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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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DOE OSTI2022

Multi-objective goal-directed optimization of de novo stable organic radicals for aqueous redox flow batteries

Abstract Advances in the field of goal-directed molecular optimization offer the promise of finding feasible candidates for even the most challenging molecular design applications. One example of a fundamental design challenge is the search for novel stable radical scaffolds for an aqueous redox flow battery that simultaneously satisfy redox requirements at the anode and cathode, as relatively few stable organic radicals are known to exist. To meet this challenge, we develop a new open-source molecular optimization framework based on AlphaZero coupled with a fast, machine-learning-derived surrogate objective trained with nearly 100,000 quantum chemistry simulations. The objective function comprises two graph neural networks: one that predicts adiabatic oxidation and reduction potentials and a second that predicts electron density and local three-dimensional environment, previously shown to be correlated with radical persistence and stability. With no hard-coded knowledge of organic chemistry, the reinforcement learning agent finds molecule candidates that satisfy a precise combination of redox, stability and synthesizability requirements defined at the quantum chemistry level, many of which have reasonable predicted retrosynthetic pathways. The optimized molecules show that alternative stable radical scaffolds may offer a unique profile of stability and redox potentials to enable low-cost symmetric aqueous redox flow batteries.

25 ENERGY STORAGE↗

DOE OSTI2025

Characterisation and comparative analysis of mitochondrial genomes of false, yellow, black and blushing morels provide insights on their structure and evolution

Morchella species have considerable significance in terrestrial ecosystems, exhibiting a range of ecological lifestyles along the saprotrophism-to-symbiosis continuum. However, the mitochondrial genomes of these ascomycetous fungi have not been thoroughly studied, thereby impeding a comprehensive understanding of their genetic makeup and ecological role. In this study, we analysed the mitogenomes of 30 Morchellaceae species, including yellow, black, blushing and false morels. These mitogenomes are either circular or linear DNA molecules with lengths ranging from 217 to 565 kbp and GC content ranging from 38% to 48%. Fifteen core protein-coding genes, 28–37 tRNA genes and 3–8 rRNA genes were identified in these Morchellaceae mitogenomes. The gene order demonstrated a high level of conservation, with the cox1 gene consistently positioned adjacent to the rnS gene and cob gene flanked by apt genes. Some exceptions were observed, such as the rearrangement of atp6 and rps3 in Morchella importuna and the reversed order of atp6 and atp8 in certain morel mitogenomes. However, the arrangement of the tRNA genes remains conserved. We additionally investigated the distribution and phylogeny of homing endonuclease genes (HEGs) of the LAGLIDADG (LAGs) and GIY-YIG (GIYs) families. A total of 925 LAG and GIY sequences were detected, with individual species containing 19–48HEGs. These HEGs were primarily located in the cox1, cob, cox2 and nad5 introns and their presence and distribution displayed significant diversity amongst morel species. These elements significantly contribute to shaping their mitogenome diversity. Overall, this study provides novel insights into the phylogeny and evolution of the Morchellaceae.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Fluid Dynamics Effects on Microstructure Prediction in Single-Laser Tracks for Additive Manufacturing of IN625

Single-track laser fusion were simulated using a heat-transfer-solidification-only (HTS) model and its extension with fluid dynamics (HTS_FD) model using a parallel open-source code, which included laminar fluid dynamics, flat-free surface of the molten alloy, heat transfer, phase-change, evaporation, and surface tension phenomena. The results illustrate that the fluid dynamics affects the solidification and ensuing microstructure. For the HTS_FD simulations, thermal gradient, G was found to exhibit a maximum at the extremity of the solidified pool ( i.e. , at the free surface), while for HTS simulations, G exhibited a maximum around the entire edge of the solidified pool. HTS_FD simulations predicted a wider range of cooling rates than the HTS simulations, exhibited an increased spread in the solidification speed, V variation within the melt-pool with respect to the HTS model results. Primary dendrite arm spacing (PDAS) were evaluated based on power law correlations and marginal stability theory models using the ( G , V ) from HTS and HTS_FD simulations to quantify the effect of the fluid dynamics on the microstructure. At low-laser powers and low-scan speeds, the PDAS obtained with the fluid dynamics model (HTS_FD) was larger by more than 30 pct with respect to the PDAS calculated with the simple HTS model. A new PDAS correlation, i.e. , \( \lambda_{1} \left[ {\mu {\text{m}}} \right] = 832\;G\left[ {\text{K/m}} \right]^{ - 0.5} V\left[ {\text{m/s}} \right]^{ - 0.25} \) , which uses the ( G , V ) results from the HTS_FD model was developed and validated against experimental results.

36 MATERIALS SCIENCE↗

DOE OSTI2020

Constraining physical models at gigabar pressures

High-energy-density (HED) experiments in convergent geometry are able to test physical models at pressures beyond hundreds of millions of atmospheres. The measurements from these experiments are generally highly integrated and require unique analysis techniques to procure quantitative infor mation. This work describes a methodology to constrain the physics in convergent HED experiments by adapting the methods common to many other fields of physics. As an example, a mechanical model of an imploding shell is constrained by data from a thin-shelled direct-drive exploding-pusher experiment on the OMEGA Laser System using Bayesian inference, resulting in the reconstruction of the shell dynamics and energy transfer during the implosion. The model is tested by analyzing synthetic data from a 1-D hydrodynamics code and is sampled using a Markov chain Monte Carlo to generate the posterior distributions of the model parameters. As a result, the goal of this work is to demonstrate a general methodology that can be used to draw conclusions from a wide variety of HED experiments.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2020

Binary pseudorandom array test standard optimized for characterization of large field-of-view optical interferometers

Recently, a technique for calibrating the modulation transfer function (MTF) of a broad variety of metrology instrumentation has been demonstrated. This technique is based on test samples structured as one-dimensional binary pseudo-random (BPR) sequences and two-dimensional BPR arrays (BPRAs). The inherent power spectral density of BPR gratings (sequences) and arrays has a deterministic white-noise-like character that allows direct determination of the MTF with uniform sensitivity over the entire spatial frequency range and field-of-view of an instrument. As such, the BPR samples satisfy the characteristics of a test standard: functionality, ease of specification and fabrication, reproducibility, and low sensitivity to manufacturing error. Here we discuss our recent developments directed to the optimization of the sample design, fabrication, application, and data processing procedures, suitable for thorough characterization of large aperture optical interferometers. Compared with the previous coded-aperture based design, the improved, 'highly randomized' BPRA pattern of the new test standard provides better accuracy and reliability of instrument MTF and aberration characterization, and enables operation optimization of large aperture optical interferometers. We describe the pattern generation algorithm and tests to verify the compliance to desired BPRA topography. The data acquisition and analysis procedures for different applications of the technique are also discussed.

Yashchuk, Valeriy V.↗

DOE OSTI2024

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.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2021

Stellar and Accretion Disk Parameters of the Close Binary HD 50526

We present a photometric and spectroscopic study of HD 50526, an ellipsoidal binary member of the group Double Periodic Variable stars. Performing data mining in photometric surveys and conducting new spectroscopic observations with several spectrographs during 2008–2015, we obtained orbital and stellar parameters of the system. The radial velocities were analyzed with the genetic PIKAIA algorithm, whereas Doppler tomography maps for the Hα and Hβ lines were constructed with the Total Variation Minimization code. An optimized simplex algorithm was used to solve the inverse problem adjusting the light curve with the best stellar parameters for the system. We find an orbital period of 6.ͩ701 ± 0.ͩ001 and a long photometric cycle of 191 ± 2 days. We detected the spectral features of the coldest star and modeled it with a logg=2.79±0.02 dex giant of mass 1.13 ± 0.02 M {sub ⊙} and effective temperature 10500 ± 125 K. In addition, we determine a mass ratio q = 0.206 ± 0.033 and that the hot star is a B-type dwarf of mass 5.48 ± 0.02 M {sub ⊙}. The V-band orbital light curve can be modeled including the presence of an accretion disk around the hotter star. This fills the Roche lobe of the hotter star and has a radius 14.74 ± 0.02 R {sub ⊙} and the temperature at the outer edge is 9400 K. Two bright spots located in the disk account for the global morphology of the light curve. The Doppler tomography maps of Hα and Hβ reveal complex structures of mass fluxes in the system.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2022

Development and performance of a HemeLB GPU code for human-scale blood flow simulation

In recent years, it has become increasingly common for high performance computers (HPC) to possess some level of heterogeneous architecture - typically in the form of GPU accelerators. In some machines these are isolated within a dedicated partition, whilst in others they are integral to all compute nodes - often with multiple GPUs per node - and provide the majority of a machine's compute performance. In light of this trend, it is becoming essential that codes deployed on HPC are updated to execute on accelerator hardware. Here, in this paper, we introduce a GPU implementation of the 3D blood flow simulation code HemeLB that has been developed using CUDA C++. We demonstrate how taking advantage of NVIDIA GPU hardware can achieve significant performance improvements compared to the equivalent CPU only code on which it has been built whilst retaining the excellent strong scaling characteristics that have been repeatedly demonstrated by the CPU version. With HPC positioned on the brink of the exascale era, we use HemeLB as a motivation to provide a discussion on some of the challenges that many users will face when deploying their own applications on upcoming exascale machines.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Stellar migration and chemical enrichment in the milky way disc: a hybrid model

ABSTRACT We develop a hybrid model of galactic chemical evolution that combines a multiring computation of chemical enrichment with a prescription for stellar migration and the vertical distribution of stellar populations informed by a cosmological hydrodynamic disc galaxy simulation. Our fiducial model adopts empirically motivated forms of the star formation law and star formation history, with a gradient in outflow mass loading tuned to reproduce the observed metallicity gradient. With this approach, the model reproduces many of the striking qualitative features of the Milky Way disc’s abundance structure: (i) the dependence of the [O/Fe]–[Fe/H] distribution on radius Rgal and mid-plane distance |z|; (ii) the changing shapes of the [O/H] and [Fe/H] distributions with Rgal and |z|; (iii) a broad distribution of [O/Fe] at sub-solar metallicity and changes in the [O/Fe] distribution with Rgal, |z|, and [Fe/H]; (iv) a tight correlation between [O/Fe] and stellar age for [O/Fe] > 0.1; (v) a population of young and intermediate-age α-enhanced stars caused by migration-induced variability in the Type Ia supernova rate; (vi) non-monotonic age–[O/H] and age–[Fe/H] relations, with large scatter and a median age of ∼4 Gyr near solar metallicity. Observationally motivated models with an enhanced star formation rate ∼2 Gyr ago improve agreement with the observed age–[Fe/H] and age–[O/H] relations, but worsen agreement with the observed age–[O/Fe] relation. None of our models predict an [O/Fe] distribution with the distinct bimodality seen in the observations, suggesting that more dramatic evolutionary pathways are required. All code and tables used for our models are publicly available through the Versatile Integrator for Chemical Evolution (VICE; https://pypi.org/project/vice).

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2022

Simulation and Reynolds-averaged Navier-Stokes modeling of a three-component Rayleigh-Taylor mixing problem with thermonuclear burn

Rayleigh-Taylor mixing in the presence of a third component with intermediate density is investigated through three-dimensional large-eddy simulation (LES) with a high-order compact finite-difference code. Two configurations are considered: (1) a symmetric configuration in which the Atwood number between the heavy and intermediate components matches the Atwood number between the intermediate and light components and (2) an asymmetric configuration in which the Atwood number between the heavy and intermediate components is an order of magnitude greater than the Atwood number between the intermediate and light components. Mass fraction covariances are extracted, and proposed Reynolds-averaged Navier-Stokes (RANS) closures for density-specific-volume and density-mass-fraction covariances are evaluated in an a priori fashion. Additionally, a multicomponent extension of the k - Φ - L - a - V RANS model [Morgan, Phys. Rev. E 104, 015107 (2021)] is presented which includes model equations for the upper-triangular elements of the mass fraction covariance matrix. This model, referred to as the k - Φ - L - a - C model, is compared against results from LES and against other RANS models. Profiles of average mass fraction, mass-fraction covariance, and density-specific-volume covariance obtained with the k - Φ - L - a - C model are found to agree well with LES data. Finally, the impact of three-component turbulent mixing on average reaction rate is investigated in both premixed and nonpremixed cases by heating the mixing layer and allowing it to undergo thermonuclear (TN) burn. A closure model for average reaction rate is proposed for use with the k - Φ - L - a - C model, and when this model is applied, improved agreement is obtained between LES and RANS in total TN neutron production.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2020

Xyce Parallel Electronic Simulator Users' Guide (Version 7.2)

This manual describes the use of the Xyce Parallel Electronic Simulator. Xyce has been designed as a SPICE-compatible, high-performance analog circuit simulator, and has been written to support the simulation needs of the Sandia National Laboratories electrical designers. This development has focused on improving capability over the current state-of-the-art in the following areas: Capability to solve extremely large circuit problems by supporting large-scale parallel computing platforms (up to thousands of processors). This includes support for most popular parallel and serial computers. A differential-algebraic-equation (DAE) formulation, which better isolates the device model package from solver algorithms. This allows one to develop new types of analysis without requiring the implementation of analysis-specific device models. Device models that are specifically tailored to meet Sandias needs, including some radiation-aware devices (for Sandia users only). Object-oriented code design and implementation using modern coding practices. Xyce is a parallel code in the most general sense of the phrase - a message passing parallel implementation - which allows it to run efficiently a wide range of computing platforms. These include serial, shared-memory and distributed-memory parallel platforms. Attention has been paid to the specific nature of circuit-simulation problems to ensure that optimal parallel efficiency is achieved as the number of processors grows.

42 ENGINEERING↗

DOE OSTI2020

Xyce Parallel Electronic Simulator Users' Guide (V.7.1)

This manual describes the use of the Xyce Parallel Electronic Simulator. Xyce has been designed as a SPICE-compatible, high-performance analog circuit simulator, and has been written to support the simulation needs of the Sandia National Laboratories electrical designers. This development has focused on improving capability over the current state-of-the-art in the following areas: 1) Capability to solve extremely large circuit problems by supporting large-scale parallel computing platforms (up to thousands of processors). This includes support for most popular parallel and serial computers. 2) A differential-algebraic-equation (DAE) formulation, which better isolates the device model package from solver algorithms. This allows one to develop new types of analysis without requiring the implementation of analysis-specific device models. 3) Device models that are specifically tailored to meet Sandia's needs, including some radiation-aware devices (for Sandia users only). 4) Object-oriented code design and implementation using modern coding practices. Xyce is a parallel code in the most general sense of the phrase a message passing parallel implementation which allows it to run efficiently a wide range of computing platforms. These include serial, shared-memory and distributed-memory parallel platforms. Attention has been paid to the specific nature of circuit-simulation problems to ensure that optimal parallel efficiency is achieved as the number of processors grows.

42 ENGINEERING↗

DOE OSTI2021

Xyce Parallel Electronic Simulator Users' Guide Version 7.4

This manual describes the use of the Xyce Parallel Electronic Simulator. Xyce has been designed as a SPICE-compatible, high-performance analog circuit simulator, and has been written to support the simulation needs of the Sandia National Laboratories electrical designers. This development has focused on improving capability over the current state-of-the-art in the following areas: • Capability to solve extremely large circuit problems by supporting large-scale parallel computing platforms (up to thousands of processors). This includes support for most popular parallel and serial computers. • A differential-algebraic-equation (DAE) formulation, which better isolates the device model package from solver algorithms. This allows one to develop new types of analysis without requiring the implementation of analysis-specific device models. • Device models that are specifically tailored to meet Sandia’s needs, including some radiation-aware devices (for Sandia users only). • Object-oriented code design and implementation using modern coding practices. Xyce is a parallel code in the most general sense of the phrase — a message passing parallel implementation — which allows it to run efficiently a wide range of computing platforms. These include serial, shared-memory and distributed-memory parallel platforms. Attention has been paid to the specific nature of circuit-simulation problems to ensure that optimal parallel efficiency is achieved as the number of processors grows.

42 ENGINEERING↗

DOE OSTI2022

Xyce™ Parallel Electronic Simulator Users' Guide, Version 7.5.

This manual describes the use of the Xyce Parallel Electronic Simulator. Xyce has been designed as a SPICE-compatible, high-performance analog circuit simulator, and has been written to support the simulation needs of the Sandia National Laboratories electrical designers. This development has focused on improving capability over the current state-of-the-art in the following areas: (1) Capability to solve extremely large circuit problems by supporting large-scale parallel computing platforms (up to thousands of processors). This includes support for most popular parallel and serial computers. (2) A differential-algebraic-equation (DAE) formulation, which better isolates the device model package from solver algorithms. This allows one to develop new types of analysis without requiring the implementation of analysis-specific device models. (3) Device models that are specifically tailored to meet Sandia's needs, including some radiation-aware devices (for Sandia users only). (4) Object-oriented code design and implementation using modern coding practices. Xyce is a parallel code in the most general sense of the phrase — a message passing parallel implementation — which allows it to run efficiently a wide range of computing platforms. These include serial, shared-memory and distributed-memory parallel platforms. Attention has been paid to the specific nature of circuit-simulation problems to ensure that optimal parallel efficiency is achieved as the number of processors grows.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2022

Xyce™ Parallel Electronic Simulator Users' Guide (V.7.6)

This manual describes the use of the Xyce™ Parallel Electronic Simulator. Xyce™ has been designed as a SPICE-compatible, high-performance analog circuit simulator, and has been written to support the simulation needs of the Sandia National Laboratories electrical designers. This development has focused on improving capability over the current state-of-the-art in the following areas: (1) Capability to solve extremely large circuit problems by supporting large-scale parallel computing platforms (up to thousands of processors). This includes support for most popular parallel and serial computers. (2) A differential-algebraic-equation (DAE) formulation, which better isolates the device model package from solver algorithms. This allows one to develop new types of analysis without requiring the implementation of analysis-specific device models. (3) Device models that are specifically tailored to meet Sandia's needs, including some radiation-aware devices (for Sandia users only). (4) Object-oriented code design and implementation using modern coding practices. Xyce™ is a parallel code in the most general sense of the phrase—a message passing parallel implementation—which allows it to run efficiently a wide range of computing platforms. These include serial, shared-memory and distributed-memory parallel platforms. Attention has been paid to the specific nature of circuit-simulation problems to ensure that optimal parallel eficiency is achieved as the number of processors grows.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2021

Spatial coupling of gyrokinetic simulations, a generalized scheme based on first-principles

In this paper, we present a scheme that spatially couples two gyrokinetic codes using first-principles. Coupled equations are presented and a necessary and sufficient condition for ensuring accuracy is derived. This new scheme couples both the field and the particle distribution function. The coupling of the distribution function is only performed once every few time-steps, using a five-dimensional (5D) grid to communicate the distribution function between the two codes. This 5D grid interface enables the coupling of different types of codes and models, such as particle and continuum codes, or delta-f and total-f models. Transferring information from the 5D grid to the marker particle weights is achieved using a new resampling technique. Demonstration of the coupling scheme is shown using two XGC gyrokinetic simulations for both the core and edge. We also apply the coupling scheme to two continuum simulations for a one-dimensional advection–diffusion problem.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2024

PETSc/TAO Users Manual Revision 3.22

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2020

A global anthropogenic emission inventory of atmospheric pollutants from sector- and fuel-specific sources (1970–2017): an application of the Community Emissions Data System (CEDS)

Global anthropogenic emission inventories remain vital for understanding the sources of atmospheric pollution and the associated impacts on the environment, human health, and society. Rapid changes in today's society require that these inventories provide contemporary estimates of multiple atmospheric pollutants with both source sector and fuel type information to understand and effectively mitigate future impacts. To fill this need, we have updated the open-source Community Emissions Data System (CEDS) (Hoesly et al., 2019) to develop a new global emission inventory, CEDSGBD-MAPS. This inventory includes emissions of seven key atmospheric pollutants (NOx; CO; SO2; NH3; non-methane volatile organic compounds, NMVOCs; black carbon, BC; organic carbon, OC) over the time period from 1970–2017 and reports annual country-total emissions as a function of 11 anthropogenic sectors (agriculture; energy generation; industrial processes; on-road and non-road transportation; separate residential, commercial, and other sectors (RCO); waste; solvent use; and international shipping) and four fuel categories (total coal, solid biofuel, the sum of liquid-fuel and natural-gas combustion, and remaining process-level emissions). The CEDSGBD-MAPS inventory additionally includes monthly global gridded (0.5°?×?0.5°) emission fluxes for each compound, sector, and fuel type to facilitate their use in earth system models. CEDSGBD-MAPS utilizes updated activity data, updates to the core CEDS default scaling procedure, and modifications to the final procedures for emissions gridding and aggregation. Relative to the previous CEDS inventory (Hoesly et al., 2018), these updates extend the emission estimates from 2014 to 2017 and improve the overall agreement between CEDS and two widely used global bottom-up emission inventories. The CEDSGBD-MAPS inventory provides the most contemporary global emission estimates to date for these key atmospheric pollutants and is the first to provide global estimates for these species as a function of multiple fuel types and source sectors. Dominant sources of global NOx and SO2 emissions in 2017 include the combustion of oil, gas, and coal in the energy and industry sectors as well as on-road transportation and international shipping for NOx. Dominant sources of global CO emissions in 2017 include on-road transportation and residential biofuel combustion. Dominant global sources of carbonaceous aerosol in 2017 include residential biofuel combustion, on-road transportation (BC only), and emissions from the waste sector. Global emissions of NOx, SO2, CO, BC, and OC all peak in 2012 or earlier, with more recent emission reductions driven by large changes in emissions from China, North America, and Europe. In contrast, global emissions of NH3 and NMVOCs continuously increase between 1970 and 2017, with agriculture as a major source of global NH3 emissions and solvent use, energy, residential, and the on-road transport sectors as major sources of global NMVOCs. Due to similar development methods and underlying datasets, the CEDSGBD-MAPS emissions are expected to have consistent sources of uncertainty as other bottom-up inventories. The CEDSGBD-MAPS source code is publicly available online through GitHub: https://github.com/emcduffie/CEDS/tree/CEDS_GBD-MAPS (last access: 1 December 2020). The CEDSGBD-MAPS emission inventory dataset (both annual country-total and monthly global gridded files) is publicly available under https://doi.org/10.5281/zenodo.3754964 (McDuffie et al., 2020c).

Mcduffie, Erin↗