Add validation with cropped output: Init

Author: cbegeman

compass/ocean/inactive_top_cells.py

@@ -0,0 +1,28 @@
+import os
+import xarray
+
+from mpas_tools.io import write_netcdf
+
+
+def remove_inactive_top_cells_output(in_filename, inactive_top_cells=1):
+    """
+    Remove inactive top cells from the output netCDF file
+
+    Parameters
+    ----------
+    in_filename : str
+        Filename for the netCDF file to be cropped
+
+    inactive_top_cells : str, optional
+        The number of inactive top cell layers. It should be equal to
+        ``config.inactive_top_cells``.
+    """
+    if not os.path.exists(in_filename):
+        raise OSError('File {} does not exist.'.format(in_filename))
+
+    out_filename = in_filename.split('.')[0] + '_crop.nc'
+
+    with xarray.open_dataset(in_filename) as ds_in:
+        ds_out = ds_in.isel(nVertLevels=slice(1,None))
+
+    write_netcdf(ds_out, out_filename)

compass/ocean/tests/global_ocean/init/__init__.py

@@ -121,6 +121,12 @@ def validate(self):
             compare_variables(test_case=self, variables=variables,
                               filename1='initial_state/initial_state.nc')
 
+        if self.with_inactive_top_cells:
+            variables = [
+                'temperature', 'salinity', 'layerThickness', 'normalVelocity']
+            compare_variables(test_case=self, variables=variables,
+                              filename1='initial_state/initial_state_crop.nc')
+
         if self.mesh.with_ice_shelf_cavities:
             variables = ['ssh', 'landIcePressure']
             compare_variables(test_case=self, variables=variables,

compass/ocean/tests/global_ocean/init/initial_state.py

@@ -3,6 +3,7 @@
 from compass.ocean.tests.global_ocean.metadata import \
     add_mesh_and_init_metadata
 from compass.model import run_model
+from compass.ocean.inactive_top_cells import remove_inactive_top_cells_output
 from compass.ocean.vertical.grid_1d import generate_1d_grid, write_1d_grid
 from compass.ocean.plot import plot_vertical_grid, plot_initial_state
 from mpas_tools.io import write_netcdf
@@ -141,6 +142,9 @@ def __init__(self, test_case, mesh, initial_condition, with_bgc,
         for file in ['initial_state.nc', 'init_mode_forcing_data.nc']:
             self.add_output_file(filename=file)
 
+        if with_inactive_top_cells:
+            self.add_output_file(filename='initial_state_crop.nc')
+
     def setup(self):
         """
         Set up the test case in the work directory, including downloading any
@@ -157,6 +161,7 @@ def run(self):
         Run this step of the testcase
         """
         config = self.config
+        logger = self.logger
         interfaces = generate_1d_grid(config=config)
 
         write_1d_grid(interfaces=interfaces, out_filename='vertical_grid.nc')
@@ -167,7 +172,6 @@ def run(self):
 
         if self.with_inactive_top_cells:
 
-            logger = self.logger
             logger.info("   * Updating minLevelCell for inactive top cells")
 
             in_filename = 'initial_state.nc'
@@ -181,10 +185,14 @@ def run(self):
                 ds = ds.isel(Time=0)
 
                 if ('minLevelCell' in ds):
-                    minLevelCell = ds.minLevelCell+1
+                    if config.has_option('vertical_grid', 'inactive_top_cells'):
+                        offset = config.getint('vertical_grid', 'inactive_top_cells')
+                    minLevelCell = ds.minLevelCell+offset
                     ds_out['minLevelCell'] = minLevelCell
                 else:
                     logger.info("   - Streams missing for inactive top cells")
+           
+            remove_inactive_top_cells_output(in_filename, inactive_top_cells=offset)
 
             write_netcdf(ds_out, out_filename)
             logger.info("   - Complete")