Merge pull request #20 from noaa-oar-arl/develop

Develop

README.md

@@ -110,6 +110,10 @@ The variables listed here are set by the user in the NACC run script, and they a
     Logical to choose if the NOAA-ARL 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
+-   `IFCANOPY [default: False]`
+    Logical to choose if the ECCC in-canopy shading effects are used in CMAQ:  based on input canopy parameters in "GeoFile" and output in METCRO2D file.
+    -   `False`: Do not input/output ECCC canopy parameters
+    -   `True`: Input/output of ECCC canopy parameters
 -   `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

@@ -22,12 +22,12 @@ NTIMES=73
 export NODES=12
 
 APPL=aqm.t12z
-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
+InMetDir=/gpfs/hps2/ptmp/Patrick.C.Campbell/fv3gfs16_testdata
+InGeoDir=/gpfs/hps3/emc/naqfc/noscrub/Patrick.C.Campbell/nacc_geofiles
 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_bioseason/
-ProgDir=/gpfs/hps3/emc/naqfc/noscrub/Patrick.C.Campbell/NACC_bioseason/parallel/src
+OutDir=/gpfs/hps2/ptmp/Patrick.C.Campbell/fv3gfs16_testdata/nacc_output_parallel_canopy_shade
+ProgDir=/gpfs/hps3/emc/naqfc/noscrub/Patrick.C.Campbell/NACC_canopy_shade/parallel/src
 
 if [ ! -s $InMetDir ]; then
   echo "No such input directory $InMetDir"
@@ -59,7 +59,7 @@ cat>namelist.mcip<<!
   file_gd    = 'GRIDDESC'
   file_mm    = '$InMetDir/gfs.t12z.atmf','.nc'
   file_sfc   = '$InMetDir/gfs.t12z.sfcf','.nc'
-  file_geo   = '$InGeoDir/gfs.t12z.geo.08.nc'
+  file_geo   = '$InGeoDir/gfs.t12z.geo.01.canopy.nc'
   file_viirs_gvf = '$InVIIRSDir_GVF/GVF-WKL-GLB_v2r3_j01_s20200824_e20200830_c202008311235100.grib2.nc'
   file_viirs_lai = '$InVIIRSDir_LAI/VIIRS_VNP15A2H.001_20190829.nc'
   ioform     =  1
@@ -78,9 +78,10 @@ cat>namelist.mcip<<!
   ifviirs_gvf = .FALSE. 
   ifviirs_lai = .FALSE.
   iffengsha_dust = .FALSE.
-  ifbioseason = .TRUE.
-  mcip_start = "2020-10-17-12:00:00.0000"
-  mcip_end   = "2020-10-20-13:00:00.0000"
+  ifbioseason = .FALSE.
+  ifcanopy    = .TRUE.
+  mcip_start = "2020-01-12-12:00:00.0000"
+  mcip_end   = "2020-01-15-13:00:00.0000"
   intvl      =  60
   coordnam   = "FV3_RPO"
   grdnam     = "FV3_CONUS"

parallel/scripts/run-nacc-fv3_slurm.ksh

@@ -64,6 +64,12 @@ cat>namelist.mcip<<!
   lpv        =  0
   lwout      =  1
   luvbout    =  1
+  ifdiag_pbl = .FALSE.
+  ifviirs_gvf = .FALSE.
+  ifviirs_lai = .FALSE.
+  iffengsha_dust = .FALSE.
+  ifbioseason = .TRUE.
+  ifcanopy    = .FALSE.
   mcip_start = "2019-07-12-12:00:00.0000"
   mcip_end   = "2019-07-15-13:00:00.0000"
   intvl      =  60

parallel/src/alloc_ctm.f90

@@ -94,6 +94,7 @@ SUBROUTINE alloc_ctm
   INTEGER                      :: npxwrf41
   INTEGER                      :: nfengsha
   INTEGER                      :: nbioseason
+  INTEGER                      :: ncanopy
   INTEGER                      :: ntke
   INTEGER                      :: npv
   INTEGER                      :: nwout
@@ -216,13 +217,20 @@ SUBROUTINE alloc_ctm
     nfengsha = 0
   ENDIF
 
+  IF ( ifcanopy ) THEN
+    ncanopy = 9  ! FCH, FRT, CLU, POPU, LAIE, C1R, C2R, C3R, C4R
+  ELSE
+    ncanopy = 0
+  ENDIF
+
   IF ( ifbioseason ) THEN
     nbioseason = 1  ! SEASON
   ELSE
     nbioseason = 0
   ENDIF
 
-  nfld2dxyt = 29 + nwr + nsoil2d + npxwrf41 + nfengsha + nbioseason
+
+  nfld2dxyt = 29 + nwr + nsoil2d + npxwrf41 + nfengsha + nbioseason + ncanopy
 
   ALLOCATE ( fld2dxyt ( nfld2dxyt ) )
 
@@ -293,6 +301,19 @@ SUBROUTINE alloc_ctm
    c_season    => fld2dxyt(29+nwr+nsoil2d+npxwrf41+nfengsha+1)
   ENDIF
 
+  IF ( ( ifcanopy ) ) THEN
+   c_fch    => fld2dxyt(29+nwr+nsoil2d+npxwrf41+nfengsha+nbioseason+1)
+   c_frt    => fld2dxyt(29+nwr+nsoil2d+npxwrf41+nfengsha+nbioseason+2)
+   c_clu    => fld2dxyt(29+nwr+nsoil2d+npxwrf41+nfengsha+nbioseason+3)
+   c_popu   => fld2dxyt(29+nwr+nsoil2d+npxwrf41+nfengsha+nbioseason+4)
+   c_laie   => fld2dxyt(29+nwr+nsoil2d+npxwrf41+nfengsha+nbioseason+5)
+   c_c1r    => fld2dxyt(29+nwr+nsoil2d+npxwrf41+nfengsha+nbioseason+6)
+   c_c2r    => fld2dxyt(29+nwr+nsoil2d+npxwrf41+nfengsha+nbioseason+7)
+   c_c3r    => fld2dxyt(29+nwr+nsoil2d+npxwrf41+nfengsha+nbioseason+8)
+   c_c4r    => fld2dxyt(29+nwr+nsoil2d+npxwrf41+nfengsha+nbioseason+9)
+  ENDIF
+
+
 !-------------------------------------------------------------------------------
 ! Time-varying 3d fields at cell centers.
 !-------------------------------------------------------------------------------

parallel/src/alloc_met.f90

@@ -228,6 +228,45 @@ SUBROUTINE alloc_met
   ENDIF
  ENDIF
 
+ IF ( ( ifcanopy ) ) THEN
+  IF ( iffch ) THEN  ! forest canopy height available
+    ALLOCATE ( fch    (met_nx, met_ny) )
+  ENDIF
+
+  IF ( iffrt ) THEN  ! forest fraction field available
+    ALLOCATE ( frt    (met_nx, met_ny) )
+  ENDIF
+
+  IF ( ifclu ) THEN  ! forest clumping indext available
+    ALLOCATE ( clu    (met_nx, met_ny) )
+  ENDIF
+
+  IF ( ifpopu ) THEN  ! population density available
+    ALLOCATE ( popu    (met_nx, met_ny) )
+  ENDIF
+
+  IF ( iflaie ) THEN  ! ECCC lai (MODIS) available
+    ALLOCATE ( laie    (met_nx, met_ny) )
+  ENDIF
+
+  IF ( ifc1r ) THEN  ! cumulative LAI fraction hc to 0.75 * hc
+    ALLOCATE ( c1r    (met_nx, met_ny) )
+  ENDIF
+
+  IF ( ifc2r ) THEN  ! cumulative LAI fraction hc to 0.50 * hc
+    ALLOCATE ( c2r    (met_nx, met_ny) )
+  ENDIF
+
+  IF ( ifc3r ) THEN  ! cumulative LAI fraction hc to 0.35 * hc
+    ALLOCATE ( c3r    (met_nx, met_ny) )
+  ENDIF
+
+  IF ( ifc4r ) THEN  ! cumulative LAI fraction hc to 0.20 * hc
+    ALLOCATE ( c4r    (met_nx, met_ny) )
+  ENDIF
+
+ ENDIF
+
   IF ( ifmol ) THEN  ! Monin-Obukhov length available
     ALLOCATE ( mol    (ix, jy) )
   ENDIF

parallel/src/alloc_x.f90

@@ -177,6 +177,19 @@ SUBROUTINE alloc_x
    ALLOCATE ( xseason  (ncols_x, nrows_x) )
   ENDIF
 
+  IF ( ( ifcanopy ) ) THEN
+   ALLOCATE ( xfch  (ncols_x, nrows_x) )
+   ALLOCATE ( xfrt  (ncols_x, nrows_x) )
+   ALLOCATE ( xclu  (ncols_x, nrows_x) )
+   ALLOCATE ( xpopu (ncols_x, nrows_x) )
+   ALLOCATE ( xlaie (ncols_x, nrows_x) )
+   ALLOCATE ( xc1r  (ncols_x, nrows_x) )
+   ALLOCATE ( xc2r  (ncols_x, nrows_x) )
+   ALLOCATE ( xc3r  (ncols_x, nrows_x) )
+   ALLOCATE ( xc4r  (ncols_x, nrows_x) )
+  ENDIF
+
+
   ALLOCATE ( xveg    (ncols_x, nrows_x) )
 
   ALLOCATE ( xwstar  (ncols_x, nrows_x) )

parallel/src/ctmproc.f90

@@ -340,6 +340,19 @@ END SUBROUTINE collapx
       IF ( ( ifbioseason ) ) THEN
        c_season%fld(col,row)  = xseason(c,r)
       ENDIF
+
+      IF ( ( ifcanopy ) ) THEN
+       c_fch%fld(col,row)  = xfch(c,r)
+       c_frt%fld(col,row)  = xfrt(c,r)
+       c_clu%fld(col,row)  = xclu(c,r)
+       c_popu%fld(col,row) = xpopu(c,r)
+       c_laie%fld(col,row) = xlaie(c,r)
+       c_c1r%fld(col,row)  = xc1r(c,r)
+       c_c2r%fld(col,row)  = xc2r(c,r)
+       c_c3r%fld(col,row)  = xc3r(c,r)
+       c_c4r%fld(col,row)  = xc4r(c,r)
+      ENDIF
+
       c_seaice%fld(col,row) = xseaice(c,r)
       c_snowh%fld(col,row)  = xsnowh(c,r)
 

parallel/src/ctmvars_mod.f90

@@ -143,6 +143,15 @@ MODULE ctmvars
   TYPE(fld2ddata), POINTER     :: c_ssm
   TYPE(fld2ddata), POINTER     :: c_uthr
   TYPE(fld2ddata), POINTER     :: c_season
+  TYPE(fld2ddata), POINTER     :: c_fch
+  TYPE(fld2ddata), POINTER     :: c_frt
+  TYPE(fld2ddata), POINTER     :: c_clu
+  TYPE(fld2ddata), POINTER     :: c_popu
+  TYPE(fld2ddata), POINTER     :: c_laie
+  TYPE(fld2ddata), POINTER     :: c_c1r
+  TYPE(fld2ddata), POINTER     :: c_c2r
+  TYPE(fld2ddata), POINTER     :: c_c3r
+  TYPE(fld2ddata), POINTER     :: c_c4r
   TYPE(fld2ddata), POINTER     :: c_seaice
   TYPE(fld2ddata), POINTER     :: c_snowh
   TYPE(fld2ddata), POINTER     :: c_wr

parallel/src/init_ctm.f90

@@ -711,6 +711,108 @@ SUBROUTINE init_ctm
     c_season%iend(2) = ny
   ENDIF
 
+  IF ( ( ifcanopy ) ) THEN
+   c_fch%fld = fillreal
+   c_fch%fldname = 'FCH'
+   c_fch%long_name = 'forest canopy height'
+   c_fch%units = 'm'
+   c_fch%dimnames(1) = 'nx'
+   c_fch%dimnames(2) = 'ny'
+   c_fch%istart(1) = 1
+   c_fch%istart(2) = 1
+   c_fch%iend(1) = nx
+   c_fch%iend(2) = ny
+
+   c_frt%fld = fillreal
+   c_frt%fldname = 'FRT'
+   c_frt%long_name = 'forest fraction'
+   c_frt%units = '1'
+   c_frt%dimnames(1) = 'nx'
+   c_frt%dimnames(2) = 'ny'
+   c_frt%istart(1) = 1
+   c_frt%istart(2) = 1
+   c_frt%iend(1) = nx
+   c_frt%iend(2) = ny
+
+   c_clu%fld = fillreal
+   c_clu%fldname = 'CLU'
+   c_clu%long_name = 'clumping index'
+   c_clu%units = '1'
+   c_clu%dimnames(1) = 'nx'
+   c_clu%dimnames(2) = 'ny'
+   c_clu%istart(1) = 1
+   c_clu%istart(2) = 1
+   c_clu%iend(1) = nx
+   c_clu%iend(2) = ny
+
+   c_popu%fld = fillreal
+   c_popu%fldname = 'POPU'
+   c_popu%long_name = 'population density'
+   c_popu%units = 'people/10km2'
+   c_popu%dimnames(1) = 'nx'
+   c_popu%dimnames(2) = 'ny'
+   c_popu%istart(1) = 1
+   c_popu%istart(2) = 1
+   c_popu%iend(1) = nx
+   c_popu%iend(2) = ny
+
+   c_laie%fld = fillreal
+   c_laie%fldname = 'LAIE'
+   c_laie%long_name = 'Leaf Area Index (ECCC)'
+   c_laie%units = 'm2 m-2'
+   c_laie%dimnames(1) = 'nx'
+   c_laie%dimnames(2) = 'ny'
+   c_laie%istart(1) = 1
+   c_laie%istart(2) = 1
+   c_laie%iend(1) = nx
+   c_laie%iend(2) = ny
+
+   c_c1r%fld = fillreal
+   c_c1r%fldname = 'C1R'
+   c_c1r%long_name = 'cumulative LAI fraction hc to 0.75 * hc'
+   c_c1r%units = '1'
+   c_c1r%dimnames(1) = 'nx'
+   c_c1r%dimnames(2) = 'ny'
+   c_c1r%istart(1) = 1
+   c_c1r%istart(2) = 1
+   c_c1r%iend(1) = nx
+   c_c1r%iend(2) = ny
+
+   c_c2r%fld = fillreal
+   c_c2r%fldname = 'C2R'
+   c_c2r%long_name = 'cumulative LAI fraction hc to 0.50 * hc'
+   c_c2r%units = '1'
+   c_c2r%dimnames(1) = 'nx'
+   c_c2r%dimnames(2) = 'ny'
+   c_c2r%istart(1) = 1
+   c_c2r%istart(2) = 1
+   c_c2r%iend(1) = nx
+   c_c2r%iend(2) = ny
+
+   c_c3r%fld = fillreal
+   c_c3r%fldname = 'C3R'
+   c_c3r%long_name = 'cumulative LAI fraction hc to 0.35 * hc'
+   c_c3r%units = '1'
+   c_c3r%dimnames(1) = 'nx'
+   c_c3r%dimnames(2) = 'ny'
+   c_c3r%istart(1) = 1
+   c_c3r%istart(2) = 1
+   c_c3r%iend(1) = nx
+   c_c3r%iend(2) = ny
+
+   c_c4r%fld = fillreal
+   c_c4r%fldname = 'C4R'
+   c_c4r%long_name = 'cumulative LAI fraction hc to 0.20 * hc'
+   c_c4r%units = '1'
+   c_c4r%dimnames(1) = 'nx'
+   c_c4r%dimnames(2) = 'ny'
+   c_c4r%istart(1) = 1
+   c_c4r%istart(2) = 1
+   c_c4r%iend(1) = nx
+   c_c4r%iend(2) = ny
+
+  ENDIF
+
   c_seaice%fld = fillreal
   c_seaice%fldname = 'SEAICE'
   c_seaice%long_name = 'sea ice'

parallel/src/init_x.f90

@@ -145,6 +145,14 @@ SUBROUTINE init_x
    xseason  (:,:)   = fillreal
   ENDIF
 
+  IF ( ( ifcanopy ) ) THEN
+   xfch  (:,:)   = fillreal  ;    xclu     (:,:)   = fillreal
+   xfrt  (:,:)   = fillreal  ;    xpopu    (:,:)   = fillreal
+   xlaie (:,:)   = fillreal  ;    xc1r     (:,:)   = fillreal
+   xc2r  (:,:)   = fillreal  ;    xc3r     (:,:)   = fillreal
+   xc4r  (:,:)   = fillreal
+  ENDIF
+
   IF ( met_hybrid >= 0 ) THEN
     xmuhyb(:,:)   = fillreal
   ENDIF

parallel/src/mcipparm_mod.f90

@@ -248,7 +248,25 @@ MODULE mcipparm
   LOGICAL            :: ifssm           ! sediment supply map in input file?
   LOGICAL            :: ifssmwrfout     ! sediment supply map in WRF history?
   LOGICAL            :: ifuthr          ! threshold velocity in input file?
-  LOGICAL            :: ifuthrwrfout    ! threshold velocity in WRF history?
+  LOGICAL            :: ifuthrwrfout    ! threshold velocity in WRF history
+  LOGICAL            :: iffch           ! forest canopy height in input file?
+  LOGICAL            :: iffchwrfout     ! forest canopy height in WRF history?
+  LOGICAL            :: iffrt           ! forest fraction in input file?
+  LOGICAL            :: iffrtwrfout     ! forest fraction in WRF history?
+  LOGICAL            :: ifclu           ! forest clumping index in input file?
+  LOGICAL            :: ifcluwrfout     ! forest clumping index in WRF history?
+  LOGICAL            :: ifpopu          ! population density in input file?
+  LOGICAL            :: ifpopuwrfout    ! population density in WRF history?
+  LOGICAL            :: iflaie          ! leaf area index (ECCC) in input file?
+  LOGICAL            :: iflaiewrfout    ! leaf area index (ECCC) in WRF history?
+  LOGICAL            :: ifc1r           ! cumulative LAI fraction hc to 0.75 * hc in input file?
+  LOGICAL            :: ifc1rwrfout     ! cumulative LAI fraction hc to 0.75 * hc in WRF history?
+  LOGICAL            :: ifc2r           ! cumulative LAI fraction hc to 0.50 * hc in input file?
+  LOGICAL            :: ifc2rwrfout     ! cumulative LAI fraction hc to 0.50 * hc in WRF history?
+  LOGICAL            :: ifc3r           ! cumulative LAI fraction hc to 0.35 * hc in input file?
+  LOGICAL            :: ifc3rwrfout     ! cumulative LAI fraction hc to 0.35 * hc in WRF history?
+  LOGICAL            :: ifc4r           ! cumulative LAI fraction hc to 0.20 * hc in input file?
+  LOGICAL            :: ifc4rwrfout     ! cumulative LAI fraction hc to 0.20 * hc in WRF history?
   LOGICAL            :: iflufrc         ! fractional land use available?
   LOGICAL            :: ifluwrfout      ! is fractional land use in WRF history?
   LOGICAL            :: iflu2wrfout     ! is fractional land use 2 in WRF history?
@@ -275,6 +293,7 @@ MODULE mcipparm
   LOGICAL            :: ifviirs_lai     ! use NAQFC VIIRS LAI?
   LOGICAL            :: iffengsha_dust  ! use NAQFC Fengsha Windblown Dust?
   LOGICAL            :: ifbioseason     ! use bioseason switch?
+  LOGICAL            :: ifcanopy        ! use canopy parameters?
 
 !-------------------------------------------------------------------------------
 ! Run Options.