diff --git a/docs/Doxyfile.in b/docs/Doxyfile.in
index 20e6fbc7e..d596f9b16 100644
--- 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
index 4ec07d3e9..49964b44e 100644
--- 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
index 7f0bec898..682389d68 100644
--- 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
index 5fd4eceb9..37734c31c 100644
--- 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
diff --git a/sorc/fvcom_tools.fd/module_ncio.f90 b/sorc/fvcom_tools.fd/module_ncio.f90
index f6ba24628..1a790aaa9 100644
--- a/sorc/fvcom_tools.fd/module_ncio.f90
+++ b/sorc/fvcom_tools.fd/module_ncio.f90
@@ -1,5 +1,5 @@
 !> @file
-!!  module: functions to read and write netcdf files
+!! @brief Functions to read and write netcdf files.
 !!
 !! @author Ming Hu @date 2017-11-01
 !!
@@ -99,14 +99,14 @@ module module_ncio
 
 contains
 
+!> Open a netcdf file, set initial debug level.
+!!
+!! @param this instance of an ncio class
+!! @param filename the file to open
+!! @param action "r" for read, "w" for write
+!! @param debug_level set to non-zero for some verbose output
+!! @author Ming Hu @date 2017-11-01
 subroutine open_nc(this,filename,action,debug_level)
-!
-! open a netcdf file, set initial debug level
-!
-! prgmmr:  Ming Hu             org: GSD           date: 2017-11-01
-!
-! abstract: 
-!
 
   implicit none
 !
@@ -139,14 +139,11 @@ subroutine open_nc(this,filename,action,debug_level)
 
 end subroutine open_nc
 
+!> Close a netcdf file.
+!!
+!! @param this instance of an ncio class
+!! @author Ming Hu org: GSD/AMB @date 2017-04-10
 subroutine close_nc(this)
-!
-! initial netcdf file
-!
-! prgmmr:  Ming Hu             org: GSD/AMB           date: 2017-04-10
-!
-! abstract: 
-!
 
   implicit none
 !
@@ -162,15 +159,13 @@ subroutine close_nc(this)
 
 end subroutine close_nc
 
+!> Get attribute in wrf netcdf file.
+!!
+!! @param this instance of an ncio class
+!! @param attname name of the attribute to get
+!! @param rval return value
+!! @author Ming Hu org: GSD/AMB @date 2017-10-04
 subroutine get_att_nc_real(this,attname,rval)
-!
-! get attribute in wrf netcdf file
-!
-! prgmmr:  Ming Hu             org: GSD/AMB           date: 2017-10-04
-!
-! abstract: 
-!
-
   implicit none
 !
   class(ncio) :: this
@@ -188,15 +183,13 @@ subroutine get_att_nc_real(this,attname,rval)
 !
 end subroutine get_att_nc_real
 
+!> Get integer attribute in wrf netcdf file.
+!!
+!! @param this instance of an ncio class
+!! @param attname name of the attribute to get
+!! @param ival value of attribute.
+!! @author Ming Hu org: GSD/AMB @date 2017-10-04
 subroutine get_att_nc_int(this,attname,ival)
-!
-! get attribute in wrf netcdf file
-!
-! prgmmr:  Ming Hu             org: GSD/AMB           date: 2017-10-04
-!
-! abstract: 
-!
-
   implicit none
 !
   class(ncio) :: this
@@ -214,15 +207,13 @@ subroutine get_att_nc_int(this,attname,ival)
 !
 end subroutine get_att_nc_int
 
+!> Get string attribute in wrf netcdf file.
+!!
+!! @param this instance of an ncio class
+!! @param attname name of the attribute to get
+!! @param string value of attribute.
+!! @author Ming Hu org: GSD/AMB @date 2017-10-04
 subroutine get_att_nc_string(this,attname,string)
-!
-! get attribute in wrf netcdf file
-!
-! prgmmr:  Ming Hu             org: GSD/AMB           date: 2017-10-04
-!
-! abstract: 
-!
-
   implicit none
 !
   class(ncio) :: this
@@ -241,15 +232,13 @@ subroutine get_att_nc_string(this,attname,string)
 end subroutine get_att_nc_string
 
 
+!> Get dimensions in netcdf file.
+!!
+!! @param[in] this instance of an ncio class
+!! @param[in] dimname name of the dimension
+!! @param[out] dimvalue length of the dimension
+!! @author Ming Hu org: GSD/AMB @date 2017-11-01
 subroutine get_dim_nc(this,dimname,dimvalue)
-!
-! get dimensions in netcdf file
-!
-! prgmmr:  Ming Hu             org: GSD/AMB           date: 2017-11-01
-!
-! abstract: 
-!
-
   implicit none
 !
   class(ncio) :: this
@@ -270,11 +259,15 @@ subroutine get_dim_nc(this,dimname,dimvalue)
 !
 end subroutine get_dim_nc
 
-!==========================begin replace_var ==========================
+!> Read in one field.
+!!
+!! @param[in] this instance of an ncio class
+!! @param[in] varname name of the variable
+!! @param[in] nd1
+!! @param[in] field
+!! @author Ming Hu org: GSD/AMB @date 2017-11-01
 subroutine replace_var_nc_char_1d(this,varname,nd1,field)
-!
-! read in one field 
-!
+
   use netcdf
 !
   implicit none
@@ -301,10 +294,15 @@ subroutine replace_var_nc_char_1d(this,varname,nd1,field)
 !
 end subroutine replace_var_nc_char_1d
 
+!> Read in one field.
+!!
+!! @param[in] this instance of an ncio class
+!! @param[in] varname name of the variable
+!! @param[in] nd1
+!! @param[in] nd2
+!! @param[in] field
+!! @author Ming Hu org: GSD/AMB @date 2017-11-01
 subroutine replace_var_nc_char_2d(this,varname,nd1,nd2,field)
-!
-! read in one field 
-!
   use netcdf
 !
   implicit none
@@ -343,10 +341,16 @@ subroutine replace_var_nc_char_2d(this,varname,nd1,nd2,field)
 !
 end subroutine replace_var_nc_char_2d
 
+!> Read in one field.
+!!
+!! @param[in] this instance of an ncio class
+!! @param[in] varname name of the variable
+!! @param[in] nd1
+!! @param[in] nd2
+!! @param[in] nd3
+!! @param[in] field
+!! @author Ming Hu org: GSD/AMB @date 2017-11-01
 subroutine replace_var_nc_char_3d(this,varname,nd1,nd2,nd3,field)
-!
-! read in one field 
-!
   use netcdf
 !
   implicit none
@@ -388,11 +392,15 @@ subroutine replace_var_nc_char_3d(this,varname,nd1,nd2,nd3,field)
   deallocate(temp)
 !
 end subroutine replace_var_nc_char_3d
-!
+
+!> Read in one field.
+!!
+!! @param[in] this instance of an ncio class
+!! @param[in] varname name of the variable
+!! @param[in] ilength
+!! @param[in] field
+!! @author Ming Hu org: GSD/AMB @date 2017-11-01
 subroutine replace_var_nc_char(this,varname,ilength,field)
-!
-! read in one field 
-!
   use netcdf
 !
   implicit none
@@ -492,11 +500,14 @@ subroutine replace_var_nc_char(this,varname,ilength,field)
 end subroutine replace_var_nc_char
 !--- replace_var_nc_char
 
-!---- replace real
+!> Replace real.
+!!
+!! @param[in] this instance of an ncio class
+!! @param[in] varname name of the variable
+!! @param[in] nd1
+!! @param[in] field
+!! @author Ming Hu org: GSD/AMB @date 2017-11-01
 subroutine replace_var_nc_real_1d(this,varname,nd1,field)
-!
-! read in one field 
-!
   use netcdf
 !
   implicit none
@@ -523,10 +534,15 @@ subroutine replace_var_nc_real_1d(this,varname,nd1,field)
 !
 end subroutine replace_var_nc_real_1d
 
+!> Replace real.
+!!
+!! @param[in] this instance of an ncio class
+!! @param[in] varname name of the variable
+!! @param[in] nd1
+!! @param[in] nd2
+!! @param[in] field
+!! @author Ming Hu org: GSD/AMB @date 2017-11-01
 subroutine replace_var_nc_real_2d(this,varname,nd1,nd2,field)
-!
-! read in one field 
-!
   use netcdf
 !
   implicit none
@@ -565,6 +581,15 @@ subroutine replace_var_nc_real_2d(this,varname,nd1,nd2,field)
 !
 end subroutine replace_var_nc_real_2d
 
+!> Replace real.
+!!
+!! @param[in] this instance of an ncio class
+!! @param[in] varname name of the variable
+!! @param[in] nd1
+!! @param[in] nd2
+!! @param[in] nd3
+!! @param[in] field
+!! @author Ming Hu org: GSD/AMB @date 2017-11-01
 subroutine replace_var_nc_real_3d(this,varname,nd1,nd2,nd3,field)
 !
 ! read in one field 
@@ -613,10 +638,14 @@ subroutine replace_var_nc_real_3d(this,varname,nd1,nd2,nd3,field)
 !
 end subroutine replace_var_nc_real_3d
 
+!> Read in one field.
+!!
+!! @param[in] this instance of an ncio class
+!! @param[in] varname name of the variable
+!! @param[in] ilength
+!! @param[in] field
+!! @author Ming Hu org: GSD/AMB @date 2017-11-01
 subroutine replace_var_nc_real(this,varname,ilength,field)
-!
-! read in one field 
-!
   use netcdf
 !
   implicit none
@@ -715,7 +744,13 @@ subroutine replace_var_nc_real(this,varname,ilength,field)
 !
 end subroutine replace_var_nc_real
 
-!---- repalce double
+!> Replace double.
+!!
+!! @param[in] this instance of an ncio class
+!! @param[in] varname name of the variable
+!! @param[in] nd1
+!! @param[in] field
+!! @author Ming Hu org: GSD/AMB @date 2017-11-01
 subroutine replace_var_nc_double_1d(this,varname,nd1,field)
 !
 ! read in one field 
@@ -746,6 +781,14 @@ subroutine replace_var_nc_double_1d(this,varname,nd1,field)
 !
 end subroutine replace_var_nc_double_1d
 
+!> Replace double.
+!!
+!! @param[in] this instance of an ncio class
+!! @param[in] varname name of the variable
+!! @param[in] nd1
+!! @param[in] nd2
+!! @param[in] field
+!! @author Ming Hu org: GSD/AMB @date 2017-11-01
 subroutine replace_var_nc_double_2d(this,varname,nd1,nd2,field)
 !
 ! read in one field 
@@ -788,6 +831,15 @@ subroutine replace_var_nc_double_2d(this,varname,nd1,nd2,field)
 !
 end subroutine replace_var_nc_double_2d
 
+!> Replace double.
+!!
+!! @param[in] this instance of an ncio class
+!! @param[in] varname name of the variable
+!! @param[in] nd1
+!! @param[in] nd2
+!! @param[in] nd3
+!! @param[in] field
+!! @author Ming Hu org: GSD/AMB @date 2017-11-01
 subroutine replace_var_nc_double_3d(this,varname,nd1,nd2,nd3,field)
 !
 ! read in one field 
@@ -837,10 +889,14 @@ subroutine replace_var_nc_double_3d(this,varname,nd1,nd2,nd3,field)
 end subroutine replace_var_nc_double_3d
 !
 
+!> Read in one field.
+!!
+!! @param[in] this instance of an ncio class
+!! @param[in] varname name of the variable
+!! @param[in] ilength
+!! @param[in] field
+!! @author Ming Hu org: GSD/AMB @date 2017-11-01
 subroutine replace_var_nc_double(this,varname,ilength,field)
-!
-! read in one field 
-!
   use netcdf
 !
   implicit none
@@ -938,12 +994,15 @@ subroutine replace_var_nc_double(this,varname,ilength,field)
   endif
 !
 end subroutine replace_var_nc_double
-!
-!---- replace int
+
+!> Read in one field.
+!!
+!! @param[in] this instance of an ncio class
+!! @param[in] varname name of the variable
+!! @param[in] nd1
+!! @param[in] field
+!! @author Ming Hu org: GSD/AMB @date 2017-11-01
 subroutine replace_var_nc_int_1d(this,varname,nd1,field)
-!
-! read in one field 
-!
   use netcdf
 !
   implicit none
@@ -970,6 +1029,14 @@ subroutine replace_var_nc_int_1d(this,varname,nd1,field)
 !
 end subroutine replace_var_nc_int_1d
 
+!> Read in one field.
+!!
+!! @param[in] this instance of an ncio class
+!! @param[in] varname name of the variable
+!! @param[in] nd1
+!! @param[in] nd2
+!! @param[in] field
+!! @author Ming Hu org: GSD/AMB @date 2017-11-01
 subroutine replace_var_nc_int_2d(this,varname,nd1,nd2,field)
 !
 ! read in one field 
@@ -1012,10 +1079,16 @@ subroutine replace_var_nc_int_2d(this,varname,nd1,nd2,field)
 !
 end subroutine replace_var_nc_int_2d
 
+!> Read in one field.
+!!
+!! @param[in] this instance of an ncio class
+!! @param[in] varname name of the variable
+!! @param[in] nd1
+!! @param[in] nd2
+!! @param[in] nd3
+!! @param[in] field
+!! @author Ming Hu org: GSD/AMB @date 2017-11-01
 subroutine replace_var_nc_int_3d(this,varname,nd1,nd2,nd3,field)
-!
-! read in one field 
-!
   use netcdf
 !
   implicit none
@@ -1059,11 +1132,15 @@ subroutine replace_var_nc_int_3d(this,varname,nd1,nd2,nd3,field)
   deallocate(temp)
 !
 end subroutine replace_var_nc_int_3d
-!
+
+!> Read in one field.
+!!
+!! @param[in] this instance of an ncio class
+!! @param[in] varname name of the variable
+!! @param[in] ilength
+!! @param[in] field
+!! @author Ming Hu org: GSD/AMB @date 2017-11-01
 subroutine replace_var_nc_int(this,varname,ilength,field)
-!
-! read in one field 
-!
   use netcdf
 !
   implicit none
@@ -1161,14 +1238,15 @@ subroutine replace_var_nc_int(this,varname,ilength,field)
   endif
 !
 end subroutine replace_var_nc_int
-!
-!==========================end of replace_var ==========================
 
-!==========================begin get_var ==========================
+!> Read in one field.
+!!
+!! @param[in] this instance of an ncio class
+!! @param[in] varname name of the variable
+!! @param[in] nd1
+!! @param[in] field
+!! @author Ming Hu org: GSD/AMB @date 2017-11-01
 subroutine get_var_nc_double_1d(this,varname,nd1,field)
-!
-! read in one field 
-!
   use netcdf
 !
   implicit none
@@ -1198,10 +1276,15 @@ subroutine get_var_nc_double_1d(this,varname,nd1,field)
 !
 end subroutine get_var_nc_double_1d
 
+!> Read in one field.
+!!
+!! @param[in] this instance of an ncio class
+!! @param[in] varname name of the variable
+!! @param[in] nd1
+!! @param[in] nd2
+!! @param[in] field
+!! @author Ming Hu org: GSD/AMB @date 2017-11-01
 subroutine get_var_nc_double_2d(this,varname,nd1,nd2,field)
-!
-! read in one field 
-!
   use netcdf
 !
   implicit none
@@ -1244,10 +1327,16 @@ subroutine get_var_nc_double_2d(this,varname,nd1,nd2,field)
 !
 end subroutine get_var_nc_double_2d
 
+!> Read in one field.
+!!
+!! @param[in] this instance of an ncio class
+!! @param[in] varname name of the variable
+!! @param[in] nd1
+!! @param[in] nd2
+!! @param[in] nd3
+!! @param[in] field
+!! @author Ming Hu org: GSD/AMB @date 2017-11-01
 subroutine get_var_nc_double_3d(this,varname,nd1,nd2,nd3,field)
-!
-! read in one field 
-!
   use netcdf
 !
   implicit none
@@ -1295,11 +1384,15 @@ subroutine get_var_nc_double_3d(this,varname,nd1,nd2,nd3,field)
   deallocate(temp)
 !
 end subroutine get_var_nc_double_3d
-!
+
+!> Read in one field.
+!!
+!! @param[in] this instance of an ncio class
+!! @param[in] varname name of the variable
+!! @param[in] ilength
+!! @param[in] field
+!! @author Ming Hu org: GSD/AMB @date 2017-11-01
 subroutine get_var_nc_double(this,varname,ilength,field)
-!
-! read in one field 
-!
   use netcdf
 !
   implicit none
@@ -1398,10 +1491,14 @@ subroutine get_var_nc_double(this,varname,ilength,field)
 !
 end subroutine get_var_nc_double
 
+!> Read in one field.
+!!
+!! @param[in] this instance of an ncio class
+!! @param[in] varname name of the variable
+!! @param[in] nd1
+!! @param[in] field
+!! @author Ming Hu org: GSD/AMB @date 2017-11-01
 subroutine get_var_nc_real_1d(this,varname,nd1,field)
-!
-! read in one field 
-!
   use netcdf
 !
   implicit none
@@ -1431,6 +1528,14 @@ subroutine get_var_nc_real_1d(this,varname,nd1,field)
 !
 end subroutine get_var_nc_real_1d
 
+!> Read in one field.
+!!
+!! @param[in] this instance of an ncio class
+!! @param[in] varname name of the variable
+!! @param[in] nd1
+!! @param[in] nd2
+!! @param[in] field
+!! @author Ming Hu org: GSD/AMB @date 2017-11-01
 subroutine get_var_nc_real_2d(this,varname,nd1,nd2,field)
 !
 ! read in one field 
@@ -1477,10 +1582,16 @@ subroutine get_var_nc_real_2d(this,varname,nd1,nd2,field)
 !
 end subroutine get_var_nc_real_2d
 
+!> Read in one field.
+!!
+!! @param[in] this instance of an ncio class
+!! @param[in] varname name of the variable
+!! @param[in] nd1
+!! @param[in] nd2
+!! @param[in] nd3
+!! @param[in] field
+!! @author Ming Hu org: GSD/AMB @date 2017-11-01
 subroutine get_var_nc_real_3d(this,varname,nd1,nd2,nd3,field)
-!
-! read in one field 
-!
   use netcdf
 !
   implicit none
@@ -1528,7 +1639,14 @@ subroutine get_var_nc_real_3d(this,varname,nd1,nd2,nd3,field)
   deallocate(temp)
 !
 end subroutine get_var_nc_real_3d
-!
+
+!> Read in one field.
+!!
+!! @param[in] this instance of an ncio class
+!! @param[in] varname name of the variable
+!! @param[in] ilength
+!! @param[in] field
+!! @author Ming Hu org: GSD/AMB @date 2017-11-01
 subroutine get_var_nc_real(this,varname,ilength,field)
 !
 ! read in one field 
@@ -1631,10 +1749,14 @@ subroutine get_var_nc_real(this,varname,ilength,field)
 !
 end subroutine get_var_nc_real
 
+!> Read in one field.
+!!
+!! @param[in] this instance of an ncio class
+!! @param[in] varname name of the variable
+!! @param[in] nd1
+!! @param[in] field
+!! @author Ming Hu org: GSD/AMB @date 2017-11-01
 subroutine get_var_nc_int_1d(this,varname,nd1,field)
-!
-! read in one field 
-!
   use netcdf
 !
   implicit none
@@ -1664,6 +1786,14 @@ subroutine get_var_nc_int_1d(this,varname,nd1,field)
 !
 end subroutine get_var_nc_int_1d
 
+!> Read in one field.
+!!
+!! @param[in] this instance of an ncio class
+!! @param[in] varname name of the variable
+!! @param[in] nd1
+!! @param[in] nd2
+!! @param[in] field
+!! @author Ming Hu org: GSD/AMB @date 2017-11-01
 subroutine get_var_nc_int_2d(this,varname,nd1,nd2,field)
 !
 ! read in one field 
@@ -1710,10 +1840,16 @@ subroutine get_var_nc_int_2d(this,varname,nd1,nd2,field)
 !
 end subroutine get_var_nc_int_2d
 
+!> Read in one field.
+!!
+!! @param[in] this instance of an ncio class
+!! @param[in] varname name of the variable
+!! @param[in] nd1
+!! @param[in] nd2
+!! @param[in] nd3
+!! @param[in] field
+!! @author Ming Hu org: GSD/AMB @date 2017-11-01
 subroutine get_var_nc_int_3d(this,varname,nd1,nd2,nd3,field)
-!
-! read in one field 
-!
   use netcdf
 !
   implicit none
@@ -1761,7 +1897,14 @@ subroutine get_var_nc_int_3d(this,varname,nd1,nd2,nd3,field)
   deallocate(temp)
 !
 end subroutine get_var_nc_int_3d
-!
+
+!> Read in one field.
+!!
+!! @param[in] this instance of an ncio class
+!! @param[in] varname name of the variable
+!! @param[in] ilength
+!! @param[in] field
+!! @author Ming Hu org: GSD/AMB @date 2017-11-01
 subroutine get_var_nc_int(this,varname,ilength,field)
 !
 ! read in one field 
@@ -1863,11 +2006,15 @@ subroutine get_var_nc_int(this,varname,ilength,field)
   endif
 !
 end subroutine get_var_nc_int
-!
+
+!> Read in one field.
+!!
+!! @param[in] this instance of an ncio class
+!! @param[in] varname name of the variable
+!! @param[in] nd1
+!! @param[in] field
+!! @author Ming Hu org: GSD/AMB @date 2017-11-01
 subroutine get_var_nc_short_1d(this,varname,nd1,field)
-!
-! read in one field 
-!
   use netcdf
 !
   implicit none
@@ -1896,7 +2043,15 @@ subroutine get_var_nc_short_1d(this,varname,nd1,field)
   endif
 !
 end subroutine get_var_nc_short_1d
-!
+
+!> Read in one field.
+!!
+!! @param[in] this instance of an ncio class
+!! @param[in] varname name of the variable
+!! @param[in] nd1
+!! @param[in] nd2
+!! @param[in] field
+!! @author Ming Hu org: GSD/AMB @date 2017-11-01
 subroutine get_var_nc_short_2d(this,varname,nd1,nd2,field)
 !
 ! read in one field 
@@ -1943,10 +2098,14 @@ subroutine get_var_nc_short_2d(this,varname,nd1,nd2,field)
 !
 end subroutine get_var_nc_short_2d
 !
+!> Read in one field.
+!!
+!! @param[in] this instance of an ncio class
+!! @param[in] varname name of the variable
+!! @param[in] ilength
+!! @param[in] field
+!! @author Ming Hu org: GSD/AMB @date 2017-11-01
 subroutine get_var_nc_short(this,varname,ilength,field)
-!
-! read in one field 
-!
   use netcdf
 !
   implicit none
@@ -2045,10 +2204,14 @@ subroutine get_var_nc_short(this,varname,ilength,field)
 !
 end subroutine get_var_nc_short
 
+!> Read in one field.
+!!
+!! @param[in] this instance of an ncio class
+!! @param[in] varname name of the variable
+!! @param[in] nd1
+!! @param[in] field
+!! @author Ming Hu org: GSD/AMB @date 2017-11-01
 subroutine get_var_nc_char_1d(this,varname,nd1,field)
-!
-! read in one field 
-!
   use netcdf
 !
   implicit none
@@ -2078,10 +2241,15 @@ subroutine get_var_nc_char_1d(this,varname,nd1,field)
 !
 end subroutine get_var_nc_char_1d
 
+!> Read in one field.
+!!
+!! @param[in] this instance of an ncio class
+!! @param[in] varname name of the variable
+!! @param[in] nd1
+!! @param[in] nd2
+!! @param[in] field
+!! @author Ming Hu org: GSD/AMB @date 2017-11-01
 subroutine get_var_nc_char_2d(this,varname,nd1,nd2,field)
-!
-! read in one field 
-!
   use netcdf
 !
   implicit none
@@ -2124,10 +2292,16 @@ subroutine get_var_nc_char_2d(this,varname,nd1,nd2,field)
 !
 end subroutine get_var_nc_char_2d
 
+!> Read in one field.
+!!
+!! @param[in] this instance of an ncio class
+!! @param[in] varname name of the variable
+!! @param[in] nd1
+!! @param[in] nd2
+!! @param[in] nd3
+!! @param[in] field
+!! @author Ming Hu org: GSD/AMB @date 2017-11-01
 subroutine get_var_nc_char_3d(this,varname,nd1,nd2,nd3,field)
-!
-! read in one field 
-!
   use netcdf
 !
   implicit none
@@ -2174,6 +2348,13 @@ subroutine get_var_nc_char_3d(this,varname,nd1,nd2,nd3,field)
 !
 end subroutine get_var_nc_char_3d
 !
+!> Read in one field.
+!!
+!! @param[in] this instance of an ncio class
+!! @param[in] varname name of the variable
+!! @param[in] ilength
+!! @param[in] field
+!! @author Ming Hu org: GSD/AMB @date 2017-11-01
 subroutine get_var_nc_char(this,varname,ilength,field)
 !
 ! read in one field 
@@ -2275,8 +2456,12 @@ subroutine get_var_nc_char(this,varname,ilength,field)
   endif
 !
 end subroutine get_var_nc_char
-!==========================end of get_var ==========================
 
+!> Handle netCDF errors.
+!!
+!! @param[in] this instance of an ncio class
+!! @param[in] status return code from neCDF
+!! @author Ming Hu org: GSD/AMB @date 2017-11-01
 subroutine handle_err(this,status)
   use netcdf
   implicit none
@@ -2289,8 +2474,15 @@ subroutine handle_err(this,status)
   end if
 end subroutine handle_err
 
+!> Convert theta T to T.
+!!
+!! @param[in] this instance of an ncio class
+!! @param[in] nx
+!! @param[in] ny
+!! @param[in] ps
+!! @param[in] t2
+!! @author Ming Hu org: GSD/AMB @date 2017-11-01
 subroutine convert_theta2t_2dgrid(this,nx,ny,ps,t2)
-! convertt theta T to T 
          implicit none
          class(ncio) :: this
 
@@ -2314,19 +2506,18 @@ subroutine convert_theta2t_2dgrid(this,nx,ny,ps,t2)
 
 end subroutine convert_theta2t_2dgrid
 
+!> Add a new variable to sfc_data.nc with dimensions (Time, yaxis_1,
+!! xaxis_1).
+!!
+!! @param[in] varname Name of variable to be created in netcdf file
+!! @param[in] dname1 1st dimension name
+!! @param[in] dname2 2nd dimension name
+!! @param[in] dname3 3rd dimension name
+!! @param lname long name output for netcdf variable
+!! @param units units to use in netcdf variable
+!!
+!! @author David.M.Wright org: UM/GLERL @date 2020-09-01
 subroutine add_new_var_3d(this,varname,dname1,dname2,dname3,lname,units)
-!
-! prgmmr:  David.M.Wright    org: UM/GLERL        date: 2020-09-01
-!
-! abstract: Add a new variable to sfc_data.nc with dimensions
-!            (Time, yaxis_1, xaxis_1)
-! 
-! Input: varname = Name of variable to be created in netcdf file
-!        dname1,dname2,dname3 = 1st,2nd, and 3rd dimension names
-!        lname = long name output for netcdf variable
-!        units = units to use in netcdf variable
-!
-  use netcdf
   implicit none
 !
   class(ncio) :: this
diff --git a/sorc/fvcom_tools.fd/process_FVCOM.f90 b/sorc/fvcom_tools.fd/process_FVCOM.f90
index 871c6a959..960980cc7 100755
--- a/sorc/fvcom_tools.fd/process_FVCOM.f90
+++ b/sorc/fvcom_tools.fd/process_FVCOM.f90
@@ -1,8 +1,12 @@
 !> @file
 !!
-!! This is the code to put lake surface temperature and aerial ice
-!! concentration from GLERL-provided FVCOM forecast files (which have
-!! already been mapped to the FV3-LAM grid) into sfc_data.nc.  
+!! @brief This is the code to put lake surface temperature and aerial
+!! ice concentration from GLERL-provided FVCOM forecast files (which
+!! have already been mapped to the FV3-LAM grid) into sfc_data.nc.
+
+!> Put lake surface temperature and aerial ice concentration from
+!! GLERL-provided FVCOM forecast files (which have already been mapped
+!! to the FV3-LAM grid) into sfc_data.nc.
 !!
 !! This script will take two variables from the command line:
 !! 1. Name of FV3 sfc data file (e.g. sfc_data.tile7.halo0.nc)
@@ -12,12 +16,13 @@
 !! names as needed:
 !!   ./fvcom_to_FV3 sfc_data.tile7.halo0.nc fvcom.nc
 !!
-!! Code is strongly based upon Eric James' (ESRL/GSL) work 
-!!  to update HRRR/WRF Great Lakes' temperature data with FVCOM.
-!!  Code also relies heavily on Ming Hu's ncio module.
+!! Code is strongly based upon Eric James' (ESRL/GSL) work to update
+!! HRRR/WRF Great Lakes' temperature data with FVCOM. Code also
+!! relies heavily on Ming Hu's ncio module.
 !!
 !! @author David Wright, University of Michigan and GLERL
 !! @date 17 Aug 2020
+!! @return 0 for success, error code otherwise
 !!
 program process_FVCOM