Hydrodynamic and sediment transport model of the mouth of the Columbia River, Washington and Oregon, 2020-2021

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Frequently anticipated questions:

What does this data set describe?

Title:
Hydrodynamic and sediment transport model of the mouth of the Columbia River, Washington and Oregon, 2020-2021
Abstract:
A three-dimensional hydrodynamic and sediment transport model application of the mouth of the Columbia River (MCR) was constructed using the Delft3D4 (D3D) modeling suite (Deltares, 2021) to simulate water levels, flow, waves, and sediment transport for time period of September 22, 2020, to March 10, 2021. The model was used to predict the dispersal of sediment from a submerged, nearshore berm composed of sediment that was dredged from the entrance to the MCR navigation channel and placed on the northern flank of the ebb-tidal delta. This data release describes the development and validation of the model application and provides input files suitable to run the models on D3D software version 4.04.01. These data accompany Stevens and others (2023).
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?
    Stevens, Andrew W., 20230124, Hydrodynamic and sediment transport model of the mouth of the Columbia River, Washington and Oregon, 2020-2021: data release DOI:10.5066/P9RVK9S9, U.S. Geological Survey, Pacific Coastal and Marine Science Center, Santa Cruz, California.

    Online Links:

    This is part of the following larger work.

    Stevens, Andrew W., Moritz, Hans R., and McMillan, James M., 2023, Bathymetry data and sediment transport modeling of a submerged nearshore berm at the mouth of the Columbia River, Oregon and Washington, 2020-2021: data release DOI:10.5066/P9RVK9S9, U.S. Geological Survey, Pacific Coastal and Marine Science Center, Santa Cruz, CA.

    Online Links:

  2. What geographic area does the data set cover?
    West_Bounding_Coordinate: -126.167549
    East_Bounding_Coordinate: -123.183540
    North_Bounding_Coordinate: 47.734695
    South_Bounding_Coordinate: 45.345337
  3. What does it look like?
    https://www.sciencebase.gov/catalog/file/get/6227fd2bd34ee0c6b38b80da?name=mcr_model_grids.png&allowOpen=true (PNG)
    Maps of Delft3D model including A, extents of Delft3D flow overall, detailed, and wave domains, and B, computational grid of the detailed model (reduced by a factor of 3 for display).
  4. Does the data set describe conditions during a particular time period?
    Beginning_Date: 22-Sep-2020
    Ending_Date: 10-Mar-2021
    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
  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 140
      Ordinates (y-coordinates) are specified to the nearest 246
      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:
    Model inputs for Delft3D4 model of the mouth of the Columbia River.
    Delft3D4 can be obtained from: https://oss.deltares.nl/
    The input files are divided into two .zip archives. The .zip file, "mcr_overall_model" contains the model setup of the overall model, and the folder "mcr_detail_model" contains the model setup of the detailed model.
    See Deltares (2021) for descriptions of the formats and entity information for files contained in the setup folders.
    Entity_and_Attribute_Detail_Citation:
    See Deltares (2021) 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)
    • 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 hydrodynamic and sediment transport model was used to predict the dispersal of sediment from a submerged, nearshore berm composed of sediment dredged from the navigation channel in the mouth of the Columbia River. The model was calibrated based on observations of berm morphology acquired with repeated multibeam bathymetric surveys. Model predictions were used to evaluate the efficiency of the nearshore berm location to enhance supply of sediment to an eroding coastline north of the inlet.

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: 20-Oct-2021 (process 1 of 5)
    A three-dimensional hydrodynamic and sediment transport model of the mouth of the Columbia River (MCR) was constructed using the Delft3D4 (D3D) modeling suite (Deltares, 2021) to simulate water levels, flow, waves, and sediment transport for the time period of September 22, 2020 to March 10, 2021. The long time period and high spatial resolution required for this study necessitated a nested modeling scheme to reduce computational expense. The nested detail model domain consists of a structured, orthogonal, curvilinear, grid that covers an area of 37 km along shore and 33 km cross shore centered on the MCR. The grid dimensions are 140 by 246 cells with resolution varying between 26 m and 1.2 km. Ten equally spaced vertical sigma layers were used to simulate 3D effects within the model domain. The grid was aligned with coastal engineering structures, including the three primary stone jetties, as well as several training dikes along the north side of the navigation channel. Flow through the structures was limited in the model by using thin dams (no transmission) or dry points. The open boundaries in the detailed model were prescribed as a time-series of Riemann invariants and salinity values for each vertical layer were derived from an overall model domain that extended roughly 150 and 100 km to the north and south of the MCR, respectively. The bathymetry for the overall, detailed, and wave grids was derived from recent data sets collected by the USGS, NOAA, and USACE between 2004 and 2020 as described in Stevens and others (2020). The source bathymetric data were converted to a common horizontal datum (NAD83) and to the land-based North American Vertical Datum of 1988 (NAVD88), then projected into the Cartesian UTM Zone 10 coordinate system (meters). Deep areas associated with the Astoria submarine canyon were removed from the model bathymetry to improve stability along the oceanic boundaries. Oceanic boundaries of the overall model were forced using astronomic tidal constituents derived from the TPXO 7.2 global tide model (Egbert and Erofeeva, 2002). A vertical offset of 1.15 m (positive values are up) derived from NOAA VDatum (version 3.2; https://vdatum.noaa.gov/) was applied at the oceanic boundary to account for the difference between local mean sea level and NAVD88. Oceanic subtidal variations were imposed at the oceanic open boundary as a time-varying correction to the astronomical tides. The subtidal time-series was derived from observations of water levels at NOAA stations 9440910 (Toke Point, WA), 9437540 (Garibaldi, OR), and 9440581 (Cape Disappointment, WA). Water-level time-series from the three stations were low-pass-filtered using a 66-hr cutoff to remove fluctuations at tidal frequencies. The low-pass-filtered values from the stations were highly correlated, and an average was applied to the oceanic model boundaries. The landward boundary of the overall model was forced with a time-series of river discharge measured at 30-minute intervals at USGS gauge 14246900 (http://waterdata.usgs.gov/usa/nwis/uv?site_no=14246900). The overall model’s oceanic and fluvial boundaries were prescribed constant salinity values of 33 and 0 practical salinity units (psu), respectively. The effects of temperature variations on circulation were neglected in the present model application.
    Date: 20-Oct-2021 (process 2 of 5)
    The spectral wave model SWAN (version 41.31) was applied to both overall and detailed models to simulate waves from the continental shelf to the coastline. Wave energy was discretized into 48 frequency bins between 0.03 and 1 Hz and 36 directional bins that covered a 180-degree sector from south to north. The seaward open boundary approximately intersects the location of Coastal Data Information Program (CDIP) buoy 179 at a water depth of 181 m. The 2D, spatially uniform, time-varying energy spectra derived from measurements at CDIP buoy 179 were used to force the wave model. Space- and time-varying wind fields derived from the High Resolution Rapid Refresh (HRRR) atmospheric model (https://rapidrefresh.noaa.gov/hrrr/) were applied to simulate wind growth within the model domain. Physics in the wave model were based on ST6 (Rogers and others, 2012) and activated with a custom run script (swan.bat) that uses the find and replace text (fart.exe) utility to implement options within SWAN that are not supported by the standard Delft3d-Wave GUI. The JONSWAP bottom friction model with a coefficient of 0.038 m2s-3 and default settings for depth induced breaking and triads were included. Convergence criteria were set to 99 percent of cells and a maximum of 30 iterations to obtain full convergence for all wave cases. The overall and detailed coupled wave and flow models were run with a computational time step of 6 s to fulfill Courant stability criteria and ensure stable and accurate results. Two-way coupling between the wave model and flow model involved a nonstationary hydrodynamic calculation in combination with regular stationary wave simulations. SWAN was activated every 30 min during the hydrodynamic simulation and performed a stationary wave simulation using the water levels and depth-averaged currents passed from the flow model.
    Date: 20-Oct-2021 (process 3 of 5)
    The online morphology addition to Delft3D was used to simulate sediment transport in the detailed domain at each computational time step (Deltares, 2021). Two sediment fractions representing native and berm sediment consisting of fine to medium sand were included were included. Bed stratigraphy was activated, and a total thickness of 20 m of sediment was made available throughout the model domain. The initial distributions of berm and native sediment were determined based on observed nearshore berm extent and thickness interpolated onto the computational grid. Bed level updating during the simulations was deactivated and the total mass of each sediment fraction was computed for each grid cell and vertical layer in the bed throughout the model domain.
    Date: 05-Jan-2022 (process 4 of 5)
    Boundary conditions for the nested model were generated from outputs from the overall model simulation using DelftDashboard software, available as part of Open Earth Tools (https://www.openearth.nl/). The nested model simulation was broken into 4 roughly equal time periods between September 22, 2020, and March 10, 2021. This segmentation was required to reduce the amount of computer resources, specifically the amount of computer RAM, required for the simulation. After segmentation, the simulations require about 100 GB of RAM available. The time series boundary conditions (.bct) and transport conditions (.bcc) for the four segments are mcr_riv_detail_oct (Sept. 22 - Nov. 1), mcr_riv_detail_nov (Nov. 1 - Dec. 14), mcr_riv_detail_dec (Dec 14. - Jan. 26), and mcr_riv_detail_feb (Jan. 26 - Mar. 10). The nested models were run sequentially, and the successive models were initialized with conditions from the end of the prior time period.
    Date: 01-Mar-2022 (process 5 of 5)
    Observations of bulk wave parameters and near-bed current velocities at approximately 2.2 m above the bed collected at the NHS buoy were compared against model predictions during low energy conditions. Qualitative and quantitative comparisons between modeled and measured water levels, wind speeds, and wave heights and periods show good agreement, with total root-mean-square errors (RMSE) of 0.11 m, 1.36 m/s, 0.22 m, and 2.21 s, respectively. However, model performance for the near-bottom currents was less accurate, with a RMSE of 0.12 and 0.14 m/s, for eastward and northward velocity components, respectively. The calibrated model was compared with observations of nearshore berm morphology and was largely able to reproduce the observed changes including the timing and magnitude of volume loss within the survey area, spreading, thinning, and onshore movement of the berm centroid. See Stevens and others (2023) for additional information.
  3. What similar or related data should the user be aware of?
    Deltares, 2021, 2021, Delft3D-Flow user manual (version 3.15): Deltares, Delft, Netherlands.

    Online Links:

    Stevens, Andrew W., Elias, Edwin, Pearson, Stuart, Kaminsky, George M., Ruggiero, Peter R., Weiner, Heather M., and Gelfenbaum, Guy R., 2020, Observations of coastal change and numerical modeling of sediment-transport pathways at the mouth of the Columbia River and its adjacent littoral cell: U.S. Geological Survey, Reston, Virginia.

    Online Links:

    Stevens, Andrew W., Moritz, Hans R., Elias, Edwin P.L., Gelfenbaum, Guy R., Ruggiero, Peter R., Pearson, Stuart G., McMillan, James M., and Kaminsky, George M., 2023, Monitoring and modeling dispersal of a submerged nearshore berm at the mouth of the Columbia River, USA: Coastal Engineering, Amsterdam, The Netherlands.

    Online Links:

    Rogers, W. Erick, Babanin, Alexander V., and Wang, David W., 2012, Observation-consistent input and whitecapping dissipation in a model for wind-generated surface waves: Description and simple calculations: Journal of Atmospheric and Oceanic Technology, Boston, Massachusetts.

    Online Links:

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, and changes in berm morphology 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 for the overall and detailed models compatible with windows executable of Delft3D4 version 4.04.01 are provided in the zip archives "mcr_overall_model.zip" and "mcr_detail_model.zip", respectively. Browse graphics showing the extents of the model grids 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: 24-Jan-2023
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_P9RVK9S9/mcr_model_metadata.faq.html>
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