started to implement the function to get model-data mismatch for each obs

da/tools/pipeline.py

@@ -227,10 +227,16 @@ def SampleOneCycle(DaCycle,Samples,StateVector, ObservationOperator,lag):
 
     DaCycle.da_settings['ObsOperator.inputfile'] = filename
 
-    # Run the forecast model
+    # Run the observation operator
 
     dummy   = RunForecastModel(DaCycle,ObservationOperator)
 
+    # Add model-data mismatch to all samples, this *might* use output from the ensemble in the future??
+
+    dummy   = Samples.AddModelDataMismatch(DaCycle)
+
+    msg = "Added Model Data Mismatch to all samples " ; logging.debug(msg)
+
     # Read forecast model samples that were written to NetCDF files by each member, also add the obs to the statevector
 
     silent = False
@@ -240,7 +246,7 @@ def SampleOneCycle(DaCycle,Samples,StateVector, ObservationOperator,lag):
         Member.ModelSample     = Samples
         silent=True
 
-    msg = "Added samples from the forecast model to each member of the StateVector" ; logging.debug(msg)
+    msg = "Added samples from the observation operator to each member of the StateVector" ; logging.debug(msg)
 
     # Advance the sample time