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MOSCATO Development and Integration in Fiscal Year 2022

During FY21, we conducted ongoing development work for the MOSCATO (Molten Salt Chemistry and Transport) solver. The code development work primarily consisted of transitioning capabilities from the original version of the solver, which was written in OpenFOAM, into Nek5000. In doing so, a fast, highly parallelizable solver was created that is capable of complex chemistry and corrosion simulations for engineering-scale molten salt systems. The Nek5000 version of MOSCATO is now fully featured and capable of higher-fidelity simulations than were previously possible. Demonstration cases including a thermal convection loop have been simulated to test these new capabilities. We built upon the work for FY22 and improved the code from several different perspectives. First, we improved the user interface by adding a new component to the official Nek5000 input file (.par). This new part contains documents parameters like, salt properties (density, viscosity, Cp, thermal conductivity), diffusion coefficients, standard potential, etc. Second, we built a conversion script to extract salt properties from the MSTDB-TP salt database and write to MOSCATO input file. Third, we migrated the code to NekRS, which is the GPU branch of Nek5000 and suitable for next generation supercomputers. Verification and Validation (V&V) work was also continued in FY22. Two tasks were performed. The first V&V task involved the validation of the Poisson-Nernst-Planck equation solver and Butler-Volmer electrode kinetics, by comparing with numerical and experimental data about thermoelectric cells. The second task involved the comparisons to corrosion results from a thermal convection loop run during the MSRE era. Satisfactory agreement was obtained from both tasks.

Yuan, Haomin↗

Data From: "Warming and snow loss increase reliance on old groundwater in a Colorado River headwater"

This repository contains the data and code associated with the paper titled "Warming and snow loss increase reliance on old groundwater in a Colorado River headwater," published in Nature Geoscience, 2026. This study seeks to answer how various ages of groundwater interact with mountainous streamflow in mountainous headwaters such as the East River. It includes various model-data processing scripts, primarily for ParFlow-CLM analysis of simulated water years 2015-2021, and two numerical warming experiments (+2.5 and +4.0 degrees C), including run scripts, forcing scripts, and post-processing, as well as comparison to observation datasets, detailed below. This data requires the use of R (.r, .rmd), Python (.py), Jupyter Notebook or Jupyter Lab (.ipynb), ParFLOW-CLM, EcoSLIM. Further information on the use of all file formats mentioned below (e.g. .tff. .nc) are provided within the associated scripts and directory where the files are located. Contents & Usage ASO/: ​​Contains the bash and python scripts used to convert airborne snow observatory (ASO) data (ASO, 2023) in various data formats (georeferenced tiff file, NetCDF, UTM, and to latitude/longitude) then regrided to the ParFlow equivalent grid. Output data are in regrid_regll_data.zip and subsequently visualized and analyzed in plot_and_compare.py for Supplementary Figures A14 and A15. The wksht_ASO_comparison.xlsx spreadsheet is used to calculate the data for Supplementary Figure A16. EcoSLIM/: Contains the scripts and input files to run the EcoSLIM particle tracking simulations (/run_scripts) and the post-processing python script (/plot_scripts/eco_agedist_plots.ipynb). Jasechko et al./: Contains the jupyter notebook (Extract_Elevation.ipynb) to determine the outlet elevations of the 260 watersheds used in Jasechko et al. (2016), and the corresponding table, Table_S1_Watersheds_alt.csv. Used to create Supplementary Information Figure A2. PLM_Wells/: Contains the QA/QC-ed groundwater level time series of the PLM-1 and PLM-6 Monitoring Wells from Faybishenko et al. (2023), reformatted to water years used for Supplementary Figures A19 and and A20. ParFlow/: Contains the input files and run scripts to run ParFlow-CLM (/run_scripts), the python and tool command language (Tcl) scripts to create and distribute the ParFlow forcing simulation files (/forcing), and various scripts and intermediary files to analyze the model outputs (/post_process). SQUIRE/: Contains the processing scripts and intermediary files for the Surface QUantitatIve pRecipitation Estimation (SQUIRE) data (Grover, 2023) used to generate Supplementary Figure A18. USGS_Streamflow/: Contains the raw and gap-filled United States Geological Survey streamflow data (U.S. Geological Survey, 2026) used at the Almont station (site number 09112500). Gap-filling is performed in the R script with data from the Taylor station (site number 09110000). (/USGS_09112500_EAST_RIVER_AT_ALMONT_GAP_FILLED/code_almont_streamflow_gap_fill.Rmd). discharge/: Contains the gap-filled discharge data at the Watershed Function SFA East River pumphouse site (Newcomer et al., 2022) used to generate Supplementary Figure A13 and to compute hourly Nash-Sutcliffe model efficiency coefficients (NSE) in Table A4. snotel_and_flux_tower/: Contains the snow telemetry data (U.S. Department of Agriculture, 2024) from the Butte (site ID 380) and Schofield (site ID 737) stations, reformatted by water year, accessed with the snotelr R package. Used to create Supplementary Figure A17. Also contains the flux tower observational data (FluxTower_Pumphouse_ESS-DIVE.ET_only.h.txt) from Ryken et al. (2022) and sap flux transpiration data (MaxB_Transpiration_5Sites.daily_sums.h.txt) from Ryken (2021), used to create Supplementary Figures A22 and A23, respectively. Raw EcoSLIM model outputs are in excess of 24TB, and are stored on National Energy Research Scientific Computing Center (NERSC) and publicly available via the external link provided in the paper.

atmospheric warming↗

Water chemistry in flume channel and hyporheic zone (i.e., porewater) associated with: “Rethinking Aerobic Respiration in the Hyporheic Zone Under Variation in Carbon and Nitrogen Stoichiometry”

Dissolved oxygen (DO), total organic carbon (TOC), total nitrogen (TN), molecular data for organic matter, and biochemical reactions for surface water and porewater (i.e., hyporheic zone) collected from a water recirculating flume located at the University of Texas, Austin. The flume contained real river water from Lower Colorado River(Austin, TX) and clean sand. Hyporheic exchange in the flume was induced through The study aims to understand relationships between aerobic metabolism of organic matter and molecular characteristics of organic matter, such as thermodynamic signature and nitrogen content, through the extent of the hyporheic zone at 10 cm- resolution, and through time. During the experiment, organic matter (dry leaves) was added to the flume and removed after 24 hours. The water samples were collected before the addition of leaves, at the time of removal of leaves, and at hour 72. The water samples were analyzed using ultrahigh resolution Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) and total organic carbon (TOC) and total nitrogen (TN) analysis. Dissolved oxygen content throughout the surface water and the hyporheic zone of the flume was measured with a large planar optode. This data package is associated with the publication ’ Rethinking Aerobic Respiration in the Hyporheic Zone Under Variation in Carbon and Nitrogen Stoichiometry’ published in Environmental Science and Technology (Turețcaia et al., 2023 https://doi.org/10.1021/acs.est.3c04765). The dataset is comprised of five folders (1) Diss_O2_pic, (2) input_files (3) output_files; (4) python_code; and (5) R_code . Diss_O2_pic contains siximages of dissolved oxygen distribution in a bedform at hours 0, 24, and 72 of the experiment conducted in a large recirculation flume. Images are in separate R and G channels (i.e., RGB). The input_files contains (1) a csv file with FTICR peaks identified within each sample, (2) a csv file with molecular information pertinent to FTICR data with Gibbs free energy calculations adjusted for environmental temperature, (3) a csv file containing concentrations of non-purgeable organic carbon measured throughout the experiment , (4) a csv file containing concentrations of total nitrogen measured throughout the experiment, (5) a csv file containing total biochemical reactions (i.e., transformations) identified in the dataset, (6) a csv containing transformation profiles, and (7) a csv file containing transformations with formulas, and (8) a jpg file with schematic representation of locations for sample collection. The output_files contains (1) and xlsx file containing percent biochemical reactions containing nitrogen identified across all 39 sample, (2) a csv file of merged FTICR data and molecular information files, (3) a csv files containing average Gibbs free energy within sampling domains and at each sampling location, (4) a csv file with average concentrations of dissolved oxygen across sampling locations at hour 0, (5) a csv file with average concentrations of dissolved oxygen across sampling locations at hour 24, (6) a csv file with average concentrations of dissolved oxygen across sampling locations at hour 72, (7) a csv file with percent chemical classes identified across sampling locations at hour 0, (8) a csv file with percent chemical classes identified across sampling locations at hour 24, (9) a csv file with percent chemical classes identified across sampling locations at hour 72, and (10) a csv file containing percent nitrogen containing biochemical reactions identified across sampling locations at hours 0, 24, and 72. The python_code contains seven ipynb files which are Jupyter Notebooks used for data analysis and figures generation. The R_code contains 3 R files with R code used for data analysis and figures generation. This data package contains the processed data used in the associated manuscript. This data has not been previously published.

54 ENVIRONMENTAL SCIENCES↗

Enhancing Monte Carlo Workflows for Nuclear Reactor Analysis with Metamodel-Driven Modeling

Monte Carlo codes are essential components of many reactor physics simulation workflows as high-fidelity continuous-energy neutron transport solvers. Among Monte Carlo radiation transport codes, MCNP is particularly notable due to its diverse simulation capabilities, large user base, and long validation history. Despite being a powerful simulation tool, MCNP provides limited capabilities to allow automated execution, model transformation, or support for user-defined logic and abstractions that limit its compatibility with modern workflows. Here, to better integrate MCNP into a modern scientific workflow, we have developed an intuitive yet full-featured MCNP Application Program Interface (API) in Python, named MCNPy, which provides a specialized set of classes for MCNP input development. Moreover, to guarantee that our reading, writing, and modeling capabilities remain self-consistent (and to render the huge scope of the MCNP API manageable), we have adopted a strategy of model-driven software development in which a generalized model of the MCNP input format has been created. From this generalized model, or “metamodel,” problem-specific implementations such as an engine for input validation or a codebase for programmatic operations may be automatically generated. Since MCNPy primarily acts as a Python front-end to the underlying Java API that directly interfaces with the metamodel, it is intrinsically linked to the metamodel and thus remains maintainable. With MCNPy, users can programmatically read, write, and modify any syntactically valid MCNP input file regardless of its origin. These capabilities allow users to automate complicated tasks like design optimization and model translation for nuclear systems. As examples, this work demonstrates the use of MCNPy to find the critical radius of a plutonium sphere and to translate a 9000+ line MCNP input file into a corresponding OpenMC model.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

HTESP (High-throughput electronic structure package): A package for high-throughput ab initio calculations

High-throughput ab initio calculations are the indispensable parts of data-driven discovery of new materials with desirable properties, as reflected in the establishment of several online material databases. The accumulation of extensive theoretical data through computations enables data-driven discovery by constructing machine learning and artificial intelligence models to predict novel compounds and forecast their properties. Efficient usage and extraction of data from these existing online material databases can accelerate the next stage materials discovery that targets different and more advanced properties, such as electron–phonon coupling for phonon-mediated superconductivity. However, extracting data from these databases, generating tailored input files for different ab initio calculations, performing such calculations, and analyzing new results can be demanding tasks. Here, in this work, we introduce a software package named “HTESP” (High-Throughput Electronic Structure Package) written in Python and Bash languages, which automates the entire workflow including data extraction, input file generation, calculation submission, result collection and plotting. Our HTESP will help speed up future computational materials discovery processes.

36 MATERIALS SCIENCE↗

Advanced Terrestrial Simulator (ATS) evaluation dataset at 7 catchments across the continental United States

This dataset comprises of the input files and other files required for Advanced Terrestrial Simulator (ATS) simulations at 7 catchments across the continental United States. ATS is an integrated surface-subsurface hydrology model. We include Jupyter notebooks (within scripts folder) for individual catchments showing information (including data sources, river network, soil, geology, landuse types etc.) on preparing the machine readable input files. ATS observation output files are provided in the output folder. Figures and analyses (.xlsx sheets) are also provided. The catchments include, Taylor River Upstream (Colorado); (b) Cossatot River (Arkansas); (c) Panther Creek (Alabama); (d) Little Tennessee River (North Carolina and Georgia); (e) Mayo River (Virginia); (f) Flat Brook (New Jersey); (g) Neversink River headwaters (New York). Readme files are provided inside the directories providing more details. Files types include: .xml, .h5, .xlsx, .png, .ipynb, .py, .nc, .txt. All of the files types can be accessed by open source software, details on software requirements are following: .xml (any text editors including notepad and textedit), .h5 (in python using hdf libraries), .xlsx (WPS Office Spreadsheets, OpenOffice Calc, LibreOffice Calc, Microsoft Office etc.), .png (any image viewer), .ipynb (Jupyter notebook), .py (any text editors including notepad and textedit), .nc (using python or other open source software).

54 ENVIRONMENTAL SCIENCES↗

Cladding Profilometry Analysis of Experimental Breeder Reactor-II Metallic Fuel Pins with HT9, D9, and SS316 Cladding

BISON finite element method fuel performance simulations were conducted using an existing automated process that couples the Fuels Irradiation & Physics Database (FIPD) and the Integral Fast Reactor Materials Information System database by writing input files and comparing the BISON output to post-irradiation fuel pin profilometry measurements contained within the databases. The importance of this work is to demonstrate the ability to benchmark fuel performance metallic fuel models within BISON using Experimental Breeder Reactor-II fuel pin data for a number of similar pins, while building off previous modeling efforts. Changes to the generic BISON input file include implementing pin specific axial power and flux profiles, pin specific fluences, frictional contact, and irradiation-induced volumetric swelling models for cladding. A statistical analysis of irradiation-induced volumetric swelling models for HT9, D9, and SS316 was performed for experiments X421/X421A, X441/X441A, and X486. Between these three experiments, there were 174 post-irradiation examination (PIE) profilometries used for validating the swelling models presented using a standard error of the estimate (SEE) method. Implementation of the volumetric swelling models for D9 and SS316 claddings was found to have a significant impact on the BISON profilometry simulated, where HT9 clad pins had an insignificant change due to low fluence values. BISON profilometry simulated for HT9, D9, and SS316 fuel pins agreed with PIE profilometry measurements, with assembly SEE values being 4.4 × 10−3 for X421A, 2.0 × 10−3 for X441A, and 2.8 × 10−3 for X486. D9 clad pins in X421/X421A had the highest SEE values, which is due to the BISON simulated profilometry being shifted axially. While this work accomplished its purpose to demonstrate the modeling of multiple fuel pins from the databases to help validate models, the results suggest that the continued development of metallic fuel models is necessary for qualifying new metallic fuel systems to better capture some physical performance phenomena, such as the hot pressing of U-Pu-Zr and the fuel cladding chemical interaction.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

SaS4D Home Team UI (SaS4D-HT-UI) v1.0

The SaS4D Home Team UI (python) is a software to view and interact with different layers of 3D geometries and generate usable MCNP-style input file. It is used by the remote Home Team in providing guidance and building models of environments they have never seen in order to investigate threat object discovered at the Working Point. The UI visualizes a colorized mesh, a semantic labelled mesh, and a semantic labelled probability mesh of the scanned environment as well as individual water-tight material-labeled objects. It allows for manipulation and re-processing of these objects. The UI also contains measurement tools to facilitate better MCNP input file generation in the manipulation workflow. The software is a key component in ensuring the Home Team has prompt awareness of the Working Point.

Chen, Xin↗

Machine Learning-Assisted High-Temperature Reservoir Thermal Energy Storage Optimization: Numerical Modeling and Machine Learning Input and Output Files

This data set includes the numerical modeling input files and output files used to synthesize data, and the reduced-order machine learning models trained from the synthesized data for reservoir thermal energy storage site identification. In this study, a machine-learning-assisted computational framework is presented to identify High-Temperature Reservoir Thermal Energy Storage (HT-RTES) site with optimal performance metrics by combining physics-based simulation with stochastic hydrogeologic formation and thermal energy storage operation parameters, artificial neural network regression of the simulation data, and genetic algorithm-enabled multi-objective optimization. A doublet well configuration with a layered (aquitard-aquifer-aquitard) generic reservoir is simulated for cases of continuous operation and seasonal-cycle operation scenarios. Neural network-based surrogate models are developed for the two scenarios and applied to generate the Pareto fronts of the HT-RTES performance for four potential HT-RTES sites. The developed Pareto optimal solutions indicate the performance of HT-RTES is operation-scenario (i.e., fluid cycle) and reservoir-site dependent, and the performance metrics have competing effects for a given site and a given fluid cycle. The developed neural network models can be applied to identify suitable sites for HT-RTES, and the proposed framework sheds light on the design of resilient HT-RTES systems. All the simulations and the neural network model were done by Idaho National Laboratory. A detailed description of the work was reported in publication linked below.

15 GEOTHERMAL ENERGY↗

(U) SENSMG: First-Order Sensitivities of Neutron Reaction Rates, Reaction-Rate Ratios, Leakage, k eff , α , and Subcritical Multiplication Using PARTISN

SENSMG is a tool for computing first-order sensitivities of neutron reaction rates, reaction-rate ratios, leakage, k eff , α, and subcritical multiplication using the PARTISN multigroup discrete-ordinates code. SENSMG computes sensitivities to all of the transport cross sections and data (total, fission, a nu, chi, and all scattering moments), two edit cross sections (absorption and capture), and the density for every nuclide and energy group. It also computes sensitivities to the mass density for every material and derivatives with respect to all interface locations and outer boundaries. It computes sensitivities to user specified reactions whose cross sections are available in a user-supplied NJOY output file. The tool can be used for one-dimensional spherical and slab (r) and two-dimensional cylindrical (r-z) geometries. The tool can be used for fixed-source and eigenvalue problems. For most responses, the tool implements Generalized Perturbation Theory (GPT) as discussed by Williams and Stacey. The tool is thus limited to computing sensitivities only for GPT-allowable responses. For subcritical multiplication, the tool implements sensitivities derived by O’Brien and Clark. SENSMG has a similar role as the old SWANLAKE (Ref. 8), FORSS (Ref. 9), and SENSIT (Ref. 10) codes. It has capabilities similar to those of SUSD3D (Refs. 11 and 12), which also uses PARTISN. Section II of this report describes the theory behind adjoint-based sensitivities, gives the equations that SENSMG solves, and defines the sensitivities that are output. Section III describes the user interface, including the input file and command line options. Section IV describes the output. Section V gives some notes about the coding that may be of interest. Section VI presents some sample problems and discusses verification, which is ongoing. Section VII lists needs and ideas for future work. Appendix A lists most of the input files whose results are presented in Sec. VI. Appendix B provides some useful details on one of the cross-section libraries that SENSMG supports.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Knowledge Graph for End-to-End Traceability of an Integrated Human-Earth System Model

Integrated human-Earth system models inform energy-water-land system dynamics and policies, yet their results are difficult to trace through input-data, model structure, scenario configurations, and solved outputs. Because this information is siloed across disconnected artifacts, process-based IAMs have historically lacked a unified, queryable representation. Such lack of traceability prevents researchers from systematically isolating the multi-sector drivers of complex outcomes (such as tracing water-scarcity results back to distant energy-system dynamics) or conducting holistic uncertainty attribution across hundreds of interacting parameters. To address this concern, our work documents the software engineering process of a knowledge graph that unifies these four layers for the Global Change Analysis Model (GCAM-USA_Reference scenario, GCAM v9.1). The graph was built as a relational property graph in DuckDB from the run’s own artifacts: the input-preparation dependency map (gcamdata chunk map), the model’s XML input files, the run configuration, and the results database (BaseX), successfully mapping the model’s declared structure. The resulting graph comprises 204,321 nodes and 1,687,814 edges across 16 node types and 15 edge types, with approximately 16.3 million time-series values stored separately to maintain structural efficiency. To ensure representation fidelity, every edge carries an epistemic-status annotation recording the warrant for the relationship (structural, provenance, dependency, or model-derived), and a machine-readable provenance ledger classifying the origin of every schema element. Evaluation against a fixed five-benchmark suite with locked baselines reports zero structural orphans, zero dangling edge endpoints, and 100% of output-producing technologies traceable to raw input files. Two interactive interfaces present the graph, including a serverless browser application built on DuckDB-Wasm. By establishing the first end-to-end provenance framework for an IAM, this work enables researchers and scientists to systematically audit complex policy scenarios, debug model structures, and trace policy-relevant outputs to their data origins in real time.

Artifical Intelligence↗

iSPECTRON: a simulation interface for linear and nonlinear spectra with ab-initio quantum chemistry software

We introduce iSPECTRON, an open source (under the Educational Community License version 2.0) program that parses data from common quantum chemistry software (NWChem, OpenMolcas, Gaussian, Cobramm, etc.), produces the input files for the simulation of linear and nonlinear spectroscopy of molecules with the Spectron code, and analyzes the spectra with a broad range of tools. Vibronic spectra are expressed in term of the electronic eigenstates, obtained through quantum chemistry computations, and vibrational/bath effects are incorporated in the framework of the displaced harmonic oscillator model, where all required quantities are computed at the Franck-Condon point. The code capabilities are illustrated by simulating linear absorption, transient absorption and two dimensional electronic spectra of the pyrene molecule. Two levels of electronic structure theory, TDDFT (with NWChem) and RASSCF/RASPT2 (with OpenMolcas), are compared where possible. Acknowledgements: F.S., A.N., D.R.N., N.G., S.M, M.G. acknowledge support from the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences, Chemical Sciences, Geosciences, and Biosciences Division under Award Nos. DE-SC0019484, KC-030103172684. The Spectron code was developed with support from the National Science Foundation (Grant CHE- 1953045). This research benefited from computational resources provided by EMSL, a DOE Office of Science User Facility sponsored by the Office of Biological and Environmental Research and located at PNNL. PNNL is operated by Battelle Memorial Institute for the United States Department of Energy under DOE Contract No. DE-AC05-76RL1830.

Segatta, Francesco↗

Sierra/SD – User’s Guide for NasGen – 5.20

NasGen provides a path for migration of structural models from Nastran bulk data format (BDF) into both an Exodus mesh file and an ASCII input file for Sierra Structural Dynamics (Salinas) and Solid Mechanics (Adagio). Many tools at Sandia National Labs (SNL) use the Exodus format. This document describes capabilities and limitations of the NasGen translation software.

97 MATHEMATICS AND COMPUTING↗

Sierra/SD – User’s Guide for NasGen – 5.18

NasGen provides a path for migration of structural models from NASTRAN bulk data format (BDF) into both an Exodus mesh file and an ASCII input file for Sierra Structural Dynamics (Salinas) and Solid Mechanics (Presto). Many tools at Sandia National Labs (SNL) use the Exodus format. NasGen was written specifically for Salinas and Presto but should be usable with a number of these packages.

97 MATHEMATICS AND COMPUTING↗

Sierra/SD – User’s Guide for NasGen (V.5.16)

NasGen provides a path for migration of structural models from Nastran bulk data format (BDF) into both an Exodus mesh file and an ASCII input file for Sierra Structural Dynamics (Salinas) and Solid Mechanics (Adagio). Many tools at Sandia National Labs (SNL) use the Exodus format. This document describes capabilities and limitations of the NasGen translation software.

97 MATHEMATICS AND COMPUTING↗

Sierra/SD – User’s Guide for NasGen – 5.22

NasGen provides a path for migration of structural models from Nastran bulk data format (BDF) into both an Exodus mesh file and an ASCII input file for Sierra Structural Dynamics (Salinas) and Solid Mechanics (Adagio). Many tools at Sandia National Labs (SNL) use the Exodus format. This document describes capabilities and limitations of the NasGen translation software.

97 MATHEMATICS AND COMPUTING↗

Sierra/SD – User’s Guide for NasGen (V.5.24)

NasGen provides a path for migration of structural models from Nastran bulk data format (BDF) into both an Exodus mesh file and an ASCII input file for Sierra Structural Dynamics (Salinas) and Solid Mechanics (Adagio). Many tools at Sandia National Labs (SNL) use the Exodus format. This document describes capabilities and limitations of the NasGen translation software.

97 MATHEMATICS AND COMPUTING↗

Sierra/SD – User’s Guide for NasGen – 5.28

NasGen provides a path for migration of structural models from Nastran bulk data format (BDF) into both an Exodus mesh file and an ASCII input file for Sierra Structural Dynamics (Salinas) and Solid Mechanics (Adagio). Many tools at Sandia National Labs (SNL) use the Exodus format. This document describes capabilities and limitations of the NasGen translation software.

97 MATHEMATICS AND COMPUTING↗