Merge branch 'feature/v16x_allsky' of https://github.com/emilyhcliu/GSI…

… into feature/v16x_allsky

modulefiles/modulefile.ProdGSI.hera

@@ -9,7 +9,6 @@
 #module-whatis " NOAA-EMC/GSI whatis description"
 
 setenv CRTM_FIX /scratch2/NCEPDEV/nwprod/NCEPLIBS/fix/crtm_v2.3.0
-#setenv CRTM_FIX /scratch2/NCEPDEV/nwprod/hpc-stack/libs/hpc-stack/intel-18.0.5.274/crtm/2.4.0/fix
 
 # Load cmake
 module use -a /contrib/cmake/modulefiles
@@ -42,6 +41,5 @@ module load w3nco/2.4.1
 module load w3emc/2.7.3
 module load bacio/2.4.1
 module load crtm/2.3.0
-#module load crtm/2.4.0
 module load netcdf/4.7.4
 module load wrf_io/1.2.0

src/gsi/antcorr_application.f90

@@ -225,16 +225,19 @@ END SUBROUTINE Remove_AntCorr
   SUBROUTINE Apply_AntCorr( AC  , &  ! Input
                             iFOV, &  ! Input
                             T     )  ! In/Output
+
+   use kinds,only: i_kind, r_kind
+
     implicit none
 
     ! Arguments
     TYPE(ACCoeff_type), INTENT(IN)     :: AC
-    INTEGER           , INTENT(IN)     :: iFOV
-    REAL(fp)          , INTENT(IN OUT) :: T(:)
+    INTEGER(i_kind)   , INTENT(IN)     :: iFOV
+    REAL(r_kind)      , INTENT(IN OUT) :: T(:)
     ! Local parameters
     CHARACTER(*), PARAMETER :: ROUTINE_NAME = 'Apply_AntCorr'
     ! Local variables
-    INTEGER :: l
+    INTEGER(i_kind) :: l
 
     ! Check input
     IF ( iFOV < 1 .OR. iFOV > AC%n_FOVS ) THEN

src/gsi/cplr_gfs_ensmod.f90

@@ -1057,8 +1057,8 @@ subroutine parallel_read_gfsnc_state_(en_full,m_cvars2d,m_cvars3d,nlon,nlat,nsig
    enddo
    deallocate(rwork3d1)
 
-!  if (k3u==0.or.k3v==0.or.k3t==0.or.k3q==0.or.k3cw==0.or.k3oz==0) &  !orig
-   if (k3u==0.or.k3v==0.or.k3t==0.or.k3q==0.or.k3oz==0) &             !emily
+!  if (k3u==0.or.k3v==0.or.k3t==0.or.k3q==0.or.k3cw==0.or.k3oz==0) &
+   if (k3u==0.or.k3v==0.or.k3t==0.or.k3q==0.or.k3oz==0) &
       write(6,'(" WARNING, problem with one of k3-")')
 
    do k=1,nsig
@@ -1361,7 +1361,7 @@ subroutine get_gfs_ens(this,grd,member,ntindex,atm_bundle,iret)
     else if ( use_gfs_ncio ) then
        if (fv3_full_hydro) then
           call general_read_gfsatm_allhydro_nc(grd,sp_ens,filename,uv_hyb_ens,.false., &
-               zflag,atm_bundle,.true.,iret)
+               zflag,atm_bundle,iret)
        else
           call general_read_gfsatm_nc(grd,sp_ens,filename,uv_hyb_ens,.false., &
                zflag,atm_bundle,.true.,iret)

src/gsi/general_read_gfsatm.f90

@@ -2571,7 +2571,7 @@ subroutine general_read_gfsatm_nc(grd,sp_a,filename,uvflag,vordivflag,zflag, &
 
 end subroutine general_read_gfsatm_nc
 subroutine general_read_gfsatm_allhydro_nc(grd,sp_a,filename,uvflag,vordivflag,zflag, &
-           gfs_bundle,init_head,iret_read)
+           gfs_bundle,iret_read)
 !$$$  subprogram documentation block
 !                .      .    .                                       .
 ! subprogram:    general_read_gfsatm_nc  adaptation of read_gfsatm for general resolutions
@@ -2595,8 +2595,6 @@ subroutine general_read_gfsatm_allhydro_nc(grd,sp_a,filename,uvflag,vordivflag,z
 !     vordivflag - logical to determine if routine should output vorticity and
 !                  divergence
 !     zflag    - logical to determine if surface height field should be output
-!     init_head- flag to read header record.  Usually .true. unless repeatedly
-!                reading similar files (ensembles)
 !
 !   output argument list:
 !     gfs_bundle  - bundle carrying guess fields
@@ -2632,7 +2630,7 @@ subroutine general_read_gfsatm_allhydro_nc(grd,sp_a,filename,uvflag,vordivflag,z
    type(sub2grid_info)                   ,intent(in   ) :: grd
    type(spec_vars)                       ,intent(in   ) :: sp_a
    character(*)                          ,intent(in   ) :: filename
-   logical                               ,intent(in   ) :: uvflag,zflag,vordivflag,init_head
+   logical                               ,intent(in   ) :: uvflag,zflag,vordivflag
    integer(i_kind)                       ,intent(  out) :: iret_read
    type(gsi_bundle)                      ,intent(inout) :: gfs_bundle
 

src/gsi/netcdfgfs_io.f90

@@ -118,7 +118,6 @@ subroutine read_
     use kinds, only: i_kind,r_kind
     use constants, only: qcmin
     use gridmod, only: sp_a,grd_a,lat2,lon2,nsig
-    ! use guess_grids, only: ifilesig,nfldsig
     use guess_grids, only: ifilesig,nfldsig,ntguessig
     use gsi_metguess_mod, only: gsi_metguess_bundle
     use gsi_bundlemod, only: gsi_bundlegetpointer
@@ -137,7 +136,6 @@ subroutine read_
     character(len=*),parameter::myname_=myname//'*read_'
     character(24) filename
     integer(i_kind):: it, istatus, inner_vars, num_fields
-    integer(i_kind):: iret_ql,iret_qi,iret_qr,iret_qs,iret_qg
     integer(i_kind):: i,j,k
 
 
@@ -206,7 +204,7 @@ subroutine read_
        if (fv3_full_hydro) then
           if (mype==0) write(*,*) 'calling general_read_gfsatm_allhydro_nc', it
           call general_read_gfsatm_allhydro_nc(grd_t,sp_a,filename,.true.,.true.,.true.,&
-              atm_bundle,.true.,istatus) ! this loads cloud and precip
+              atm_bundle,istatus) ! this loads cloud and precip
           if (mype==0) write(*,*) 'done with general_read_gfsatm_allhydro_nc', it 
        else
           if (mype==0) write(*,*) 'calling general_read_gfsatm_nc'

src/gsi/qcmod.f90

@@ -2807,9 +2807,9 @@ subroutine qc_avhrr(nchanl,is,ndat,nsig,ich,sea,land,ice,snow,luse,   &
 end subroutine qc_avhrr
 
 subroutine qc_amsua(nchanl,is,ndat,nsig,npred,sea,land,ice,snow,mixed,luse,   &
-     zsges,cenlat,tb_obsbc1,si_mean,cosza,clw,tbc,ptau5,emissivity_k,ts, &                    
+     zsges,cenlat,tb_obsbc1,cosza,clw,tbc,ptau5,emissivity_k,ts, &                    
      pred,predchan,id_qc,aivals,errf,errf0,clwp_amsua,varinv,cldeff_obs,cldeff_fg,factch6, &
-     cld_rbc_idx,sfc_speed,error0,clw_guess_retrieval,scatp,radmod)                     
+     cld_rbc_idx,sfc_speed,error0,clw_guess_retrieval,scatp,radmod,si_mean)                     
 
 !$$$ subprogram documentation block
 !               .      .    .
@@ -2890,7 +2890,8 @@ subroutine qc_amsua(nchanl,is,ndat,nsig,npred,sea,land,ice,snow,mixed,luse,   &
   logical,                             intent(in   ) :: sea,land,ice,snow,mixed,luse
   integer(i_kind),                     intent(in   ) :: ndat,nsig,npred,nchanl,is
   integer(i_kind),dimension(nchanl),   intent(inout) :: id_qc
-  real(r_kind),                        intent(in   ) :: zsges,cenlat,tb_obsbc1,si_mean
+  real(r_kind),                        intent(in   ) :: zsges,cenlat,tb_obsbc1
+  real(r_kind), optional,              intent(in   ) :: si_mean
   real(r_kind),dimension(nchanl),      intent(in   ) :: cldeff_obs,cldeff_fg
   real(r_kind),                        intent(in   ) :: cosza,clw,clwp_amsua,clw_guess_retrieval
   real(r_kind),                        intent(in   ) :: sfc_speed,scatp
@@ -3614,9 +3615,9 @@ subroutine qc_mhs(nchanl,ndat,nsig,is,sea,land,ice,snow,mhs,luse,   &
 
 end subroutine qc_mhs
 subroutine qc_atms(nchanl,is,ndat,nsig,npred,sea,land,ice,snow,mixed,luse,   &
-                 zsges,cenlat,tb_obsbc1,si_mean,cosza,clw,tbc,ptau5,emissivity_k,ts, &                    
+                 zsges,cenlat,tb_obsbc1,cosza,clw,tbc,ptau5,emissivity_k,ts, &                    
                  pred,predchan,id_qc,aivals,errf,errf0,clwp_amsua,varinv,cldeff_obs,cldeff_fg,factch6, &
-                 cld_rbc_idx,sfc_speed,error0,clw_guess_retrieval,scatp,radmod)                     
+                 cld_rbc_idx,sfc_speed,error0,clw_guess_retrieval,scatp,radmod,si_mean)                     
 
 !$$$ subprogram documentation block
 !               .      .    .
@@ -3687,7 +3688,8 @@ subroutine qc_atms(nchanl,is,ndat,nsig,npred,sea,land,ice,snow,mixed,luse,   &
   logical,                             intent(in   ) :: sea,land,ice,snow,mixed,luse
   integer(i_kind),                     intent(in   ) :: nchanl,is,ndat,nsig,npred
   integer(i_kind),dimension(nchanl),   intent(inout) :: id_qc
-  real(r_kind),                        intent(in   ) :: zsges,cenlat,tb_obsbc1,si_mean 
+  real(r_kind),                        intent(in   ) :: zsges,cenlat,tb_obsbc1
+  real(r_kind), optional,              intent(in   ) :: si_mean 
   real(r_kind),dimension(nchanl),      intent(in   ) :: cldeff_obs, cldeff_fg  
   real(r_kind),                        intent(in   ) :: cosza,clw,clwp_amsua,clw_guess_retrieval
   real(r_kind),                        intent(in   ) :: sfc_speed,scatp
@@ -3703,7 +3705,7 @@ subroutine qc_atms(nchanl,is,ndat,nsig,npred,sea,land,ice,snow,mixed,luse,   &
 
 ! For now, just pass all channels to qc_amsua
   call qc_amsua (nchanl,is,ndat,nsig,npred,sea,land,ice,snow,mixed,luse,   &
-                 zsges,cenlat,tb_obsbc1,si_mean,cosza,clw,tbc,ptau5,emissivity_k,ts, &                   
+                 zsges,cenlat,tb_obsbc1,cosza,clw,tbc,ptau5,emissivity_k,ts, &                   
                  pred,predchan,id_qc,aivals,errf,errf0,clwp_amsua,varinv,cldeff_obs,cldeff_fg,factch6, & 
                  cld_rbc_idx,sfc_speed,error0,clw_guess_retrieval,scatp,radmod)                    
 

src/gsi/setuprad.f90

@@ -1373,7 +1373,7 @@ subroutine setuprad(obsLL,odiagLL,lunin,mype,aivals,stats,nchanl,nreal,nobs,&
            end if
 
            call qc_amsua(nchanl,is,ndat,nsig,npred,sea,land,ice,snow,mixed,luse(n),   &
-              zsges,cenlat,tb_obsbc1,si_mean,cosza,clw_obs,tbc,ptau5,emissivity_k,ts, &                   
+              zsges,cenlat,tb_obsbc1,cosza,clw_obs,tbc,ptau5,emissivity_k,ts, &                   
               pred,predchan,id_qc,aivals,errf,errf0,clw_obs,varinv,cldeff_obs,cldeff_fg,factch6, & 
               cld_rbc_idx,sfc_speed,error0,clw_guess_retrieval,scatp,radmod)                    
 
@@ -1414,7 +1414,7 @@ subroutine setuprad(obsLL,odiagLL,lunin,mype,aivals,stats,nchanl,nreal,nobs,&
            si_mean= half*(si_obs+si_fg) 
 
            call qc_atms(nchanl,is,ndat,nsig,npred,sea,land,ice,snow,mixed,luse(n),    &
-              zsges,cenlat,tb_obsbc1,si_mean,cosza,clw_obs,tbc,ptau5,emissivity_k,ts, & 
+              zsges,cenlat,tb_obsbc1,cosza,clw_obs,tbc,ptau5,emissivity_k,ts, & 
               pred,predchan,id_qc,aivals,errf,errf0,clw_obs,varinv,cldeff_obs,cldeff_fg,factch6, &
               cld_rbc_idx,sfc_speed,error0,clw_guess_retrieval,scatp,radmod)                   
 

src/gsi/write_incr.f90

@@ -91,7 +91,7 @@ subroutine write_fv3_inc_ (grd,sp_a,filename,mype_out,gfs_bundle,ibin)
     use obsmod, only: ianldate 
     use state_vectors, only: allocate_state, deallocate_state
 
-    use state_vectors, only: svars3d, ns3d
+    use state_vectors, only: svars3d
     use mpeu_util, only: getindex
 
     implicit none
@@ -134,7 +134,7 @@ subroutine write_fv3_inc_ (grd,sp_a,filename,mype_out,gfs_bundle,ibin)
                        hyaivarid, hybivarid, uvarid, vvarid, delpvarid, delzvarid, &
                        tvarid, sphumvarid, liqwatvarid, o3varid, icvarid, &
                        qrvarid, qsvarid, qgvarid
-    integer(i_kind) :: icw,iql,iqi,iqr,iqs,iqg
+    integer(i_kind) :: iql,iqi,iqr,iqs,iqg
     integer(i_kind) :: dimids3(3),nccount(3),ncstart(3), cnksize(3), j1, j2
 
     type(gsi_bundle) :: svalinc(nobs_bins)
@@ -446,17 +446,17 @@ subroutine write_fv3_inc_ (grd,sp_a,filename,mype_out,gfs_bundle,ibin)
     call mpi_barrier(mpi_comm_world,ierror)
     ! liquid water increment
     if (iql>0) then
-    do k=1,grd%nsig
-       krev = grd%nsig+1-k
-       if (zero_increment_strat('liq_wat_inc')) then 
-         call zero_inc_strat(qlsm(:,:,k), k, troplev) 
-       end if
-       if (should_zero_increments_for('liq_wat_inc')) qlsm(:,:,k) = 0.0_r_kind
-       out3d(:,:,krev) = transpose(qlsm(j1:j2,:,k))
-    end do
-    call nccheck_incr(nf90_put_var(ncid_out, liqwatvarid, sngl(out3d), &
-                      start = ncstart, count = nccount))
-    call mpi_barrier(mpi_comm_world,ierror)
+       do k=1,grd%nsig
+          krev = grd%nsig+1-k
+          if (zero_increment_strat('liq_wat_inc')) then 
+            call zero_inc_strat(qlsm(:,:,k), k, troplev) 
+          end if
+          if (should_zero_increments_for('liq_wat_inc')) qlsm(:,:,k) = 0.0_r_kind
+          out3d(:,:,krev) = transpose(qlsm(j1:j2,:,k))
+       end do
+       call nccheck_incr(nf90_put_var(ncid_out, liqwatvarid, sngl(out3d), &
+                         start = ncstart, count = nccount))
+       call mpi_barrier(mpi_comm_world,ierror)
     endif
     ! ozone increment
     do k=1,grd%nsig
@@ -472,59 +472,59 @@ subroutine write_fv3_inc_ (grd,sp_a,filename,mype_out,gfs_bundle,ibin)
     call mpi_barrier(mpi_comm_world,ierror)
     ! ice mixing ratio increment
     if (iqi>0) then
-    do k=1,grd%nsig
-       krev = grd%nsig+1-k
-       if (zero_increment_strat('icmr_inc')) then 
-         call zero_inc_strat(qism(:,:,k), k, troplev) 
-       end if
-       if (should_zero_increments_for('icmr_inc')) qism(:,:,k) = 0.0_r_kind
-       out3d(:,:,krev) = transpose(qism(j1:j2,:,k))
-    end do
-    call nccheck_incr(nf90_put_var(ncid_out, icvarid, sngl(out3d), &
-                      start = ncstart, count = nccount))
-    call mpi_barrier(mpi_comm_world,ierror)
+       do k=1,grd%nsig
+          krev = grd%nsig+1-k
+          if (zero_increment_strat('icmr_inc')) then 
+            call zero_inc_strat(qism(:,:,k), k, troplev) 
+          end if
+          if (should_zero_increments_for('icmr_inc')) qism(:,:,k) = 0.0_r_kind
+         out3d(:,:,krev) = transpose(qism(j1:j2,:,k))
+       end do
+       call nccheck_incr(nf90_put_var(ncid_out, icvarid, sngl(out3d), &
+                         start = ncstart, count = nccount))
+       call mpi_barrier(mpi_comm_world,ierror)
     endif
     ! rain water mixing ratio increment
     if (iqr>0) then
-    do k=1,grd%nsig
-       krev = grd%nsig+1-k
-       if (zero_increment_strat('rwmr_inc')) then 
-         call zero_inc_strat(qrsm(:,:,k), k, troplev) 
-       end if
-       if (should_zero_increments_for('rwmr_inc')) qrsm(:,:,k) = 0.0_r_kind
-       out3d(:,:,krev) = transpose(qrsm(j1:j2,:,k))
-    end do
-    call nccheck_incr(nf90_put_var(ncid_out, qrvarid, sngl(out3d), &
-                      start = ncstart, count = nccount))
-    call mpi_barrier(mpi_comm_world,ierror)
+       do k=1,grd%nsig
+          krev = grd%nsig+1-k
+          if (zero_increment_strat('rwmr_inc')) then 
+            call zero_inc_strat(qrsm(:,:,k), k, troplev) 
+          end if
+          if (should_zero_increments_for('rwmr_inc')) qrsm(:,:,k) = 0.0_r_kind
+          out3d(:,:,krev) = transpose(qrsm(j1:j2,:,k))
+       end do
+       call nccheck_incr(nf90_put_var(ncid_out, qrvarid, sngl(out3d), &
+                         start = ncstart, count = nccount))
+       call mpi_barrier(mpi_comm_world,ierror)
     endif
     ! snow water mixing ratio increment
     if (iqs>0) then
-    do k=1,grd%nsig
-       krev = grd%nsig+1-k
-       if (zero_increment_strat('snmr_inc')) then 
-         call zero_inc_strat(qssm(:,:,k), k, troplev) 
-       end if
-       if (should_zero_increments_for('snmr_inc')) qssm(:,:,k) = 0.0_r_kind
-       out3d(:,:,krev) = transpose(qssm(j1:j2,:,k))
-    end do
-    call nccheck_incr(nf90_put_var(ncid_out, qsvarid, sngl(out3d), &
-                      start = ncstart, count = nccount))
-    call mpi_barrier(mpi_comm_world,ierror)
+       do k=1,grd%nsig
+          krev = grd%nsig+1-k
+          if (zero_increment_strat('snmr_inc')) then 
+            call zero_inc_strat(qssm(:,:,k), k, troplev) 
+          end if
+          if (should_zero_increments_for('snmr_inc')) qssm(:,:,k) = 0.0_r_kind
+          out3d(:,:,krev) = transpose(qssm(j1:j2,:,k))
+       end do
+       call nccheck_incr(nf90_put_var(ncid_out, qsvarid, sngl(out3d), &
+                         start = ncstart, count = nccount))
+       call mpi_barrier(mpi_comm_world,ierror)
     endif
     ! graupel mixing ratio increment
     if (iqg>0) then
-    do k=1,grd%nsig
-       krev = grd%nsig+1-k
-       if (zero_increment_strat('grle_inc')) then 
-         call zero_inc_strat(qgsm(:,:,k), k, troplev) 
-       end if
-       if (should_zero_increments_for('grle_inc')) qgsm(:,:,k) = 0.0_r_kind
-       out3d(:,:,krev) = transpose(qgsm(j1:j2,:,k))
-    end do
-    call nccheck_incr(nf90_put_var(ncid_out, qgvarid, sngl(out3d), &
-                      start = ncstart, count = nccount))
-    call mpi_barrier(mpi_comm_world,ierror)
+       do k=1,grd%nsig
+          krev = grd%nsig+1-k
+          if (zero_increment_strat('grle_inc')) then 
+            call zero_inc_strat(qgsm(:,:,k), k, troplev) 
+          end if
+          if (should_zero_increments_for('grle_inc')) qgsm(:,:,k) = 0.0_r_kind
+          out3d(:,:,krev) = transpose(qgsm(j1:j2,:,k))
+       end do
+       call nccheck_incr(nf90_put_var(ncid_out, qgvarid, sngl(out3d), &
+                         start = ncstart, count = nccount))
+       call mpi_barrier(mpi_comm_world,ierror)
     endif
 !    ! cleanup and exit
     call nccheck_incr(nf90_close(ncid_out))