Activate handling of wrfchem initial conditions (only fetch, no read and write)

pycif/plugins/models/wrfchem/ini_mapper.py

@@ -53,6 +53,12 @@ def ini_mapper(model, transform_type, general_mapper={}, backup_comps={},
         dict_surface, **{"input_dates": {
             model.datei: np.array([[model.datei, model.datef]])}}
     )
+
+    dict_ini = dict(
+        dict_surface, **{"input_dates": {
+            model.datei: np.array([[model.datei, model.datei]])}}
+    )
+
     
     # Executable
     mapper = {
@@ -96,12 +102,11 @@ def ini_mapper(model, transform_type, general_mapper={}, backup_comps={},
         for s in model.chemistry.emis_species.attributes
     }
     mapper["inputs"].update(emis)
-    # raise ValueError("look here")
-    # freum: comment inicond until I move them from preprocessing to cif
-    # inicond = {
-    #     ("inicond", s): dict_ini for s in model.chemistry.acspecies.attributes
-    # }
-    # mapper["inputs"].update(inicond)
+
+    inicond = {
+        ("inicond", s): dict_ini for s in model.chemistry.acspecies.attributes
+    }
+    mapper["inputs"].update(inicond)
 
     # freum: from here, additional code in lmdz's ini_mapper that the
     # WRF plugin doesn't use. Commented instead of deleted in case it's

pycif/plugins/models/wrfchem/io/inputs/make_inicond.py

@@ -12,15 +12,10 @@ from ......utils import path
 
 # Copied from chimere on 2022-01-03
 
-def make_inicond(self, datastore, runsubdir, mode, datei, datef):
-    ddi = min(datei, datef)
+def make_inicond(self, datastore, runsubdir, mode, datei):
 
-    raise NotImplementedError("Adapt to wrf")
-
-    # Fixed name for INI_CONCS files
-    fileout = "{}/INI_CONCS.0.nc".format(runsubdir)
-    fileoutincr = "{}/INI_CONCS.0.increment.nc".format(runsubdir)
-    nho = self.nho
+    # Fixed name for initial conditions file
+    fileout = "{}/wrfinput_d01".format(runsubdir)
     
     # # Getting the forward initial concentrations (needed even for adjoint)
     # # if chained period
@@ -52,7 +47,7 @@ def make_inicond(self, datastore, runsubdir, mode, datei, datef):
             continue
         
         tracer = datastore[trid]
-        tracer_data = tracer["data"][ddi]
+        tracer_data = tracer["data"][datei]
         
         # If no data is provided, just copy from original file
         if "spec" not in tracer_data:
@@ -61,57 +56,59 @@ def make_inicond(self, datastore, runsubdir, mode, datei, datef):
             fileini = "{}/{}".format(dirorig, fileorig)
             
             # If does not exist, just link
-            linked = False
+            # linked = False
             if not os.path.isfile(fileout):
                 path.link(fileini, fileout)
-                linked = True
-            
-            # Otherwise, check for difference
-            if not linked:
-                if not os.path.isfile(fileini):
-                    warning("The initial condition file {} does not exist to "
-                            "initialize the species {}. The concentrations will"
-                            " be initialized to zero. Please check your yaml if"
-                            " you expect a different behaviour"
-                            .format(fileini, spec))
-                    continue
-                
-                if not filecmp.cmp(fileini, fileout):
-                    with Dataset(fileini, "r") as ds:
-                        if spec not in ds.variables:
-                            warning("{} is not accounted "
-                                    "for in the initial conditions file {}. "
-                                    "Please check your IC whether it should be"
-                                    .format(spec, fileini))
-                            continue
-                        
-                        iniin = ds.variables[spec][:]
-                        iniin = xr.DataArray(
-                            iniin[np.newaxis, ...],
-                            coords={"time": [min(datei, datef)]},
-                            dims=("time", "lev", "lat", "lon"),
-                        )
-                    
-                    # If ini file is still a link, should be copied
-                    # to be able to modify it locally
-                    if os.path.islink(fileout):
-                        file_orig = pathlib.Path(fileout).resolve()
-                        os.unlink(fileout)
-                        shutil.copy(file_orig, fileout)
-                    
-                    # Now writes the new value for the corresponding species
-                    self.inicond.write(spec, fileout, iniin,
-                                       comp_type="inicond")
-            
-            # Repeat operations for tangent linear
-            if mode == "tl":
-                # If does not exist, just link
-                if not os.path.isfile(fileoutincr):
-                    shutil.copy(fileini, fileoutincr)
-                
-                with Dataset(fileoutincr, "a") as fout:
-                    if spec in fout.variables:
-                        fout.variables[spec][:] = 0.0
+                # linked = True
+
+            # freum: didn't need this in fluxes, so commenting it here too
+            # # Otherwise, check for difference
+            # if not linked:
+            #     if not os.path.isfile(fileini):
+            #         warning("The initial condition file {} does not exist to "
+            #                 "initialize the species {}. The concentrations will"
+            #                 " be initialized to zero. Please check your yaml if"
+            #                 " you expect a different behaviour"
+            #                 .format(fileini, spec))
+            #         continue
+            #     
+            #     if not filecmp.cmp(fileini, fileout):
+            #         with Dataset(fileini, "r") as ds:
+            #             if spec not in ds.variables:
+            #                 warning("{} is not accounted "
+            #                         "for in the initial conditions file {}. "
+            #                         "Please check your IC whether it should be"
+            #                         .format(spec, fileini))
+            #                 continue
+            #             
+            #             iniin = ds.variables[spec][:]
+            #             iniin = xr.DataArray(
+            #                 iniin[np.newaxis, ...],
+            #                 coords={"time": [min(datei, datef)]},
+            #                 dims=("time", "lev", "lat", "lon"),
+            #             )
+            #         
+            #         # If ini file is still a link, should be copied
+            #         # to be able to modify it locally
+            #         if os.path.islink(fileout):
+            #             file_orig = pathlib.Path(fileout).resolve()
+            #             os.unlink(fileout)
+            #             shutil.copy(file_orig, fileout)
+            #         
+            #         # Now writes the new value for the corresponding species
+            #         self.inicond.write(spec, fileout, iniin,
+            #                            comp_type="inicond")
+
+            # freum: no tl mode for wrf
+            # # Repeat operations for tangent linear
+            # if mode == "tl":
+            #     # If does not exist, just link
+            #     if not os.path.isfile(fileoutincr):
+            #         shutil.copy(fileini, fileoutincr)
+            #     
+            #     with Dataset(fileoutincr, "a") as fout:
+            #         if spec in fout.variables:
+            #             fout.variables[spec][:] = 0.0
         
         else:
             # Replace existing link by copy
@@ -121,17 +118,21 @@ def make_inicond(self, datastore, runsubdir, mode, datei, datef):
             # Write initial conditions
             ini_fwd = tracer_data["spec"]
             self.inicond.write(spec, fileout, ini_fwd, comp_type="inicond")
-            
-            if mode == "tl":
-                path.copyfromlink(fileoutincr)
-                ini_tl = tracer_data.get("incr", 0.0 * ini_fwd)
-                self.inicond.write(
-                    spec, fileoutincr, ini_tl, comp_type="inicond"
-                )
 
-        # Check that the dates are consistent with what CHIMERE expects
-        replace_dates(fileout, [min(datei, datef)], self.ignore_input_dates)
-        if mode == "tl":
-            replace_dates(fileoutincr, [min(datei, datef)],
-                          self.ignore_input_dates)
-        
+            # freum: no tl mode for wrf
+            # if mode == "tl":
+            #     path.copyfromlink(fileoutincr)
+            #     ini_tl = tracer_data.get("incr", 0.0 * ini_fwd)
+            #     self.inicond.write(
+            #         spec, fileoutincr, ini_tl, comp_type="inicond"
+            #     )
+
+        # Check that the dates are consistent with what wrf expects
+        # Commented, because WRF checks that too.
+        # wrfinput_times, _ = self.wrfhelper.wrf_times([fileout])
+        # ok = False
+        # if len(wrfinput_times) == 1):
+        #     if wrfinput_times[0] == datei:
+        #         ok = True
+        # if not ok:
+        #     raise ValueError("Dates in {} are not what WRF expects.")        

pycif/plugins/models/wrfchem/io/native2inputs.py

@@ -69,11 +69,8 @@ def native2inputs(
 
     # Deals with initial conditions
     elif input_type == "inicond":
-        msg = "Implement make_inicond here - IF needed"
-        logging.info(msg)
-        # pass
-        # raise NotImplementedError(msg)
-        make_inicond(self, datastore, runsubdir, mode, ddi, ddf)
+        ddi = min(datei, datef)
+        make_inicond(self, datastore, runsubdir, mode, ddi)
 
     else:
         msg = "No method implemented for input type '{}'.".format(input_type)