Precise distance-based two-dimensional automated mesh generation toolbox intended for coastal ocean/shallow water flow models

[!NOTE]
This is the default and recommended PROJECTION branch. Please use it unless you otherwise require legacy (MASTER branch) or the absolute newest features (DEV branch).

[!WARNING]
The boundary of the meshing domain must be a polygon (first point equals the last and non-self intersecting) but it does not need to be simplified. Read the user guide for more information about the inputs.

Table of contents

• Getting help
• Contributing
• Code framework
• Starting out
• Testing
• References
• Gallery
• Changelog

OceanMesh2D is a set of user-friendly MATLAB functions to generate two-dimensional (2D) unstructured meshes for coastal ocean circulation problems. These meshes are based on a variety of feature driven geometric and bathymetric mesh size functions, which are generated according to user-defined parameters. Mesh generation is achieved through a force-balance algorithm combined with a number of topological improvement strategies aimed at improving the worst case triangle quality. The software embeds the mesh generation process into an object-orientated framework that contains pre- and post-processing workflows, which makes mesh generation flexible, reproducible, and script-able.

Getting help

[!TIP]
PLEASE READ THE USER GUIDE! A recent pdf of the user guide is located in this branch. For a continually updated version click here (wait for compilation and then click download PDF)

Besides posting issues with the code on Github, you can also ask questions via our Slack channel here.

Note: If the slack link invite isn't working, please send either one of us and an email and we'll fix it. By default, the invite link expires every 30 days.

Otherwise please reach out to either Dr. William Pringle ([email protected]) or Dr. Keith Roberts ([email protected]) with questions or concerns or feel free to start an Issue in the issues tab above.

Contributing

All contributions are welcome!

To contribute to the software:

1. Fork the repository.
2. Clone the forked repository, add your contributions and push the changes to your fork.
3. Create a Pull request

Before creating the pull request, make sure that the examples pass...

Some things that will increase the chance that your pull request is accepted:

• Write minimal working examples that demonstrate the functionality.
• Write good commit and pull request messages.

Code framework

OceanMesh2D consists of four standalone classes that are called in sequence. It requires no paid toolboxes to build meshes and has been tested to work with a trial version of MATLAB.

OceanMesh2D::
├── geodata -- process geospatial data.
├── edgefx  -- build mesh size functions.
├── meshgen -- generate mesh based on mesh size functions and boundaries.
└── msh     -- store, write, read, inspect, and visualize meshes and their
               axuillary components for numerical simulation.

Starting Out

1. Clone or download and unzip the current repository.

2. Run the setup.sh bash script or setup.bat batch script to download the required m_map package and the base datasets:

   • GSHHG global shoreline
   • SRTM15_PLUS global topobathy DEM

3. Create or modify startup.m file located under your home folder by executing command in MATLAB:

   edit(fullfile(userpath,'startup.m'))
   

   And add the line:

   run(<PATH_TO_OCEANMESH2D>/setup_oceanmesh2d.m)
   

   Replace <PATH_TO_OCEANMESH2D> with the folder name where you cloned/unzipped the repository.

4. Restart MATLAB to get paths added.

Additional data required for some of the following examples must be downloaded manually from Zenodo. Specifically, Examples 2, 3, 4, 5 and 5b require additional datasets from the google drive folder while base datasets are sufficient for the other examples.

Featured in  ┌── Examples/Example_1_NZ.m   -- A simple mesh around South Island
             |                                New Zealand that uses GSHHS shoreline.
user guide   ├── Examples/Example_2_NY.m   -- A high-resolution mesh around
             |                                the New York/Manhattan area that uses a DEM
             |                                created from LiDAR data.
             └── Examples/Example_3_ECGC.m -- Builds a mesh for the western North Atlantic
                                              with a local high-resolution nest around New York

Featured in         ┌── Examples/Example_4_PRVI.m -- Builds a mesh for the western North Atlantic
                    |                                with three high-resolution nests around
Geoscientific Model |                                Puerto Rico and US Virgin Islands
                    ├── Examples/Example_5_JBAY.m -- An extremely high-fidelity (15-m) mesh from
Development paper[1]|                                LiDAR data around Jamaica Bay with CFL-limiting.
                    └── Examples/Example_6_GBAY.m -- An example of the polyline/thalweg mesh size
                                                     function along the Houston Ship Channel.

See Testing to test OceanMesh2D on your system.

Testing

To ensure the software is fully functional on your system before building some crazy meshes it is strongly recommended to run the tests (RunTests.m) in the Tests/ directory.

We test all pull requests using this test suite on a local host before accepting. For substantial pull requests we will also test the Examples from the Examples/ directory.

References!

If you make use of OceanMesh2D please include a reference to [1], and to any of [2]-[5] if pertinent (latex .bib file). We would also appreciate using our logo in a presentation featuring OceanMesh2D.

[1] - Roberts, K. J., Pringle, W. J., and Westerink, J. J., 2019.
      OceanMesh2D 1.0: MATLAB-based software for two-dimensional unstructured mesh generation in coastal ocean modeling,
      Geosci. Model Dev. (GMD), https://doi.org/10.5194/gmd-12-1847-2019.
[2] - Roberts, K. J., Pringle, W. J, 2018.
      OceanMesh2D: User guide - Precise distance-based two-dimensional automated mesh generation toolbox intended for coastal
      ocean/shallow water. https://doi.org/10.13140/RG.2.2.21840.61446/2.
[3] - Roberts, Keith J. Unstructured Mesh Generation and Dynamic Load Balancing for Coastal Ocean Hydrodynamic Simulation, 2019.
      PhD Thesis, University of Notre Dame. https://curate.nd.edu/show/4q77fr0022c.
[4] - Roberts, Keith J., Pringle W.J., Westerink J. J. Contreras, M.T., Wirasaet, D., 2019.
      On the automatic and a priori design of unstructured mesh resolution for coastal ocean circulation models,
      Ocean Modelling, 144, 101509. https://doi.org/10.1016/j.ocemod.2019.101509.
[5] - Pringle, W. J., Wirasaet, D., Roberts, K. J., and Westerink, J. J., 2021.
      Global Storm Tide Modeling with ADCIRC v55: Unstructured Mesh Design and Performance,
      Geoscientific Model Development, 14(2), 1125-1145. https://doi.org/10.5194/gmd-14-1125-2021.

In addition, best practice when using software in a scientific publication is to cite the permanent doi corresponding to the version used (e.g., for reproducibility). All our releases are archived at the following Zenodo repository doi link.

Authors (202X). CHLNDDEV/OceanMesh2D: OceanMesh2D VX.X. Zenodo. https://doi.org/10.5281/zenodo.1341384

Please fill in the version (VX.X), author list and year corresponding to the version used.

We would also like to acknowledge various scripts and algorithms from mesh2d included in OceanMesh2D that have been developed by @dengwirda. Please also see JIGSAW-GEO:

[i] - Engwirda, D., 2017.
      JIGSAW-GEO (1.0): Locally orthogonal staggered unstructured grid generation for general circulation modelling on the sphere.
      Geoscientific Model Development, 10(6), 2117–2140. https://doi.org/10.5194/gmd-10-2117-2017.

GALLERY:

• These images can be made by running the examples

• The following images are provided from happy users. Please send us your meshes.

Jiangchao Qiu from his publication.

Changelog

The format is based on Keep a Changelog

Unreleased (on current HEAD of the Projection branch)

Fixed

• User inputted edge constraints are now saved when no weirs are being constrained during mesh generation.

Added

• Check in Read_shapefile.m to handle, warn, and correct cases where there are empty objects in a shapefile. https://github.com/CHLNDDEV/OceanMesh2D/pull/315
• nws8 namelist for switching to CLE15 vortex model and option vortex model options implemented into a developement branch (https://github.com/adcirc/adcirc/pull/393) of ADCIRC. https://github.com/CHLNDDEV/OceanMesh2D/pull/317

Changed

• Combine limit and velwd namelists into wetdry namelist to match ADCIRC release code. https://github.com/CHLNDDEV/OceanMesh2D/pull/317
• Defunct Google drive link to Zenodo one in the README.

[6.0.0] - 2024-02-28

Added

• Added ability to generate constrainsts for shorelines automatically using the new high-fidelity method. https://github.com/CHLNDDEV/OceanMesh2D/pull/264
• auxiliary file reader function that can be used standalone e.g., m = m.read({'fort.13','fort.15'})), as well as called from within msh() function. https://github.com/CHLNDDEV/OceanMesh2D/pull/287
• swanoutput namelist for SWAN model outputs. https://github.com/CHLNDDEV/OceanMesh2D/pull/287
• Added new function in msh called remesh_patch to remesh within specified polygonal domains and insert back into parent mesh. https://github.com/CHLNDDEV/OceanMesh2D/pull/301
• Read and write to 2dm format. https://github.com/CHLNDDEV/OceanMesh2D/pull/300
• namelist and RSTIMNC input arguments for Make_f15.m fort.15 generator. updated the help message for all input argumebts to Make_f15. https://github.com/CHLNDDEV/OceanMesh2D/pull/283
• New stability namelist options to Make_f15.m fort.15 generator. https://github.com/CHLNDDEV/OceanMesh2D/pull/283
• Optionality for mesh2dgen to choose the method of mesh generation kind, and the maximum iteration count iter. https://github.com/CHLNDDEV/OceanMesh2D/pull/272
• Option improve_with_reduced_quality to meshgen for allowing for mesh improvements even when quality is decreasing or large number of nodes eliminated, which sometimes is necessary to force the advancement in mesh quality.
• Option delaunay_elim_on_exit to meshgen to skip the last call to delaunay_elim to potentially avoid deleting boundary elements.
• Geoid offset nodal attribute in Calc_f13 subroutine. https://github.com/CHLNDDEV/OceanMesh2D/pull/251
• Support for writing Self Attraction and Loading (SAL) files in NetCDF for the ADCIRC model. https://github.com/CHLNDDEV/OceanMesh2D/pull/231
• Added 'high-fidelity' option for automatically forming and constraining edges into the mesh. https://github.com/CHLNDDEV/OceanMesh2D/pull/264

Changed

• treating logicals in namelists as a logicals type within MATLAB but ouput as a string. https://github.com/CHLNDDEV/OceanMesh2D/pull/287
• Calc_Sponge.m to allow for sponge in polygon region and coefficents based on spatially varying depth. https://github.com/CHLNDDEV/OceanMesh2D/pull/287
• removed namelists from default setup in Make_f15.m fort.15 generator to be invoked by user as an input argument instead. https://github.com/CHLNDDEV/OceanMesh2D/pull/283
• Use implicit smoother (ds=1) in msh.clean when fix points are present. https://github.com/CHLNDDEV/OceanMesh2D/pull/283
• Default filename for the dynamicWaterLevelCorrection is now null so that it is not evoked by default. https://github.com/CHLNDDEV/OceanMesh2D/pull/272
• Default mesh improvement strategy is ds 2.
• Retrieve boundary indices in msh.get_boundary_of_mesh method. https://github.com/CHLNDDEV/OceanMesh2D/pull/259
• msh.offset63 struct and associated write/make routines for dynamicwaterlevel offset functionality. https://github.com/CHLNDDEV/OceanMesh2D/pull/259
• dynamicWaterLevelCorrection to fort.15 namelist, and PRBCKGRND option to met fort.15 namelist. https://github.com/CHLNDDEV/OceanMesh2D/pull/261
• Improved code readability by auto-indenting core functions and reworking 'setup' and 'Examples' functions, including adding necessary files for separation from core functions. https://github.com/CHLNDDEV/OceanMesh2D/pull/308
• Renamed functions for clarity and fixed multiple small bugs; changes are compatible with OpenEarthTools but distinct. https://github.com/CHLNDDEV/OceanMesh2D/pull/308

Fixed

• catch for offset_nodes of int type in writeoffset63.m. https://github.com/CHLNDDEV/OceanMesh2D/pull/287
• writing out the wave coupling timestep RSTIMNC on the WTIMNC line of fort.15 when NWS > 300. https://github.com/CHLNDDEV/OceanMesh2D/pull/283
• make_bc call with empty varargin, e.g., when calling inner. https://github.com/CHLNDDEV/OceanMesh2D/pull/283
• Make_offset63 call with constant offset (length 1 time_vector). https://github.com/CHLNDDEV/OceanMesh2D/pull/283
• ourKNNsearch call in nanfill option of Griddata (msh.interp). https://github.com/CHLNDDEV/OceanMesh2D/pull/283
• m_map link in setup.sh Issue #277. https://github.com/CHLNDDEV/OceanMesh2D/pull/283
• Updated Calc_f13.m to avoid an "Unrecognized variable" error by ensuring "broken" is always defined. https://github.com/CHLNDDEV/OceanMesh2D/pull/282
• Fixed test for likely geographic coordinates in Make_f15.m. https://github.com/CHLNDDEV/OceanMesh2D/pull/282
• updated Gridded_to_Mesh_SeaBed_DepthAveraged.m to fix the infinite loop in using Cal_IT_Fric.m by filling in the NaNs at greater depths with values from above. https://github.com/CHLNDDEV/OceanMesh2D/pull/280
• Recursive cleaning issues: infinite loop and preservation of fixed points.
• msh.interp method for K argument of length 1, and for the test to determine whether the bathymetry grid is irregular. https://github.com/CHLNDDEV/OceanMesh2D/pull/259
• Printing of namelist character strings or numbers. https://github.com/CHLNDDEV/OceanMesh2D/pull/261
• Make_offset63.m time interval computation. https://github.com/CHLNDDEV/OceanMesh2D/pull/261 and https://github.com/CHLNDDEV/OceanMesh2D/pull/272
• Removed dependency on statistics toolbox when using the 'nanfill' option in msh.interp. https://github.com/CHLNDDEV/OceanMesh2D/pull/269
• Missing routines for reading in elvstaname and velstaname in readfort15.m by adding readlinevecname() method. https://github.com/CHLNDDEV/OceanMesh2D/pull/281
• Incorrect reference to ibtype was changed to ibtypee in map_mesh_properties function. https://github.com/CHLNDDEV/OceanMesh2D/pull/298

[5.0.0] - 2021-07-29

Added

• meshgen.build() now will rewind the iteration set in the case mesh improvement cannot improve the qualities. https://github.com/CHLNDDEV/OceanMesh2D/pull/234
• msh.plot() now has a cmap in which the user can specify their any cmocean colormap
• radius_separated_points function that trims the points in the mesh to have a specified resolution that can be used before m_quiver so that vectors are evenly plotted. https://github.com/CHLNDDEV/OceanMesh2D/pull/225
• Deleting boundary conditions by specifyng their indices in msh.object.bd field. See https://github.com/CHLNDDEV/OceanMesh2D/pull/205
• Ability for user to set their own axis limits when plotting with msh.plot(). https://github.com/CHLNDDEV/OceanMesh2D/pull/224

Fixed

• Minor fix to msh.make_bc using the auto method. https://github.com/CHLNDDEV/OceanMesh2D/pull/237
• correction in setting stereographic projection bounds in setProj to make sure points are not pushed outside and become NaNs (was limited to radius of 178 deg but made sure can go up to full 180 deg). https://github.com/CHLNDDEV/OceanMesh2D/pull/225
• Correctly deleting weirs from boundary object through make_bc delete method. See https://github.com/CHLNDDEV/OceanMesh2D/pull/205
• Array format fix for reading in ibtype and nvell from fort.14 file and when executing carry_over_weirs. See https://github.com/CHLNDDEV/OceanMesh2D/pull/206
• Fix for irregular grid spacings in DEMs. See https://github.com/CHLNDDEV/OceanMesh2D/pull/204
• tidal constituents for Make_f15 can now contain "major8" in addition to other constituents in the string/cell array https://github.com/CHLNDDEV/OceanMesh2D/pull/221
• Correctly collect NDBC and NOS stations in mesh when creating fort15 file using Make_f15 for meteorological, velocity and elevation records https://github.com/CHLNDDEV/OceanMesh2D/pull/242

Changed

• msh.plot() using type bd option now creates a legend for the different boundary condition types. https://github.com/CHLNDDEV/OceanMesh2D/pull/247
• forcing facecolor to white in m_trimesh so that it does not intefere with background color option. https://github.com/CHLNDDEV/OceanMesh2D/pull/245
• made topographic elevation bound option for max_ele, wl, slp, and g edgefx kwargs consistent and added explanation of this option is included in edgefx help. https://github.com/CHLNDDEV/OceanMesh2D/pull/230
• m_plot() function calls m_grid() with background color input kwarg (if backcolor option used) instead of manual application. https://github.com/CHLNDDEV/OceanMesh2D/pull/225
• tidal_data_to_ob function called from Make_f15 populates boundary condition tidal constituents that do not exist in the tidal database with zero values so that user can add user-defined values later (previously did not populate). https://github.com/CHLNDDEV/OceanMesh2D/pull/225
• Improved cmocean for pivot handling with discrete colormap. https://github.com/CHLNDDEV/OceanMesh2D/pull/225
• Renamed Calc_NLCD_Mannings to Calc_Mannings_Landcover and making option for 'ccap' landcover type in addition to 'nlcd' (default) and added the ability to using user specified inteprolation (e.g., nearest, linear, cell-averaging, etc.) of the landcover data to the mesh vertices. https://github.com/CHLNDDEV/OceanMesh2D/pull/221

[4.0.0] - 2021-03-14

Added

• mesh2d interface improvements to filter small polygons.
• Support for creation of fort.20 files for forcing rivers by @Jiangchao3
• Mesh "cleaning" modes moderate and aggressive transfer nodal attributes via improvements to msh.map_mesh_properties
• msh.remove_attribute() method to remove f13 attribute(s)
• new msh.interp() slope_calc kwarg option to set the method of computing the topographic gradients (slopes), either rms [default] or abs
• new extract_subdomain() keep_numbering kwarg option to keep the full mesh triangulation numbering on the subdomain [off by default].

Changed

• msh.plot() overhaul. All options specified via kwarg.
• msh.plot() option subset option is now called subdomain
• msh.plot() arbitary f13 option now utilizes colormap kwarg
• utilities/extract_subdomain now is called with kwargs.
• Cleaning up msh.bound_courant_number() to use msh.get_boundary_of_mesh() for Delaunay-triangulation and allowing msh.clean() to do the transfer of attributes automatically.
• msh.plus(obj1,obj2) can now carry over obj2 f13 attributes if also exist in obj1
• msh() more efficient storing of boundary conditions read in from fort.xx files, and msh.write() can write out arbitrary vertex indices (instead of just 1 to NP).

Fixed

• Boundary labeling fix
• Prompt when labeling bcs using outer kwarg in make_bc
• fix for boundary condition mapping in msh.map_mesh_properties() especially for weirs/barriers
• fix for barrier mapping in msh.plus() routine
• fix for msh.make_bc(m,auto,gdat) where gdat is empty. In this case it uses the depths on the mesh to determine the open boundaries.
• check for poly2ccw mapping toolbox function in kml2struct
• fix for msh.plot() on log colormap when plotting f13 attributes

Deleted

• Deprecating msh.CheckTimestep() for msh.bound_courant_number. Added error message and instruction in the CheckTimestep help

[3.3.0] - 2020-12-21

Fixed

• Users without mapping toolbox could not read in shapefiles because of a bug that
  made them required to have a 3d shapefiles.
• plotting gdat with no shoreline.
• plotting a mesh's bathymetry with a non-zero datum using cmocean.
• cell-averaging interpolation method in msh.interp fixed for unequal lon-lat DEM grid spacings

Added

• Mesh patch smoother
• Ability to remesh abritary patches of elements within the domain while respecting user-defined mesh sizes and the patches boundaries.
• Ability to use the TPXO9 Atlas for the tidal bcs and sponge (inside tidal_data_to_ob.m and Calc_Sponge.m) by using '**' wildcards in place of the constituent name within the tidal atlas filename (the atlas has an individual file for each constituent).
• Introducing 'auto_outer' option for the make_bc msh method which populates the bc for the outermost mesh boundary polygon (ignores islands)
• Changelog to README
• "mapMeshProperties" msh method ports over mesh properties for a mesh subset
• 'invert' option in the msh.interp method to turn off the DEM value inversion typically performed

Changed

• for the make_bc msh method 'auto'/'auto_outer' options, allowing for the 'depth' method of classification to use the interpolated depths on the mesh if gdat is empty.
• improving help for make_bc msh method, Make_f15.m and Calc_Sponge.m
• renamed "ExtractSubDomain.m" to "extract_subdomain.m"
• improving "extract_subdomain.m" help and facilitating NaN-delimited polygons
• ability to return boundary as a cell in "get_boundary_of_mesh" msh method
• "Example_1_NZ.m" includes example of plotting bcs of a msh subset
• using "mapMeshproperties" method in "fixmeshandcarry"
• using "fixmeshandcarry" in the "cat" msh method
• improving warning and error messages for the "interp" msh method
• adding geofactor into "writefort15" for the GAHM vortex model