Merge pull request #11 from noaa-oar-arl/develop

Develop

README.md

@@ -106,6 +106,10 @@ The variables listed here are set by the user in the NACC run script, and they a
     Logical to choose if the NOAA-ARL Fengsha Windblown dust is used in CMAQ:  based on input soil parameters in "GeoFile" and output in METCRO2D file.
     -   `False`: Do not input/output Fengsha WB Dust soil parameters
     -   `True`: Input/output of Fengsha WB Dust soil parameters
+-   `IFBIOSEASON [default: False]`
+    Logical to choose if the NOAA-ARL time-dependend bioseasons withc is used in CMAQ:  based on summer/winter seasonal information and T2,  and is output in METCRO2D file.
+    -   `False`: Do not calculate and output SEASON variable in METCRO2D
+    -   `True`:  Calculate and output SEASON variable in METCRO2D
 -   `MCIP_START [format: YYYY-MM-DD-HH:MM:SS.SSSS]`  
     Beginning date and time (UTC) of data to output from NACC. The start date and time must be contained within the input data from WRF or FV3-GFS.
 -   `MCIP_END [format: YYYY-MM-DD-HH:MM:SS.SSSS]`  

parallel/scripts/run-nacc-fv3.ksh

@@ -1,5 +1,5 @@
 #!/bin/ksh -l
-#BSUB -J viirs-gvf-test
+#BSUB -J nacc-test
 #BSUB -o jnacc_par.out1
 #BSUB -e jnacc_par.err1
 #BSUB -q debug
@@ -22,12 +22,12 @@ NTIMES=73
 export NODES=12
 
 APPL=aqm.t12z
-InMetDir=/gpfs/hps2/ptmp/Patrick.C.Campbell/NACC_FV3GFS16_runs/sens5_nacc_cmaq531_nofire_fengsha/com/aqm/prod/aqm.20190826
+InMetDir=/gpfs/hps2/ptmp/Patrick.C.Campbell/NACC_FV3GFS16_runs/sens8_nacc_cmaq531_nofire_viirs_lai/com/aqm/prod/aqm.20201017
 InGeoDir=/gpfs/hps3/emc/naqfc/noscrub/Youhua.Tang/nwdev/NAQFC-WCOSS/fix
 InVIIRSDir_GVF=/gpfs/hps3/emc/naqfc/noscrub/Patrick.C.Campbell/viirs_gvf_test/grib2
 InVIIRSDir_LAI=/gpfs/hps3/emc/naqfc/noscrub/Patrick.C.Campbell/viirs_lai_test/
-OutDir=/gpfs/hps2/ptmp/$USER/NACC_test_lai/
-ProgDir=/gpfs/hps3/emc/naqfc/noscrub/Patrick.C.Campbell/NACC_viirs_lai/parallel/src
+OutDir=/gpfs/hps2/ptmp/$USER/NACC_test_bioseason/
+ProgDir=/gpfs/hps3/emc/naqfc/noscrub/Patrick.C.Campbell/NACC_bioseason/parallel/src
 
 if [ ! -s $InMetDir ]; then
   echo "No such input directory $InMetDir"
@@ -75,11 +75,12 @@ cat>namelist.mcip<<!
   lwout      =  1
   luvbout    =  1
   ifdiag_pbl = .FALSE.
-  ifviirs_gvf = .TRUE. 
-  ifviirs_lai = .TRUE.
+  ifviirs_gvf = .FALSE. 
+  ifviirs_lai = .FALSE.
   iffengsha_dust = .FALSE.
-  mcip_start = "2019-08-26-12:00:00.0000"
-  mcip_end   = "2019-08-29-13:00:00.0000"
+  ifbioseason = .TRUE.
+  mcip_start = "2020-10-17-12:00:00.0000"
+  mcip_end   = "2020-10-20-13:00:00.0000"
   intvl      =  60
   coordnam   = "FV3_RPO"
   grdnam     = "FV3_CONUS"

parallel/src/alloc_ctm.f90

@@ -93,6 +93,7 @@ SUBROUTINE alloc_ctm
   INTEGER                      :: nsoil2d
   INTEGER                      :: npxwrf41
   INTEGER                      :: nfengsha
+  INTEGER                      :: nbioseason
   INTEGER                      :: ntke
   INTEGER                      :: npv
   INTEGER                      :: nwout
@@ -215,8 +216,13 @@ SUBROUTINE alloc_ctm
     nfengsha = 0
   ENDIF
 
+  IF ( ifbioseason ) THEN
+    nbioseason = 1  ! SEASON
+  ELSE
+    nbioseason = 0
+  ENDIF
 
-  nfld2dxyt = 29 + nwr + nsoil2d + npxwrf41 + nfengsha
+  nfld2dxyt = 29 + nwr + nsoil2d + npxwrf41 + nfengsha + nbioseason
 
   ALLOCATE ( fld2dxyt ( nfld2dxyt ) )
 
@@ -283,6 +289,10 @@ SUBROUTINE alloc_ctm
    c_uthr     => fld2dxyt(29+nwr+nsoil2d+npxwrf41+5)
   ENDIF
 
+  IF ( ( ifbioseason ) ) THEN
+   c_season    => fld2dxyt(29+nwr+nsoil2d+npxwrf41+nfengsha+1)
+  ENDIF
+
 !-------------------------------------------------------------------------------
 ! Time-varying 3d fields at cell centers.
 !-------------------------------------------------------------------------------

parallel/src/alloc_x.f90

@@ -164,13 +164,19 @@ SUBROUTINE alloc_x
   ALLOCATE ( xrgrnd  (ncols_x, nrows_x) )
   ALLOCATE ( xwr     (ncols_x, nrows_x) )
   ALLOCATE ( xlai    (ncols_x, nrows_x) )
+
   IF ( ( iffengsha_dust ) ) THEN
    ALLOCATE ( xclayf  (ncols_x, nrows_x) )
    ALLOCATE ( xsandf  (ncols_x, nrows_x) )
    ALLOCATE ( xdrag   (ncols_x, nrows_x) )
    ALLOCATE ( xssm    (ncols_x, nrows_x) )
    ALLOCATE ( xuthr   (ncols_x, nrows_x) )
   ENDIF
+
+  IF ( ( ifbioseason ) ) THEN
+   ALLOCATE ( xseason  (ncols_x, nrows_x) )
+  ENDIF
+
   ALLOCATE ( xveg    (ncols_x, nrows_x) )
 
   ALLOCATE ( xwstar  (ncols_x, nrows_x) )

parallel/src/ctmproc.f90

@@ -330,6 +330,9 @@ END SUBROUTINE collapx
        c_ssm%fld(col,row)    = xssm(c,r)
        c_uthr%fld(col,row)   = xuthr(c,r)
       ENDIF
+      IF ( ( ifbioseason ) ) THEN
+       c_season%fld(col,row)  = xseason(c,r)
+      ENDIF
       c_seaice%fld(col,row) = xseaice(c,r)
       c_snowh%fld(col,row)  = xsnowh(c,r)
 

parallel/src/ctmvars_mod.f90

@@ -142,6 +142,7 @@ MODULE ctmvars
   TYPE(fld2ddata), POINTER     :: c_drag
   TYPE(fld2ddata), POINTER     :: c_ssm
   TYPE(fld2ddata), POINTER     :: c_uthr
+  TYPE(fld2ddata), POINTER     :: c_season
   TYPE(fld2ddata), POINTER     :: c_seaice
   TYPE(fld2ddata), POINTER     :: c_snowh
   TYPE(fld2ddata), POINTER     :: c_wr

parallel/src/dealloc_ctm.f90

@@ -173,11 +173,12 @@ SUBROUTINE dealloc_ctm
   NULLIFY    ( c_lai    )
   NULLIFY    ( c_seaice )
   NULLIFY    ( c_snowh  )
-  NULLIFY    ( c_clayf  )
-  NULLIFY    ( c_sandf  )
-  NULLIFY    ( c_drag   )
-  NULLIFY    ( c_ssm    )
-  NULLIFY    ( c_uthr   )
+  IF ( ASSOCIATED ( c_clayf        ) )  NULLIFY    ( c_clayf  )
+  IF ( ASSOCIATED ( c_sandf        ) )  NULLIFY    ( c_sandf  )
+  IF ( ASSOCIATED ( c_drag         ) )  NULLIFY    ( c_drag   )
+  IF ( ASSOCIATED ( c_ssm          ) )  NULLIFY    ( c_ssm    )
+  IF ( ASSOCIATED ( c_uthr         ) )  NULLIFY    ( c_uthr   )
+  IF ( ASSOCIATED ( c_season       ) )  NULLIFY    ( c_season )
 
   IF ( ASSOCIATED ( c_wr        ) ) NULLIFY ( c_wr        )
   IF ( ASSOCIATED ( c_soim1     ) ) NULLIFY ( c_soim1     )

parallel/src/dealloc_x.f90

@@ -148,6 +148,9 @@ SUBROUTINE dealloc_x
   IF ( ALLOCATED ( xdrag  ) )  DEALLOCATE ( xdrag )
   IF ( ALLOCATED ( xssm   ) )  DEALLOCATE ( xssm )
   IF ( ALLOCATED ( xuthr  ) )  DEALLOCATE ( xuthr )
+
+  IF ( ALLOCATED ( xseason  ) )  DEALLOCATE ( xseason )
+
   DEALLOCATE ( xveg    )
 
   DEALLOCATE ( xwstar   )

parallel/src/init_ctm.f90

@@ -698,6 +698,19 @@ SUBROUTINE init_ctm
    c_uthr%iend(2) = ny
   ENDIF
 
+  IF ( ifbioseason ) THEN
+    c_season%fld = fillreal
+    c_season%fldname = 'SEASON'
+    c_season%long_name = 'bioseason flag'
+    c_season%units = '1'
+    c_season%dimnames(1) = 'nx'
+    c_season%dimnames(2) = 'ny'
+    c_season%istart(1) = 1
+    c_season%istart(2) = 1
+    c_season%iend(1) = nx
+    c_season%iend(2) = ny
+  ENDIF
+
   c_seaice%fld = fillreal
   c_seaice%fldname = 'SEAICE'
   c_seaice%long_name = 'sea ice'

parallel/src/init_x.f90

@@ -141,6 +141,10 @@ SUBROUTINE init_x
    xuthr   (:,:)   = fillreal
   ENDIF
 
+  IF ( ( ifbioseason ) ) THEN
+   xseason  (:,:)   = fillreal
+  ENDIF
+
   IF ( met_hybrid >= 0 ) THEN
     xmuhyb(:,:)   = fillreal
   ENDIF

parallel/src/mcipparm_mod.f90

@@ -274,6 +274,7 @@ MODULE mcipparm
   LOGICAL            :: ifviirs_gvf     ! use NAQFC VIIRS GVF?
   LOGICAL            :: ifviirs_lai     ! use NAQFC VIIRS LAI?
   LOGICAL            :: iffengsha_dust  ! use NAQFC Fengsha Windblown Dust?
+  LOGICAL            :: ifbioseason     ! use bioseason switch?
 
 !-------------------------------------------------------------------------------
 ! Run Options.

parallel/src/pblsup.f90

@@ -94,7 +94,7 @@ SUBROUTINE pblsup
 !           26 Jun 2018  Now use netCDF tokens for missing data.  (T. Spero)
 !           14 Sep 2018  Removed support for MM5v3 input.  (T. Spero)
 !-------------------------------------------------------------------------------
-
+  USE metinfo
   USE mcipparm
   USE xvars
   USE const
@@ -309,6 +309,27 @@ END SUBROUTINE getpblht
           xwstar(c,r) = 0.0
         ENDIF
 
+        ! User-defined calculation of the BEIS bioseason/freeze flag based on 2-m temperature
+        ! Needs updating with more robust T2/Q2 parameterization
+        IF ( ifbioseason ) THEN 
+         IF ( met_season == 1 ) THEN ! N. Hemisphere "summer" months 
+           IF ( xtemp2(c,r) < 269.15 ) THEN !check if temperature < -4C, 28F.
+            xseason(c,r)=0. ! winter
+           ELSE  
+            xseason(c,r)=1. ! summer
+           END IF
+         END IF
+
+         IF ( met_season == 2 ) THEN ! N. Hemisphere "winter" months
+           IF ( xtemp2(c,r) > 273.15 ) THEN !check if temperature > 0C, 32F.
+            xseason(c,r)=1. ! summer
+           ELSE 
+            xseason(c,r)=0. ! winter
+           END IF
+         END IF
+
+        ENDIF
+
       ENDDO
     ENDDO
 

parallel/src/rdfv3.f90

@@ -2368,7 +2368,6 @@ END SUBROUTINE windrotation
 !-------------------------------------------------------------------------------
 ! If this is the first time in this routine, then determine season.
 !-------------------------------------------------------------------------------
-! But if global 
   IF ( first ) THEN
 
     ! These seasons are used in MM5 and WRF for land-use lookup tables.
@@ -2392,10 +2391,11 @@ END SUBROUTINE windrotation
         met_season = 2   ! winter
       ENDIF
     ENDIF
+
 !-------------------------------------------------------------------------------
 ! If roughness length was not available in output, fill it from lookup tables.
 ! If the urban model was used in WRF, replace roughness length with urban-
-! specific arrays.
+! specific arrays. 
 !-------------------------------------------------------------------------------
 
     IF ( .NOT. gotznt ) THEN

parallel/src/readnml.f90

@@ -111,7 +111,7 @@ SUBROUTINE readnml (ctmlays)
 
   NAMELIST /userdefs/    inmetmodel, dx_in, dy_in, met_cen_lat_in, met_cen_lon_in, &
                          lpv, lwout, luvbout, ifdiag_pbl, ifviirs_gvf, &
-                         ifviirs_lai, iffengsha_dust,    &
+                         ifviirs_lai, iffengsha_dust, ifbioseason,    &
                          eradm, mcip_start, mcip_end, ntimes, intvl,  &
                          coordnam, grdnam, ctmlays,           &
                          btrim, lprt_col, lprt_row,           &
@@ -257,6 +257,7 @@ SUBROUTINE readnml (ctmlays)
   ifviirs_gvf = .false.  ! To use NAQFC VIIRS GVF input
   ifviirs_lai = .false.  ! To use NAQFC VIIRS LAI input
   iffengsha_dust = .false.  ! To use NAQFC Fengsha Windblown Dust
+  ifbioseason = .false.  ! To use bioseason switch
 !-------------------------------------------------------------------------------
 ! Set default value for earth radius in meters (ERADM).  The default value is
 ! consistent with the value used for a spherical earth in MM5 and in WRF-ARW.

parallel/src/xvars_mod.f90

@@ -203,6 +203,8 @@ MODULE xvars
   REAL, ALLOCATABLE :: xveg       ( : , : )  ! vegetation coverage [decimal]
   REAL, ALLOCATABLE :: xsltyp     ( : , : )  ! soil texture type [category]
 
+  REAL, ALLOCATABLE :: xseason    ( : , : )  ! bioseason flag [1=summer, 0=winter]
+
   REAL, ALLOCATABLE :: xwsat_px   ( : , : )  ! soil saturation (PX) [m3/m3]
   REAL, ALLOCATABLE :: xwwlt_px   ( : , : )  ! soil wilt pt (PX) [m3/m3]
   REAL, ALLOCATABLE :: xwfc_px    ( : , : )  ! soil fld capacity (PX) [m3/m3]

serial/scripts/run-nacc-fv3.csh

@@ -38,7 +38,8 @@ cat>namelist.mcip<<!
   file_mm    = '$InMetDir/gfs.t12z.atmf','.nc'
   file_sfc   = '$InMetDir/gfs.t12z.sfcf','.nc'
   file_geo   = '$InGeoDir/gfs.t12z.geo.07.nc'
-  file_viirs_gvf = '$InVIIRSDir/GVF-WKL-GLB_v2r3_j01_s20200824_e20200830_c202008311235100.grib2.nc'
+  file_viirs_gvf = '$IVIIRSDir/GVF-WKL-GLB_v2r3_j01_s20200824_e20200830_c202008311235100.grib2.nc'
+  file_viirs_lai = '$InVIIRSDir/VIIRS_VNP15A2H.001_20190829.nc'
   ioform     =  1
  &END
 
@@ -53,7 +54,9 @@ cat>namelist.mcip<<!
   luvbout    =  1
   ifdiag_pbl = .FALSE.
   ifviirs_gvf = .FALSE.
+  ifviirs_lai = .FALSE.
   iffengsha_dust = .FALSE. 
+  ifbioseason = .FALSE.
   mcip_start = "2019-07-12-12:00:00.0000"
   mcip_end   = "2019-07-15-13:00:00.0000"
   intvl      =  60

serial/scripts/run-nacc-fv3.ksh

@@ -57,6 +57,7 @@ cat>namelist.mcip<<!
   ifviirs_gvf = .FALSE.
   ifviirs_lai = .FALSE.
   iffengsha_dust = .FALSE.
+  ifbioseason = .FALSE.
   mcip_start = "2019-08-12-12:00:00.0000"
   mcip_end   = "2019-08-15-13:00:00.0000"
   intvl      =  60

serial/src/alloc_ctm.f90

@@ -93,6 +93,7 @@ SUBROUTINE alloc_ctm
   INTEGER                      :: nsoil2d
   INTEGER                      :: npxwrf41
   INTEGER                      :: nfengsha
+  INTEGER                      :: nbioseason
   INTEGER                      :: ntke
   INTEGER                      :: npv
   INTEGER                      :: nwout
@@ -215,8 +216,13 @@ SUBROUTINE alloc_ctm
     nfengsha = 0
   ENDIF
 
+  IF ( ifbioseason ) THEN
+    nbioseason = 1  ! SEASON
+  ELSE
+    nbioseason = 0
+  ENDIF
 
-  nfld2dxyt = 29 + nwr + nsoil2d + npxwrf41 + nfengsha
+  nfld2dxyt = 29 + nwr + nsoil2d + npxwrf41 + nfengsha + nbioseason
 
   ALLOCATE ( fld2dxyt ( nfld2dxyt ) )
 
@@ -283,6 +289,10 @@ SUBROUTINE alloc_ctm
    c_uthr     => fld2dxyt(29+nwr+nsoil2d+npxwrf41+5)
   ENDIF
 
+  IF ( ( ifbioseason ) ) THEN
+   c_season    => fld2dxyt(29+nwr+nsoil2d+npxwrf41+nfengsha+1)
+  ENDIF
+
 !-------------------------------------------------------------------------------
 ! Time-varying 3d fields at cell centers.
 !-------------------------------------------------------------------------------

serial/src/alloc_x.f90

@@ -164,13 +164,19 @@ SUBROUTINE alloc_x
   ALLOCATE ( xrgrnd  (ncols_x, nrows_x) )
   ALLOCATE ( xwr     (ncols_x, nrows_x) )
   ALLOCATE ( xlai    (ncols_x, nrows_x) )
+
   IF ( ( iffengsha_dust ) ) THEN
    ALLOCATE ( xclayf  (ncols_x, nrows_x) )
    ALLOCATE ( xsandf  (ncols_x, nrows_x) )
    ALLOCATE ( xdrag   (ncols_x, nrows_x) )
    ALLOCATE ( xssm    (ncols_x, nrows_x) )
    ALLOCATE ( xuthr   (ncols_x, nrows_x) )
   ENDIF
+
+  IF ( ( ifbioseason ) ) THEN
+   ALLOCATE ( xseason  (ncols_x, nrows_x) )
+  ENDIF
+
   ALLOCATE ( xveg    (ncols_x, nrows_x) )
 
   ALLOCATE ( xwstar  (ncols_x, nrows_x) )

serial/src/ctmproc.f90

@@ -330,6 +330,9 @@ END SUBROUTINE collapx
        c_ssm%fld(col,row)    = xssm(c,r)
        c_uthr%fld(col,row)   = xuthr(c,r)
       ENDIF
+      IF ( ( ifbioseason ) ) THEN
+       c_season%fld(col,row)  = xseason(c,r)
+      ENDIF
       c_seaice%fld(col,row) = xseaice(c,r)
       c_snowh%fld(col,row)  = xsnowh(c,r)
 

serial/src/ctmvars_mod.f90

@@ -142,6 +142,7 @@ MODULE ctmvars
   TYPE(fld2ddata), POINTER     :: c_drag
   TYPE(fld2ddata), POINTER     :: c_ssm
   TYPE(fld2ddata), POINTER     :: c_uthr
+  TYPE(fld2ddata), POINTER     :: c_season
   TYPE(fld2ddata), POINTER     :: c_seaice
   TYPE(fld2ddata), POINTER     :: c_snowh
   TYPE(fld2ddata), POINTER     :: c_wr

serial/src/dealloc_ctm.f90

@@ -173,11 +173,12 @@ SUBROUTINE dealloc_ctm
   NULLIFY    ( c_lai    )
   NULLIFY    ( c_seaice )
   NULLIFY    ( c_snowh  )
-  NULLIFY    ( c_clayf  )
-  NULLIFY    ( c_sandf  )
-  NULLIFY    ( c_drag   )
-  NULLIFY    ( c_ssm    )
-  NULLIFY    ( c_uthr   )
+  IF ( ASSOCIATED ( c_clayf        ) )  NULLIFY    ( c_clayf  )
+  IF ( ASSOCIATED ( c_sandf        ) )  NULLIFY    ( c_sandf  )
+  IF ( ASSOCIATED ( c_drag         ) )  NULLIFY    ( c_drag   )
+  IF ( ASSOCIATED ( c_ssm          ) )  NULLIFY    ( c_ssm    )
+  IF ( ASSOCIATED ( c_uthr         ) )  NULLIFY    ( c_uthr   )
+  IF ( ASSOCIATED ( c_season       ) )  NULLIFY    ( c_season )
 
   IF ( ASSOCIATED ( c_wr        ) ) NULLIFY ( c_wr        )
   IF ( ASSOCIATED ( c_soim1     ) ) NULLIFY ( c_soim1     )