fix outspcies typo

dynamic/palm_dynamic.py

@@ -214,7 +214,7 @@ print('cent_lon, cent_lat:', cent_lon, cent_lat)
 irange = origin_x + dx * (np.arange(nx, dtype='f8') + .5)
 jrange = origin_y + dy * (np.arange(ny, dtype='f8') + .5)
 palm_grid_y, palm_grid_x = np.meshgrid(jrange, irange, indexing='ij')
-transformer2 = Transformer.from_crs(inproj, lonlatproj,always_xy=True)
+transformer2 = Transformer.from_crs(inproj, lonlatproj, always_xy=True)
 palm_grid_lon, palm_grid_lat = transformer2.transform(palm_grid_x, palm_grid_y)
 
 ######################################
@@ -360,13 +360,15 @@ for wrf_file in wrf_files_proc:
                 # create list of variables
                 # dynamical variables
                 wrfchem_dynamic = ['PH', 'PHB', 'HGT', 'T', 'W', 'TSLB', 'SMOIS', 'MU', 'MUB','P', 'PB', 'PSFC']
+                
                 # add chemical species if included
                 if len(wrfchem_spec)>0:
                     wrfchem_variables = wrfchem_dynamic + wrfchem_spec
 
                 # add aerosol species if included
-                N_avr = 6.022e23 # Avargardo constant
-                inv_den = f_wrf.variables['ALT'][0] # inverse density
+                N_avr   = 6.022e23                  # Avargardo constant
+                inv_den = f_wrf.variables['ALT'][0] # Inverse density
+                t00     = f_wrf.variables['T00'][0] # Perturbation pt to standard (T00 wrf-chem variable)
 
                 for varname in wrfchem_variables:
                     # gaseous aerosols
@@ -487,7 +489,7 @@ for wrf_file in wrf_files_proc:
         print('Vertical interpolation...')
         palm_wrf_utils.palm_wrf_vertical_interp(hinterp_file, vinterp_file, wrf_file, z_levels,
                                                 z_levels_stag, z_soil_levels, origin_z, terrain,
-                                                wrf_hybrid_levs, vinterp_terrain_smoothing, nz, ny, nx)
+                                                wrf_hybrid_levs, vinterp_terrain_smoothing, nz, ny, nx, t00)
 
 if radiation_from_wrf:
     print('Start processing of radiation inputs from the WRF radiation files.')

dynamic/palm_dynamic_output.py

@@ -325,7 +325,7 @@ def palm_dynamic_output(wrf_files, interp_files, dynamic_driver_file, times_sec,
                     if (var == 'soil_m' or var == 'soil_t' or var == 'u' or var == 'v' or var == 'w'):
                         continue
                     else:
-                        if (var == 'h2so4' or var=='hno3' or var== 'nh3' or var== 'ocnv' or var== 'ocsv'):
+                        if (var == 'h2so4' or var=='hno3' or var== 'nh3' or var== 'ocnv' or var== 'ocsv' or var == 'no' or var == 'no2' or var == 'no3'):
                             var = var.upper()
 
                         init_var= infile.variables['init_atmosphere_'+ var.lower()]

dynamic/palm_wrf_utils.py

@@ -219,7 +219,7 @@ def calc_gp(f, ph):
     return np.array(gp)
 
 def palm_wrf_vertical_interp(infile, outfile, wrffile, z_levels, z_levels_stag,
-        z_soil_levels, origin_z, terrain, wrf_hybrid_levs, vinterp_terrain_smoothing,nz,ny,nx):
+        z_soil_levels, origin_z, terrain, wrf_hybrid_levs, vinterp_terrain_smoothing, nz, ny, nx, t00_raw):
 
     zdim       = len(z_levels)
     zwdim      = len(z_levels_stag)
@@ -232,7 +232,6 @@ def palm_wrf_vertical_interp(infile, outfile, wrffile, z_levels, z_levels_stag,
         os.remove(infile+'_vinterp.log')
     except:
         pass
-
     nc_infile  = netCDF4.Dataset(infile, 'r')
     nc_wrf     = netCDF4.Dataset(wrffile, 'r')
     nc_outfile = netCDF4.Dataset(outfile, "w", format="NETCDF4")
@@ -303,7 +302,7 @@ def palm_wrf_vertical_interp(infile, outfile, wrffile, z_levels, z_levels_stag,
     vdata = nc_outfile.createVariable('init_atmosphere_qv', "f4", ("Time", "z","south_north","west_east"))
     vdata[0,:,:,:] = init_atmosphere_qv
     # ======================= POTENTIAL TEMPERATURE ==========================
-    pt_raw = nc_infile.variables['T'][0] + 290.    # from perturbation pt to standard (T00 wrf-chem variable)
+    pt_raw = nc_infile.variables['T'][0] + t00_raw
     pt_raw = np.r_[pt_raw[0:1], pt_raw]
     init_atmosphere_pt = interpolate_1d(z_levels, height, pt_raw)