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Merge pull request #9 from noaa-oar-arl/develop
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Merge Develop into Master
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drnimbusrain authored Nov 24, 2020
2 parents 77ec880 + f67085a commit b6fa8f7
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8 changes: 6 additions & 2 deletions README.md
Original file line number Diff line number Diff line change
Expand Up @@ -97,7 +97,11 @@ The variables listed here are set by the user in the NACC run script, and they a
- `IFVIIRS_GVF [default: False]`
Logical to choose if the vegetation fraction is taken from FV3 or VIIRS GVF.
- `False`: Use FV3 vegetation fraction
- `True`: Use VIIRS GVF
- `True`: Use VIIRS GVF
- `IFVIIRS_LAI [default: False]`
Logical to choose if the LAI is taken from FV3 or VIIRS.
- `False`: Use FV3 LAI
- `True`: Use VIIRS LAI
- `IFFENGSHA_DUST [default: False]`
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
Expand Down Expand Up @@ -179,7 +183,7 @@ cd $NACC_home/serial/scripts
|InMetFiles|netCDF (WRF or FV3-GFS)|List of WRF or FV3-GFS output files for input to NACC|required|
|InSfcFiles|netCDF (FV3-GFS)|List of FV3-GFS output files for input to NACC|required (only FV3-GFS)|
|InGeoFile|netCDF (WRFor FV3-GFS)|Output from WRF Geogrid processor|optional; only required if fractional land use, LAI, etc are not part of the WRF or FV3-GFS output. Offline Pre-processed NOAA-ARL "geofiles" with LAI and LANDUSEF (based on 12-month climatological IGBP-MODIS) for the global GFSv16 Gaussian NetCDF Grid are available via FTP by request (Contact: Patrick C. Campbell; Patrick.C.Campbell@noaa.gov)|
|InVIIRSFile|netCDF (FV3-GFS)|Input from VIIRS GVF data |optional; only if global NetCDF VIIRS Input file is provided. Global ~ 4km VIIRS NetCDF Grid are available via FTP by request. (Contact: Patrick C. Campbell; Patrick.C.Campbell@noaa.gov)|
|InVIIRSFile|netCDF (FV3-GFS)|Input from VIIRS data |optional; only if global NetCDF VIIRS Input COARDS file is provided. Global ~ 4km VIIRS NetCDF Grid are available via FTP by request. (Contact: Patrick C. Campbell; Patrick.C.Campbell@noaa.gov)|

**Table 2. NACC output files**

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13 changes: 8 additions & 5 deletions parallel/scripts/run-nacc-fv3.ksh
Original file line number Diff line number Diff line change
Expand Up @@ -24,9 +24,10 @@ 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
InGeoDir=/gpfs/hps3/emc/naqfc/noscrub/Youhua.Tang/nwdev/NAQFC-WCOSS/fix
InVIIRSDir=/gpfs/hps3/emc/naqfc/noscrub/Patrick.C.Campbell/viirs_gvf_test/grib2
OutDir=/gpfs/hps2/ptmp/$USER/NACC-VIIRS-Test/output_fengsha_test
ProgDir=/gpfs/hps3/emc/naqfc/noscrub/Patrick.C.Campbell/NACC/parallel/src
InVIIRSDir_GVF=/gpfs/hps3/emc/naqfc/noscrub/Patrick.C.Campbell/viirs_gvf_test/grib2
InVIIRSDir_LAI=/gpfs/hps3/emc/naqfc/noscrub/Patrick.C.Campbell/viirs_lai_test/
OutDir=/gpfs/hps2/ptmp/$USER/NACC_test_lai/
ProgDir=/gpfs/hps3/emc/naqfc/noscrub/Patrick.C.Campbell/NACC_viirs_lai/parallel/src

if [ ! -s $InMetDir ]; then
echo "No such input directory $InMetDir"
Expand Down Expand Up @@ -59,7 +60,8 @@ cat>namelist.mcip<<!
file_mm = '$InMetDir/gfs.t12z.atmf','.nc'
file_sfc = '$InMetDir/gfs.t12z.sfcf','.nc'
file_geo = '$InGeoDir/gfs.t12z.geo.08.nc'
file_viirs_gvf = '$InVIIRSDir/GVF-WKL-GLB_v2r3_j01_s20200824_e20200830_c202008311235100.grib2.nc'
file_viirs_gvf = '$InVIIRSDir_GVF/GVF-WKL-GLB_v2r3_j01_s20200824_e20200830_c202008311235100.grib2.nc'
file_viirs_lai = '$InVIIRSDir_LAI/VIIRS_VNP15A2H.001_20190829.nc'
ioform = 1
&END
Expand All @@ -73,7 +75,8 @@ cat>namelist.mcip<<!
lwout = 1
luvbout = 1
ifdiag_pbl = .FALSE.
ifviirs_gvf = .FALSE.
ifviirs_gvf = .TRUE.
ifviirs_lai = .TRUE.
iffengsha_dust = .FALSE.
mcip_start = "2019-08-26-12:00:00.0000"
mcip_end = "2019-08-29-13:00:00.0000"
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6 changes: 3 additions & 3 deletions parallel/src/alloc_met.f90
Original file line number Diff line number Diff line change
Expand Up @@ -202,7 +202,7 @@ SUBROUTINE alloc_met
!test
ENDIF

IF ( iflai ) THEN ! leaf area index available
IF ( iflai ) THEN ! leaf area index available (Either from model or VIIRS)
ALLOCATE ( lai (ix, jy) )
ENDIF

Expand Down Expand Up @@ -241,9 +241,9 @@ SUBROUTINE alloc_met
ALLOCATE ( veg (ix, jy) )
ENDIF

IF ( ifveg_viirs ) THEN ! VIIRS GVF, i.e.,vegetation fraction available
IF ( ifveg_viirs ) THEN ! VIIRS GVF, i.e.,vegetation fraction available
ALLOCATE ( veg (ix, jy) )
ENDIF
ENDIF

IF ( ifwr ) THEN ! canopy wetness available
ALLOCATE ( wr (ix, jy) )
Expand Down
5 changes: 3 additions & 2 deletions parallel/src/coord_mod.f90
Original file line number Diff line number Diff line change
Expand Up @@ -189,8 +189,9 @@ MODULE coord
!FV3GFS
REAL, SAVE, ALLOCATABLE :: fv3lat(:),fv3lon(:), xindex(:,:), yindex(:,:), xuindex(:,:), yuindex(:,:), &
xvindex(:,:),yvindex(:,:),xdindex(:,:),ydindex(:,:)
!VIIRS (Optional for GVF--> veg frac currently)
REAL, SAVE, ALLOCATABLE :: viirslat(:),viirslon(:),xindex_viirs(:,:),yindex_viirs(:,:)
!VIIRS (Optional for GVF--> veg frac or LAI currently)
REAL, SAVE, ALLOCATABLE :: viirslat_gvf(:),viirslon_gvf(:),xindex_viirs_gvf(:,:),yindex_viirs_gvf(:,:)
REAL, SAVE, ALLOCATABLE :: viirslat_lai(:),viirslon_lai(:),xindex_viirs_lai(:,:),yindex_viirs_lai(:,:)
!-------------------------------------------------------------------------------
! COORDNAM_GD:
! The coordinate system name used for I/O-API description and GRIDDESC.
Expand Down
1 change: 1 addition & 0 deletions parallel/src/files_mod.f90
Original file line number Diff line number Diff line change
Expand Up @@ -69,6 +69,7 @@ MODULE files
CHARACTER(LEN=256), PARAMETER :: file_nml = 'namelist.mcip'
CHARACTER(LEN=256) :: file_geo
CHARACTER(LEN=256) :: file_viirs_gvf
CHARACTER(LEN=256) :: file_viirs_lai

CHARACTER(LEN=16), PARAMETER :: gridbdy2d = 'GRID_BDY_2D '
CHARACTER(LEN=16), PARAMETER :: gridcro2d = 'GRID_CRO_2D '
Expand Down
2 changes: 2 additions & 0 deletions parallel/src/mcipparm_mod.f90
Original file line number Diff line number Diff line change
Expand Up @@ -265,12 +265,14 @@ MODULE mcipparm
LOGICAL :: iftkef ! TKE (if exists) on full levels?
LOGICAL :: ifveg ! vegetation fraction in input file?
LOGICAL :: ifveg_viirs ! using vegetation fraction in VIIRS?
LOGICAL :: iflai_viirs ! using LAI in VIIRS?
LOGICAL :: ifw10m ! 10-m wind components in input file?
LOGICAL :: ifwr ! canopy wetness in input file?
LOGICAL :: ifznt ! roughness length in input file?
LOGICAL :: needseaice ! sea ice in input file?
LOGICAL :: ifdiag_pbl ! use diagnostic PBL?
LOGICAL :: ifviirs_gvf ! use NAQFC VIIRS GVF?
LOGICAL :: ifviirs_lai ! use NAQFC VIIRS LAI?
LOGICAL :: iffengsha_dust ! use NAQFC Fengsha Windblown Dust?

!-------------------------------------------------------------------------------
Expand Down
69 changes: 61 additions & 8 deletions parallel/src/rdfv3.f90
Original file line number Diff line number Diff line change
Expand Up @@ -197,6 +197,7 @@ SUBROUTINE rdfv3 (mcip_now,nn)
INTEGER, SAVE :: cdfid, cdfid2
INTEGER :: cdfidg
INTEGER :: cdfid_vgvf
INTEGER :: cdfid_vlai
INTEGER :: dimid
INTEGER :: dimids ( nf90_max_var_dims )
REAL, SAVE, ALLOCATABLE :: dum1d ( : )
Expand Down Expand Up @@ -661,7 +662,7 @@ END SUBROUTINE windrotation
if(.not.allocated(atmp)) allocate(atmp(ncols_x,nrows_x))
if(.not.allocated(utmp)) allocate(utmp(ncols_x+1,nrows_x+1))

IF ( ifveg_viirs ) THEN !If using VIIRS GVF for vegetation fraction-->Need to allocate array for VIIRS
IF ( ifveg_viirs .OR. iflai_viirs ) THEN !If using VIIRS GVF or LAI ->Need to allocate array for VIIRS
IF ( .NOT. ALLOCATED ( dum2d_viirs ) ) &
ALLOCATE ( dum2d_viirs (met_nx_viirs, met_ny_viirs) ) ! 2D

Expand All @@ -685,9 +686,14 @@ END SUBROUTINE windrotation
yuindex(ncols_x+1,nrows_x+1),xvindex(ncols_x+1,nrows_x+1),yvindex(ncols_x+1,nrows_x+1), &
xdindex(ncols_x+1,nrows_x+1),ydindex(ncols_x+1,nrows_x+1))

IF ( ifveg_viirs ) THEN !If using VIIRS GVF for vegetation fraction
allocate(xindex_viirs(ncols_x,nrows_x), yindex_viirs(ncols_x,nrows_x))
IF ( ifveg_viirs ) THEN !If using VIIRS GVF
allocate(xindex_viirs_gvf(ncols_x,nrows_x), yindex_viirs_gvf(ncols_x,nrows_x))
ENDIF

IF ( iflai_viirs) THEN !If using VIIRS LAI
allocate(xindex_viirs_lai(ncols_x,nrows_x), yindex_viirs_lai(ncols_x,nrows_x))
ENDIF


! Compute distance from origin (at reflat, standlon) to domain center, and
! store in MET_XXCTR and MET_YYCTR. Then calculate latitude, longitude,
Expand Down Expand Up @@ -755,12 +761,34 @@ END SUBROUTINE windrotation

mapcrs(i,j) = mapfac_lam (latcrs(i,j), met_tru1, met_tru2)

call getxyindex(latcrs(i,j),loncrs(i,j),xindex_viirs(i,j),yindex_viirs(i,j),viirslat,viirslon,met_nx_viirs,met_ny_viirs)
call getxyindex(latcrs(i,j),loncrs(i,j),xindex_viirs_gvf(i,j),yindex_viirs_gvf(i,j),viirslat_gvf,viirslon_gvf,met_nx_viirs,met_ny_viirs)

ENDDO
ENDDO
ENDIF


IF ( iflai_viirs ) THEN !If using VIIRS LAI for vegetation fraction
xoff=-1.5
yoff=-1.5
DO j = 1, nrows_x
DO i = 1, ncols_x

xxin = met_xxctr + (FLOAT(i) + xoff) * met_resoln
yyin = met_yyctr + (FLOAT(j) + yoff) * met_resoln

CALL xy2ll_lam (xxin, yyin, met_tru1, met_tru2, met_proj_clon, &
met_ref_lat, latcrs(i,j), loncrs(i,j))

mapcrs(i,j) = mapfac_lam (latcrs(i,j), met_tru1, met_tru2)

call getxyindex(latcrs(i,j),loncrs(i,j),xindex_viirs_lai(i,j),yindex_viirs_lai(i,j),viirslat_lai,viirslon_lai,met_nx_viirs,met_ny_viirs)

ENDDO
ENDDO
ENDIF


IF ( .NOT. gotfaces ) THEN ! get lat, lon, map-scale factor on faces

xoff = -2.0 ! U-face: no offset in X from dot-point center value
Expand Down Expand Up @@ -1701,8 +1729,8 @@ END SUBROUTINE windrotation
ENDIF
ENDIF !Fengsha WB dust variables

IF ( iflai ) THEN
IF ( iflaiwrfout ) THEN ! leaf area index in FV3 history file
IF ( iflai ) THEN
IF ( iflaiwrfout ) THEN ! leaf area index in FV3 history file
CALL get_var_2d_real_cdf (cdfid2, 'LAI', dum2d, it, rcode)
IF ( rcode == nf90_noerr ) THEN
call myinterp(dum2d,met_nx,met_ny,atmp,xindex,yindex,ncols_x,nrows_x,1)
Expand All @@ -1717,7 +1745,7 @@ END SUBROUTINE windrotation
WRITE (*,f9400) TRIM(pname), 'LAI', TRIM(nf90_strerror(rcode))
CALL graceful_stop (pname)
ENDIF
ELSE ! leaf area index in GEOGRID file from WPS
ELSE ! leaf area index in GEOGRID file from WPS
flg = file_geo
rcode = nf90_open (flg, nf90_nowrite, cdfidg)
IF ( rcode /= nf90_noerr ) THEN
Expand All @@ -1743,8 +1771,33 @@ END SUBROUTINE windrotation
WRITE (*,f9950) TRIM(pname)
CALL graceful_stop (pname)
ENDIF
ENDIF
IF ( iflai_viirs ) THEN !Instead Using VIIRS LAI
!Open VIIRS LAI File
flg = file_viirs_lai
rcode = nf90_open (flg, nf90_nowrite, cdfid_vlai)
IF ( rcode /= nf90_noerr ) THEN
WRITE (*,f9910) TRIM(pname)
CALL graceful_stop (pname)
ENDIF
CALL get_var_2d_real_cdf (cdfid_vlai, 'lai', dum2d_viirs, it, rcode)
IF ( rcode == nf90_noerr ) THEN
call myinterp(dum2d_viirs,met_nx_viirs,met_ny_viirs,atmp,xindex_viirs_lai,yindex_viirs_lai,ncols_x,nrows_x,1)
lai(1:ncols_x,1:nrows_x) = atmp(1:ncols_x,1:nrows_x)
where(lai.lt.0) lai=0.
WRITE (*,f6000) 'lai ', lai(lprt_metx, lprt_mety), ' from VIIRS LAI'
ELSE
WRITE (*,f9440) TRIM(pname), 'lai', TRIM(nf90_strerror(rcode))
CALL graceful_stop (pname)
ENDIF
rcode = nf90_close (cdfid_vlai)
IF ( rcode /= nf90_noerr ) THEN
WRITE (*,f9960) TRIM(pname)
CALL graceful_stop (pname)
ENDIF
ENDIF

ENDIF

IF ( ifwr ) THEN
CALL get_var_2d_real_cdf (cdfid2, 'cnwat', dum2d, it, rcode)
Expand All @@ -1768,7 +1821,7 @@ END SUBROUTINE windrotation
ENDIF
CALL get_var_2d_real_cdf (cdfid_vgvf, 'VEG_surface', dum2d_viirs, it, rcode)
IF ( rcode == nf90_noerr ) THEN
call myinterp(dum2d_viirs,met_nx_viirs,met_ny_viirs,atmp,xindex_viirs,yindex_viirs,ncols_x,nrows_x,1)
call myinterp(dum2d_viirs,met_nx_viirs,met_ny_viirs,atmp,xindex_viirs_gvf,yindex_viirs_gvf,ncols_x,nrows_x,1)
veg(1:ncols_x,1:nrows_x) = atmp(1:ncols_x,1:nrows_x)*0.01
where(veg.gt.100 .OR. veg.lt.0) veg=0.
WRITE (*,f6000) 'veg ', veg(lprt_metx, lprt_mety), 'fraction (from VIIRS GVF)'
Expand Down
8 changes: 6 additions & 2 deletions parallel/src/readnml.f90
Original file line number Diff line number Diff line change
Expand Up @@ -107,11 +107,11 @@ SUBROUTINE readnml (ctmlays)
INTEGER :: nrowsin
CHARACTER(LEN=16), PARAMETER :: pname = 'READNML'

NAMELIST /filenames/ file_gd, file_mm, file_sfc, file_geo, file_viirs_gvf, ioform
NAMELIST /filenames/ file_gd, file_mm, file_sfc, file_geo, file_viirs_gvf, file_viirs_lai, ioform

NAMELIST /userdefs/ inmetmodel, dx_in, dy_in, met_cen_lat_in, met_cen_lon_in, &
lpv, lwout, luvbout, ifdiag_pbl, ifviirs_gvf, &
iffengsha_dust, &
ifviirs_lai, iffengsha_dust, &
eradm, mcip_start, mcip_end, ntimes, intvl, &
coordnam, grdnam, ctmlays, &
btrim, lprt_col, lprt_row, &
Expand Down Expand Up @@ -219,6 +219,7 @@ SUBROUTINE readnml (ctmlays)
file_geo = " "
file_sfc(:) = " "
file_viirs_gvf = " "
file_viirs_lai = " "
!-------------------------------------------------------------------------------
! Set default value for user-selected model (2 = WRF, 3 = FV3).
inmetmodel = 2
Expand Down Expand Up @@ -254,6 +255,7 @@ SUBROUTINE readnml (ctmlays)

ifdiag_pbl = .false. ! To re-diagnose the PBLH
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
!-------------------------------------------------------------------------------
! Set default value for earth radius in meters (ERADM). The default value is
Expand Down Expand Up @@ -368,6 +370,8 @@ SUBROUTINE readnml (ctmlays)
file_viirs_gvf = TRIM( ADJUSTL(file_viirs_gvf) )
IF ( file_viirs_gvf(1:7) == "no_file" ) file_viirs_gvf = " "

file_viirs_lai = TRIM( ADJUSTL(file_viirs_lai) )
IF ( file_viirs_lai(1:7) == "no_file" ) file_viirs_lai = " "
!-------------------------------------------------------------------------------
! Verify values of user-defined options.
!-------------------------------------------------------------------------------
Expand Down
7 changes: 7 additions & 0 deletions parallel/src/setgriddefs.f90
Original file line number Diff line number Diff line change
Expand Up @@ -762,6 +762,13 @@ SUBROUTINE setgriddefs
ENDIF
WRITE (*,f6150) 'VIIRS GVF-VEGETATION FRACTION', TRIM(yesno)

IF ( iflai_viirs ) THEN
yesno = ''
ELSE
yesno = 'NOT'
ENDIF
WRITE (*,f6150) 'VIIRS LAI', TRIM(yesno)

IF ( ifw10m ) THEN
yesno = ''
ELSE
Expand Down
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