feature/coupled-crow fractional grid (#218)

* updated checkout build and link to use new unified model
- changed a few names from fv3 to ufs

* updates for linking to new fix

* point to a particular hash of ufs model

* remove theia modules

* update ww3 build for fv3->ufs naming change

* adding WW3 to build

* updates for having cice fix file have resolution folders and
removing cice5 references

* remove CODEwave as it is an unused variable

* more fv3->ufs dir name changes

* update location of fd_nems.yaml file for CMEPS-interface change

* modules used for successful forecast and atm post, but ocn post failed

* remove nowave parm file

* rename w/wave file

* change of parameters for mom6 to match rt tests

* add all the parm files for ocean

* updates for MOM6 to use same MOM_input templates as used in rt tests/parm dir

* add one-step option to no wave case

* updates to make nems.configure template files more closely
match ufs-weather-model tests/parm templates for easier
updates and also added updates for frac grid/not frac grid option

* use latest ufs-weather-model

* update to latest code

* changing n_aero  from 1 to 0 following ufs-community/ufs-weather-model#270

* updating MOM_input_templates based on ufs-community/ufs-weather-model#290

* updating iovsr  after NCAR/ccpp-physics#514 namelist options iovrsw and iovrlw will be replaced by a single iovr option

* updates for most recent commit to ufs-weather-model
includes updates to make CICE input file ice_in match the latest
in the rt test options, updates to include fractional grid options (set to false for now),
update to have namelist options iovrsw and iovrlw will be replaced by a single iovr
which was needed after NCAR/ccpp-physics#514

* deleting redundant/renamed files.  These files are now nems.configure.cpld(_wave).IN

* updated wave case file to include frac grid and made a new
non-frac grid case file

* use frac grid oro if frac grid true

* add nonfrac grid case to readme

* remove keep data option from case file

README.md

@@ -66,9 +66,10 @@ or
 ./setup_case.sh -p HERA ../cases/$CASE.yaml test2d
 ```
 where $CASE is one of the following:
-- prototype_5: Used for UFS S2S Prototype 5 (Runs 35 day cases with atm-ocn-ice-wav coupling)
+- prototype_5: Used for UFS S2S Prototype 5 (Runs 35 day cases with atm-ocn-ice-wav coupling, use with p5 workflow only)
 - coupled_free_forecast: 2 day tests for atm-ocn-ice coupling 
-- coupled_free_forecast_wave: 2 day test for atm-ocn-ice-wav coupling (same as p5 except shorter) 
+- coupled_free_forecast_wave: 2 day test for atm-ocn-ice-wav coupling (frac grid)
+- coupled_free_forecast_nofrac_wave: 2 day test for atm-ocn-ice-wav coupling (non frac grid)
 - atm_free_forecast:  Run the atm only case with same ICs as coupled tests 
 Please see the bottom of the README for information about particular versions and ICs
 

ush/forecast_postdet.sh

@@ -176,8 +176,17 @@ EOF
 	# Grid and orography data
 	for n in $(seq 1 $ntiles); do
 	  $NLN $FIXfv3/$CASE/${CASE}_grid.tile${n}.nc     $DATA/INPUT/${CASE}_grid.tile${n}.nc
-	  $NLN $FIXfv3/$CASE/${CASE}_oro_data.tile${n}.nc $DATA/INPUT/oro_data.tile${n}.nc
 	done
+        if  [ $FRAC_GRID ]; then 
+          FIXoro=${FIXoro:-$FIX_DIR/fix_fv3_fracoro}
+          for n in $(seq 1 $ntiles); do 
+            $NLN $FIXoro/${CASE}.mx${OCNRES}_frac/${CASE}.mx${OCNRES}_tile${n}.nc $DATA/INPUT/oro_data.tile${n}.nc
+          done 
+        else 
+          for n in $(seq 1 $ntiles); do
+            $NLN $FIXfv3/$CASE/${CASE}_oro_data.tile${n}.nc $DATA/INPUT/oro_data.tile${n}.nc
+          done
+        fi 
         if [ $cplflx = ".false." ] ; then
 	  $NLN $FIXfv3/$CASE/${CASE}_mosaic.nc  $DATA/INPUT/grid_spec.nc
         else 

workflow/cases/coupled_free_forecast_nofrac_wave.yaml

@@ -0,0 +1,62 @@
+case:
+  places:
+    workflow_file: layout/free_forecast_gfs.yaml
+    #BASE_CPLIC: /scratch2/NCEPDEV/climate/climpara/S2S/IC
+
+  settings: 
+    SDATE: 2013-04-01t00:00:00
+    EDATE: 2013-04-01t00:00:00
+
+    onestep: .true.
+    cplmode: nems_orig
+    FRAC_GRID: .false.
+    cplwav: .true.
+    cplwav2atm: .true.
+    cplflx: .true.
+    print_esmf: .true.
+    nems_temp: 'cpld_wave'
+    mom6ic_prepared: .false.
+    KEEPDATA: NO
+
+  nsst:
+    NST_MODEL: 0
+
+  output_settings:
+    OCN_INTERVAL: 24
+    FHOUT_GFS: 6
+    FHMIN_GFS: 0
+    FHMAX_GFS: 48
+    FHMAX_HF_GFS: 0
+    FHOUT_HF_GFS: -1
+
+  fv3_gfs_settings:
+    CASE: C384
+    LEVS: 65
+    DELTIM: 450
+    SEEDLET: 10
+    CCPP_SUITE: FV3_GFS_v15p2_coupled
+    nst_anl: no
+    DO_SKEB: false
+    DO_SHUM: false
+    DO_SPPT: false
+    layout:
+       x: 6
+       y: 12
+       nth: 1
+       WGRP: 1
+       WGRP_NTASKS: 24
+       WRTIOBUF: "32M"
+    cdmbgwd: "1.0,1.2"
+
+  ocn_settings:
+    OCNPETS: 240
+
+  ice_settings:
+    ICEPETS: 48
+
+  wave_settings: 
+    WAVPETS: 136
+
+  post:
+    downset: 2
+    GOESF: no

workflow/cases/coupled_free_forecast_wave.yaml

@@ -8,8 +8,8 @@ case:
     EDATE: 2013-04-01t00:00:00
 
     onestep: .true.
-    cplmode: nems_orig
-    FRAC_GRID: .false.
+    cplmode: nems_frac
+    FRAC_GRID: .true.
     cplwav: .true.
     cplwav2atm: .true.
     cplflx: .true.
@@ -35,6 +35,7 @@ case:
     DELTIM: 450
     SEEDLET: 10
     CCPP_SUITE: FV3_GFS_v15p2_coupled
+    CPL_ATMIC: CFSRfracL64
     nst_anl: no
     DO_SKEB: false
     DO_SHUM: false