from __future__ import absolute_import, division, print_function, \
unicode_literals
from mpas_tools.mesh.creation import build_spherical_mesh as \
create_spherical_mesh
from mpas_tools.mesh.creation import build_planar_mesh as create_planar_mesh
from mpas_tools.cime.constants import constants
from mpas_tools.ocean.inject_bathymetry import inject_bathymetry
from mpas_tools.ocean.inject_meshDensity import inject_spherical_meshDensity, \
inject_planar_meshDensity
from mpas_tools.ocean.inject_preserve_floodplain import \
inject_preserve_floodplain
from mpas_tools.viz.paraview_extractor import extract_vtk
from mpas_tools.logging import LoggingContext
[docs]
def build_spherical_mesh(cellWidth, lon, lat, out_filename='base_mesh.nc',
plot_cellWidth=True, vtk_dir='base_mesh_vtk',
preserve_floodplain=False, floodplain_elevation=20.0,
do_inject_bathymetry=False, logger=None,
use_progress_bar=True):
"""
Build an MPAS mesh using JIGSAW with the given cell sizes as a function of
latitude and longitude
The result is a mesh file stored in ``out_filename`` as well as several
intermediate files: ``mesh.log``, ``mesh-HFUN.msh``, ``mesh.jig``,
``mesh-MESH.msh``, ``mesh.msh``, and ``mesh_triangles.nc``.
Parameters
----------
cellWidth : ndarray
m x n array of cell width in km
lon : ndarray
longitude in degrees (length n and between -180 and 180)
lat : ndarray
longitude in degrees (length m and between -90 and 90)
out_filename : str, optional
The file name of the resulting MPAS mesh
plot_cellWidth : bool, optional
Whether to produce a plot of ``cellWidth``. If so, it will be written
to ``cellWidthGlobal.png``.
vtk_dir : str, optional
The name of the directory where mesh data will be extracted for viewing
in ParaVeiw.
preserve_floodplain : bool, optional
Whether a flood plain (bathymetry above z = 0) should be preserved in
the mesh
floodplain_elevation : float, optional
The elevation in meters to which the flood plain is preserved
do_inject_bathymetry : bool, optional
Whether one of the default bathymetry datasets, ``earth_relief_15s.nc``
or ``topo.msh``, should be added to the MPAS mesh
logger : logging.Logger, optional
A logger for the output if not stdout
use_progress_bar : bool, optional
Whether to display progress bars (problematic in logging to a file)
"""
with LoggingContext(__name__, logger=logger) as logger:
earth_radius = constants['SHR_CONST_REARTH']
create_spherical_mesh(cellWidth, lon, lat, earth_radius, out_filename,
plot_cellWidth, logger=logger)
logger.info('Step 4. Inject meshDensity into the mesh file')
inject_spherical_meshDensity(cellWidth, lon, lat,
mesh_filename=out_filename)
_shared_steps(out_filename, vtk_dir, preserve_floodplain,
floodplain_elevation, do_inject_bathymetry, logger,
use_progress_bar)
[docs]
def build_planar_mesh(cellWidth, x, y, geom_points, geom_edges,
out_filename='base_mesh.nc', vtk_dir='base_mesh_vtk',
preserve_floodplain=False, floodplain_elevation=20.0,
do_inject_bathymetry=False, logger=None,
use_progress_bar=True):
"""
Build a planar MPAS mesh
Parameters
----------
cellWidth : ndarray
m x n array of cell width in km
x, y : ndarray
arrays defining planar coordinates in meters
geom_points : ndarray
list of point coordinates for bounding polygon for the planar mesh
geom_edges : ndarray
list of edges between points in ``geom_points`` that define the
bounding polygon
out_filename : str, optional
The file name of the resulting MPAS mesh
vtk_dir : str, optional
The name of the directory where mesh data will be extracted for viewing
in ParaVeiw.
preserve_floodplain : bool, optional
Whether a flood plain (bathymetry above z = 0) should be preserved in
the mesh
floodplain_elevation : float, optional
The elevation in meters to which the flood plain is preserved
do_inject_bathymetry : bool, optional
Whether one of the default bathymetry datasets, ``earth_relief_15s.nc``
or ``topo.msh``, should be added to the MPAS mesh
logger : logging.Logger, optional
A logger for the output if not stdout
use_progress_bar : bool, optional
Whether to display progress bars (problematic in logging to a file)
"""
with LoggingContext(__name__, logger=logger) as logger:
create_planar_mesh(cellWidth, x, y, geom_points, geom_edges,
out_filename, logger=logger)
logger.info('Step 4. Inject meshDensity into the mesh file')
inject_planar_meshDensity(cellWidth, x, y, mesh_filename=out_filename)
_shared_steps(out_filename, vtk_dir, preserve_floodplain,
floodplain_elevation, do_inject_bathymetry, logger,
use_progress_bar)
def _shared_steps(out_filename, vtk_dir, preserve_floodplain,
floodplain_elevation, do_inject_bathymetry, logger,
use_progress_bar):
step = 5
if do_inject_bathymetry:
logger.info('Step {}. Injecting bathymetry'.format(step))
inject_bathymetry(mesh_file=out_filename)
step += 1
if preserve_floodplain:
logger.info('Step {}. Injecting flag to preserve floodplain'.format(
step))
inject_preserve_floodplain(mesh_file=out_filename,
floodplain_elevation=floodplain_elevation)
step += 1
logger.info('Step {}. Create vtk file for visualization'.format(step))
extract_vtk(ignore_time=True, lonlat=True, dimension_list=['maxEdges='],
variable_list=['allOnCells'], filename_pattern=out_filename,
out_dir=vtk_dir, use_progress_bar=use_progress_bar)
logger.info("***********************************************")
logger.info("** The global mesh file is {} **".format(out_filename))
logger.info("***********************************************")