Hydrodynamic model of the San Francisco Bay and Delta, California

Dates

Publication Date: 2021-06-03
Start Date: 2018-10-01
End Date: 2019-04-30

Citation

Tehranirad, B., Nederhoff, K.M., Herdman, L.M., and Erikson, L., 2021, Hydrodynamic model of the San Francisco Bay and Delta, California: U.S. Geological Survey data release, https://doi.org/10.5066/P9WWB9V4.

Summary

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-me [...]

Summary

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 values using Manning’s coefficients.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. The figure below depicts the model extent, location of offshore and discharge boundaries, levees, and NOAA tide stations used for model validation within the model domain.

Figure 1: Map of model extent in the San Francisco Bay and Delta

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. Table 1 lists the USGS discharge stations incorporated in the SFBDHM.

Table 1. List of model discharge boundaries and their corresponding USGS discharge station identification numbers
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_his.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. Table 2 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). Model results are provided in the SFBD_his.nc file.

Table 2. Statistics describing comparisons of observed and simulated water levels from the San Francisco Bay and Delta DFM model for the time period of Oct-2018 to Apr-2019
NOAA Station ID	Station Name	Root Mean Square Error (cm)	Mean Absolute Error (cm)	Bias (cm)
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

References Cited

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: https://water.ca.gov/Library/Modeling-and-Analysis/Bay-Delta-Region-models-and-tools/Delta-Simulation-Model-II, accessed September 14, 2019.

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<0183:EIMOBO>2.0.CO;2.

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, 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, 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: ISPRS Journal of Photogrammetry and Remote Sensing, v. 162, p. 184–199, https://doi.org/10.1016/j.isprsjprs.2020.02.019.

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, https://doi.org/10.1007/s10236-011-0423-6.

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: MDPI Water, v. 12, p. 1–15, https://doi.org/10.3390/w12092481.

Contacts

Point of Contact :: PCMSC Science Data Coordinator
Originator :: Babak (Contractor) Tehranirad, Cornelis M Nederhoff, Liv M Herdman, Li Erikson
Metadata Contact :: PCMSC Science Data Coordinator
Publisher :: U.S. Geological Survey
Distributor :: U.S. Geological Survey - ScienceBase
SDC Data Owner :: Pacific Coastal and Marine Science Center
USGS Mission Area :: Natural Hazards

Attached Files

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SFBD_model_metadata.xml Original FGDC Metadata	View	27.9 KB	application/fgdc+xml
SFBD_model_input_files.zip		115.5 MB	application/zip
SFBD_model_results.zip		18.82 MB	application/zip
SFBD_model_study_area.png “Map of model extent in the San Francisco Bay and Delta”		1.09 MB	image/png

Related External Resources

Type: Related Primary Publication

Nederhoff, K., Saleh, R., Tehranirad, B., Herdman, L., Erikson, L., Barnard, P.L., and van der Wegen, M., 2021, Drivers of extreme water levels in a large, urban, high-energy coastal estuary – A case study of the San Francisco Bay: Coastal Engineering, v. 170, p. 103984, https://doi.org/10.1016/j.coastaleng.2021.103984.	https://doi.org/10.1016/j.coastaleng.2021.103984

Purpose

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.

Hydrodynamic model of the San Francisco Bay and Delta, California

Dates

Citation

Summary