def run(self):
"""
Run this step of the test case
"""
config = self.config
logger = self.logger
section = config['gotm']
nx = section.getint('nx')
ny = section.getint('ny')
dc = section.getfloat('dc')
dsMesh = make_planar_hex_mesh(nx=nx, ny=ny, dc=dc, nonperiodic_x=False,
nonperiodic_y=False)
write_netcdf(dsMesh, 'grid.nc')
dsMesh = cull(dsMesh, logger=logger)
dsMesh = convert(dsMesh, graphInfoFileName='graph.info',
logger=logger)
write_netcdf(dsMesh, 'mesh.nc')
replacements = dict()
replacements['config_periodic_planar_vert_levels'] = \
config.get('gotm', 'vert_levels')
replacements['config_periodic_planar_bottom_depth'] = \
config.get('gotm', 'bottom_depth')
self.update_namelist_at_runtime(options=replacements)
run_model(self)
def run(self):
"""
Run this step of the test case
"""
logger = self.logger
section = self.config['enthalpy_benchmark']
nx = section.getint('nx')
ny = section.getint('ny')
dc = section.getfloat('dc')
levels = section.get('levels')
dsMesh = make_planar_hex_mesh(nx=nx, ny=ny, dc=dc, nonperiodic_x=True,
nonperiodic_y=True)
write_netcdf(dsMesh, 'grid.nc')
dsMesh = cull(dsMesh, logger=logger)
dsMesh = convert(dsMesh, logger=logger)
write_netcdf(dsMesh, 'mpas_grid.nc')
args = ['create_landice_grid_from_generic_MPAS_grid.py',
'-i', 'mpas_grid.nc',
'-o', 'landice_grid.nc',
'-l', levels,
'--thermal']
check_call(args, logger)
make_graph_file(mesh_filename='landice_grid.nc',
graph_filename='graph.info')
_setup_initial_conditions(section, 'landice_grid.nc')
def run(self):
"""
Run this step of the test case
"""
logger = self.logger
section = self.config['eismint2']
nx = section.getint('nx')
ny = section.getint('ny')
dc = section.getfloat('dc')
dsMesh = make_planar_hex_mesh(nx=nx,
ny=ny,
dc=dc,
nonperiodic_x=False,
nonperiodic_y=False)
dsMesh = convert(dsMesh, logger=logger)
write_netcdf(dsMesh, 'mpas_grid.nc')
dsMesh.close()
radius = section.get('radius')
args = [
'define_cullMask.py', '-f', 'mpas_grid.nc', '-m', 'radius', '-d',
radius
]
check_call(args, logger)
dsMesh = xarray.open_dataset('mpas_grid.nc')
dsMesh = cull(dsMesh, logger=logger)
dsMesh = convert(dsMesh, logger=logger)
write_netcdf(dsMesh, 'mpas_grid2.nc')
levels = section.get('levels')
args = [
'create_landice_grid_from_generic_MPAS_grid.py', '-i',
'mpas_grid2.nc', '-o', 'landice_grid.nc', '-l', levels,
'--thermal', '--beta'
]
check_call(args, logger)
make_graph_file(mesh_filename='landice_grid.nc',
graph_filename='graph.info')
def test_conversion():
dsMesh = xarray.open_dataset(
'mesh_tools/mesh_conversion_tools/test/mesh.QU.1920km.151026.nc')
dsMesh = convert(dsIn=dsMesh)
write_netcdf(dsMesh, 'mesh.nc')
dsMask = xarray.open_dataset(
'mesh_tools/mesh_conversion_tools/test/land_mask_final.nc')
dsCulled = cull(dsIn=dsMesh, dsMask=dsMask)
write_netcdf(dsCulled, 'culled_mesh.nc')
fcMask = read_feature_collection(
'mesh_tools/mesh_conversion_tools/test/Arctic_Ocean.geojson')
dsMask = mask(dsMesh=dsMesh, fcMask=fcMask)
write_netcdf(dsMask, 'antarctic_mask.nc')
def main(args):
earth_radius = 6371.0e3
out_dir = os.path.abspath(args.output)
out_base = os.path.basename(args.output)
out_basepath = out_dir + "/" + out_base
out_filename = out_dir + "/" + out_base + "_mpas.nc"
p = bool(args.plots)
print(p)
if not os.path.exists(out_dir):
os.makedirs(out_dir)
else:
print("Base dir already exists: ", out_dir)
if (args.opt == "unif" or args.opt == "localref"):
#Density based grid
if (args.opt == "unif"):
cellWidth, lon, lat = jutil.cellWidthVsLatLon(args.r)
elif (args.opt == "localref"):
cellWidth, lon, lat = jutil.localrefVsLatLon(args.r, p=p)
mesh_file = jutil.jigsaw_gen_sph_grid(cellWidth,
lon,
lat,
basename=out_basepath)
elif (args.opt == "icos"):
#Icosahedral grid
mesh_file = jutil.jigsaw_gen_icos_grid(basename=out_basepath, level=4)
else:
print("Unknown option")
exit(1)
#Convert jigsaw mesh to netcdf
jigsaw_to_netcdf(msh_filename=mesh_file,
output_name=out_basepath + '_triangles.nc',
on_sphere=True,
sphere_radius=1.0)
#convert to mpas grid specific format
write_netcdf(
convert(xarray.open_dataset(out_basepath + '_triangles.nc'),
dir=out_dir,
graphInfoFileName=out_basepath + "_graph.info"), out_filename)
def run(self):
"""
Run this step of the test case
"""
config = self.config
section = config['soma']
options = dict(
config_eos_linear_alpha=section.get('eos_linear_alpha'),
config_soma_density_difference=section.get('density_difference'),
config_soma_surface_temperature=section.get('surface_temperature'),
config_soma_surface_salinity=section.get('surface_salinity'),
config_soma_salinity_gradient=section.get('salinity_gradient'),
config_soma_thermocline_depth=section.get('thermocline_depth'),
config_soma_density_difference_linear=section.get(
'density_difference_linear'),
config_soma_phi=section.get('phi'),
config_soma_shelf_depth=section.get('shelf_depth'),
config_soma_bottom_depth=section.get('bottom_depth'))
for out_name in ['namelist_mark_land.ocean', 'namelist.ocean']:
self.update_namelist_at_runtime(options=options, out_name=out_name)
ds_mesh = convert(xarray.open_dataset('base_mesh.nc'),
graphInfoFileName='base_graph.info',
logger=self.logger)
write_netcdf(ds_mesh, 'mesh.nc')
run_model(self,
namelist='namelist_mark_land.ocean',
streams='streams_mark_land.ocean',
graph_file='base_graph.info')
ds_mesh = cull(xarray.open_dataset('masked_initial_state.nc'),
graphInfoFileName='graph.info',
logger=self.logger)
write_netcdf(ds_mesh, 'culled_mesh.nc')
run_model(self,
namelist='namelist.ocean',
streams='streams.ocean',
graph_file='graph.info')
def run(self):
"""
Run this step of the test case
"""
mesh_type = self.mesh_type
logger = self.logger
config = self.config
section = config['dome']
if mesh_type == '2000m':
nx = section.getint('nx')
ny = section.getint('ny')
dc = section.getfloat('dc')
dsMesh = make_planar_hex_mesh(nx=nx,
ny=ny,
dc=dc,
nonperiodic_x=True,
nonperiodic_y=True)
write_netcdf(dsMesh, 'grid.nc')
dsMesh = cull(dsMesh, logger=logger)
dsMesh = convert(dsMesh, logger=logger)
write_netcdf(dsMesh, 'mpas_grid.nc')
levels = section.get('levels')
args = [
'create_landice_grid_from_generic_MPAS_grid.py', '-i',
'mpas_grid.nc', '-o', 'landice_grid.nc', '-l', levels
]
check_call(args, logger)
make_graph_file(mesh_filename='landice_grid.nc',
graph_filename='graph.info')
_setup_dome_initial_conditions(config,
logger,
filename='landice_grid.nc')
def run(self):
"""
Run this step of the test case
"""
config = self.config
logger = self.logger
section = config['ziso']
nx = section.getint('nx')
ny = section.getint('ny')
dc = section.getfloat('dc')
dsMesh = make_planar_hex_mesh(nx=nx, ny=ny, dc=dc, nonperiodic_x=False,
nonperiodic_y=True)
write_netcdf(dsMesh, 'base_mesh.nc')
dsMesh = cull(dsMesh, logger=logger)
dsMesh = convert(dsMesh, graphInfoFileName='culled_graph.info',
logger=logger)
write_netcdf(dsMesh, 'culled_mesh.nc')
ds = _write_initial_state(config, dsMesh, self.with_frazil)
_write_forcing(config, ds.yCell, ds.zMid)
def run(self):
"""
Run this step of the test case
"""
config = self.config
logger = self.logger
replacements = dict()
replacements['config_periodic_planar_vert_levels'] = \
config.getfloat('vertical_grid', 'vert_levels')
replacements['config_periodic_planar_bottom_depth'] = \
config.getfloat('vertical_grid', 'bottom_depth')
self.update_namelist_at_runtime(options=replacements)
section = config['vertical_grid']
vert_levels = section.getint('vert_levels')
bottom_depth = section.getfloat('bottom_depth')
section = config['internal_wave']
nx = section.getint('nx')
ny = section.getint('ny')
dc = section.getfloat('dc')
use_distances = section.getboolean('use_distances')
amplitude_width_dist = section.getfloat('amplitude_width_dist')
amplitude_width_frac = section.getfloat('amplitude_width_frac')
bottom_temperature = section.getfloat('bottom_temperature')
surface_temperature = section.getfloat('surface_temperature')
temperature_difference = section.getfloat('temperature_difference')
salinity = section.getfloat('salinity')
logger.info(' * Make planar hex mesh')
dsMesh = make_planar_hex_mesh(nx=nx,
ny=ny,
dc=dc,
nonperiodic_x=False,
nonperiodic_y=True)
logger.info(' * Completed Make planar hex mesh')
write_netcdf(dsMesh, 'base_mesh.nc')
logger.info(' * Cull mesh')
dsMesh = cull(dsMesh, logger=logger)
logger.info(' * Convert mesh')
dsMesh = convert(dsMesh,
graphInfoFileName='culled_graph.info',
logger=logger)
logger.info(' * Completed Convert mesh')
write_netcdf(dsMesh, 'culled_mesh.nc')
ds = dsMesh.copy()
yCell = ds.yCell
ds['bottomDepth'] = bottom_depth * xarray.ones_like(yCell)
ds['ssh'] = xarray.zeros_like(yCell)
init_vertical_coord(config, ds)
yMin = yCell.min().values
yMax = yCell.max().values
yMid = 0.5 * (yMin + yMax)
if use_distances:
perturbation_width = amplitude_width_dist
else:
perturbation_width = (yMax - yMin) * amplitude_width_frac
# Set stratified temperature
temp_vert = (bottom_temperature +
(surface_temperature - bottom_temperature) *
((ds.refZMid + bottom_depth) / bottom_depth))
depth_frac = xarray.zeros_like(temp_vert)
refBottomDepth = ds['refBottomDepth']
for k in range(1, vert_levels):
depth_frac[k] = refBottomDepth[k -
1] / refBottomDepth[vert_levels - 1]
# If cell is in the southern half, outside the sin width, subtract
# temperature difference
frac = xarray.where(
numpy.abs(yCell - yMid) < perturbation_width,
numpy.cos(0.5 * numpy.pi * (yCell - yMid) / perturbation_width) *
numpy.sin(numpy.pi * depth_frac), 0.)
temperature = temp_vert - temperature_difference * frac
temperature = temperature.transpose('nCells', 'nVertLevels')
temperature = temperature.expand_dims(dim='Time', axis=0)
normalVelocity = xarray.zeros_like(ds.xEdge)
normalVelocity, _ = xarray.broadcast(normalVelocity, ds.refBottomDepth)
normalVelocity = normalVelocity.transpose('nEdges', 'nVertLevels')
normalVelocity = normalVelocity.expand_dims(dim='Time', axis=0)
ds['temperature'] = temperature
ds['salinity'] = salinity * xarray.ones_like(temperature)
ds['normalVelocity'] = normalVelocity
write_netcdf(ds, 'ocean.nc')
def waves_mesh(cfg):
pwd = os.getcwd()
src_path = pwd
dst_path = pwd
opts = jigsawpy.jigsaw_jig_t()
hfun = jigsawpy.jigsaw_msh_t()
mesh = jigsawpy.jigsaw_msh_t()
init = jigsawpy.jigsaw_msh_t()
#------------------------------------ setup files for JIGSAW
opts.geom_file = \
str(Path(dst_path)/"geom.msh") # GEOM file
opts.jcfg_file = \
str(Path(dst_path)/"jcfg.jig") # JCFG file
opts.hfun_file = \
str(Path(dst_path)/"hfun.msh") # HFUN file
opts.mesh_file = \
str(Path(dst_path)/"mesh.msh") # MESH file
opts.init_file = \
str(Path(dst_path)/"init.msh") # INIT file
#------------------------------------ define JIGSAW geometry
if cfg['coastlines']:
print('Defining coastline geometry')
create_coastline_geometry(cfg['shpfiles'], opts.geom_file,
cfg['sphere_radius'])
else:
geom = jigsawpy.jigsaw_msh_t()
geom.mshID = 'ELLIPSOID-MESH'
geom.radii = cfg['sphere_radius'] * np.ones(3, float)
jigsawpy.savemsh(opts.geom_file, geom)
#------------------------------------ define mesh size function
print('Defining mesh size function')
lon_min = -180.0
lon_max = 180.0
dlon = cfg['hfun_grid_spacing']
nlon = int((lon_max - lon_min) / dlon) + 1
lat_min = -90.0
lat_max = 90.0
nlat = int((lat_max - lat_min) / dlon) + 1
dlat = cfg['hfun_grid_spacing']
xlon = np.linspace(lon_min, lon_max, nlon)
ylat = np.linspace(lat_min, lat_max, nlat)
print(' hfun grid dimensions: {}, {}'.format(xlon.size, ylat.size))
define_hfunction.depth_threshold_refined = cfg['depth_threshold_refined']
define_hfunction.distance_threshold_refined = cfg[
'distance_threshold_refined']
define_hfunction.depth_threshold_global = cfg['depth_threshold_global']
define_hfunction.distance_threshold_global = cfg[
'distance_threshold_global']
define_hfunction.refined_res = cfg['refined_res']
define_hfunction.maxres = cfg['maxres']
hfunction = define_hfunction.cell_widthVsLatLon(xlon, ylat,
cfg['shpfiles'],
cfg['sphere_radius'],
cfg['ocean_mesh'])
hfunction = hfunction / km
hfun.mshID = "ellipsoid-grid"
hfun.radii = np.full(3,
cfg['sphere_radius'],
dtype=jigsawpy.jigsaw_msh_t.REALS_t)
hfun.xgrid = np.radians(xlon)
hfun.ygrid = np.radians(ylat)
hfun.value = hfunction.astype(jigsawpy.jigsaw_msh_t.REALS_t)
#------------------------------------ specify JIGSAW initial conditions
print('Specifying initial fixed coordinate locations')
create_initial_points(cfg['ocean_mesh'], xlon, ylat, hfunction,
cfg['sphere_radius'], opts.init_file)
jigsawpy.loadmsh(opts.init_file, init)
jigsawpy.savevtk(str(Path(dst_path) / "init.vtk"), init)
#------------------------------------ set HFUN grad.-limiter
print('Limiting mesh size function gradients')
hfun.slope = np.full( # |dH/dx| limits
hfun.value.shape,
cfg['hfun_slope_lim'],
dtype=hfun.REALS_t)
jigsawpy.savemsh(opts.hfun_file, hfun)
jigsawpy.cmd.marche(opts, hfun)
#------------------------------------ make mesh using JIGSAW
opts.hfun_scal = "absolute"
opts.hfun_hmax = float("inf") # null HFUN limits
opts.hfun_hmin = float(+0.00)
opts.mesh_dims = +2 # 2-dim. simplexes
opts.mesh_eps1 = +.67 # relax edge error
opts.mesh_rad2 = +1.2
opts.optm_qlim = +9.5E-01 # tighter opt. tol
opts.optm_iter = +32
opts.optm_qtol = +1.0E-05
opts.verbosity = 2
#jigsawpy.cmd.tetris(opts, 3, mesh)
jigsawpy.cmd.jigsaw(opts, mesh)
if cfg['coastlines']:
segment.segment(mesh)
#------------------------------------ save mesh for Paraview
print("Writing ex_h.vtk file.")
jigsawpy.savevtk(str(Path(dst_path) / "_hfun.vtk"), hfun)
jigsawpy.savevtk(str(Path(dst_path) / "waves_mesh.vtk"), mesh)
jigsawpy.savemsh(str(Path(dst_path) / "waves_mesh.msh"), mesh)
#------------------------------------ convert mesh to MPAS format
jigsaw_to_netcdf(msh_filename='waves_mesh.msh',
output_name='waves_mesh_triangles.nc',
on_sphere=True,
sphere_radius=cfg['sphere_radius'])
write_netcdf(
convert(xarray.open_dataset('waves_mesh_triangles.nc'),
dir='./',
logger=None), 'waves_mesh.nc')
#------------------------------------ cull mesh to ocean bounary
if os.path.exists('./cull_waves_mesh'):
f = open('cull_waves_mesh.nml', 'w')
f.write('&inputs\n')
f.write(" waves_mesh_file = 'waves_mesh.nc'\n")
f.write(" ocean_mesh_file = '" + cfg['ocean_mesh'] + "'\n")
f.write("/\n")
f.write('&output\n')
f.write(" waves_mesh_culled_vtk = 'waves_mesh_culled.vtk'\n")
f.write(" waves_mesh_culled_gmsh = 'waves_mesh_culled.msh'\n")
f.write("/\n")
f.close()
subprocess.call('./cull_waves_mesh', shell=True)
#------------------------------------ output ocean mesh polygons
subprocess.call('paraview_vtk_field_extractor.py -f ' + cfg['ocean_mesh'] +
' --ignore_time -v areaCell -o ' + cfg['ocean_mesh'] +
'.vtk',
shell=True)
return
def run(self):
"""
Run this step of the test case
"""
config = self.config
logger = self.logger
section = config['ice_shelf_2d']
nx = section.getint('nx')
ny = section.getint('ny')
dc = section.getfloat('dc')
dsMesh = make_planar_hex_mesh(nx=nx, ny=ny, dc=dc, nonperiodic_x=False,
nonperiodic_y=True)
write_netcdf(dsMesh, 'base_mesh.nc')
dsMesh = cull(dsMesh, logger=logger)
dsMesh = convert(dsMesh, graphInfoFileName='culled_graph.info',
logger=logger)
write_netcdf(dsMesh, 'culled_mesh.nc')
bottom_depth = config.getfloat('vertical_grid', 'bottom_depth')
section = config['ice_shelf_2d']
temperature = section.getfloat('temperature')
surface_salinity = section.getfloat('surface_salinity')
bottom_salinity = section.getfloat('bottom_salinity')
# points 1 and 2 are where angles on ice shelf are located.
# point 3 is at the surface.
# d variables are total water-column thickness below ice shelf
y1 = section.getfloat('y1')
y2 = section.getfloat('y2')
y3 = y2 + section.getfloat('edge_width')
d1 = section.getfloat('cavity_thickness')
d2 = d1 + section.getfloat('slope_height')
d3 = bottom_depth
ds = dsMesh.copy()
ds['bottomDepth'] = bottom_depth * xarray.ones_like(ds.xCell)
yCell = ds.yCell
column_thickness = xarray.where(
yCell < y1, d1, d1 + (d2 - d1) * (yCell - y1) / (y2 - y1))
column_thickness = xarray.where(
yCell < y2, column_thickness,
d2 + (d3 - d2) * (yCell - y2) / (y3 - y2))
column_thickness = xarray.where(yCell < y3, column_thickness, d3)
ds['ssh'] = -bottom_depth + column_thickness
# set up the vertical coordinate
init_vertical_coord(config, ds)
modify_mask = xarray.where(yCell < y3, 1, 0).expand_dims(
dim='Time', axis=0)
landIceFraction = modify_mask.astype(float)
landIceMask = modify_mask.copy()
ref_density = constants['SHR_CONST_RHOSW']
landIcePressure, landIceDraft = compute_land_ice_pressure_and_draft(
ssh=ds.ssh, modify_mask=modify_mask, ref_density=ref_density)
salinity = surface_salinity + ((bottom_salinity - surface_salinity) *
(ds.zMid / (-bottom_depth)))
salinity, _ = xarray.broadcast(salinity, ds.layerThickness)
salinity = salinity.transpose('Time', 'nCells', 'nVertLevels')
normalVelocity = xarray.zeros_like(ds.xEdge)
normalVelocity, _ = xarray.broadcast(normalVelocity, ds.refBottomDepth)
normalVelocity = normalVelocity.transpose('nEdges', 'nVertLevels')
normalVelocity = normalVelocity.expand_dims(dim='Time', axis=0)
ds['temperature'] = temperature * xarray.ones_like(ds.layerThickness)
ds['salinity'] = salinity
ds['normalVelocity'] = normalVelocity
ds['fCell'] = xarray.zeros_like(ds.xCell)
ds['fEdge'] = xarray.zeros_like(ds.xEdge)
ds['fVertex'] = xarray.zeros_like(ds.xVertex)
ds['modifyLandIcePressureMask'] = modify_mask
ds['landIceFraction'] = landIceFraction
ds['landIceMask'] = landIceMask
ds['landIcePressure'] = landIcePressure
ds['landIceDraft'] = landIceDraft
write_netcdf(ds, 'initial_state.nc')
def saveesm(path,
geom,
mesh,
preserve_floodplain=False,
floodplain_elevation=20.0,
do_inject_elevation=False,
with_cavities=False,
lat_threshold=43.00,
with_critical_passages=True):
"""
SAVEESM: export a jigsaw mesh obj. to MPAS-style output.
1. Writes "mesh_triangles.nc" and "base_mesh.nc" files.
2. (Optionally) injects elevation + floodplain data.
3. Calls MPAS-Tools + Geometric-Data to cull mesh into
ocean/land partitions.
4. Writes "culled_mesh.nc" (ocean) and "invert_mesh.nc"
(land) MPAS-spec. output files.
Data is written to "../path/out/" and/or "../path/tmp/".
"""
# Authors: Darren Engwirda
ttic = time.time()
print("")
print("Running MPAS mesh-tools...")
inject_edge_tags(mesh)
# adapted from BUILD_MESH.py
if (geom.mshID.lower() == "ellipsoid-mesh"):
print("Forming mesh_triangles.nc")
jigsaw_mesh_to_netcdf(mesh=mesh,
on_sphere=True,
sphere_radius=np.mean(geom.radii) * 1e3,
output_name=os.path.join(path, "tmp",
"mesh_triangles.nc"))
if (geom.mshID.lower() == "euclidean-mesh"):
print("Forming mesh_triangles.nc")
jigsaw_mesh_to_netcdf(mesh=mesh,
on_sphere=False,
output_name=os.path.join(path, "tmp",
"mesh_triangles.nc"))
print("Forming base_mesh.nc")
write_netcdf(convert(
xarray.open_dataset(os.path.join(path, "tmp", "mesh_triangles.nc"))),
fileName=os.path.join(path, "out", "base_mesh.nc"))
"""
if do_inject_elevation:
print("Injecting cell elevations")
inject_elevation(
cell_elev=mesh.value,
mesh_file=os.path.join(
path, "out", "base_mesh.nc"))
"""
if preserve_floodplain:
print("Injecting floodplain flag")
inject_preserve_floodplain(mesh_file=os.path.join(
path, "out", "base_mesh.nc"),
floodplain_elevation=floodplain_elevation)
args = [
"paraview_vtk_field_extractor.py", "--ignore_time", "-l", "-d",
"maxEdges=0", "-v", "allOnCells", "-f",
os.path.join(path, "out", "base_mesh.nc"), "-o",
os.path.join(path, "out", "base_mesh_vtk")
]
print("")
print("running:", " ".join(args))
subprocess.check_call(args, env=os.environ.copy())
# adapted from CULL_MESH.py
# required for compatibility with MPAS
netcdfFormat = "NETCDF3_64BIT"
gf = GeometricFeatures(cacheLocation="{}".format(
os.path.join(HERE, "..", "data", "geometric_data")))
# start with the land coverage from Natural Earth
fcLandCoverage = gf.read(componentName="natural_earth",
objectType="region",
featureNames=["Land Coverage"])
# remove the region south of 60S so we can replace
# it based on ice-sheet topography
fcSouthMask = gf.read(componentName="ocean",
objectType="region",
featureNames=["Global Ocean 90S to 60S"])
fcLandCoverage = \
fcLandCoverage.difference(fcSouthMask)
# add land coverage from either the full ice sheet
# or just the grounded part
if with_cavities:
fcAntarcticLand = gf.read(
componentName="bedmap2",
objectType="region",
featureNames=["AntarcticGroundedIceCoverage"])
else:
fcAntarcticLand = gf.read(componentName="bedmap2",
objectType="region",
featureNames=["AntarcticIceCoverage"])
fcLandCoverage.merge(fcAntarcticLand)
# save the feature collection to a geojson file
fcLandCoverage.to_geojson(
os.path.join(path, "tmp", "land_coverage.geojson"))
# Create the land mask based on the land coverage,
# i.e. coastline data.
dsBaseMesh = xarray.open_dataset(os.path.join(path, "out", "base_mesh.nc"))
dsLandMask = mask(dsBaseMesh, fcMask=fcLandCoverage)
dsLandMask = add_land_locked_cells_to_mask(
dsLandMask, dsBaseMesh, latitude_threshold=lat_threshold, nSweeps=20)
if with_critical_passages:
# merge transects for critical passages into
# critical_passages.geojson
fcCritPassages = gf.read(componentName="ocean",
objectType="transect",
tags=["Critical_Passage"])
# create masks from the transects
dsCritPassMask = \
mask(dsBaseMesh, fcMask=fcCritPassages)
# Alter critical passages to be at least two
# cells wide, to avoid sea ice blockage.
dsCritPassMask = widen_transect_edge_masks(
dsCritPassMask, dsBaseMesh, latitude_threshold=lat_threshold)
dsLandMask = subtract_critical_passages(dsLandMask, dsCritPassMask)
# merge transects for critical land blockages
# into critical_land_blockages.geojson
fcCritBlockages = gf.read(componentName="ocean",
objectType="transect",
tags=["Critical_Land_Blockage"])
# create masks from the transects for critical
# land blockages
dsCritBlockMask = \
mask(dsBaseMesh, fcMask=fcCritBlockages)
dsLandMask = add_critical_land_blockages(dsLandMask, dsCritBlockMask)
# create seed points for a flood fill of the ocean
# use all points in the ocean directory, on the
# assumption that they are, in fact *in* the ocean
fcSeed = gf.read(componentName="ocean",
objectType="point",
tags=["seed_point"])
# update the land mask to ensure all ocean cells really
# are "reachable" from the rest of the global ocean
dsLandMask = mask_reachable_ocean(dsMesh=dsBaseMesh,
dsMask=dsLandMask,
fcSeed=fcSeed)
# cull the (ocean) mesh based on the land mask, and a
# cull the (land) mesh using the inverse mask
if preserve_floodplain:
# with "preserve_floodplains", the (ocean) mesh will
# contain overlap with the (land) mesh, otherwise the
# two are "perfectly" disjoint
dsCulledMesh = cull(dsBaseMesh,
dsMask=dsLandMask,
dsPreserve=dsBaseMesh,
graphInfoFileName=os.path.join(
path, "out", "culled_graph.info"))
dsInvertMesh = cull(dsBaseMesh,
dsInverse=dsLandMask,
graphInfoFileName=os.path.join(
path, "out", "invert_graph.info"))
else:
dsCulledMesh = cull(dsBaseMesh,
dsMask=dsLandMask,
graphInfoFileName=os.path.join(
path, "out", "culled_graph.info"))
dsInvertMesh = cull(dsBaseMesh,
dsInverse=dsLandMask,
graphInfoFileName=os.path.join(
path, "out", "invert_graph.info"))
write_netcdf(dsCulledMesh, os.path.join(path, "out", "culled_mesh.nc"),
netcdfFormat)
write_netcdf(dsInvertMesh, os.path.join(path, "out", "invert_mesh.nc"),
netcdfFormat)
args = [
"paraview_vtk_field_extractor.py", "--ignore_time", "-d", "maxEdges=",
"-v", "allOnCells", "-f",
os.path.join(path, "out", "culled_mesh.nc"), "-o",
os.path.join(path, "out", "culled_mesh_vtk")
]
print("")
print("running", " ".join(args))
subprocess.check_call(args, env=os.environ.copy())
args = [
"paraview_vtk_field_extractor.py", "--ignore_time", "-d", "maxEdges=",
"-v", "allOnCells", "-f",
os.path.join(path, "out", "invert_mesh.nc"), "-o",
os.path.join(path, "out", "invert_mesh_vtk")
]
print("running", " ".join(args))
subprocess.check_call(args, env=os.environ.copy())
ttoc = time.time()
print("CPUSEC =", (ttoc - ttic))
return
def run(self):
"""
Run this step of the test case
"""
logger = self.logger
config = self.config
section = config['humboldt']
logger.info('calling build_cell_wdith')
cell_width, x1, y1, geom_points, geom_edges = self.build_cell_width()
logger.info('calling build_planar_mesh')
build_planar_mesh(cell_width,
x1,
y1,
geom_points,
geom_edges,
logger=logger)
dsMesh = xarray.open_dataset('base_mesh.nc')
logger.info('culling mesh')
dsMesh = cull(dsMesh, logger=logger)
logger.info('converting to MPAS mesh')
dsMesh = convert(dsMesh, logger=logger)
logger.info('writing grid_converted.nc')
write_netcdf(dsMesh, 'grid_converted.nc')
# If no number of levels specified in config file, use 10
levels = section.get('levels')
logger.info('calling create_landice_grid_from_generic_MPAS_grid.py')
args = [
'create_landice_grid_from_generic_MPAS_grid.py', '-i',
'grid_converted.nc', '-o', 'gis_1km_preCull.nc', '-l', levels,
'-v', 'glimmer'
]
check_call(args, logger=logger)
# This step uses a subset of the whole Greenland dataset trimmed to
# the region around Humboldt Glacier, to speed up interpolation.
# This could also be replaced with the full Greenland Ice Sheet
# dataset.
logger.info('calling interpolate_to_mpasli_grid.py')
args = [
'interpolate_to_mpasli_grid.py', '-s',
'humboldt_1km_2020_04_20.epsg3413.icesheetonly.nc', '-d',
'gis_1km_preCull.nc', '-m', 'b', '-t'
]
check_call(args, logger=logger)
# This step is only necessary if you wish to cull a certain
# distance from the ice margin, within the bounds defined by
# the GeoJSON file.
cullDistance = section.get('cullDistance')
if float(cullDistance) > 0.:
logger.info('calling define_cullMask.py')
args = [
'define_cullMask.py', '-f', 'gis_1km_preCull.nc', '-m'
'distance', '-d', cullDistance
]
check_call(args, logger=logger)
else:
logger.info('cullDistance <= 0 in config file. '
'Will not cull by distance to margin. \n')
# This step is only necessary because the GeoJSON region
# is defined by lat-lon.
logger.info('calling set_lat_lon_fields_in_planar_grid.py')
args = [
'set_lat_lon_fields_in_planar_grid.py', '-f', 'gis_1km_preCull.nc',
'-p', 'gis-gimp'
]
check_call(args, logger=logger)
logger.info('calling MpasMaskCreator.x')
args = [
'MpasMaskCreator.x', 'gis_1km_preCull.nc', 'humboldt_mask.nc',
'-f', 'Humboldt.geojson'
]
check_call(args, logger=logger)
logger.info('culling to geojson file')
dsMesh = xarray.open_dataset('gis_1km_preCull.nc')
humboldtMask = xarray.open_dataset('humboldt_mask.nc')
dsMesh = cull(dsMesh, dsInverse=humboldtMask, logger=logger)
write_netcdf(dsMesh, 'humboldt_culled.nc')
logger.info('Marking horns for culling')
args = ['mark_horns_for_culling.py', '-f', 'humboldt_culled.nc']
check_call(args, logger=logger)
logger.info('culling and converting')
dsMesh = xarray.open_dataset('humboldt_culled.nc')
dsMesh = cull(dsMesh, logger=logger)
dsMesh = convert(dsMesh, logger=logger)
write_netcdf(dsMesh, 'humboldt_dehorned.nc')
logger.info('calling create_landice_grid_from_generic_MPAS_grid.py')
args = [
'create_landice_grid_from_generic_MPAS_grid.py', '-i',
'humboldt_dehorned.nc', '-o', 'Humboldt_1to10km.nc', '-l', levels,
'-v', 'glimmer', '--beta', '--thermal', '--obs', '--diri'
]
check_call(args, logger=logger)
logger.info('calling interpolate_to_mpasli_grid.py')
args = [
'interpolate_to_mpasli_grid.py', '-s',
'humboldt_1km_2020_04_20.epsg3413.icesheetonly.nc', '-d',
'Humboldt_1to10km.nc', '-m', 'b', '-t'
]
check_call(args, logger=logger)
logger.info('Marking domain boundaries dirichlet')
args = [
'mark_domain_boundaries_dirichlet.py', '-f', 'Humboldt_1to10km.nc'
]
check_call(args, logger=logger)
logger.info('calling set_lat_lon_fields_in_planar_grid.py')
args = [
'set_lat_lon_fields_in_planar_grid.py', '-f',
'Humboldt_1to10km.nc', '-p', 'gis-gimp'
]
check_call(args, logger=logger)
logger.info('creating graph.info')
make_graph_file(mesh_filename='Humboldt_1to10km.nc',
graph_filename='graph.info')
def run(self):
"""
Run this step of the test case
"""
config = self.config
logger = self.logger
section = config['baroclinic_channel']
nx = section.getint('nx')
ny = section.getint('ny')
dc = section.getfloat('dc')
dsMesh = make_planar_hex_mesh(nx=nx,
ny=ny,
dc=dc,
nonperiodic_x=False,
nonperiodic_y=True)
write_netcdf(dsMesh, 'base_mesh.nc')
dsMesh = cull(dsMesh, logger=logger)
dsMesh = convert(dsMesh,
graphInfoFileName='culled_graph.info',
logger=logger)
write_netcdf(dsMesh, 'culled_mesh.nc')
section = config['baroclinic_channel']
use_distances = section.getboolean('use_distances')
gradient_width_dist = section.getfloat('gradient_width_dist')
gradient_width_frac = section.getfloat('gradient_width_frac')
bottom_temperature = section.getfloat('bottom_temperature')
surface_temperature = section.getfloat('surface_temperature')
temperature_difference = section.getfloat('temperature_difference')
salinity = section.getfloat('salinity')
coriolis_parameter = section.getfloat('coriolis_parameter')
ds = dsMesh.copy()
xCell = ds.xCell
yCell = ds.yCell
bottom_depth = config.getfloat('vertical_grid', 'bottom_depth')
ds['bottomDepth'] = bottom_depth * xarray.ones_like(xCell)
ds['ssh'] = xarray.zeros_like(xCell)
init_vertical_coord(config, ds)
xMin = xCell.min().values
xMax = xCell.max().values
yMin = yCell.min().values
yMax = yCell.max().values
yMid = 0.5 * (yMin + yMax)
xPerturbMin = xMin + 4.0 * (xMax - xMin) / 6.0
xPerturbMax = xMin + 5.0 * (xMax - xMin) / 6.0
if use_distances:
perturbationWidth = gradient_width_dist
else:
perturbationWidth = (yMax - yMin) * gradient_width_frac
yOffset = perturbationWidth * numpy.sin(6.0 * numpy.pi *
(xCell - xMin) / (xMax - xMin))
temp_vert = (bottom_temperature +
(surface_temperature - bottom_temperature) *
((ds.refZMid + bottom_depth) / bottom_depth))
frac = xarray.where(yCell < yMid - yOffset, 1., 0.)
mask = numpy.logical_and(yCell >= yMid - yOffset,
yCell < yMid - yOffset + perturbationWidth)
frac = xarray.where(
mask, 1. - (yCell - (yMid - yOffset)) / perturbationWidth, frac)
temperature = temp_vert - temperature_difference * frac
temperature = temperature.transpose('nCells', 'nVertLevels')
# Determine yOffset for 3rd crest in sin wave
yOffset = 0.5 * perturbationWidth * numpy.sin(
numpy.pi * (xCell - xPerturbMin) / (xPerturbMax - xPerturbMin))
mask = numpy.logical_and(
numpy.logical_and(
yCell >= yMid - yOffset - 0.5 * perturbationWidth,
yCell <= yMid - yOffset + 0.5 * perturbationWidth),
numpy.logical_and(xCell >= xPerturbMin, xCell <= xPerturbMax))
temperature = (temperature + mask * 0.3 *
(1. - ((yCell - (yMid - yOffset)) /
(0.5 * perturbationWidth))))
temperature = temperature.expand_dims(dim='Time', axis=0)
normalVelocity = xarray.zeros_like(ds.xEdge)
normalVelocity, _ = xarray.broadcast(normalVelocity, ds.refBottomDepth)
normalVelocity = normalVelocity.transpose('nEdges', 'nVertLevels')
normalVelocity = normalVelocity.expand_dims(dim='Time', axis=0)
ds['temperature'] = temperature
ds['salinity'] = salinity * xarray.ones_like(temperature)
ds['normalVelocity'] = normalVelocity
ds['fCell'] = coriolis_parameter * xarray.ones_like(xCell)
ds['fEdge'] = coriolis_parameter * xarray.ones_like(ds.xEdge)
ds['fVertex'] = coriolis_parameter * xarray.ones_like(ds.xVertex)
write_netcdf(ds, 'ocean.nc')
def run(self):
"""
Run this step of the test case
"""
config = self.config
logger = self.logger
section = config['isomip_plus']
nx = section.getint('nx')
ny = section.getint('ny')
dc = section.getfloat('dc')
filter_sigma = section.getfloat('topo_smoothing') * self.resolution
min_ice_thickness = section.getfloat('min_ice_thickness')
min_land_ice_fraction = section.getfloat('min_land_ice_fraction')
draft_scaling = section.getfloat('draft_scaling')
process_input_geometry('input_geometry.nc',
'input_geometry_processed.nc',
filterSigma=filter_sigma,
minIceThickness=min_ice_thickness,
scale=draft_scaling)
dsMesh = make_planar_hex_mesh(nx=nx + 2,
ny=ny + 2,
dc=dc,
nonperiodic_x=False,
nonperiodic_y=False)
translate(mesh=dsMesh, yOffset=-2 * dc)
write_netcdf(dsMesh, 'base_mesh.nc')
dsGeom = xarray.open_dataset('input_geometry_processed.nc')
min_ocean_fraction = config.getfloat('isomip_plus',
'min_ocean_fraction')
dsMask = interpolate_ocean_mask(dsMesh, dsGeom, min_ocean_fraction)
dsMesh = cull(dsMesh, dsInverse=dsMask, logger=logger)
dsMesh.attrs['is_periodic'] = 'NO'
dsMesh = convert(dsMesh,
graphInfoFileName='culled_graph.info',
logger=logger)
write_netcdf(dsMesh, 'culled_mesh.nc')
ds = interpolate_geom(dsMesh, dsGeom, min_ocean_fraction)
for var in ['landIceFraction']:
ds[var] = ds[var].expand_dims(dim='Time', axis=0)
ds['landIceMask'] = \
(ds.landIceFraction >= min_land_ice_fraction).astype(int)
ref_density = constants['SHR_CONST_RHOSW']
landIcePressure, landIceDraft = compute_land_ice_pressure_and_draft(
ssh=ds.ssh, modify_mask=ds.ssh < 0., ref_density=ref_density)
ds['landIcePressure'] = landIcePressure
ds['landIceDraft'] = landIceDraft
if self.time_varying_forcing:
self._write_time_varying_forcing(ds_init=ds)
ds['bottomDepth'] = -ds.bottomDepthObserved
section = config['isomip_plus']
min_column_thickness = section.getfloat('min_column_thickness')
min_levels = section.getint('minimum_levels')
interfaces = generate_1d_grid(config)
# Deepen the bottom depth to maintain the minimum water-column
# thickness
min_depth = numpy.maximum(-ds.ssh + min_column_thickness,
interfaces[min_levels + 1])
ds['bottomDepth'] = numpy.maximum(ds.bottomDepth, min_depth)
init_vertical_coord(config, ds)
ds['modifyLandIcePressureMask'] = \
(ds['landIceFraction'] > 0.01).astype(int)
max_bottom_depth = -config.getfloat('vertical_grid', 'bottom_depth')
frac = (0. - ds.zMid) / (0. - max_bottom_depth)
# compute T, S
init_top_temp = section.getfloat('init_top_temp')
init_bot_temp = section.getfloat('init_bot_temp')
init_top_sal = section.getfloat('init_top_sal')
init_bot_sal = section.getfloat('init_bot_sal')
ds['temperature'] = (1.0 - frac) * init_top_temp + frac * init_bot_temp
ds['salinity'] = (1.0 - frac) * init_top_sal + frac * init_bot_sal
# compute coriolis
coriolis_parameter = section.getfloat('coriolis_parameter')
ds['fCell'] = coriolis_parameter * xarray.ones_like(ds.xCell)
ds['fEdge'] = coriolis_parameter * xarray.ones_like(ds.xEdge)
ds['fVertex'] = coriolis_parameter * xarray.ones_like(ds.xVertex)
normalVelocity = xarray.zeros_like(ds.xEdge)
normalVelocity = normalVelocity.broadcast_like(ds.refBottomDepth)
normalVelocity = normalVelocity.transpose('nEdges', 'nVertLevels')
ds['normalVelocity'] = normalVelocity.expand_dims(dim='Time', axis=0)
write_netcdf(ds, 'initial_state.nc')
plot_folder = '{}/plots'.format(self.work_dir)
if os.path.exists(plot_folder):
shutil.rmtree(plot_folder)
# plot a few fields
section_y = config.getfloat('isomip_plus_viz', 'section_y')
# show progress only if we're not writing to a log file
show_progress = self.log_filename is None
plotter = MoviePlotter(inFolder=self.work_dir,
streamfunctionFolder=self.work_dir,
outFolder=plot_folder,
expt=self.experiment,
sectionY=section_y,
dsMesh=ds,
ds=ds,
showProgress=show_progress)
plotter.plot_3d_field_top_bot_section(ds.zMid,
nameInTitle='zMid',
prefix='zmid',
units='m',
vmin=-720.,
vmax=0.,
cmap='cmo.deep_r')
plotter.plot_3d_field_top_bot_section(ds.temperature,
nameInTitle='temperature',
prefix='temp',
units='C',
vmin=-2.,
vmax=1.,
cmap='cmo.thermal')
plotter.plot_3d_field_top_bot_section(ds.salinity,
nameInTitle='salinity',
prefix='salin',
units='PSU',
vmin=33.8,
vmax=34.7,
cmap='cmo.haline')
# compute restoring
dsForcing = xarray.Dataset()
restore_top_temp = section.getfloat('restore_top_temp')
restore_bot_temp = section.getfloat('restore_bot_temp')
restore_top_sal = section.getfloat('restore_top_sal')
restore_bot_sal = section.getfloat('restore_bot_sal')
dsForcing['temperatureInteriorRestoringValue'] = \
(1.0 - frac) * restore_top_temp + frac * restore_bot_temp
dsForcing['salinityInteriorRestoringValue'] = \
(1.0 - frac) * restore_top_sal + frac * restore_bot_sal
restore_rate = section.getfloat('restore_rate')
restore_xmin = section.getfloat('restore_xmin')
restore_xmax = section.getfloat('restore_xmax')
frac = numpy.maximum(
(ds.xCell - restore_xmin) / (restore_xmax - restore_xmin), 0.)
frac = frac.broadcast_like(dsForcing.temperatureInteriorRestoringValue)
# convert from 1/days to 1/s
dsForcing['temperatureInteriorRestoringRate'] = \
frac * restore_rate / constants['SHR_CONST_CDAY']
dsForcing['salinityInteriorRestoringRate'] = \
dsForcing.temperatureInteriorRestoringRate
# compute "evaporation"
restore_evap_rate = section.getfloat('restore_evap_rate')
mask = numpy.logical_and(ds.xCell >= restore_xmin,
ds.xCell <= restore_xmax)
mask = mask.expand_dims(dim='Time', axis=0)
# convert to m/s, negative for evaporation rather than precipitation
evap_rate = -restore_evap_rate / (constants['SHR_CONST_CDAY'] * 365)
# PSU*m/s to kg/m^2/s
sflux_factor = 1.
# C*m/s to W/m^2
hflux_factor = 1. / (ref_density * constants['SHR_CONST_CPSW'])
dsForcing['evaporationFlux'] = mask * ref_density * evap_rate
dsForcing['seaIceSalinityFlux'] = \
mask*evap_rate*restore_top_sal/sflux_factor
dsForcing['seaIceHeatFlux'] = \
mask*evap_rate*restore_top_temp/hflux_factor
write_netcdf(dsForcing, 'init_mode_forcing_data.nc')