scidoc update

mzhangw · Aug 16, 2024 · 9085a24 · 9085a24
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diff --git a/physics/CONV/SAMF/samfshalcnv.f b/physics/CONV/SAMF/samfshalcnv.f
@@ -1,6 +1,7 @@
 !>  \file samfshalcnv.f
-!!  This file contains the Scale-Aware mass flux Shallow Convection scheme.
+!!
 
+!>  This module contains the Scale-Aware mass flux Shallow Convection scheme.
       module samfshalcnv
 
       use samfcnv_aerosols, only : samfshalcnv_aerosols

diff --git a/physics/GWD/cires_ugwp_initialize.F90 b/physics/GWD/cires_ugwp_initialize.F90
@@ -6,7 +6,7 @@
 !  init gw-background dissipation
 !===============================    
 
-!> Define constants
+!> This module contains UGWP v0 initialization schemes 
     module ugwp_common_v0
 !
      use machine,  only: kind_phys
@@ -95,6 +95,7 @@ end subroutine init_global_gwdis_v0
 !    ugwpv0_oro_init
 !
 !=========================================================================
+!> This module contains orographic wave source schemes for UGWP v0.
      module ugwpv0_oro_init
 
      use ugwp_common_v0, only : bnv2min, grav, grcp, fv, grav, cpd, grcp, pi

diff --git a/physics/GWD/ugwp_driver_v0.F b/physics/GWD/ugwp_driver_v0.F
@@ -1,4 +1,6 @@
 !>\file ugwp_driver_v0.F
+
+!> This module contains the UGWP v0 driver module
       module ugwp_driver_v0
       use cires_orowam2017
       contains
@@ -9,7 +11,7 @@ module ugwp_driver_v0
 !
 !=====================================================================
 !>\ingroup cires_ugwp_run_mod
-!>\defgroup ugwp_driverv0_mod GFS UGWP V0 Driver Module
+!>\defgroup ugwp_driverv0_mod UGWP V0 Driver Module
 !! This is the CIRES UGWP V0 driver module
 !!
 !! Note for the sub-grid scale orography scheme in UGWP-v0: Due to degraded forecast

diff --git a/physics/GWD/ugwpv1_gsldrag_post.F90 b/physics/GWD/ugwpv1_gsldrag_post.F90
@@ -1,5 +1,6 @@
 !>  \file ugwpv1_gsldrag_post.F90
-!! This file contains
+
+!> This module contains code to be executed after the UGWP v1 scheme
 module ugwpv1_gsldrag_post
 
 contains

diff --git a/physics/MP/GFDL/module_gfdl_cloud_microphys.F90 b/physics/MP/GFDL/module_gfdl_cloud_microphys.F90
@@ -27,6 +27,7 @@
 ! =======================================================================
 !>\defgroup mod_gfdl_cloud_mp GFDL Cloud MP modules
 !!\ingroup gfdlmp
+
 !> This module contains the column GFDL Cloud microphysics scheme.
 module gfdl_cloud_microphys_mod
 

diff --git a/physics/MP/NSSL/mp_nssl.F90 b/physics/MP/NSSL/mp_nssl.F90
@@ -3,7 +3,8 @@
 
 
 !>\defgroup nsslmp NSSL MP Module
-!! This module contains the front end to NSSL microphysics scheme.
+
+!> This module contains the front end to NSSL microphysics scheme.
 module mp_nssl
 
     use machine, only : kind_phys

diff --git a/physics/MP/Thompson/mp_thompson.F90 b/physics/MP/Thompson/mp_thompson.F90
@@ -3,7 +3,8 @@
 
 
 !>\defgroup aathompson Aerosol-Aware Thompson MP Module
-!! This module contains the aerosol-aware Thompson microphysics scheme.
+
+!> This module contains the aerosol-aware Thompson microphysics scheme.
 module mp_thompson
 
       use mpi_f08

diff --git a/physics/MP/Thompson/mp_thompson_post.F90 b/physics/MP/Thompson/mp_thompson_post.F90
@@ -1,3 +1,7 @@
+!> \file mp_thompson_post.F90
+!!
+
+!>This module contain the post processing of Thompson microphysics
 module mp_thompson_post
 
    use mpi_f08
@@ -15,7 +19,7 @@ module mp_thompson_post
 
 contains
 
-!! \section arg_table_mp_thompson_post_init Argument Table
+!> \section arg_table_mp_thompson_post_init Argument Table
 !! \htmlinclude mp_thompson_post_init.html
 !!
    subroutine mp_thompson_post_init(ttendlim, errmsg, errflg)
@@ -125,7 +129,7 @@ subroutine mp_thompson_post_run(ncol, nlev, tgrs_save, tgrs, prslk, dtp, ttendli
 
    end subroutine mp_thompson_post_run
 
-!! \section arg_table_mp_thompson_post_finalize Argument Table
+!> \section arg_table_mp_thompson_post_finalize Argument Table
 !! \htmlinclude mp_thompson_post_finalize.html
 !!
    subroutine mp_thompson_post_finalize(errmsg, errflg)

diff --git a/physics/MP/Thompson/mp_thompson_pre.F90 b/physics/MP/Thompson/mp_thompson_pre.F90
@@ -1,8 +1,9 @@
 !>\file mp_thompson_pre.F90
 !!
 
-! CCPP license goes here, as well as further documentation
 !>\ingroup aathompson
+
+!> This module contains the pre-processing of Thompson cloud microphysics
 module mp_thompson_pre
 
       use machine, only : kind_phys

diff --git a/physics/PBL/SATMEDMF/mfscuq.f b/physics/PBL/SATMEDMF/mfscuq.f
@@ -1,5 +1,7 @@
 !>\file mfscuq.f
-!! This file contains the mass flux and downdraft parcel preperties
+!!
+
+!> This module contains the mass flux and downdraft parcel properties
 !! parameterization for stratocumulus-top-driven turbulence (updated version).
       module mfscuq_mod
       contains

diff --git a/physics/PBL/SATMEDMF/satmedmfvdifq.F b/physics/PBL/SATMEDMF/satmedmfvdifq.F
@@ -1,8 +1,8 @@
 !> \file satmedmfvdifq.F
-!! This file contains the CCPP-compliant SATMEDMF scheme (updated version) which
+
+!> This file contains the CCPP-compliant SATMEDMF scheme (updated version) which
 !! computes subgrid vertical turbulence mixing using scale-aware TKE-based moist
 !! eddy-diffusion mass-flux (TKE-EDMF) parameterization (by Jongil Han).
-
       module satmedmfvdifq
       use mfpbltq_mod
       use tridi_mod

diff --git a/physics/PBL/tridi.f b/physics/PBL/tridi.f
@@ -1,5 +1,8 @@
 !>\file tridi.f
 !! These subroutines are originally internal subroutines in moninedmf.f
+
+!> This module contains routine to compute tridiagonal matrix elements for TKE, heat, moist
+!! and momentum
       module tridi_mod
       contains
 

diff --git a/physics/Radiation/RRTMG/rrtmg_lw_cloud_optics.F90 b/physics/Radiation/RRTMG/rrtmg_lw_cloud_optics.F90
@@ -1,24 +1,25 @@
 !>\file rrtmg_lw_cloud_optics.F90
 !!
 
+!>This module contains the cloud optics property module for RRTMG-LW
 module mo_rrtmg_lw_cloud_optics
   use machine,          only: kind_phys
   use mersenne_twister, only: random_setseed, random_number, random_stat
 
   implicit none
 
-  !< Parameter used for RRTMG cloud-optics
+  !> Parameter used for RRTMG cloud-optics
   integer,parameter :: &
        nBandsLW_RRTMG = 16
-  !< ipat is bands index for ebert & curry ice cloud (for iflagice=1)
+  !> ipat is bands index for ebert & curry ice cloud (for iflagice=1)
   integer,dimension(nBandsLW_RRTMG),parameter :: &
        ipat = (/ 1, 2, 3, 3, 3, 4, 4, 4, 5, 5, 5, 5, 5, 5, 5, 5 /)
   real(kind_phys), parameter :: &
        absrain  = 0.33e-3, & !< Rain drop absorption coefficient \f$(m^{2}/g)\f$ .
        abssnow0 = 1.5,     & !< Snow flake absorption coefficient (micron), fu coeff
        abssnow1 = 2.34e-3    !< Snow flake absorption coefficient \f$(m^{2}/g)\f$, ncar coef
 
-  !< Reset diffusivity angle for Bands 2-3 and 5-9 to vary (between 1.50
+  !> Reset diffusivity angle for Bands 2-3 and 5-9 to vary (between 1.50
   !! and 1.80) as a function of total column water vapor.  the function
   !! has been defined to minimize flux and cooling rate errors in these bands
   !! over a wide range of precipitable water values.
@@ -35,7 +36,7 @@ module mo_rrtmg_lw_cloud_optics
        diffusivityHigh  = 1.80, & !< Maximum diffusivity angle for bands 2-3 and 5-9
        diffusivityB1410 = 1.66    !< Diffusivity for bands 1, 4, and 10
 
-  !< RRTMG LW cloud property coefficients
+  !> RRTMG LW cloud property coefficients
   real(kind_phys) , dimension(58,nBandsLW_RRTMG),parameter :: &
        absliq1 = reshape(source=(/ &
        1.64047e-03, 6.90533e-02, 7.72017e-02, 7.78054e-02, 7.69523e-02, & !1

diff --git a/physics/Radiation/RRTMG/rrtmg_sw_cloud_optics.F90 b/physics/Radiation/RRTMG/rrtmg_sw_cloud_optics.F90
@@ -1,6 +1,7 @@
 !>\file rrtmg_sw_cloud_optics.F90
 !!
 
+!> This module contains the cloud optics property module for RRTMG-SW
 module mo_rrtmg_sw_cloud_optics
   use machine,          only: kind_phys
   use mersenne_twister, only: random_setseed, random_number, random_stat

diff --git a/physics/Radiation/RRTMGP/rrtmgp_aerosol_optics.F90 b/physics/Radiation/RRTMGP/rrtmgp_aerosol_optics.F90
@@ -1,6 +1,7 @@
 !>\file rrtmgp_aerosol_optics.F90
 !!
 
+!> This module contains aerosol optics properties for RRTMGP
 module rrtmgp_aerosol_optics
   use machine,                   only: kind_phys
   use radiation_tools,           only: check_error_msg

diff --git a/physics/Radiation/RRTMGP/rrtmgp_lw_cloud_optics.F90 b/physics/Radiation/RRTMGP/rrtmgp_lw_cloud_optics.F90
@@ -1,10 +1,11 @@
 !> \file rrtmgp_lw_cloud_optics.F90
-!! This module contains two routines: The first initializes data and functions
+!!
+
+!> This module contains two routines: The first initializes data and functions
 !! needed to compute the longwave cloud radiative properteis in RRTMGP. The second routine
 !! is a ccpp scheme within the "radiation loop", where the shortwave optical prperties
 !! (optical-depth, single-scattering albedo, asymmetry parameter) are computed for ALL
 !! cloud types visible to RRTMGP.
-!!
 module rrtmgp_lw_cloud_optics
   use machine,                  only: kind_phys
   use mo_rte_kind,              only: wl

diff --git a/physics/Radiation/RRTMGP/rrtmgp_lw_gas_optics.F90 b/physics/Radiation/RRTMGP/rrtmgp_lw_gas_optics.F90
@@ -1,9 +1,10 @@
 !> \file rrtmgp_lw_gas_optics.F90 
-!! This module contains two routines: One to initialize the k-distribution data
+!!
+
+!> This module contains two routines: One to initialize the k-distribution data
 !! and functions needed to compute the longwave gaseous optical properties in RRTMGP.
 !! The second routine is a ccpp scheme within the "radiation loop", where the longwave
 !! optical prperties (optical-depth) are computed for clear-sky conditions (no aerosols).
-!!                                                
 module rrtmgp_lw_gas_optics
   use machine,               only: kind_phys
   use mo_rte_kind,           only: wl

diff --git a/physics/Radiation/RRTMGP/rrtmgp_lw_main.F90 b/physics/Radiation/RRTMGP/rrtmgp_lw_main.F90
@@ -1,6 +1,7 @@
 !> \file rrtmgp_lw_main.F90
 !! This file contains the longwave RRTMGP radiation scheme.
-!!
+
+!> This module contains the RRTMGP-LW radiation scheme
 module rrtmgp_lw_main
   use mpi_f08
   use machine,                only: kind_phys, kind_dbl_prec

diff --git a/physics/Radiation/RRTMGP/rrtmgp_sampling.F90 b/physics/Radiation/RRTMGP/rrtmgp_sampling.F90
@@ -11,8 +11,8 @@
 !    BSD 3-clause license, see http://opensource.org/licenses/BSD-3-Clause
 ! -------------------------------------------------------------------------------------------------
 !
-! This module provides a simple implementation of sampling for the
-!   Monte Carlo Independent Pixel Approximation (McICA, doi:10.1029/2002jd003322)
+!> This module provides a simple implementation of sampling for the
+!!   Monte Carlo Independent Pixel Approximation (McICA, doi:10.1029/2002jd003322)
 ! Cloud optical properties, defined by band and assumed homogenous within each cell (column/layer),
 !   are randomly sampled to preserve the mean cloud fraction and one of several possible overlap assumptions
 ! Users supply random numbers with order ngpt,nlay,ncol

diff --git a/physics/Radiation/RRTMGP/rrtmgp_sw_cloud_optics.F90 b/physics/Radiation/RRTMGP/rrtmgp_sw_cloud_optics.F90
@@ -1,6 +1,7 @@
 !>\file rrtmgp_sw_cloud_optics.F90
 !!
 
+!> This module contains the cloud optics properties calculation for RRTMGP-SW
 module rrtmgp_sw_cloud_optics
   use machine,                  only: kind_phys
   use mo_rte_kind,              only: wl

diff --git a/physics/Radiation/RRTMGP/rrtmgp_sw_gas_optics.F90 b/physics/Radiation/RRTMGP/rrtmgp_sw_gas_optics.F90
@@ -1,7 +1,8 @@
 !> \file rrtmgp_sw_gas_optics.F90
-!! This module contains a routine to initialize the k-distribution data used
-!! by the RRTMGP shortwave radiation scheme.
+!!
 
+!> This module contains a routine to initialize the k-distribution data used
+!! by the RRTMGP shortwave radiation scheme.
 module rrtmgp_sw_gas_optics
   use machine,                only: kind_phys
   use mo_rte_kind,            only: wl

diff --git a/physics/Radiation/RRTMGP/rrtmgp_sw_main.F90 b/physics/Radiation/RRTMGP/rrtmgp_sw_main.F90
@@ -1,6 +1,7 @@
 !>\file rrtmgp_sw_main.F90
 !!
 
+!> This module contain the RRTMGP-SW radiation scheme
 module rrtmgp_sw_main
   use mpi_f08
   use machine,                only: kind_phys, kind_dbl_prec

diff --git a/physics/Radiation/radiation_tools.F90 b/physics/Radiation/radiation_tools.F90
@@ -1,6 +1,7 @@
 !>\file radiation_tools.F90
 !!
 
+!> This module contains tools for radiation
 module radiation_tools
   use machine, only: &
        kind_phys                   ! Working type

diff --git a/physics/SFC_Layer/MYNN/mynnsfc_wrapper.F90 b/physics/SFC_Layer/MYNN/mynnsfc_wrapper.F90
@@ -1,6 +1,7 @@
 !> \file mynnsfc_wrapper.F90
-!!  Contains all of the code related to running the MYNN surface layer scheme
+!!
 
+!>  This Model ontains all of the code related to running the MYNN surface layer scheme
       MODULE mynnsfc_wrapper
 
           USE module_sf_mynn

diff --git a/physics/SFC_Layer/UFS/sfc_diag.f b/physics/SFC_Layer/UFS/sfc_diag.f
@@ -1,11 +1,11 @@
 !>  \file sfc_diag.f
 !!  This file contains the land surface diagnose calculation scheme.
 
+!> This module contains the land surface diagnose calcualtion
       module sfc_diag
       contains
 
 !> \defgroup sfc_diag_mod GFS sfc_diag module
-!! This module contains the land surface diagose calculation.
 !! \section arg_table_sfc_diag_run Argument Table
 !! \htmlinclude sfc_diag_run.html
 !!

diff --git a/physics/SFC_Layer/UFS/sfc_diag_post.F90 b/physics/SFC_Layer/UFS/sfc_diag_post.F90
@@ -1,12 +1,12 @@
 !> \file sfc_diag_post.F90
 !!  Contains code related to the surface diagnostic scheme.
 
+!> This module contains code related to the surface diagnostic scheme.
       module sfc_diag_post
 
       contains
 
 !>\defgroup sfc_diag_post_mod GFS sfc_diag_post Module
-!! This module contains code related to the surface diagnostic scheme.
 !> @{
 #if 0
 !> \section arg_table_sfc_diag_post_run Argument Table

diff --git a/physics/SFC_Layer/UFS/sfc_nst_post.f90 b/physics/SFC_Layer/UFS/sfc_nst_post.f90
@@ -1,6 +1,7 @@
 !>  \file sfc_nst_post.f90
-!!  This file contains code to be executed after the GFS NSST model.
+!!  This file contains code to be executed after the near-surface sea temperature scheme.
 
+!> This module contains code to be executed after the near-surface sea temperature scheme
 module sfc_nst_post
 
   use machine               , only : kind_phys, kp => kind_phys

diff --git a/physics/SFC_Layer/UFS/sfc_nst_pre.f90 b/physics/SFC_Layer/UFS/sfc_nst_pre.f90
@@ -1,6 +1,7 @@
 !>  \file sfc_nst_pre.f90
-!!  This file contains preparation for the GFS NSST model.
+!!  This file contains preparation for the near-surface sea temperature scheme.
 
+!> This module contain preparation for the near-surface sea temperature scheme 
 module sfc_nst_pre
 
   use machine               , only : kind_phys
@@ -11,7 +12,7 @@ module sfc_nst_pre
 
 contains
 
-  !> \defgroup GFS_NSST_PRE GFS Near-Surface Sea Temperature Pre
+  !> \defgroup GFS_NSST_PRE Near-Surface Sea Temperature Pre
   !!
   !! The NSST scheme is one of the three schemes used to represent the
   !! surface in the GFS physics suite. The other two are the Noah land

diff --git a/physics/SFC_Models/Land/Noah/namelist_soilveg.f b/physics/SFC_Models/Land/Noah/namelist_soilveg.f
@@ -1,6 +1,8 @@
 !>\file namelist_soilveg.f
 
 !>\ingroup Noah_LSM
+
+!> This module contains namelist options for Noah LSM
       module namelist_soilveg
       implicit none
       save

diff --git a/physics/SFC_Models/Land/Noah/sflx.f b/physics/SFC_Models/Land/Noah/sflx.f
@@ -1,5 +1,7 @@
 !>\file sflx.f
-!! This file is the entity of GFS Noah LSM Model(Version 2.7).
+!!
+
+!> This module contains the entity of GFS Noah LSM Model(Version 2.7).
       module sflx
       contains
 !>\ingroup Noah_LSM

diff --git a/physics/SFC_Models/Land/Noah/surface_perturbation.F90 b/physics/SFC_Models/Land/Noah/surface_perturbation.F90
@@ -3,6 +3,7 @@
 !! albedo and vegetation fraction perturbations.
 
 !>\defgroup gfs_sfcpert GFS Surface Perturbation Module
+
 !> This module contains routines used in the percentile matching algorithm for the
 !! albedo and vegetation fraction perturbations.
 module surface_perturbation

diff --git a/physics/SFC_Models/Land/Noahmp/noahmp_tables.f90 b/physics/SFC_Models/Land/Noahmp/noahmp_tables.f90
@@ -2,7 +2,8 @@
 !!  This file contains Fortran versions of the data tables included with NoahMP in mptable.tbl, soilparm.tbl, and genparm.tbl. 
 
 !> \ingroup NoahMP_LSM
-!! \brief Data from MPTABLE.TBL, SOILPARM.TBL, GENPARM.TBL for NoahMP
+
+!> brief Data from MPTABLE.TBL, SOILPARM.TBL, GENPARM.TBL for NoahMP
 !!
 !! Note that a subset of the data in the *.TBL files is represented in this file. For example,
 !! only the data in the noah_mp_modis_parameters section of MPTABLE.TBL and the STAS section of

diff --git a/physics/SFC_Models/Land/RUC/namelist_soilveg_ruc.F90 b/physics/SFC_Models/Land/RUC/namelist_soilveg_ruc.F90
@@ -1,6 +1,7 @@
 !>\file namelist_soilveg_ruc.F90
 !>\ingroup RUC_lsm
 
+!> This module contains the namelist options of soil/vegetation in RUC
       module namelist_soilveg_ruc
 
       use machine ,   only : kind_phys