code cleanup

mzhangw · Jun 24, 2024 · 9b53b71 · 9b53b71
1 parent 8525a7e
commit 9b53b71
Show file tree

Hide file tree

Showing 25 changed files with 354 additions and 479 deletions.
diff --git a/physics/GWD/ugwpv1_gsldrag.F90 b/physics/GWD/ugwpv1_gsldrag.F90
@@ -62,9 +62,6 @@ module ugwpv1_gsldrag
 !>@brief The subroutine initializes the unified UGWP
 !> \section arg_table_ugwpv1_gsldrag_init Argument Table
 !! \htmlinclude ugwpv1_gsldrag_init.html
-!!
-! -----------------------------------------------------------------------
-!
     subroutine ugwpv1_gsldrag_init  (                                          &
                 me, master, nlunit, input_nml_file, logunit,                   &
                 fn_nml2, jdat, lonr, latr, levs, ak, bk, dtp,                  &

diff --git a/physics/Interstitials/UFS_SCM_NEPTUNE/GFS_ccpp_suite_sim_pre.F90 b/physics/Interstitials/UFS_SCM_NEPTUNE/GFS_ccpp_suite_sim_pre.F90
@@ -20,12 +20,7 @@ module GFS_ccpp_suite_sim_pre
   public GFS_ccpp_suite_sim_pre_run, load_ccpp_suite_sim
 contains
 
-  ! ######################################################################################
-  !
-  ! SUBROUTINE GFS_ccpp_suite_sim_pre_run
-  !
-  ! ######################################################################################
-!> \section arg_table_GFS_ccpp_suite_sim_pre_run
+!> \section arg_table_GFS_ccpp_suite_sim_pre_run Argument Table
 !! \htmlinclude GFS_ccpp_suite_sim_pre_run.html
 !! 
   subroutine GFS_ccpp_suite_sim_pre_run(do_ccpp_suite_sim, dtend, ntqv, dtidx, dtp,      &

diff --git a/physics/Interstitials/UFS_SCM_NEPTUNE/GFS_cloud_diagnostics.F90 b/physics/Interstitials/UFS_SCM_NEPTUNE/GFS_cloud_diagnostics.F90
@@ -28,7 +28,7 @@ module GFS_cloud_diagnostics
 !! This was bundled together with the prognostic cloud modules within the RRTMG implementation.
 !! For the RRTMGP implementation we propose to keep these diagnostics independent.
 !> @{
-!> \section arg_table_GFS_cloud_diagnostics_run
+!> \section arg_table_GFS_cloud_diagnostics_run Argument Table
 !! \htmlinclude GFS_cloud_diagnostics_run.html
 !!  
   subroutine GFS_cloud_diagnostics_run(nCol, nLev, iovr, iovr_rand, iovr_maxrand,        &

diff --git a/physics/Interstitials/UFS_SCM_NEPTUNE/GFS_physics_post.F90 b/physics/Interstitials/UFS_SCM_NEPTUNE/GFS_physics_post.F90
@@ -1,4 +1,3 @@
-! ###########################################################################################
 !> \file GFS_physics_post.F90
 !!
 !! This module contains GFS specific calculations (e.g. diagnostics) and suite specific
@@ -13,10 +12,7 @@ module GFS_physics_post
   public GFS_physics_post_run
 contains
 
-! ###########################################################################################
-! SUBROUTINE GFS_physics_post_run
-! ###########################################################################################
-!! \section arg_table_GFS_physics_post_run Argument Table
+!> \section arg_table_GFS_physics_post_run Argument Table
 !! \htmlinclude GFS_physics_post_run.html
 !!
   subroutine GFS_physics_post_run(nCol, nLev, ntoz, ntracp100, nprocess, nprocess_summed,   &
@@ -26,39 +22,39 @@ subroutine GFS_physics_post_run(nCol, nLev, ntoz, ntracp100, nprocess, nprocess_
 
     ! Inputs
     integer, intent(in) :: &
-         nCol,           & ! Horizontal dimension
-         nLev,           & ! Number of vertical layers
-         ntoz,           & ! Index for ozone mixing ratio
-         ntracp100,      & ! Number of tracers plus 100
-         nprocess,       & ! Number of processes that cause changes in state variables 
-         nprocess_summed,& ! Number of causes in dtidx per tracer summed for total physics tendency
-         ip_physics,     & ! Index for process in diagnostic tendency output
-         ip_photochem,   & ! Index for process in diagnostic tendency output
-         ip_prod_loss,   & ! Index for process in diagnostic tendency output
-         ip_ozmix,       & ! Index for process in diagnostic tendency output
-         ip_temp,        & ! Index for process in diagnostic tendency output
-         ip_overhead_ozone ! Index for process in diagnostic tendency output    
+         nCol,           & !< Horizontal dimension
+         nLev,           & !< Number of vertical layers
+         ntoz,           & !< Index for ozone mixing ratio
+         ntracp100,      & !< Number of tracers plus 100
+         nprocess,       & !< Number of processes that cause changes in state variables 
+         nprocess_summed,& !< Number of causes in dtidx per tracer summed for total physics tendency
+         ip_physics,     & !< Index for process in diagnostic tendency output
+         ip_photochem,   & !< Index for process in diagnostic tendency output
+         ip_prod_loss,   & !< Index for process in diagnostic tendency output
+         ip_ozmix,       & !< Index for process in diagnostic tendency output
+         ip_temp,        & !< Index for process in diagnostic tendency output
+         ip_overhead_ozone !< Index for process in diagnostic tendency output    
     integer, intent(in), dimension(:,:) :: &
-         dtidx             ! Bookkeeping indices for GFS diagnostic tendencies
+         dtidx             !< Bookkeeping indices for GFS diagnostic tendencies
     logical, intent(in) :: &
-         ldiag3d           ! Flag for 3d diagnostic fields
+         ldiag3d           !< Flag for 3d diagnostic fields
     logical, intent(in), dimension(:) :: &
-         is_photochem      ! Flags for photochemistry processes to sum
+         is_photochem      !< Flags for photochemistry processes to sum
 
     ! Inputs (optional)
     real(kind=kind_phys), intent(in), dimension(:,:), pointer, optional :: &
-         do3_dt_prd,     & ! Physics tendency: production and loss effect
-         do3_dt_ozmx,    & ! Physics tendency: ozone mixing ratio effect
-         do3_dt_temp,    & ! Physics tendency: temperature effect
-         do3_dt_ohoz       ! Physics tendency: overhead ozone effect
+         do3_dt_prd,     & !< Physics tendency: production and loss effect
+         do3_dt_ozmx,    & !< Physics tendency: ozone mixing ratio effect
+         do3_dt_temp,    & !< Physics tendency: temperature effect
+         do3_dt_ohoz       !< Physics tendency: overhead ozone effect
 
     ! Outputs
     real(kind=kind_phys), intent(inout), dimension(:,:,:) :: &
-         dtend             ! Diagnostic tendencies for state variables
+         dtend             !< Diagnostic tendencies for state variables
     character(len=*), intent(out) :: &
-         errmsg            ! CCPP error message
+         errmsg            !< CCPP error message
     integer, intent(out) :: &
-         errflg            ! CCPP error flag
+         errflg            !< CCPP error flag
 
     ! Locals
     integer :: idtend, ichem, iphys, itrac
@@ -123,6 +119,7 @@ subroutine GFS_physics_post_run(nCol, nLev, ntoz, ntracp100, nprocess, nprocess_
 
   contains
 
+!>
     subroutine sum_it(isum,itrac,sum_me)
       integer, intent(in) :: isum ! third index of dtend of summary process
       integer, intent(in) :: itrac ! tracer or state variable being summed

diff --git a/physics/Interstitials/UFS_SCM_NEPTUNE/GFS_rad_time_vary.fv3.F90 b/physics/Interstitials/UFS_SCM_NEPTUNE/GFS_rad_time_vary.fv3.F90
@@ -10,12 +10,9 @@ module GFS_rad_time_vary
 
       contains
 
-!>\defgroup mod_GFS_rad_time_vary GFS Radiation Time Update
-!! This module contains code related to GFS radiation setup.
-!> @{
+!> This module contains code related to GFS radiation setup.
 !> \section arg_table_GFS_rad_time_vary_timestep_init Argument Table
 !! \htmlinclude GFS_rad_time_vary_timestep_init.html
-!!
       subroutine GFS_rad_time_vary_timestep_init (lrseeds, rseeds,                     &
               lslwr, lsswr, isubc_lw, isubc_sw, icsdsw, icsdlw, cnx, cny, isc, jsc,    &
               imap, jmap, sec, kdt, imp_physics, imp_physics_zhao_carr, ipsd0, ipsdlim,&
@@ -97,6 +94,5 @@ subroutine GFS_rad_time_vary_timestep_init (lrseeds, rseeds,
          endif
 
       end subroutine GFS_rad_time_vary_timestep_init
-!> @}
 
    end module GFS_rad_time_vary
diff --git a/physics/Interstitials/UFS_SCM_NEPTUNE/GFS_rad_time_vary.scm.F90 b/physics/Interstitials/UFS_SCM_NEPTUNE/GFS_rad_time_vary.scm.F90
@@ -10,12 +10,9 @@ module GFS_rad_time_vary
 
       contains
 
-!>\defgroup mod_GFS_rad_time_vary GFS Radiation Time Update
-!! This module contains code related to GFS radiation setup.
-!> @{
+!> This module contains code related to GFS radiation setup.
 !> \section arg_table_GFS_rad_time_vary_timestep_init Argument Table
 !! \htmlinclude GFS_rad_time_vary_timestep_init.html
-!!
       subroutine GFS_rad_time_vary_timestep_init (lrseeds, rseeds,                     &
               lslwr, lsswr, isubc_lw, isubc_sw, icsdsw, icsdlw, cnx, cny, isc, jsc,    &
               imap, jmap, sec, kdt, imp_physics, imp_physics_zhao_carr, ipsd0, ipsdlim,&
@@ -97,6 +94,5 @@ subroutine GFS_rad_time_vary_timestep_init (lrseeds, rseeds,
          endif
 
       end subroutine GFS_rad_time_vary_timestep_init
-!> @}
 
    end module GFS_rad_time_vary
diff --git a/physics/Interstitials/UFS_SCM_NEPTUNE/GFS_radiation_surface.F90 b/physics/Interstitials/UFS_SCM_NEPTUNE/GFS_radiation_surface.F90
@@ -9,14 +9,11 @@ module GFS_radiation_surface
 
       contains
 
-!>\defgroup GFS_radiation_surface_mod GFS Radiation Surface Module
 !! This module contains calls to module_radiation_surface::setemis() to set up
 !! surface emissivity for LW radiation and to module_radiation_surface::setalb()
 !! to set up surface albedo for SW radiation.
-!> @{
 !> \section arg_table_GFS_radiation_surface_init Argument Table
 !! \htmlinclude GFS_radiation_surface_init.html
-!!
       subroutine GFS_radiation_surface_init (me, ialb, iems, semis_file, con_pi, errmsg, errflg)
 
       use module_radiation_surface, only: sfc_init
@@ -192,5 +189,4 @@ subroutine GFS_radiation_surface_run (                            &
 
       end subroutine GFS_radiation_surface_run
 
-!> @}
        end module GFS_radiation_surface
diff --git a/physics/Interstitials/UFS_SCM_NEPTUNE/GFS_rrtmgp_cloud_mp.F90 b/physics/Interstitials/UFS_SCM_NEPTUNE/GFS_rrtmgp_cloud_mp.F90
@@ -1,8 +1,5 @@
 !> \file GFS_rrtmgp_cloud_mp.F90
-!!
-!> \defgroup GFS_rrtmgp_cloud_mp GFS_rrtmgp_cloud_mp.F90
-!!
-!! \brief This module contains the interface for ALL cloud microphysics assumptions and 
+!! This module contains the interface for ALL cloud microphysics assumptions and 
 !! the RRTMGP radiation scheme. Specific details below in subroutines.
 !!
 module GFS_rrtmgp_cloud_mp
@@ -31,17 +28,11 @@ module GFS_rrtmgp_cloud_mp
 
 contains  
 
-!>\defgroup gfs_rrtmgp_cloud_mp_mod GFS RRTMGP Cloud MP Module
-!! \section arg_table_GFS_rrtmgp_cloud_mp_run
+!> \section arg_table_GFS_rrtmgp_cloud_mp_run Argument Table
 !! \htmlinclude GFS_rrtmgp_cloud_mp_run_html
-!!
-!> \ingroup GFS_rrtmgp_cloud_mp
-!!
 !! Here the cloud-radiative properties (optical-path, particle-size and sometimes cloud-
 !! fraction) are computed for cloud producing physics schemes (e.g GFDL-MP, Thompson-MP,
 !! MYNN-EDMF-pbl, GF-convective, and SAMF-convective clouds).
-!!
-!! \section GFS_rrtmgp_cloud_mp_run
   subroutine GFS_rrtmgp_cloud_mp_run(nCol, nLev, nTracers, ncnd, i_cldliq, i_cldice,     &
        i_cldrain, i_cldsnow, i_cldgrpl, i_cldtot, i_cldliq_nc, i_cldice_nc, i_twa, kdt,  &
        imfdeepcnv, imfdeepcnv_gf, imfdeepcnv_samf, doSWrad, doLWrad, effr_in, lmfshal,   &
@@ -310,8 +301,7 @@ subroutine GFS_rrtmgp_cloud_mp_run(nCol, nLev, nTracers, ncnd, i_cldliq, i_cldic
 
   end subroutine GFS_rrtmgp_cloud_mp_run
 
-!> \ingroup GFS_rrtmgp_cloud_mp
-!! Compute cloud radiative properties for Grell-Freitas convective cloud scheme.
+!> Compute cloud radiative properties for Grell-Freitas convective cloud scheme.
 !!                 (Adopted from module_SGSCloud_RadPre)
 !!  
 !! - The total convective cloud condensate is partitoned by phase, using temperature, into
@@ -390,8 +380,7 @@ subroutine cloud_mp_GF(nCol, nLev, lsmask, t_lay, p_lev, p_lay, qs_lay, relhum,
     enddo
   end subroutine cloud_mp_GF
 
-!> \ingroup GFS_rrtmgp_cloud_mp 
-!! Compute cloud radiative properties for MYNN-EDMF PBL cloud scheme.
+!> Compute cloud radiative properties for MYNN-EDMF PBL cloud scheme.
 !!                    (Adopted from module_SGSCloud_RadPre)
 !!
 !! - Cloud-fraction, liquid, and ice condensate mixing-ratios from MYNN-EDMF cloud scheme
@@ -463,8 +452,7 @@ subroutine cloud_mp_MYNN(nCol, nLev, lsmask, t_lay, p_lev, p_lay, qs_lay, relhum
   end subroutine cloud_mp_MYNN
 
 
-!> \ingroup GFS_rrtmgp_cloud_mp 
-!! Compute cloud radiative properties for SAMF convective cloud scheme.
+!> Compute cloud radiative properties for SAMF convective cloud scheme.
 !!
 !! - The total-cloud convective mixing-ratio is partitioned by phase into liquid/ice 
 !!   cloud properties. LWP and IWP are computed.
@@ -527,8 +515,7 @@ subroutine cloud_mp_SAMF(nCol, nLev, t_lay, p_lev, p_lay, qs_lay, relhum,
 
   end subroutine cloud_mp_SAMF
 
-!> \ingroup GFS_rrtmgp_cloud_mp 
-!! This routine computes the cloud radiative properties for a "unified cloud".
+!> This routine computes the cloud radiative properties for a "unified cloud".
 !! - "unified cloud" implies that the cloud-fraction is PROVIDED.
 !! - The cloud water path is computed for all provided cloud mixing-ratios and hydrometeors.
 !! - If particle sizes are provided, they are used. If not, default values are assigned.
@@ -658,8 +645,8 @@ subroutine cloud_mp_uni(nCol, nLev, nTracers, ncnd, i_cldliq, i_cldice, i_cldrai
     enddo       ! nLev
 
   end subroutine cloud_mp_uni
-!> \ingroup GFS_rrtmgp_cloud_mp 
-!! This routine computes the cloud radiative properties for the Thompson cloud micro-
+
+!> This routine computes the cloud radiative properties for the Thompson cloud micro-
 !! physics scheme.
 !!
 !! - The cloud water path is computed for all provided cloud mixing-ratios and hydrometeors.
@@ -791,8 +778,7 @@ subroutine cloud_mp_thompson(nCol, nLev, nTracers, ncnd, i_cldliq, i_cldice, i_c
 
   end subroutine cloud_mp_thompson
 
-!> \ingroup GFS_rrtmgp_cloud_mp 
-!! This function computes the cloud-fraction following.
+!> This function computes the cloud-fraction following.
 !! Xu-Randall(1996) A Semiempirical Cloudiness Parameterization for Use in Climate Models
 !! https://doi.org/10.1175/1520-0469(1996)053<3084:ASCPFU>2.0.CO;2
 !!
@@ -835,11 +821,8 @@ function cld_frac_XuRandall(p_lay, qs_lay, relhum, cld_mr, alpha)
     return
   end function
 
-  ! ######################################################################################
-  ! This routine is a wrapper to update the Thompson effective particle sizes used by the
-  ! RRTMGP radiation scheme.
-  !
-  ! ######################################################################################
+  !> This routine is a wrapper to update the Thompson effective particle sizes used by the
+  !! RRTMGP radiation scheme.
   subroutine cmp_reff_Thompson(nLev, nCol, i_cldliq, i_cldice, i_cldsnow, i_cldice_nc,   &
        i_cldliq_nc, i_twa, q_lay, p_lay, t_lay, tracer, con_eps, con_rd, ltaerosol,      &
        mraerosol, lsmask, effrin_cldliq, effrin_cldice, effrin_cldsnow)

diff --git a/physics/Interstitials/UFS_SCM_NEPTUNE/GFS_rrtmgp_post.F90 b/physics/Interstitials/UFS_SCM_NEPTUNE/GFS_rrtmgp_post.F90
@@ -1,8 +1,5 @@
 !> \file GFS_rrtmgp_post.F90
-!!
-!> \defgroup GFS_rrtmgp_post GFS_rrtmgp_post.F90
-!!
-!! \brief RRTMGP post-processing routine.
+!! RRTMGP post-processing routine.
 !!
 module GFS_rrtmgp_post
   use machine,                   only: kind_phys
@@ -15,23 +12,16 @@ module GFS_rrtmgp_post
   public GFS_rrtmgp_post_run
 
 contains
-  ! ######################################################################################## 
-!>\defgroup gfs_rrtmgp_post_mod GFS RRTMGP Post Module
-!> \section arg_table_GFS_rrtmgp_post_run
+
+!> \section arg_table_GFS_rrtmgp_post_run Argument Table
 !! \htmlinclude GFS_rrtmgp_post.html
-!!
-!! \ingroup GFS_rrtmgp_post
-!!
-!! \brief The all-sky radiation tendency is computed, the clear-sky tendency is computed 
+!!The all-sky radiation tendency is computed, the clear-sky tendency is computed 
 !! if requested.
 !!
 !! RRTMGP surface and TOA fluxes are copied to fields that persist between radiation/physics
 !! calls.
 !! 
 !! (optional) Save additional diagnostics.
-!!
-!! \section GFS_rrtmgp_post_run
-  ! ######################################################################################## 
   subroutine GFS_rrtmgp_post_run (nCol, nLev, nDay, iSFC, iTOA, idxday, doLWrad, doSWrad,  &
        do_lw_clrsky_hr, do_sw_clrsky_hr, save_diag, fhlwr, fhswr, sfc_alb_nir_dir,         &
        sfc_alb_nir_dif, sfc_alb_uvvis_dir, sfc_alb_uvvis_dif, p_lev, tsfa, coszen, coszdg, &