil gas probes with online trace gas detection

Abstract. Gas concentrations and isotopic signatures can unveil microbial metabolisms and their responses to environmental changes in soil. Currently, few methods measure in situ soil trace gases such as the products of nitrogen and carbon cycling or volatile organic compounds (VOCs) that constrain microbial biochemical processes like nitrification, methanogenesis, respiration, and microbial communication. Versatile trace gas sampling systems that integrate soil probes with sensitive trace gas analyzers could fill this gap with in situ soil gas measurements that resolve spatial (centimeters) and temporal (minutes) patterns. We developed a system that integrates new porous and hydrophobic sintered polytetrafluoroethylene (sPTFE) diffusive soil gas probes that non-disruptively collect soil gas samples with a transfer system to direct gas from multiple probes to one or more central gas analyzer(s) such as laser and mass spectrometers. Here, we demonstrate the feasibility and versatility of this automated multiprobe system for soil gas measurements of isotopic ratios of nitrous oxide (δ18O, δ15N, and the 15N site preference of N2O), methane, carbon dioxide (δ13C), and VOCs. First, we used an inert silica matrix to challenge probe measurements under controlled gas conditions. By changing and controlling system flow parameters, including the probe flow rate, we optimized recovery of representative soil gas samples while reducing sampling artifacts on subsurface concentrations. Second, we used this system to provide a real-time window into the impact of environmental manipulation of irrigation and soil redox conditions on in situ N2O and VOC concentrations. Moreover, to reveal the dynamics in the stable isotope ratios of N2O (i.e., 14N14N16O, 14N15N16O, 15N14N16O, and 14N14N18O), we developed a new high-precision laser spectrometer with a reduced sample volume demand. Our integrated system – a tunable infrared laser direct absorption spectrometry (TILDAS) in parallel with Vocus proton transfer reaction mass spectrometry (PTR-MS), in line with sPTFE soil gas probes – successfully quantified isotopic signatures for N2O, CO2, and VOCs in real time as responses to changes in the dry–wetting cycle and redox conditions. Broadening the collection of trace gases that can be monitored in the subsurface is critical for monitoring biogeochemical cycles, ecosystem health, and management practices at scales relevant to the soil system.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2019

EGS Collab Earth Modeling: Integrated 3D Model of the Testbed

The EGS Collab project is conducting a series of stimulation and interwell flow tests in an intermediate scale (~10-20 m) testbed located on the 4850 level in the Sanford Underground Research Facility (SURF) in Lead, South Dakota. The testbed consists of eight ~200 ft (~60 m) HQ-diameter (9.6 cm) boreholes that are drilled into the Poorman Formation from the western rib of the West Access Drift. Of the eight boreholes, one borehole is used as an injection/stimulation well, another sub-parallel borehole located about 10 m away from the injection well is used as a production well, and rest of the other boreholes are used as monitoring wells. For 3D visualization of the testbed as well as to provide spatially accurate and consistent parameter data for geomechanical and geophysical process modeling tasks, we are using Leapfrog Software (Seequent Limited). For analysis of fractures and creation of conditioned stochastic discrete fracture network (CS-DFN) model of the testbed, we are using FracMan (Golder Associates Inc.). As of mid-May 2019, the EGS Collab Leapfrog database contains the general layout of the drifts/shafts at the 4850 and 4100 levels; generalized geologic framework model of a domain that spans both the 4850 and 4100 levels; the CS-DFN of the testbed; and layouts of the EGS Collab testbed boreholes, kISMET testbed boreholes, and other existing boreholes at the 4850 level. This information has been obtained from the SURF Vulcan database, detailed laser scan and point surveys of borehole collar locations, directional surveys of borehole trajectories, and mapping of features in the drifts, boreholes, and cores. Similarly, other types of data that have been incorporated into the Leapfrog database include static features of the testbed such as natural discontinuities (e.g., fractures, weeps), location of monitoring instruments, and stimulation notches. Baseline geophysical characterization results (e.g., seismic, ERT, temperature, etc.) are also imported into the Leapfrog database. The location and size of packers, various point-source signals detected during stimulation and flow tests (e.g., temperature anomalies, micro-earthquake events, etc.) are also compiled in the database. All feature locations are reported using the local Homestake Mine coordinate system. In this paper, we present some of the geostructural characteristics as well as the status of the testbed as represented by Leapfrog/FracMan database/visualizations.

15 GEOTHERMAL ENERGY↗

DOE OSTI2017

Electron heating and energy inventory during asymmetric reconnection in a laboratory plasma

Abstract Electron heating and the energy inventory during asymmetric reconnection are studied in the laboratory plasma with a density ratio of about 8 across the current sheet. Features of asymmetric reconnection such as the large density gradients near the low‐density side separatrices, asymmetric in‐plane electric field, and bipolar out‐of‐plane magnetic field are observed. Unlike the symmetric case, electrons are also heated near the low‐density side separatrices. The measured parallel electric field may explain the observed electron heating. Although large fluctuations driven by lower hybrid drift instabilities are also observed near the low‐density side separatrices, laboratory measurements and numerical simulations reported here suggest that they do not play a major role in electron energization. The average electron temperature increase in the exhaust region is proportional to the incoming magnetic energy per an electron/ion pair but exceeds scalings of the previous space observations. This discrepancy is explained by differences in the boundary condition and system size. The profile of electron energy gain from the electric field shows that there is additional electron energy gain associated with the electron diamagnetic current besides a large energy gain near the X line. This additional energy gain increases electron enthalpy, not the electron temperature. Finally, a quantitative analysis of the energy inventory during asymmetric reconnection is conducted. Unlike the symmetric case where the ion energy gain is about twice more than the electron energy gain, electrons and ions obtain a similar amount of energy during asymmetric reconnection.

Yoo, Jongsoo↗

DOE OSTI2020

A parallel strategy for density functional theory computations on accelerated nodes

Using the Löwdin orthonormalization of tall-skinny matrices as a proxy-app for wavefunction-based Density Functional Theory solvers, we investigate a distributed memory parallel strategy focusing on Graphics Processing Unit (GPU)-accelerated nodes as available on some of the top ranked supercomputers at the present time. Here we present numerical results in the strong limit regime, as it is particularly relevant for First-Principles Molecular Dynamics. We also examine how matrix product-based iterative solvers provide a competitive alternative to dense eigensolvers on GPUs, allowing to push the strong scaling limit of these computations to a larger number of distributed tasks. Our strategy, which relies on replicated Gram matrices and efficient collective communications using the NCCL library, leads to a time-to-solution under 0.5 s for the Löwdin orthonormalization of a tall-skinny matrix of 3000 columns on Summit at Oak Ridge Leadership Facility (OLCF). Given the similarity in computational operations between one iteration of a DFT solver and this proxy-app, this shows the possibility of solving accurately the DFT equations well under a minute for 3000 electronic wave functions, and thus perform First-Principles molecular dynamics of physical systems much larger than traditionally solved on CPU systems.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2023

Unraveling the functional dark matter through global metagenomics

Metagenomes encode an enormous diversity of proteins, reflecting a multiplicity of functions and activities1,2. Exploration of this vast sequence space has been limited to a comparative analysis against reference microbial genomes and protein families derived from those genomes. Here, to examine the scale of yet untapped functional diversity beyond what is currently possible through the lens of reference genomes, we develop a computational approach to generate reference-free protein families from the sequence space in metagenomes. We analyse 26,931 metagenomes and identify 1.17 billion protein sequences longer than 35 amino acids with no similarity to any sequences from 102,491 reference genomes or the Pfam database3. Using massively parallel graph-based clustering, we group these proteins into 106,198 novel sequence clusters with more than 100 members, doubling the number of protein families obtained from the reference genomes clustered using the same approach. We annotate these families on the basis of their taxonomic, habitat, geographical and gene neighbourhood distributions and, where sufficient sequence diversity is available, predict protein three-dimensional models, revealing novel structures. Overall, our results uncover an enormously diverse functional space, highlighting the importance of further exploring the microbial functional dark matter.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2022

Numerical modeling of pedestal stability and broadband turbulence of wide-pedestal QH-mode plasmas on DIII-D

The wide-pedestal quiescent high confinement mode discovered on DIII-D in recent years is a stationary and quiescent H-mode (QH-mode) with the pedestal width exceeding EPED prediction by at least 25%. Its characteristics, such as low rotation, high energy confinement and edge localized mode-free operation, make it an attractive operation mode for future reactors. Linear and nonlinear simulations using BOUT++ reduced two fluid MHD models and awere carried out to investigate the bursty broadband turbulence often observed in the edge of wide-pedestal QH-mode plasmas. Two kinds of MHD-scale instabilities in different spatial locations within the pedestal were found in the simulations: one mild peeling–ballooning (PB) mode γ PB < 0.04ω A ) located near the minimum in E r</:sub> well propagating in ion diamagnetic drift direction; and one drift-Alfvén wave locates at smaller radius compared to E r</:sub> well propagating in the electron diamagnetic drift direction and unstable only when the parallel electron dynamics is included in the simulation. The coupling between drift wave and shear Alfvén wave provides a possible cause of the experimentally observed local profile flattening in the upper-pedestal. The rotation direction, mode location, as well as the wavenumber of these two modes from BOUT++ simulations agree reasonably well with the experimental measurements, while the lack of quantitative agreement is likely due to the lack of trapped electron physics in current fluid model. This work presents improved physics understanding of the pedestal stability and turbulence dynamics for wide-pedestal QH-mode.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2017

Picosecond phase-velocity dispersion of hypersonic phonons imaged with ultrafast electron microscopy

We describe the direct imaging—with four-dimensional ultrafast electron microscopy—of the emergence, evolution, dispersion, and decay of photoexcited, hypersonic coherent acoustic phonons in nanoscale germanium wedges. Coherent strain waves generated via ultrafast in situ photoexcitation were imaged propagating with initial phase velocities of up to 35 km/s across discrete micrometer-scale crystal regions. We then observe that, while each wave front travels at a constant velocity, the entire wave train evolves with a time-varying phase-velocity dispersion, displaying a single-exponential decay to the longitudinal speed of sound (5 km/s) and with a mean lifetime of 280 ps. We also find that the wave trains propagate along a single in-plane direction oriented parallel to striations introduced during specimen preparation, independent of crystallographic direction. Elastic-plate modeling indicates the dynamics arise from excitation of a single, symmetric (dilatational) guided acoustic mode. Further, by precisely determining the experiment time-zero position with a plasma-lensing method, we find that wave-front emergence occurs approximately 100 ps after femtosecond photoexcitation, which matches well with Auger recombination times in germanium. We conclude by discussing the similarities between the imaged hypersonic strain-wave dynamics and electron/hole plasma-wave dynamics in strongly photoexcited semiconductors.

36 MATERIALS SCIENCE↗

DOE OSTI2024

ICED: An Integrated CGRA Framework Enabling DFVS-Aware Acceleration

oarse-grained reconfigurable arrays (CGRAs) are a promising solution to enable energy-efficient acceleration of applications from different domains. By leveraging reconfiguration at the functional level, they can adapt to significantly different computational patterns. Existing CGRA mapping approaches extract instruction-level parallelism, exploit loop-pipelining opportunities, guarantee the data dependency, and target high throughput of a given loop. However, the recurrence data-dependency in the DFG and the mismatch between required and available computing/communication resources complicate the mapping, and might lead to significant unbalances in the utilization of the CGRA's tiles. This results in wasted power for tiles with low utilization. Applying dynamic voltage and frequency scaling (DVFS) can potentially solve this challenge and improve energy efficiency by adjusting voltage and frequency of different tiles independently. CGRAs have also been successful in accelerating data-dependent streaming applications. However, in these applications, the execution time of each kernel in the pipeline might dynamically vary depending on the characteristics of the input. This also leads to under-utilization of resources for the dynamically changing kernels that do not limit the application throughput. DVFS can also improve energy efficiency for these applications by dynamically changing the voltage and frequency levels of tiles that host non performance-constraining kernels. This paper proposes ICEDTEA -- an integrated DVFS-aware framework to map applications on CGRAs that support power islands. ICEDTEA proposes a CGRA architecture supporting DVFS islands at varying granularity (from a single tile to a group of tiles) and the related DVFS-aware compilation and mapping toolchain. ICEDTEA is the first work that introduces DVFS support for spatio-temporal CGRAs at power-island levels. The experimental evaluation shows that ICEDTEA improves average utilization by 2.3$\times$ and energy-efficiency by 1.32$\times$ over a conventional CGRA. With streaming applications, ICEDTEA improves energy efficiency by 1.12$\times$ over a state-of-the-art CGRA that introduces partial dynamic reconfiguration to adapt to variations in kernels' throughput.

Tan, Cheng↗

DOE OSTI2017

SIERRA Low Mach Module: Fuego Theory Manual (V.4.44)

The SIERRA Low Mach Module: Fuego along with the SIERRA Participating Media Radiation Module: Syrinx, henceforth referred to as Fuego and Syrinx, respectively, are the key elements of the ASCI fire environment simulation project. The fire environment simulation project is directed at characterizing both open large-scale pool fires and building enclosure fires. Fuego represents the turbulent, buoyantly-driven incompressible flow, heat transfer, mass transfer, combustion, soot, and absorption coefficient model portion of the simulation software. Syrinx represents the participating-media thermal radiation mechanics. This project is an integral part of the SIERRA multi-mechanics software development project. Fuego depends heavily upon the core architecture developments provided by SIERRA for massively parallel computing, solution adaptivity, and mechanics coupling on unstructured grids.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2017

SIERRA Low Mach Module: Fuego User Manual (V.4.44)

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2017

SIERRA Low Mach Module: Fuego Theory Manual Version 4.46.

97 MATHEMATICS AND COMPUTING↗