Hydrodynamic model of the San Francisco Bay and Delta, California

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What does this data set describe?

Title:
Hydrodynamic model of the San Francisco Bay and Delta, California
Abstract:
A one- and two-dimensional hydrodynamic model of the San Francisco Bay and Delta was constructed using the Delft3D Flexible Mesh Suite (Delft3D FM; Kernkamp and others, 2011; https://www.deltares.nl/en/software/delft3d-flexible-mesh-suite/) to simulate still water levels. Required model input files are provided to run the model for the time period from October 1, 2018, to April 30, 2019. This data release describes the construction and validation of the model application and provides input files suitable to run the model on Delft3D FM Suite 2020.04.
Model Description: The San Francisco Bay and Delta Still Water Level Model (SFBD-SWL) utilizes the open-source Delft3D Flexible Mesh Suite (Delft3D FM; Kernkamp and others, 2011; https://www.deltares.nl/en/software/delft3d-flexible-mesh-suite/, 2020.04 release, SVN revision 601351) to compute Still Water Levels (SWLs) in San Francisco Bay and the Sacramento-San Joaquin Delta. SWL captures the effects of meteorological and fluvial forcing on the coastal water levels; however, it excludes the impacts of wave setup and runup on the water level. The model covers the Delta up to the approximate upstream limit of tidal influence and extends seaward to the Pacific Ocean. It must be noted that the main purpose of the model was to simulate SWL in open embayments of the San Francisco Bay. The model utilizes 1D elements used to represent tributaries and rivers flowing into the Bay and Delta. Model schematizations of the Delta (model grid and cross-section profiles) were derived from Delta Simulation Model II (DSM2, California Department of Water Resources, 2013).
Topographic and bathymetric datasets from the USGS and California Department of Water Resources were applied across the San Francisco Bay and Delta Hydrodynamic model. In particular, the 2-meter resolution LEAN-corrected topography in the Bay (Buffington and others, 2016) and the seamless 10-meter resolution digital elevation model by Fregoso and others (2017) were applied. Data from the National Land Cover Database Land Cover (CONUS; Homer and others, 2020) were converted to roughness. The unstructured grid consists of more than 185,000 net nodes in the horizontal with a spatial resolution as fine as 100 meters. The 100-meter resolution model network is not fine enough to resolve smaller features such as narrow levees and dams. Therefore, an additional polyline has been included to account for constraining and rerouting effects of local levees and infrastructure. This file provides the location of each subgrid feature and, in combination with the latest topography, describes fine-scale elevations for the hydrodynamic simulations. The model is forced by astronomic tides and remote non-tidal residual (NTR) water levels at the offshore boundaries, fluvial discharges, and wind and atmospheric mean sea level pressure fields at the surface.
Offshore Boundaries The model's offshore boundary conditions in the Pacific Ocean are based on 67 measured tidal constituents at San Francisco with spatial variability derived from TPXO 8.0 (Egbert and Erofeeva, 2002). Tidal constituents were calibrated based on the difference between modeled and observed tidal constituents at the NOAA tide stations located throughout the bay. Remote NTR derived from measurements at the San Francisco NOAA tide station (#9414290) are applied uniformly across the ocean boundary. The tidal forcing files are included in the model package, as well as the NTR offshore boundary forcing files for the time period from Oct-2018 to Apr-2019.
Discharge Boundaries Fluvial discharges from 16 USGS gauged rivers that flow into the Bay are included in the model (https://waterdata.usgs.gov/nwis/dv/?referred_module=sw). Six fluvial inflows to the Delta are based on Dayflow model outputs (https://data.ca.gov/dataset/dayflow). The discharge forcing files for the time period from Oct-2018 to Apr-2019 are included in the model package. The discharge stations incorporated in the SFBD-SWL are as follows (Name, USGS Station Number):
Coyote Creek, 11172175 
Guadalupe River, 11169025 
Saratoga Creek, 11169500 
San Francisquito Creek, 11164500 
San Mateo Creek, 11162753 
Corte Madera Creek, 11460000 
San Rafael Creek, 11459800 
Novato Creek, 11459500 
Petaluma River, 11459150 
Sonoma Creek, 11458500 
Napa River, 11458000 
Wildcat Creek, 11181400 
San Lorenzo Creek #1, 11181000 
San Lorenzo Creek #2, 11181008 
Alameda Creek #1, 11180500 
Alameda Creek #2, 11179000 
Wind and Atmospheric Pressure Meteorological forcing conditions (wind and pressure) provided in this example dataset are based on ERA5 (Hersbach and others, 2020). ERA5 provides hourly estimates of a large number of atmospheric, land, and oceanic climate variables at 30-kilometer resolution. The ERA5 wind and pressure data for the time period from Oct-2018 to Apr-2019 is provided in the model package.
Model Validation Measured and simulated water levels for the time period of Oct-2018 to Apr-2019 are provided in SFBD_model_results.zip. Measured water levels (referenced to the vertical datum NAVD88) were obtained from the NOAA tide stations (https://tidesandcurrents.noaa.gov/) within San Francisco Bay. The following list contains the measurement stations and model error statistics during the simulation period of Oct-2018 to Apr-2019 (NOAA Station ID, Station Name, Root Mean Square Error in cm, Mean Absolute Error in cm, Bias in cm). Root-mean-square errors (RMSE) are less than 10 cm for water levels at all observation sites (tide gauges).
9414290, San Francisco, 5.2, 4.0, 0.7 
9414750, Alameda, 6.6, 5.0, 2.4 
9414863, Richmond, 5.4, 4.1, 0.0 
9414523, Redwood City, 7.4, 5.3, -2.0 
9415144, Port Chicago, 7.0, 5.2, -3.0 
9415102, Martinez, 6.5, 5.0, 1.2
Supplemental_Information:
Any use of trade, product, or firm names is for descriptive purposes only and does not imply endorsement by the U.S. Government.
  1. How might this data set be cited?
    Tehranirad, Babak, Nederhoff, Kees M, Herdman, Liv M, and Erikson, Li, 20210603, Hydrodynamic model of the San Francisco Bay and Delta, California: data release DOI:10.5066/P9WWB9V4, U.S. Geological Survey, Pacific Coastal and Marine Science Center, Santa Cruz, California.

    Online Links:

  2. What geographic area does the data set cover?
    West_Bounding_Coordinate: -123.5330200
    East_Bounding_Coordinate: -121.2973022
    North_Bounding_Coordinate: 38.61223644
    South_Bounding_Coordinate: 37.06359516
  3. What does it look like?
    https://www.sciencebase.gov/catalog/file/get/604675c6d34eb120311a42cb?name=SFBD_model_study_area.png&allowOpen=true (PNG)
    Map of model extent in the San Francisco Bay and Delta
  4. Does the data set describe conditions during a particular time period?
    Beginning_Date: 01-Oct-2018
    Ending_Date: 30-Apr-2019
    Currentness_Reference:
    time period for which the data were modeled
  5. What is the general form of this data set?
    Geospatial_Data_Presentation_Form: model
  6. How does the data set represent geographic features?
    1. How are geographic features stored in the data set?
      This is a Point data set. It contains the following vector data types (SDTS terminology):
      • Point (84)
    2. What coordinate system is used to represent geographic features?
      Grid_Coordinate_System_Name: Universal Transverse Mercator
      Universal_Transverse_Mercator:
      UTM_Zone_Number: 10
      Transverse_Mercator:
      Scale_Factor_at_Central_Meridian: 0.9996
      Longitude_of_Central_Meridian: -123.0
      Latitude_of_Projection_Origin: 0.0
      False_Easting: 500000.0
      False_Northing: 0.0
      Planar coordinates are encoded using row and column
      Abscissae (x-coordinates) are specified to the nearest 115
      Ordinates (y-coordinates) are specified to the nearest 75
      Planar coordinates are specified in Meter
      The horizontal datum used is North American Datum of 1983.
      The ellipsoid used is GRS_1980.
      The semi-major axis of the ellipsoid used is 6378137.0.
      The flattening of the ellipsoid used is 1/298.257222101.
      Vertical_Coordinate_System_Definition:
      Altitude_System_Definition:
      Altitude_Datum_Name: North American Vertical Datum of 1988
      Altitude_Resolution: 0.01
      Altitude_Distance_Units: meters
      Altitude_Encoding_Method:
      Explicit elevation coordinate included with horizontal coordinates
  7. How does the data set describe geographic features?
    Entity_and_Attribute_Overview:
    SFBD_model_input_files.zip archive contains files of various types and formats. SFBD_model_results.zip contains one file (SFBD_his.nc).
    Entity_and_Attribute_Detail_Citation:
    See Deltares (2020) for descriptions of the formats and entity information for files contained in the .zip archives.

Who produced the data set?

  1. Who are the originators of the data set? (may include formal authors, digital compilers, and editors)
    • Babak Tehranirad
    • Kees M Nederhoff
    • Liv M Herdman
    • Li Erikson
  2. Who also contributed to the data set?
  3. To whom should users address questions about the data?
    PCMSC Science Data Coordinator
    U.S. Geological Survey, Pacific Coastal and Marine Science Center
    2885 Mission Street
    Santa Cruz, CA

    831-427-4747 (voice)
    pcmsc_data@usgs.gov

Why was the data set created?

The purpose of this data release is to provide researchers, engineers, and other potential users the Delft3D Flexible Mesh hydrodynamics model of the San Francisco Bay and Delta. This model was developed through collaborative work between USGS, Deltares USA, and Alameda County Flood Control District. The model can be used to simulate water levels throughout the open embayments within San Francisco Bay. Whereas this data release does not intend to provide comprehensive meteorological, fluvial, and oceanic input data from outside sources, nor does the use of those products imply endorsement by the U.S. Government, those files are provided herein to serve as examples of required file formats.

How was the data set created?

  1. From what previous works were the data drawn?
  2. How were the data generated, processed, and modified?
    Date: 15-Feb-2021 (process 1 of 2)
    Users should read the Abstract section of the metadata carefully to understand model inputs, boundary conditions, and parameters of the model. Simulated water levels and discharges were compared against time-series measurements of observed water levels from locations throughout the study area. Total root-mean-square error (RMSE) was less than 10 cm for water levels at all of the measurement sites.
    Date: 29-Jun-2021 (process 2 of 2)
    Edits made to Abstract section of metadata to parallel text used in upcoming manuscript. Additional citation for new text added to Cross_Reference section. No data were changed.
  3. What similar or related data should the user be aware of?
    Kernkamp, H.W.J., Van Dam, A., Stelling, G.S., and De Goede, E.D., 2011, Efficient scheme for the shallow water equations on unstructured grids with application to the Continental Shelf: Ocean Dynamics, Springer Nature, Switzerland.

    Online Links:

    Other_Citation_Details:
    Kernkamp, H.W.J., Van Dam, A., Stelling, G.S., and De Goede, E.D., 2011, Efficient scheme for the shallow water equations on unstructured grids with application to the Continental Shelf: Ocean Dynamics, v. 61, p. 1175-1188
    Buffington, Kevin J., Dugger, Bruce D., Thorne, Karen M., and Takekawa, John Y., 2016, Statistical correction of lidar-derived digital elevation models with multispectral airborne imagery in tidal marshes: Remote Sensing of Environment, Amsterdam, Netherlands.

    Online Links:

    Other_Citation_Details:
    Buffington, K.J., Dugger, B.D., Thorne, K.M., and Takekawa, J.Y., 2016, Statistical correction of lidar-derived digital elevation models with multispectral airborne imagery in tidal marshes: Remote Sensing of Environment, v. 186, p. 616-625, https://doi.org/10.1016/j.rse.2016.09.020.
    California Department of Water Resources, 2013, DSM2: Delta Simulation Model II: California Department of Water Resources, Sacramento, California.

    Online Links:

    Other_Citation_Details:
    California Department of Water Resources, 2013, DSM2: Delta Simulation Model II: https://water.ca.gov/Library/Modeling-and-Analysis/Bay-Delta-Region-models-and-tools/Delta-Simulation-Model-II, accessed September 14, 2019.
    Egbert, Gary D., and Erofeeva., Svetlana Y., 2002, Efficient inverse modeling of barotropic ocean tides: Journal of Atmospheric and Oceanic Technology, Boston, Massachusetts.

    Online Links:

    Other_Citation_Details:
    Egbert, G.D., and Erofeeva, S.Y., 2002, Efficient inverse modeling of barotropic ocean tides: Journal of Atmospheric and Oceanic Technology, v. 19, p. 183-204, https://doi.org/10.1175/1520-0426(2002)019
    Fregoso, Theresa A., Wang, Rueen-Fang, Ateljevich, Eli, and Jaffe, Bruce E., 2017, A new seamless, high-resolution digital elevation model of the San Francisco Bay-Delta Estuary, California: U.S. Geological Survey, Reston, Virginia.

    Online Links:

    Other_Citation_Details:
    Fregoso, T., Wang, R.-F., Ateljevich, E., and Jaffe, B.E., 2017, A new seamless, high-resolution digital elevation model of the San Francisco Bay-Delta Estuary, California: U.S. Geological Survey Open-File Report 2017–1067, 27 p., https://doi.org/10.3133/ofr20171067.
    Hersbach, Hans, Bell, Bill, Berrisford, Paul, Hirahara, Shoji, Horányi, András, Muñoz-Sabater, Joaquín, Nicolas, Julien, Peubey, Carole, Radu, Raluca, Schepers, Dinand, Simmons, Adrian, Soci, Cornel, Abdalla, Saleh, Abellan, Xavier, Balsamo, Gianpaolo, Bechtold, Peter, Biavati, Gionata, Bidlot, Jean, Bonavita, Massimo, Chiara, Giovanna De, Dahlgren, Per, Dee, Dick, Diamantakis, Michail, Dragani, Rossana, Flemming, Johannes, Forbes, Richard, Fuentes, Manuel, Geer, Alan, Haimberger, Leo, Healy, Sean, Hogan, Robin J., Hólm, Elías, Janisková, Marta, Keeley, Sarah, Laloyaux, Patrick, Lopez, Philippe, Lupu, Cristina, Radnoti, Gabor, Rosnay, Patricia de, Rozum, Iryna, Vamborg, Freja, Villaume, Sebastien, and Thépaut, Jean-Noël, 2020, The ERA5 global reanalysis: Quarterly Journal of the Royal Meteorological Society, Hoboken, New Jersey.

    Online Links:

    Other_Citation_Details:
    Hersbach, H., Bell, B., Berrisford, P., Hirahara, S., Horányi, A., Muñoz-Sabater, J., Nicolas, J., Peubey, C., Radu, R., Schepers, D., Simmons, A., Soci, C., Abdalla, S., Abellan, X., Balsamo, G., Bechtold, P., Biavati, G., Bidlot, J., Bonavita, M., De Chiara, G., Dahlgren, P., Dee, D., Diamantakis, M., Dragani, R., Flemming, J., Forbes, R., Fuentes, M., Geer, A., Haimberger, L., Healy, S., Hogan, R.J., Hólm, E., Janisková, M., Keeley, S., Laloyaux, P., Lopez, P., Lupu, C., Radnoti, G., de Rosnay, P., Rozum, I., Vamborg, F., Villaume, S., and Thépaut, J.N., 2020, The ERA5 global reanalysis: Quarterly Journal of the Royal Meteorological Society, v. 146, p. 1999-2049, https://doi.org/10.1002/qj.3803.
    Homer, Collin, Dewitz, Jon, Jin, Suming, Xian, George, Costello, Catherine, Danielson, Patrick, Gass, Leila, Funk, Michelle, Wickham, James, Stehman, Stephen, Auch, Roger, and Riitters, Kurt, 2020, Conterminous United States land cover change patterns 2001–2016 from the 2016 national land cover database: ISPRS Journal of Photogrammetry and Remote Sensing, Amsterdam, Netherlands.

    Online Links:

    Other_Citation_Details:
    Homer, C., Dewitz, J., Jin, S., Xian, G., Costello, C., Danielson, P., Gass, L., Funk, M., Wickham, J., Stehman, S., Auch, R., and Riitters, K., 2020, Conterminous United States land cover change patterns 2001–2016 from the 2016 National Land Cover Database: Journal of Photogrammetry and Remote Sensing, v. 162, p. 184–199, https://doi.org/10.1016/j.isprsjprs.2020.02.019.
    Tehranirad, Babak, Herdman, Liv, Nederhoff, Kees, Erikson, Li, Cifelli, Robert, Pratt, Greg, Leon, Michael, and Barnard, Patrick, 2020, Effect of Fluvial Discharges and Remote Non-Tidal Residuals on Compound Flood Forecasting in San Francisco Bay: Water, Basel, Switzerland.

    Online Links:

    Other_Citation_Details:
    Tehranirad, B., Herdman, L., Nederhoff, K., Erikson, L., Cifelli, R., Pratt, G., Leon, M., and Barnard, P., 2020, Effect of fluvial discharges and remote non-tidal residuals on compound flood forecasting in San Francisco Bay: Water, v. 12, p. 1–15, https://doi.org/10.3390/w12092481.

How reliable are the data; what problems remain in the data set?

  1. How well have the observations been checked?
    Model outputs were compared to observed water levels in San Francisco Bay to assess the accuracy of simulated results as described in the process steps below.
  2. How accurate are the geographic locations?
    No formal positional accuracy tests were conducted.
  3. How accurate are the heights or depths?
    No formal positional accuracy tests were conducted.
  4. Where are the gaps in the data? What is missing?
    Dataset is considered complete for the information presented, as described in the abstract.
  5. How consistent are the relationships among the observations, including topology?
    All data fall within expected ranges.

How can someone get a copy of the data set?

Are there legal restrictions on access or use of the data?
Access_Constraints: none
Use_Constraints:
USGS-authored or produced data and information are in the public domain from the U.S. Government and are freely redistributable with proper metadata and source attribution. Please recognize and acknowledge the U.S. Geological Survey as the originator(s) of the dataset and in products derived from these data. This information is not intended for navigational purposes.
  1. Who distributes the data set? (Distributor 1 of 1)
    U.S. Geological Survey - Science Base
    U.S. Geological Survey
    Denver Federal Center, Building 810, Mail Stop 302
    Denver, CO
    USA

    1-888-275-8747 (voice)
    sciencebase@usgs.gov
  2. What's the catalog number I need to order this data set? Model files compatible with windows executable of Delft3D Flexible Mesh version 2021.04 are provided in the zip archive "SFBD_model_input_files.zip".
  3. What legal disclaimers am I supposed to read?
    Unless otherwise stated, all data, metadata and related materials are considered to satisfy the quality standards relative to the purpose for which the data were collected. Although these data and associated metadata have been reviewed for accuracy and completeness and approved for release by the U.S. Geological Survey (USGS), no warranty expressed or implied is made regarding the display or utility of the data on any other system or for general or scientific purposes, nor shall the act of distribution constitute any such warranty. The SFBD-SWL model has been approved for release by the U.S. Geological Survey (USGS). Although the model and accompanying software has been subjected to rigorous review, the USGS reserves the right to update the model as needed pursuant to further analysis and review. No warranty, expressed or implied, is made by the USGS or the U.S. Government as to the functionality of the software and related material nor shall the fact of release constitute any such warranty. Furthermore, the model is released on condition that neither the USGS nor the U.S. Government shall be held liable for any damages resulting from its authorized or unauthorized use.
  4. How can I download or order the data?

Who wrote the metadata?

Dates:
Last modified: 29-Jun-2021
Metadata author:
PCMSC Science Data Coordinator
U.S. Geological Survey, Pacific Coastal and Marine Science Center
2885 Mission St.
Santa Cruz, CA

831-427-4747 (voice)
pcmsc_data@usgs.gov
Metadata standard:
Content Standard for Digital Geospatial Metadata (FGDC-STD-001-1998)

This page is <https://cmgds.marine.usgs.gov/catalog/pcmsc/DataReleases/ScienceBase/DR_P9WWB9V4/SFBD_model_metadata.faq.html>
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