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 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
resolution = float(self.resolution)
section = config['planar_convergence']
nx_1km = section.getint('nx_1km')
ny_1km = section.getint('ny_1km')
nx = int(nx_1km / resolution)
ny = int(ny_1km / resolution)
dc = resolution * 1e3
ds_mesh = make_planar_hex_mesh(nx=nx,
ny=ny,
dc=dc,
nonperiodic_x=False,
nonperiodic_y=False)
center(ds_mesh)
write_netcdf(ds_mesh, 'mesh.nc')
make_graph_file('mesh.nc', 'graph.info')
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 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 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')