Mesh Creation

Building a Mesh

This is all out of date and needs refining!!!

The mpas_tools.mesh.creation.build_mesh.build_mesh() function is used create an MPAS mesh using the JIGSAW and JIGSAW-Python packages.

The user must define a local python module define_base_mesh that provides a function that returns a 2D array cellWidth of cell sizes in kilometers.

If the mesh is on a sphere, this function is called cellWidthVsLatLon() and also returns 1D lon and lat arrays.

The mesh is planar, the function is called cellWidthVsXY() and returns 4 arrays in addition to cellWidth: 1D x and y arrays defining planar coordinates in meters; as well as geom_points, list of point coordinates for bounding polygon for the planar mesh; and geom_edges, list of edges between points in geom_points that define the bounding polygon.

The result is an MPAS mesh file base_mesh.nc as well as several intermediate files: mesh.log, mesh-HFUN.msh, mesh.jig, mesh-MESH.msh, mesh.msh, and mesh_triangles.nc.

The mpas_tools.viz.paraview_extractor.extract_vtk() function is used to produce a VTK file in the base_mesh_vtk directory that can be viewed in ParaVeiw.

Optionally, a field, cellSeedMask, can be added to the mesh file that can later be used preserve a “flood plain” of positive elevations in the MPAS mesh. See mpas_tools.mesh.creation.inject_preserve_floodplain.inject_preserve_floodplain().

Optioanlly, a field, bottomDepthObserved, can be added to the mesh file with bathymetry data from one of two topography files: earth_relief_15s.nc or topo.msh. If bathymetry should be added to the mesh, a local link with one of these file names must exist. See py:func:mpas_tools.mesh.creation.inject_bathymetry.inject_bathymetry`.

A simple example of define_base_mesh.py for a spherical mesh with constant, 240-km resolution is:

import numpy as np


def cellWidthVsLatLon():
    """
    Create cell width array for this mesh on a regular latitude-longitude grid.

    Returns
    -------
    cellWidth : numpy.ndarray
        m x n array of cell width in km
    lon : numpy.ndarray
        longitude in degrees (length n and between -180 and 180)
    lat : numpy.ndarray
        longitude in degrees (length m and between -90 and 90)
    """

    ddeg = 10
    constantCellWidth = 240

    lat = np.arange(-90, 90.01, ddeg)
    lon = np.arange(-180, 180.01, ddeg)

    cellWidth = constantCellWidth * np.ones((lat.size, lon.size))
    return cellWidth, lon, lat

With this module defined locally, a mesh can be generated either with the command-line tool build_mesh:

$ build_mesh

or by calling py:func:mpas_tools.mesh.creation.build_mesh.build_mesh:

from mpas_tools.mesh.creation.build_mesh import build_mesh


build_mesh()

The full usage details of the command-line tool are:

$ build_mesh --help

usage: build_mesh [-h] [--preserve_floodplain]
                  [--floodplain_elevation FLOODPLAIN_ELEVATION]
                  [--inject_bathymetry] [--geometry GEOMETRY]
                  [--plot_cellWidth]

optional arguments:
  -h, --help            show this help message and exit
  --preserve_floodplain
                        Whether a flood plain (bathymetry above z = 0) should
                        be preserved in the mesh
  --floodplain_elevation FLOODPLAIN_ELEVATION
                        The elevation in meters to which the flood plain is
                        preserved, default is 20 m
  --inject_bathymetry   Whether one of the default bathymetry datasets,
                        earth_relief_15s.nc or topo.msh, should be added to
                        the MPAS mesh
  --geometry GEOMETRY   Whether the mesh is on a sphere or a plane, default is
                        a sphere
  --plot_cellWidth      Whether to produce a plot of cellWidth