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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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
A sharp interface Lagrangian-Eulerian method for rigid-body fluid-structure interaction
Herein this paper introduces a sharp interface method to simulate fluid-structure interaction (FSI) involving rigid bodies immersed in viscous incompressible fluids. The capabilities of this methodology are benchmarked using a range of test cases and demonstrated using large-scale models of biomedical FSI. The numerical approach developed herein, which we refer to as an immersed Lagrangian-Eulerian (ILE) method, integrates aspects of partitioned and immersed FSI formulations by solving separate momentum equations for the fluid and solid subdomains, as in a partitioned formulation, while also using non-conforming discretizations of the dynamic fluid and structure regions, as in an immersed formulation. A simple Dirichlet-Neumann coupling scheme is used, in which the motion of the immersed solid is driven by fluid traction forces evaluated along the fluid-structure interface, and the motion of the fluid along that interface is constrained to match the solid velocity and thereby satisfy the no-slip condition. To develop a practical numerical method, we adopt a penalty approach that approximately imposes the no-slip condition along the fluid-structure interface. In the coupling strategy, a separate discretization of the fluid-structure interface is tethered to the volumetric solid mesh via stiff spring-like penalty forces. Our fluid-structure coupling scheme relies on an immersed interface method (IIM) for discrete geometries, which enables the accurate determination of both velocities and stresses along complex internal interfaces. Numerical methods for FSI can suffer from instabilities related to the added mass effect, but computational tests indicate that the methodology introduced here remains stable for selected test cases across a broad range of solid-fluid mass density ratios, including extremely small, nearly equal, equal, and large density ratios. Biomedical FSI demonstration cases include results obtained using this method to simulate the dynamics of a bileaflet mechanical heart valve in a pulse duplicator, and to model transport of blood clots in a patient-averaged anatomical model of the inferior vena cava.
High pressure ammonia/methanol oxidation up to 100 atm
Here, high pressure ammonia/methanol oxidation and NOx formations were investigated using a recently developed supercritical pressure jet-stirred reactor (SP-JSR) at 20 and 100 atm with temperatures between 550 and 950 K and equivalence ratios of 0.138 and 1.15. The experimental results show that NH 3 oxidation at high pressure is significantly accelerated by the active OH radicals produced from CH 3 OH oxidation. Furthermore, the kinetic interactions between NH 3 and CH 3 OH are governed mainly by the reactions CH 3 OH + NH 2 = CH 2 OH + NH 3 , CH 3 OH + NH 2 = CH 3 O + NH 3 , and CH 2 O + NH 2 = HCO + NH 3 . A HP-Mech model for high-pressure NH 3 /CH 3 OH oxidation was developed in this study. It consists of the most recent NH 3 and CH 3 OH models including some new reactions and updated rate constants from the literature as well as NH 3 -CH 3 OH interactions where rate constants of CH 3 OH + NH 2 = CH 2 OH + NH 3 , CH 3 OH + NH 2 = CH 3 O + NH 3 , NH 2 + CH 2 O = NH 3 + HCO, and NH 2 + CH 2 O = NH 2 CHO + H were theoretically calculated in this study. Our model with these updates improves the prediction for the measured N 2 O/NO x temperature dependence at 100 atm. In addition, the reaction pathway and sensitivity analysis show that N 2 O/NO x /HONO interactions with HO 2 are very important, especially for a fuel-lean mixture at 100 atm. The HONO mole fraction for the fuel-lean mixture at 100 atm was then measured by off-axis integrated cavity output spectroscopy (ICOS) at wavenumber of 6638.26 cm -1 . The experimental data show a significant HONO formation at intermediate temperature that is strongly underpredicted by numerical simulation at 100 atm. Therefore, the HONO related reactions with notable uncertainty at high pressure such as NO + OH (+M) = HONO (+M) and H 2 NO + NO 2 = HONO + HNO need deeper exploration in the future.
Vibrational spectroscopy of uranium tetrafluoride hydrates
Uranium tetrafluoride (UF 4 ) is an important intermediate in the production of UF6 and nuclear fuel. Historical characterization of UF 4 with Raman spectroscopy was plagued with ambiguity until the first accurate Raman spectrum was published by our group in 2016. Although generally considered to be relatively stable, UF 4 can hydrolyze to form numerous UF 4 hydrates that may play a role in future uranium waste forms. In contrast to anhydrous UF 4 , the hydrates, with their OH stretch and HOH bending modes, can be spectroscopically characterized by the type and degree of water bonding in the crystal lattice, which can yield additional information about their crystal structure. Herein, vibrational spectroscopy (Raman and infrared) was used to characterize three different UF 4 hydrates: UF 4 (H 2 O) 0.33 , U 3 F 12 (H 2 O), and UF 4 (H 2 O) 2.5 . Spectra show the different hydrates vary in the number of observed bands, full-width half-maximum of the bands, and band intensity. These differences are due to varying interactions between the OH stretch and HOH bending modes with UF 4 and the polymeric UF 4 structure in the crystal lattice. These vibrational data, in combination with spectral fitting and crystallographic structures measured with powder X-ray diffraction and single crystal X-ray diffraction, provide unique details on the location of water molecules in the crystal lattice of hydrated UF 4 , and provide an interesting contrast to the vibrational spectra of anhydrous UF 4 .
Detailed Characterization of an Annealed Reduced Graphene Oxide Catalyst for Selective Peroxide Formation Activity
Recently, electrochemical hydrogen peroxide (H 2 O 2 ) generation from oxygen molecules has been extensively studied. Thus far, the best peroxide activity under alkaline conditions has been reported at the surface of a mild reduced graphene oxide annealed at 600 °C (mrGO-600). However, the detailed material information, such as chemical functionality and structural morphology, is unknown, which results in ambiguous debates on its catalytic active sites. Therefore, to solve this problem, we intensively characterize the structure of mrGO-600 to clarify the origin of its catalytic activity. Various characterizations, including X-ray photoelectron spectroscopy, Raman spectroscopy, infrared spectroscopy, near-edge X-ray absorption fine spectroscopy, and high-resolution transmittance electron microscopy coupled with in situ infrared spectroelecrochemistry, reveal that the annealing process generates not only various hole edge defects that are related to the ring ether group but also numerous point defects that result in a small-sized disconnected graphitic carbon region. These defects are believed to form a unique atomic level configuration in mrGO-600, which enables it to facilitate high peroxide-generated activity from oxygen molecules in an alkaline electrolyte.
Multi-task graph neural networks for simultaneous prediction of global and atomic properties in ferromagnetic systems *
Abstract We introduce a multi-tasking graph convolutional neural network, HydraGNN, to simultaneously predict both global and atomic physical properties and demonstrate with ferromagnetic materials. We train HydraGNN on an open-source ab initio density functional theory (DFT) dataset for iron-platinum with a fixed body centered tetragonal lattice structure and fixed volume to simultaneously predict the mixing enthalpy (a global feature of the system), the atomic charge transfer, and the atomic magnetic moment across configurations that span the entire compositional range. By taking advantage of underlying physical correlations between material properties, multi-task learning (MTL) with HydraGNN provides effective training even with modest amounts of data. Moreover, this is achieved with just one architecture instead of three, as required by single-task learning (STL). The first convolutional layers of the HydraGNN architecture are shared by all learning tasks and extract features common to all material properties. The following layers discriminate the features of the different properties, the results of which are fed to the separate heads of the final layer to produce predictions. Numerical results show that HydraGNN effectively captures the relation between the configurational entropy and the material properties over the entire compositional range. Overall, the accuracy of simultaneous MTL predictions is comparable to the accuracy of the STL predictions. In addition, the computational cost of training HydraGNN for MTL is much lower than the original DFT calculations and also lower than training separate STL models for each property.
Single-particle dynamics of microbunching
The mechanism of steady-state microbunching (SSMB) has been proposed [D. F. Ratner and A. W. Chao, Phys. Rev. Lett. 105, 154801 (2010)] to generate high-power coherent radiation at a high repetition rate or in continuous-wave mode using electron storage rings. In this paper, the related single-particle dynamics are theoretically and numerically studied, and important results are presented. The investigated effects are longitudinal quantum radiation excitation, nonlinear momentum compaction, and linear and nonlinear coupling of the transverse and longitudinal motion. Although this analysis is oriented toward SSMB, some of the analyzed effects are also crucial in cases such as coherent harmonic generation, bunch slicing, bunch compression, free-electron laser beam transport lines, and quasi-isochronous rings, which involve precise longitudinal phase-space manipulations.
PETSc/TAO Users Manual V.3.21
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 (PDEs) and related problems on high-performance computers. PETSc/TAO is a suite of data structures and routines that provide the building blocks for implementing large-scale application codes on parallel (and serial) computers. PETSc uses the MPI standard for all distributed memory communication. PETSc/TAO includes a large suite of parallel linear solvers, nonlinear solvers, time integrators, and optimizers that may be used in application codes written in Fortran, C, C++, and Python (via petsc4py; see Getting Started ). The library is organized hierarchically, enabling users to employ the abstraction level most appropriate for a particular problem. By using techniques of object-oriented programming, PETSc provides enormous flexibility for users.