Source code for compass.ocean.tests.global_ocean.files_for_e3sm.ocean_mesh

import os

import numpy as np
import xarray as xr
from import write_netcdf

from import symlink
from compass.ocean.tests.global_ocean.files_for_e3sm.files_for_e3sm_step import (  # noqa: E501
from compass.ocean.vertical import (

[docs]class OceanMesh(FilesForE3SMStep): """ A step for creating an MPAS-Ocean mesh from variables from an MPAS-Ocean initial state file """
[docs] def __init__(self, test_case): """ Create a new step Parameters ---------- test_case : compass.ocean.tests.global_ocean.files_for_e3sm.FilesForE3SM The test case this step belongs to """ # noqa: E501 super().__init__(test_case, name='ocean_mesh')
# for now, we won't define any outputs because they include the mesh # short name, which is not known at setup time. Currently, this is # safe because no other steps depend on the outputs of this one.
[docs] def run(self): """ Run this step of the testcase """ super().run() dest_filename = f'{self.mesh_short_name}.{self.creation_date}.nc' with xr.open_dataset('') as ds: keep_vars = self.mesh_vars + [ 'refBottomDepth', 'vertCoordMovementWeights', 'bottomDepth', 'maxLevelCell', 'layerThickness', 'restingThickness' ] if 'minLevelCell' in ds: keep_vars.append('minLevelCell') if self.with_ice_shelf_cavities: ice_shelf_keep_vars = [ 'landIceMask', 'landIceDraft', 'landIceFraction', 'landIceFloatingMask', 'landIceFloatingFraction' ] for var in ice_shelf_keep_vars: if var in ds: keep_vars.append(var) else: self.logger.warn(f'Warning: {var} not present in ' f'ocean mesh file.') ds = ds[keep_vars] ds.load() for attr in list(ds.attrs): # drop config options from global attributes if attr.startswith('config_'): ds.attrs.pop(attr) ref_bot_depth = ds.refBottomDepth.values interfaces = np.append([0], ref_bot_depth) if 'minLevelCell' not in ds: ds['minLevelCell'] = xr.ones_like(ds.maxLevelCell) ds.minLevelCell.attrs['long_name'] = \ 'Index to the first active ocean cell in each column.' ds['refTopDepth'] = ('nVertLevels', interfaces[0:-1]) ds.refTopDepth.attrs['units'] = 'm' ds.refTopDepth.attrs['long_name'] = \ "Reference depth of ocean for each vertical level. Used in " \ "'z-level' type runs." ds['refZMid'] = ('nVertLevels', -0.5 * (interfaces[1:] + interfaces[0:-1])) ds.refZMid.attrs['units'] = 'm' ds.refZMid.attrs['long_name'] = \ 'Reference mid z-coordinate of ocean for each vertical ' \ 'level. This has a negative value.' ds['refLayerThickness'] = ('nVertLevels', interfaces[1:] - interfaces[0:-1]) ds.refLayerThickness.attrs['units'] = 'm' ds.refLayerThickness.attrs['long_name'] = \ 'Reference layer thickness of ocean for each vertical level.' ds['cellMask'] = compute_cell_mask( ds.minLevelCell - 1, ds.maxLevelCell - 1, ds.sizes['nVertLevels']) ds.cellMask.attrs['long_name'] = \ 'Mask on cells that determines if computations should be ' \ 'done on cells.' ds['ssh'] = compute_ssh_from_layer_thickness( ds.layerThickness, ds.bottomDepth, ds.cellMask) ds.ssh.attrs['units'] = 'm' ds.ssh.attrs['long_name'] = 'sea surface height' ds['zMid'] = compute_zmid_from_layer_thickness( ds.layerThickness, ds.ssh, ds.cellMask) ds.zMid.attrs['units'] = 'm' ds.zMid.attrs['long_name'] = \ 'z-coordinate of the mid-depth of the layer' write_netcdf(ds, dest_filename) symlink(os.path.abspath(dest_filename), f'{self.ocean_mesh_dir}/{dest_filename}')