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Model scripts associated with “Revisiting controls on hyporheic respiration with knowledge-guided machine learning at continental scale”

NOTE: The manuscript associated with this data package is currently in review. The data/scripts may be revised based on reviewer feedback. Upon manuscript acceptance, this data package will be updated with the final scripts and additional metadata. This data package is associated with the publication “Revisiting controls on hyporheic respiration with knowledge-guided machine learning at continental scale” submitted to Environmental Science & Technology (Zheng et al. 2026). The project combines mechanistic process modeling with knowledge-guided machine learning (KGML) to evaluate how organic matter chemistry, microbial biomass, and physical substrate accessibility regulate realized respiration rates across river corridors. All data used in this paper have been previously published and can be accessed at https://data.ess-dive.lbl.gov/datasets/doi:10.15485/1729719 (Goldman et al., 2020). This data package contains 3 R-markdown (Rmd) preprocessing scripts for the previously published data and subsequent modelling workflows. The full workflow with input and output data can be found in the associated GitHub repository at https://github.com/jianqiuz/KGML-WHONDRS.

Biogeochemistry↗

Datasets and U-Net Model for "A Deep Learning Based Framework to Identify Undocumented Orphaned Oil and Gas Wells from Historical Maps: a Case Study for California and Oklahoma"

This dataset has results and the model associated with the publication Ciulla et al., (2024). It contains a U-Net semantic segmentation model (unet_model.h5) and associated code implemented in tensorflow 2.0 for the model training and identification of oil and gas well symbols in USGS historical topographic maps (HTMC). Given a quadrangle map (7.5 minutes), downloadable at this url: https://ngmdb.usgs.gov/topoview/, and a list of coordinates of the documented wells present in the area, the model returns the coordinates of oil and gas symbols in the HTMC maps. For reproducibility of our workflow, we provide a sample map in California and the documented well locations for the entire State of California (CalGEM_AllWells_20231128.csv) downloaded from https://www.conservation.ca.gov/calgem/maps/Pages/GISMapping2.aspx. Additionally, the locations of 1,301 potential undocumented orphaned wells identified using our deep learning framework or the counties of Los Angeles and Kern in California, and Osage and Oklahoma in Oklahoma are provided in the file found_potential_UOWs.zip. The results of the visual inspection of satellite imagery in Osage County is in the file visible_potential_UOWs.zip. The dataset also includes a custom tool to validate the detected symbols in the HTMC maps (vetting_tool.py). More details about the methodology can be found in the associated paper: Ciulla, F., Santos, A., Jordan, P., Kneafsey, T., Biraud, S.C., and Varadharajan, C. (2024) A Deep Learning Based Framework to Identify Undocumented Orphaned Oil and Gas Wells from Historical Maps: a Case Study for California and Oklahoma. Accepted for publication in Environmental Science and Technology. The geographical coordinates provided correspond to the locations of potential undocumented orphaned oil and gas wells (UOWs) extracted from historical maps. The actual presence of wells need to be confirmed with on-the-ground investigations. For your safety, do not attempt to visit or investigate these sites without appropriate safety training, proper equipment, and authorization from local authorities. Approaching these well sites without proper personal protective equipment (PPE) may pose significant health and safety risks. Oil and gas wells can emit hazardous gasses including methane, which is flammable, odorless and colorless, as well as hydrogen sulfide, which can be fatal even at low concentrations. Additionally, there may be unstable ground near the wellhead that may collapse around the wellbore. This dataset was prepared as an account of work sponsored by the United States Government. While this document is believed to contain correct information, neither the United States Government nor any agency thereof, nor the Regents of the University of California, nor any of their employees, makes any warranty, express or implied, or assumes any legal 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 its trade name, trademark, manufacturer, or otherwise, does not necessarily constitute or imply its endorsement, recommendation, or favoring by the United States Government or any agency thereof, or the Regents of the University of California. The views and opinions of authors expressed herein do not necessarily state or reflect those of the United States Government or any agency thereof or the Regents of the University of California.

Artificial Intelligence↗

2018 Annual Site Environmental Report

Los Alamos National Laboratory’s (the Laboratory’s) annual site environmental reports are prepared annually by the Laboratory’s environmental organizations, as required by U.S. Department of Energy Order 231.1B, Administrative Change 1, Environment, Safety, and Health Reporting, and Order 458.1, Administrative Change 3, Radiation Protection of the Public and the Environment. The following chapters in this report discuss our success in complying with environmental laws, regulations, and orders (Chapter 2, Compliance Summary); how we manage the Laboratory’s environmental performance (Chapter 3, Environmental Programs); how we monitor for air emissions of radioactive materials and climate conditions (Chapter 4, Air Quality); how we monitor for effects of Laboratory operations on groundwater quality (Chapter 5, Groundwater Monitoring); how we monitor the movement of chemicals and radionuclides by storm water runoff and the levels of chemicals and radionuclides in deposited sediment (Chapter 6, Watershed Quality); how we monitor for the presence, levels, and effects of chemicals and radionuclides in plants, animals, soil, and vegetation (Chapter 7, Ecosystem Health); and finally, what radionuclide dose or risk from chemical exposure members of the public may experience as a result of Laboratory operations (Chapter 8, Public Dose and Risk Assessment). This report follows plain language guidelines, as required for federal agencies by the Plain Language Act of 2010. More information about plain language can be found at http://www.plainlanguage.gov/index.cfm. You will notice we have substantially reduced the use of acronyms and abbreviations and are using active voice and personal pronouns. We hope you find this report useful. If you have suggestions for improving this report, additional questions, or want a copy of this report, please contact us at envoutreach@lanl.gov, or call the Communications Office at 505-665-7000. This report, its supplemental tables, and the 2018 Annual Site Environmental Report Summary are available at http://www.lanl.gov/environment/environmental-report.php. Note: This document has been revised since it was initially published on September 23, 2019. The revisions included corrections to figure and table references, changes in heading levels, adding blank pages where appropriate, and changes of an editorial nature.

54 ENVIRONMENTAL SCIENCES↗

Long-Term Monitoring & Stewardship at Los Alamos National Laboratory [Slides]

Development and implementation of the Institutional Control Evaluation Project will include: Evaluate institutional surface water controls and infrastructure installed by LANL. Implement pilot project in the Los Alamos Canyon Watershed Spring, 2020. Initial evaluations will include canyon bottom controls with plan to expand program as funding allows. This will be a building block for successful Long-Term Monitoring and Stewardship (LTM&S) Program.

54 ENVIRONMENTAL SCIENCES↗

Meteorological Tower Network Expansion Pilot Project Siting Considerations to Ensure Data Quality and Representativeness of Three New Meteorological Towers at Los Alamos National Laboratory

Associated with the Meteorological Tower Network Expansion Pilot Project by the Environmental Protection and Compliance (EPC) Compliance Programs (CP) Meteorology and Air Quality (MAQ) team, the purpose of this technical report is to establish requisite justification for the siting of three 10-meter high instrumented meteorological towers at three new locations on the Los Alamos National Laboratory (LANL) site. These towers and their associated instrumentation are similar in scope to the existing 10-meter meteorological tower that is collecting meteorological data in Mortandad Canyon (MDCN). The conclusions and recommendations in this technical report will inform LANL management, EPC-CP MAQ staff, and other LANL divisions of the criteria employed for the selection of the final location for siting these three new towers. Meeting such comprehensive criteria will ensure that all data acquired will be spatially representative for meeting the diverse Safety Basis (SB), emergency management, and operations organizations programmatic needs and analytical data input requirements to its codes.

54 ENVIRONMENTAL SCIENCES↗

Storm Water Pollution Prevention Plan Middle DP Road Recovery Effort, June 26, 2020

The United States Environmental Protection Agency (EPA) has issued a final 2017 Construction General Permit (CGP) that covers discharges of stormwater from construction sites. The 2017 National Pollutant Discharge Elimination System (NPDES) General Permit for Storm Water Discharges from Construction Activity (Appendix D) includes the following requirements:(1) conduct a critical habitat and threatened/endangered species study; (2) develop and implement a Storm Water Pollution Prevention Plan (SWPPP) in accordance with good engineering practices; (3) submit a Notice of Intent (NOI); (4) install and maintain erosion and stormwater controls; (5) perform and document storm water inspections during construction and site stabilization; (6) amend the SWPPP as necessary; and (7) submit a Notice of Termination (NOT) following project completion and final stabilization of disturbed areas. Authorization to discharge storm water is required under this Permit for both large and small construction projects disturbing more than one (1) acre or part of a larger common plan of development that collectively disturbs more than one (1) acre. All parties that meet the definition of Operator must be permitted. Each permittee is not required to develop and implement a separate SWPP Plan. It is required that there be at least one SWPP Plan for a site that incorporates the required elements for all Operators. The 2017 CGP number for New Mexico (Region 6) is NMR100000. This Plan, which has been developed for Triad National Security, LLC (Triad), describes the nature and sequencing of construction activities, potential sources of pollution, and identifies the Best Management Practices (BMPs) to minimize the potential for erosion and storm water pollution. The Plan was developed in accordance with the provisions of the Clean Water Act (33 U.S.C. § §1251 et seq., as amended by the Water Quality Act of 1987, P.L. 100-4), and the regulations established by the U.S. Environmental Protection Agency (EPA) for National Pollutant Discharge Elimination System (NPDES) General Permits for Storm Water Discharges From Construction Activities.

54 ENVIRONMENTAL SCIENCES↗

Storm Water Pollution Prevention Plan Middle DP Road Recovery Effort, June 26, 2020 (Copy for Informational Puproses Only)

The United States Environmental Protection Agency (EPA) has issued a final 2017 Construction General Permit (CGP) that covers discharges of stormwater from construction sites. The 2017 National Pollutant Discharge Elimination System (NPDES) General Permit for Storm Water Discharges from Construction Activity (Appendix D) includes the following requirements: (1) conduct a critical habitat and threatened/endangered species study; (2) develop and implement a Storm Water Pollution Prevention Plan (SWPPP) in accordance with good engineering practices; (3) submit a Notice of Intent (NOI); (4) install and maintain erosion and stormwater controls; (5) perform and document storm water inspections during construction and site stabilization; (6) amend the SWPPP as necessary; and (7) submit a Notice of Termination (NOT) following project completion and final stabilization of disturbed areas. Authorization to discharge storm water is required under this Permit for both large and small construction projects disturbing more than one (1) acre or part of a larger common plan of development that collectively disturbs more than one (1) acre. All parties that meet the definition of Operator must be permitted. Each permittee is not required to develop and implement a separate SWPP Plan. It is required that there be at least one SWPP Plan for a site that incorporates the required elements for all Operators. The 2017 CGP number for New Mexico (Region 6) is NMR100000. This Plan, which has been developed for Triad National Security, LLC (Triad), describes the nature and sequencing of construction activities, potential sources of pollution, and identifies the Best Management Practices (BMPs) to minimize the potential for erosion and storm water pollution. The Plan was developed in accordance with the provisions of the Clean Water Act (33 U.S.C. § §1251 et seq., as amended by the Water Quality Act of 1987, P.L. 100-4), and the regulations established by the U.S. Environmental Protection Agency (EPA) for National Pollutant Discharge Elimination System (NPDES) General Permits for Storm Water Discharges From Construction Activities.

54 ENVIRONMENTAL SCIENCES↗

Hydraulic Testing of the Lost Lake Aquifer Near Recovery Well RWM019

An aquifer pumping test was conducted on the Lost Lake Aquifer Zone (LLAZ) at the recently installed recovery well RWM019 in accordance with the approved test plan (Dixon, 2020). The objective of the testing was to determine baseline well performance parameters and aquifer hydraulic conductivity. This testing consisted of a step-drawdown test to determine well performance properties, a constant pumping rate aquifer test to determine aquifer hydraulic properties, and a post-test aquifer recovery monitoring period also used to estimate aquifer hydraulic properties. Well performance parameters determined included specific capacity, well efficiency, and head loss coefficients. The specific capacity of RWM019 was determined to be approximately 2.6 gpm/ft of drawdown based on the final step of the step-drawdown test. Well efficiency was inversely related to pumping rate and decreased from 87% to 81% over a pumping range of approximately 49 to 79 gpm. The aquifer head loss coefficient was determined to be 2.3 ft/ft 3 /min and the well loss coefficient was determined to be 0.05 min 2 /ft 5 .

42 ENGINEERING↗

Environmental Effects Assessment for Proposed Offshore Wind Farm off the Coast of Grays Harbor, Washington

Grays Harbor Wind LLC (GHW) is proposing to develop a floating offshore wind farm offshore of west Grays Harbor County, Washington (Grays Harbor). The proposed GHW Offshore Wind Project (Project) would entail construction, installation and operation of a 1,000-megawatt (MW) offshore wind farm consisting of approximately 75 floating units, each containing a floating foundation and wind turbine generator (WTG). The Project location is approximately 25 miles (21.7 nautical miles [nmi]) offshore west of Grays Harbor, at waters depths of 360 to 700 feet. The Pacific Northwest National Laboratory (PNNL) was contracted by Herrera Environmental Consultants, Inc. on behalf of GHW to carry out this preliminary scoping study to evaluate baseline conditions and potential effects on fish and marine mammals from development and operation of a floating offshore wind farm installed within a designated area off the coast of Washington1. Floating offshore wind units installed in an ocean environment as part of the Project would interact with marine wildlife. This Study report provides an initial data aggregation and analysis, using publicly available data, of the Project effects, both negative and positive, on the marine environment. The scope of this assessment is limited by the fact that the Project development is presently at the conceptual level. Data on marine organisms were aggregated and evaluated; however seabirds were evaluated by Herrera Environmental Consulting and, along with bats, were not included in the scope of this study. Significant additional work is necessary to characterize ocean, seafloor, and environmental conditions; select appropriate floating offshore wind technologies; identify construction methods and locations; and assess facility locations, including electrical interconnection. Data aggregation and analysis of seabirds and bats is also needed. Evaluation of the full range of potential environmental effects would be conducted following an award of a lease from the Bureau of Ocean Energy Management (BOEM) as part of the leasing, National Environmental Policy Act (NEPA)/State Environmental Policy Act (SEPA) environmental review and permitting processes. While this initial data aggregation and analysis uses best available public scientific information and current assumptions about the Project configuration, the effects discussed herein are based on the status of review to-date and may change as Project-specific details are developed.

17 WIND ENERGY↗

Wetland Delineation Report for Middle Mortandad Mesa Adjacent to Technical Area 55 at Los Alamos National Laboratory

This report provides the results of a wetland delineation conducted to support operational logistics for construction of a high-pressure water line that is planned to occur near a wetland at Los Alamos National Laboratory (LANL). The wetland reach is on the mesa edge in Technical Area (TA)-55 above the Mortandad Canyon watershed. This area has not been previously delineated; however, it drains to a canyon bottom where LANL updated a delineation in 2017 for the wetland adjacent to Technical Areas (TAs) 25, 48, and 55.

54 ENVIRONMENTAL SCIENCES↗

Planning is Key for Storm Water Regulatory Compliance [Slides]

Most construction projects at LANL are subject to a EPA regulated storm water discharge permit (NPDES Construction General Permit). Each identified non-compliance is a regulatory liability to both the subcontractor & Triad.

54 ENVIRONMENTAL SCIENCES↗

Los Alamos National Laboratory Floodplain Assessment for the High Explosive Transfer Facility Blast Radius Fence Project at Technical Area 08

The National Nuclear Security Administration (NNSA), a semi-autonomous agency within the U.S. Department of Energy (DOE), is proposing to take action at Los Alamos National Laboratory (LANL) within the upper Pajarito Canyon 100-year (yr.) floodplain at Technical Area (TA) 08. This action consists of installation of a 3-strand smooth wire fence to create an operational boundary in a radius of 1250 feet (ft.) from the TA-08 High Explosive (HE) Transfer Facility (Figure 1). The proposed fence is intended to provide a barrier between the public and direct access to the HE Transfer Facility.

54 ENVIRONMENTAL SCIENCES↗

TA-60-2 Warehouse Asset Tree and Supporting Information

The purpose of the document is to show an example of a Multi-Sector General Permit environmental compliance program inspection structure to new software provider (new provider is under contract w/ LANL) to begin setting up new database.

54 ENVIRONMENTAL SCIENCES↗

LANL Meteorological Program: 2020 Data Completeness/Quality Report

Los Alamos National Laboratory (LANL) operates four mesa-top meteorology towers: Technical Area (TA) 06, TA-49, TA-53, and TA-54. An additional tower is located in Mortandad Canyon (TA-5 MDCN), and a rain gauge at North Community (NCOM). A description of the meteorology monitoring network is found in Dewart and Boggs (2014). Mesa-top towers are instrumented at 1.2 meters (m), 11.5 m, 23 m, and 46 m. In addition, TA-06 is instrumented at 92 m. The TA-5 MDCN tower is 10 m in height and is instrumented at 1.2 m and 10 m. Data are collected every 15 minutes. Range checking is done on each measurement every 15 minutes; data that are beyond normal ranges are eliminated from the data set and replaced by a code for missing data. In addition, data are reviewed weekly by meteorologists to identify bad data not identified by range checking. The data steward eliminates these data from the data set and replaces them with a code for missing data. The instrument technicians also review that data and schedule instrument replacement as required. Data completeness is determined by the number of total 15-minute records available versus the total number of possible measurements for the entire year. As a rule, the meteorologists do not attempt to estimate data that are eliminated as bad data. Original datalogger records, containing bad data, can be recalled from program archival storage.

54 ENVIRONMENTAL SCIENCES↗