Merge pull request #411 from xylar/test_time_series_stats_monthly

Add monthly output test and update daily output test to match

compass/ocean/tests/global_ocean/__init__.py

@@ -16,6 +16,8 @@
 from compass.ocean.tests.global_ocean.threads_test import ThreadsTest
 from compass.ocean.tests.global_ocean.analysis_test import AnalysisTest
 from compass.ocean.tests.global_ocean.daily_output_test import DailyOutputTest
+from compass.ocean.tests.global_ocean.monthly_output_test import \
+    MonthlyOutputTest
 from compass.ocean.tests.global_ocean.files_for_e3sm import FilesForE3SM
 from compass.ocean.tests.global_ocean.make_diagnostics_files import \
     MakeDiagnosticsFiles
@@ -68,6 +70,10 @@ def __init__(self, mpas_core):
                 DailyOutputTest(
                     test_group=self, mesh=mesh, init=init,
                     time_integrator=time_integrator))
+            self.add_test_case(
+                MonthlyOutputTest(
+                    test_group=self, mesh=mesh, init=init,
+                    time_integrator=time_integrator))
 
             dynamic_adjustment = QU240DynamicAdjustment(
                 test_group=self, mesh=mesh, init=init,

compass/ocean/tests/global_ocean/daily_output_test/streams.forward

@@ -19,18 +19,30 @@
     <var_array name="avgGlobalStats"/>
     <var_array name="vertSumMinGlobalStats"/>
     <var_array name="vertSumMaxGlobalStats"/>
+    <var_array name="vertNonLocalFlux"/>
     <var_array name="activeTracersTend"/>
     <var_array name="activeTracerHorizontalAdvectionTendency"/>
     <var_array name="activeTracerVerticalAdvectionTendency"/>
     <var_array name="activeTracerVertMixTendency"/>
+    <var_array name="activeTracerHorMixTendency"/>
     <var_array name="activeTracerSurfaceFluxTendency"/>
     <var_array name="temperatureShortWaveTendency"/>
     <var_array name="activeTracerNonLocalTendency"/>
+    <var_array name="activeTracerForcingMLTend"/>
+    <var_array name="activeTracerHorMixMLTend"/>
+    <var_array name="activeTracerNonLocalMLTend"/>
+    <var_array name="activeTracerVertAdvectionMLTend"/>
+    <var_array name="activeTracerHorAdvectionMLTend"/>
+    <var_array name="activeTracerVertMixMLTend"/>
+    <var_array name="activeTracersML"/>
+    <var_array name="activeTracersTendML"/>
     <var_array name="activeTracerVerticalAdvectionTopFlux"/>
     <var_array name="activeTracerHorizontalAdvectionEdgeFlux"/>
+    <var_array name="totalFreshWaterTemperatureFlux"/>
     <var name="daysSinceStartOfSim"/>
-    <var name="ssh"/>
     <var name="binBoundaryMerHeatTrans"/>
+    <var name="binBoundaryZonalMean"/>
+    <var name="ssh"/>
     <var name="velocityMeridional"/>
     <var name="velocityZonal"/>
     <var name="layerThickness"/>
@@ -45,30 +57,37 @@
     <var name="dThreshMLD"/>
     <var name="normalVelocity"/>
     <var name="vertVelocityTop"/>
+    <var name="zMid"/>
+    <var name="atmosphericPressure"/>
     <var name="normalGMBolusVelocity"/>
     <var name="vertGMBolusVelocityTop"/>
     <var name="GMBolusVelocityZonal"/>
     <var name="GMBolusVelocityMeridional"/>
-    <var name="gmKappaScaling"/>
-    <var name="RediKappaScaling"/>
     <var name="cGMphaseSpeed"/>
     <var name="velocityZonalTimesTemperature_GM"/>
     <var name="velocityMeridionalTimesTemperature_GM"/>
+    <var name="normalGMBolusVelocityTimesTemperature"/>
+    <var name="normalGMBolusVelocitySquared"/>
+    <var name="gmKappaScaling"/>
+    <var name="gmBolusKappa"/>
+    <var name="mocStreamvalLatAndDepthGM"/>
+    <var name="mocStreamvalLatAndDepthRegionGM"/>
     <var name="penetrativeTemperatureFlux"/>
     <var name="latentHeatFlux"/>
     <var name="sensibleHeatFlux"/>
     <var name="longWaveHeatFluxUp"/>
     <var name="longWaveHeatFluxDown"/>
     <var name="seaIceHeatFlux"/>
     <var name="shortWaveHeatFlux"/>
+    <var name="frazilTemperatureTendency"/>
     <var name="evaporationFlux"/>
     <var name="seaIceSalinityFlux"/>
     <var name="seaIceFreshWaterFlux"/>
     <var name="riverRunoffFlux"/>
     <var name="iceRunoffFlux"/>
     <var name="rainFlux"/>
     <var name="snowFlux"/>
-    <var name="vertNonLocalFlux"/>
+    <var name="bottomLayerShortwaveTemperatureFlux"/>
     <var name="salinitySurfaceRestoringTendency"/>
     <var name="areaCellGlobal"/>
     <var name="areaEdgeGlobal"/>
@@ -94,8 +113,18 @@
     <var name="SSHSquared"/>
     <var name="velocityZonalSquared"/>
     <var name="velocityMeridionalSquared"/>
+    <var name="normalVelocitySquared"/>
     <var name="velocityZonalTimesTemperature"/>
     <var name="velocityMeridionalTimesTemperature"/>
+    <var name="normalVelocityTimesTemperature"/>
+    <var name="oceanHeatContentSfcToBot"/>
+    <var name="oceanHeatContentSfcTo700m"/>
+    <var name="oceanHeatContent700mTo2000m"/>
+    <var name="oceanHeatContent2000mToBot"/>
+    <var name="BruntVaisalaFreqTop"/>
+    <var name="bruntVaisalaFreqML"/>
+    <var name="icebergFreshWaterFlux"/>
+    <var name="icebergHeatFlux"/>
 </stream>
 
 </streams>

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

@@ -0,0 +1,64 @@
+from compass.validate import compare_variables
+from compass.ocean.tests.global_ocean.forward import ForwardTestCase, \
+    ForwardStep
+
+
+class MonthlyOutputTest(ForwardTestCase):
+    """
+    A test case to test the output for the TimeSeriesStatMonthly analysis
+    member in E3SM.
+    """
+
+    def __init__(self, test_group, mesh, init, time_integrator):
+        """
+        Create test case
+
+        Parameters
+        ----------
+        test_group : compass.ocean.tests.global_ocean.GlobalOcean
+            The global ocean test group that this test case 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
+
+        time_integrator : {'split_explicit', 'RK4'}
+            The time integrator to use for the forward run
+        """
+        super().__init__(test_group=test_group, mesh=mesh, init=init,
+                         time_integrator=time_integrator,
+                         name='monthly_output_test')
+
+        step = ForwardStep(test_case=self, mesh=mesh, init=init,
+                           time_integrator=time_integrator, cores=4,
+                           threads=1)
+
+        module = self.__module__
+        step.add_output_file(filename='output.nc')
+        step.add_output_file(
+            filename='analysis_members/'
+                     'mpaso.hist.am.timeSeriesStatsMonthly.0001-01-01.nc')
+        step.add_namelist_file(module, 'namelist.forward')
+        if mesh.mesh_name in ['QU240', 'QUwISC240']:
+            # a shorter time step is needed to prevent crashes
+            step.add_namelist_options(dict(config_dt='00:30:00'))
+        step.add_streams_file(module, 'streams.forward')
+        self.add_step(step)
+
+    def validate(self):
+        """
+        Test cases can override this method to perform validation of variables
+        and timers
+        """
+        variables = [
+            'timeMonthly_avg_activeTracers_temperature',
+            'timeMonthly_avg_activeTracers_salinity',
+            'timeMonthly_avg_layerThickness', 'timeMonthly_avg_normalVelocity',
+            'timeMonthly_avg_ssh']
+
+        compare_variables(
+            test_case=self, variables=variables,
+            filename1='forward/analysis_members/'
+                      'mpaso.hist.am.timeSeriesStatsMonthly.0001-01-01.nc')

compass/ocean/tests/global_ocean/monthly_output_test/namelist.forward

@@ -0,0 +1,3 @@
+config_run_duration = '0000-01-00_00:00:00'
+config_AM_timeSeriesStatsMonthly_enable = .true.
+config_AM_timeSeriesStatsMonthly_restart_stream = 'none'

compass/ocean/tests/global_ocean/monthly_output_test/streams.forward

@@ -0,0 +1,11 @@
+<streams>
+
+<stream name="timeSeriesStatsMonthlyOutput"
+        type="output"
+        precision="double"
+        filename_template="analysis_members/mpaso.hist.am.timeSeriesStatsMonthly.$Y-$M-$D.nc"
+        output_interval="00-01-00_00:00:00"
+        clobber_mode="truncate">
+</stream>
+
+</streams>