Add omega support to barotropic_gyre, pending forcing stream

Author: cbegeman

polaris/ocean/tasks/barotropic_gyre/analysis.py

@@ -46,8 +46,8 @@ def __init__(self, component, indir, boundary_condition='free slip'):
     def run(self):
 
         ds_mesh = xr.open_dataset('mesh.nc')
-        ds_init = xr.open_dataset('init.nc')
-        ds = xr.open_dataset('output.nc')
+        ds_init = self.open_model_dataset('init.nc')
+        ds = self.open_model_dataset('output.nc')
 
         field_mpas = compute_barotropic_streamfunction(
             ds_init.isel(Time=0), ds, prefix='', time_index=-1)

polaris/ocean/tasks/barotropic_gyre/barotropic_gyre.cfg

@@ -1,5 +1,8 @@
 [barotropic_gyre]
 
+# time integrator
+time_integrator = RK4
+
 # distance in kilometers between cell centers
 resolution = 20
 

polaris/ocean/tasks/barotropic_gyre/forward.py

@@ -119,7 +119,6 @@ def dynamic_model_config(self, at_setup):
         model = config.get('ocean', 'model')
         if model == 'mpas-ocean':
             self.add_yaml_file('polaris.ocean.config', 'single_layer.yaml')
-
         nu = config.getfloat("barotropic_gyre", "nu_2")
         rho_0 = config.getfloat("barotropic_gyre", "rho_0")
 
@@ -133,26 +132,54 @@ def dynamic_model_config(self, at_setup):
                                       config_model='mpas-ocean')
 
         if self.run_time_steps is not None:
+            output_frequency_units = 'seconds'
             run_duration = ceil(self.run_time_steps * dt)
+            output_frequency = f'{run_duration}'
             stop_time_str = time.strftime('0001-01-01_%H:%M:%S',
                                           time.gmtime(run_duration))
             output_interval_str = time.strftime('0000_%H:%M:%S',
                                                 time.gmtime(run_duration))
         else:
+            output_frequency_units = 'months'
+            output_frequency = '1'
             stop_time_str = time.strftime('0004-01-01_00:00:00')
             output_interval_str = time.strftime('0000-01-00_00:00:00')
 
+        time_integrator = config.get('barotropic_gyre', 'time_integrator')
+        time_integrator_map = dict([('RK4', 'RungeKutta4')])
+        model = config.get('ocean', 'model')
+        if model == 'omega':
+            if time_integrator in time_integrator_map.keys():
+                time_integrator = time_integrator_map[time_integrator]
+            else:
+                print('Warning: mapping from time integrator '
+                      f'{time_integrator} to omega not found, '
+                      'retaining name given in config')
+
         replacements = dict(
             dt=dt_str,
             stop_time=stop_time_str,
             output_interval=output_interval_str,
+            output_frequency=output_frequency,
+            output_frequency_units=output_frequency_units,
+            time_integrator=time_integrator,
             nu=f'{nu:02g}',
         )
 
         # make sure output is double precision
         self.add_yaml_file(self.package, self.yaml_filename,
                            template_replacements=replacements)
 
+    def setup(self):
+        """
+        TEMP: symlink initial condition to name hard-coded in Omega
+        """
+        super().setup()
+        model = self.config.get('ocean', 'model')
+        # TODO: remove as soon as Omega no longer hard-codes this file
+        if model == 'omega':
+            self.add_input_file(filename='OmegaMesh.nc', target='init.nc')
+
 
 def compute_max_time_step(config):
     """

polaris/ocean/tasks/barotropic_gyre/forward.yaml

@@ -4,10 +4,29 @@ ocean:
     config_run_duration: none
   time_integration:
     config_dt: {{ dt }}
-    config_time_integrator: RK4
+    config_time_integrator: {{ time_integrator }}
+  advection:
+    config_thickness_flux_type: constant
   hmix_del2:
     config_use_mom_del2: true
     config_mom_del2: {{ nu }}
+  hmix_del4:
+    config_use_mom_del4: false
+
+mpas-ocean:
+  run_modes:
+    config_ocean_run_mode: forward
+  decomposition:
+    config_block_decomp_file_prefix: graph.info.part.
+  bottom_drag:
+    config_implicit_constant_bottom_drag_coeff: 0.
+  forcing:
+    config_use_bulk_wind_stress: true
+  debug:
+    config_disable_vel_hadv: true
+    config_disable_vel_hmix: false
+    config_disable_tr_all_tend: true
+
   streams:
     mesh:
       filename_template: init.nc
@@ -32,21 +51,30 @@ ocean:
       - layerThickness
       - ssh
 
-mpas-ocean:
-  advection:
-    config_thickness_flux_type: constant
-  bottom_drag:
-    config_implicit_constant_bottom_drag_coeff: 0.
-  forcing:
-    config_use_bulk_wind_stress: true
-  debug:
-    config_disable_vel_hadv: true
-    config_disable_vel_hmix: false
-    config_disable_tr_all_tend: true
-
 Omega:
   Tendencies:
-    VelDiffTendencyEnable: true
-    VelHyperDiffTendencyEnable: false
+    TracerHorzAdvTendencyEnable : false
+    TracerDiffTendencyEnable : false
+    TracerHyperDiffTendencyEnable : false
+  Advection:
+    FluxThicknessType: Center
   Dimension:
     NVertLevels: 1
+  IOStreams:
+    InitialState:
+      Filename: init.nc
+      Contents:
+        - LayerThickness
+        - NormalVelocity
+    History:
+      Filename: output.nc
+      Freq: {{ output_frequency }}
+      FreqUnits: {{ output_frequency_units }}
+      IfExists: append
+      # effectively never
+      FileFreq: 9999
+      FileFreqUnits: years
+      Contents:
+        - LayerThickness
+        - NormalVelocity
+        - SshCellDefault