save progress

physics/CONV/SAMF/samfaerosols.F

@@ -1,3 +1,5 @@
+!>\file samfaerosols.F
+!!
       module samfcnv_aerosols
 
       implicit none

physics/CONV/SAS/shalcnv.F

@@ -1,16 +1,12 @@
-!> \defgroup SASHAL Mass-Flux Shallow Convection
-!! @{
-!!  \brief The Mass-Flux shallow convection scheme parameterizes the effect of shallow convection on the environment much like the \ref SAS scheme with a few key modifications. Perhaps most importantly, no quasi-equilibrium assumption is necessary since the shallow cloud base mass flux is parameterized from the surface buoyancy flux. Further, there are no convective downdrafts, the entrainment rate is greater than for deep convection, and the shallow convection is limited to not extend over the level where \f$p=0.7p_{sfc}\f$.
+!> \file shalcnv.F
+!!  Contains the entire SAS shallow convection scheme.
+
+!>  \brief The Mass-Flux shallow convection scheme parameterizes the effect of shallow convection on the environment much like the \ref SAS scheme with a few key modifications. Perhaps most importantly, no quasi-equilibrium assumption is necessary since the shallow cloud base mass flux is parameterized from the surface buoyancy flux. Further, there are no convective downdrafts, the entrainment rate is greater than for deep convection, and the shallow convection is limited to not extend over the level where \f$p=0.7p_{sfc}\f$.
 !!
 !!  This scheme was designed to replace the previous eddy-diffusivity approach to shallow convection with a mass-flux based approach as it is used for deep convection. Differences between the shallow and deep SAS schemes are presented in Han and Pan (2011) \cite han_and_pan_2011 . Like the deep scheme, it uses the working concepts put forth in Arakawa and Schubert (1974) \cite arakawa_and_schubert_1974 but includes modifications and simplifications from Grell (1993) \cite grell_1993 such as only one cloud type (the deepest possible, up to \f$p=0.7p_{sfc}\f$), rather than a spectrum based on cloud top heights or assumed entrainment rates, although it assumes no convective downdrafts. It contains many modifications associated with deep scheme as discussed in Han and Pan (2011) \cite han_and_pan_2011 , including the calculation of cloud top, a greater CFL-criterion-based maximum cloud base mass flux, and the inclusion of convective overshooting.
 !!
 !!  \section diagram_sashal Calling Hierarchy Diagram
 !!  \image html Shallow_SAS_Flowchart.png "Diagram depicting how the SAS shallow convection scheme is called from the GSM physics time loop" height=2cm
-!!  \section intraphysics Intraphysics Communication
-!!  This space is reserved for a description of how this scheme uses information from other scheme types and/or how information calculated in this scheme is used in other scheme types.
-
-!> \file shalcnv.F
-!!  Contains the entire SAS shallow convection scheme.
       module shalcnv
 
       implicit none
@@ -90,7 +86,7 @@ end subroutine shalcnv_init
 !! \section arg_table_shalcnv_run Argument Table
 !! \htmlinclude shalcnv_run.html
 !!
-!!  @{
+!>  @{
       subroutine shalcnv_run(                                           &
      &     grav,cp,hvap,rv,fv,t0c,rd,cvap,cliq,eps,epsm1,               &
      &     im,km,jcap,delt,delp,prslp,psp,phil,qlc,qli,                 &
@@ -1340,4 +1336,3 @@ end subroutine shalcnv_run
 
       end module shalcnv
 !> @}
-!! @}

physics/CONV/progsigma_calc.f90

@@ -1,3 +1,8 @@
+!>\file progsigma_calc.f90
+!! This file contains the subroutine that calculates the prognostic
+!! updraft area fraction that is used for closure computations in
+!! saSAS deep and shallow convection, based on a moisture budget
+!! as described in Bengtsson et al. 2022 \cite Bengtsson_2022.
       module progsigma
 
         implicit none
@@ -6,12 +11,6 @@ module progsigma
 
       contains
 
-!>\file progsigma_calc.f90
-!! This file contains the subroutine that calculates the prognostic
-!! updraft area fraction that is used for closure computations in 
-!! saSAS deep and shallow convection, based on a moisture budget
-!! as described in Bengtsson et al. 2022 \cite Bengtsson_2022.
-
 !>\ingroup SAMFdeep
 !>\ingroup SAMF_shal
 !> This subroutine computes a prognostic updraft area fraction

physics/GWD/drag_suite.F90

@@ -6,9 +6,7 @@ module drag_suite
 
       contains
 
-!> \defgroup gfs_drag_suite_mod GSL drag_suite Module
 !> This module contains the CCPP-compliant GSL orographic gravity wave drag scheme.
-!> @{
 !!
 !> \brief This subroutine initializes the orographic gravity wave drag scheme.
 !!

physics/GWD/ugwpv1_gsldrag_post.F90

@@ -5,7 +5,6 @@ module ugwpv1_gsldrag_post
 contains
 
 !>\defgroup ugwpv1_gsldrag_post ugwpv1_gsldrag Scheme Post
-!! @{
 !> \section arg_table_ugwpv1_gsldrag_post_run Argument Table
 !! \htmlinclude ugwpv1_gsldrag_post_run.html
 !!
@@ -141,5 +140,4 @@ subroutine ugwpv1_gsldrag_post_run ( im, levs, ldiag_ugwp,       &
 !=====================================================================
       end subroutine ugwpv1_gsldrag_post_run      
 
-!! @}
 end module ugwpv1_gsldrag_post

physics/PBL/MYNN_EDMF/module_bl_mynn.F90

@@ -351,11 +351,11 @@ MODULE module_bl_mynn
 
 ! ==================================================================
 !>\ingroup gp_mynnedmf
-!! This subroutine is the GSD MYNN-EDNF PBL driver routine,which
+!! This subroutine is the MYNN-EDNF PBL driver routine,which
 !! encompassed the majority of the subroutines that comprise the 
 !! procedures that ultimately solve for tendencies of 
 !! \f$U, V, \theta, q_v, q_c, and q_i\f$.
-!!\section gen_mynn_bl_driver GSD mynn_bl_driver General Algorithm
+!!\section gen_mynn_bl_driver  mynn_bl_driver General Algorithm
 !> @{
   SUBROUTINE mynn_bl_driver(            &
        &initflag,restart,cycling,       &
@@ -1508,7 +1508,7 @@ END SUBROUTINE mynn_bl_driver
 !>\ingroup gp_mynnedmf
 !! This subroutine initializes the mixing length, TKE, \f$\theta^{'2}\f$,
 !! \f$q^{'2}\f$, and \f$\theta^{'}q^{'}\f$.
-!!\section gen_mym_ini GSD MYNN-EDMF mym_initialize General Algorithm 
+!!\section gen_mym_ini  MYNN-EDMF mym_initialize General Algorithm 
 !> @{
   SUBROUTINE  mym_initialize (                                & 
        &            kts,kte,xland,                            &
@@ -1712,7 +1712,7 @@ END SUBROUTINE mym_initialize
 !!\param gh      \f$G_H\f$ divided by \f$L^{2}/q^{2}\f$ (\f$s^{-2}\f$)
 !!\param sm      stability function for momentum, at Level 2
 !!\param sh      stability function for heat, at Level 2
-!!\section gen_mym_level2 GSD MYNN-EDMF mym_level2 General Algorithm
+!!\section gen_mym_level2  MYNN-EDMF mym_level2 General Algorithm
 !! @ {
   SUBROUTINE  mym_level2 (kts,kte,                &
        &            dz,                           &
@@ -2599,7 +2599,7 @@ END SUBROUTINE boulac_length
 !>\ingroup gp_mynnedmf
 !! This subroutine calculates the vertical diffusivity coefficients and the 
 !! production terms for the turbulent quantities.      
-!>\section gen_mym_turbulence GSD mym_turbulence General Algorithm
+!>\section gen_mym_turbulence  mym_turbulence General Algorithm
 !! Two subroutines mym_level2() and mym_length() are called within this
 !!subrouine to collect variable to carry out successive calculations:
 !! - mym_level2() calculates the level 2 nondimensional wind shear \f$G_M\f$
@@ -5512,7 +5512,7 @@ end subroutine tridiag3
 !!the TKE-method more during stable conditions (PBLH < 400 m).
 !!A variable tke threshold (TKEeps) is used since no hard-wired
 !!value could be found to work best in all conditions.
-!>\section gen_get_pblh  GSD get_pblh General Algorithm
+!>\section gen_get_pblh  get_pblh General Algorithm
 !> @{
   SUBROUTINE GET_PBLH(KTS,KTE,zi,thetav1D,qke1D,zw1D,dz1D,landsea,kzi)
 

physics/PBL/SATMEDMF/satmedmfvdif.F

@@ -42,7 +42,6 @@ subroutine satmedmfvdif_init (satmedmf,
       end subroutine satmedmfvdif_init
 
 !> \defgroup satmedmf GFS Scale-aware TKE-based Moist Eddy-Diffusivity Mass-flux (TKE-EDMF) Scheme Module 
-!! @{
 !! \brief This subroutine contains all of the logic for the
 !! scale-aware TKE-based moist eddy-diffusion mass-flux (TKE-EDMF) scheme.
 !!
@@ -60,7 +59,6 @@ end subroutine satmedmfvdif_init
 !! -# A mass-flux approach is also used to represent the stratocumulus-top-induced turbulence
 !! (mfscu.f).
 !! \section detail_satmedmfvidf GFS satmedmfvdif Detailed Algorithm 
-!> @{
       subroutine satmedmfvdif_run(im,km,ntrac,ntcw,ntiw,ntke,           &
      &     grav,rd,cp,rv,hvap,hfus,fv,eps,epsm1,                        &
      &     dv,du,tdt,rtg,u1,v1,t1,q1,swh,hlw,xmu,garea,                 &
@@ -1542,6 +1540,5 @@ subroutine satmedmfvdif_run(im,km,ntrac,ntcw,ntiw,ntke,           &
 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
       return
       end subroutine satmedmfvdif_run
-!> @}
 
       end module satmedmfvdif