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At least 289 records · Page 16

PETSc/TAO Users Manual (Rev. 3.20)

This manual describes the use of the Portable, Extensible Toolkit for Scientific Computation (PETSc) and the Toolkit for Advanced Optimization (TAO) for the numerical solution of partial differential equations and related problems on high-performance computers. PETSc/TAO is a suite of data structures and routines that provide the building blocks for the implementation of large-scale application codes on parallel (and serial) computers. PETSc uses the MPI standard for all distributed memory communication.

97 MATHEMATICS AND COMPUTING↗

Scaling Analysis of Two–Phase Flow in Fractal Permeability Fields

Fluid mixing in permeable media is essential in many practical applications. The mixing process is a consequence of velocity fluctuations owing to geological heterogeneities and mobility contrast of fluids. Heterogeneities in natural rocks are often spatially correlated, and their properties, such as permeability, may be described using fractal distributions. This work models the fractal characteristics of such permeability fields in which the covariance function is expressed as a power-law function. A generalized scaling relation is derived relating various fractal permeability fields using the magnitude of their fluctuations. Here, this relation reveals the self-similar behavior of two-phase flow in such permeable media. To that end, a recently developed, high-resolution numerical simulator is employed to validate the analytically derived scaling relations. Two flow problems are considered in which flow is governed by 1) a linear, and 2) a nonlinear transport equation. Due to the probabilistic representation of the fractal permeability fields, a sensitivity study is conducted for each flow scenario to determine the number of realizations required for statistical convergence. Scaling analysis is performed using ensemble averages of simulated saturation profiles and their mixing lengths. Results support the validity of the developed scaling relation across the range of investigated flow conditions at intermediate times. The dynamics of linear flow in the asymptotic regime is affected by the correlation structure of heterogeneity. In nonlinear flow, scaling behavior appears to be dominated by the degree of nonlinearity.

58 GEOSCIENCES↗

The Catalogue for Astrophysical Turbulence Simulations (CATS)

Turbulence is a key process in many fields of astrophysics. Advances in numerical simulations of fluids over the last several decades have revolutionized our understanding of turbulence and related processes such as star formation and cosmic ray propagation. However, data from numerical simulations of astrophysical turbulence are often not made public. We introduce a new simulation-oriented database for the astronomical community: the Catalogue for Astrophysical Turbulence Simulations (CATS), located at www.mhdturbulence.com. CATS includes magnetohydrodynamic (MHD) turbulent box simulation data products generated by the public codes athena++, arepo, enzo, and flash. CATS also includes several synthetic observational data sets, such as turbulent HI data cubes. We also include measured power spectra and three-point correlation functions from some of these data. We discuss the importance of open-source statistical and visualization tools for the analysis of turbulence simulations such as those found in CATS.

79 ASTRONOMY AND ASTROPHYSICS↗

Parameter estimation from spontaneous imbibition into volcanic tuff

Two-phase fluid flow properties underlie quantitative prediction of water and gas movement, but constraining these properties typically requires multiple time-consuming laboratory methods. The estimation of two-phase flow properties (van Genuchten parameters, porosity, and intrinsic permeability) is illustrated in cores of vitric nonwelded volcanic tuff using Bayesian parameter estimation that fits numerical models to observations from spontaneous imbibition experiments. The uniqueness and correlation of the estimated parameters is explored using different modeling assumptions and subsets of the observed data. The resulting estimation process is sensitive to both moisture retention and relative permeability functions, thereby offering a comprehensive method for constraining both functions. The data collected during this relatively simple laboratory experiment, used in conjunction with a numerical model and a global optimizer, result in a viable approach for augmenting more traditional capillary pressure data obtained from hanging water column, membrane plate extractor, or mercury intrusion methods. This method may be useful when imbibition rather than drainage parameters are sought, when larger samples (e.g., including heterogeneity or fractures) need to be tested that cannot be accommodated in more traditional methods, or when in educational laboratory settings.

58 GEOSCIENCES↗

Isotropic seismic radiation from rock damage and dilatancy

SUMMARY We present semi-analytical and numerical results on isotropic radiation expected to be generated by seismic sources with damaged dilatant materials that sustain during failure an overall shear deformation. The results are derived for inclusions with different stiffness components, including those responsible for shear-volumetric coupling in dilatant material, and different geometries, in a surrounding elastic solid. The obtained relations indicate that the isotropic seismic potency and seismic moment components are proportional to the shear potency components multiplied by the aspect ratio between the thickness and length of the source zone. For a typical rupture zone with a thin tabular geometry, the expected small aspect ratio explains the general seismological observations of small isotropic radiation. However, isotropic radiation induced by dynamic dilation for short and thick sources is more pronounced and may reach for spherical sources sustaining shear deformation 18 per cent of the shear components. Sources that include also tensile components and explosions can produce larger isotropic radiation. The results provide rigorous relations that can be used to estimate different source properties in numerical simulations, experiments and field studies.

Geochemistry & Geophysics↗

Energy balance and Alfvén Mach numbers in compressible magnetohydrodynamic turbulence with a large-scale magnetic field

Energy equipartition is a powerful theoretical tool for understanding astrophysical plasmas. It is invoked, for example, to measure magnetic fields in the interstellar medium (ISM), as evidence for small-scale turbulent dynamo action, and, in general, to estimate the energy budget of star-forming molecular clouds. Here, in this study, we motivate and explore the role of the volume-averaged root-mean-squared (rms) magnetic coupling term between the turbulent, δB , and large-scale, B 0 , fields, $\langle$(δB·B 0 ) 2 $\rangle$$_{V}^{1/2}$. By considering the second moments of the energy balance equations we show that the rms coupling term is in energy equipartition with the volume-averaged turbulent kinetic energy for turbulence with a sub-Alfvénic large-scale field. Under the assumption of exact energy equipartition between these terms, we derive relations for the magnetic and coupling term fluctuations, which provide excellent, parameter-free agreement with time-averaged data from 280 numerical simulations of compressible magnetohydrodynamic (MHD) turbulence. Furthermore, we explore the relation between the turbulent mean field and total Alfvén Mach numbers, and demonstrate that sub-Alfvénic turbulence can only be developed through a strong, large-scale magnetic field, which supports an extremely super-Alfvénic turbulent magnetic field. This means that the magnetic field fluctuations are significantly subdominant to the velocity fluctuations in the sub-Alfvénic large-scale field regime. Throughout our study, we broadly discuss the implications for observations of magnetic fields and understanding the dynamics in the magnetized ISM.

79 ASTRONOMY AND ASTROPHYSICS↗

ZFP: A compressed array representation for numerical computations

HPC trends favor algorithms and implementations that reduce data motion relative to FLOPS. We investigate the use of lossy compressed data arrays in place of traditional IEEE floating point arrays to store the primary data of calculations. Simulation is fundamentally an exercise in controlled approximation, and error introduced by finite-precision arithmetic (or lossy compression) is just one of several sources of error that need to be managed to ensure sufficient accuracy in a computed result. We describe ZFP, a compressed numerical format designed for in-memory storage of multidimensional arrays, and summarize theoretical results that demonstrate that the error of repeated lossy compression can be bounded and controlled. Furthermore, we establish a relationship between grid resolution and compression-induced errors and show that, contrary to conventional floating point, ZFP reduces finite-difference errors with finer grids. We present example calculations that demonstrate data reduction by 4x or more with negligible impact on solution accuracy. Our results further demonstrate several orders-of-magnitude increase in accuracy using ZFP over IEEE floating point and Posits for the same storage budget.

Lindstrom, Peter↗

Linear and Nonlinear Solvers for Simulating Multiphase Flow within Large-Scale Engineered Subsurface Systems

Simulation of multiphase flow in the subsurface is well-known to be computationally challenging. While there have been many studies that have explored approaches to overcoming these challenges, they often utilize relatively simple case studies. In this paper, we focus on the unique numerical challenges posed by modeling large-scale engineered subsurface systems, characterized by discrete features embedded in a heterogeneous natural subsurface setting. The man-made features such as shafts, tunnels, and barriers often cause multiple challenges in modeling the domain for multiphase porous media flow. This flow scenario can have a wide range of applications such as nuclear waste repositories, enhanced recovery of a petroleum reservoir, geothermal engineering, and carbon sequestration. An example of these severe numerical challenges is the case of performance assessment (PA) for Waste Isolation Pilot Plant (WIPP), the only operating deep geological repository in the US, which simulates extreme material properties of bedded salt rock formation and extreme contrast due to open excavation next to the formation. The models have extremes not only of permeability and porosity but also of the constitutive models needed for multiphase flow; additionally, they have process models like salt creep closure reducing porosity over time, fracturing in clay and anhydrite interbeds of the bedded salt, gas generation from the waste materials, and unintentional human borehole intrusions in some scenarios. Numerical simulations require the solution of coupled systems of nonlinear PDEs; in our work, we use the open-source simulator PFLOTRAN which is based on Finite Volume discretization. The solution of the nonlinear equations requires use of the Newton-Raphson iteration at each time step, which entails the solution of the linearized Jacobian system at each iteration. The effects of all the processes (i.e., large number of unknowns, highly nonlinear constitutive relations, large contrasts in material properties in short distances) lead to an ill-conditioned Jacobian matrix that severely challenges traditional linear solver, i.e., stabilized biconjugate gradient with block Jacobi incomplete LU preconditioner (BCGS-ILU) leading to non-convergence for traditional Newton-Raphson nonlinear solver causing unacceptably long computation time for each model. This paper presents linear solvers such as constrained pressure residual (CPR) two-stage preconditioner with alternate-block-factorization (ABF) and quasi- implicit pressure and explicit saturation (QIMPES) decouplers and flexible generalized residual solver (FGMRES). The new general-purpose nonlinear solver, Newton trust-region dogleg Cauchy (NTRDC), is also introduced to resolve extreme nonlinearities in the models. We demonstrate the effectiveness of each method relative to the default BCGS-Newton solver. The two best cases had nearly 50 times speed-up and achieved completion of a simulation in 14 hours that never completed due to non-convergence with the default solver. We also investigate the strong scalability of each method and discuss some of the deficiencies found for Block Jacobi preconditioner using parallel domain decomposition, and node packing effects of modern processor architecture.

Preconditioner, Nonlinear, Porous media, Multiphas↗

Experiments and numerical modeling of surrogate droplet combustion for a 93 octane gasoline calibration fuel

Gasoline is the world’s most prolific liquid transportation fuel for ground transportation vehicles. Yet, a fundamental understanding of its burning characteristics is still lacking. Complicating this matter is the highly multicomponent nature of gasoline (comprised of hundreds of chemical species) and the seasonable variability of its composition due to variations in the crude oil feedstocks used in refining. The need to bring order to this complex problem has led to development of calibration fuels (Tier II in presented study) which on average will provide repeatable metrics that replicate performance of refined gasoline for various engine designs. This study presents results of experiments using the configuration of an isolated droplet to study the combustion dynamics of calibration fuel and three different surrogates (S4, S5, S6) for the calibration fuel. Droplet burning is under microgravity conditions, where gas transport is determined entirely by fuel evaporation in order to promote spherical symmetry in the burning process. The initial droplet diameters ranged between 0.55 mm and 0.60 mm. The droplets were spark-ignited and their burning histories were recorded by digital video cameras to obtain quantitative data. For each fuel, the evolutions of droplet, flame, and soot-shell diameters were measured to calculate the burn rates, flame-droplet diameter ratios (FSR) and soot-droplet diameter ratios. Additionally, a detailed numerical modeling is presented. This simulation includes multicomponent phase equilibrium, unsteady gas and liquid transport, radiative heat transfer, internal liquid diffusion and detailed combustion chemistry of different fuels during their burning process. Experiment results show that the calibration fuel and surrogates have a close burn rates and FSR, and S5 presents a relatively similar results with calibration fuel. Predictions from the numerical simulation using the surrogate are compared with experiment measurements, which showed a good agreement with the experiment results, including the droplet burning rate and FSR.

Guo, Songtao↗

Reactive Transport Modeling of Anthropogenic Carbon Mineralization in Stacked Columbia River Basalt Reservoirs

Numerical simulation of CO2 storage in basalts and related reactive lithologies requires modeling complex, coupled hydrologic and chemical processes, including multi-phase flow and transport, partitioning of CO2 into the aqueous phase, and chemical interactions with aqueous fluids and rock minerals. We conducted reactive transport simulations of the Wallula pilot-scale CO2 injection into the flow tops of the Grande Ronde Basalt using our PNNL STOMP-CO2 simulator with the ECKEChem reactive module. Our mineralization simulation of the ~1,000 tons of injected CO2 into the interflow zones was based on the hydrologic transport model we previously developed. For this work, the simulations considered geochemical reactions involving the basalt components, precipitates, formation brine, and injected CO2. In our benchmark case, carbonate minerals precipitated, resulting in ~20% of the CO2 being mineralized in 10 years. Increasing the reaction rate of a single primary mineral phase (clinopyroxene) by an order of magnitude resulted in a carbon mineralization reaction extent of ~90% over the same time interval. Based on these initial sensitivity analysis results, it is clear that a thorough understanding of primary mineral dissolution rates is required for accurately predicting long-term fate and transport of injected CO2 into basalt formations. Our reactive transport numerical simulations will be key components of commercial-scale CO2 storage operation permitting, de-risking, and optimization in mafic and ultramafic reservoirs.

Cao, Ruoshi↗

Analysis of muntjac deer genome and chromatin architecture reveals rapid karyotype evolution

Abstract Closely related muntjac deer show striking karyotype differences. Here we describe chromosome-scale genome assemblies for Chinese and Indian muntjacs, Muntiacus reevesi (2 n = 46) and Muntiacus muntjak vaginalis (2 n = 6/7), and analyze their evolution and architecture. The genomes show extensive collinearity with each other and with other deer and cattle. We identified numerous fusion events unique to and shared by muntjacs relative to the cervid ancestor, confirming many cytogenetic observations with genome sequence. One of these M. muntjak fusions reversed an earlier fission in the cervid lineage. Comparative Hi-C analysis showed that the chromosome fusions on the M. muntjak lineage altered long-range, three-dimensional chromosome organization relative to M. reevesi in interphase nuclei including A/B compartment structure. This reshaping of multi-megabase contacts occurred without notable change in local chromatin compaction, even near fusion sites. A few genes involved in chromosome maintenance show evidence for rapid evolution, possibly associated with the dramatic changes in karyotype.

59 BASIC BIOLOGICAL SCIENCES↗

Self-focusing of cosh-Gaussian laser beam and its effect on the excitation of ion-acoustic wave and stimulated Brillouin backscattering in collisionless plasma

An analytical and numerical study has been carried out for self-focusing of an intense cosh-Gaussian laser beam in collisionless plasma and its impact on the excitation of ion-acoustic wave and stimulated Brillouin backscattering process. The analytical model has been developed under Wentzel–Kramers–Brillouin and paraxial ray approximations. The nonlinearities of ponderomotive force on electron and the relativistic oscillation of the electron mass have been used in this study. The nonlinear differential equations have been set up for the beam width parameters of the main beam, ion-acoustic wave, backscattered wave and back reflectivity of stimulated Brillouin scattering (SBS). These equations have been solved numerically for different values of decentred parameter (b), relative plasma density (ω{sub p0}/ω{sub 0}) and incident laser intensity (a). The results have been compared with only relativistic nonlinearity and Gaussian profile of laser beam. The focusing of laser beam, ion-acoustic wave and scattered wave are found to be strong under relativistic-ponderomotive regime compared to only relativistic regime. Further, it is observed that focusing/intensity of main laser beam, ion acoustic wave and SBS back reflectivity increases with increasing the values of b and ω{sub p0}/ω{sub 0}. Itis also found that back reflectivity of SBS process gets suppressed with the increase in the value of a. This study may be useful in laser induced fusion scheme where back scattering of SBS plays very important role.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Impacts of Multidimensional Progenitor Perturbations on Core-collapse Supernova Explosions

Numerical studies of core-collapse supernovae have demonstrated the importance of nonradial motions in precollapse progenitors on the explosion outcome. We use the Chimera neutrino radiation hydrodynamics code running seven two-dimensional simulations of 15 M⊙ progenitors with different progenitor structures introduced by different one- and two-dimensional precollapse stellar evolution environments to examine the impacts of stellar structure and nonspherical motion in the precollapse progenitor on the development of explosions. We compare the explosion evolution of these models in terms of shock dynamics, diagnostic energy, neutrino heating, accretion, explosion geometry, nuclear abundances, and turbulent convection. We also analyze how stochastic variation impacts our simulations. Contrary to results reported in prior studies examining the impacts of multidimensional progenitors, we observe similar shock revival times and explosion development in our simulations despite differences in initial compositions and structures. We find no discernible impact from the accretion of nonradial perturbations from a multi-D progenitor onto the stalled shock in the revival and strength of explosion, as fully developed neutrino-driven convection behind the stalled shock is similar for all our models. For models with physically sourced noise in the iron core, a strong oscillation of the shock occurs after bounce and deflects infall laterally, and accelerates the saturation of the lateral turbulent kinetic energy. An examination of model stochasticity shows that any prior expected impacts on explosive outcome due to convection-related perturbations lie below the detectable threshold of numerical variation.

Chen, Chien-Hui [North Carolina State University]↗

Toward control co-design of utility-scale wind turbines: Collective vs. individual blade pitch control

A large-eddy simulation framework has been coupled with controller modules to systematically investigate the impacts of collective (CPC) and individual (IPC) pitch control strategies on utility-scale wind turbine energy production and fatigue loads. Wind turbine components were parameterized using an actuator surface model to simulate the rotor blades and the turbine nacelle. The baseline CPC and IPC algorithms, consisting of single-input single-output proportional–integral controllers and two integral controllers, respectively, were incorporated into the numerical framework. A series of simulations were carried out to investigate the relative performance of the two controllers under various turbulent inflow conditions, spanning hub-height velocities of 7 to 14 m/s. The numerical simulation results of this study showed that, in comparison to the CPC, the IPC controller could successfully reduce the damage equivalent loads of utility-scale turbines at regions 2 and 3 of turbine operation by about 3% and 40%, respectively, without any penalty on the power production of the turbine. It was also shown that, despite its minor impact on the turbulence kinetic energy of the wake, the IPC controller did not influence the recovery of the turbine wake.

17 WIND ENERGY↗

Elemental profiling and genome-wide association studies reveal genomic variants modulating ionomic composition in Populus trichocarpa leaves

The ionome represents elemental composition in plant tissues and can be an indicator of nutrient status as well as overall plant performance. Thus, identifying genetic determinants governing elemental uptake and storage is an important goal for breeding and engineering biomass feedstocks with improved performance. In this study, we coupled high-throughput ionome characterization of leaf tissues with high-resolution genome-wide association studies (GWAS) to uncover genetic loci that modulate ionomic composition in leaves of poplar ( Populus trichocarpa ). Significant agreement was observed across the three ionomic profiling platforms tested: inductively coupled plasma-mass spectrometry (ICP-MS), neutron activation analysis (NAA) and laser-induced breakdown spectroscopy (LIBS). Relative quantification of 20 elements using ICP-MS across a population of 584 genotypes, revealed larger variation in micro-nutrients and trace elements content than for macro-nutrients across genotypes. The GWAS performed using a set of high-density (>8.2 million) single nucleotide polymorphisms, identified over 600 loci significantly associated with variations in these mineral elements, pointing to numerous uncharacterized candidate genes. A significant enrichment for genes related to ion homeostasis and transport was observed, including several members of the cation-proton antiporters (CPA) family and MATE efflux transporters, previously reported to be critical for plant growth and fitness in other species. Our results also included a polymorphic copy of the high-affinity molybdenum transporter MOT1 found directly associated to molybdenum content. For the first time in a perennial plant, our results provide evidence of genetic control of mineral content in a model tree species.

59 BASIC BIOLOGICAL SCIENCES↗

Evaluation of Tritium Behavior in Forest Vegetation for the Purpose of Determining Appropriate Non-Zero Deposition Velocities for Tritium Oxide

Modeling and field measurements have been conducted between 2019 and 2021 to assess the practicality of using a non-zero deposition velocity for safety basis estimates of tritium oxide fate and transport modeling. A model was developed which used a complex deposition algorithm designed to assess how tritium oxide would mix based on the turbulent motions and wind speed effects that the forest canopy has on the atmosphere. The model was driven based on measurements of wind and turbulence taken from the Aiken AmeriFlux Tower which measures these properties at five levels located within and just above the forest. The model was then validated against a series of field experiments which were designed to test the model predictions and estimate the deposition velocity occurring over the forest environment at the Savannah River Site. The field releases used deuterium oxide as a surrogate for tritium oxide and was released as a fine mist which rapidly evaporated, creating a gaseous tracer in the atmosphere. Using air samplers, the elevations in deuterium concentration in the air relative to background measurements was assessed and then modeled. Generally, the numerical model tended to underpredict the amount of deuterium being mixed from above the canopy to the forest floor, indicating that the predictions it provides are still conservative relative to what was measured during the field experiments. Across a suite of modeling runs, the 95 th and 99 th percentile deposition velocities were estimated to be 1.2 and 0.7 cm s -1 , respectively. Estimated deposition velocities in the 2021 field experiments, which specifically assessed a release above the forest canopy and its mixing to the surface, predicted deposition velocities ranging from 1.75 to 6.61 cm s -1 . While these field releases do not cover all possible meteorological conditions, it seems appropriate to use a non-zero deposition velocity when performing safety-basis modeling of tritium oxide. The recommendation presented in this report is to use 1.0 cm s -1 . This is between the 95 th and 99 th percentile value estimated from the modeling study, suggesting it should be appropriate for the majority of release scenarios given the model’s apparent conservatism relative to field measurements.

54 ENVIRONMENTAL SCIENCES↗

What is the iε for the S-matrix?

Can the S-matrix be complexified in a way consistent with causality? Since the 1960's, the affirmative answer to this question has been well-understood for 2→2 scattering of the lightest particle in theories with a mass gap at low momentum transfer, where the S-matrix is analytic everywhere except at normal-threshold branch cuts. We ask whether an analogous picture extends to realistic theories, such as the Standard Model, that include massless fields, UV/IR divergences, and unstable particles. Especially in the presence of light states running in the loops, the traditional iε prescription for approaching physical regions might break down, because causality requirements for the individual Feynman diagrams can be mutually incompatible. We demonstrate that such analyticity problems are not in contradiction with unitarity. Instead, they should be thought of as finite-width effects that disappear in the idealized 2→2 scattering amplitudes with no unstable particles, but might persist at higher multiplicity. To fix these issues, we propose an iε -like prescription for deforming branch cuts in the space of Mandelstam invariants without modifying the analytic properties. This procedure results in a complex strip around the real part of the kinematic space, where the S-matrix remains causal. In addition to giving a pedagogical introduction to the analytic properties of the perturbative S-matrix from a modern point of view, we illustrate all the points on explicit examples, both symbolically and numerically. Furthermore, to help with the investigation of related questions, we introduce a number of tools, including holomorphic cutting rules, new approaches to dispersion relations, as well as formulae for local behavior of Feynman integrals near branch points.

Anomalous thresholds↗