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At least 973 records · Page 54

Model simulations of Plum Island Ecosystems LTER low marsh site using ELM-PFLOTRAN

Model simulations using the E3SM Land Model (ELM) coupled to the PFLOTRAN reactive transport model via the Alquimia interface. The simulations were conducted for a tidal salt marsh at the Plum Island Ecosystems LTER near Rowley, Massachusetts, USA. Model simulations were forced using site-specific tidal cycles and salinity, and the simulations used a biogeochemical reaction network including aerobic decomposition, sulfate reduction, iron reduction, and methanogenesis. Model outputs include simulated carbon stocks, carbon dioxide and methane fluxes, and porewater concentrations of key solutes related to sulfur, iron, and carbon cycling. The model simulations included a saline simulation (with tidal sulfate inputs), a fresh simulation (with low salinity and low sulfate inputs), and a saline simulation with lower vegetation productivity to represent the effect of salinity on vegetation. These simulations were conducted to demonstrate that a new model framework incorporating subsurface redox and biogeochemical interactions into a land surface model could reproduce measured surface greenhouse gas fluxes and biogeochemical dynamics in tidal marsh ecosystems, and to test whether including redox interactions in a land surface model would allow the model to resolve contrasts in biogeochemical cycling and greenhouse gas production between saline and freshwater wetlands.The data package includes gzipped tar archives (which can be expanded using standard tar and gzip utilities) of model outputs from three model configurations: saline subsurface and reduced vegetation productivity related to salinity; saline subsurface with vegetation productivity not reduced; and freshwater. Also included are code for the modified E3SM model, Alquimia interface, and PFLOTRAN reactive transport simulator in gzipped tar format; plain text parameter and configuration files; python code files for visualizing model output and defining model configurations; and model output, tide and salinity forcing, and configuration files in netCDF format. See the README.md file in the data package for a detailed description of all files contained in the package. All files are in netCDF (.nc), gzipped tar archive (.tar.gz or .tgz), or text (all other files).Updated: May 13, 2024. Model output, E3SM code, PFLOTRAN input files, and python codes for visualizing results were updated to reflect changes made for the manuscript revision. The updated archive reflects the code and model output from the final accepted manuscript. Changes included updated reaction parameters reflecting improved parameterization and additional comparisons with field measurements. E3SM code changes included better support for multiple grid cells and improved flow and transport parameterization.

54 ENVIRONMENTAL SCIENCES↗

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↗

Daily, 30 m Resolution NDSI Data for the East River Watershed, CO for 2000-2020

This dataset contains daily Normalized Difference Snow Index (NDSI) values at 30 m spatial resolution for the East River watershed in Colorado, USA. The temporal range of these data includes water years 2001-2020. These data were created using the Spatial and Temporal Adaptive Reflectance Fusion Model (STARFM). This model fuses low spatial and high temporal resolution data from MODIS (500 m, daily) with high spatial and low temporal resolution data from Landsat (30 m, 16 days) to create a 30m synthetic daily snow product. This product allows for the analysis of historical snow covered area trends in the East River Watershed at fine spatiotemporal resolutions where it was not available previously. This research was performed as a part of the Department of Energy’s Subsurface Biogeochemical Research Program with the primary intent of better understanding the timing and spatial patterns of water delivery to the Critical Zone in mountain watersheds. Each .zip file contains one "water year" of data (October 1 - September 30; i.e., water year 2010 starts October 1, 2010 and ends September 30, 2011). Each zip file contains the following: STARFM daily Normalized Difference Snow Index (NDSI) fusion data files in GeoTiff format with one layer for each day between Landsat data acquisition dates (i.e., for dates of Landsat acquisition, the Landsat image is included for that date). The study area is located in an area of Landsat path overlap, so Landsat dates acquisitions are every 7-9 days. Landsat NDSI files containing the high spatial (30m), low temporal (7-9 days due to Landsat path overlap) resolution data used as input to STARFM in GeoTiff format with one layer for each day. Dates for which no Landsat data were obtained are included as NoData layers. MODIS NDSI files containing the high temporal (daily), low spatial (500m) resolution data used as input to STARFM in GeoTiff format with one layer for each day. Please note the MODIS data were resampled to 30m pixels for input into the STARFM model. The data have a scale factor of 10,000 and a no data value of -32767. The projection of all datasets is WGS 84 (EPSG: 4326), which has a latitude/longitude based degree resolution of 0.0002694946 X 0.0002694946, and approximates to the 30 m spatial resolution mentioned above. The Layer Index files in .csv format. They contain information for each layer in the above GeoTiff files regarding the corresponding date for each layer, the fraction of pixels in the image that contain valid data (missing data is due to either cloud cover or poor data quality; these values are not percent snow cover). Dates of Landsat overpass are indicated in these files. If no Landsat data were able to be obtained due to cloud cover or lack of Landsat Tier 1 data available on Google Earth Engine, this is also noted.

EARTH SCIENCE > CRYOSPHERE > SNOW/ICE↗

Hydrogeologic Model Based on Reduced Complexity

This data set provides the basic hydrogeologic model used for development of the TOUGH2 reservoir modeling results for the Kimberlina site. The hydrogeologic model is based on the static geologic model provided as a separate data set but has some simplifications regarding the geologic layers. Some geologic layers have been merged for the hydrogeologic model because the hydrogeologic properties were very similar. The data set contains several files. The word file explains the structure of the data files. The pdf contains a table with the hydrogeologic properties. The data set also includes 15 thickness files for 15 geological layers (including 3 Vedder sand layers and 3 Vedder shale layers), three elevations files (with reference elevation at ground surface/model top at 9000 m), and one fault trace file for seven faults. Most users may only need 2-3 faults close to the injection well (also see the figure). The arrangement of these layer thickness and elevations files can be see from the three layer files (for Tecplot). To develop a grid structure, start with the Vedder top elevation (REFVedderTop.dat) and add/subtract the thicknesses of layers above/below.

3D Groundwater Model↗

Revised Kimberlina Groundwater Simulations

Kimberlina Groundwater Qaulity Simulations (Version 3: 2015 October) by Lawrence Livermore National Labratory. Submitted to the EDX team at the National Energy Technology Laboratory for research use. This dataset contains 562 updated groundwater quality simulations based on the Kimberlina site. It is a six-layer model including the aquifers and aquitards inbetween the ground surface and the reservoir. The input files and associated leakage information for these simulations are included in the zip file "nrap_kim_well31_fluxes and inputs.tar.gz". These 562 simulations are the successful results out of 1000 monte carlo simulations, with time length greater than 5 years. Each simulation consists 6 output files, therefore, there are 3372 files (6*562) in total. One single example simulation of full time length (200 year) is also provided in the zip file "single_simulation_200yr_sim0012.tar.gz". These 6 groundwater quality parameters are: - pH (use absolute value) - TDS (mg/kg) - Pressure (Pa) - CO2 Liquid Saturation (fraction range 0.0-1.0) - CO2 Gas Concentration (mol/L) - CO2 Liquid Concentration (mol/kg) Their correponding file names, take the first simulation for example, are: ph0001.ntab (for pH) , tds0001.ntab (for TDS), usnt0001.p.ntab (for pressure), usnt0001.s_liquid.ntab (for liquid saturation), usnt0001.c_co2_gas.ntab (for CO2 gas concentration) and usnt0001.c_co2_liquid.ntab (for CO2 liquid concentration). Each output file contains at least 19 columns (variables). The total number of columns depends on the simulation time length. The column data include 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 jth grid of y-axis 4. k: the kth grid of z-axis 5. element_ref: element type 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 rest (14, 15, 16...) variables are the simulated parameter values over time, take pH as an example, are: 14. ph000y: initial pH value. 15. ph001y: simulated pH value at the end of the 1st year. 16. ph002y: simulated pH value at the end of the 2nd year. ... (and so on)... The zip input files have the input fluxes of brine and CO2 (in kg/s) allocated to model layers 1,2,3 and 5 (layers 4 and 6 are assumed to be no-flow aquitards) through the following nodes: (src1 WELL 7 7 25 25 10 32) #Etchegoin (src2 WELL 7 7 25 25 33 72) #Macoma Chanac (src3 WELL 7 7 25 25 73 83) #Santa Margarita Mclure (src4 WELL 7 7 25 25 84 89) #Fruitvale Round Mountain (aquitard) (src5 WELL 7 7 25 25 90 96) #Olcese Sand (thief zone) (src6 WELL 7 7 25 25 97 99) #tremblor Freeman (aquitard) ex: brn1 is assigned to src 1 from i=(7,7), j=(25,25), k=(10,32) Edited by Ya-Mei Yang at National Energy Technology Laboratory

brine leakage↗

Ground-based_transient_electromagnetic_data_and_resistivity_models_for_SubTER_BelleCreek_2017-2018

Ground-based transient electromagnetic (TEM) data were acquired in selected locations around Belle Creek, Montana to define the resistivity structure of the near surface. Data were acquired using the ABEM WalkTEM system (Guideline Geo Ab, Sundbyberg, Sweden). TEM data were processed and numerically inverted to derive one-dimensional resistivity structure using SPIA (Aarhus Geosoftware, Aarhus, Denmark). This release includes raw and processed TEM data and resistivity models for each data location using the following structure: Ground-based_transient_electromagnetic_data_and_resistivity_models_for_SubTER_BelleCreek_2017-2018.xml SBC_TEM_2019_SoundingLocationsModels.gdb.zip - file geodatabase with all models and plots attached. This is a mirror of the contents of the model directory. Ground-based_transient_electromagnetic_data_and_resistivity_models_for_SubTER_BelleCreek_2017-2018.zip Data SBC_USF - raw data USF_format_description.pdf - manual describing the USF file format SBC_SoundingID-USF_lookup.csv - table describing the USF file naming convention and channel mapping *.usf files - raw, unprocessed data files SBC_TEM - processed data AarhusInv_manual.pdf - manual describing the TEM file format *.tem files - processed data files Models SBC_Model_Plots - plots of the data and the models for each sounding location TEM_model_data_dictionary.csv - data dictionary describing tabulated models SBC_TEM_models.csv - tabulated models

geophysical surveying↗

Water Security Toolkit User Manual Version 1.2.

The Water Security Toolkit (WST) is a suite of open source software tools that can be used by water utilities to create response strategies to reduce the impact of contamination in a water distribution network . WST includes hydraulic and water quality modeling software , optimizati on methodologies , and visualization tools to identify: (1) sensor locations to detect contamination, (2) locations in the network in which the contamination was introduced, (3) hydrants to remove contaminated water from the distribution system, (4) locations in the network to inject decontamination agents to inactivate, remove, or destroy contaminants, (5) locations in the network to take grab sample s to help identify the source of contamination and (6) valves to close in order to isolate contaminate d areas of the network. This user manual describes the different components of WST , along w ith examples and case studies. License Notice The Water Security Toolkit (WST) v.1.2 Copyright c 2012 Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000, there is a non-exclusive license for use of this work by or on behalf of the U.S. government. This software is distributed under the Revised BSD License (see below). In addition, WST leverages a variety of third-party software packages, which have separate licensing policies: Acro Revised BSD License argparse Python Software Foundation License Boost Boost Software License Coopr Revised BSD License Coverage BSD License Distribute Python Software Foundation License / Zope Public License EPANET Public Domain EPANET-ERD Revised BSD License EPANET-MSX GNU Lesser General Public License (LGPL) v.3 gcovr Revised BSD License GRASP AT&T Commercial License for noncommercial use; includes randomsample and sideconstraints executable files LZMA SDK Public Domain nose GNU Lesser General Public License (LGPL) v.2.1 ordereddict MIT License pip MIT License PLY BSD License PyEPANET Revised BSD License Pyro MIT License PyUtilib Revised BSD License PyYAML MIT License runpy2 Python Software Foundation License setuptools Python Software Foundation License / Zope Public License six MIT License TinyXML zlib License unittest2 BSD License Utilib Revised BSD License virtualenv MIT License Vol Common Public License vpykit Revised BSD License Additionally, some precompiled WST binary distributions might bundle other third-party executables files: Coliny Revised BSD License (part of Acro project) Dakota GNU Lesser General Public License (LGPL) v.2.1 PICO Revised BSD License (part of Acro project) i Revised BSD License Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of Sandia National Laboratories nor Sandia Corporation nor the names of its con- tributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IM- PLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL SANDIA CORPORATION BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUD- ING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ii Acknowledgements This work was supported by the U.S. Environmental Protection Agency through its Office of Research and Development (Interagency Agreement # DW8992192801). The material in this document has been subject to technical and policy review by the U.S. EPA, and approved for publication. The views expressed by individual authors, however, are their own, and do not necessarily reflect those of the U.S. Environmental Protection Agency. Mention of trade names, products, or services does not convey official U.S. EPA approval, endorsement, or recommendation. The Water Security Toolkit is an extension of the Threat Ensemble Vulnerability Assessment-Sensor Place- ment Optimization Tool (TEVA-SPOT), which was also developed with funding from the U.S. Environ- mental Protection Agency through its Office of Research and Development (Interagency Agreement # DW8992192801). The authors acknowledge the following individuals for their contributions to the devel- opment of TEVA-SPOT: Jonathan Berry (Sandia National Laboratories), Erik Boman (Sandia National Laboratories), Lee Ann Riesen (Sandia National Laboratories), James Uber (University of Cincinnati), and Jean-Paul Watson (Sandia National Laboratories). iii Acronyms ATUS American Time-Use Survey BLAS Basic linear algebra sub-routines CFU Colony-forming unit CVAR Conditional value at risk CWS Contamination warning system EA Evolutionary algorithm EDS Event detection system EPA U.S. Environmental Protection Agency EC Extent of Contamination ERD EPANET results database file GLPK GNU Linear Programming Kit GRASP Greedy randomized adaptive sampling process HEX Hexadecimal HTML HyperText markup language INP EPANET input file LP Linear program MC Mass consumed MILP Mixed integer linear program MIP Mixed integer program MSX Multi-species extension for EPANET NFD Number of failed detections NS Number of sensors NZD Non-zero demand PD Population dosed PE Population exposed PK Population killed TAI Threat assessment input file TCE Tailed-conditioned expectation TD Time to detection TEC Timed extent of contamination TEVA Threat ensemble vulnerability assessment TSB Tryptic soy broth TSG Threat scenario generation file TSI Threat simulation input file VAR Value at risk VC Volume consumed WST Water Security Toolkit YML YAML configuration file format for WST iv Symbols Notation Definition Example { , } set brackets { 1,2,3 } means a set containing the values 1,2, and 3. [?] is an element of s [?] S means that s is an element of the set S . [?] for all s = 1 [?] s [?] S means that the statement s = 1 is true for all s in set S . P summation P n i =1 s i means s 1 + s 2 + * * * + s n . \ set minus S \ T means the set that contains all those elements of S that are not in set T . %7C given %7C is used to define conditional probability. P ( s %7C t ) means the prob- ability of s occurring given that t occurs. %7C ... %7C cardinality Cardinality of a set is the number of elements of the set. If set S = { 2,4,6 } , then %7C S %7C = 3. v

Klise, Katherine A.↗

A simple json format for storing and exchanging code calculation and experimental results

Calculation codes and code systems give their results in a plethora of different formats and/or files. For instance, MCNP gives a user the MCNP specific output file, the mctal file, the ptrac file, etc. while PARTISN has a PARTISN specific output file and a number of binary files with various kinds of information about the calculation. However, the results we are interested in are always the same. These can be single values such as the effective multiplication factor k eff or the effective delayed neutron fraction β eff . It can be histogram data (such as particle spectra, reaction rates, sensitivity profiles, etc.) or even pointwise data (for example the nuclide composition as a function of time, etc.). It is also worthwhile to note that this would also apply to experimental data that we may wish to compare with as well. Calculation and experimental results can basically be split into two components: attributes (or metadata) and the actual result itself. Attributes represent information about the result that are not necessarily required for its’ interpretation but that are still good to have. Often, these attributes are what we will want to filter results on. This means that these attributes are often the answer to specific questions we may have about the result. The following is a non exhaustive list of such basic questions: what type of result is it: e.g. the effective multiplication factor k eff , the effective delayed neutron fraction β eff , etc.; which case does it relate to: e.g. a specific ICSBEP case such as PU-MET-FAST-001-001; which code and version produced this result: e.g. MCNP 6.2, etc.; which nuclear data library was used to obtain the result: e.g. ENDF/B-VIII.0 or JEFF 3.3; which nuclide and reaction does it apply to (for reaction rates and sensitivity profiles); which volume in the geometry was it calculated in? The second component of the calculation or experimental result is the actual numerical data of the result. It is this data that we want to compare, exchange, plot, interpret, etc. It consists of values with optional uncertainties and units. It also includes the underlying structure (if any structure is required to interpret the result). Depending on the type of result, it may be a single value (e.g. the effective multiplication factor), an array of values (e.g. a reaction rate or particle spectrum) or even a multidimensional array. In order to exchange results between different organisations, for instance for benchmarking, people often resort to spreadsheets or custom text files that need to be filled out. While this approach works well if little information is to be exchanged, it can become cumbersome when dealing with large amounts of data (like for instance particle spectra for thousands of cases). In addition, such an approach does not always capture the metadata we may be interested in to allow for automated processing of these files. The purpose of this report is to propose a standardised json structure to store any type of result and present an associated python interface to interact with these results directly. For such a structure to be useful, it must fulfill a specific set of functional requirements that we try to meet with this proposal. The format must allow for the calculation result to stand by itself. This means that we should not have to look in multiple places to be able to understand it. For example, if the result relates to a particle spectrum, the group structure in which the result is given should be stored with it. The format should be code agnostic. This means that we do not need to know where it came from to understand it. The format should be result type agnostic. This means that the format must be generic enough so that we can even use it for results we have not thought of yet. The format should be relatively easy to interact with through different scripting or programming languages (i.e. the machine interface) while still providing a clean structure that can be used directly by any human.

97 MATHEMATICS AND COMPUTING↗

Using CUBIT to Create Unstructured Mesh Models for MCNP Simulations

The Monte Carlo N-Particle (MCNP) transport code version 6 (also known as MCNP6) 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 creating CSG models is a time-consuming and error-prone process as the complexities of geometries increase. An MCNP UM calculation requires UM geometry input files. The UM capability was originally designed to work with UM models created with the Abaqus/CAE software and ASCII input files that it generates. The Abaqus-formatted input files needed for MCNP UM calculations must have the correct Abaqus syntax and meet the additional MCNP requirements. Several software packages can generate a UM model formatted as an Abaqus input file. Cubit, the Sandia National Laboratory automated mesh generation toolkit, can generate a UM model formatted as an Abaqus input file. However, the Abaqus input files created by Cubit cannot be used for MCNP simulations. A Python script has been developed to convert an Abaqus file created by Cubit to an Abaqus file that the MCNP code can process. This report describes the process of using Cubit to create UM models for MCNP calculations.

97 MATHEMATICS AND COMPUTING↗

Bacteroides expand the functional versatility of a universal transcription factor and transcribed DNA to program capsule diversity

This record contains a list of Snakemake rules (Snakefile) to process a raw *.fastq.gz (from GEO record: GSE281607) using Cutadapt, map a processed *.fastq file using Bowtie, convert mapped reads to *.bed files using Samtools and Bedtools, and count the occurance of each Bacteriodes fragilis str NCTC 9343 genome position anywhere in a mapped read and as the 3' end of a mapped read using Bedtools. It further contains *ebwt files to assist with Bowtie mapping, *genome file to be used with Bedtools, a *.fasta file (useful to regenerate *ebwt files), and the completely processed *bed and *txt read files (generated by Snakemake and R) as references. In addition, a *.pdb file is included and represents the predicted interaction between UpeY and UpaZ.

Landick, Robert↗

Size-resolved ice nucleating particle (INP) concentrations from the MOSAiC campaign

Sample collection: Ground-based immersion mode ice nucleation measurements were conducted on samples collected at the U.S. DOE ARM AMF2 onboard the R/V Polarstern P-deck during MOSAiC from 23 Oct 2019 to 01 Oct 2020. Samples were collected using a Davis Rotating-drum Unit for Monitoring (DRUM; DRUMAir, LLC) cascading impactor in 4 stages (i.e., size bins). Instrument information on the model used, the DA400, can be found at the DRUMAir website (http://www.drumair.com/). Stages A, B, C, and D had particle size cuts at 2.96, 1.21, 0.34, and 0.15 &micro;m in particle diameter, respectively. Strips of sample substrate (PFA, perfluoroalkoxy; McMaster) were adhered to each disc in each stage and coated with petrolatum to enable particles to stick on impact. The discs move slowly over time, such that aerosol loading is streaked onto the PFA. Every 24 hours, a blank is created on the PFA to separate daily samples. During MOSAiC, the pump typically pulled 20 &ndash; 35 lpm (average of 32 lpm) at the inlet with all the discs in place in each stage. Daily samples were collected for each of the four stages, equaling 28,800 &ndash; 50,400 total L of air (average of 46,080 L total L of air) per sample. Discs rotated for approximately 24 days before the sampling per strip was complete and changed to a new disc. Discs were stored frozen after collection. Sample preparation for analysis: Following collection and transport from MOSAiC to the Kreidenweis/DeMott laboratory, care of PI Creamean, in Fort Collins, CO, strips were removed from the discs and cut up to separate daily samples. Each daily portion of the strip was stored in separate sterile 15-mL centrifuge tubes and stored in a standard commercial freezer until analysis (approximately 4 &ndash; 12 months after collection). Sample analysis: Drop freezing assays (DFAs) were conducted on one daily sample set every 3 &ndash; 4 days of the study for all four stages using the Colorado State University (CSU) cold plate (CP). Sample set days were chosen to cover the entire year of MOSAiC and avoiding days where the AOS purge system was activated. Immediately after removal from the freezer, 2 mL of 0.1-&micro;m filtered deionized water was added with a single-use sterile syringe directly to the tubes, then mixed using a vortex mixer for at least 30 minutes at 500 rpm to resuspend particles from the PFA into the deionized water. Following sample preparation, another single-use syringe was used to create 100 aliquots on a 3-inch diameter copper plate, then covered with a transparent plastic dome. The drops were approximately the same volume (2.5 &micro;L each), though careful inspection. The plate was cooled at approximately 3 &ndash; 10 K min-1 from room temperature until all drops froze on the plate. Temperature was measured by an Omega thermocouple probes and meter. Drop freezing was visually detected but recorded through monitoring software to provide the time frozen, channel of the meter used, temperature, and cooling rate for each drop. Not all 100 drops were always detected; the total number of rows in each data file equals the number of drops recorded, which typically was > 80 %. Each sample was tested three times (i.e., a new set of 100 drops was created for each test). Data provided are files containing these parameters. From the freezing temperatures recorded, the fraction frozen was and INP concentrations were calculated per L of air using the equation from Vali (1971): [INPs] = &minus;(ln(f)/Valiquot)*(Vsuspension/Vair) where f is the proportion of droplets not frozen, Valiquot is the volume of each aliquot (i.e., 2.5e-6 L), Vsuspension is the volume of the suspension (i.e., 0.002 L), and Vair is the volume of air per sample (i.e., 36000 L). Data usage guidance: There are three files included with this dataset: (1) dumcp_inp_concentrations.csv which includes cumulative INP concentrations binned every 0.5 &deg;C from 0 to &ndash;30 &deg;C for all samples and size ranges (i.e., DRUM stages) processed via DFA using the CSU CP; (2) dumcp_inp_standard_deviation.csv which includes the standard deviations for all samples and temperatures in dumcp_inp_concentrations.csv; and (3) dumcp_blank_concentrations_standard_deviation.csv which includes the INP concentrations and standard deviations for the deionized water and PFA blanks binned every 0.5 &deg;C from 0 to &ndash;30 &deg;C. The first column in each file represents the freezing temperature in &deg;C binned every 0.5 &deg;C from 0 to &ndash;30 &deg;C (first cell in this column = header = &ldquo;temp&rdquo;). The second column in each file represents the standard deviation of each temperature bin in &deg;C (first cell in this column = header = &ldquo;temperr&rdquo;). For file (1) dumcp_inp_concentrations.csv, the remaining columns indicate the INP concentrations per L of air for each temperature bin. For each sample column, the header in the first row indicates the stage (i.e., size bin as &ldquo;A_&rdquo;, &ldquo;B_&rdquo;, &ldquo;C_&rdquo;, or &ldquo;D_&rdquo;) and date (&ldquo;_yyyymmdd) of collection. For file (2) dumcp_inp_standard_deviation.csv, the remaining columns indicate the INP concentration standard deviation per L of air for each temperature bin. For each sample column, the header in the first row indicates the stage (i.e., size bin as &ldquo;A_&rdquo;, &ldquo;B_&rdquo;, &ldquo;C_&rdquo;, or &ldquo;D_&rdquo;) and date (&ldquo;_yyyymmdd) of collection. For file (3) dumcp_blank_concentrations_standard_deviation.csv, the remaining columns indicate the INP concentrations and standard deviations for the deionized water blank (&ldquo;di_0.1&rdquo; and &ldquo;di_0.1sd&rdquo; for the concentrations and standard deviations, respectively) and PFA blank (&ldquo;pfa&rdquo; and &ldquo;pfasd&rdquo; for the concentrations and standard deviations, respectively). Please see Creamean et al. (2019a; 2018a; 2018b; 2019b) for additional details on DRUM sample collection and offline processing. For questions or help with data interpretation, contact Dr. Jessie Creamean (jessie.creamean@colostate.edu). References: Creamean, J. M., Mignani, C., Bukowiecki, N., and Conen, F.: Using spectra characteristics to identify ice nucleating particle populations during winter storms in the Alps, Atmos. Chem. Phys., 19, 8123&ndash;8140, 2019a. Creamean, J. M., Kirpes, R. M., Pratt, K. A., Spada, N. S., Maahn, M., de Boer, G., Schnell, R. C., and China, S.: Marine and terrestrial influences on ice nucleating particles during continuous springtime measurements in an Arctic oilfield location, Atmospheric Chemistry and Physics, 18, 18023-18042, 10.5194/acp-18-18023-2018, 2018a. Creamean, J. M., Primm, K. M., Tolbert, M. A., Hall, E. G., Wendell, J., Jordan, A., Sheridan, P. J., Smith, J., and Schnell, R. C.: HOVERCAT: A novel aerial system for evaluation of aerosol-cloud interactions, Atmospheric Measurement Techniques, 11, 3969-3985, 10.5194/amt-11-3969-2018, 2018b. Creamean, J. M., Cross, J. N., Pickart, R., McRaven, L., Lin, P., Pacini, A., Hanlon, R., Schmale, D. G., Ceniceros, J., Aydell, T., Colombi, N., Bolger, E., and DeMott, P. J.: Ice nucleating particles carried from below a phytoplankton bloom to the Arctic atmosphere, Geophys. Res. Lett., 46, 8572-8581, https://doi.org/10.1029/2019GL083039, 2019b. Vali, G.: Quantitative Evaluation of Experimental Results an the Heterogeneous Freezing Nucleation of Supercooled Liquids, Journal of the Atmospheric Sciences, 28, 402-409, 10.1175/1520-0469(1971)028<0402:qeoera>2.0.co;2, 1971.

4-stage DRUM aerosol collector (DA400),Ice nuclei,↗

Urban Parameters Arizona Urban Corridor 100m

132 Urban parameters based on building physical dimensions and location were generated for the cities in six Arizona Counties at 100m resolution using the NATURF model. To use the binary file with WRF, the binary file and the index file must be placed in their own directory in WRF_GEOG and accessed in the same way NUDAPT44 would be accessed.

Dumas, Melissa [ORNL] (ORCID:0000000233190846)↗

Urban Parameters Washington, DC 100m

132 Urban parameters based on building physical dimensions and location were generated for Washington, District of Columbia at 100m resolution using the NATURF model. To use the binary file with WRF, the binary file and the index file must be placed in their own directory in WRF_GEOG and accessed in the same way NUDAPT44 would be accessed.

Dumas, Melissa [ORNL] (ORCID:0000000233190846)↗

Sensitivity Analysis of Drivers Water Shortage in the Los Angeles Region During Drought

The code and detailed step-by-step instructions for generating the model output data, processing results, and analysis and plotting are provided at https://github.com/IMMM-SFA/Ferencz_et_al_2026_ER_Water. The PyArtes model is a python adaptation of the Artes model. PyArtes uses many of the same input data and optimization model architecture as Artes. Documentation for the PyArtes model is provided in the Supplement to the paper. The primary data product are simulated monthly water shortages for indoor and outdoor demand under a large ensemble of drought scenarios (>13,000). The droughts are hypothetical and are not based on historical time series data of supply sources - though historical data did help inform ranges explored for supply parameters. Demands are informed by recent 2017-2021 water supply data. Demands used for the model can be accessed at https://github.com/IMMM-SFA/Ferencz_et_al_2026_ER_Water. Simulations resolve demand for over 90 water providers in the study region. The results report 36 months of water shortage data for each indoor and outdoor demand node. The study also developed a multilayer perceptron (MLP) neural network trained on a subset of the simulated shortage ensemble to emulate worst annual water shortage for a given set of parameter multipliers -- provided the parameter values fall within the ranges sampled in the ensemble. Emulated water shortages for synthetic ensembles are in the MLP-generated shortages folder. The MLP model was used to generate larger ensembles to support Sobol analysis that would have been extremely computationally expensive to simulate. Datasets provided in this repository*: Simulated shortages. These results are used for the analysis for Figures 5, 8, and 9 in the paper, and also to train the MLP emulator. .zip file containing outputs for the 13,312 scenario ensemble. Separate .csv files for indoor and outdoor shortage for each scenario. Rows = demand ids (~100), Columns = months (36) Units = acre-feet/month of shortage (shortage = monthly demand - supply). 1 acft = 1233.48 m^3 .csv files of aggregated shortages derived from the 13,312 ensemble Rows = scenarios (13,312), Columns = demand ids (~100) Units = acre-feet/year (either worst annual shortage or total shortage over the 3-year drought) .csv file of the parameter multipliers scenarios for the ensemble .csv file of the parameter ranges and baseline values the multipliers were applied to MLP-generated shortages. These results are used for Figures 4, 6, and 7 in the paper. mwd higher folder: scenario ensembles, emulated worst year total shortages (acft), and Sobol results Emulated shortages. Rows = scenarios, columns = demand ids, units acft Sobol results. Rows = demand ids, columns Sobol (S1, ST, or 95% confidence interval) value for each parameter mwd lower folder: scenario ensembles, emulated worst year total shortages (acft), and Sobol results same organization as mwd higher MLP performance: performance metrics (R^2, RMSE, BIAS, MAPE) for the testing subset (20% or 2,662 scenarios) and simulated vs emulated worst year shortage (acre-feet/year) for every demand node, MWD wholesale regions, and the entire study region (LAC). Supporting data for figures. Figure plotting scripts in the associated GitHub repo. These files support analysis and visualization. Geospatial Data used for plotting simulated water shortages and Sobol results. Dictionary of full names for demand nodes in the model and estimates of water supply by source type informed by Artes input files and California Urban Water Management Planning data: https://water.ca.gov/Programs/Water-Use-And-Efficiency/Urban-Water-Use-Efficiency/Urban-Water-Management-Plans *Readme files provided for each folder.

drought↗

Public Reference Data for Megawatt-Scale Hydrogen Electrolysis - Simulated Marine Hydrokinetic Tidal Turbine

The U.S. Department of Energy and National Laboratory of the Rockies (NLR) demonstrate hydrogen electrolysis, hydrogen compression and storage, and variable hydrogen fuel cell power production using megawatt-scale equipment at NLR’s Flatirons Campus as part of the Advanced Research on Integrated Energy Systems (ARIES) initiative. This dataset is part of that effort and is intended for academic, national laboratory, industrial, and other stakeholders to plan, design, and validate models of megawatt-scale hydrogen technologies and diverse energy infrastructure. These data provide a baseline for how existing hydrogen electrolysis technologies perform when coupled with other energy technologies. This dataset contains inputs and outputs from simulations of a floating marine hydrokinetic turbine over approximately half a tidal cycle (~6.6 hours). Inflow conditions were derived from field measurements in Alaska’s Cook Inlet and represent a tidal environment in which the current speed ramps from near 0 m/s to a peak of 3 m/s and back. The original acoustic doppler current profiler dataset is publicly available on the Marine and Hydrokinetic Data Repository. In a full tidal cycle, the flow reverses and the rotor would reorient; this reversal was not modeled. In the Cook Inlet campaign , turbulence intensity was similar in both directions. Two inflow cases are included. In the first case, labeled “raw” in the files, the measured current time series was used directly in the InflowWind module of OpenFAST. Speed and direction were applied as a function of time and elevation, uniformly in the horizontal direction. With full spatial coherence, this approach captures high turbulent variability and results in pronounced power fluctuations, so it is considered a conservative, near-worst-case representation of loading. In the second case, labeled “average” in the files, a 30-minute moving average was applied to extract the slowly varying mean speed. The residual fluctuations about this mean were used to generate spatially varying, full-field turbulence inputs with TurbSim, giving a more physically realistic representation of the inflow across the rotor disk. Two random realizations were used to produce distinct inflow conditions for two OpenFAST simulations representing a two-turbine array. The same turbulence intensity is applied across the full time series, producing larger fluctuations at the start and end, where the mean speed is low. The second case is the more appropriate framework for performance and power assessment but overpredicts turbulence at lower flow speeds and underpredicts it at higher speeds. As the floating platform moves and the rotor changes its x-position, Taylor’s frozen turbulence hypothesis used by InflowWind assumes a constant rather than a time-varying mean velocity, introducing some inaccuracy in the velocity plane sampling. The turbine modeled is the 500-kW Reference Model 1, a horizontal-axis two-bladed hydrokinetic turbine on a four-column floating semisubmersible substructure . Simulations were performed using OpenFAST v4.1 with the Reference Open Source Controller (ROSCO) v2.10. All input files required to reproduce the simulations are included. The electrolyzer is a 1.25-MW proton exchange membrane type MC250 system manufactured by Nel . This unit supports up to 2.5 MW, but NLR has only a single 1.25-MW stack. The datasets report hydrogen balance-of-plant and system data, all captured at 1 Hz, including hydrogen mass production measured with an Emerson Coriolis flow meter. The system controls hydrogen production by varying direct current applied to the stack, from a maximum of 3,000 A to a minimum safe operating current of 300 A, or 10%. Because the current–voltage characteristic changes as the stack ages and efficiency degrades, the actual minimum safe operating power changes over time. The simulated tidal turbine time series data was translated from power (kilowatts) to current (amperes) using a curve fit with calibration data and sent to the electrolyzer power supply at 1-Hz. Each zip file represents a single tidal electrolysis experiment and is named: {technology}_{inflow method}_{number of 500 kW tidal turbines connected} For instance, “tidal-500kW-RM1_average_2.zip” is a 6-hour experiment using the 500-kW tidal reference model, scaled by 2x (1-MW) to better match the electrolyzer maximum of 1.25MW, fed with the 30-minute moving average current case. Each zip folder contains the following files: A .csv file of raw data. An .xlsx file explaining all the fields in the raw data. A .png plot showing the time series of hydrogen production in kilograms per hour, electrolysis power consumption, and input wave power. A .csv file combines all tidal profiles as "combined_tidal_experiments.csv." A separate experiment, “characterization_200.zip,” shows the MC250 electrolyzer steady-state response with 30-minute load steps over 5 hours and is accessible with this entry.

08 HYDROGEN↗

Replication Data for: Measurement of the mean number of muons with energies above 500 GeV in air showers detected with the IceCube Neutrino Observatory

<b>Measurement of the mean number of muons with energies above 500 GeV in air showers detected with the IceCube Neutrino Observatory</b> <br><br> This data release accompanies results submitted to Physical Review D describing the measurement of the average multiplicity of TeV muons with IceCube. It contains the data necessary to reproduce the main plots from the paper (Figs. 7 and 9), i.e. the numerical results for the average number of muons with energies above 500 GeV as a function of primary cosmic ray energy. <br><br> For any questions about this data release, please write to analysis@icecube.wisc.edu. <br><br> Files included in this release: <ul> <li>A README file <li>Files including data to reproduce the results plots from the paper (see below for details) <li>An example python script showing how to read and plot the data </ul> <br> <u>What is in the files icecube_Nmu500_X_Y.txt:</u> <br> Y indicates wether the file contains values obtained from experimental data (Y="data") or air-shower simulations (Y="MC"). <br> X indicates the hadronic interaction model for which the plot is made. If Y="data", this means that the experimental data was interpreted using this model. If Y="MC", it means that the simulations were performed with this model. The three models included are Sibyll 2.1, QGSJet-II.04, and EPOS-LHC (see paper for references). The file with X="modelaverage" gives the average over the three individual results with the deviations from the average included in the systematic uncertainties. <br><br> Please see the README file for details on how the data is structured in the files.

Astroparticle Physics↗

FGGE/ERBM tape specification and shipping letter description

The Nimbus-7 FGGE/ERBM tape contains 27 ERB parameters which are extracted and reformatted from the Nimbus-7 ERB-MATRIX tape. There are four types of files on a FGGE/ERBM tape: a test file; tape-header file which describes the data set characteristics and the contents of the tape; a grid-descriptor file which contains the information of the ERB scanning channel target number and their associated latitude limits and longitude intervals; and one or more data files. A single end-of-file (EOF) tape mark is written after each file, and two EOF marks are written after the last data file on the tape.

Han, D.↗

Engineering description of the ascent/descent bet product

The Ascent/Descent output product is produced in the OPIP routine from three files which constitute its input. One of these, OPIP.IN, contains mission specific parameters. Meteorological data, such as atmospheric wind velocities, temperatures, and density, are obtained from the second file, the Corrected Meteorological Data File (METDATA). The third file is the TRJATTDATA file which contains the time-tagged state vectors that combine trajectory information from the Best Estimate of Trajectory (BET) filter, LBRET5, and Best Estimate of Attitude (BEA) derived from IMU telemetry. Each term in the two output data files (BETDATA and the Navigation Block, or NAVBLK) are defined. The description of the BETDATA file includes an outline of the algorithm used to calculate each term. To facilitate describing the algorithms, a nomenclature is defined. The description of the nomenclature includes a definition of the coordinate systems used. The NAVBLK file contains navigation input parameters. Each term in NAVBLK is defined and its source is listed. The production of NAVBLK requires only two computational algorithms. These two algorithms, which compute the terms DELTA and RSUBO, are described. Finally, the distribution of data in the NAVBLK records is listed.

Seacord, A. W., II↗