Merge branch 'develop' into bugfix/gc_doxygen

Fixes ufs-community#1025.

reg_tests/global_cycle/C192.gsi_lndincsoilnoahmp.sh

@@ -37,9 +37,8 @@ export DONST="NO"
 export use_ufo=.true.
 
 export DO_SFCCYCLE=".FALSE." 
-export DO_LNDINC=".TRUE." 
-export DO_SOI_INC=".true."
-export GCYCLE_INTERP_LNDINC=".true."
+export GCYCLE_DO_SOILINCR=".true."
+export GCYCLE_INTERP_LANDINCR=".true."
 export LSOIL_INCR=3
 
 export VERBOSE=YES

reg_tests/global_cycle/C192.gsitile_lndincsoilnoahmp.sh

@@ -37,9 +37,8 @@ export DONST="NO"
 export use_ufo=.true.
 
 export DO_SFCCYCLE=".FALSE." 
-export DO_LNDINC=".TRUE." 
-export DO_SOI_INC=".true."
-export GCYCLE_INTERP_LNDINC=".false."
+export GCYCLE_DO_SOILINCR=".true."
+export GCYCLE_INTERP_LANDINCR=".false."
 export LSOIL_INCR=3
 
 export VERBOSE=YES

reg_tests/global_cycle/C192.jedi_lndincsoilnoahmp.sh

@@ -39,10 +39,9 @@ export DONST="NO"
 export use_ufo=.true.
 
 export DO_SFCCYCLE=".FALSE." 
-export DO_LNDINC=".TRUE." 
-export DO_SOI_INC=".true."
-export GCYCLE_INTERP_LNDINC=".false."
-export SOI_INC_FNAME="soil_sfcincr_jedi"
+export GCYCLE_DO_SOILINCR=".true."
+export GCYCLE_INTERP_LANDINCR=".false."
+export SOILINCR_FNAME="soil_sfcincr_jedi"
 export LSOIL_INCR=3
 
 export VERBOSE=YES

reg_tests/global_cycle/C768.lndincsnow.sh

@@ -31,9 +31,8 @@ export FNSNOA=$COMIN/gdas.t00z.snogrb_t1534.3072.1536
 export FNACNA=$COMIN/gdas.t00z.seaice.5min.blend.grb
 export NST_FILE=$COMIN/gdas.t00z.dtfanl.nc
 
-export DO_SNO_INC=.true. # must be lower-case.
-export DO_SOI_INC=.false.
-export GCYCLE_INTERP_LNDINC=.false.
+export GCYCLE_DO_SNOWINCR=.true. # must be lower-case.
+export GCYCLE_INTERP_LANDINCR=.false.
 export JCAP=1534
 export LONB=3072
 export LATB=1536
@@ -42,7 +41,6 @@ export DONST="NO"
 export use_ufo=.true.
 
 export DO_SFCCYCLE=".FALSE." 
-export DO_LNDINC=".TRUE." 
 
 export VERBOSE=YES
 export CYCLVARS=FSNOL=99999.,FSNOS=99999.,

sorc/global_cycle.fd/cycle.f90

@@ -9,7 +9,7 @@
 !!
 !!  There are three main options (which can be called in combination):
 !!  1. Update the surface fields with sfccylce (do_sfccycle = .true.)
-!!  2. Update the land states with increments read in from file (do_lndinc = .true.)
+!!  2. Update the land states with increments read in from file (do_landincr = .true.)
 !!     Can read in either a GSI-output increment file and regrid it,
 !!     or (preferred) a file on the native model grid ( either produced
 !!     by JEDI, or pre- regridded from a GSI-output file)
@@ -62,12 +62,12 @@
 !!                 terrain.
 !!  -DONST         Call routines to process NSST records.
 !!  -DO_SFCCYCLE   Call sfccycle routine to update surface fields
-!!  -DO_LNDINC     Call routines to add land increments to sfc restarts
-!!                 (includes do_soi_inc and/or do_sno_inc)
-!!  -DO_SOI_INC    Apply increments to soil states. Requires DO_LNDINC=.true.
-!!  -DO_SNO_INC    Apply increments to snow states. Requires DO_LNDINC=.true.
+!!  -DO_LANDINCR   Call routines to add land increments to sfc restarts
+!!                 (includes do_soilincr and/or do_snowincr)
+!!  -DO_SOILINCR    Apply increments to soil states. Requires DO_LANDINCR=.true.
+!!  -DO_SNOWINCR    Apply increments to snow states. Requires DO_LANDINCR=.true.
 !!                 (NOTE: oudated, coded here for Noah LSM only).
-!!  -INTERP_LNDINC Land increment is on Gaussian grid (from GSI)  and should
+!!  -INTERP_LANDINCR Land increment is on Gaussian grid (from GSI)  and should
 !!                 be regridded to the native model grid
 !!  -LSOIL_INCR    Number of soil layers (from top) to apply soil increments to.
 !!                 LSOIL_INCR is currently set to 3 by default.
@@ -110,12 +110,12 @@ PROGRAM SFC_DRV
  INTEGER :: ISOT, IVEGSRC, LENSFC, ZSEA1_MM, ZSEA2_MM, IERR
  INTEGER :: NPROCS, MYRANK, NUM_THREADS, NUM_PARTHDS, MAX_TASKS
  REAL    :: FH, DELTSFC, ZSEA1, ZSEA2
- LOGICAL :: USE_UFO, DO_NSST, DO_LNDINC, DO_SFCCYCLE, FRAC_GRID
+ LOGICAL :: USE_UFO, DO_NSST, DO_LANDINCR, DO_SFCCYCLE, FRAC_GRID
 !
  NAMELIST/NAMCYC/ IDIM,JDIM,LSOIL,LUGB,IY,IM,ID,IH,FH,&
                   DELTSFC,IALB,USE_UFO,DONST,             &
                   DO_SFCCYCLE,ISOT,IVEGSRC,ZSEA1_MM,      &
-                  ZSEA2_MM, MAX_TASKS, DO_LNDINC, FRAC_GRID
+                  ZSEA2_MM, MAX_TASKS, DO_LANDINCR, FRAC_GRID
 !
  DATA IDIM,JDIM,LSOIL/96,96,4/
  DATA IY,IM,ID,IH,FH/1997,8,2,0,0./
@@ -137,7 +137,7 @@ PROGRAM SFC_DRV
 
  USE_UFO = .FALSE.
  DONST   = "NO"
- DO_LNDINC   = .FALSE.
+ DO_LANDINCR   = .FALSE.
  DO_SFCCYCLE = .TRUE.
  FRAC_GRID = .FALSE.
 
@@ -179,7 +179,7 @@ PROGRAM SFC_DRV
 
  CALL SFCDRV(LUGB,IDIM,JDIM,LENSFC,LSOIL,DELTSFC,  &
              IY,IM,ID,IH,FH,IALB,                  &
-             USE_UFO,DO_NSST,DO_SFCCYCLE,DO_LNDINC, &
+             USE_UFO,DO_NSST,DO_SFCCYCLE,DO_LANDINCR, &
              FRAC_GRID,ZSEA1,ZSEA2,ISOT,IVEGSRC,MYRANK)
 
  PRINT*
@@ -294,7 +294,7 @@ END PROGRAM SFC_DRV
  !!            differences between the filtered and unfiltered terrain.
  !! @param[in] DO_NSST When true, process NSST records.
  !! @param[in] DO_SFCCYCLE Call sfccycle routine to update surface fields
- !! @param[in] DO_LNDINC Read in land increment files, and add increments to
+ !! @param[in] DO_LANDINCR Read in land increment files, and add increments to
  !!            requested states.
  !! @param[in] FRAC_GRID When true, run with fractional grid.
  !! @param[in] ZSEA1 When running NSST model, this is the lower bound
@@ -307,7 +307,7 @@ END PROGRAM SFC_DRV
  !! @author Mark Iredell, George Gayno
  SUBROUTINE SFCDRV(LUGB, IDIM,JDIM,LENSFC,LSOIL,DELTSFC,  &
                    IY,IM,ID,IH,FH,IALB,                  &
-                   USE_UFO,DO_NSST,DO_SFCCYCLE,DO_LNDINC,&
+                   USE_UFO,DO_NSST,DO_SFCCYCLE,DO_LANDINCR,&
                    FRAC_GRID,ZSEA1,ZSEA2,ISOT,IVEGSRC,MYRANK)
 !
  USE READ_WRITE_DATA
@@ -328,7 +328,7 @@ SUBROUTINE SFCDRV(LUGB, IDIM,JDIM,LENSFC,LSOIL,DELTSFC,  &
  INTEGER, INTENT(IN) :: ISOT, IVEGSRC, MYRANK
 
  LOGICAL, INTENT(IN) :: USE_UFO, DO_NSST,DO_SFCCYCLE
- LOGICAL, INTENT(IN) :: DO_LNDINC, FRAC_GRID
+ LOGICAL, INTENT(IN) :: DO_LANDINCR, FRAC_GRID
 
  REAL, INTENT(IN)    :: FH, DELTSFC, ZSEA1, ZSEA2
 
@@ -387,7 +387,7 @@ SUBROUTINE SFCDRV(LUGB, IDIM,JDIM,LENSFC,LSOIL,DELTSFC,  &
  INTEGER, DIMENSION(LENSFC) :: STC_UPDATED, SLC_UPDATED
  REAL, DIMENSION(LENSFC,LSOIL) :: STCINC, SLCINC 
 
- LOGICAL :: FILE_EXISTS, DO_SOI_INC, INTERP_LNDINC, DO_SNO_INC
+ LOGICAL :: FILE_EXISTS, DO_SOILINCR, INTERP_LANDINCR, DO_SNOWINCR
  CHARACTER(LEN=3)       :: RANKCH
  INTEGER :: lsoil_incr
 
@@ -396,13 +396,13 @@ SUBROUTINE SFCDRV(LUGB, IDIM,JDIM,LENSFC,LSOIL,DELTSFC,  &
 ! increments.
 !--------------------------------------------------------------------------------
 
- NAMELIST/NAMSFCD/ NST_FILE, lsoil_incr, DO_SNO_INC, DO_SOI_INC, INTERP_LNDINC
+ NAMELIST/NAMSFCD/ NST_FILE, lsoil_incr, DO_SNOWINCR, DO_SOILINCR, INTERP_LANDINCR
 
  DATA NST_FILE/'NULL'/
 
- DO_SNO_INC = .FALSE.
- DO_SOI_INC      = .FALSE.
- INTERP_LNDINC   = .FALSE.
+ DO_SNOWINCR = .FALSE.
+ DO_SOILINCR      = .FALSE.
+ INTERP_LANDINCR   = .FALSE.
  lsoil_incr = 3 !default
 
 
@@ -475,16 +475,16 @@ SUBROUTINE SFCDRV(LUGB, IDIM,JDIM,LENSFC,LSOIL,DELTSFC,  &
    ALLOCATE(SICFCS_FG(LENSFC))
  ENDIF
 
-IF (DO_LNDINC) THEN
+IF (DO_LANDINCR) THEN
    ! identify variables to be updated, and allocate arrays.
-   IF  (DO_SOI_INC ) THEN
+   IF  (DO_SOILINCR ) THEN
        PRINT*
        PRINT*," APPLYING SOIL INCREMENTS"
        ALLOCATE(STC_BCK(LENSFC, LSOIL), SMC_BCK(LENSFC, LSOIL), SLC_BCK(LENSFC,LSOIL))
        ALLOCATE(LANDINC_MASK_FG(LENSFC))
    ENDIF
    ! FOR NOW, CODE SO CAN DO BOTH, BUT MIGHT NEED TO THINK ABOUT THIS SOME MORE.
-   IF  (DO_SNO_INC) THEN
+   IF  (DO_SNOWINCR) THEN
        ! ideally, would check here that sfcsub snow DA update is not also requested
        ! but latter is controlled by fnsol, which is read in within that routine.
        ! should be done at script level.
@@ -522,7 +522,7 @@ SUBROUTINE SFCDRV(LUGB, IDIM,JDIM,LENSFC,LSOIL,DELTSFC,  &
    call MPI_ABORT(MPI_COMM_WORLD, 18, IERR)
  ENDIF
 
- IF ( (IS_NOAHMP .OR. INTERP_LNDINC) .AND. DO_SNO_INC) THEN
+ IF ( (IS_NOAHMP .OR. INTERP_LANDINCR) .AND. DO_SNOWINCR) THEN
    print *, 'FATAL ERROR: Snow increment update does not work with NOAH_MP/with interp'
    call MPI_ABORT(MPI_COMM_WORLD, 29, IERR)
  ENDIF
@@ -560,7 +560,7 @@ SUBROUTINE SFCDRV(LUGB, IDIM,JDIM,LENSFC,LSOIL,DELTSFC,  &
  ENDIF
 
  ! CALCULATE MASK FOR LAND INCREMENTS
- IF (DO_LNDINC)  &
+ IF (DO_LANDINCR)  &
     CALL CALCULATE_LANDINC_MASK(SWEFCS, VETFCS, SOTFCS, &
                     LENSFC,VEG_TYPE_LANDICE,  LANDINC_MASK)
 
@@ -686,11 +686,11 @@ SUBROUTINE SFCDRV(LUGB, IDIM,JDIM,LENSFC,LSOIL,DELTSFC,  &
 ! READ IN AND APPLY LAND INCREMENTS
 !--------------------------------------------------------------------------------
 
- IF (DO_LNDINC) THEN
+ IF (DO_LANDINCR) THEN
 
     ! SNOW INCREMENTS
     ! do snow first, as temperature updates will use snow analaysis
-    IF (DO_SNO_INC) THEN
+    IF (DO_SNOWINCR) THEN
     ! updates are made to snow depth only over land (and not-land ice).
     ! SWE is then updated from the snow depth analysis, using the model
     ! forecast density
@@ -734,7 +734,7 @@ SUBROUTINE SFCDRV(LUGB, IDIM,JDIM,LENSFC,LSOIL,DELTSFC,  &
     !re-calculate soilsnow mask if snow has been updated.
     LANDINC_MASK_FG = LANDINC_MASK
 
-    IF (DO_SFCCYCLE .OR. DO_SNO_INC)  THEN
+    IF (DO_SFCCYCLE .OR. DO_SNOWINCR)  THEN
         CALL CALCULATE_LANDINC_MASK(SWEFCS, VETFCS, SOTFCS, LENSFC, &
                                     VEG_TYPE_LANDICE, LANDINC_MASK)
     ENDIF
@@ -745,8 +745,8 @@ SUBROUTINE SFCDRV(LUGB, IDIM,JDIM,LENSFC,LSOIL,DELTSFC,  &
     SLC_BCK = SLCFCS
 
     ! SOIL INCREMENTS
-    IF ( DO_SOI_INC ) THEN
-        IF ( INTERP_LNDINC ) THEN
+    IF ( DO_SOILINCR ) THEN
+        IF ( INTERP_LANDINCR ) THEN
 
            !--------------------------------------------------------------------------------
            ! read increments in
@@ -777,7 +777,7 @@ SUBROUTINE SFCDRV(LUGB, IDIM,JDIM,LENSFC,LSOIL,DELTSFC,  &
             CALL WRITE_DATA(LENSFC,IDIM,JDIM,LSOIL,DO_NSST,.true.,NSST, &
                             STCINC=STCINC,SLCINC=SLCINC)
 
-        ELSE  ! if interp_lndinc
+        ELSE  ! if interp_landincr
 
            !--------------------------------------------------------------------------------
            ! read increments in

ush/global_cycle.sh

@@ -140,10 +140,9 @@
 #                   between the filtered and unfiltered terrain.  Default is true.
 #     DONST         Process NST records when using NST model.  Default is 'no'.
 #     DO_SFCCYCLE   Call sfcsub routine 
-#     DO_LNDINC     Call routines to add snow and /or soil increments
-#     DO_SOI_INC    Call routine to add soil increments
-#     DO_SNO_INC    Call routine to add snow inrcements
-#     GCYCLE_INTERP_LNDIC  Flag to regrid input land increment from Gaus to native model 
+#     GCYCLE_DO_SOILINCR   Call routine to add soil increments
+#     GCYCLE_DO_SNOWINCR   Call routine to add snow inrcements
+#     GCYCLE_INTERP_LANDINCR  Flag to regrid input land increment from Gaus to native model 
 #                   grid inside gcycle
 #                   
 #     zsea1/zsea2   When running with NST model, this is the lower/upper bound
@@ -269,13 +268,14 @@ CYCLVARS=${CYCLVARS:-""}
 use_ufo=${use_ufo:-.true.}
 DONST=${DONST:-"NO"}
 DO_SFCCYCLE=${DO_SFCCYCLE:-.true.}
-DO_LNDINC=${DO_LNDINC:-.false.}
-DO_SOI_INC=${DO_SOI_INC:-.false.}
-DO_SNO_INC=${DO_SNO_INC:-.false.}
-if [ "$DO_SOI_INC" == ".true." ] || [ "$DO_SNO_INC" == ".true." ] ; then
-        DO_LNDINC=".true."
+GCYCLE_DO_SOILINCR=${GCYCLE_DO_SOILINCR:-.false.}
+GCYCLE_DO_SNOWINCR=${GCYCLE_DO_SNOWINCR:-.false.}
+if [ "$GCYCLE_DO_SOILINCR" == ".true." ] || [ "$GCYCLE_DO_SNOWINCR" == ".true." ] ; then
+        DO_LANDINCR=".true."
+else
+        DO_LANDINCR=".false."
 fi
-GCYCLE_INTERP_LNDINC=${GCYCLE_INTERP_LNDINC:-.false.}
+GCYCLE_INTERP_LANDINCR=${GCYCLE_INTERP_LANDINCR:-.false.}
 zsea1=${zsea1:-0}
 zsea2=${zsea2:-0}
 MAX_TASKS_CY=${MAX_TASKS_CY:-99999}
@@ -386,7 +386,7 @@ cat << EOF > fort.36
   idim=$CRES, jdim=$CRES, lsoil=$LSOIL,
   iy=$iy, im=$im, id=$id, ih=$ih, fh=$FHOUR,
   deltsfc=$DELTSFC,ialb=$IALB,use_ufo=$use_ufo,donst="$DONST",
-  do_sfccycle=$DO_SFCCYCLE,do_lndinc=$DO_LNDINC,isot=$ISOT,ivegsrc=$IVEGSRC,
+  do_sfccycle=$DO_SFCCYCLE,do_landincr=$DO_LANDINCR,isot=$ISOT,ivegsrc=$IVEGSRC,
   zsea1_mm=$zsea1,zsea2_mm=$zsea2,MAX_TASKS=$MAX_TASKS_CY,
   frac_grid=$FRAC_GRID
  /
@@ -396,9 +396,9 @@ EOF
 cat << EOF > fort.37
  &NAMSFCD
   NST_FILE="$NST_FILE",
-  DO_SOI_INC=$DO_SOI_INC,
-  DO_SNO_INC=$DO_SNO_INC,
-  INTERP_LNDINC=$GCYCLE_INTERP_LNDINC,
+  DO_SOILINCR=$GCYCLE_DO_SOILINCR,
+  DO_SNOWINCR=$GCYCLE_DO_SNOWINCR,
+  INTERP_LANDINCR=$GCYCLE_INTERP_LANDINCR,
   lsoil_incr=$LSOIL_INCR, 
  /
 EOF

ush/global_cycle_driver.sh

@@ -52,11 +52,10 @@ else
 fi
 
 export DO_SFCCYLE=${DO_SFCCYCLE:-".true."}
-export DO_LNDINC=${DO_LNDINC:-".false."}
-export DO_SOI_INC=${DO_SOI_INC:-".false."}
-export DO_SNO_INC=${DO_SNO_INC:-".false."}
-export GCYCLE_INTERP_LNDINC=${GCYCLE_INTERP_LNDINC:-".false."}
-SOI_INC_FNAME=${SOI_INC_FNAME:-"soil_xainc"}
+export GCYCLE_DO_SOILINCR=${GCYCLE_DO_SOILINCR:-".false."}
+export GCYCLE_DO_SNOWINCR=${GCYCLE_DO_SNOWINCR:-".false."}
+export GCYCLE_INTERP_LANDINCR=${GCYCLE_INTERP_LANDINCR:-".false."}
+SOILINCR_FNAME=${SOILINCR_FNAME:-"soil_xainc"}
 export FRAC_GRID=${FRAC_GRID:-".false."}
 
 CRES=$(echo $CASE | cut -c 2-)
@@ -96,15 +95,15 @@ for n in $(seq 1 $ntiles); do
     ln -fs $FIXorog/${CASE}/C${CRES}.mx${OCNRES}_oro_data.tile${n}.nc   $DATA/fnorog.00$n
   fi
 
-  if [[ "$DO_SNO_INC" == ".true." ]] ; then  
+  if [[ "$GCYCLE_DO_SNOWINCR" == ".true." ]] ; then  
         ln -fs $COMIN/$PDY.${cyc}0000.xainc.tile${n}.nc      $DATA/snow_xainc.00$n
   fi
 
-  if [ "$DO_SOI_INC" == ".true." ] && [ "$GCYCLE_INTERP_LNDINC" == ".false." ] ; then
-        ln -fs $COMIN/${SOI_INC_FNAME}.00${n} $DATA/soil_xainc.00$n
+  if [ "$GCYCLE_DO_SOILINCR" == ".true." ] && [ "$GCYCLE_INTERP_LANDINCR" == ".false." ] ; then
+        ln -fs $COMIN/${SOILINCR_FNAME}.00${n} $DATA/soil_xainc.00$n
   fi
 
-  if [ "$DO_SOI_INC" == ".true." ] && [ "$GCYCLE_INTERP_LNDINC" == ".true." ] ; then
+  if [ "$GCYCLE_DO_SOILINCR" == ".true." ] && [ "$GCYCLE_INTERP_LANDINCR" == ".true." ] ; then
         ln -fs $COMIN/sfcincr_gsi.00$n $DATA/sfcincr_gsi.00$n
   fi
 done