Merge branch 'develop' into feature/doxsfc

Fixes ufs-community#281
GeorgeGayno-NOAA · Feb 25, 2021 · a9c300a · a9c300a
2 parents 3a869a7 + c1a1d29
commit a9c300a
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diff --git a/docs/Doxyfile.in b/docs/Doxyfile.in
@@ -402,13 +402,13 @@ EXTRACT_ALL            = NO
 # be included in the documentation.
 # The default value is: NO.
 
-EXTRACT_PRIVATE        = NO
+EXTRACT_PRIVATE        = YES
 
 # If the EXTRACT_PACKAGE tag is set to YES all members with package or internal
 # scope will be included in the documentation.
 # The default value is: NO.
 
-EXTRACT_PACKAGE        = NO
+EXTRACT_PACKAGE        = YES
 
 # If the EXTRACT_STATIC tag is set to YES all static members of a file will be
 # included in the documentation.

diff --git a/sorc/chgres_cube.fd/program_setup.F90 b/sorc/chgres_cube.fd/program_setup.F90
@@ -1,7 +1,8 @@
 !> @file
-!! @brief Set up program execution
+!! @brief Set up program execution.
 !!
-!! Set up program execution
+!! This module contains code to read the setup namelist file, handle
+!! the varmap file for GRIB2 data, and calculate the soil parameters.
 !!
 !! @author George Gayno NCEP/EMC
  module program_setup
@@ -144,7 +145,8 @@ module program_setup
 
 !> Reads program configuration namelist.
 !!
-!! @param filename the name of the configuration file (defaults to ./fort.41).
+!! @param filename the name of the configuration file (defaults to
+!! ./fort.41).
 !! @author George Gayno NCEP/EMC
  subroutine read_setup_namelist(filename)
  implicit none
@@ -443,6 +445,27 @@ end subroutine get_var_cond
 !> Driver routine to compute soil parameters for each
 !! soil type. Works for Zobler and STATSGO soil categories.
 !!
+!! The calculations are those used in the Noah Land Surface Model. For
+!! more information see <a
+!! href="https://doi.org/10.1029/2002JD003296">Implementation of Noah
+!! land surface model advances in the National Centers for
+!! Environmental Prediction operational mesoscale Eta model</a>.
+!!
+!! For more details about the soil parameters/properties see <a
+!! href="https://journals.ametsoc.org/view/journals/mwre/129/4/1520-0493_2001_129_0569_caalsh_2.0.co_2.xml">Coupling
+!! an Advanced Land Surface–Hydrology Model with the Penn State–NCAR
+!! MM5 Modeling System. Part I: Model Implementation and
+!! Sensitivity</a>.
+!!
+!! The original source for soil properties is here:
+!!
+!! Cosby, B. J., G. M. Hornberger, R. B. Clapp, and T. R. Ginn, 1984:
+!! <a
+!! href="https://agupubs.onlinelibrary.wiley.com/doi/10.1029/WR020i006p00682">A
+!! statistical exploration of the relationships of soil moisture
+!! characteristics to the physical properties of soils</a>. Water
+!! Resour. Res.,20, 682–690.
+!!
 !! @param [in] localpet  ESMF local persistent execution thread
 !! @author George Gayno NCEP/EMC
  subroutine calc_soil_params_driver(localpet)
@@ -588,8 +611,8 @@ subroutine calc_soil_params_driver(localpet)
 
  end subroutine calc_soil_params_driver
 
-!> Compute soil parameters.  Will be used to rescale soil moisture
-!! differences in soil type between the input grid and target
+!> Compute soil parameters. These will be used to rescale soil
+!! moisture differences in soil type between the input grid and target
 !! model grid.
 !!
 !! @param [in] num_soil_cats  number of soil type categories

diff --git a/sorc/fvcom_tools.fd/CMakeLists.txt b/sorc/fvcom_tools.fd/CMakeLists.txt
@@ -1,3 +1,8 @@
+# This is the CMake file for the fvcom_tools utility in the UFS_UTILS
+# project.
+#
+# David Wright
+
 set(fortran_src
    kinds.f90
    module_ncio.f90

diff --git a/sorc/fvcom_tools.fd/kinds.f90 b/sorc/fvcom_tools.fd/kinds.f90
@@ -1,35 +1,31 @@
 !> @file
-!!                .      .    .                                       .
-!! Module to hold specification kinds for variable declaration.
+!! @brief Module to hold specification kinds for variable declaration.
+!!
 !! This module is based on (copied from) Paul vanDelst's 
 !! type_kinds module found in the community radiative transfer
 !! model
 !!
-!! The numerical data types defined in this module are:
-!! -     r_single  - specification kind for single precision (4-byte) real variable
-!! -     i_kind    - generic specification kind for default integer
-!! -     r_kind    - generic specification kind for default floating point
-!!
+!! @author David Wright, University of Michigan
 module kinds
   implicit none
   private
 !
 ! for name string
-  integer, parameter, public  :: len_sta_name  = 8
+  integer, parameter, public  :: len_sta_name  = 8 !< Name length.
 
 ! Integer type definitions below
 
 ! Integer types
-  integer, parameter, public  :: i_kind = 4
-  integer, parameter, public  :: i_short = 2
-  integer, parameter, public  :: i_byte  = 1
+  integer, parameter, public  :: i_kind = 4 !< generic specification kind for default integer.
+  integer, parameter, public  :: i_short = 2 !< generic specification kind for default short.
+  integer, parameter, public  :: i_byte  = 1 !< generic specification kind for default byte.
 ! Real types
-  integer, parameter, public  :: r_single = 4  ! single precision
-  integer, parameter, public  :: r_kind = 8
+  integer, parameter, public  :: r_single = 4  !< specification kind for single precision (4-byte) real variable.
+  integer, parameter, public  :: r_kind = 8 !< generic specification kind for default floating point
 
 !
-  real(r_single),parameter,public :: rmissing=-99999.0
-  real(i_kind),parameter,public :: imissing=-99999
-  real(r_kind),parameter,public :: drmissing=-99999.0
+  real(r_single),parameter,public :: rmissing=-99999.0 !< Fill value for single real missing data.
+  real(i_kind),parameter,public :: imissing=-99999 !< Fill value for integer missing data.
+  real(r_kind),parameter,public :: drmissing=-99999.0 !< Fill value for double real missing data.
 
 end module kinds