Merge pull request #735 from xylar/create-icoswisc30e3r5

New Mesh: IcoswISC30E3r5

compass/ocean/tests/global_ocean/global_ocean.cfg

@@ -47,6 +47,12 @@ btr_dt_per_km = 1.5
 
 # Maximum allowed Haney number for configurations with ice-shelf cavities
 rx1_max = 20
+# the number of iterations of topography smoothing (0 means no smoothing)
+topo_smooth_num_passes = 0
+# The distance in km over which the Gaussian filter is applied
+topo_smooth_distance_limit = 200.0
+# The standard deviation in km of the Gaussian filter
+topo_smooth_std_deviation = 100.0
 
 # number of cores to use
 init_ntasks = 36

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

@@ -1,6 +1,12 @@
 import os
-from importlib.resources import contents
+from importlib.resources import contents, read_text
 
+import xarray as xr
+from jinja2 import Template
+from mpas_tools.io import write_netcdf
+from mpas_tools.logging import check_call
+
+from compass.io import symlink
 from compass.model import run_model
 from compass.ocean.plot import plot_initial_state, plot_vertical_grid
 from compass.ocean.tests.global_ocean.metadata import (
@@ -79,7 +85,7 @@ def __init__(self, test_case, mesh, initial_condition):
 
         cull_step = self.mesh.steps['cull_mesh']
         target = os.path.join(cull_step.path, 'topography_culled.nc')
-        self.add_input_file(filename='topography.nc',
+        self.add_input_file(filename='topography_culled.nc',
                             work_dir_target=target)
 
         self.add_input_file(
@@ -162,6 +168,8 @@ def run(self):
         Run this step of the testcase
         """
         config = self.config
+        self._smooth_topography()
+
         interfaces = generate_1d_grid(config=config)
 
         write_1d_grid(interfaces=interfaces, out_filename='vertical_grid.nc')
@@ -186,3 +194,43 @@ def _get_resources(self):
         self.cpus_per_task = config.getint('global_ocean',
                                            'init_cpus_per_task')
         self.min_cpus_per_task = self.cpus_per_task
+
+    def _smooth_topography(self):
+        """ Smooth the topography using a Gaussian filter """
+        config = self.config
+        section = config['global_ocean']
+        num_passes = section.getint('topo_smooth_num_passes')
+        if num_passes == 0:
+            # just symlink the culled topography to be the topography used for
+            # the initial condition
+            symlink(target='topography_culled.nc', link_name='topography.nc')
+            return
+
+        distance_limit = section.getfloat('topo_smooth_distance_limit')
+        std_deviation = section.getfloat('topo_smooth_std_deviation')
+
+        template = Template(read_text(
+            'compass.ocean.tests.global_ocean.init', 'smooth_topo.template'))
+
+        text = template.render(num_passes=f'{num_passes}',
+                               distance_limit=f'{distance_limit}',
+                               std_deviation=f'{std_deviation}')
+
+        # add trailing end line
+        text = f'{text}\n'
+
+        with open('smooth_depth_in', 'w') as file:
+            file.write(text)
+
+        check_call(args=['ocean_smooth_topo_before_init'],
+                   logger=self.logger)
+
+        with (xr.open_dataset('topography_culled.nc') as ds_topo):
+            with xr.open_dataset('topography_orig_and_smooth.nc') as ds_smooth:
+                for field in ['bed_elevation', 'landIceDraftObserved',
+                              'landIceThkObserved']:
+                    attrs = ds_topo[field].attrs
+                    ds_topo[field] = ds_smooth[f'{field}New']
+                    ds_topo[field].attrs = attrs
+
+            write_netcdf(ds_topo, 'topography.nc')

compass/ocean/tests/global_ocean/init/smooth_topo.template

@@ -0,0 +1,8 @@
+&smooth
+    filename_depth_in    = "topography_culled.nc"
+    filename_depth_out   = "topography_orig_and_smooth.nc"
+    filename_mpas_mesh   = "mesh.nc"
+    distanceLimit        = {{ distance_limit }}
+    stdDeviation         = {{ std_deviation }}
+    numSmoothingPasses   = {{ num_passes }}
+/

compass/ocean/tests/global_ocean/mesh/qu/dynamic_adjustment.yaml

@@ -1,5 +1,5 @@
 dynamic_adjustment:
-  land_ice_flux_mode: data
+  land_ice_flux_mode: pressure_only
   get_dt_from_min_res: True
 
   steps:
@@ -16,7 +16,7 @@ dynamic_adjustment:
       Rayleigh_damping_coeff: 1.0e-5
 
     simulation:
-      run_duration: 10_00:00:00
+      run_duration: 80_00:00:00
       output_interval: 10_00:00:00
       restart_interval: 10_00:00:00
       Rayleigh_damping_coeff: None

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

@@ -34,19 +34,18 @@ prefix = QU
 # a description of the mesh
 mesh_description = MPAS quasi-uniform mesh for E3SM version ${e3sm_version} at
                    ${min_res}-km global resolution with <<<levels>>> vertical
-                   level
-
+                   levels.
 # E3SM version that the mesh is intended for
 e3sm_version = 3
 # The revision number of the mesh, which should be incremented each time the
 # mesh is revised
-mesh_revision = 2
+mesh_revision = 5
 # the minimum (finest) resolution in the mesh
 min_res = ${qu_resolution}
 # the maximum (coarsest) resolution in the mesh, can be the same as min_res
 max_res = ${qu_resolution}
 # The URL of the pull request documenting the creation of the mesh
-pull_request = https://github.com/MPAS-Dev/compass/pull/691
+pull_request = https://github.com/MPAS-Dev/compass/pull/735
 
 # the resolution of the QU or Icos mesh in km
-qu_resolution = 120
+qu_resolution = 30

compass/ocean/tests/global_ocean/streams.forward

@@ -18,6 +18,7 @@
     <var name="xtime"/>
     <var name="normalVelocity"/>
     <var name="layerThickness"/>
+    <var name="kineticEnergyCell"/>
 </stream>
 
 <stream name="forcing_data"