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DOE OSTI2017

Charliecloud

Charliecloud is a set of scripts to let users run a virtual cluster of virtual machines (VMs) on a desktop or supercomputer. Key functions include: 1. Creating (typically by installing an operating system from vendor media) and updating VM images; 2. Running a single VM; 3. Running multiple VMs in a virtual cluster. The virtual machines can talk to one another over the network and (in some cases) the outside world. This is accomplished by calling external programs such as QEMU and the Virtual Distributed Ethernet (VDE) suite. The goal is to let users have a virtual cluster containing nodes where they have privileged access, while isolating that privilege within the virtual cluster so it cannot affect the physical compute resources. Host configuration enforces security; this is not included in Charliecloud, though security guidelines are included in its documentation and Charliecloud is designed to facilitate such configuration. Charliecloud manages passing information from host computers into and out of the virtual machines, such as parameters of the virtual cluster, input data specified by the user, output data from virtual compute jobs, VM console display, and network connections (e.g., SSH or X11). Parameters for the virtual cluster (number of VMs, RAM and disk per VM, etc.) are specified by the user or gathered from the environment (e.g., SLURM environment variables). Example job scripts are included. These include computation examples (such as a "hello world" MPI job) as well as performance tests. They also include a security test script to verify that the virtual cluster is appropriately sandboxed. Tests include: 1. Pinging hosts inside and outside the virtual cluster to explore connectivity; 2. Port scans (again inside and outside) to see what services are available; 3. Sniffing tests to see what traffic is visible to running VMs; 4. IP address spoofing to test network functionality in this case; 5. File access tests to make sure host access permissions are enforced. This test script is not a comprehensive scanner and does not test for specific vulnerabilities. Importantly, no information about physical hosts or network topology is included in this script (or any of Charliecloud); while part of a sensible test, such information is specified by the user when the test is run. That is, one cannot learn anything about the LANL network or computing infrastructure by examining Charliecloud code.

Priedhorsky, Reid↗

DOE OSTI2021

Optode Images, and Dissolved Oxygen Data from Sand and Sediment Flow-through Column Experiments associated with: "2-D Imaging of Dissolved Oxygen Concentration in Flow-Through Sediment Columns"

This data package is associated with the publication "2-D Imaging of Dissolved Oxygen Concentration in Flow-Through Sediment Columns" submitted to Frontiers in Water (Garayburu-Caruso et al., 2022). This work presents a novel application of planar optode technology to sediment columns that allows the study of well-constrained flow fields without the need to assume completely homogeneous flow. We introduce a flow-through column with the interior coated in an oxygen sensing film and a series of sampling ports as a unique tool capable of capturing changes in dissolved oxygen (DO) at high frequency (10 s) and spatial (< 1 mm) resolution across the length of a column. In addition, we provide custom scripts that allows image processing steps to be automated and consistently reproduced over a variety of experimental conditions. This dataset is comprised of four folders (1) 01_Riverbed_Sediment_Experiment, (2) 02_Sand_Experiment, (3) 01_Riverbed_Sediment_Raw_Images, and (4) 02_Sand_Experiment_Raw_Images. 01_Riverbed_Sediment_Experiment contains (1) a subfolder with csv files that contain statistical parameters from the linear regressions applied to each optode image, (2) a subfolder with csv files from DO data measured by in-line sensors, (3) a subfolder with csv files containing column and injection specific input parameters for the image processing script, and (4) a subfolder with scripts used to process the images and create associated figures. 02_Sand_Experiment contains (1) a subfolder with csv files containing column and injection-specific input parameters for the image processing script, and (2) a subfolder with scripts used to process the images and create associated figures. 01_Riverbed_Sediment_Raw_Images (spited in 3 parts due to size) contains a subfolder with raw red, and green images from the optode system during the MilliQ Injection, Vanillin Injection or Vanillin + Sampling Injection respectively. 02_Sand_Experiment_Raw_Images contains a subfolder with raw red, and green images from the optode system. Outside of the main folders there is a csv containing file-level metadata and a csv data dictionary defining column headers for all csv files contained in the data package.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2016

Summary of Documentation for DYNA3D-ParaDyn's Software Quality Assurance Regression Test Problems

The Software Quality Assurance (SQA) regression test suite for DYNA3D (Zywicz and Lin, 2015) and ParaDyn (DeGroot, et al., 2015) currently contains approximately 600 problems divided into 21 suites, and is a required component of ParaDyn’s SQA plan (Ferencz and Oliver, 2013). The regression suite allows developers to ensure that software modifications do not unintentionally alter the code response. The entire regression suite is run prior to permanently incorporating any software modification or addition. When code modifications alter test problem results, the specific cause must be determined and fully understood before the software changes and revised test answers can be incorporated. The regression suite is executed on LLNL platforms using a Python script and an associated data file. The user specifies the DYNA3D or ParaDyn executable, number of processors to use, test problems to run, and other options to the script. The data file details how each problem and its answer extraction scripts are executed. For each problem in the regression suite there exists an input deck, an eight-processor partition file, an answer file, and various extraction scripts. These scripts assemble a temporary answer file in a specific format from the simulation results. The temporary and stored answer files are compared to a specific level of numerical precision, and when differences are detected the test problem is flagged as failed. Presently, numerical results are stored and compared to 16 digits. At this accuracy level different processor types, compilers, number of partitions, etc. impact the results to various degrees. Thus, for consistency purposes the regression suite is run with ParaDyn using 8 processors on machines with a specific processor type (currently the Intel Xeon E5530 processor). For non-parallel regression problems, i.e., the two XFEM problems, DYNA3D is used instead. When environments or platforms change, executables using the current source code and the new resource are created and the regression suite is run. If differences in answers arise, the new answers are retained provided that the differences are inconsequential. This bootstrap approach allows the test suite answers to evolve in a controlled manner with a high level of confidence. Developers also run the entire regression suite with (serial) DYNA3D. While these results normally differ from the stored (parallel) answers, abnormal termination or wildly different values are strong indicators of potential issues.

42 ENGINEERING↗

DOE OSTI2024

Documentation for Python Automation in CYME for DER Hosting Capacity Analysis of Different Feeder Configurations

This file provides the documentation for several Python scripts that were developed by Sandia National Laboratories to enhance the automation and customization capabilities for performing various distribution system planning and analysis tasks in CYME. Specifically, these scripts (.py files detailed in Figure 1) enable the user to evaluate different distribution system configurations and the resulting impacts on hosting capacity results and other metrics. In general, these scripts—and the accompanying documentation—provide the foundation upon which future customized tools can be created. For example, the scripts show how to extract and modify parameters of various circuit components, set up and run analyses using built-in CYME tools (iteratively), and export reports for further evaluations and comparisons. Thus, the capabilities and syntaxes used in the scripts can be adapted and leveraged for countless other objectives.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2016

Development and Verification of MATLAB Functions for Pressure Drop Estimation in Crossflow Tube Bundles

The experimental data on drag coefficients in crossflow tube bundles is severely limited. It is largely contained in nomograms for a small range of tube bundle pitch ratios for both in-line and staggered bundles. These monograms and the corresponding correlations/curve fits are not readily accessible. This lack of experimental data presents a limitation when designing crossflow heat exchangers for nuclear reactors. Specifically, Molten Salt Reactors (MSRs) that utilize cross-flow configurations with turbulent molten salts flowing in the shell side are of interest. Current methods of calculating the drag coefficients are outdated and time consuming when conducting design studies (i.e. picking points off a graph). A computer script could easily run the necessary rapid calculations of the pressure drop for a large possible range of Reynolds numbers, pitch ratios and tube bundle configurations. In an effort to facilitate increased access and accuracy to crossflow pressure drop calculations, a set of MATLAB scripts have been created. These are specifically for the pressure drop and drag coefficients for flow over rows of in-line and staggered tube bundles. For verification of the scripts, the nomograms produced by Zukauskas, of which the scripts are built off, served as a comparison to the plot generated by the MATLAB scripts. (authors)

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

DOE OSTI2023

GeoThermalCloud for EGS – An Open-source, User-friendly, Scalable AI Workflow for Modeling Enhanced Geothermal Systems

Enhanced Geothermal Systems (EGS) offer a vast potential to expand the use of geothermal energy. Heat is extracted from this engineered system by injecting relatively cold water into subsurface fractures, which are in contact with hot dry rock, and brought back to surface through production wells. Creating EGS requires improving the natural permeability of hot crystalline rocks. In this short conference paper, we present a reproducible workflow for modeling EGS. Our workflow called the GeoThermalCloud (GTC) for EGS, leverages recent advances in machine learning, deep learning, and high-performance computing. This GTC framework is currently being made open-source, user-friendly, and reproducible through python scripts as well as Google Colab/Jupyter Notebooks. This GTC for EGS modeling scripts are made available at https://github.com/SmartTensors/GeoThermalCloud.jl/tree/master/EGS and will constantly be updated to cater for geothermal community. Current GTC framework provides scripts to train deep learning (DL) models for techno-economics and data worth analysis. The Geothermal Design Tool (https://github.com/GeoDesignTool/GeoDT.git), a fast and simplified multi-physics solver, is used to develop a database for training DL models. This short paper provides details on the scripts to curate, process, and train DL models. The scripts can easily be modified to train on databases generated by other popular open-source simulators such as PFLOTRAN, STOMP, TOUGH, and GEOSX or commercial software such as ResFrac and COMSOL.

15 GEOTHERMAL ENERGY↗

DOE OSTI2021

Dependence of dark matter - electron scattering on the galactic dark matter velocity distribution

The rate of dark matter-electron scattering depends on the underlying velocity distribution of the dark matter halo. Importantly, dark matter-electron scattering is particularly sensitive to the high-velocity tail, which differs significantly amongst the various dark matter halo models. In this work, we summarize the leading halo models and discuss the various parameters which enter them. We recommend updated values for these parameters based on recent studies and measurements. Furthermore, we quantify the dependence of the dark matter-electron scattering rate on the choice of halo model and parameters, and demonstrate how these choices propagate to the predicted cross-section limits. The rate is most sensitive to changes in the circular velocity v 0 ; in silicon targets, we find that the changes in the rate predictions can range from Script $\mathcal{O}$(0.01%) to Script $\mathcal{O}$(100%) for contact interactions and Script $\mathcal{O}$(10%) to Script $\mathcal{O}$(100%) for long-range interactions.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2016

SU-F-J-94: Development of a Plug-in Based Image Analysis Tool for Integration Into Treatment Planning

Purpose: To extend the functionality of a commercial treatment planning system (TPS) to support (i) direct use of quantitative image-based metrics within treatment plan optimization and (ii) evaluation of dose-functional volume relationships to assist in functional image adaptive radiotherapy. Methods: A script was written that interfaces with a commercial TPS via an Application Programming Interface (API). The script executes a program that performs dose-functional volume analyses. Written in C#, the script reads the dose grid and correlates it with image data on a voxel-by-voxel basis through API extensions that can access registration transforms. A user interface was designed through WinForms to input parameters and display results. To test the performance of this program, image- and dose-based metrics computed from perfusion SPECT images aligned to the treatment planning CT were generated, validated, and compared. Results: The integration of image analysis information was successfully implemented as a plug-in to a commercial TPS. Perfusion SPECT images were used to validate the calculation and display of image-based metrics as well as dose-intensity metrics and histograms for defined structures on the treatment planning CT. Various biological dose correction models, custom image-based metrics, dose-intensity computations, and dose-intensity histograms were applied to analyze the image-dose profile. Conclusion: It is possible to add image analysis features to commercial TPSs through custom scripting applications. A tool was developed to enable the evaluation of image-intensity-based metrics in the context of functional targeting and avoidance. In addition to providing dose-intensity metrics and histograms that can be easily extracted from a plan database and correlated with outcomes, the system can also be extended to a plug-in optimization system, which can directly use the computed metrics for optimization of post-treatment tumor or normal tissue response models. Supported by NIH - P01 - CA059827.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2017

ACME Priority Metrics (A-PRIME)

A-PRIME, is a collection of scripts designed to provide Accelerated Climate Model for Energy (ACME) model developers and analysts with a variety of analysis of the model needed to determine if the model is producing the desired results, depending on the goals of the simulation. The software is csh scripts based at the top level to enable scientist to provide the input parameters. Within the scripts, the csh scripts calls code to perform the postprocessing of the raw data analysis and create plots for visual assessment.

Evans, KatherineJ.↗

DOE OSTI2024

Interpolation Models and Error Bounds for Verifiable Scientific Machine Learning

This repository contains python scripts and numerical data accompanying the paper: "Leveraging Interpolation Models and Error Bounds for Verifiable Scientific Machine Learning," Tyler Chang, Andrew Gillette, Romit Maulik, 2024. The following subdirectories are included: - "interpolants" contains our interpolation scripts used for all studies - "experiments" contains scripts demonstrating our experiments with synthetic data - "airfoil" contains scripts demonstrating our experiments with the publicly available UIUC airfoil dataset. Further instructions are provided in READMEs within the sub-directories.

Gillette, Andrew↗

DOE OSTI2025

JGI-Trichoderma v1.0

There is a series of Python and bash scripts to parse genomics datasets used to evaluate the coevolution of gene families and the feature importance of gene families using an SVM classifier. - Cover analysis: takes a list of single-copy genes in a set of genomes, aligns and builds the gene trees to determine if two gene families have a signature of covariation with one another. It parses the files to run phykit cover script described here: https://jlsteenwyk.com/PhyKIT/usage/index.html - SVM-classifier: This Python script is an SVM-based genomic classifier designed for biological data analysis. It combines machine learning with feature selection to identify important genomic markers and classify biological samples. Core Functionality: The script uses Support Vector Machines from scikit-learn to classify genomic data, incorporating SelectKBest for automated feature selection and leave-one-out cross-validation for performance assessment. It operates in multiple modes: feature ranking, optimal combination discovery, and sample prediction. Primary Applications: Genomic sample classification and biomarker discovery Feature importance analysis in high-dimensional biological datasets Prediction of sample categories based on genomic profiles Research applications requiring robust classification of biological data Key Advantages: High-dimensional handling: SVMs excel with genomic data's typical high feature-to-sample ratios Integrated feature selection: Reduces noise and computational overhead while identifying key markers Probability estimation: Provides confidence scores essential for biological interpretation Validation robustness: Leave-one-out cross-validation ensures reliable performance metrics Operational flexibility: Multiple analysis modes support different research phases from exploration to prediction

Stecca Steindorff, Andrei [Lawrence Berkeley Natio↗

DOE OSTI2025

Guideline 36 Conformance Test v2.0

ASHRAE Guideline 36 provides guidance for how typical commercial building HVAC systems should be controlled to reduce energy costs and improve the indoor environmental quality for occupants. An industry-led effort is developing test scripts for how control manufacturers can test that the control logic in their control products follows Guideline 36. This software intends to support that effort in two ways. First, by providing a testbed for control manufacturers to run the test scripts against their own control products and compare their generated results to the expected results provided by the test scripts. Second, by providing a testbed that can be used during the development of test scripts to rapidly and repeatably verify they exercise Guideline 36 logic as desired and generate accurate expected results that control products can be compared to. An initial version of the software has already been developed and released open-source by a previous CEC-funded project that implemented the first use case (https://github.com/LBNL-ETA/guideline36_conformance_test/blob/master/LICENSE.txt), while this software disclosure will add the functionality of the second use case, as well as update the software where needed, all open-source. We intend to extend and contribute to the existing open-source software repository.

Blum, David [Lawrence Berkeley National Laboratory↗

DOE OSTI2020

Description and Use of SCALE Sampler Parametric Capability for Engineering Analysis and Optimization

The Sampler sequence was introduced into the SCALE nuclear modeling and simulation suite in SCALE 6.2 to perform uncertainty quantification via random sampling of nuclear data, material number densities, and dimensions. Sampler was expanded with the introduction of a parametric capability in SCALE 6.2.2. This paper discusses input for the Sampler parametric sequence and presents two case studies of analyses performed using the sequence. These case studies include preconceptual design of a package for transporting high assay low-enriched uranium (HALEU) oxide and scoping calculations to support subcritical limit development for a future update of the ANSI/ANS-8.1 (ANS-8.1) standard. The parametric capability within Sampler provides many benefits to analysts. For instance, parametric sweeps are frequently used to identify optimum parameter values as part of safety analysis or system design, but such sweeps can require substantial engineering time or may rely on custom-written scripts or scripts such as Write One, Run Many (or WORM) developed outside of any software quality assurance program. With the parametric capabilities in Sampler, however, a large number of inputs can be generated automatically without recourse to scripting by individual analysts. The parametric capability can also be used in lieu of the CSAS5S search sequence to identify optimum parameters more simply with straightforward inputs and outputs. Sampler can also be used to calculate input parameters from engineering specifications. For example, diameters can be converted to radii, or masses can be used to calculate number densities. Overall, the Sampler parametric capability provides a robust feature within SCALE, eliminating the need for user-developed scripting.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2024

HERO WEC 2024 Hydraulic Configuration Deployment Data

The following submission includes raw and processed data from the in water deployment of NREL's Hydraulic and Electric Reverse Osmosis Wave Energy Converter (HERO WEC), in the form of parquet files, TDMS files, CSV files, bag files and MATLAB workspaces. This dataset was collected in March 2024 at the Jennette's pier test site in North Carolina. This submission includes the following: - Data description document (HERO WEC FY24 Hydraulic Deployment Data Descriptions.doc) - This document includes detailed descriptions of the type of data and how it was processed and/or calculated. - Processed MATLAB workspace - The processed data is provided in the form of a single MATLAB workspace containing data from the full deployment. This workspace contains data from all sensors down sampled to 10 Hz along with all array Value Added Products (VAPs). - MATLAB visualization scripts - The MATLAB workspaces can be visualized using the file "HERO_WEC_2024_Hydraulic_Config_Data_Viewer.m/mlx". The user simply needs to download the processed MATLAB workspaces, specify the desired start and end times and run this file. Both the .m and .mlx file format has been provided depending on the user's preference. - Summary Data - The fully processed data was used to create a summary data set with averages and important calculations performed on 30-minute intervals to align with the intervals of wave resource data reported from nearby CDIP ocean observing buoys located 20km East of Jennette's pier and 40km Northeast of Jennette's pier. The wave resource data provided in this data set is to be used for reference only due the difference in water depth and proximity to shore between the Jennette's pier test site and the locations of the ocean observing buoys. This data is provided in the Summary Data zip folder, which includes this data set in the form of a MATLAB workspace, parquet file, and excel spreadsheet. - Processed Parquet File - The processed data is provided in the form of a single parquet file containing data from all HERO WEC sensors collected during the full deployment. Data in these files has been down sampled to 10 Hz and all array VAPs are included. - Interim Filtered Data - Raw data from each sensor group partitioned into 30-minute parquet files. These files are outputs from an intermediate stage of data processing and contain the raw data with no Quality Control (QC) or calculations performed in a format that is easier to use than the raw data. - Raw Data - Raw, unprocessed data from this deployment can be found in the Raw Data zip folder. This data is provided in the form of TDMS, CSV, and bag files in the original format output by the MODAQ system. - Python Data Processing Script - This links to an NREL public github repository containing the python script used to go from raw data to fully processed parquet files. Additional documentation on how to use this script is included in the github repository. This data set has been developed by the National Renewable Energy Laboratory, operated by Alliance for Sustainable Energy, LLC, for the U.S. Department of Energy (DOE) under Contract No. DE-AC36-08GO28308. Funding provided by the U.S. Department of Energy Office of Energy Efficiency and Renewable Energy Water Power Technologies Office.

16 TIDAL AND WAVE POWER↗

DOE OSTI2022

FTICR-MS Data from Multi-continent River Water and Sediment and from Coastal River Fresh and Saline Sediment Associated with: “Dissolved Organic Matter Functional Trait Relationships are Conserved Across Rivers”

This data package is associated with the publication “Dissolved Organic Matter Functional Trait Relationships are Conserved Across Rivers” submitted to PNAS (Stegen et al., 2023). The study aims to understand large-scale spatial structure of the dissolved organic matter (DOM) thermodynamic traits and inter-trait relationships by investigating (1) river water and sediments collected along 97 rivers spanning 3 continents and (2) coastal sediment collected from fresh and saline locations in Pacific and Gulf/Atlantic rivers. Sediment extracts and water samples were analyzed using ultrahigh resolution Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS). This dataset is comprised of three folders (1) Coastal, (2) WHONDR_S19S, and (3) Data_Dictionaries. Coastal contains (1) a subfolder with processed FTICR-MS data as csv files and sample collection metadata, (2) a subfolder with R scripts used to process the data and create associated figures, (3) a subfolder with the raw, unprocessed FTICR-MS data as .xml files, and (4) a readme file with more information about the dataset and instructions for using Formularity (https://omics.pnl.gov/software/formularity). WHONDRS_S19S contains (1) a csv file with processed FTICR data, (2) a csv with sample collection metadata, (3) a csv with sample geospatial data, (4) a csv with simulated lambda model outputs, (5) a subfolder with R scripts used to process the data and create associated figures, and (6) a readme file with more information regarding WHONDRS raw FTICR data and processing scripts. Data_Dictionaries contains data dictionaries for each csv file in the data package. The 97 global river corridors were part of a WHONDRS (https://whondrs.pnnl.gov) study. The raw, unprocessed FTICR-MS data with additional data can be found at doi:10.15485/1729719 for sediments and doi:10.15485/1603775 for water. This data package contains the processed data used in the associated manuscript. The coastal data has not been previously published, and this data package contains both the raw and processed data. Version 3 of this data package published February 2023 includes updates to the title of the manuscript, additional data and data dictionary and updated scripts linked to new analysis.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2022

Transport and Retention of Particulate Organic Matter in Sand: Lab Experiments and Modelling

Flow-through reactor (FTR) experiments were conducted at three different downward vertical flow rates to study the transport and retention of particulate organic matter (Chlorella powder) in riverbed sediments. This data package includes data files (.csv) regarding effluent collected from the FTRs during the experiments (time, duration, volume of each sample collection; concentration of nonreactive bromide tracer; concentration of suspended Chlorella determined by absorbance measurements) and sediment (sand) slices collected from the FTRs after the experiments (mass of Chlorella retained in 1 cm depth intervals determined by loss-on-ignition method). More detailed descriptions of data are provided in the data dictionary, and detailed methods are available in the associated MSc thesis listed in ‘Related References.’ The data dictionary and file level meta data (FLMD) are included in the data package as both .csv and .xlsx files. This data package also includes timelapse videos (.mp4) of the experiments, and modelling scripts associated with the experiments. The modelling scripts are included as MATLAB ‘live scripts’ (.mlx, which can be run using MATLAB), and are also included as .pdf and .html files with output plots included (which can be viewed without a MATLAB license and installation). The data files and modelling scripts are organized into a .zip folder for each of the three FTR experiments (three flow rates).

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2023

Spatial Study 2022: Water Column, Sediment, and Total Ecosystem Respiration Rates across the Yakima River Basin, Washington, USA (v2)

This dataset supports a broader study examining the drivers of spatial variability in sediment respiration rates in the Yakima River Basin and is associated with the manuscript “Sediment-associated processes account for most of the spatial variation in ecosystem respiration in the Yakima River basin” submitted to Nature Communications Earth & Environment (Garayburu-Caruso et al., in review). The dataset provides ecosystem metabolism estimates generated from streamMetabolizer (Appling et al.; 2018) using data collected during the same five-week period at 48 sites within multiple rivers throughout the Yakima River Basin in Washington, USA. Additionally, it includes the scripts used for the analysis and producing the figures in the manuscript. The contents include streamMetabolizer inputs and outputs and additional relevant data needed to generate the main manuscript results. The data included are: total ecosystem respiration, water respiration, calculated sediment-associated respiration, gross primary production outputs from the river corridor model for the Yakima River Basin, median grain size (d50), depth, dissolved oxygen, water temperature, pressure, and annual oxygen consumption. The associated GitHub repository can be found at https://github.com/river-corridors-sfa/SSS_metabolism. Samples collected during this study were labeled as “Second Spatial Study” or “SSS.” Raw time series sensor data, total suspended solids, and depth data from SSS were published at https://data.ess-dive.lbl.gov/datasets/doi:10.15485/1969566. A subset of data from the SSS samples were published in the contiguous United States (CONUS)-Scale Model-Sample (CM) study data package available at https://data.ess-dive.lbl.gov/view/doi:10.15485/1923689 that presents data from across the CONUS. They include dissolved organic carbon (DOC, measured as non-purgeable organic carbon, NPOC), total nitrogen (TN), grain size, aerobic sediment respiration, dissolved oxygen (DO), and temperature. Parent IDs and Site IDs are consistent between the SSS and CM data packages, and they can be mapped directly so data across packages can be used together. Field metadata for the samples in this da This dataset is comprised of one main data folder with four subfolders. The main data folder contains of (1) file-level metadata; (2) data dictionary; (3) total/water column/sediment respiration; (4) gross primary production (GPP); (5) median grain size (d50); and (6) annual oxygen consumption. The “Figures” subfolder contains the figures used in the paper and all intermediate files (including geospatial files). The “Published_Data” contains a readme directing the user to download the public data to reproduce analyses and figures. The “Scripts” folder contains all scripts used in the analyses that were not part of running StreamMetabolizer. Lastly, the “Stream_Metabolizer” folder contains all files associated with running StreamMetabolizer including (1) model input files, (2) model output files, (3) processing scripts, (4) histogram plots of the outputs, and (5) an R project. All files are .csv, .pdf, .R, .Rmd, .Rproj, .html, .png, .txt, .qgz, .cpg, .dbf, .prj, .shp, .shp.ea.iso.xml, .shp.iso.xml, .shx, .sbn. ta package can be found at either link. We acknowledge the Yakama Nation as owners and caretakers of the lands where we collected these data. We thank the Confederated Tribes and Bands of the Yakama Nation Tribal Council and Yakama Nation Fisheries for working with us to facilitate sample collection and optimization of data usage according to their values and worldview.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2024

Manuscript Workflows from and Processed Organic Matter Composition of Experimentally Burned Open Air and Muffle Furnace Vegetation Chars across Differing Burn Severity and Feedstock Types from Pacific Northwest, USA (v3)

This dataset includes processed organic matter chemistry data from an experimental study designed to compare how the chemical composition of organic matter changes across different burn conditions and vegetation materials representative of major land cover types of the Pacific Northwest, USA. Chars were created in a closed muffle furnace or on an open burn table from four different feedstock species representing vegetation commonly impacted by fire regimes across the Pacific Northwest, USA. Source data and associated metadata (including methods and geospatial information) can be found at https://data.ess-dive.lbl.gov/datasets/doi:10.15485/1894135 (Grieger et al. 2022). This dataset provides processing scripts and processed data for both solid and dissolved phase organic matter characterization data from experimentally generated chars. These processed data can be used to compare how different burn conditions may influence resultant organic matter chemistry and help further our understanding of potential biogeochemical impacts on river corridors post-fire. The processed data were subsequently analyzed; and the results and ecological implications of the findings were published in peer-reviewed manuscripts. The scripts and workflows used to develop the manuscripts are also included in this data package.This data package was originally published June 2024. It was updated September 2024 (new and modified files) and in January 2025 (modified files). See the change history section in the readme for more details.This dataset is comprised of one data package readme, one data dictionary (dd), one file level metadata (flmd), and folders containing (A) processed data; (B) general processing scripts; and (C) additional folders with specific manuscript analysis scripts and processed data. Step-by-step instructions to assist the user in recreating the workflow used to generate the results in the manuscripts is also provided. The processed data folder includes (1) a folder of processed Parallel Factor Analysis (PARAFAC) and spectra indices outputs from excitation emissions matrix (EEM) fluorescence and absorbance data; (2) a folder of processed solid state carbon-13 (13-C NMR) integrals; (3) folder of high resolution characterization of organic matter via 21 Tesla Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) generated through the Environmental Molecular Sciences Laboratory (EMSL; https://www.pnnl.gov/environmental-molecular-sciences-laboratory) processed data outputs from Formultitude (https://github.com/PNNL-Comp-Mass-Spec/Formultitude), blank corrections and data aggregation, and calculated molecular indices. All files are .pdf, .csv, .html, .Rmd, .R, or .RData.

54 ENVIRONMENTAL SCIENCES↗