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

pycif/plugins/models/wrfchem/__init__.py

@@ -61,17 +61,16 @@ requirements = {
         "preftree": "datavect/components",
     },
 
-    # # Boundary conditions
-    # "latcond": {
-    #     "name": "wrfchem",
-    #     "version": "icbc",
-    #     "type": "fields",
-    #     "empty": False,
-    #     "any": False,
-    #     "subplug": True,
-    #     "preftree": "datavect/components",
-    # },
-    #
+    # Boundary conditions
+    "latcond": {
+        "name": "wrfchem",
+        "version": "icbc",
+        "type": "fields",
+        "empty": True,
+        "any": False,
+        "newplg": True,
+    },
+
     "inicond": {
         "name": "wrfchem",
         "version": "icbc",

pycif/plugins/models/wrfchem/ini_mapper.py

@@ -46,7 +46,6 @@ def ini_mapper(model, transform_type, general_mapper={}, backup_comps={},
     # as needed below
     # default_dict = {"input_dates": input_intervals, "force_dump": True}
     default_dict = {"force_dump": True, "sparse_data": False}
-    meteo_dict = {"input_dates": meteo_intervals, "force_dump": True}
     dict_surface = dict(default_dict, **{"domain": model.domain,
                                          "fixed_domain": True})
     dict_setup = dict(
@@ -54,6 +53,8 @@ def ini_mapper(model, transform_type, general_mapper={}, backup_comps={},
             model.datei: np.array([[model.datei, model.datef]])}}
     )
 
+    dict_lat = dict(dict_surface, **{"is_lbc": True,
+                                     "input_dates": meteo_intervals})
     dict_ini = dict(
         dict_surface, **{"input_dates": {
             model.datei: np.array([[model.datei, model.datei]])}}
@@ -108,6 +109,12 @@ def ini_mapper(model, transform_type, general_mapper={}, backup_comps={},
     }
     mapper["inputs"].update(inicond)
 
+    lbc = {
+        ("latcond", s): dict_lat
+        for s in model.chemistry.acspecies.attributes
+    }
+    mapper["inputs"].update(lbc)
+
     # 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
     # needed at some point.

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

+import os
+import shutil
+import filecmp
+from netCDF4 import Dataset
+import numpy as np
+import xarray as xr
+import pandas as pd
+import pathlib
+
+from logging import warning
+
+from ......utils import path
+# from .utils import replace_dates
+
+# Copied from chimere on 2022-01-03, adapted to wrf
+
+def make_latcond(self, datastore, runsubdir, datei, mode):
+    """
+    Generates boundary conditions files for wrf
+    (Could merge with make_inicond, it's pretty much the same)
+
+    :param self:
+    :param datastore:
+    :type datastore: dict
+    :param runsubdir:
+    :type runsubdir: str
+    :param mode:
+    :return:
+    """
+
+    # List of dates for which emissions are needed
+    # freum: all uses commented
+    # list_dates = pd.date_range(ddi, periods=self.nhours + 1, freq="H")
+    
+    # Name of variable in netCDF
+    # freum: all uses commented
+    # nc_varname = "top_conc" if input_type == "topcond" else "lat_conc"
+
+    # Fixed name for BC files
+    fileout = "{}/wrfbdy_d01".format(runsubdir)
+
+    # Loop on all active species
+    # If in datastore, take data, otherwise, link to original BOUN_CONCS
+    for spec in self.chemistry.acspecies.attributes:
+        trid = ("latcond", spec)
+
+        # If spec not explicitly defined in datastore,
+        # fetch general component information if available
+        if trid in datastore:
+            pass
+        elif trid not in datastore and ("latcond", "") in datastore:
+            trid = ("latcond", "")
+        else:
+            continue
+
+        tracer = datastore[trid]
+        tracer_data = tracer["data"][datei]
+        
+        # If no data is provided, just copy from original file
+        if "spec" not in tracer_data:
+            dirorig = tracer["dirorig"]
+            fileorig = tracer["fileorig"]
+            fileini = "{}/{}".format(dirorig, fileorig)
+            
+            # If does not exist, just link
+            # linked = False
+            if not os.path.isfile(fileout):
+                path.link(fileini, fileout)
+
+            # freum: comment again, same as in fluxes and inicond
+            # # Otherwise, check for difference
+            # if not linked:
+            #     if not os.path.isfile(fileini):
+            #         warning("The boundary 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:
+            #             ljust_specs_in = ds.variables["species"][:].astype(str)
+            #             specs_in = ["".join(p).strip() for p in ljust_specs_in]
+            #             
+            #             if spec not in specs_in:
+            #                 warning("{} is not accounted "
+            #                         "for in the boundary conditions file {}. "
+            #                         "Please check your LBC whether it should be"
+            #                         .format(spec, fileini))
+            #                 continue
+            #                 
+            #             ispec = specs_in.index(spec)
+            #             
+            #             if input_type == "latcond":
+            #                 lbcin = ds.variables["lat_conc"][..., ispec]
+            #                 lbcin = lbcin[..., np.newaxis, :]
+            #             else:
+            #                 lbcin = ds.variables["top_conc"][..., ispec]
+            #                 lbcin = lbcin[:, np.newaxis, ...]
+            #             
+            #             lbcin = xr.DataArray(
+            #                 lbcin,
+            #                 coords={"time": list_dates},
+            #                 dims=("time", "lev", "lat", "lon"),
+            #             )
+            #             
+            #         # If lbc 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.latcond.write(spec, fileout, lbcin,
+            #                            comp_type=input_type)
+
+        else:
+            # Replace existing link by copy
+            # of original file to modify it
+            path.copyfromlink(fileout)
+
+            # Write initial conditions
+            lbc_fwd = tracer_data["spec"]
+            self.latcond.write(spec, fileout, lbc_fwd, comp_type="latcond")
+
+            # freum: no tl mode for wrf
+            # if mode == "tl":
+            #     path.copyfromlink(fileoutincr)
+            #     lbc_tl = tracer_data.get("incr", 0.0 * lbc_fwd)
+            #     self.latcond.write(
+            #         spec, fileoutincr, lbc_tl, comp_type=input_type
+            #     )
+        
+        # Check that the dates are consistent with what CHIMERE expects
+        # freum: check for dates in file commented, because wrf checks that too
+        # replace_dates(fileout, list_dates, self.ignore_input_dates)
+        
+        # freum: no tl mode for wrf
+        # # Repeat operations for tangent linear
+        # # Needed to initialize the TL to zero for other species
+        # if mode != "tl":
+        #     continue
+        # 
+        # if "spec" not in tracer_data:
+        #     # If does not exist, just link
+        #     if not os.path.isfile(fileoutincr):
+        #         shutil.copy(fileini, fileoutincr)
+        # 
+        #     with Dataset(fileoutincr, "a") as fout:
+        #         nc_var_out = fout.variables[nc_varname][:]
+        #         nc_names = [
+        #             str(b"".join(s).strip().lower(), "utf-8")
+        #             for s in fout.variables["species"][:]
+        #         ]
+        #         if spec.lower() not in nc_names:
+        #             continue
+        # 
+        #         # Apply to original data
+        #         nc_var_out[..., nc_names.index(spec.lower())][:] = 0.0
+        # 
+        #         fout.variables[nc_varname][:] = nc_var_out
+        # 
+        # replace_dates(fileoutincr, list_dates, self.ignore_input_dates)

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

@@ -15,6 +15,7 @@ from .inputs.params import update_namelist_file
 import logging
 from .inputs.make_fluxes import make_fluxes
 from .inputs.make_inicond import make_inicond
+from .inputs.make_latcond import make_latcond
 
 
 def native2inputs(
@@ -72,6 +73,10 @@ def native2inputs(
         ddi = min(datei, datef)
         make_inicond(self, datastore, runsubdir, mode, ddi)
 
+    elif input_type == "latcond":
+        ddi = min(datei, datef)
+        make_latcond(self, datastore, runsubdir, ddi, mode)
+
     else:
         msg = "No method implemented for input type '{}'.".format(input_type)
         logging.info(msg)