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

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Metadata:

Identification_Information:
Citation:
Citation_Information:
Originator: Benjamin K. Norris
Originator: Curt D. Storlazzi
Originator: Andrew M. Pomeroy
Publication_Date: 20230524
Title:
OpenFOAM models of low- and high-relief sites from the coral reef flat off Waiakane, Molokai, Hawaii
Geospatial_Data_Presentation_Form: comma-delimited text
Series_Information:
Series_Name: data release
Issue_Identification: DOI: 10.5066/P933TO2Q
Publication_Information:
Publication_Place:
Pacific Coastal and Marine Science Center, Santa Cruz, California
Publisher: U.S. Geological Survey
Online_Linkage: https://doi.org/10.5066/P933TO2Q
Description:
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].
Purpose:
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.
Time_Period_of_Content:
Time_Period_Information:
Single_Date/Time:
Calendar_Date: 2023
Currentness_Reference: publication year
Status:
Progress: Complete
Maintenance_and_Update_Frequency: None planned
Spatial_Domain:
Bounding_Coordinates:
West_Bounding_Coordinate: -180.0
East_Bounding_Coordinate: 180.0
North_Bounding_Coordinate: 90.0
South_Bounding_Coordinate: -90.0
Keywords:
Theme:
Theme_Keyword_Thesaurus: ISO 19115 Topic Category
Theme_Keyword: oceans
Theme_Keyword: geoscientificInformation
Theme:
Theme_Keyword_Thesaurus: Data Categories for Marine Planning
Theme_Keyword: Wave Energy Production
Theme:
Theme_Keyword_Thesaurus: USGS Thesaurus
Theme_Keyword: coastal processes
Theme:
Theme_Keyword_Thesaurus: Marine Realms Information Bank (MRIB) keywords
Theme_Keyword: geomorphology
Theme:
Theme_Keyword_Thesaurus: None
Theme_Keyword: U.S. Geological Survey
Theme_Keyword: USGS
Theme_Keyword: Coastal and Marine Hazards and Resources Program
Theme_Keyword: CHMRP
Theme_Keyword: Pacific Coastal and Marine Science Center
Theme_Keyword: PCMSC
Theme:
Theme_Keyword_Thesaurus: USGS Metadata Identifier
Theme_Keyword: USGS:62045796d34ec05caca1cfe4
Place:
Place_Keyword_Thesaurus: Geographic Names Information System (GNIS)
Place_Keyword: State of Hawaii
Place_Keyword: Molokai
Place_Keyword: Waiakane
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.
Point_of_Contact:
Contact_Information:
Contact_Organization_Primary:
Contact_Organization:
U.S. Geological Survey, Pacific Coastal and Marine Science Center
Contact_Person: PCMSC Science Data Coordinator
Contact_Address:
Address_Type: mailing and physical
Address: 2885 Mission Street
City: Santa Cruz
State_or_Province: CA
Postal_Code: 95060
Contact_Voice_Telephone: 831-427-4747
Contact_Electronic_Mail_Address: pcmsc_data@usgs.gov
Browse_Graphic:
Browse_Graphic_File_Name: Browse_Graphic_File_Description:
Illustration showing layout and configuration of the 2D OpenFOAM models.
Browse_Graphic_File_Type: PNG
Native_Data_Set_Environment:
Microsoft Windows 10, Windows Subsystem for Linux, Ubuntu OpenFOAM v-1912
Cross_Reference:
Citation_Information:
Originator: Rosenberger, K.J.
Originator: Storlazzi, C.D.
Originator: Cheriton, O.M.
Originator: Logan, J.B.
Publication_Date: 2019
Title: Coral Reef Circulation and Sediment Dynamics Experiment
Other_Citation_Details: U.S. Geological Survey data release
Online_Linkage: https://doi.org/10.5066/P9FSG90O
Cross_Reference:
Citation_Information:
Originator: Norris, B.K.
Originator: Storlazzi, C.D.
Originator: Pomeroy, A.W.M.
Originator: Rosenberger, K.J.
Originator: Logan, J.B.
Originator: Cheriton, O.M.
Publication_Date: 2023
Title:
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
Other_Citation_Details: Coastal Engineering
Online_Linkage: https://doi.org/10.1016/j.coastaleng.2023.104331
Cross_Reference:
Citation_Information:
Originator: Higuera, P.
Originator: Lara, J.L.
Originator: Losada, I.J.
Publication_Date: 2013
Title:
Realistic wave generation and active wave absorption for Navier-Stokes models. Application to OpenFOAM.
Other_Citation_Details: Coastal Engineering, 71, 102-118.
Online_Linkage: https://doi.org/10.1016/j.coastaleng.2012.07.002
Cross_Reference:
Citation_Information:
Originator: Le Mehaute, B.
Publication_Date: 1967
Title: An Introduction to Hydrodynamics and Water Waves
Other_Citation_Details: Springer, Berlin, Heidelberg.
Online_Linkage: None
Data_Quality_Information:
Attribute_Accuracy:
Attribute_Accuracy_Report:
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).
Logical_Consistency_Report: No formal logical accuracy tests were conducted.
Completeness_Report:
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.
Lineage:
Process_Step:
Process_Description:
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).
Process_Date: 2022
Spatial_Data_Organization_Information:
Indirect_Spatial_Reference: The model results presented are for Waiakane, Molokai, Hawaii
Direct_Spatial_Reference_Method: Point
Point_and_Vector_Object_Information:
SDTS_Terms_Description:
SDTS_Point_and_Vector_Object_Type: Point
Point_and_Vector_Object_Count: 140
Entity_and_Attribute_Information:
Detailed_Description:
Entity_Type:
Entity_Type_Label: Waiakane_OpenFOAM_model_configuration
Entity_Type_Definition: CSV file containing information on model scenarios
Entity_Type_Definition_Source: Producer defined
Attribute:
Attribute_Label: modelNumber
Attribute_Definition: The model number
Attribute_Definition_Source: USGS
Attribute_Domain_Values:
Range_Domain:
Range_Domain_Minimum: 1
Range_Domain_Maximum: 140
Attribute_Units_of_Measure: sequential unique number
Attribute_Measurement_Resolution: 1
Attribute:
Attribute_Label: domain
Attribute_Definition: low or high relief model domain
Attribute_Definition_Source: USGS
Attribute_Domain_Values:
Unrepresentable_Domain: lowRelief or highRelief
Attribute:
Attribute_Label: scenarioNumber
Attribute_Definition: The model scenario number
Attribute_Definition_Source: USGS
Attribute_Domain_Values:
Range_Domain:
Range_Domain_Minimum: 1
Range_Domain_Maximum: 70
Attribute_Units_of_Measure: Sequential incremental numbering for each scenario
Attribute_Measurement_Resolution: 1
Attribute:
Attribute_Label: waterDepth
Attribute_Definition: The model scenario number
Attribute_Definition_Source: USGS
Attribute_Domain_Values:
Range_Domain:
Range_Domain_Minimum: 1
Range_Domain_Maximum: 4
Attribute_Units_of_Measure: meters
Attribute_Measurement_Resolution: 1
Attribute:
Attribute_Label: waveHeight
Attribute_Definition: The wave height
Attribute_Definition_Source: USGS
Attribute_Domain_Values:
Range_Domain:
Range_Domain_Minimum: 0.4
Range_Domain_Maximum: 1.2
Attribute_Units_of_Measure: meters
Attribute_Measurement_Resolution: 0.2
Attribute:
Attribute_Label: wavePeriod
Attribute_Definition: The wave period
Attribute_Definition_Source: USGS
Attribute_Domain_Values:
Range_Domain:
Range_Domain_Minimum: 4
Range_Domain_Maximum: 20
Attribute_Units_of_Measure: seconds
Attribute_Measurement_Resolution: 4
Attribute:
Attribute_Label: rampTime
Attribute_Definition: The model rampTime
Attribute_Definition_Source: USGS
Attribute_Domain_Values:
Range_Domain:
Range_Domain_Minimum: 8
Range_Domain_Maximum: 40
Attribute_Units_of_Measure: seconds
Attribute_Measurement_Resolution: 8
Attribute:
Attribute_Label: runTime
Attribute_Definition: The model runTime
Attribute_Definition_Source: USGS
Attribute_Domain_Values:
Range_Domain:
Range_Domain_Minimum: 48
Range_Domain_Maximum: 192
Attribute_Units_of_Measure: seconds
Attribute_Measurement_Resolution: 48
Attribute:
Attribute_Label: purgeWrite
Attribute_Definition: The model purgeWrite
Attribute_Definition_Source: CSV
Attribute_Domain_Values:
Range_Domain:
Range_Domain_Minimum: 320
Range_Domain_Maximum: 1600
Attribute_Units_of_Measure: Unitless
Attribute_Measurement_Resolution: 320
Attribute:
Attribute_Label: waveSteepness
Attribute_Definition: The wave steepness for each scenario
Attribute_Definition_Source: USGS
Attribute_Domain_Values:
Range_Domain:
Range_Domain_Minimum: 0.003
Range_Domain_Maximum: 0.105
Attribute_Units_of_Measure: Unitness
Attribute_Measurement_Resolution: 0.001
Attribute:
Attribute_Label: gamma
Attribute_Definition: The wave breaking parameter
Attribute_Definition_Source: USGS
Attribute_Domain_Values:
Range_Domain:
Range_Domain_Minimum: 0.1
Range_Domain_Maximum: 0.67
Attribute_Units_of_Measure: Unitless
Attribute_Measurement_Resolution: 0.01
Attribute:
Attribute_Label: waveTheory
Attribute_Definition: The wave theory used for each scenario
Attribute_Definition_Source: CSV
Attribute_Domain_Values:
Enumerated_Domain:
Enumerated_Domain_Value: cnoidal
Enumerated_Domain_Value_Definition: a traveling wave whose amplitude is constricted by depth.
Enumerated_Domain_Value_Definition_Source: Le Mehaute, 1967
Attribute_Domain_Values:
Enumerated_Domain:
Enumerated_Domain_Value: StokesII
Enumerated_Domain_Value_Definition:
A nonlinear and periodic surface wave on a surface with constant mean depth.
Enumerated_Domain_Value_Definition_Source: Le Mehaute, 1967
Attribute_Domain_Values:
Enumerated_Domain:
Enumerated_Domain_Value: StokesV
Enumerated_Domain_Value_Definition:
A nonlinear and periodic surface wave on a surface with constant mean depth. Enumerated_Domain_Value_Definition_Source:
Enumerated_Domain_Value_Definition_Source: Le Mehaute, 1967
Overview_Description:
Entity_and_Attribute_Overview: The first line of the csv file is a header line.
Entity_and_Attribute_Detail_Citation: U.S. Geological Survey
Distribution_Information:
Distributor:
Contact_Information:
Contact_Organization_Primary:
Contact_Organization: U.S. Geological Survey - ScienceBase
Contact_Address:
Address_Type: mailing and physical
Address: Denver Federal Center, Building 810, Mail Stop 302
City: Denver
State_or_Province: CO
Postal_Code: 80225
Contact_Voice_Telephone: 1-888-275-8747
Contact_Electronic_Mail_Address: sciencebase@usgs.gov
Resource_Description: The model files are encoded as C++ format.
Distribution_Liability:
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.
Standard_Order_Process:
Digital_Form:
Digital_Transfer_Information:
Format_Name: text
Format_Version_Date: 2022
Format_Information_Content: ZIP file contains the models
File_Decompression_Technique: UnZIP is required to extract the models from the ZIP folder.
Transfer_Size: 3030
Digital_Transfer_Option:
Online_Option:
Computer_Contact_Information: Access_Instructions:
Data can be downloaded using the Network_Resource_Name links. The first link is a direct link to a zip file containing the model scenarios in C++ format. The second link points to a landing page with the model scenarios, a csv file describing the parameters for each model scenario, metadata, and browse image.
Fees: None.
Standard_Order_Process:
Digital_Form:
Digital_Transfer_Information:
Format_Name: comma-delimited text
Format_Version_Number: CSV
Format_Information_Content:
Comma-delimited text file contains the parameters for each model scenario.
File_Decompression_Technique: none
Transfer_Size: 0.008
Digital_Transfer_Option:
Online_Option:
Computer_Contact_Information: Access_Instructions:
Data can be downloaded using the Network_Resource_Name links. The first link is a direct link to a zip file containing the csv file of model scenarios. The second link points to a landing page with the csv file, the model scenarios, metadata, and browse image.
Fees: None.
Technical_Prerequisites:
Data can be read with a normal text editor such as NotePad++. Recommend SublimeText3. Models can be run using OpenFOAM v-1912.
Metadata_Reference_Information:
Metadata_Date: 20230524
Metadata_Contact:
Contact_Information:
Contact_Organization_Primary:
Contact_Organization:
U.S. Geological Survey, Pacific Coastal and Marine Science Center
Contact_Person: PCMSC Science Data Coordinator
Contact_Address:
Address_Type: mailing and physical
Address: 2885 Mission Street
City: Santa Cruz
State_or_Province: CA
Postal_Code: 95060
Contact_Voice_Telephone: 831-427-4747
Contact_Electronic_Mail_Address: pcmsc_data@usgs.gov
Metadata_Standard_Name: Content Standard for Digital Geospatial Metadata
Metadata_Standard_Version: FGDC-STD-001-1998

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