Add validation with cropped output

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

@@ -99,6 +99,14 @@ 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',
+                              filename2='initial_state/initial_state_comp.nc',
+                              quiet=False, check_outputs=False)
+
         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

@@ -7,6 +7,7 @@
 from compass.ocean.tests.global_ocean.metadata import (
     add_mesh_and_init_metadata,
 )
+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.step import Step
 
@@ -139,6 +140,9 @@ def __init__(self, test_case, mesh, initial_condition,
                      'graph.info']:
             self.add_output_file(filename=file)
 
+        if with_inactive_top_cells:
+            self.add_output_file(filename='initial_state_crop.nc')
+
     def setup(self):
         """
         Get resources at setup from config options
@@ -175,6 +179,7 @@ def run(self):
             config.set('vertical_grid', 'vert_levels', f'{vert_levels + 1}',
                        comment='the number of vertical levels + 1')
             config.set('vertical_grid', 'inactive_top_cells', '1')
+        logger = self.logger
         interfaces = generate_1d_grid(config=config)
 
         write_1d_grid(interfaces=interfaces, out_filename='vertical_grid.nc')
@@ -186,7 +191,6 @@ 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'
@@ -200,11 +204,18 @@ 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")
 

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

@@ -1,8 +1,10 @@
+import os
 from compass.ocean.tests.global_ocean.forward import (
     ForwardStep,
     ForwardTestCase,
 )
 from compass.validate import compare_timers, compare_variables
+from compass.ocean.inactive_top_cells import remove_inactive_top_cells_output
 
 
 class PerformanceTest(ForwardTestCase):
@@ -71,6 +73,18 @@ def validate(self):
             compare_variables(test_case=self, variables=variables,
                               filename1=f'{step_subdir}/output.nc')
 
+            if self.config.has_option('vertical_grid', 'inactive_top_cells'):
+                offset = self.config.getint('vertical_grid', 'inactive_top_cells')
+                if offset > 0:
+                    remove_inactive_top_cells_output('forward/output.nc',
+                                                     inactive_top_cells=offset)
+                    filename2=None
+                    if os.path.exists('forward/output_comp.nc'):
+                        filename2='forward/output_comp.nc'
+                    compare_variables(test_case=self, variables=variables,
+                                      filename1='forward/output_crop.nc',
+                                      filename2=filename2)
+
             if self.mesh.with_ice_shelf_cavities:
                 variables = [
                     'ssh', 'landIcePressure', 'landIceDraft',