def build_mesh(preserve_floodplain=False,
floodplain_elevation=20.0,
do_inject_bathymetry=False):
print('Step 1. Build cellWidth array as function of latitude and '
'longitude')
cellWidth, lon, lat = define_base_mesh.cellWidthVsLatLon()
da = xarray.DataArray(cellWidth,
dims=['lat', 'lon'],
coords={
'lat': lat,
'lon': lon
},
name='cellWidth')
da.to_netcdf('cellWidthVsLatLon.nc')
print('Step 2. Generate mesh with JIGSAW')
jigsaw_driver(cellWidth, lon, lat)
print('Step 3. Convert triangles from jigsaw format to netcdf')
jigsaw_to_netcdf(msh_filename='mesh-MESH.msh',
output_name='mesh_triangles.nc',
on_sphere=True)
print('Step 4. Convert from triangles to MPAS mesh')
write_netcdf(convert(xarray.open_dataset('mesh_triangles.nc')),
'base_mesh.nc')
print('Step 5. Inject correct meshDensity variable into base mesh file')
inject_meshDensity(cw_filename='cellWidthVsLatLon.nc',
mesh_filename='base_mesh.nc')
if do_inject_bathymetry:
print('Step 6. Injecting bathymetry')
inject_bathymetry(mesh_file='base_mesh.nc')
if preserve_floodplain:
print('Step 7. Injecting flag to preserve floodplain')
inject_preserve_floodplain(mesh_file='base_mesh.nc',
floodplain_elevation=floodplain_elevation)
print('Step 8. Create vtk file for visualization')
args = [
'paraview_vtk_field_extractor.py', '--ignore_time', '-l', '-d',
'maxEdges=0', '-v', 'allOnCells', '-f', 'base_mesh.nc', '-o',
'base_mesh_vtk'
]
print("running", ' '.join(args))
subprocess.check_call(args, env=os.environ.copy())
print("***********************************************")
print("** The global mesh file is base_mesh.nc **")
print("***********************************************")
def build_mesh(preserve_floodplain=False,
floodplain_elevation=20.0,
do_inject_bathymetry=False,
geometry='sphere',
plot_cellWidth=True):
if geometry == 'sphere':
on_sphere = True
else:
on_sphere = False
print(
'Step 1. Build cellWidth array as function of horizontal coordinates')
if on_sphere:
cellWidth, lon, lat = define_base_mesh.cellWidthVsLatLon()
da = xarray.DataArray(cellWidth,
dims=['lat', 'lon'],
coords={
'lat': lat,
'lon': lon
},
name='cellWidth')
cw_filename = 'cellWidthVsLatLon.nc'
da.to_netcdf(cw_filename)
plot_cellWidth = True
if plot_cellWidth:
import matplotlib
from cartopy import config
import cartopy.crs as ccrs
matplotlib.use('Agg')
fig = plt.figure()
fig.set_size_inches(16.0, 8.0)
plt.clf()
ax = plt.axes(projection=ccrs.PlateCarree())
ax.set_global()
im = ax.imshow(cellWidth,
origin='lower',
transform=ccrs.PlateCarree(),
extent=[-180, 180, -90, 90],
cmap='jet')
ax.coastlines()
gl = ax.gridlines(crs=ccrs.PlateCarree(),
draw_labels=True,
linewidth=1,
color='gray',
alpha=0.5,
linestyle='-')
gl.xlabels_top = False
gl.ylabels_right = False
plt.title('Grid cell size, km')
plt.colorbar(im, shrink=.60)
plt.savefig('cellWidthGlobal.png')
else:
cellWidth, x, y, geom_points, geom_edges = define_base_mesh.cellWidthVsXY(
)
da = xarray.DataArray(cellWidth,
dims=['y', 'x'],
coords={
'y': y,
'x': x
},
name='cellWidth')
cw_filename = 'cellWidthVsXY.nc'
da.to_netcdf(cw_filename)
print('Step 2. Generate mesh with JIGSAW')
if on_sphere:
jigsaw_driver(cellWidth, lon, lat)
else:
jigsaw_driver(cellWidth,
x,
y,
on_sphere=False,
geom_points=geom_points,
geom_edges=geom_edges)
print('Step 3. Convert triangles from jigsaw format to netcdf')
jigsaw_to_netcdf(msh_filename='mesh-MESH.msh',
output_name='mesh_triangles.nc',
on_sphere=on_sphere)
print('Step 4. Convert from triangles to MPAS mesh')
write_netcdf(convert(xarray.open_dataset('mesh_triangles.nc')),
'base_mesh.nc')
print('Step 5. Inject correct meshDensity variable into base mesh file')
inject_meshDensity(cw_filename=cw_filename,
mesh_filename='base_mesh.nc',
on_sphere=on_sphere)
if do_inject_bathymetry:
print('Step 6. Injecting bathymetry')
inject_bathymetry(mesh_file='base_mesh.nc')
if preserve_floodplain:
print('Step 7. Injecting flag to preserve floodplain')
inject_preserve_floodplain(mesh_file='base_mesh.nc',
floodplain_elevation=floodplain_elevation)
print('Step 8. Create vtk file for visualization')
args = [
'paraview_vtk_field_extractor.py', '--ignore_time', '-l', '-d',
'maxEdges=0', '-v', 'allOnCells', '-f', 'base_mesh.nc', '-o',
'base_mesh_vtk'
]
print("running", ' '.join(args))
subprocess.check_call(args, env=os.environ.copy())
print("***********************************************")
print("** The global mesh file is base_mesh.nc **")
print("***********************************************")
def build_mesh(
preserve_floodplain=False,
floodplain_elevation=20.0,
do_inject_bathymetry=False,
geometry='sphere',
plot_cellWidth=True):
if geometry == 'sphere':
on_sphere = True
else:
on_sphere = False
print('Step 1. Build cellWidth array as function of horizontal coordinates')
if on_sphere:
cellWidth, lon, lat = define_base_mesh.cellWidthVsLatLon()
da = xarray.DataArray(cellWidth,
dims=['lat', 'lon'],
coords={'lat': lat, 'lon': lon},
name='cellWidth')
cw_filename = 'cellWidthVsLatLon.nc'
da.to_netcdf(cw_filename)
plot_cellWidth = True
if plot_cellWidth:
register_sci_viz_colormaps()
fig = plt.figure(figsize=[16.0, 8.0])
ax = plt.axes(projection=ccrs.PlateCarree())
ax.set_global()
im = ax.imshow(cellWidth, origin='lower',
transform=ccrs.PlateCarree(),
extent=[-180, 180, -90, 90], cmap='3Wbgy5',
zorder=0)
ax.add_feature(cartopy.feature.LAND, edgecolor='black', zorder=1)
gl = ax.gridlines(
crs=ccrs.PlateCarree(),
draw_labels=True,
linewidth=1,
color='gray',
alpha=0.5,
linestyle='-', zorder=2)
gl.top_labels = False
gl.right_labels = False
plt.title(
'Grid cell size, km, min: {:.1f} max: {:.1f}'.format(
cellWidth.min(),cellWidth.max()))
plt.colorbar(im, shrink=.60)
fig.canvas.draw()
plt.tight_layout()
plt.savefig('cellWidthGlobal.png', bbox_inches='tight', dpi=300)
plt.close()
else:
cellWidth, x, y, geom_points, geom_edges = define_base_mesh.cellWidthVsXY()
da = xarray.DataArray(cellWidth,
dims=['y', 'x'],
coords={'y': y, 'x': x},
name='cellWidth')
cw_filename = 'cellWidthVsXY.nc'
da.to_netcdf(cw_filename)
print('Step 2. Generate mesh with JIGSAW')
if on_sphere:
jigsaw_driver(cellWidth, lon, lat)
else:
jigsaw_driver(
cellWidth,
x,
y,
on_sphere=False,
geom_points=geom_points,
geom_edges=geom_edges)
print('Step 3. Convert triangles from jigsaw format to netcdf')
jigsaw_to_netcdf(msh_filename='mesh-MESH.msh',
output_name='mesh_triangles.nc', on_sphere=on_sphere)
print('Step 4. Convert from triangles to MPAS mesh')
write_netcdf(convert(xarray.open_dataset('mesh_triangles.nc')),
'base_mesh.nc')
print('Step 5. Inject correct meshDensity variable into base mesh file')
inject_meshDensity(cw_filename=cw_filename,
mesh_filename='base_mesh.nc', on_sphere=on_sphere)
if do_inject_bathymetry:
print('Step 6. Injecting bathymetry')
inject_bathymetry(mesh_file='base_mesh.nc')
if preserve_floodplain:
print('Step 7. Injecting flag to preserve floodplain')
inject_preserve_floodplain(mesh_file='base_mesh.nc',
floodplain_elevation=floodplain_elevation)
print('Step 8. Create vtk file for visualization')
extract_vtk(ignore_time=True, lonlat=True, dimension_list=['maxEdges='],
variable_list=['allOnCells'], filename_pattern='base_mesh.nc',
out_dir='base_mesh_vtk')
print("***********************************************")
print("** The global mesh file is base_mesh.nc **")
print("***********************************************")