Feature/updates for gw (#162)

* Define CRTM_FIX and add prod_util path to GDAS Hera and Orion modules (#154)

* Add sensor keyword to amsua_n19.yaml (#154)

* updates for fv3jedi var and lgetkf g-w cycling (#154)

modulefiles/GDAS/hera.lua

@@ -78,6 +78,8 @@ setenv('MPIEXEC_EXEC', mpiexec)
 setenv('MPIEXEC_NPROC', mpinproc)
 
 setenv('R2D2_CONFIG', '/scratch1/NCEPDEV/stmp4/Cory.R.Martin/R2D2_SHARED/config_hera.yaml')
+setenv("CRTM_FIX","/scratch1/NCEPDEV/da/Cory.R.Martin/GDASApp/fix/crtm")
+prepend_path("PATH","/scratch2/NCEPDEV/nwprod/hpc-stack/libs/hpc-stack/intel-18.0.5.274/prod_util/1.2.2/bin")
 
 whatis("Name: ".. pkgName)
 whatis("Version: ".. pkgVersion)

modulefiles/GDAS/orion.lua

@@ -74,6 +74,8 @@ setenv('MPIEXEC_EXEC', mpiexec)
 setenv('MPIEXEC_NPROC', mpinproc)
 
 setenv('R2D2_CONFIG', '/work2/noaa/da/cmartin/GDASApp/R2D2_SHARED/config_orion.yaml')
+setenv("CRTM_FIX","/work2/noaa/da/cmartin/GDASApp/fix/crtm")
+prepend_path("PATH","/apps/contrib/NCEP/libs/hpc-stack/intel-2018.4/prod_util/1.2.2/bin")
 
 execute{cmd="ulimit -s unlimited",modeA={"load"}}
 

parm/atm/lgetkf/lgetkf.yaml

@@ -9,7 +9,7 @@ background:
      template:
        datetime: $(BKG_ISOTIME)
        filetype: fms restart
-       state variables: [ua,va,t,DZ,delp,sphum,ice_wat,liq_wat,o3mr,phis,
+       state variables: [ua,va,t,DZ,delp,ps,sphum,ice_wat,liq_wat,o3mr,phis,
                         slmsk,sheleg,tsea,vtype,stype,vfrac,stc,smc,snwdph,
                         u_srf,v_srf,f10m]
        datapath: bkg/mem%mem%/RESTART
@@ -45,12 +45,12 @@ local ensemble DA:
 
 #output:
 #  filetype: auxgrid
-#  gridtype: latlon
+#  gridtype: gaussian
 #  filename: $(ANL_DIR)/mem%{member}%/atmanl.
 
 output ensemble increments:
   filetype: auxgrid
-  gridtype: latlon
+  gridtype: gaussian
   filename: $(ANL_DIR)/mem%{member}%/atminc.
 
 geometry: $(GEOM_ANL)

parm/atm/obs/config/amsua_n19.yaml

@@ -180,6 +180,7 @@ obs filters:
       name: ObsErrorFactorTransmitTopRad@ObsFunction
       channels: *amsua_n19_channels
       options:
+        sensor: amsua_n19
         channels: *amsua_n19_channels
 #  Surface Jacobian check
 - filter: BlackList
@@ -192,6 +193,7 @@ obs filters:
       name: ObsErrorFactorSurfJacobianRad@ObsFunction
       channels: *amsua_n19_channels
       options:
+        sensor: amsua_n19
         channels: *amsua_n19_channels
         obserr_demisf: [0.010, 0.020, 0.015, 0.020, 0.200]
         obserr_dtempf: [0.500, 2.000, 1.000, 2.000, 4.500]
@@ -334,6 +336,7 @@ obs filters:
   - name: ChannelUseflagCheckRad@ObsFunction
     channels: *amsua_n19_channels
     options:
+      sensor: amaua_n19
       channels: *amsua_n19_channels
       use_flag: [ 1,  1,  1,  1,  1,
                   1, -1, -1,  1,  1,

parm/atm/variational/3dvar_dripcg.yaml

@@ -40,6 +40,6 @@ final:
   increment:
     output:
       filetype: auxgrid
-      gridtype: latlon
+      gridtype: gaussian
       filename: $(ANL_DIR)/atminc.
     geometry: $(GEOM_ANL)

ush/jediinc2fv3.py

@@ -70,7 +70,7 @@ def create_fv3inc(ncges, ncin, ncout):
 
     # Rename and change dimensionality of fields
     for name, variable in ncin.variables.items():
-        if len(variable.dimensions) in [3, 4]:
+        if len(variable.dimensions) in [4]:
             dimsout = variable.dimensions[1:]
             dimsout_inc = dimsout
         else:
@@ -84,7 +84,7 @@ def create_fv3inc(ncges, ncin, ncout):
                 tinc = name
 
             x = ncout.createVariable(vardict[name], 'f4', dimsout)
-            if len(variable.dimensions) in [3, 4]:
+            if len(variable.dimensions) in [4]:
                 ncout[vardict[name]][:] = ncin[name][0, ...]
             else:
                 ncout[vardict[name]][:] = ncin[name][:]

ush/ufsda/archive.py

@@ -30,7 +30,7 @@ def atm_diags(config):
         r2d2_config['provider'] = config['provider']
         r2d2_config['start'] = config['window_begin']
         r2d2_config['end'] = r2d2_config['start']
-        input_file = ob['obs space']['obsdataout']['obsfile']
+        input_file = ob['obs space']['obsdataout']['engine']['obsfile']
         r2d2_config['source_dir'] = config['OBS_DIR']
         r2d2_config['source_file_fmt'] = input_file.replace('.nc4', '_0000.nc4')
         r2d2_config['obs_types'] = [ob['obs space']['name']]