Source code for compass.landice.tests.circular_shelf.setup_mesh

import numpy
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 circular_shelf test cases Attributes ---------- mesh_type : str The resolution or mesh type of the test case """
[docs] def __init__(self, test_case): """ Create the step Parameters ---------- test_case : compass.TestCase The test case this step belongs to """ super().__init__(test_case=test_case, name='setup_mesh') self.mesh_type = test_case.mesh_type 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 """ logger = self.logger config = self.config section = config['circular_shelf'] 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, '--diri'] check_call(args, logger) make_graph_file(mesh_filename='landice_grid.nc', graph_filename='graph.info') _setup_circular_shelf_initial_conditions(config, logger, filename='landice_grid.nc')
def _setup_circular_shelf_initial_conditions(config, logger, filename): """ Add the initial condition to the given MPAS mesh file Parameters ---------- config : compass.config.CompassConfigParser Configuration options for this test case, a combination of the defaults for the machine, core and configuration logger : logging.Logger A logger for output from the step filename : str file to setup circular_shelf """ section = config['circular_shelf'] use_mu = section.getboolean('use_mu') use_7cells = section.getboolean('use_7cells') # Open the file, get needed dimensions gridfile = NetCDFFile(filename, 'r+') nVertLevels = len(gridfile.dimensions['nVertLevels']) if nVertLevels != 5: logger.info('nVertLevels in the supplied file was {}. ' 'This test case is typically run with 5 levels.' .format(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'] cellsOnCell = gridfile.variables['cellsOnCell'] # Get b.c. variables SMB = gridfile.variables['sfcMassBal'] # Center the circular_shelf in the center of the cell that is closest to # the center of the domain. # Only do this if it appears this has not already been done: if xVertex[:].min() >= 0.0: logger.info("Shifting x/y coordinates to center domain at 0,0.") # 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 circular_shelf center r = ((xCell[:] - x0)**2 + (yCell[:] - y0)**2)**0.5 centerCellIndex = numpy.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 our local values of the origin location and distance array # (or assume these are correct because this grid has previously been # shifted) x0 = 0.0 y0 = 0.0 r = ((xCell[:] - x0)**2 + (yCell[:] - y0)**2)**0.5 centerCellIndex = numpy.abs(r[:]).argmin() # Make a circular ice mass # Define circular_shelf dimensions - all in meters r0 = 21000.0 thickness[:] = 0.0 # initialize to 0.0 # Calculate the circular_shelf thickness for cells within the desired # radius (thickness will be NaN otherwise) thickness_field = thickness[0, :] thickness_field[r < r0] = 1000.0 thickness[0, :] = thickness_field # flat bed at -2000 m everywhere with a single grounded point bedTopography[:] = -2000.0 bedTopography[0, centerCellIndex] = -880.0 if use_7cells: logger.info('Making the grounded portion of the domain cover 7 cells ' '- the center cell and its 6 neighbors.') bedTopography[0, cellsOnCell[centerCellIndex, :] - 1] = -880.0 else: logger.info('Making the grounded portion of the domain cover 1 cell' '- the center cell.') if use_mu: logger.info('Setting no-slip on the grounded portion of the domain' 'by setting a high mu field there.') mu = gridfile.variables['muFriction'] # mu is 0 everywhere except a high value in the grounded cell mu[:] = 0.0 mu[centerCellIndex] = 1.0e8 if use_7cells: mu[cellsOnCell[centerCellIndex, :] - 1] = 1.0e8 else: # use Dirichlet b.c. logger.info('Setting no-slip on the grounded portion of the domain' 'by setting no-slip Dirichlet velocity boundary' 'conditions there.') dirMask = gridfile.variables['dirichletVelocityMask'] uvel = gridfile.variables['uReconstructX'] vvel = gridfile.variables['uReconstructY'] dirMask[:] = 0 uvel[:] = 0.0 vvel[:] = 0.0 # Apply mask to basal level of grounded portion only dirMask[:, centerCellIndex, -1] = 1 if use_7cells: dirMask[:, cellsOnCell[centerCellIndex, :] - 1, -1] = 1 # Setup layerThicknessFractions layerThicknessFractions[:] = 1.0 / nVertLevels # boundary conditions SMB[:] = 0.0 # m/yr # Convert from units of m/yr to kg/m2/s using an assumed ice density SMB[:] = SMB[:] * 910.0 / (3600.0 * 24.0 * 365.0) gridfile.close() logger.info('Successfully added circular shelf initial conditions to: {}' .format(filename))