import numpy as np
from netCDF4 import Dataset as NetCDFFile
from mpas_tools.planar_hex import make_planar_hex_mesh
from mpas_tools.io import write_netcdf
from mpas_tools.mesh.conversion import convert, cull
from mpas_tools.logging import check_call
from compass.model import make_graph_file
from compass.step import Step
[docs]class SetupMesh(Step):
"""
A step for creating a mesh and initial condition for dome test cases
Attributes
----------
initial_condition : {'zero', 'exact'}
The type of initial condition to set up. 'zero' means nearly zero ice
thickness. 'exact' uses a precomputed near exact solution from a file.
"""
[docs] def __init__(self, test_case, initial_condition):
"""
Create the step
Parameters
----------
test_case : compass.TestCase
The test case this step belongs to
initial_condition : {'zero', 'exact'}
The type of initial condition to set up. 'zero' means nearly zero
ice thickness. 'exact' uses a precomputed near exact solution from
a file.
"""
super().__init__(test_case=test_case, name='setup_mesh')
self.initial_condition = initial_condition
if initial_condition == 'exact':
self.add_input_file(filename='near_exact_solution_r_P_W.txt',
package='compass.landice.tests.hydro_radial')
elif initial_condition != 'zero':
raise ValueError("Unknown initial condition type specified "
"{}.".format(initial_condition))
self.add_output_file(filename='graph.info')
self.add_output_file(filename='landice_grid.nc')
# no setup() method is needed
[docs] def run(self):
"""
Run this step of the test case
"""
initial_condition = self.initial_condition
logger = self.logger
section = self.config['hydro_radial']
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,
'--hydro',
'--diri']
check_call(args, logger)
make_graph_file(mesh_filename='landice_grid.nc',
graph_filename='graph.info')
_setup_hydro_radial_initial_conditions(
logger, filename='landice_grid.nc',
initial_condition=initial_condition)
def _setup_hydro_radial_initial_conditions(logger, filename,
initial_condition):
"""
Add the initial condition to the given MPAS mesh file
Parameters
----------
logger : logging.Logger
A logger for output from the step
filename : str
file to setup hydro_radial
initial_condition : {'zero', 'exact'}
the type of initial condition
"""
# Open the file, get needed dimensions
gridfile = NetCDFFile(filename, 'r+')
nVertLevels = len(gridfile.dimensions['nVertLevels'])
# Get variables
xCell = gridfile.variables['xCell']
yCell = gridfile.variables['yCell']
xEdge = gridfile.variables['xEdge']
yEdge = gridfile.variables['yEdge']
xVertex = gridfile.variables['xVertex']
yVertex = gridfile.variables['yVertex']
thickness = gridfile.variables['thickness']
bedTopography = gridfile.variables['bedTopography']
layerThicknessFractions = gridfile.variables['layerThicknessFractions']
# Find center of domain
x0 = xCell[:].min() + 0.5 * (xCell[:].max() - xCell[:].min())
y0 = yCell[:].min() + 0.5 * (yCell[:].max() - yCell[:].min())
# Calculate distance of each cell center from dome center
r = ((xCell[:] - x0)**2 + (yCell[:] - y0)**2)**0.5
# Center the dome in the center of the cell that is closest to the center
# of the domain.
# NOTE: for some meshes, maybe we don't want to do this - could add
# command-line argument controlling this later.
putOriginOnACell = True
if putOriginOnACell:
centerCellIndex = np.abs(r[:]).argmin()
xShift = -1.0 * xCell[centerCellIndex]
yShift = -1.0 * yCell[centerCellIndex]
xCell[:] = xCell[:] + xShift
yCell[:] = yCell[:] + yShift
xEdge[:] = xEdge[:] + xShift
yEdge[:] = yEdge[:] + yShift
xVertex[:] = xVertex[:] + xShift
yVertex[:] = yVertex[:] + yShift
# Now update origin location and distance array
x0 = 0.0
y0 = 0.0
r = ((xCell[:] - x0)**2 + (yCell[:] - y0)**2)**0.5
# center thickness (m)
h0 = 500.0
# sliding velocity at margin (m/s)
v0 = 100.0 / (3600.0 * 24.0 * 365.0)
# ideal ice cap radius (m)
R0 = 25.0e3
# onset of sliding (m)
R1 = 5.0e3
# actual margin location (m)
L = 0.9 * R0
thickness[0, r < R0] = h0 * (1.0 - (r[r < R0] / R0)**2)
thickness[0, r > L] = 0.0
# flat bed
bedTopography[:] = 0.0
# Setup layerThicknessFractions
layerThicknessFractions[:] = 1.0 / nVertLevels
# melt
gridfile.variables['basalMeltInput'][:] = 0.0
# 20 cm/yr as SI mass rate
gridfile.variables['basalMeltInput'][:] = \
0.2 / (365.0 * 24.0 * 3600.0) * 1000.0
# Use this line to only add a source term to the center cell - useful for
# debugging divergence
# value from ramp
# gridfile.variables['basalMeltInput'][0,r==0.0] = 4.0e-10 * 1000.0 *100
# velocity
gridfile.variables['uReconstructX'][:] = 0.0
velo = v0 * (r - R1)**5 / (L - R1)**5
velo[r < R1] = 0.0
gridfile.variables['uReconstructX'][0, :, -1] = velo
gridfile.variables['uReconstructX'][0, thickness[0, :] == 0.0, :] = 0.0
if initial_condition == 'zero':
logger.info("Using 'zero' option for initial condition.")
# set some small initial value to keep adaptive time stepper from
# taking a huge time step initially
gridfile.variables['waterThickness'][0, :] = 0.01
gridfile.variables['waterPressure'][0, :] = 0.0
elif initial_condition == 'exact':
logger.info("Using 'exact' option for initial condition.")
# IC on thickness
# import exact solution
fnameSoln = 'near_exact_solution_r_P_W.txt'
soln = np.loadtxt(fnameSoln, delimiter=',')
rsoln = soln[:, 0]
Psoln = soln[:, 1]
Wsoln = soln[:, 2]
Wmpas = np.interp(r, rsoln, Wsoln) # apply exact solution
Wmpas[np.isnan(Wmpas)] = 0.0
gridfile.variables['waterThickness'][0, :] = Wmpas
# IC on water pressure
# apply exact solution
Pmpas = np.interp(r, rsoln, Psoln)
Pmpas[np.isnan(Pmpas)] = 0.0
gridfile.variables['waterPressure'][0, :] = Pmpas
else:
raise ValueError("Unknown initial condition type specified "
"{}.".format(initial_condition))
gridfile.close()
logger.info('Successfully added hydro_radial initial conditions to: '
'{}'.format(filename))