Merge pull request #717 from xylar/add-step-for-reconstruction-coeffs

Add step for reconstruction coeffs

compass/ocean/tests/global_ocean/files_for_e3sm/__init__.py

@@ -38,6 +38,9 @@
 from compass.ocean.tests.global_ocean.files_for_e3sm.seaice_mesh import (  # noqa: E501
     SeaiceMesh,
 )
+from compass.ocean.tests.global_ocean.files_for_e3sm.write_coeffs_reconstruct import (  # noqa: E501
+    WriteCoeffsReconstruct,
+)
 from compass.ocean.tests.global_ocean.forward import get_forward_subdir
 from compass.testcase import TestCase
 
@@ -115,6 +118,10 @@ def __init__(self, test_group, mesh=None, init=None,
         self.add_step(RemapIcebergClimatology(
             test_case=self))
 
+        if mesh is not None and init is not None:
+            self.add_step(WriteCoeffsReconstruct(
+                test_case=self, mesh=mesh, init=init))
+
     def configure(self):
         """
         Modify the configuration options for this test case

compass/ocean/tests/global_ocean/files_for_e3sm/files_for_e3sm_step.py

@@ -38,8 +38,9 @@ class FilesForE3SMStep(Step):
         A list of the variables that belong to the MPAS horizontal mesh
     """
 
-    def __init__(self, test_case, name, subdir=None, cpus_per_task=1,
-                 min_cpus_per_task=1, ntasks=1, min_tasks=1,):
+    def __init__(self, test_case, name='files_for_e3sm_step', subdir=None,
+                 cpus_per_task=1, min_cpus_per_task=1, ntasks=1, min_tasks=1,
+                 **kwargs):
         """
         Create a new test case
 
@@ -79,7 +80,7 @@ def __init__(self, test_case, name, subdir=None, cpus_per_task=1,
         super().__init__(test_case=test_case, name=name, subdir=subdir,
                          cpus_per_task=cpus_per_task,
                          min_cpus_per_task=min_cpus_per_task, ntasks=ntasks,
-                         min_tasks=min_tasks)
+                         min_tasks=min_tasks, **kwargs)
 
         self.mesh_short_name = None
         self.creation_date = None
@@ -130,6 +131,7 @@ def setup(self):
         if with_ice_shelf_cavities != 'autodetect':
             self.with_ice_shelf_cavities = \
                 (with_ice_shelf_cavities.lower() == 'true')
+        super().setup()
 
     def run(self):  # noqa: C901
         """
@@ -209,3 +211,5 @@ def run(self):  # noqa: C901
                 os.makedirs(dest_dir)
             except FileExistsError:
                 pass
+
+        super().run()

compass/ocean/tests/global_ocean/files_for_e3sm/write_coeffs_reconstruct/__init__.py

@@ -0,0 +1,67 @@
+import os
+
+from mpas_tools.logging import check_call
+
+from compass.io import symlink
+from compass.ocean.tests.global_ocean.files_for_e3sm.files_for_e3sm_step import (  # noqa: E501
+    FilesForE3SMStep,
+)
+from compass.ocean.tests.global_ocean.forward import ForwardStep
+
+
+class WriteCoeffsReconstruct(ForwardStep, FilesForE3SMStep):
+    """
+    A step for writing out ``coeffs_reconstruct`` for a given MPAS mesh
+    """
+
+    def __init__(self, test_case, mesh, init):
+        """
+        Create a new step
+
+        Parameters
+        ----------
+        test_case : compass.TestCase
+            The test case this step belongs to
+
+        mesh : compass.ocean.tests.global_ocean.mesh.Mesh
+            The test case that produces the mesh for this run
+
+        init : compass.ocean.tests.global_ocean.init.Init
+            The test case that produces the initial condition for this run
+        """
+        super().__init__(test_case=test_case, mesh=mesh, init=init,
+                         time_integrator='split_explicit',
+                         name='write_coeffs_reconstruct')
+
+        package = 'compass.ocean.tests.global_ocean.files_for_e3sm.' \
+                  'write_coeffs_reconstruct'
+
+        self.add_namelist_file(package, 'namelist.reconstruct')
+        self.add_streams_file(package, 'streams.reconstruct')
+
+    def run(self):
+        """
+        Run this step of the testcase
+        """
+        super().run()
+
+        # perform a test reconstruction to make sure things are working
+        args = ['vector_reconstruct',
+                '-i', 'restart.nc',
+                '-o', 'velocity_components.nc',
+                '-w', 'coeffs_reconstruct.nc',
+                '-v', 'normalVelocity',
+                '--out_variables', 'velocity']
+        check_call(args=args, logger=self.logger)
+
+        reconstruct_dir = \
+            '../assembled_files/diagnostics/mpas_analysis/reconstruct'
+        try:
+            os.makedirs(reconstruct_dir)
+        except FileExistsError:
+            pass
+
+        reconstruct_filename = f'{self.mesh_short_name}_coeffs_reconstruct.nc'
+        # make links in diagnostics directory
+        symlink(os.path.abspath('coeffs_reconstruct.nc'),
+                f'{reconstruct_dir}/{reconstruct_filename}')

compass/ocean/tests/global_ocean/files_for_e3sm/write_coeffs_reconstruct/namelist.reconstruct

@@ -0,0 +1 @@
+config_run_duration = '0000_00:00:01'

compass/ocean/tests/global_ocean/files_for_e3sm/write_coeffs_reconstruct/streams.reconstruct

@@ -0,0 +1,13 @@
+<streams>
+
+<stream name="coeffs_reconstruct"
+        type="output"
+        filename_template="coeffs_reconstruct.nc"
+        output_interval="0000_00:00:01"
+		reference_time="0001-01-01_00:00:00"
+        clobber_mode="truncate">
+
+    <var name="coeffs_reconstruct"/>
+</stream>
+
+</streams>

compass/ocean/tests/global_ocean/forward.py

@@ -39,7 +39,7 @@ class ForwardStep(Step):
     def __init__(self, test_case, mesh, time_integrator, init=None,
                  name='forward', subdir=None, ntasks=None, min_tasks=None,
                  openmp_threads=None, get_dt_from_min_res=True,
-                 land_ice_flux_mode='pressure_only'):
+                 land_ice_flux_mode='pressure_only', **kwargs):
         """
         Create a new step
 
@@ -91,7 +91,7 @@ def __init__(self, test_case, mesh, time_integrator, init=None,
             min_tasks = ntasks
         super().__init__(test_case=test_case, name=name, subdir=subdir,
                          ntasks=ntasks, min_tasks=min_tasks,
-                         openmp_threads=openmp_threads)
+                         openmp_threads=openmp_threads, **kwargs)
 
         if (ntasks is None) != (openmp_threads is None):
             raise ValueError('You must specify both ntasks and openmp_threads '
@@ -179,6 +179,7 @@ def setup(self):
             else:
                 # RK4, so use the smaller time step
                 self.add_namelist_options({'config_dt': btr_dt})
+        super().setup()
 
     def constrain_resources(self, available_resources):
         """
@@ -206,11 +207,13 @@ def runtime_setup(self):
             else:
                 # RK4, so use the smaller time step
                 self.update_namelist_at_runtime({'config_dt': btr_dt})
+        super().runtime_setup()
 
     def run(self):
         """
         Run this step of the testcase
         """
+        super().run()
         update_pio = self.config.getboolean('global_ocean',
                                             'forward_update_pio')
         run_model(self, update_pio=update_pio)

docs/developers_guide/ocean/api.rst

@@ -203,6 +203,8 @@ test cases and steps
    files_for_e3sm.remap_sea_surface_salinity_restoring.RemapSeaSurfaceSalinityRestoring.run
    files_for_e3sm.remap_iceberg_climatology.RemapIcebergClimatology
    files_for_e3sm.remap_iceberg_climatology.RemapIcebergClimatology.run
+   files_for_e3sm.write_coeffs_reconstruct.WriteCoeffsReconstruct
+   files_for_e3sm.write_coeffs_reconstruct.WriteCoeffsReconstruct.run
 
    init.Init
    init.Init.configure

docs/developers_guide/ocean/test_groups/global_ocean.rst

@@ -1380,6 +1380,12 @@ The test case is made up of 10 steps:
     the MPAS mesh.  This dataset is used in E3SM for compsets with data iceberg
     freshwater fluxes (``DIB``).
 
+:py:class:`compass.ocean.tests.global_ocean.files_for_e3sm.write_coeffs_reconstruct.WriteCoeffsReconstruct`
+    is used to do a one-time-step forward run to write out coefficients
+    ``coeff_reconstruct`` for reconstructing vector fields at cell centers from
+    normal values at edges.  These can be used in combination with the
+
+
 files_for_e3sm for an existing mesh
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~