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At least 523 records · Page 29

Improved diffusion coefficients generated from Monte Carlo codes

Monte Carlo codes are becoming more widely used for reactor analysis. Some of these applications involve the generation of diffusion theory parameters including macroscopic cross sections and diffusion coefficients. Two approximations used to generate diffusion coefficients are assessed using the Monte Carlo code MC21. The first is the method of homogenization; whether to weight either fine-group transport cross sections or fine-group diffusion coefficients when collapsing to few-group diffusion coefficients. The second is a fundamental approximation made to the energy-dependent P1 equations to derive the energy-dependent diffusion equations. Standard Monte Carlo codes usually generate a flux-weighted transport cross section with no correction to the diffusion approximation. Results indicate that this causes noticeable tilting in reconstructed pin powers in simple test lattices with L2 norm error of 3.6%. This error is reduced significantly to 0.27% when weighting fine-group diffusion coefficients by the flux and applying a correction to the diffusion approximation. Noticeable tilting in reconstructed fluxes and pin powers was reduced when applying these corrections. (authors)

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

Estimates of SNL/NM maximum winds and recurrence intervals for use in non-nuclear building design loads

Extreme wind is one environmental aspect used in safe building and structure design. The Department of Energy (DOE) Standard (STD) 1020-2012 includes various building standards adopted by DOE, and guidance necessary to comply with Facility Safety. Recent updates to the American Society of Civil Engineers (ASCE) Standards and International Building Codes (IBC) were used to initiate a review of local maximum wind speeds and verify estimates to be used in new building design. This report summarizes the site specific wind data and techniques used in estimating the maximum wind speeds anticipated at Sandia National Laboratories, New Mexico. The local data suggests site specific increases in wind speed maxima over information documented in past standards and building codes.

42 ENGINEERING↗

Developing a Computational Chemistry Framework for the Exascale Era

Within computational chemistry the NWChem package has arguably been the de facto standard for running high-accuracy numerical simulations on the most powerful supercomputers. In order to better address the challenges presented by emerging exascale architectures, the decision has been made to rewrite NWChem. Design of the resulting package, NWChemEx, has been driven by exascale computing; however, significant additional design considerations have arisen from the team's involvement with the Molecular Sciences Software Institute (MolSSI). MolSSI is a National Science Foundation initiative focused on establishing coding and data standards for the computational chemistry community. As a result, NWChemEx is built upon a general computational chemistry framework called the Simulation Development Environment (SDE) that is designed with a focus on extensibility and interoperability. The present manuscript describes the modular approach of the SDE and how it has been used to implement the self-consistent field algorithm within NWChemEx.

97 MATHEMATICS AND COMPUTING↗

Measuring Impact of U.S. DOE Geothermal Technologies Office Funding: Considerations for Development of a Geothermal Resource Reporting Metric

This paper reviews existing methodologies and reporting codes used to describe extracted energy resources such as coal and oil and describes a comparable proposed methodology to describe geothermal resources. The goal is to provide the U.S. Department of Energy's (DOE) Geothermal Technologies Office (GTO) with a consistent and comprehensible means of assessing the impacts of its funding programs. This framework will allow for GTO to assess the effectiveness of research, development, and deployment (RD&D) funding, prioritize funding requests, and demonstrate the value of RD&D programs to the U.S. Congress. Standards and reporting codes used in other countries and energy sectors provide guidance to inform development of a geothermal methodology, but industry feedback and our analysis suggest that the existing models have drawbacks that should be addressed. In order to formulate a comprehensive metric for use by GTO, we analyzed existing resource assessments and reporting methodologies for the geothermal, mining, and oil and gas industries, and we sought input from industry, investors, academia, national labs, and other government agencies. Using this background research as a guide, we describe a methodology for assessing and reporting on GTO funding according to resource knowledge and resource grade (or quality). This methodology would allow GTO to target funding or measure impact by progression of projects or geological potential for development.

15 GEOTHERMAL ENERGY↗

Ectomycorrhizal effects on decomposition are highly dependent on fungal traits, climate, and litter properties: A model-based assessment. Dataset.

To simulate the effects of mycorrhizal fungi on soil organic matter cycling, we incorporated mycorrhizal processes into the Carbon, Organisms, Rhizosphere, and Protection in the Soil Environment (CORPSE) model to develop a new soil model Myco-CORPSE. The new model was calibrated and evaluated against soil measurements taken at temperate forests in New Hampshire (NH) and Georgia (GA). A series of scenario analysis were also conducted to explore the conditions under which ectomycorrhizal (ECM) N acquisition processes can induce different soil C accumulation in ECM systems compared to arbuscular (AM) systems.In this data package, we included:-The Python codes of the standard Myco-CORPSE model we developed: "Standard Myco_CORPSE python codes.zip". The main program is the "gradient_sim.py" which calculates the bulk soil microbes and CN content along a user defined gradient of clay, soil temperature, soil moisture and mycorrhizal dominance, and relies on two subprograms "CORPSE_deriv.py" and "CORPSE_integrate.py". "CORPSE_deriv.py" calculated the changes in all simulated soil stock within every time step and "CORPSE_integrate.py" integrate the changes in all simulated soil stock within simulated time period. The program "Plot.py" is used to plot the major outputs produced by the main program "gradient_sim.py".-The modified Python codes of Myco-CORPSE models with site-level environmental inputs (in NH and GA) used to conduct simulations in NH and GA sites: "NH_GA model simulations.zip". -The Python codes used to evaluate the Myco-CORPSE simulation outputs in NH and GA sites against site-level measurements: "Plot NH_GA simulation against measurements.zip". It includes both the evaluation Python code, the model outputs on NH and GA sites, and the measured soil properties in both sites.-The modified Python codes of Myco-CORPSE models "Scenario analysis_model simulations.zip" that is used to conduct scenario analysis of how different litter properties, mycorrhizal fungal traits, climate, and seasonal variation in temperature and vegetation phenology impact the mycorrhizal effects on soil CN properties. The sub file folder "Scenario analysis_litter traits" contains the codes for scenario analysis of different litter properties; The sub file folder "Scenario analysis_ECM types" contains the codes for scenario analysis of different ECM fungal traits; The sub file folder "Scenario analysis_climate&seasonality" contains the codes for scenario analysis of different climate and seasonalities;-"Scenario analysis_model results and plotting codes.zip" contains all the output files from the the scenario analysis of Myco-CORPSE model as described above and the plotting codes used to the generate the heatmaps and scatterplots shown in the manuscript "Ectomycorrhizal effects on decomposition are highly dependent on fungal traits, climate, and litter properties: A model-based assessment"The majority of the model outputs did not have specific geographic information or temporal coverage because the analysis we conducted are mainly hypothetical model simulations. We only provided geographic description, coordinates and temporal coverage for those soil measurements which we used for model evaluations (included in the "Plot NH_GA simulation against measurements.zip").

54 ENVIRONMENTAL SCIENCES↗

Code Verification and Solution Verification framework in pin-resolved neutron transport code MPACT

Program verification in scientific computing encompasses the application of formal and mathematical techniques to a scientific computing code for its credibility, accuracy, and validity. Code Verification identifies bugs and performance issues in the software development stage. Solution Verification assesses the applicability of the code and the accuracy of the solution to problems of interest. Both activities utilize application cases and quantify the error against prescribed acceptance criteria. However, simply executing more application cases does not guarantee stronger or more comprehensive credibility. Here, we establish a verification framework that involves Code Verification and Solution Verification, both of which work together such that the overarching goal of “converge to the correct answer for the intended application” can be reasonably inferred. The application of such a verification framework is demonstrated using the pin-resolved neutron transport code MPACT, where standard unit tests and regression tests are covered, and where the Method of Exact Solutions and the Method of Manufactured Solutions are successfully used. Additionally, the applicability of Method of Manufactured Solutions is extended to the OECD/NEA C5G7 benchmark problems of practical material and geometric configurations. Solution Verification activities are demonstrated on a practical hierarchy of application models of increasing complexity ranging from 2D pin cell problems to 3D assembly problems. The convergence behavior and rate of convergence with respect to each individual variable are studied and provided. This framework can be adapted broadly to other fields involving scientific computing codes.

97 MATHEMATICS AND COMPUTING↗

GenASiS: General Astrophysical Simulation System. II. Self-gravitating Baryonic Matter*

GenASiS (General Astrophysical Simulation System) is a code being developed initially and primarily, though not exclusively, for the simulation of core-collapse supernovae on the world's leading capability supercomputers. This paper---the second in a series---documents capabilities for Newtonian self-gravitating fluid dynamics, including tabulated microphysical equations of state treating nuclei and nuclear matter (`baryonic matter'). Computation of the gravitational potential of a spheroid, and simulation of the gravitational collapse of dust and of an ideal fluid, provide tests of self-gravitation against known solutions. In multidimensional computations of the adiabatic collapse, bounce, and explosion of spherically symmetric pre-supernova progenitors---which we propose become a standard benchmark for code comparisons---we find that the explosions are prompt and remain spherically symmetric (as expected), with an average shock expansion speed and total kinetic energy that are inversely correlated with the progenitor mass at the onset of collapse and the compactness parameter.

Cardall, Christian [ORNL] (ORCID:000000020086105X)↗

Intercomparison of 3D pore-scale flow and solute transport simulation methods

Multiple numerical approaches have been developed to simulate porous media fluid flow and solute transport at the pore scale. These include methods that 1) explicitly model the three-dimensional geometry of pore spaces and 2) those that conceptualize the pore space as a topologically consistent set of stylized pore bodies and pore throats. In previous work we validated a model of class 1, based on direct numerical simulation using computational fluid dynamics (CFD) codes, against magnetic resonance velocimetry (MRV) measurements of pore-scale velocities. Here we expand that validation to include additional models of class 1 based on the immersed-boundary method (IMB), lattice Boltzmann method (LBM), smoothed particle hydrodynamics (SPH), as well as a model of class 2 (a pore-network model or PNM). The PNM approach used in the current study was recently improved and demonstrated to accurately simulate solute transport in a two-dimensional experiment. While the PNM approach is computationally much less demanding than direct numerical simulation methods, the effect of conceptualizing complex three-dimensional pore geometries on solute transport in the manner of PNMs has not been fully determined. We apply all four approaches (CFD, LBM, SPH and PNM) to simulate pore-scale velocity distributions and nonreactive solute transport, and intercompare the model results with previously reported experimental observations. Experimental observations are limited to measured pore-scale velocities, so solute transport comparisons are made only among the various models. Comparisons are drawn both in terms of macroscopic variables (e.g., permeability, solute breakthrough curves) and microscopic variables (e.g., local velocities and concentrations).

computational fluid dynamics↗

A Conversation on Standard 90.1-2016

The roundtable discussion: A Conversation on Standard 90.1-2016, highlights some of the major changes one can expect to see in building envelope, mechanical system, and lighting requirements. In addition, the article highlights a new performance-based compliance path, climate zone revisions, and the strategic initiatives resulting in the new format. This roundtable was conducted by ASHRAE Journal with Drake Erbe, Member ASHRAE; Dick Lord, Fellow ASHRAE; Len Sciarra, AIA, Member ASHRAE; Eric Richman, Member ASHRAE; Michael Rosenberg, Member ASHRAE; Rahul Athalye, Associate Member ASHRAE; Bing Liu, P.E., Member ASHRAE; and Jason Glazer, P.E., Member ASHRAE.

ASHRAE↗

The 2016 Edition of the ICSBEP Handbook

Over the past several decades, numerous experiments have been performed worldwide to support criticality safety. These experiments represent a significant investment in infrastructure, expertise, and cost, and are valuable resources of data for present and future research. These valuable assets provide the basis for recording, development, and validation of methods and nuclear data. If the experimental data are lost, the high cost to repeat many of these measurements may be prohibitive. The International Criticality Safety Benchmark Evaluation Project (ICSBEP) was established to: 1. Identify a comprehensive set of critical benchmark data and, to the extent possible, verify the data; 2. Evaluate the data and quantify overall uncertainties through various types of sensitivity analyses; 3. Compile the data into a standardized format; 4. Perform calculations of each experiment with standard criticality safety codes; and 5. Formally document the work into a single source of verified benchmark critical data. Annually, contributors from around the world continue to collaborate in the evaluation and review of select benchmark experiments for inclusion in the International Handbook of Evaluated Criticality Safety Benchmark Experiments (ICSBEP Handbook). Further information regarding the ICSBEP, including highlighted criticality safety benchmark evaluations, can be found in the September and October 2003 editions of Nuclear Science and Engineering. Several new evaluations have been prepared for inclusion in the September 2016 edition of the ICSBEP Handbook. (authors)

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

An improved dataset for predicting mammal infecting viruses from genetic sequence information

There have been several attempts to develop machine learning (ML) models to identify human infecting viruses from their genomic sequences, with varying degrees of success. Direct comparison between models is problematic, because these models are typically trained and evaluated on different datasets with alternative data splitting schemes, features, and model performance metrics. In this paper we present a standardized dataset of mammal infecting and non-infecting viral pathogens, refined from the previous work of Mollentze et al. to include the latest literature evidence, roughly doubling the number of curated host-virus records available to the community, and new host target labels, primate and mammal. The new host labels were included for several reasons, including previous reports that classification performance is better at broader taxonomic ranks and the idea that there may be more data for primate infection that might serve as a suitable proxy for zoonotic potential and avoidance of false positives for human infection due to absence of evidence. On this dataset, we report the performance of eight machine learning models for predicting mammal-infecting viruses from their genomic sequences. We find that randomly assigning cases in our improved dataset to training/testing sets, when compared to the original assignments into training/testing in Mollentze et al., increases the overall average ROC AUC of prediction of human infection from 0.663 ± 0.070 to 0.784 ± 0.013, consistent with the reduction in phylogenetic distance between train and test sets (relative entropy change from 3.00 to 0.08). The broadest host category of mammal infection can be predicted most reliably at 0.850 ± 0.020. We share our improved dataset and code to enable standardized comparisons of machine learning methods to predict human host infections. Overall, we have presented preliminary evidence that classification of virus host infection is more tractable at higher taxonomic ranks, that unsurprisingly reducing the phylogenetic distance between training and test sets can improve predictive performance, that peptide kmer features appear to be harmful to out of sample model performance, and we are left with the question of whether models for virus host prediction can reasonably be expected to perform well in out of sample scenarios given the likelihood that viruses do not share a common ancestor. Consistent with this concern, when the data is resampled such that there is no overlap between viral families in training and test sets (relative entropy > 24), models perform no better than random chance at prediction of human infection regardless of whether kmers are included (ROC AUC 0.50 ± 0.08) or not (ROC AUC 0.50 ± 0.04).

59 BASIC BIOLOGICAL SCIENCES↗

TropiRoot 1.0: Database of tropical root characteristics across environments

Tropical ecosystems contain the world's largest biodiversity of vascular plants. Yet, our understanding of tropical functional diversity and its contribution to global diversity patterns is constrained by data availability. This discrepancy underscores an urgent need to bridge data gaps by incorporating comprehensive tropical root data into global datasets. Here, we provide a database of tropical root characteristics. This new database, TropiRoot 1.0, will be instrumental in evaluating an array of hypotheses pertaining to root functional ecology and plant biogeography, both within the tropics and relative to other global biomes. The data compilation was conducted by the TropiRoot Initiative, in partnership with the Fine-Root Ecology Database (FRED) and the Global Root Trait (GRooT) database, Colorado State University (CSU) and the Smithsonian Tropical Research Institute (STRI). Literature search and data extraction were conducted between 2020 and 2024. Literature was identified using Web of Science, Scopus, and complemented using the expert knowledge of members of TropiRoot. To provide broad environmental and geographical distributions, literature searches included root characteristics (traits) across global change drivers, natural gradients, and from different continents. We adopted FRED standardized data columns and streamlined the format to enhance accessibility for data extraction across various user groups. This optimized framework resulted in a smaller, yet comprehensive datasheet. To make the database compatible with other global root trait initiatives, column identification was standardized following the codes provided by FRED. These efforts culminated in data extracted from 104 new sources, resulting in more than 8000 rows of data (either species or community data). Most of the data in TropiRoot 1.0 include root characteristics such as root biomass, morphology, root dynamics, mass fraction, architecture, anatomy, physiology, and root chemistry. This initiative represents a 30% increase in the currently available data for tropical roots in FRED. TropiRoot 1.0 contains root characteristics from 25 different countries, where seven are located in Asia, six in South America, five in Central America and the Caribbean, four in Africa, two in North America, and 1 in Oceania. Due to the volume of data, when ancillary data were available, including soil data, these data were either extracted and included in the database or its availability was recorded in an additional column. Multiple contributors checked the entries for outliers during the collation process to ensure data quality. For text-based observations, we examined all cells to ensure that their content relates to their specific categories. For numerical observations, we ordered each numerical value from least to greatest and plotted the values, checking apparent outliers against the data in their respective sources and correcting or removing incorrect or impossible values. Some data (soil and aboveground) have different columns for the same variable presented in different units, including originally published units, but root characteristics data had units converted to match those reported in FRED. By filling a gap from global databases, TropiRoot 1.0 expands our knowledge of otherwise so far underrepresented regions and our ability to assess global trends. This advancement can be used to improve tropical forest representation in vegetation models. The data are freely available and should be cited when used.

FRED↗

Optimization of Condensed Matter Physics Application with OpenMP Tasking Model

The Density Matrix Renormalization Group (DMRG++) is a condensed matter physics application used to study superconductivity properties of materials. It’s main computations consist of calculating hamiltonian matrix which requires sparse matrix-vector multiplications. This paper presents task-based parallelization and optimization strategies of the Hamiltonian algorithm. The algorithm is implemented as a mini-application in C++ and parallelized with OpenMP. The optimization leverages tasking features, such as dependencies or priorities included in the OpenMP standard 4.5. The code refactoring targets performance as much as programmability. The optimized version achieves a speedup of 8.0× with 8 threads and 20.5× with 40 threads on a Power9 computing node while reducing the memory consumption to 90 MB with respect to the original code, by adding less than ten OpenMP directives.

Criado, Joel↗

Analysis of US Industrial Assessment Centers (IACs) implementation

Industrial energy assessments are a fundamental action toward developing a decarbonization strategy at any level. They provide an understanding of where energy efficiency opportunities exist and help to make informed business decisions about the costs and benefits of implementing sustainable policies and practices. This paper examines the effectiveness of the Department of Energy's Industrial Assessment Centers Program at providing useful energy-efficiency audits as well as the barriers faced by the program and plans for future growth and improvement. This paper presents an analysis of the program between 1981 and 2022, covering 20,290 industrial assessments and 151,198 recommendations, with $2.6 billion of recommended savings. The analysis includes a breakdown of the IAC recommendations and implemented projects based on both the industrial subsectors according to the Standard Industrial Classification code, energy type, and systems evaluated. The results include a 47 % implementation rate, a gap analysis to understand the missed opportunities, and a discussion about reasons for recommendation rejection. A comparison of the IAC Program with other country-level energy auditing or assessment programs was conducted, and suggestions for improving implementation rates were mentioned.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

High Accuracy Transition Metal Effective Cores for the Many-Body Diffusion Monte Carlo Method

Practical applications of the real-space diffusion Monte Carlo (DMC) method require the removal of core electrons, where currently localization approximations of semilocal potentials are generally used in the projector. Accurate calculations of complex solids and large molecules demand minimizing the impact of approximated atomic cores. Prior works have shown that the errors from such approximations can be sizable in both finite and periodic systems. In this work, we show that a class of differential pseudopotentials, known as pseudo-Hamiltonians, can be constructed for the 3d transition metal atoms, entirely removing the need for any localization scheme in the DMC projector. As a proof of principle, we demonstrate the approach for the case of Co. In order to minimize errors in the pseudo-Hamiltonian at the many-body level, we generalize the recently proposed correlation-consistent pseudopotential generation scheme to successively close semilocal representations of the differential potentials. Our generation scheme successfully produces potentials tailored specifically for real space projector quantum Monte Carlo methods with low error at the many-body level, i.e., with many-body scattering properties very close to relativistic all-electron results. In particular, we show that the agreement with respect to atomic and molecular quantities reach chemical accuracy in many cases-on par with the most accurate semilocal pseudopotentials available. Further, our pseudo-Hamiltonian generation scheme utilizes standard quantum chemistry codes designed only to work with semilocal pseudopotentials, enabling straightforward generation of pseudo-Hamiltonians for additional elements in future works.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Automatic energy calibration algorithm for an RBS setup

This work describes a computer algorithm for automatic extraction of the energy calibration parameters from a Rutherford Back-Scattering Spectroscopy (RBS) spectrum. Parameters like the electronic gain, electronic offset and detection resolution (FWHM) of a RBS setup are usually determined using a standard sample. In our case, the standard sample comprises of a multi-elemental thin film made of a mixture of Ti-Al-Ta that is analyzed at the beginning of each run at defined beam energy. A computer program has been developed to extract automatically the calibration parameters from the spectrum of the standard sample. The code evaluates the first derivative of the energy spectrum, locates the trailing edges of the Al, Ti and Ta peaks and fits a first order polynomial for the energy-channel relation. The detection resolution is determined fitting the convolution of a pre-calculated theoretical spectrum. To test the code, data of two years have been analyzed and the results compared with the manual calculations done previously, obtaining good agreement.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Temporal resolution criterion for correctly simulating relativistic electron motion in a high-intensity laser field

Particle-in-cell codes are now standard tools for studying ultra-intense laser-plasma interactions. Motivated by direct laser acceleration of electrons in sub-critical plasmas, we examine temporal resolution requirements that must be satisfied to accurately calculate electron dynamics in strong laser fields. Using the motion of a single electron in a perfect plane electromagnetic wave as a test problem, we show surprising deterioration of the numerical accuracy with increasing wave amplitude a{sub 0} for a given time-step. We go on to show analytically that the time-step must be significantly less than λ/ca{sub 0} to achieve good accuracy. We thus propose adaptive electron sub-cycling as an efficient remedy.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Dynamical consequences of a constraint on the Langevin thermostat in molecular cluster simulation

We investigate some unusual behaviour observed while performing molecular dynamics simulations with the DL_POLY_4.03 code. Under the standard Langevin thermostat, atoms appear to be thermalised to different temperatures, depending on their mass and on the total number of particles in the system. We find that an imposed constraint whereby no thermal noise acts on the centre of mass of the system is the cause of the unexpected behaviour. This is demonstrated by solving the stochastic dynamics for the constrained thermostat and comparing the results with simulation data. The effect of the constraint can be considerable for small systems with disparate masses. By removing the constraint the Langevin thermostat may be restored to its intended behaviour and this has been implemented as an option in DL_POLY_4.05. SMK was supported by the U.S. Department of Energy, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences, and Biosciences.

dissociation↗