Hydrodynamic and sediment transport model of San Francisco Bay, California, Nov-Dec 2014

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Frequently anticipated questions:

What does this data set describe?

Title:
Hydrodynamic and sediment transport model of San Francisco Bay, California, Nov-Dec 2014
Abstract:
A three-dimensional hydrodynamic and sediment transport model of San Pablo and Suisun Bays was constructed using the Delft3D4 (D3D) modeling suite (Deltares, 2021a) to simulate water levels, flow, waves, and suspended sediment for time period of Nov 1 to Dec 31, 2014. This data release describes the construction and validation of the model application and provides input files suitable to run the model on D3D software version 4.04.01.
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?
    Allen, Rachel M., and Stevens, Andrew W., 20210608, Hydrodynamic and sediment transport model of San Francisco Bay, California, Nov-Dec 2014: data release DOI:10.5066/P9GLTWS0, 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: -124.2
    East_Bounding_Coordinate: -121.3
    North_Bounding_Coordinate: 38.9
    South_Bounding_Coordinate: 36.3
  3. What does it look like?
    https://www.sciencebase.gov/catalog/file/get/6080aae7d34e8564d683fc0a?name=SPB_D3D_modeldomain.png&allowOpen=true (PNG)
    San Francisco Bay model domain and bathymetry used in (A) the overall model and (B) the nested model. Model boundaries and observation points for data-model comparisons are marked in (B). Vertical datum is NAVD88.
    https://www.sciencebase.gov/catalog/file/get/6080aae7d34e8564d683fc0a?name=SPB_D3D_tidalpropagation.png&allowOpen=true (PNG)
    Comparison of modeled and measured tidal propagation through northern San Francisco Bay. (A) Map of observation locations (NOAA tide gauges) and modeled transect. (B) Amplitudes and (C) phases of modeled (lines) and measured (markers) M2, K1, and O1 tidal constituents from San Francisco Bay mouth into Suisun Bay. Along-transect distances at 20 km intervals are denoted in (A).
    https://www.sciencebase.gov/catalog/file/get/6080aae7d34e8564d683fc0a?name=SPB_D3D_SSC.jpg&allowOpen=true (JPG)
    Suspended sediment concentration in San Pablo Bay, produced using model outputs of nst run 128. The top three figures show timeseries of observations (black) compared with model results (colors) at sites N1T (blue), S1T (red), and M2T(green); locations shown on the bottom. The bottom map image depicts the model outputs from 08:00:00 on 25 Dec 2014, with model sediment concentrations from the height above bed comparable to the measurement heights. The map also shows the location of site CHT (grey).
  4. Does the data set describe conditions during a particular time period?
    Beginning_Date: 01-Nov-2014
    Ending_Date: 31-Dec-2014
    Currentness_Reference:
    ground condition at time data were collected
  5. What is the general form of this data set?
    Geospatial_Data_Presentation_Form: various file types for model input and validation
  6. How does the data set represent geographic features?
    1. How are geographic features stored in the data set?
    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: -124.0
      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 78
      Ordinates (y-coordinates) are specified to the nearest 38
      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:
    Timeseries model inputs and outputs for Delft3D4 model runs in San Pablo Bay, CA, from Nov-Dec 2014.
    Delft3D4 can be obtained from: https://oss.deltares.nl/.
    The information is divided into two folders. The folder SPB_D3D_nst_run128_setup contains the model setup, and the folder SPB_D3D_nst_run128_output contains the model output.
    See Deltares (2020) for descriptions of the formats and entity information for files contained in the setup folders.
    Model output timeseries are reported for approximately 40 observation sites within the model domains at a 15 min time interval for water level, velocity, wind, waves, salinity, sediment transport, and bed level. The files are NEFIS compliant (https://content.oss.deltares.nl/delft3d/manuals/NEFIS_User_Manual.pdf), and can be read with Delft3D4, Matlab, or other software that can read scientific data.
    The model output folder contains two files:
    1) NEFIS definition file (.def)
    2) NEFIS data file (.dat)
    Entity_and_Attribute_Detail_Citation:
    See Deltares (2020) for descriptions of the formats and entity information for files contained in the .zip archive.

Who produced the data set?

  1. Who are the originators of the data set? (may include formal authors, digital compilers, and editors)
    • Rachel M. Allen
    • Andrew W. Stevens
  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 model was constructed to investigate sediment transport and fluxes within San Pablo Bay.

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: 01-Jun-2020 (process 1 of 5)
    A three-dimensional hydrodynamic and sediment transport model of San Pablo and Suisun Bays was constructed using the Delft3D4 (D3D) modeling suite (Deltares, 2021a) to simulate water levels, flow, waves, and suspended sediment for time period of Nov 1 to Dec 31, 2014. The San Pablo and Suisun Bay model was nested within an overall model for San Francisco Bay, also built using D3D. The overall model was modified from the published tide model for San Francisco Bay (Elias and others, 2013). The 2D tide model was extended to 3D with 10 vertical sigma layers (representing 2,3,5,8,13,20,20,20,7, and 2 percent of the total water depth, from near-bed to near-surface). A non-tidal residual based on water-level observations at NOAA site 9414290 (San Francisco) was added to the tidal harmonics of the published model to force the oceanic boundaries. These observations were low-pass filtered with a 66-hr cutoff to remove tidal fluctuations. The overall model was spun up from Jan 1 to Nov 1, 2014, with salinity at the river boundaries of 0 PSU and 33 PSU in the ocean. Wind forcings from the COAMPS model for Northern California (Naval Research Laboratory, 2020) were applied to the overall model, but the wave model (SWAN) was not turned on. Freshwater inputs through the rivers were derived from USGS Stations: the Sacramento River at Freeport (USGS gauge 11447650), the San Joaquin River at Stockton (USGS gauge 11304810), and the San Joaquin River at Vernalis (USGS gauge 11303500). Three sediment types were included in the overall model: mud (ws = 0.2 mm/s, ρ = 2650 kg/m3), flocs (ws = 1 mm/s, ρ = 1300 kg/m3), and sand (D50 = 0.2 mm, ρ = 2650 kg/m3). Sediment availability on the bed was prescribed based on the bathymetry: at depths shallower than 5 m, 1.05 m of mud was available on the bed, 2.55 m of flocs, and 0.05 m of sand. In deeper parts of the system, there was 0.05 m each of mud and flocs, and 1.1 m of sand. Sediment inputs at the rivers were set as constant values: 0.03 kg/ m3 for flocs, 0.02 kg/ m3 for mud, and 0 kg/ m3 for sand. Roughness in the model was prescribed using a Manning’s n value of 0.0225. Following the spin-up period, the overall model was run from Nov 1 to Dec 31, 2014 to prescribe the boundary conditions for the nested model.
    Date: 01-Jun-2020 (process 2 of 5)
    The nested model was forced with Riemann boundary conditions computed from the overall model at the Richmond boundary. At the Sacramento and San Joaquin River boundaries, total discharge was set to that of the overall model. Salinity and sediment concentrations at the Richmond boundary were based on a spatial and temporal interpolation of values in the overall model to the nested grid. Salinity at the Sacramento and San Joaquin River boundaries was set to 0 ppt, and sediment was input as a linear profile with concentrations derived from the overall model. Freshwater was supplied at the Petaluma, Sonoma, and Napa Rivers, using observations of river outflow, Q, from USGS gauges (11459150, 11458500, and 11458000, respectively). Time- and space-varying wind conditions were applied to the nested runs based on COAMPS (see above). Waves were implemented through two-way coupling with the SWAN model (Deltares, 2021b) with Madsen bottom friction, assuming a roughness coefficient of 5 x 10-4 m. Sediment availability on the bed was initialized with a single bed layer. The model was allowed to spin up over 3 months; the evolved bed following this spin up period was used as the initial condition. The initial availability of flocs and sand is shown in the "Sand Fractions" folders of the model inputs.
    Date: 01-Feb-2021 (process 3 of 5)
    The model was calibrated to minimize errors in water levels through the hydrodynamic roughness, using observational data from NOAA stations at San Francisco (station number 9414150), Richmond (9414863), Martinez-Amorco (9415102), and Port Chicago (9415144) (National Oceanic and Atmospheric Administration, 2020), using common tidal constituents (Pawlowicz and others, 2002). Using Manning's n of 0.0225 in the overall model, tidal propagation of the M2, K1, and O1 constituents through the north bay adequately matched the observed values through a 3-month period. Other tidal constituents, including S2 and N2 also followed the observations.
    Date: 01-Feb-2021 (process 4 of 5)
    To evaluate model performance, we compared the observed water depth, velocity, salinity, wave conditions, and suspended sediment concentration at sites N1T, S1T, and M2T (Allen and others, 2019) with modeled values at the same location with the time lag, normalized unbiased root-mean-square-deviation (ubRMSDN), the normalized bias (BiasN), and amplitude ratio. Modeled water levels in the shallows were within 10-20 cm of the measured values. The amplitude ratio for water levels was close to 1 at each site in the shallows, and the time lag between observations and models was under 6 minutes. BiasN and ubRMSDN were both less than 0.5 for each location, indicating excellent performance for water level. Velocities in the east and north directions performed reasonably well between the observations and the model, with BiasN between -0.14 and 0.33, ubRMSDN between -0.52 and 0.33 (with an exception at 0.97, for site M2T in the east direction), and amplitude ratio between 0.68 and 1.34.
    Date: 13-Oct-2021 (process 5 of 5)
    Performed minor edits to the metadata to correct typos. No data were changed Person who carried out this activity:
    U.S. Geological Survey
    Attn: Susan A. Cochran
    Geologist
    2885 Mission Street
    Santa Cruz, CA

    831-460-7545 (voice)
    scochran@usgs.gov
  3. What similar or related data should the user be aware of?
    Elias, Edwin, Hansen, Jeff E., and Erikson, Li H., 2013, San Francisco Bay basic tide model.

    Online Links:

    Other_Citation_Details:
    Elias, E., Hansen, J.E., and Erikson, L.H., 2013, San Francisco Bay basic tide model: U.S. Geological Survey data release, https://doi.org/10.5066/F7DN4330
    Laboratory, Naval Research, 2020, COAMPS real-time forecasts for central and northern California in support of the Central and Northern California Ocean Observing System (CeNCOOS).

    Online Links:

    National Oceanic and Atmospheric Administration, 2020, NOAA Tides and Currents.

    Online Links:

    U.S. Geological Survey, 2018, National Water Information System data available on the World Wide Web (USGS Water Data for the Nation).

    Online Links:

    Allen, Rachel M., Lacy, Jessica R., Stacey, Mark T., and Variano, Evan A., 2019, Seasonal, spring-neap, and tidal variation in cohesive sediment transport parameters in estuarine shallows.

    Online Links:

    Other_Citation_Details:
    Allen, R.M., Lacy, J.R., Stacey, M.T., and Variano, E.A., 2019, Seasonal, spring-neap, and tidal variation in cohesive sediment transport parameters in estuarine shallows: Journal of Geophysical Research--Oceans, v. 124, p. 7265-7284, https://doi.org/10.1029/2018JC014825
    Madsen, Ole S., Poon, Ying-Keung, and Graber, Hans C., 1988, Spectral wave attenuation by bottom friction: Theory.

    Online Links:

    Other_Citation_Details:
    Madsen, O.S., Poon, Y-K, Graber, H.C., 1988, Spectral wave attenuation by bottom friction: Theory: Coastal Engineering Conference Proceedings, v.21, p.34, https://doi.org/10.9753/icce.v21.34
    Deltares, 2021a, 2021, Delft3D-Flow user manual (version 3.15): Deltares, Delft, Netherlands.

    Online Links:

    Deltares, 2021b, 2021, Delft3D-Wave user manual (version 3.05): Deltares, Delft, Netherlands.

    Online Links:

    Pawlowicz, Rich, Beardsley, Bob, and Lentz, Steve, 2002, Classical tidal harmonic analysis including error estimates in MATLAB using T_TIDE.

    Online Links:

    Other_Citation_Details:
    Pawlowicz, R., Beardsley, B., and Lentz, S., 2002, Classical tidal harmonic analysis including error estimates in MATLAB using T_TIDE: Computers and Geosciences, v. 28, p. 929-937, https://doi.org/10.1016/S0098-3004(02)00013-4

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, velocities, wave statistics, salinity, and suspended sediment concentration 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. Users are advised to read the rest of the metadata record carefully for additional details.
  5. How consistent are the relationships among the observations, including topology?
    All data falls 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 input files compatible with windows executable of Delft3D4 version 4.04.01 are provided in the zip archive "SPB_D3D_nst_run128_setup.zip". Browse graphics showing the model bathymetry and validation are also provided along with associated metadata.
  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.
  4. How can I download or order the data?

Who wrote the metadata?

Dates:
Last modified: 13-Oct-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_P9GLTWS0/SPB_D3D_metadata.faq.html>
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