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All sourcesNASA NTRSDOE OSTI
DOE OSTI2026

Permafrost Thaw, Uneven Subsidence and Projected Drying of Ice-wedge Polygon Tundra: Modeling Archive

This dataset is a model archive of the paper Permafrost Thaw, Uneven Subsidence and Projected Drying of Ice-wedge Polygon Tundra (in prep) to support a modeling study investigating how projected increases in Arctic temperature and precipitation will jointly influence hydrologic conditions in ice-rich tundra landscapes. With this dataset, this study is to address the research question: Will Arctic tundra landscapes become wetter or drier with increasing precipitation and temperature in the future when thaw-induced ground subsidence and associated microtopographic evolution are represented? The simulations focus on ice-wedge polygon tundra, a widespread form of ice-rich permafrost terrain that is highly sensitive to thaw-driven landscape change. This dataset contains model input and output data for four study watersheds in Alaska: Anaktuvuk, Utqiagvik (formerly Barrow), Brooks Foothills, and Prudhoe Bay. Simulations were performed using the Advanced Terrestrial Simulator (ATS, v1.5), a physics-rich integrated surface–subsurface hydrologic model. For each watershed, ten modeling cases were performed representing two landscape evolution conditions (with subsidence and without subsidence) combined with five climate forcing scenarios derived from Shared Socioeconomic Pathways (SSP5, SSP5 with precipitation trend, SSP2, SSP2 with precipitation trend, and SSP2 with double precipitation trend). Particularly, for each watershed under the forcing SSP2 with precipitation trend, there are two additional simulations considering spatially heterogeneous subsidence distributions: one assumes randomly distributed scaling and the other includes elevation dependent distribution scaling. These simulations span 1980–2099 and include spin-up runs (1980–2009) followed by transient projections (2010–2099). To facilitate reproducibility of simulations, all datasets are organized by watershed. For each study watershed, the dataset contains: (1) Pre-partitioned mesh files for 32-core modeling (.par.32.XX), located in EACH_WATERSHED/mesh/basin; and also a non-partitioned mesh file (.exo) located in EACH_WATERSHED/mesh; (2) Climate forcings corresponding to the five SSP scenarios (.h5), located in EACH_WATERSHED/data; (3) Final states (.h5) from column spin-up modeling used to initialize historical watershed-scale spin-up runs from 1980 to 2009, located in EACH_WATERSHED/PreSpinupHistorical; (4) Final states (.h5) of historical watershed-scale spin-up runs from 1980 to 2009 used to initialize projection runs, located in EACH_WATERSHED/Spinup_daymetERA5; (5) ATS modeling input files (.xml), located in EACH_WATERSHED/EACH_SIMULATION_SCENARIO/inputfiles; (6) ATS modeling output files (.dat), located in in EACH_WATERSHED/EACH_SIMULATION_SCENARIO/combined_obs; (7) For the Brooks Foothills watershed, additional spatial model outputs are provided (.h5) for selected years (2033 and 2093) used to generate spatial figures in this study, located in Brooksfoothills/EACH_SIMULATION_SCENARIO/results-WITH/WITHOUT_SUBSIDENCE-year2033/2093. All data files with suffix .h5 can be accessible through Python h5py, and all data files with suffix of .dat can be imported by Python pandas. Mesh file with .exo can be visualized through Paraview or read by Python netCDF. The Next-Generation Ecosystem Experiments in the Arctic (NGEE Arctic) project is a research effort to reduce uncertainty in the Department of Energy’s Energy Exascale Earth System Model (E3SM) by developing a predictive understanding of Arctic tundra ecosystems underlain by permafrost and to quantify feedbacks from the Arctic tundra to the Earth system. NGEE Arctic is supported by the Department of Energy's Office of Biological and Environmental Research. Over Phases 1–3, observations made by the NGEE Arctic team across a gradient of permafrost landscapes in Arctic Alaska improved the representation of tundra processes in the land surface component of E3SM (the E3SM Land Model, ELM). Model improvements emphasized unique aspects of permafrost environments and explored reductions in model complexity while retaining predictive power. The Arctic-informed ELM developed by NGEE Arctic has been used to make novel predictions on processes ranging from permafrost thaw to soil biogeochemical cycling to Earth system feedbacks associated with the unique characteristics of tundra plants. In Phase 4, the NGEE Arctic team is evaluating our new predictive understanding under novel conditions across the Arctic domain. In collaboration with partners at long-term pan-Arctic research sites we are examining whether an Arctic-informed ELM can faithfully simulate interactions among surface and subsurface processes at site, regional, and pan-Arctic scales. In turn, we are using variety of tools to dynamically extend and evaluate ELM inference, with an emphasis on data synthesis and pan-Arctic model evaluation, reintegration of code with an evolving E3SM, scaling across heterogeneous Arctic landscapes, and the appropriate representation of the impacts of increasingly frequent Arctic disturbances.

EARTH SCIENCE > ATMOSPHERE > PRECIPITATION↗
DOE OSTI2020

Neutronics Enhanced Meshing Operations (NEMO) Users Manual V.1.0

The is a Python framework developed at Idaho National Laboratory that uses the Cubit Python to build Cubit models and export them in EXODUS II format. These EXODUS mesh files can be used by any -based application, but NEMO is specialized for coupled neutronics calculations. Therefore, the primary purpose of NEMO is to prepare mesh files for reactor geometries and generate a homogenization overlay file for the Serpent Monte Carlo code. This homogenization overlay file ensures the consistency of the mesh with the generation of homogenized cross sections and reference fluxes for the Superhomogenization method. NEMO also supports the preparation of mesh files for thermal and thermo-mechanical models, particularly the discontinuous finite element gap heat transfer model in Griffin. This manual introduces the user to the basic capabilities in NEMO for prismatic geometries.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗
DOE OSTI2019

l3d2vtk: An MCNPTools Utility to Enable LNK3DNT File Visualization & Post-Processing

This paper describes recent work to develop and incorporate a utility program into the MCNPTools package that enables LNK3DNT file visualization & post-processing. A LNK3DNT file is a binary Cartesian, cylindrical, or spherical structured mesh file that describes material and material relative density distributions by mesh voxel. This mesh file format is principally used by the PARTISN discrete-ordinates radiation-transport code. However, the MCNP ® Monte Carlo radiation-transport code can use LNK3DNT files to specify geometry, and the MCNP code can produce LNK3DNT files representing a user-defined region of the MCNP constructive solid geometry (CSG). Because of the use of LNK3DNT files as MCNP input and output and with other computer codes, improving the ability to visualize and/or quantitatively post-process LNK3DNT files benefits end users. In particular, it is helpful to visually verify that the material and density distributions are as expected. Also, an analyst can orient viewers with respect to other in formation, e.g., by co-plotting a voxelized representation of MCNP CSG with mesh tally and/or particle track results. However, until now, the only capability to interactively interrogate LNK3DNT files is through a 2-D slice plotter provided by the Monte Carlo Application ToolKit (MCATK), which is not currently distributed outside of Los Alamos National Laboratory. The utility created as part of this work converts LNK3DNT binary files to an ASCII XML-based StructuredMesh VTK (.vts) file. The geometries supported are 1-D spherical and cylindrical ( r ), 1-D Cartesian ( x ), 2-D cylindrical ( r-z and r-θ ) and Cartesian ( x-y ), and 3-D cylindrical ( r-z-θ ) and Cartesian ( x-y-z ). This file format is chosen to minimize external dependencies (e.g., on an HDF5 library) and to provide a file that can be interrogated by the user in a text editor or standard visualization applications (e.g., ParaView or VisIt). However, other file formats may provide more utility such as XDMF, which can use HDF5 and is discussed further as something to explore as future work. This paper is organized as follows: a brief introduc tion to the MCNPTools library and utility programs is given, the LNK3DNT-to-VTK (l3d2vtk) utility functionality is de scribed, and then an example post-processing workflow using the ParaView application is given.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2021

The Importance of Freeze/Thaw Cycles on Lateral Transport in Ice-Wedge Polygons: Modeling Archive

This Modeling Archive is in support of an NGEE Arctic publication "The importance of freeze/thaw cycles on lateral transport in ice-wedge polygons". The dataset includes xml input/configuration files. These files are compatible with the ATS version 1.0 and higher. The mesh folder contains mesh files used for high-centered polygon (hcp) and low-centered polygon (lcp). The mesh files represent the transect of the polygonal tundra (Fig 1). Here we used two types of mesh with impermeable layer and without. The mesh with an impermeable layer corresponds to the synthetic permafrost (no freezeup case). The freeze up case uses mesh without impermeable layer to simulated frozen ground start at the same depth where the impermeable layer is for the no freezeup case. The meteorological data used drive the model saved in the "inputs" folder. The processed tracer flow rates are saved in the "tracer-flow-ratesCfolder. To plot figures 1 and 2, we used VisIt software. To plot all the flow rates, we used ipython notebook script. All required inputs are saved in "freezeup" and "no freezeup" folders. Each folder includes the corresponding "lcp" and "hcp" folders. The "freezeup" folder has also flat-centered polygon (fcp) case, low porosity "lpor", and low permeability "lper" cases. Included are *.xml, *.exo, *.h5, *pdf, *.ipynb, *.sh, *.py, and *.out files. NGEE Arctic Project Summary: The Next-Generation Ecosystem Experiments: Arctic (NGEE Arctic), was a research effort to reduce uncertainty in Earth System Models by developing a predictive understanding of carbon-rich Arctic ecosystems and feedbacks to climate. NGEE Arctic was supported by the Department of Energy's Office of Biological and Environmental Research. The NGEE Arctic project had two field research sites: 1) located within the Arctic polygonal tundra coastal region on the Barrow Environmental Observatory (BEO) and the North Slope near Utqiagvik (Barrow), Alaska and 2) multiple areas on the discontinuous permafrost region of the Seward Peninsula north of Nome, Alaska. Through observations, experiments, and synthesis with existing datasets, NGEE Arctic provided an enhanced knowledge base for multi-scale modeling and contributed to improved process representation at global pan-Arctic scales within the Department of Energy's Earth system Model (the Energy Exascale Earth System Model, or E3SM), and specifically within the E3SM Land Model component (ELM).

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2016

MESHMAKER (MM) V1.5

MeshMaker v1.5 is a code that describes the system geometry and discretizes the domain in problems of flow and transport through porous and fractured media that are simulated using the TOUGH+ [Moridis and Pruess, 2014] or TOUGH2 [Pruess et al., 1999; 2012] families of codes. It is a significantly modified and drastically enhanced version of an earlier simpler facility that was embedded in the TOUGH2 codes [Pruess et al., 1999; 2012], from which it could not be separated. The code (MeshMaker.f90) is a stand-alone product written in FORTRAN 95/2003, is written according to the tenets of Object-Oriented Programming, has a modular structure and can perform a number of mesh generation and processing operations. It can generate two-dimensional radially symmetric (r,z) meshes, and one-, two-, and three-dimensional rectilinear (Cartesian) grids in (x,y,z). The code generates the file MESH, which includes all the elements and connections that describe the discretized simulation domain and conforming to the requirements of the TOUGH+ and TOUGH2 codes. Multiple-porosity processing for simulation of flow in naturally fractured reservoirs can be invoked by means of a keyword MINC, which stands for Multiple INteracting Continua. The MINC process operates on the data of the primary (porous medium) mesh as provided on disk file MESH, and generates a secondary mesh containing fracture and matrix elements with identical data formats on file MINC.

MORIDIS, GEORGE↗
DOE OSTI2023

Data, figures, animations, and scripts associated with the manuscript "Integrated Effects of Site Hydrology and Vegetation on Exchange Fluxes and Carbon Cycling at the Coastal Terrestrial Aquatic Interface"

This package contains the data, figures, animations, and scripts used in "Integrated Effects of Site Hydrology and Vegetation on Exchange Fluxes and Carbon Cycling at the Coastal Terrestrial Aquatic Interface" (Li et al., 2023). This study examines the interactions between soil, vegetation and hydrologic conditions in coastal areas, with a focus on the Chesapeake Bay region. The researchers used a mechanistic model called ATS-PFLOTRAN to explore how these interactions affect exchange process in different regions and the carbon/nitrogen cycle across the terrestrial-aquatic interface (TAI). Simulation scenarios isolate the effects of control factors and reaction constants derived from laboratory experiments. The results show a carbon cycle "hot zone" in coastal wetlands and in the transition zone between wetlands and uplands. Transpiration enhances fluxes between the surface and subsurface domains and increases dissolved oxygen in TAI. The decomposition of leaf-derived organic carbon provides an additional source of carbon for aerobic respiration and denitrification in the TAI. Microbial activity plays a key role in controlling redox conditions and their variability. This modeling study improves the understanding of complex TAI interactions and facilitates the representation of coastal ecosystems in larger-scale Earth system models.Several files can be found from this data package.1. Readme,md: This file describe the Title, Target Journal, Target submission date, Co-author, Science Questions, Hypotheses, Key words, Key message, Model and Data, Repo Structure. The user can read this file first and then go to details.2. mesh.zip: This file contains the mesh file for simulation cases. 3. Figure.zip: This file contains figures used in the manuscript . 4. animation.zip: This file contains animations used in the manuscript . 5. Data.zip: This file contains all required input data, such as concentration and flow boundaries. Also, it contains the DEM and processes results on area fraction. 6. Simulation_setup_and_results.zip: This file contains setup of cases used in the manuscript . The result files are too large, if you need that data, please contact to the Author. 7. notebooks.zip: This file contains the Jupyter notebooks for performing sensitivity analysis and other pre-process and post-process analyses.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

LLNL Kimberlina 1.2 NUFT Simulations June 2018 (v2)

This dataset contains the output 6,000, 3-dimensional reactive multi-phase flow and transport aquifer simulations of brine and CO2 leakage into a protective aquiver in California’s San Joaquin Valley and input data files detailing the geologic mesh, aquifer physical properties and CO2 and brine injection rates. This data set was generated as an ongoing effort with the US DOE National Risk Assessment Partnership (NRAP) to evaluate the effectiveness of monitoring techniques to detect brine and CO2 leakage from legacy wells into underground sources of drinking water overlaying a CO2 storage reservoir. Each simulation contains a unique set of input parameters, generated stochastically. The outputs consist of these upper three geologic layers (from top): the Etchegoin, Macoma-Chanac, Santa Margarita-McLure formations. These simulations span the several distances (1, 3 and 6 km or wells W31-0.2, W31-0.5 and W31-1.0, respectively) from the CO2 injector, initiated from bottom hole pressure and saturation to calculate wellbore leakage from the storage reservoir, with low and high regional groundwater gradients and wellbore leakage into 5 leaky nodes. The dataset includes 1,000 unique simulations for each distance, which each contain a unique aquifer heterogeneity, aquifer and caprock permeability, and two model generations are included with a high permeability (prod07) and hybrid permeability (prod09). The range of permeability distributions is listed in Table 1. Each model generation consists of 3,000 simulations. Included in the dataset are the leakage rates determined from 2D wellbore models which utilize the pressure and CO2 saturation from LBL's reservoir simulations, NUFT mesh files with distributed lithology, NUFT rocktab files which describe the material properties for the geologic layers and the NUFT input files and post-processed output 'ntab' files. Each ntab file contains spatial (rows) and temporal (columns) model output tables for each model cell, the locations (x,y,z) and dimensions for each cells (dx, dy, dz). Table 1. Permeability distribution ranges for prod07 and prod09 model generations Geologic Layer: Permeability Range (log10 m^2) prod07 prod09 Etchegoin -12.92 to -10.92 -13.70 to -11.44 Macoma-Chanac -12.72 to -10.72 -13.50 to -11.24 Santa Margarita-McLure -12.70 to -10.70 -13.48 to -11.22 The input files used to generate the model include which are included in the dataset are: Time series of CO2 leakage input into the model (ex: Q_brn.W31-0.2.sim1000.layers123.tab) Time series of CO2 leakage input into the model (ex: Q_CO2.W31-0.2.sim1000.layers123.tab) Physical properties of the aquifer materials detailing the aquifer porosity, solid density, partitioning coefficients, permeabilities and van-Genuchten parameters detailed in a NUFT rocktab file: (ex: sim1000.usnt.rocktab) Numerical mesh and geologic data assigned to each model cell detailed in a NUFT genmsh format (ex: sim1000.mesh_k16.prod07.trans.genmsh) The primary output parameters are: pH (use absolute value) Change in TDS (mg/kg) Change in Pressure (Pa) Change CO2 gas saturation (fraction range 0.0-1.0) for example, the directory /p/lscratchh/mansoor1/nrap/kimberlina/prod09/mainfiles/sim1000/W31- 0.2 contains: sim1000.W31-0.2.trans.pH.red.ntab sim1000.W31-0.2.no_bg.trans.TDS.red.ntab sim1000.W31-0.2.usnt.P.deltabg.red.ntab sim1000.W31-0.2.usnt.CO2_sat.deltabg.red.ntab Each row in the NTAB files consist of model output per numerical grid cell. Each output file contains 33 columns (variables), including the information of numerical records, geologic location and sizes and the simulated parameter values over time. The first 13 variables are about numerical records and relative geologic information for a simulation grid: 1. index: simulation index 2. i: the ith grid of x-axis 3. j: the ith grid of y-axis 4. k: the ith grid of z-axis 5. element_ref: element reference 6. nuft_ind: nuft index 7. x: grid location in the x axis direction 8. y: grid location in the y axis direction 9. z: grid location in the z axis direction 10. dx: grid length in the x axis direction 11. dy: grid length in the y axis direction 12. dz: grid length in the z axis direction 13. volume: volume of the simulation grid The remainder (14, 15, 16...) variables are the simulated parameter values over time, take Pressure as an example, are: 14. 0.0y: initial pressure per cell. 15. 10.0y: simulated pressure at the end of the 10th year. 16. 20.0y: simulated pressure at the end of the 20th year. ... (repeated for every 10 years until 200 years)... The model extends 10,000 m, 5,000 m and 1,411 m in the x,y and z dimensions, respectively. The mesh consists of 164,832 cells with mesh dimensions of 101 x 51 x 32 (nx, ny, nz), with cell dimensions ranging from 100 m laterally (along x and y-axis) and model layers are as designated in the z-axis: Layer 1: atmosphere (1e-30 m thick) Layer 2: upper caprock (10 m thick) Layers 3-13: Etchegoin (536.23 m thck) Layers 14-27: Macoma-Chanac (679.04 m thick) Layers 28-32: Santa Margarita-McLure (185.94 m thick) The wellbore is placed along node i=51, j=26, and extends vertically along 5 nodes from the top to the bottom of the model. Special instructions when extracting files: Each Gzip archive (ex: prod07.sim1000-sim00099.tar.gz) contains 100 simulations. Gzip archives should be transferred into base directories (ie. In Linux: mkdir prod07; mv prod07.*.tar.gz prod07/.) before extracting, or files will be overwritten. Each sub-simulation tree should have the following file structure pattern (using the linux 'tree' command): |-- prod07 | |-- sim0001 | |-- W31-0.2 | | |-- Q_brn.W31-0.2.sim0001.layers123.tab | | |-- Q_co2.W31-0.2.sim0001.layers123.tab | | |-- sim0001.W31-0.2.no_bg.trans.TDS.red.ntab | | |-- sim0001.W31-0.2.trans.pH.red.ntab | | |-- sim0001.W31-0.2.usnt.CO2_sat.deltabg.red.ntab | | |-- sim0001.W31-0.2.usnt.P.deltabg.red.ntab | |-- W31-0.5 | | |-- Q_brn.W31-0.5.sim0001.layers123.tab | | |-- Q_co2.W31-0.5.sim0001.layers123.tab | | |-- sim0001.W31-0.5.no_bg.trans.TDS.red.ntab | | |-- sim0001.W31-0.5.trans.pH.red.ntab | | |-- sim0001.W31-0.5.usnt.CO2_sat.deltabg.red.ntab | | |-- sim0001.W31-0.5.usnt.P.deltabg.red.ntab | |-- W31-1.0 | | |-- Q_brn.W31-1.0.sim0001.layers123.tab | | |-- Q_co2.W31-1.0.sim0001.layers123.tab | | |-- sim0001.W31-1.0.no_bg.trans.TDS.red.ntab | | |-- sim0001.W31-1.0.trans.pH.red.ntab | | |-- sim0001.W31-1.0.usnt.CO2_sat.deltabg.red.ntab | | |-- sim0001.W31-1.0.usnt.P.deltabg.red.ntab | |-- sim0001.mesh_k16.prod07.trans.genmsh Disclaimer This document was prepared as an account of work sponsored by an agency of the United States government. Neither the United States government nor Lawrence Livermore National Security, LLC, nor any of their employees makes any warranty, expressed or implied, or assumes any legal liability or responsibility for the accuracy, completeness, or usefulness of any information, apparatus, product, or process disclosed, or represents that its use would not infringe privately owned rights. Reference herein to any specific commercial product, process, or service by trade name, trademark, manufacturer, or otherwise does not necessarily constitute or imply its endorsement, recommendation, or favoring by the United States government or Lawrence Livermore National Security, LLC. The views and opinions of authors expressed herein do not necessarily state or reflect those of the United States government or Lawrence Livermore National Security, LLC, and shall not be used for advertising or product endorsement purposes. Lawrence Livermore National Laboratory is operated by Lawrence Livermore National Security, LLC, for the U.S. Department of Energy, National Nuclear Security Administration under Contract DE-AC52-07NA27344. This report was reviewed and released as LLNL-MI-753464.

aquifer↗
DOE OSTI2026

A bespoke model of Arctic river basins based on hillslope delineation: Model Archive

This dataset is a model archive of the paper A bespoke model of Arctic river basins based on hillslope delineation (in prep), which introduces a watershed decomposition and parameterization method for large scale permafrost hydrology simulation. With this dataset, this study aims to address the research question: whether a computationally efficient hillslope-based modeling framework can reliably simulate discharge at Arctic river-basin scales. This dataset contains model input and output data for five modeling scenarios at a study site located in the Sagavanirktok River basin. The five modeling scenarios include three modeling cases under temperate conditions using full 3D, decomposed 3D, and decomposed 2D modeling strategies; and two modeling cases under actual Arctic conditions with permafrost using full 3D and decomposed 2D modeling strategies. Simulations were performed using the Advanced Terrestrial Simulator (ATS, v1.6 for three temperate scenarios and v1.5 for two Arctic scenarios), a physics-rich integrated surface–subsurface hydrologic model with cryo-hydrology features. For the three temperate models, simulations were conducted for the period of 10/01/1993 - 09/30/2002; and for the two Arctic models, simulations were conducted for the period of 01/01/1994 - 12/31/2002. To facilitate reproducibility of simulations, all datasets are organized hierarchically. The dataset contains: (1) Mesh files (.exo) for full 3D model, decomposed 3D models, and decomposed 2D models, located in huc/190604020802_gauge15906000/mesh/. Mesh files can be visualized through Paraview or read by Python. (2) Climate forcings (.h5) for full 3D model and decomposed 3D/2D models are located in huc/190604020802_gauge15906000/daymet_onePiece/, and huc/190604020802_gauge15906000/vp_pr_revised_daymet_1980_2006_with_wind/ separately. Accessible by Python. (3) Raw measured gage discharge (.csv) from USGS, located in huc/190604020802_gauge15906000/gaged_basin15906000_discharge_usgs/. Accessible by Python. (4) Delineated subdomain raster (.tif) and shape files (.shp), and the final parameterized results (.npy) for decomposed models, located in huc/190604020802_gauge15906000/data_preprocessed-meshing. Accessible by Python. (5) Temperate models are located in nonpermaf_huc190604020802_gauge15906000/, which includes three cases: decomposed 2D models (inside model_0*-hillslope_*), decomposed 3D models (inside model_1*-subcatchment_*), and full 3D model (inside model_2*-onepiece_*). Two step spin-up results (checkpoint_final.h5) are located in model_*1-*_spinup_steadystate and model_*2-*_spinup_cycle, separately, which are used to initialize real transient models. The input files (.xml) and output results (.dat) of the real transient models are located in model_*3-*_transient/. Especially, for two example hillslope models (ID=-11 and 11), additional h5py files are included in model_03-hillslope_transient/hillslope-11/, model_03-hillslope_transient/hillslope11, model_13-subcatchment_transient/subcatchment-11/, model_13-subcatchment_transient/subcatchment/11, respectively, which are used to plot the saturation figure (Figure 5) in the manuscript. Accessible by Python. (6) Arctic models are located in huc190604020802_gauge15906000/, which includes two cases: decomposed 2D models (inside model_04-hillslope_transient), and full 3D model (inside model_05-onepiece_transient_mannp1_ra). Three step spin-up results (checkpoint_final.h5) are located in model_01-column_freezeup/, model_02-column_spinup/, model_03-hillslope_spinup/, respectively, which are used to initialize real 2D transient hillslope models. The input files (.xml) and output results (.dat) of transient 2D hillslope models are located in model_04-hillslope_transient/. The input files (.xml) and output results (.dat) of the full 3D transient model is located in model_05-onepiece_transient_mannp1_ra/. The full 3D transient model is initialized by model_02-column_spinup/. Accessible by Python. (7) The MOSART routed discharge results (.csv) under Arctic conditions is located in huc190604020802_gauge15906000/MOSART/. Accessible by Python. (8) All Python codes (.py) used to parameterize full 3D model to decomposed 2D models are located in script/. These codes fit with watershed workflow (a watershed delineation tool) v1.4 under the branch gaob/v1.4 from https://github.com/gaobhub/watershed-workflow.git.

EARTH SCIENCE > CRYOSPHERE↗
DOE OSTI2024

Chromium Poisoning ERMINE Model Data

This is the data from the paper "Systematic and Predictive Trends to Chromium Poisoning in Solid Oxide Fuel Cell Cathodes" by Hokon Kim et al., appearing in the Journal of Power Sources. The files here are the microstructures, mesh files, and outputs from the ERMINE finite element model of chromium poisoning in SOFC cathodes. Further description can be found in Readme.rtf and in the paper..

Chromium,SOFC↗
DOE OSTI2023

Generating MCNP Input Files for Unstructured Mesh Geometries

The Los Alamos National Laboratory’s (LANL) Monte Carlo N-Particle (MCNP)1 transport code version 6.3 (also known as MCNP6.3) has the capability for tracking particles on unstructured mesh (UM) geometry models embedded into constructive solid geometry (CSG) cells. This feature has been developed for performing calculations of complex geometry models because manually creating CSG models is time-consuming and error-prone as the complexities of geometries increase. A UM geometry model is a collection of finite elements representing a solid geometry. The first step of the MCNP UM calculation is using other software packages to create a finite element mesh representation of a solid 3D geometry because the MCNP code cannot be used to generate a UM model. Computer-aided design (CAD) software is typically used to create a solid geometry model, which is later imported into mesh generation software to create a UM model. Some mesh generation software packages may also be used to create solid geometries and thus CAD files are not needed. The MCNP UM feature was originally designed for models generated by the Abaqus/CAE software suite. The MCNP code version 6.0 and later can process UM models formatted as Abaqus input files. Starting with a 6.3 version, the MCNP code can process HDF5 mesh input files. We only focus on the UM models formatted as Abaqus input files in this report since currently no external software can be used to generate HDF5 mesh input files for MCNP UM calculations. The MCNP code version 6.3 can be used to convert the Abaqus mesh input files into the HDF5 mesh input files, but this option is typically used by the MCNP code development team to test the HDF5 mesh input file feature. Several software packages (such as Abaqus, Attila4MC, or Cubit) can be used to create the Abaqus input files for MCNP UM calculations. An MCNP UM calculation using an Abaqus model requires two input file types: MCNP and Abaqus input files. The Abaqus input files needed for MCNP UM calcu lations must have the correct Abaqus syntax and meet the additional requirements by the MCNP code. The MCNP code can process only Abaqus input files that make use of part and assembly definitions, where elements in each part must be grouped into one or more element sets (i.e., elset) using *Elset keyword lines with specified naming formats. The MCNP and Abaqus input files required for MCNP UM simulations must be related; pseudo-cells in an MCNP input file must be constructed from mesh model data from an Abaqus input file. For large complex UM models, it is tedious to manually create MCNP UM input files. The um pre op (unstructured mesh pre operations) program with the -m option can be used to create a skeleton MCNP input file from an Abaqus input file [6]. Since the um pre op program was written in Fortran and was not written for optimized performance, this program is a deprecated feature in the MCNP code version 6.3 and may be removed in the next release of the code. To improve calculation flow of multiphysics calculations, a Python3 code called write mcnp um input has been developed to generate an MCNP input file instead of using the um_pre_op -m option. This Python code was initially released to the public in 2020. We have updated this Python code for MCNP6.3 and it was used to generate the MCNP input files used to verify the MCNP6.3 code. The write_mcnp_um_input code is included with the MCNP6.3 code package which will be released to the public through the Radiation Safety Information Computational Center (RSICC) at Oak Ridge National Laboratory. This report is a revision of LA-UR-20-27139 report.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2024

Versatile TRISO fuel particle modeling in Bison

Tri-structural isotropic (TRISO) fuel particles are a key component in several previous and current reactors as well as in a variety of novel nuclear reactor designs. Interest in TRISO fuel is on the rise, necessitating considerable computer modeling of TRISO fuel behavior in order to support related design and licensing activities. The Bison nuclear fuel performance code, which offers a full set of capabilities for modeling TRISO fuels, makes it easier to explore the various important aspects of TRISO fuel behavior. One key advantage of Bison is its ability to create meshes in 1D, 2D, and 3D. Users can customize these meshes for specific geometries, mesh densities, and use cases. This enables a wide variety of analyses, including thermal, structural, mass diffusion, homogenization, and statistical failure analyses. Furthermore, the meshing capability simplifies analysts’ workflows. The inherent mesh generation capability eliminates the need for separate mesh-generating software and mesh file management. Also, the fact that the meshes are customizable makes it straightforward to automate an investigation over a range of geometric parameters or mesh densities. Here, the present paper highlights the ease with which Bison may be used to create meshes for both simple and relatively complex TRISO fuel particles, and it explores the types of analyses enabled by these meshes.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2020

Utah FORGE: Data for 3-D Model Development - Lithology, Temperature, Pressure, and Stress

This submission comprises two downloadable .zip archives. Each archive contains spreadsheets with 3-D data and a .txt document describing the data. The Mesh Files .zip download contains data regarding the lithologic contacts of the granitoid and overlying sedimentary basin fill. The Initial Conditions .zip download contains data regarding temperature, pressure, and stress. These data were generated during Utah FORGE Phase 2 and exported from Seequent Leapfrog Geothermal. They are intended for use in 3-D earth modeling.

15 GEOTHERMAL ENERGY↗
DOE OSTI2022

Drying of tundra landscapes will limit subsidence-induced acceleration of permafrost thaw: Modeling Archive

This Modeling Archive is in support of a NGEE Arctic publication in review "Drying of tundra landscapes will limit subsidence-induced acceleration of permafrost thaw". The study used a cryohydrology model to assess the potential risk of abrupt permafrost thaw triggered by melting ground ice, a key open question associated with permafrost response to a warming Arctic. The spatially resolved simulations are for a small catchment 465 ice-wedge polygons in polygonal tundra near Utqiagvik, Alaska in the high-emissions RCP8.5 climate scenario. The simulations are compared to runoff, evapotranspiration and subsidence in the current climate and agree well. The study used the ATS code configured as an intermediate-scale cryohydrology model (Advanced Terrestrial Simulator, Version v2). The archive includes input files for spinup (1985 to 2005) and projections (2006 to 2100 - the manuscript reports 2006 to 2098). Three of the projections include the effects of subsidence and microtopography change with different depth profiles of ice content corresponding to the median, 20th percentile and 80th percentile. The fourth projection has subsidence turnoff and uses the reference case (median) ice content. Spatially averaged or aggregated output variables are included for the projections. Selected checkpoint files for the projections and postprocessing scripts are also included. Files included are *.xml; *.h5; *.exo; *.py; *.sh, *. nb, mesh files, and one file in the original Excel format plus *.csv and *.pdf to conserve formatting contained in the original file. The Next-Generation Ecosystem Experiments: Arctic (NGEE Arctic), was a research effort to reduce uncertainty in Earth System Models by developing a predictive understanding of carbon-rich Arctic ecosystems and feedbacks to climate. NGEE Arctic was supported by the Department of Energy's Office of Biological and Environmental Research. The NGEE Arctic project had two field research sites: 1) located within the Arctic polygonal tundra coastal region on the Barrow Environmental Observatory (BEO) and the North Slope near Utqiagvik (Barrow), Alaska and 2) multiple areas on the discontinuous permafrost region of the Seward Peninsula north of Nome, Alaska. Through observations, experiments, and synthesis with existing datasets, NGEE Arctic provided an enhanced knowledge base for multi-scale modeling and contributed to improved process representation at global pan-Arctic scales within the Department of Energy's Earth system Model (the Energy Exascale Earth System Model, or E3SM), and specifically within the E3SM Land Model component (ELM).

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2017

Quinoa, Version 0.2

Quinoa is a set of computational tools that enables research and numerical analysis in fluid dynamics. At this time it remains a test-bed to experiment with various algorithms using fully asynchronous runtime systems. Currently, Quinoa consists of the following tools: (1) Walker, a numerical integrator for systems of stochastic differential equations in time. It is a mathematical tool to analyze and design the behavior of stochastic differential equations. It allows the estimation of arbitrary coupled statistics and probability density functions and is currently used for the design of statistical moment approximations for multiple mixing materials in variable-density turbulence. (2) Inciter, an overdecomposition-aware finite element field solver for partial differential equations using 3D unstructured grids. Inciter is used to research asynchronous mesh-based algorithms and to experiment with coupling asynchronous to bulk-synchronous parallel code. Two planned new features of Inciter, compared to the previous release (LA-CC-16-015), to be implemented in 2017, are (a) a simple Navier-Stokes solver for ideal single-material compressible gases, and (b) solution-adaptive mesh refinement (AMR), which enables dynamically concentrating compute resources to regions with interesting physics. Using the NS-AMR problem we plan to explore how to scale such high-load-imbalance simulations, representative of large production multiphysics codes, to very large problems on very large computers using an asynchronous runtime system. (3) RNGTest, a test harness to subject random number generators to stringent statistical tests enabling quantitative ranking with respect to their quality and computational cost. (4) UnitTest, a unit test harness, running hundreds of tests per second, capable of testing serial, synchronous, and asynchronous functions. (5) MeshConv, a mesh file converter that can be used to convert 3D tetrahedron meshes from and to either of the following formats: Gmsh, http://www.geuz.org/gmsh, Netgen, http://sourceforge.net/apps/mediawiki/netgen-mesher, ExodusII, http://sourceforge.net/projects/exodusii, HyperMesh, http://www.altairhyperworks.com/product/HyperMesh.

Bakosi, Jozsef↗
DOE OSTI2022

ATS (Advanced Terrestrial Simulator) integrated hydrology and reactive transport model output in Copper Creek, Colorado

This dataset is generated using the ATS (Advanced Terrestrial Simulator) model at Copper Creek, Colorado, the largest catchment in the East River watershed. ATS is an integrated hydrology and reactive transport model to simulate the Concentration-Discharge (C-Q) relationship, and is used to quantify the geochemical export and understand how watersheds respond to climate disturbances. Key hydrogeochemical variables, including discharge, precipitation, evapotranspiration, and geochemical concentrations, were simulated and output at a daily frequency at the Copper Creek outlet. A group of hydrology and geochemical model variables over the spatial domain are output at a bi-monthly frequency. The model used 1-km resolution daily frequency Daymet meteorological forcing, and mineral composition from previous studies. The simulations are performed on NERSC. The datasets include the input files for running the ATS (Advanced Terrestrial Simulator) simulation, including the mesh file, input script and geochemical model files. The output files from the ATS (Advanced Terrestrial Simulator) are the daily time-series discharge and geochemical concentration simulated at the outlet of Copper Creek, and the bi-monthly spatial output over the simulation domain.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2016

User Manual for the PROTEUS Mesh Tools

PROTEUS is built around a finite element representation of the geometry for visualization. In addition, the PROTEUS-SN solver was built to solve the even-parity transport equation on a finite element mesh provided as input. Similarly, PROTEUS-MOC and PROTEUS-NEMO were built to apply the method of characteristics on unstructured finite element meshes. Given the complexity of real world problems, experience has shown that using commercial mesh generator to create rather simple input geometries is overly complex and slow. As a consequence, significant effort has been put into place to create multiple codes that help assist in the mesh generation and manipulation. There are three input means to create a mesh in PROTEUS: UFMESH, GRID, and NEMESH. At present, the UFMESH is a simple way to generate two-dimensional Cartesian and hexagonal fuel assembly geometries. The UFmesh input allows for simple assembly mesh generation while the GRID input allows the generation of Cartesian, hexagonal, and regular triangular structured grid geometry options. The NEMESH is a way for the user to create their own mesh or convert another mesh file format into a PROTEUS input format. Given that one has an input mesh format acceptable for PROTEUS, we have constructed several tools which allow further mesh and geometry construction (i.e. mesh extrusion and merging). This report describes the various mesh tools that are provided with the PROTEUS code giving both descriptions of the input and output. In many cases the examples are provided with a regression test of the mesh tools. The most important mesh tools for any user to consider using are the MT_MeshToMesh.x and the MT_RadialLattice.x codes. The former allows the conversion between most mesh types handled by PROTEUS while the second allows the merging of multiple (assembly) meshes into a radial structured grid. Note that the mesh generation process is recursive in nature and that each input specific for a given mesh tool (such as .axial or .merge) can be used as “mesh” input for any of the mesh tools discussed in this manual.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

Towards a NEAMS-based high-fidelity model of the MARVEL reactor

This report outlines the progress of Idaho National Laboratory in developing a high-fidelity and high-resolution model of the Microreactor Applications Research Validation and Evaluation reactor. The model was developed under the Nuclear Energy Advanced Modeling and Simulation microreactor application driver at Idaho National Laboratory. The overarching objective of this activity is the development of a high-fidelity multiphysics MARVEL model using NEAMS tools, and to verify and validate NEAMS tools against MARVEL reference simulation and experimental data, respectively. This is a unique opportunity to conduct multiphysics analysis on a soon-to-be-deployed microreactor. This multiphysics model developed under the NEAMS-funded INL microreactor application driver leverages three single-physics models coupled via the MOOSE’s MultiApp and Transfer systems. The latter systems enable in-memory data transfer between MOOSE-based and MOOSE-wrapped applications. The first single-physics model, that functions as main application, leverages Griffin to model the neutron transport in the core through the discontinuous finite element (DFEM) discrete ordinates solver (SN). Several optimization flags that were developed by the Griffin developer team were beta-tested to enhance the solver’s performance. These include the combined use of using_average_xs and update_averaged_xs_on that enable to avoid expensive on-the-fly cross sections evaluations at each linear iterations in favor of evaluations of the macroscopic cross sections at each Picard iteration. The second single-physics model uses BISON to handle solid heat transfer and asymptotic hydrogen redistribution analysis in the fuel. While the model returns consistent results for the temperature and hydrogen distribution in the fuel, a mismatch was noticed in the calculated temperature in the reflector due to the value of the gap conductance used in our model. Ongoing investigations are being performed to assess the origin of this discrepancy. Finally, the System Analysis Module (SAM) was used to model the flow of the sodium-potassium eutectic in the primary loop. A first verification was also performed showing good agreement in terms of mass flow rate and inlet temperature. All mesh files were generated using the MOOSE Reactor module, removing the need for external meshing tools. Notably, this workscope represents one of the initial applications of the MOOSE Reactor module for modeling highly irregular geometries. The use of the reactor module significantly streamlined the mesh generation process. The full multiphysics mode, that combines all the single physics models, was leveraged to conduct initial steady-state multiphysics simulations to compute power, and temperature distribution in the reactor. Initial testing was performed for transient simulations as well. In this case, the new checkpoint restart capability for eigenvalue calculations was tested showing the capability for streamlined restart of transient calculations. Future work will focus on improving the fidelity of the model by performing comprehensive code-to-code comparisons. For instance, the full-core Griffin neutronics model will be benchmarked against MCNP reference results, that were provided by the MARVEL design team. Additionally, the SAM T/H model will be verified against reference RELAP-5 results for selected accident scenarios. Besides code-to-code verification exercises, the model fidelity will be improved by replacing the single-channel SAM model with a more complex SAM-Pronghorn coupled model, in which the sub-channel capability is deployed to obtain radial temperature resolution in the coolant. This model will be developed in synergy with the NEAMS thermal hydraulics team.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗
DOE OSTI2024

Sodium-Cooled Fast Reactor Reference Plant Model

This report details the progress of Idaho National Laboratory (INL) in creating a reference plant multiphysics model for the Advanced Burner Test Reactor (ABTR). This model was developed under Task 13 of the U.S. Nuclear Regulatory Commission project “Development and Modeling Support for Advanced Non-Light Water Reactors,” and is an extension of the reference plant model developed in Task 4b, which was improved upon in the following ways. (1) The discrete ordinates method was used in lieu of the super-homogenization (SPH)-corrected diffusion approximation in order to better capture the anisotropic scattering contribution and the neutron leakage change due to thermal expansion. (2) The novel neutronic spatial discretization approach, termed the ring-heterogeneous (RH) approximation, was conceptualized and introduced to capture the differential expansion of the materials in the core. This new technique proved capable of preserving fission rates and maintaining the eigenvalue within 2.5% and 266 pcm with 9 neutron energy groups, respectively. Separating the different materials in the core enables the differential expansion of materials to be explicitly accounted for, eliminating the need for problem-specific cross-section functionalization techniques. (3) The SAM model for the core and system thermal-hydraulics analysis was updated to include 61 channels instead of just four representative ones. This enables users to obtain improved spatial resolution for sodium temperature and density scalar fields. (4) All the mesh files were created via the Multiphysics Object-Oriented Simulation Environment (MOOSE) Reactor module, eliminating all reliance on external tools for mesh creation. (5) Finally, the fuel axial expansion now leverages the HT9 and UPuZr material properties that have been validated against experimental data. The reference plant model was used to perform a full-core unprotected loss of flow (ULOF) transient calculation, including neutronics, thermal and mechanical feedback mechanisms. Future work will be devoted to further enhancements of the model. Potential improvements to the model include the addition of the control rod driveline expansion feedback and the upgrading of the support plate model so as to explicitly include 3D effects. Additionally, a Nuclear Energy Advanced Modeling and Simulation funded parallel effort has completely automated the creation of the ring-heterogeneous (RH) mesh from the fully heterogeneous (FH) geometry, thus maximizing user friendliness for the sodium fast reactor sodium-cooled fast reactor (SFR) workflow and will be incorporated in future work.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗