OpenFOAM models of low- and high-relief sites from the coral reef flat off Waiakane, Molokai, Hawaii

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Frequently anticipated questions:

What does this data set describe?

Title:
OpenFOAM models of low- and high-relief sites from the coral reef flat off Waiakane, Molokai, Hawaii
Abstract:
OpenFOAM Computational Fluid Dynamics (CFD) models were developed to simulate wave energy dissipation across natural rough reef surfaces on the reef flat off Waiakane, Molokai, Hawaii, to understand this process in the context of reef restoration design. A total of 140 models were developed (70 per low- and 70 per high-bed-relief domains). Models were calibrated and validated with oceanographic datasets collected in 2018. This data release presents the 140 model scenarios that can be readily input into OpenFOAM to recreate the results, in addition to a csv file indicating the parameters used for each model scenario. These model data accompany Norris and others (2023) [Norris, B.K., Storlazzi, C.D., Pomeroy, A.W.M., Rosenberger, K.J., Logan, J.B., and Cheriton, O.M., 2023, Combining field observations and high-resolution numerical modeling to demonstrate the effect of coral reef roughness on turbulence and its implications for reef restoration design: Coastal Engineering, https://doi.org/10.1016/j.coastaleng.2023.104331].
  1. How might this data set be cited?
    Norris, Benjamin K., Storlazzi, Curt D., and Pomeroy, Andrew M., 20230524, OpenFOAM models of low- and high-relief sites from the coral reef flat off Waiakane, Molokai, Hawaii: data release DOI: 10.5066/P933TO2Q, 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: -180.0
    East_Bounding_Coordinate: 180.0
    North_Bounding_Coordinate: 90.0
    South_Bounding_Coordinate: -90.0
  3. What does it look like?
    https://www.sciencebase.gov/catalog/file/get/62045796d34ec05caca1cfe4?name=Waiakane_OpenFOAM_model_configuration.png&allowOpen=true (PNG)
    Illustration showing layout and configuration of the 2D OpenFOAM models.
  4. Does the data set describe conditions during a particular time period?
    Calendar_Date: 2023
    Currentness_Reference:
    publication year
  5. What is the general form of this data set?
    Geospatial_Data_Presentation_Form: comma-delimited text
  6. How does the data set represent geographic features?
    1. How are geographic features stored in the data set?
      Indirect_Spatial_Reference: The model results presented are for Waiakane, Molokai, Hawaii
      This is a Point data set. It contains the following vector data types (SDTS terminology):
      • Point (140)
    2. What coordinate system is used to represent geographic features?
  7. How does the data set describe geographic features?
    Waiakane_OpenFOAM_model_configuration
    CSV file containing information on model scenarios (Source: Producer defined)
    modelNumber
    The model number (Source: USGS)
    Range of values
    Minimum:1
    Maximum:140
    Units:sequential unique number
    Resolution:1
    domain
    low or high relief model domain (Source: USGS) lowRelief or highRelief
    scenarioNumber
    The model scenario number (Source: USGS)
    Range of values
    Minimum:1
    Maximum:70
    Units:Sequential incremental numbering for each scenario
    Resolution:1
    waterDepth
    The model scenario number (Source: USGS)
    Range of values
    Minimum:1
    Maximum:4
    Units:meters
    Resolution:1
    waveHeight
    The wave height (Source: USGS)
    Range of values
    Minimum:0.4
    Maximum:1.2
    Units:meters
    Resolution:0.2
    wavePeriod
    The wave period (Source: USGS)
    Range of values
    Minimum:4
    Maximum:20
    Units:seconds
    Resolution:4
    rampTime
    The model rampTime (Source: USGS)
    Range of values
    Minimum:8
    Maximum:40
    Units:seconds
    Resolution:8
    runTime
    The model runTime (Source: USGS)
    Range of values
    Minimum:48
    Maximum:192
    Units:seconds
    Resolution:48
    purgeWrite
    The model purgeWrite (Source: CSV)
    Range of values
    Minimum:320
    Maximum:1600
    Units:Unitless
    Resolution:320
    waveSteepness
    The wave steepness for each scenario (Source: USGS)
    Range of values
    Minimum:0.003
    Maximum:0.105
    Units:Unitness
    Resolution:0.001
    gamma
    The wave breaking parameter (Source: USGS)
    Range of values
    Minimum:0.1
    Maximum:0.67
    Units:Unitless
    Resolution:0.01
    waveTheory
    The wave theory used for each scenario (Source: CSV)
    ValueDefinition
    cnoidala traveling wave whose amplitude is constricted by depth.
    StokesIIA nonlinear and periodic surface wave on a surface with constant mean depth.
    StokesVA nonlinear and periodic surface wave on a surface with constant mean depth. Enumerated_Domain_Value_Definition_Source:
    Entity_and_Attribute_Overview: The first line of the csv file is a header line.
    Entity_and_Attribute_Detail_Citation: U.S. Geological Survey

Who produced the data set?

  1. Who are the originators of the data set? (may include formal authors, digital compilers, and editors)
    • Benjamin K. Norris
    • Curt D. Storlazzi
    • Andrew M. Pomeroy
  2. Who also contributed to the data set?
  3. To whom should users address questions about the data?
    U.S. Geological Survey, Pacific Coastal and Marine Science Center
    Attn: PCMSC Science Data Coordinator
    2885 Mission Street
    Santa Cruz, CA

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

Why was the data set created?

The models presented here are designed to recreate the data from the 2022 Molokai modeling project, however the OpenFOAM model files can also be utilized to inform future modeling efforts in general.

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: 2022 (process 1 of 1)
    Two model domains were developed using integrated 3D bathymetric surfaces for low- and high-relief sites (Pomeroy and others, 2022). Each domain was defined in a longshore uniform, two-dimensional vertical (2DV) coordinate system (x, z), with x pointing shoreward, z pointing upward, and the origin at the still water level. The initial mesh was 55 m long and 6.5 m high, with a uniform resolution of 0.25 m. The bathymetry surfaces were snapped to the model domain with snappyHexMesh tool using three levels of grid refinement (min. cell size of 0.125, 0.06, and 0.03 m) in the free surface region and the fine-scale areas of the model domains. The bed and atmosphere in the models were treated with zeroGradient and inletOutlet boundary conditions, respectively, with walls set as empty (non-computational) boundaries. At the model inlet, outlet, and along the bed, the fixedFluxPressure boundary condition was applied to the pressure (hydrostatic) field to adjust the pressure gradient so that the boundary flux matched the velocity boundary condition. Turbulence parameters used respective wall functions to model boundary layer effects near the bathymetry. Time-averaged values of the dimensionless wall distance z-plus ranged from 35 to 120, where z-plus between 30 and 300 defines the log-law layer where wall functions are applicable. To minimize numerical dissipation in the models, a second-order unbounded numerical scheme was used for gradients, second-order bounded central differencing schemes for divergence, and an unbounded second-order limited scheme was used for the Laplacian surface normal gradients. Wave boundary conditions were handled by the IHFOAM toolbox (Higuera and others, 2013). A series of models were developed for both the low- and high-relief domains to simulate hydrodynamics across each bathymetry. Four water depths (h = 1, 2, 3, 4 m), five significant wave heights (Hs = 0.4, 0.8, 1.2, 1.6, 2 m), and five peak wave periods (Tp = 4, 8, 12, 16, 20 s) were selected to span the range of recorded conditions. Combinations of conditions that were physically unreasonable (in other words, those with excessive wave steepness or those above the theoretical breaking limit) were eliminated, resulting in 70 cases per domain and thus 140 total cases. A summary of the model scenarios is provided in the accompanying CSV file. The scenario models were set up by varying the vertical position of the bathymetry to create domains with four different water depths. Different wave generation theories according to Le Mehaute (1967) for each combination of h, Hs, and Tp were applied at the inlet boundary to drive wave flows through the model domains. Each model was executed for a total time of 2Tp plus 10Tp to generate two wave cycles during spin-up followed by 10 wave cycles that were used for subsequent data analysis. To improve runtime efficiency, three models were run simultaneously on six distributed parallel processors on an 18-core Intel i9-10980XE CPU at 3.75 GHz with 64 GB of RAM. Execution times varied by model scenario and ranged from approximately 12 to 160 hours. The bed and atmosphere in the models were treated with zeroGradient and inletOutlet boundary conditions, respectively, with walls set as empty (non-computational) boundaries. At the model inlet, outlet, and along the bed, the fixedFluxPressure boundary condition was applied to the pressure (hydrostatic) field to adjust the pressure gradient so that the boundary flux matched the velocity boundary condition. Turbulence parameters used respective wall functions to model boundary layer effects near the bathymetry. Time-averaged values of the dimensionless wall distance z-plus ranged from 35 to 120, where z-plus is between 30 and 300, which defines the log-law layer where wall functions are applicable. To minimize numerical dissipation in the models, a second-order unbounded numerical scheme was used for gradients, second-order bounded central differencing schemes for divergence, and an unbounded second-order limited scheme was used for the Laplacian surface normal gradients. Wave boundary conditions were handled by the IHFOAM toolbox (Higuera and others, 2013). Each model file has the following file structure, where each folder corresponds to a different component of the OpenFOAM model. This file structure is a modified version taken from the IHFOAM toolbox found in the OpenFOAM tutorials folder. The 0 and 0.org folders contain the model boundary conditions. The 0 folder is a copy of the 0.org folder as a backup of the initial settings. The constant folder contains the model constants as well as the model mesh (in the polyMesh subdirectory). The system folder contains the model settings. For more details, we refer the reader to the OpenFOAM User guide (https://cfd.direct/openfoam/user-guide/) and the IHFOAM wiki site (https://openfoamwiki.net/index.php/Contrib/IHFOAM).
  3. What similar or related data should the user be aware of?
    Rosenberger, K.J., Storlazzi, C.D., Cheriton, O.M., and Logan, J.B., 2019, Coral Reef Circulation and Sediment Dynamics Experiment.

    Online Links:

    Other_Citation_Details: U.S. Geological Survey data release
    Norris, B.K., Storlazzi, C.D., Pomeroy, A.W.M., Rosenberger, K.J., Logan, J.B., and Cheriton, O.M., 2023, Combining field observations and high-resolution numerical modeling to demonstrate the effect of coral reef roughness on turbulence and its implications for reef restoration design.

    Online Links:

    Other_Citation_Details: Coastal Engineering
    Higuera, P., Lara, J.L., and Losada, I.J., 2013, Realistic wave generation and active wave absorption for Navier-Stokes models. Application to OpenFOAM..

    Online Links:

    Other_Citation_Details: Coastal Engineering, 71, 102-118.
    Le Mehaute, B., 1967, An Introduction to Hydrodynamics and Water Waves.

    Online Links:

    • None

    Other_Citation_Details: Springer, Berlin, Heidelberg.

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

  1. How well have the observations been checked?
    The models were calibrated and validated by comparing the results of two calibration cases (not presented here) to oceanographic time series data collected in 2018 (Rosenberger and others, 2019). The model settings in this data release are based on those two calibration cases and hence present a realistic estimate of the natural conditions under the simulated scenarios represented by each model case. More details on the calibration and validation can be found in Norris and others (2023).
  2. How accurate are the geographic locations?
  3. How accurate are the heights or depths?
  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?
    No formal logical accuracy tests were conducted.

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 navigation purposes.
  1. Who distributes the data set? (Distributor 1 of 1)
    U.S. Geological Survey - ScienceBase
    Denver Federal Center, Building 810, Mail Stop 302
    Denver, CO

    1-888-275-8747 (voice)
    sciencebase@usgs.gov
  2. What's the catalog number I need to order this data set? The model files are encoded as C++ format.
  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?
  5. What hardware or software do I need in order to use the data set?
    Data can be read with a normal text editor such as NotePad++. Recommend SublimeText3. Models can be run using OpenFOAM v-1912.

Who wrote the metadata?

Dates:
Last modified: 24-May-2023
Metadata author:
U.S. Geological Survey, Pacific Coastal and Marine Science Center
Attn: PCMSC Science Data Coordinator
2885 Mission Street
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_P933TO2Q/Waiakane_OpenFOAM_models_metadata.faq.html>
Generated by mp version 2.9.51 on Wed May 24 15:49:19 2023