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: https://www.sciencebase.gov/catalog/file/get/62045796d34ec05caca1cfe4?name=Waiakane_OpenFOAM_model_configuration.png&allowOpen=true 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: Network_Address: Network_Resource_Name: https://www.sciencebase.gov/catalog/item/62045796d34ec05caca1cfe4?name=Waiakane_OpenFOAM_models.zip 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: Network_Address: Network_Resource_Name: https://www.sciencebase.gov/catalog/item/62045796d34ec05caca1cfe4?name=Waiakane_OpenFOAM_models_scenarios.csv Network_Resource_Name: https://www.sciencebase.gov/catalog/item/62045796d34ec05caca1cfe4 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