oceanmesh: Automatic coastal ocean mesh generation

🌊 🌀

Coastal ocean mesh generation from ESRI Shapefiles and digital elevation models.

Functionality

• A toolkit for the development of meshes and their auxiliary files that are used in the simulation of coastal ocean circulation. The software integrates mesh generation with geophysical datasets such as topobathymetric rasters/digital elevation models and shapefiles representing coastal features. It provides some necessary pre- and post-processing tools to inevitably perform a succesful numerical simulations with the developed model.
  • Automatically deal with arbitrarily complex shoreline vector datasets that represent complex coastal boundaries and incorporate the data in an automatic-sense into the mesh generation process.
  • A variety of commonly used mesh size functions to distribute element sizes that can easily be controlled via a simple scripting application interface.
  • Mesh checking and clean-up methods to avoid simulation problems.

Questions?

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

Otherwise please reach out to either Dr. Keith Roberts ([email protected]) or Dr. William Pringle ([email protected]) with questions or concerns!

Installation

For installation, oceanmesh needs cmake, CGAL:

sudo apt install cmake libcgal-dev

CGAL and can also be installed with conda:

conda install -c conda-forge cgal

After that, clone the repo and oceanmesh can be updated/installed using pip.

pip install -U -e .

On some clusters/HPC in order to install CGAL, you may need to load/install gmp and mpfr. For example, to install:

sudo apt install libmpfr-dev libgmp3-dev

⚠️

WARNING: THIS PROGRAM IS IN ACTIVE DEVELOPMENT. INSTALLATION IS ONLY RECOMMENDED FOR DEVELOPERS AT THIS TIME. WHEN A STABLE API IS REACHED, THE PROGRAM WILL BE AVAILABLE VIA pypi

Examples

Build a simple mesh around New York witha minimum element size of 1 km expanding linear from the shoreline to a maximum size of 5 km.

Here we use the GSHHS shoreline here and the Python package meshio to write the mesh to a VTK file for visualization in ParaView.

import pathlib
import zipfile
import requests

import meshio

from oceanmesh import (
    Shoreline,
    distance_sizing_function,
    signed_distance_function,
    generate_mesh,
    make_mesh_boundaries_traversable,
    delete_faces_connected_to_one_face,
)

# Download and load the GSHHS shoreline
url = "http://www.soest.hawaii.edu/pwessel/gshhg/gshhg-shp-2.3.7.zip"
filename = url.split("/")[-1]
print(filename)
with open(filename, "wb") as f:
    r = requests.get(url)
    f.write(r.content)

with zipfile.ZipFile("gshhg-shp-2.3.7.zip", "r") as zip_ref:
    zip_ref.extractall("gshhg-shp-2.3.7")

fname = "gshhg-shp-2.3.7/GSHHS_shp/f/GSHHS_f_L1.shp"

bbox, min_edge_length = (-75.000, -70.001, 40.0001, 41.9000), 1e3

shore = Shoreline(fname, bbox, min_edge_length)

edge_length = distance_sizing_function(shore, max_edge_length=5e3)

domain = signed_distance_function(shore)

points, cells = generate_mesh(domain, edge_length)

# remove degenerate mesh faces and other common problems in the mesh
points, cells = make_mesh_boundaries_traversable(points, cells)

points, cells = delete_faces_connected_to_one_face(points, cells)

meshio.write_points_cells(
    "simple_new_york.vtk",
    points,
    [("triangle", cells)],
    file_format="vtk",
)

See the testing/ folder for more inspiration.

Testing

To run the oceanmesh unit tests (and turn off plots), check out this repository and type tox. tox can be installed via pip.

License

This software is published under the GPLv3 license