Add config option for number of inactive layers

Author: cbegeman

compass/ocean/tests/global_ocean/configure.py

@@ -26,6 +26,7 @@ def configure_global_ocean(test_case, mesh, init=None):
             config.get('global_ocean', 'prefix')))
 
     if init is not None and init.with_inactive_top_cells:
+        config.set('vertical_grid', 'inactive_top_cells', '1')
         config.set('vertical_grid', 'vert_levels', '{}'.format(
             config.getint('vertical_grid', 'vert_levels')+1))
 

compass/ocean/tests/global_ocean/mesh/qu240/qu240.cfg

@@ -16,6 +16,7 @@ min_layer_thickness = 3.0
 # The maximum layer thickness
 max_layer_thickness = 500.0
 
+inactive_top_cells = 0
 
 # options for global ocean testcases
 [global_ocean]

compass/ocean/vertical/grid_1d.py

@@ -22,17 +22,22 @@ def generate_1d_grid(config):
     interfaces : numpy.ndarray
         A 1D array of positive depths for layer interfaces in meters
     """
+    offset = 0
+    if config.has_option('vertical_grid', 'inactive_top_cells'):
+        offset = config.getint('vertical_grid', 'inactive_top_cells')
+
     section = config['vertical_grid']
     grid_type = section.get('grid_type')
     if grid_type == 'uniform':
         vert_levels = section.getint('vert_levels')
-        interfaces = _generate_uniform(vert_levels)
+        interfaces = _generate_uniform(vert_levels - offset)
     elif grid_type == 'tanh_dz':
         vert_levels = section.getint('vert_levels')
         min_layer_thickness = section.getfloat('min_layer_thickness')
         max_layer_thickness = section.getfloat('max_layer_thickness')
         bottom_depth = section.getfloat('bottom_depth')
-        interfaces = _create_tanh_dz_grid(vert_levels, bottom_depth,
+        interfaces = _create_tanh_dz_grid(vert_levels - offset,
+                                          bottom_depth,
                                           min_layer_thickness,
                                           max_layer_thickness)
 
@@ -47,6 +52,9 @@ def generate_1d_grid(config):
         # renormalize to the requested range
         interfaces = (bottom_depth/interfaces[-1]) * interfaces
 
+    if config.has_option('vertical_grid', 'inactive_top_cells'):
+        interfaces = np.append(np.zeros((offset)),interfaces)
+
     return interfaces