Cleanup work gerrit code review part 2 - 2019/06/29

physics/GFS_MP_generic.F90

@@ -84,7 +84,7 @@ module GFS_MP_generic_post
       subroutine GFS_MP_generic_post_init
       end subroutine GFS_MP_generic_post_init
 
-!>\defgroup gfs_calpreciptype GFS/GFDL calpreciptype Main
+!>\defgroup gfs_calpreciptype GFS Precipitation Type Diagnostics Module
 !! \brief If dominant precip type is requested (i.e., Zhao-Carr MP scheme), 4 more algorithms in calpreciptype()
 !! will be called.  the tallies are then summed in calwxt_dominant(). For GFDL cloud MP scheme, determine convective 
 !! rain/snow by surface temperature;  and determine explicit rain/snow by rain/snow coming out directly from MP.

physics/GFS_debug.F90

@@ -174,7 +174,6 @@ subroutine GFS_diagtoscreen_run (Model, Statein, Stateout, Sfcprop, Coupling,
                      call print_var(mpirank,omprank, blkno, 'Sfcprop%f10m'     , Sfcprop%f10m)
                      call print_var(mpirank,omprank, blkno, 'Sfcprop%tprcp'    , Sfcprop%tprcp)
                      call print_var(mpirank,omprank, blkno, 'Sfcprop%srflag'   , Sfcprop%srflag)
-                     call print_var(mpirank,omprank, blkno, 'Sfcprop%sr'       , Sfcprop%sr)
                      call print_var(mpirank,omprank, blkno, 'Sfcprop%slc'      , Sfcprop%slc)
                      call print_var(mpirank,omprank, blkno, 'Sfcprop%smc'      , Sfcprop%smc)
                      call print_var(mpirank,omprank, blkno, 'Sfcprop%stc'      , Sfcprop%stc)
@@ -321,10 +320,16 @@ subroutine GFS_diagtoscreen_run (Model, Statein, Stateout, Sfcprop, Coupling,
                      call print_var(mpirank,omprank, blkno, 'Diag%epi         ',    Diag%epi)
                      call print_var(mpirank,omprank, blkno, 'Diag%smcwlt2     ',    Diag%smcwlt2)
                      call print_var(mpirank,omprank, blkno, 'Diag%smcref2     ',    Diag%smcref2)
+                     call print_var(mpirank,omprank, blkno, 'Diag%sr          ',    Diag%sr)
                      call print_var(mpirank,omprank, blkno, 'Diag%tdomr       ',    Diag%tdomr)
                      call print_var(mpirank,omprank, blkno, 'Diag%tdomzr      ',    Diag%tdomzr)
                      call print_var(mpirank,omprank, blkno, 'Diag%tdomip      ',    Diag%tdomip)
                      call print_var(mpirank,omprank, blkno, 'Diag%tdoms       ',    Diag%tdoms)
+                     if (Model%lsm == Model%lsm_ruc) then
+                       call print_var(mpirank,omprank, blkno, 'Diag%wet1        ',  Sfcprop%wetness)
+                     else
+                       call print_var(mpirank,omprank, blkno, 'Diag%wet1        ',  Diag%wet1)
+                     end if
                      call print_var(mpirank,omprank, blkno, 'Diag%skebu_wts   ',    Diag%skebu_wts)
                      call print_var(mpirank,omprank, blkno, 'Diag%skebv_wts   ',    Diag%skebv_wts)
                      call print_var(mpirank,omprank, blkno, 'Diag%sppt_wts    ',    Diag%sppt_wts)

physics/GFS_phys_time_vary.fv3.F90

@@ -2,8 +2,9 @@
 !!  Contains code related to GFS physics suite setup (physics part of time_vary_step)
 
 !>\defgroup mod_GFS_phys_time_vary GFS Physics Time Update
-!! This module contains GFS physics time vary subroutines including ozone, h2o, i
-!! aerosol and IN&CCN updates. 
+!! This module contains GFS physics time vary subroutines including ozone, stratospheric water vapor, 
+!! aerosol, IN&CCN and surface properties updates. 
+!> @{
    module GFS_phys_time_vary
 
 #ifdef OPENMP
@@ -42,6 +43,8 @@ module GFS_phys_time_vary
 !! | errmsg         | ccpp_error_message                                     | error message for error handling in CCPP                                | none     |    0 | character             | len=*     | out    | F        |
 !! | errflg         | ccpp_error_flag                                        | error flag for error handling in CCPP                                   | flag     |    0 | integer               |           | out    | F        |
 !!
+!>\section gen_GFS_phys_time_vary_init GFS_phys_time_vary_init General Algorithm
+!! @{
       subroutine GFS_phys_time_vary_init (Data, Model, Interstitial, nthrds, errmsg, errflg)
 
          use GFS_typedefs,          only: GFS_control_type, GFS_data_type, GFS_interstitial_type
@@ -111,6 +114,7 @@ subroutine GFS_phys_time_vary_init (Data, Model, Interstitial, nthrds, errmsg, e
 !$OMP sections
 
 !$OMP section
+!> - Call read_o3data() to read ozone data 
          call read_o3data  (Model%ntoz, Model%me, Model%master)
 
          ! Consistency check that the hardcoded values for levozp and
@@ -130,6 +134,7 @@ subroutine GFS_phys_time_vary_init (Data, Model, Interstitial, nthrds, errmsg, e
          end if
 
 !$OMP section
+!> - Call read_h2odata() to read stratospheric water vapor data
          call read_h2odata (Model%h2o_phys, Model%me, Model%master)
 
          ! Consistency check that the hardcoded values for levh2o and
@@ -149,6 +154,7 @@ subroutine GFS_phys_time_vary_init (Data, Model, Interstitial, nthrds, errmsg, e
          end if
 
 !$OMP section
+!> - Call read_aerdata() to read aerosol climatology
          if (Model%aero_in) then
             ! Consistency check that the value for ntrcaerm set in GFS_typedefs.F90
             ! and used to allocate Tbd%aer_nm matches the value defined in aerclm_def
@@ -173,6 +179,7 @@ subroutine GFS_phys_time_vary_init (Data, Model, Interstitial, nthrds, errmsg, e
          endif
 
 !$OMP section
+!> - Call read_cidata() to read IN and CCN data
          if (Model%iccn) then
            call read_cidata  ( Model%me, Model%master)
            ! No consistency check needed for in/ccn data, all values are
@@ -204,7 +211,7 @@ subroutine GFS_phys_time_vary_init (Data, Model, Interstitial, nthrds, errmsg, e
          end if
 
 
-         !--- read in and initialize ozone
+!> - Call setindxoz() to initialize ozone data
          if (Model%ntoz > 0) then
 !$OMP do schedule (dynamic,1)
            do nb = 1, nblks
@@ -214,7 +221,7 @@ subroutine GFS_phys_time_vary_init (Data, Model, Interstitial, nthrds, errmsg, e
 !$OMP end do
          endif
 
-         !--- read in and initialize stratospheric water
+!> - Call setindxh2o() to initialize stratospheric water vapor data
          if (Model%h2o_phys) then
 !$OMP do schedule (dynamic,1)
            do nb = 1, nblks
@@ -224,7 +231,7 @@ subroutine GFS_phys_time_vary_init (Data, Model, Interstitial, nthrds, errmsg, e
 !$OMP end do
          endif
 
-         !--- read in and initialize aerosols
+!> - Call setindxaer() to initialize aerosols data
          if (Model%aero_in) then
 !$OMP do schedule (dynamic,1)
            do nb = 1, nblks
@@ -236,7 +243,7 @@ subroutine GFS_phys_time_vary_init (Data, Model, Interstitial, nthrds, errmsg, e
 !$OMP end do
          endif
 
-         !--- read in and initialize IN and CCN
+!> - Call setindxci() to initialize IN and CCN data
          if (Model%iccn) then
 !$OMP do schedule (dynamic,1)
            do nb = 1, nblks
@@ -267,6 +274,7 @@ subroutine GFS_phys_time_vary_init (Data, Model, Interstitial, nthrds, errmsg, e
          is_initialized = .true.
 
       end subroutine GFS_phys_time_vary_init
+!! @}
 
 
 !> \section arg_table_GFS_phys_time_vary_finalize Argument Table
@@ -324,6 +332,8 @@ end subroutine GFS_phys_time_vary_finalize
 !! | errmsg         | ccpp_error_message                                     | error message for error handling in CCPP                                | none     |    0 | character             | len=*     | out    | F        |
 !! | errflg         | ccpp_error_flag                                        | error flag for error handling in CCPP                                   | flag     |    0 | integer               |           | out    | F        |
 !!
+!>\section gen_GFS_phys_time_vary_run GFS_phys_time_vary_run General Algorithm
+!> @{
       subroutine GFS_phys_time_vary_run (Data, Model, nthrds, errmsg, errflg)
 
         use mersenne_twister,      only: random_setseed, random_number
@@ -413,7 +423,7 @@ subroutine GFS_phys_time_vary_run (Data, Model, nthrds, errmsg, errflg)
           enddo
         endif  ! imfdeepcnv, cal_re, random_clds
 
-        !--- o3 interpolation
+!> - Call ozinterpol() to make ozone interpolation
         if (Model%ntoz > 0) then
 !$OMP do schedule (dynamic,1)
           do nb = 1, nblks
@@ -424,7 +434,7 @@ subroutine GFS_phys_time_vary_run (Data, Model, nthrds, errmsg, errflg)
 !$OMP end do
         endif
 
-        !--- h2o interpolation
+!> - Call h2ointerpol() to make stratospheric water vapor data interpolation
         if (Model%h2o_phys) then
 !$OMP do schedule (dynamic,1)
           do nb = 1, nblks
@@ -435,7 +445,7 @@ subroutine GFS_phys_time_vary_run (Data, Model, nthrds, errmsg, errflg)
 !$OMP end do
         endif
 
-        !--- aerosol interpolation
+!> - Call aerinterpol() to make aerosol interpolation
         if (Model%aero_in) then
 !$OMP do schedule (dynamic,1)
          do nb = 1, nblks
@@ -450,7 +460,7 @@ subroutine GFS_phys_time_vary_run (Data, Model, nthrds, errmsg, errflg)
 !$OMP end do
         endif
 
-        !--- ICCN interpolation
+!> - Call ciinterpol() to make IN and CCN data interpolation
         if (Model%iccn) then
 !$OMP do schedule (dynamic,1)
           do nb = 1, nblks
@@ -466,7 +476,7 @@ subroutine GFS_phys_time_vary_run (Data, Model, nthrds, errmsg, errflg)
 
 !$OMP end parallel
 
-        !--- repopulate specific time-varying sfc properties for AMIP/forecast runs
+!> - Call gcycle() to repopulate specific time-varying surface properties for AMIP/forecast runs
         if (Model%nscyc >  0) then
           if (mod(Model%kdt,Model%nscyc) == 1) THEN
             call gcycle (nblks, Model, Data(:)%Grid, Data(:)%Sfcprop, Data(:)%Cldprop)
@@ -500,5 +510,7 @@ subroutine GFS_phys_time_vary_run (Data, Model, nthrds, errmsg, errflg)
         endif
 
       end subroutine GFS_phys_time_vary_run
+!> @}
 
    end module GFS_phys_time_vary
+!> @}

physics/GFS_rad_time_vary.fv3.F90

@@ -10,14 +10,13 @@ module GFS_rad_time_vary
 
       contains
 
-!>\defgroup GFS_rad_time_vary GFS RRTMG Update 
-!!\ingroup RRTMG
-!! @{
 !! \section arg_table_GFS_rad_time_vary_init Argument Table
 !!
       subroutine GFS_rad_time_vary_init
       end subroutine GFS_rad_time_vary_init
 
+!>\defgroup mod_GFS_rad_time_vary GFS Radiation Time Update
+!> @{
 !> \section arg_table_GFS_rad_time_vary_run Argument Table
 !! | local_name        | standard_name                                          | long_name                                                                     | units    | rank |  type                 |   kind    | intent | optional |
 !! |-------------------|--------------------------------------------------------|-------------------------------------------------------------------------------|----------|------|-----------------------|-----------|--------|----------|
@@ -105,10 +104,10 @@ subroutine GFS_rad_time_vary_run (Model, Data, nthrds, errmsg, errflg)
          endif
 
       end subroutine GFS_rad_time_vary_run
+!> @}
 
 !> \section arg_table_GFS_rad_time_vary_finalize Argument Table
 !!
       subroutine GFS_rad_time_vary_finalize()
       end subroutine GFS_rad_time_vary_finalize
-!! @}
    end module GFS_rad_time_vary

physics/aer_cloud.F

@@ -158,10 +158,6 @@ end subroutine aer_cloud_init
 !!\param dpre_in          mass-weighted diameter of prexisting ice crystals (m)
 !!\param ccn_diagr8       array of supersaturations for CCN diagnostics (in-out)
 !!\param Ndropr8          Current droplet number concentration (\f$Kg^{-1}\f$)
-!!\param qc               Liquid water mixing ratio (Kg/Kg)
-!!\param use_average_v    .false. integrate over the updraft distribution. True: use the mean vertical velocity
-!!\param CCN_param        CCN activation parameterization. 1- Fountoukis and Nenes (2005), 2-Abdul_Razzak and Ghan (2002) (def = 2)
-!!\param IN_param         IN activation spectrum (default is 5)
 !!\param cdncr8           Activated cloud droplet number concentration (Kg-1)
 !!\param smaxliqr8        Maximum supersaturation w.r.t liquid during droplet activation
 !!\param incr8            Nucleated ice crystal concentration (Kg-1)
@@ -172,14 +168,20 @@ end subroutine aer_cloud_init
 !!\param Ncdepr8          Nucleated nc by deposition ice nucleation (Kg-1)
 !!\param Ncdhfr8          Nucleated nc by immersion in aerosol (Kg -1)
 !!\param sc_icer8         Critical saturation ratio in cirrus
-!!\param fdust_depr8      Fraction of deposition ice nuclei that are dust
 !!\param fdust_immr8      Fraction of immersion mixed-phase ice nuclei that are dust
+!!\param fdust_depr8      Fraction of deposition ice nuclei that are dust
 !!\param fdust_dhfr8      Fraction of immersion ice nuclei that are dust (not mixed-phase)
 !!\param nlimr8           Limiting ice nuclei concentration (m-3)
-
-!===================================================================================
-
-
+!!\param use_average_v    .false. integrate over the updraft distribution. True: use the mean vertical velocity
+!!\param CCN_param        CCN activation parameterization. 1- Fountoukis and Nenes (2005), 2-Abdul_Razzak and Ghan (2002) (def = 2)
+!!\param IN_param         IN activation spectrum (default is 5)
+!!\param fd_dust
+!!\param fd_soot
+!!\param pfrz_inc_r8
+!!\param sigma_nuc
+!!\param rhi_cell
+!!\param nccn
+!!
        subroutine aerosol_activate(tparc_in, pparc_in, sigwparc_in,     &
      & wparc_ls, Aer_Props, npre_in, dpre_in, ccn_diagr8, Ndropr8,      &
      & cdncr8, smaxliqr8, incr8, smaxicer8, nheticer8, INimmr8,         &

physics/cnvc90.f

@@ -12,7 +12,7 @@ module cnvc90
       subroutine cnvc90_init()
       end subroutine cnvc90_init
 
-!>\defgroup GFS_cnvc90 GFS cnvc90 Main
+!>\defgroup GFS_cnvc90 GFS Convective Cloud Diagnostics Module
 !> @{
 !! This module contains the calculation of fraction of convective cloud,
 !! pressure at bottom of convective cloud and at top of convective
@@ -37,7 +37,7 @@ end subroutine cnvc90_init
 !! | errmsg         | ccpp_error_message                                                    | error message for error handling in CCPP                | none  |    0 | character | len=*     | out    | F        |
 !! | errflg         | ccpp_error_flag                                                       | error flag for error handling in CCPP                   | flag  |    0 | integer   |           | out    | F        |
 !!
-!>\section gen_cnvc90_run GFS cnvc90_run General Algorithm
+! \section gen_cnvc_run GFS cnvc90_run General Algorithm
       SUBROUTINE cnvc90_run(CLSTP,IM,IX,RN,KBOT,KTOP,KM,PRSI,           &
      &                      ACV,ACVB,ACVT,CV,CVB,CVT,errmsg,errflg)