release/public-v5: update of scientific documentation

physics/GFS_stochastics.F90

@@ -1,6 +1,8 @@
 !> \file GFS_stochastics.f90
 !! This file contains code previously in GFS_stochastics_driver.
 
+!>\defgroup gfs_stoch GFS Stochastics Physics Module
+!! This module
     module GFS_stochastics
 
       contains
@@ -12,9 +14,6 @@ subroutine GFS_stochastics_finalize()
       end subroutine GFS_stochastics_finalize
 
 
-!>\defgroup gfs_stoch GFS Stochastics Physics Module
-!! This module
-!> @{
 !> \section arg_table_GFS_stochastics_run Argument Table
 !! \htmlinclude GFS_stochastics_run.html
 !!
@@ -250,4 +249,3 @@ subroutine GFS_stochastics_run (im, km, kdt, do_sppt, use_zmtnblck, do_shum,
       end subroutine GFS_stochastics_run
 
     end module GFS_stochastics
-!> @}

physics/docs/ccppv5_doxyfile

@@ -130,7 +130,7 @@ INPUT                  =  pdftxt/mainpage.txt     \
                           pdftxt/GFS_SAMFdeep.txt \
                           pdftxt/GFS_SAMFshal.txt \
                           pdftxt/GFDL_cloud.txt   \
-                          pdftxt/GFS_CALPRECIPTYPE.txt   \
+###                          pdftxt/GFS_CALPRECIPTYPE.txt   \
 ###                          pdftxt/rad_cld.txt             \
                           pdftxt/CPT_CSAW.txt            \
                           pdftxt/CPT_MG3.txt             \
@@ -181,8 +181,8 @@ INPUT                  =  pdftxt/mainpage.txt     \
                         ../dcyc2.f        \
 ### Land Surface
                         ../sfc_diff.f \
-                        ../module_MYNNSFC_wrapper.F90 \
-                        ../module_sf_mynn.F90         \
+###                        ../module_MYNNSFC_wrapper.F90 \
+###                        ../module_sf_mynn.F90         \
                         ../sfc_nst.f                  \
                         ../sfc_ocean.F                \
                         ../module_nst_model.f90       \

physics/docs/pdftxt/CPT_adv_suite.txt

@@ -18,7 +18,6 @@ The csawmg physics suite uses the parameterizations in the following order:
  - \ref GFS_SAMFshal
  - \ref CPT_MG3
  - \ref mod_cs_conv_aw_adj
- - \ref GFS_CALPRECIPTYPE
 
 \section sdf_cpt_suite Suite Definition File 
 \code

physics/docs/pdftxt/GFS_NOAHMP.txt

@@ -20,20 +20,6 @@ The CCPP interface to the NoahMP LSM is a driving software layer on top of the a
 
 Note that noahmp_glacer() and noahmp_sflx() are the actual NoahMP codes.
 
-\section Default NoahMP LSM Options used in UFS atmosphere
-+ Dynamic Vegetation (opt_dveg): 2 [On]
-+ Canopy Stomatal Resistance (opt_crs): 1 [Ball-Berry]
-+ Soil Moisture Factor for Stomatal Resistance (opt_btr): 1 [Noah soil moisture]
-+ Runoff and Groundwater (opt_run): 1 [topmodel with groundwater (Niu et al. 2007 \cite niu_et_al_2007)]
-+ Surface Layer Drag Coeff (opt_sfc): 1 [Monin-Obukhov]
-+ Supercooled Liquid Water or Ice Fraction (opt_frz): 1 [no iteration (Niu and Yang, 2006 \cite niu_and_yang_2006)]
-+ Frozen Soil Permeability (opt_inf): 1 [linear effects, more permeable (Niu and Yang, 2006, \cite niu_and_yang_2006)]
-+ Radiation Transfer (opt_rad): 1 [modified two-stream (gap = f(solar angle, 3d structure ...)<1-fveg)]
-+ Ground Snow Surface Albedo (opt_alb): 2 [class]
-+ Partitioning Precipitation into Rainfall & Snowfall (opt_snf): 4 [use microphysics output]
-+ Lower Boundary Condition of Soil Temperature (opt_tbot): 2 [tbot at zbot (8m) read from a file (original Noah)]
-+ Snow/Soil Temperature Time Scheme (only layer 1) (opt_stc): 1 [semi-implicit; flux top boundary condition] 
-
 \section intra_noahmp Intraphysics Communication
  +  GFS NoahMP LSM Driver (\ref arg_table_noahmpdrv_run)
 \section gen_al_noahmp General Algorithm of Driver

physics/docs/pdftxt/GFSv15p2_suite.txt

@@ -21,7 +21,6 @@ The GFS_v15p2 physics suite uses the parameterizations in the following order:
  - \ref GFS_SAMFdeep
  - \ref GFS_SAMFshal
  - \ref GFDL_cloud
- - \ref GFS_CALPRECIPTYPE
 
 \section sdf_gfsv15p2 Suite Definition File 
 \code

physics/docs/pdftxt/GFSv16beta_suite.txt

@@ -24,7 +24,6 @@ The GFS_v16beta physics suite uses the parameterizations in the following order:
  - \ref GFS_SAMFdeep
  - \ref GFS_SAMFshal
  - \ref GFDL_cloud
- - \ref GFS_CALPRECIPTYPE
 
 \section sdf_gfsv16b Suite Definition File 
 \code

physics/docs/pdftxt/GSD_adv_suite.txt

@@ -26,7 +26,6 @@ The GSD_v1 physics suite uses the parameterizations in the following order:
    - \ref cu_gf_deep_group
    - \ref cu_gf_sh_group
  - \ref THOMPSON
- - \ref GFS_CALPRECIPTYPE
 
 \section sdf_gsdsuite Suite Definition File 
 \code

physics/docs/pdftxt/all_shemes_list.txt

@@ -3,84 +3,78 @@
 
 \section allscheme_overview Physical Parameterizations 
 
-In the CCPP, each parameterization is in its own modern Fortran module, which facilitates model development and
-code maintenance. While some individual parameterization can be invoked for the SCM, most host models will assemble the 
-parameterizations in suites. 
+In the CCPP, each parameterization is in its own modern Fortran module (i.e., CCPP-compliant; see rules for scheme to considered CCPP-compliant at 
+<a href="https://ccpp-techdoc.readthedocs.io/en/v4.0/CompliantPhysicsParams.html"> CCPP-Compliant Physics Parameterizations </a>), 
+which facilitates model development and code maintenance. While some individual parameterization can be invoked for the SCM, most host models will assemble the parameterizations in suites. 
 
 
 \b Radiation
  - \subpage GFS_RRTMG 
-   +  rrtmg_sw_pre / rrtmg_sw / rrtmg_sw_post / rrtmg_lw_pre / rrtmg_lw / rrtmg_lw_post    
+   +  CCPP-compliant modules: rrtmg_sw_pre / rrtmg_sw / rrtmg_sw_post / rrtmg_lw_pre / rrtmg_lw / rrtmg_lw_post    
  - \subpage SGSCLOUD_page 
-   +  sgscloud_radpre
+   +  CCPP-compliant module: sgscloud_radpre
 
 \b PBL \b and \b Turbulence
  - \subpage GFS_HEDMF 
-   +  \ref hedmf
+   +  CCPP-compliant module: \ref hedmf
  - \subpage GFS_SATMEDMFVDIFQ 
-   +  \ref satmedmfvdifq
+   +  CCPP-compliant module: \ref satmedmfvdifq
  - \subpage MYNNEDMF 
-   +  mynnedmf_wrapper
+   +  CCPP-compliant module: mynnedmf_wrapper
 
 \b Land \b Surface \b Model
  - \subpage GFS_NOAH 
-   +  lsm_noah
+   +  CCPP-compliant module: lsm_noah
  - \subpage RUCLSM 
-   +  lsm_ruc
+   +  CCPP-compliant module: lsm_ruc
  - \subpage NoahMP 
-   +  \ref noahmpdrv
+   +  CCPP-compliant module: \ref noahmpdrv
 
 \b Cumulus \b Parameterizations
  - \subpage GFS_SAMFdeep 
-   +  \ref samfdeepcnv
+   +  CCPP-compliant module: \ref samfdeepcnv
  - \subpage GFS_SAMFshal 
-   +  \ref samfshalcnv
+   +  CCPP-compliant module: \ref samfshalcnv
  - \subpage CSAW_scheme 
-   +  cs_conv_pre / cs_conv / cs_conv_post / cs_conv_aw_adj
+   +  CCPP-compliant modules: cs_conv_pre / cs_conv / cs_conv_post / cs_conv_aw_adj
  - \subpage CU_GF 
-   +  \ref cu_gf_driver_pre / cu_gf_driver
+   +  CCPP-compliant modules: \ref cu_gf_driver_pre / cu_gf_driver
 
 \b Microphysics
  - \subpage GFDL_cloud 
-   +  fv_sat_adj / gfdl_cloud_microphys
+   +  CCPP-compliant modules: fv_sat_adj / gfdl_cloud_microphys
  - \subpage CPT_MG3 
-   +  \ref m_micro_pre / m_micro / \ref m_micro_post
+   +  CCPP-compliant modules: \ref m_micro_pre / m_micro / \ref m_micro_post
  - \subpage THOMPSON 
-   +  mp_thompson_pre / mp_thompson / mp_thompson_post
+   +  CCPP-compliant modules: mp_thompson_pre / mp_thompson / mp_thompson_post
 
 \b Ozone \b Photochemical \b Production \b and \b Loss
  - \subpage GFS_OZPHYS 
-   +  ozphys_2015
+   +  CCPP-compliant module: ozphys_2015
 
 \b Water \b Vapor \b Photochemical \b Production \b and \b Loss
  - \subpage GFS_H2OPHYS 
-   +  h2ophys
+   +  CCPP-compliant module: h2ophys
 
 \b Gravity \b Wave \b Drag
  - \subpage GFS_UGWP_v0 
-   +  cires_ugwp / cires_ugwp_post
+   +  CCPP-compliant modules: cires_ugwp / cires_ugwp_post
 
 \b Surface \b Layer 
  - \subpage GFS_SFCLYR 
-   +  sfc_diff
+   +  CCPP-compliant module: sfc_diff
 
 \b Simplified \b Ocean \b and \b Sea \b Ice \b Representation
  - \subpage GFS_NSST 
-   +  sfc_nst_pre / sfc_nst / sfc_nst_post
+   +  CCPP-compliant modules: sfc_nst_pre / sfc_nst / sfc_nst_post
  - \subpage GFS_OCEAN 
-   +  sfc_ocean
+   +  CCPP-compliant module: sfc_ocean
  - \subpage GFS_SFCSICE 
-   +  sfc_sice
+   +  CCPP-compliant module: sfc_sice
 
 \b Others
  - \subpage GFS_RAYLEIGH 
-   +  rayleigh_damp
-
-In addition to the physical schemes themselves, this scientific documentation also covers four modules that define physics/radiation functions, parameters and constants:
- - \ref func_phys
- - \ref phy_sparam
- - \ref physcons
- - \ref radcons
+   +  CCPP-compliant module: rayleigh_damp
 
 The input information for the parameterizations includes the values of the gridbox mean prognostic variables (wind components, temperature,
 specific humidity, cloud fraction, water contents for cloud liquid, cloud ice, rain, snow, graupel, and ozone concentration), the provisional