Merge pull request #262 from cbegeman/add-omega-sphere-transport

Add support for omega sphere transport tests

Add omega support for the sphere_transport test suite

Author: cbegeman

polaris/ocean/config/single_layer.yaml

@@ -9,6 +9,5 @@ mpas-ocean:
     config_disable_thick_vadv: true
     config_disable_vel_vadv: true
     config_disable_vel_vmix: true
-    config_disable_tr_all_tend: true
   pressure_gradient:
     config_pressure_gradient_type: ssh_gradient

polaris/ocean/convergence/analysis.py

@@ -150,11 +150,17 @@ def run(self):
         """
         plt.switch_backend('Agg')
         convergence_vars = self.convergence_vars
+        variables_failed = []
         for var in convergence_vars:
-            self.plot_convergence(
+            convergence_failed = self.plot_convergence(
                 variable_name=var["name"],
                 title=var["title"],
                 zidx=var["zidx"])
+            if convergence_failed:
+                variables_failed.append(var["name"])
+        if len(variables_failed) >= 1:
+            raise ValueError('Convergence rate below minimum tolerance for '
+                             f'variables {", ".join(variables_failed)}.')
 
     def plot_convergence(self, variable_name, title, zidx):
         """
@@ -281,8 +287,7 @@ def plot_convergence(self, variable_name, title, zidx):
                          f'{conv_thresh}')
             convergence_failed = True
 
-        if convergence_failed:
-            raise ValueError('Convergence rate below minimum tolerance.')
+        return convergence_failed
 
     def compute_error(self, refinement_factor, variable_name, zidx=None,
                       error_type='l2'):

polaris/ocean/suites/omega_pr.txt

@@ -1,3 +1,4 @@
 ocean/planar/manufactured_solution/convergence_both
+ocean/spherical/icos/rotation_2d/convergence_both
 ocean/spherical/icos/cosine_bell/decomp
 ocean/spherical/icos/cosine_bell/restart

polaris/ocean/tasks/sphere_transport/analysis.py

@@ -39,13 +39,13 @@ def __init__(self, component, subdir, case_name,
         self.case_name = case_name
         convergence_vars = [{'name': 'tracer1',
                              'title': 'tracer1',
-                             'zidx': 1},
+                             'zidx': 0},
                             {'name': 'tracer2',
                              'title': 'tracer2',
-                             'zidx': 1},
+                             'zidx': 0},
                             {'name': 'tracer3',
                              'title': 'tracer3',
-                             'zidx': 1}]
+                             'zidx': 0}]
         super().__init__(component=component, subdir=subdir,
                          dependencies=dependencies,
                          convergence_vars=convergence_vars,
@@ -71,8 +71,14 @@ def convergence_parameters(self, field_name=None):
             The maximum convergence rate
         """
         config = self.config
+        model = config.get('ocean', 'model')
+        if model == 'omega' and self.case_name == 'rotation_2d':
+            order = 2
+        else:
+            order = 3
         section = config[self.case_name]
-        conv_thresh = section.getfloat(f'convergence_thresh_{field_name}')
+        conv_thresh = section.getfloat(
+            f'convergence_thresh_{field_name}_order{order}')
 
         section = config['convergence']
         error_type = section.get('error_type')

polaris/ocean/tasks/sphere_transport/correlated_tracers_2d.cfg

@@ -9,9 +9,9 @@ vel_amp = 10.
 correlation_coefficients = -0.8, 0.0, 0.9
 
 # convergence threshold below which the test fails
-convergence_thresh_tracer1 = 1.5
-convergence_thresh_tracer2 = 1.3
-convergence_thresh_tracer3 = 1.0
+convergence_thresh_tracer1_order3 = 1.5
+convergence_thresh_tracer2_order3 = 1.3
+convergence_thresh_tracer3_order3 = 1.0
 
 # time in days at which to evaluate mixing
 mixing_evaluation_time = 6.0

polaris/ocean/tasks/sphere_transport/divergent_2d.cfg

@@ -5,6 +5,6 @@
 vel_amp = 5.
 
 # convergence threshold below which the test fails
-convergence_thresh_tracer1 = 1.8
-convergence_thresh_tracer2 = 1.5
-convergence_thresh_tracer3 = 0.3
+convergence_thresh_tracer1_order3 = 1.8
+convergence_thresh_tracer2_order3 = 1.5
+convergence_thresh_tracer3_order3 = 0.3

polaris/ocean/tasks/sphere_transport/forward.py

@@ -60,3 +60,13 @@ def __init__(self, component, name, subdir, base_mesh, init,
                          graph_target=f'{base_mesh.path}/graph.info',
                          refinement_factor=refinement_factor,
                          refinement=refinement)
+
+    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')

polaris/ocean/tasks/sphere_transport/forward.yaml

@@ -1,16 +1,18 @@
-mpas-ocean:
-  run_modes:
-    config_ocean_run_mode: forward
+ocean:
   time_management:
     config_stop_time: none
     config_run_duration: {{ run_duration }}
+  time_integration:
+    config_dt: {{ dt }}
+    config_time_integrator: {{ time_integrator }}
+
+mpas-ocean:
+  run_modes:
+    config_ocean_run_mode: forward
   decomposition:
     config_block_decomp_file_prefix: graph.info.part.
   advection:
     config_vert_coord_movement: impermeable_interfaces
-  time_integration:
-    config_dt: {{ dt }}
-    config_time_integrator: {{ time_integrator }}
   debug:
     config_disable_thick_sflux: true
     config_disable_vel_all_tend: true
@@ -57,3 +59,31 @@ mpas-ocean:
       - refLayerThickness
       - kineticEnergyCell
       - relativeVorticityCell
+
+Omega:
+  Tendencies:
+    ThicknessFluxTendencyEnable : false
+    PVTendencyEnable : false
+    KETendencyEnable : false
+    SSHTendencyEnable : false
+    VelDiffTendencyEnable: false
+    VelHyperDiffTendencyEnable: false
+    TracerHorzAdvTendencyEnable : true
+    TracerDiffTendencyEnable : false
+    TracerHyperDiffTendencyEnable : false
+  Dimension:
+    NVertLevels: 1
+  IOStreams:
+    InitialState:
+      Filename: init.nc
+      Contents:
+        - State
+        - Tracers
+    History:
+      Filename: output.nc
+      Freq: {{ output_freq }}
+      FreqUnits: seconds
+      Contents:
+        - Tracers
+        - LayerThickness
+        - NormalVelocity

polaris/ocean/tasks/sphere_transport/init.py

@@ -1,8 +1,7 @@
 import numpy as np
 import xarray as xr
-from mpas_tools.io import write_netcdf
 
-from polaris import Step
+from polaris.ocean.model import OceanIOStep
 from polaris.ocean.tasks.sphere_transport.resources.flow_types import (
     flow_divergent,
     flow_nondivergent,
@@ -17,7 +16,7 @@
 from polaris.ocean.vertical import init_vertical_coord
 
 
-class Init(Step):
+class Init(OceanIOStep):
     """
     A step for an initial condition for for the cosine bell test case
     """
@@ -156,4 +155,4 @@ def run(self):
         ds['fEdge'] = xr.zeros_like(ds_mesh.xEdge)
         ds['fVertex'] = xr.zeros_like(ds_mesh.xVertex)
 
-        write_netcdf(ds, 'initial_state.nc')
+        self.write_model_dataset(ds, 'initial_state.nc')

polaris/ocean/tasks/sphere_transport/nondivergent_2d.cfg

@@ -5,9 +5,9 @@
 vel_amp = 10.
 
 # convergence threshold below which the test fails
-convergence_thresh_tracer1 = 1.5
-convergence_thresh_tracer2 = 1.1
-convergence_thresh_tracer3 = 0.3
+convergence_thresh_tracer1_order3 = 1.5
+convergence_thresh_tracer2_order3 = 1.1
+convergence_thresh_tracer3_order3 = 0.3
 
 # time in days at which to evaluate filament preservation
 filament_evaluation_time = 6.0