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Doxygen Updates (#853)
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Fixes #835.
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GeorgeGayno-NOAA authored Oct 17, 2023
1 parent 751bb18 commit 773fe3c
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4 changes: 2 additions & 2 deletions docs/Doxyfile.in
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Expand Up @@ -854,7 +854,7 @@ WARN_LOGFILE =
# spaces. See also FILE_PATTERNS and EXTENSION_MAPPING
# Note: If this tag is empty the current directory is searched.

INPUT = @abs_top_srcdir@/docs/user_guide.md
INPUT = @abs_top_srcdir@/docs/main.md

# This tag can be used to specify the character encoding of the source files
# that doxygen parses. Internally doxygen uses the UTF-8 encoding. Doxygen uses
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# (index.html). This can be useful if you have a project on for instance GitHub
# and want to reuse the introduction page also for the doxygen output.

USE_MDFILE_AS_MAINPAGE = @abs_top_srcdir@/docs/sp_user_guide.md
USE_MDFILE_AS_MAINPAGE = @abs_top_srcdir@/docs/main.md

#---------------------------------------------------------------------------
# Configuration options related to source browsing
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5 changes: 5 additions & 0 deletions docs/README.md
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For documentation see:

https://ufs-community.github.io/UFS_UTILS

https://noaa-emcufs-utils.readthedocs.io/en/latest
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4 changes: 2 additions & 2 deletions sorc/chgres_cube.fd/docs/Doxyfile.in
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Expand Up @@ -854,7 +854,7 @@ WARN_LOGFILE =
# spaces. See also FILE_PATTERNS and EXTENSION_MAPPING
# Note: If this tag is empty the current directory is searched.

INPUT = @abs_top_srcdir@/sorc/chgres_cube.fd/docs/user_guide.md \
INPUT = @abs_top_srcdir@/sorc/chgres_cube.fd/docs/chgres_cube.md \
@abs_top_srcdir@/sorc/chgres_cube.fd

# This tag can be used to specify the character encoding of the source files
Expand Down Expand Up @@ -1015,7 +1015,7 @@ FILTER_SOURCE_PATTERNS =
# (index.html). This can be useful if you have a project on for instance GitHub
# and want to reuse the introduction page also for the doxygen output.

USE_MDFILE_AS_MAINPAGE = user_guide.md
USE_MDFILE_AS_MAINPAGE = chgres_cube.md

#---------------------------------------------------------------------------
# Configuration options related to source browsing
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4 changes: 4 additions & 0 deletions sorc/chgres_cube.fd/docs/README.md
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The chgres_cube program creates initial condition files to coldstart
the forecast model.

Documentation may be found at https://ufs-community.github.io/UFS_UTILS
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4 changes: 2 additions & 2 deletions sorc/cpld_gridgen.fd/docs/Doxyfile.in
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Expand Up @@ -855,7 +855,7 @@ WARN_LOGFILE =
# spaces. See also FILE_PATTERNS and EXTENSION_MAPPING
# Note: If this tag is empty the current directory is searched.

INPUT = @abs_top_srcdir@/sorc/cpld_gridgen.fd/docs/user_guide.md \
INPUT = @abs_top_srcdir@/sorc/cpld_gridgen.fd/docs/cpld_gridgen.md \
@abs_top_srcdir@/sorc/cpld_gridgen.fd

# This tag can be used to specify the character encoding of the source files
Expand Down Expand Up @@ -1016,7 +1016,7 @@ FILTER_SOURCE_PATTERNS =
# (index.html). This can be useful if you have a project on for instance GitHub
# and want to reuse the introduction page also for the doxygen output.

USE_MDFILE_AS_MAINPAGE = user_guide.md
USE_MDFILE_AS_MAINPAGE = cpld_gridgen.md

#---------------------------------------------------------------------------
# Configuration options related to source browsing
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4 changes: 4 additions & 0 deletions sorc/cpld_gridgen.fd/docs/README.md
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This program creates the files required for the Fix and IC files for
the coupled model.

Documentation may be found at https://ufs-community.github.io/UFS_UTILS
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4 changes: 2 additions & 2 deletions sorc/emcsfc_ice_blend.fd/docs/Doxyfile.in
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Expand Up @@ -854,7 +854,7 @@ WARN_LOGFILE =
# spaces. See also FILE_PATTERNS and EXTENSION_MAPPING
# Note: If this tag is empty the current directory is searched.

INPUT = @abs_top_srcdir@/sorc/emcsfc_ice_blend.fd/docs/user_guide.md \
INPUT = @abs_top_srcdir@/sorc/emcsfc_ice_blend.fd/docs/emc_ice_blend.md \
@abs_top_srcdir@/sorc/emcsfc_ice_blend.fd

# This tag can be used to specify the character encoding of the source files
Expand Down Expand Up @@ -1015,7 +1015,7 @@ FILTER_SOURCE_PATTERNS =
# (index.html). This can be useful if you have a project on for instance GitHub
# and want to reuse the introduction page also for the doxygen output.

USE_MDFILE_AS_MAINPAGE = user_guide.md
USE_MDFILE_AS_MAINPAGE = emc_ice_blend.md

#---------------------------------------------------------------------------
# Configuration options related to source browsing
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4 changes: 4 additions & 0 deletions sorc/emcsfc_ice_blend.fd/docs/README.md
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This program blends National Ice Center sea ice cover and EMC
sea ice concentration data to create a global sea ice analysis.

Documentation may be found at https://ufs-community.github.io/UFS_UTILS
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4 changes: 2 additions & 2 deletions sorc/emcsfc_snow2mdl.fd/docs/Doxyfile.in
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Expand Up @@ -854,7 +854,7 @@ WARN_LOGFILE =
# spaces. See also FILE_PATTERNS and EXTENSION_MAPPING
# Note: If this tag is empty the current directory is searched.

INPUT = @abs_top_srcdir@/sorc/emcsfc_snow2mdl.fd/docs/user_guide.md \
INPUT = @abs_top_srcdir@/sorc/emcsfc_snow2mdl.fd/docs/emcsfc_snow2mdl.md \
@abs_top_srcdir@/sorc/emcsfc_snow2mdl.fd

# This tag can be used to specify the character encoding of the source files
Expand Down Expand Up @@ -1015,7 +1015,7 @@ FILTER_SOURCE_PATTERNS =
# (index.html). This can be useful if you have a project on for instance GitHub
# and want to reuse the introduction page also for the doxygen output.

USE_MDFILE_AS_MAINPAGE = user_guide.md
USE_MDFILE_AS_MAINPAGE = emcsfc_snow2mdl.md

#---------------------------------------------------------------------------
# Configuration options related to source browsing
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4 changes: 4 additions & 0 deletions sorc/emcsfc_snow2mdl.fd/docs/README.md
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This program blends National Ice Center snow cover and Air Force
snow depth data to create a global depth analysis.

Documentation may be found at https://ufs-community.github.io/UFS_UTILS
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4 changes: 2 additions & 2 deletions sorc/fvcom_tools.fd/docs/Doxyfile.in
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Expand Up @@ -854,7 +854,7 @@ WARN_LOGFILE =
# spaces. See also FILE_PATTERNS and EXTENSION_MAPPING
# Note: If this tag is empty the current directory is searched.

INPUT = @abs_top_srcdir@/sorc/fvcom_tools.fd/docs/user_guide.md \
INPUT = @abs_top_srcdir@/sorc/fvcom_tools.fd/docs/fvcom_tools.md \
@abs_top_srcdir@/sorc/fvcom_tools.fd

# This tag can be used to specify the character encoding of the source files
Expand Down Expand Up @@ -1015,7 +1015,7 @@ FILTER_SOURCE_PATTERNS =
# (index.html). This can be useful if you have a project on for instance GitHub
# and want to reuse the introduction page also for the doxygen output.

USE_MDFILE_AS_MAINPAGE = user_guide.md
USE_MDFILE_AS_MAINPAGE = fvcom_tools.md

#---------------------------------------------------------------------------
# Configuration options related to source browsing
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5 changes: 5 additions & 0 deletions sorc/fvcom_tools.fd/docs/README.md
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This program replaces lake surface and lake ice temperature along
with aerial ice concentration generated from the Great Lakes
Operational Forecast System (GLOFS) into the model surface restart file.

Documentation may be found at https://ufs-community.github.io/UFS_UTILS
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4 changes: 2 additions & 2 deletions sorc/gblevents.fd/docs/Doxyfile.in
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Expand Up @@ -854,7 +854,7 @@ WARN_LOGFILE =
# spaces. See also FILE_PATTERNS and EXTENSION_MAPPING
# Note: If this tag is empty the current directory is searched.

INPUT = @abs_top_srcdir@/sorc/gblevents.fd/docs/user_guide.md \
INPUT = @abs_top_srcdir@/sorc/gblevents.fd/docs/gblevents.md \
@abs_top_srcdir@/sorc/gblevents.fd

# This tag can be used to specify the character encoding of the source files
Expand Down Expand Up @@ -1015,7 +1015,7 @@ FILTER_SOURCE_PATTERNS =
# (index.html). This can be useful if you have a project on for instance GitHub
# and want to reuse the introduction page also for the doxygen output.

USE_MDFILE_AS_MAINPAGE = user_guide.md
USE_MDFILE_AS_MAINPAGE = gblevents.md

#---------------------------------------------------------------------------
# Configuration options related to source browsing
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3 changes: 3 additions & 0 deletions sorc/gblevents.fd/docs/README.md
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The gblevents program performs pre and post processing of prepbufr events.

Documentation may be found at https://ufs-community.github.io/UFS_UTILS
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1 change: 1 addition & 0 deletions sorc/gblevents.fd/gblevents.f
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Expand Up @@ -2047,6 +2047,7 @@ SUBROUTINE GBLEVN06(XOB,YOB) ! FORMERLY SUBROUTINE HTERP
C> - (USED ONLY IN PREVENTS MODE)
C> @param OEMIN - REAL MINIMUM VALUE FOR OBS ERROR (FOR VARIABLE BEING
C> - INTERPOLATED)
C> @return OEFG01 OBSERVATION ERROR
C>
C> REMARKS: 'OEFG01' RETURNED IS OBSERVATION ERROR FOR VARIABLE "IE" IN
C> REPORT TYPE "TYP", INTERPOLATED TO PRESSURE LEVEL "P".
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4 changes: 2 additions & 2 deletions sorc/global_cycle.fd/docs/Doxyfile.in
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Expand Up @@ -854,7 +854,7 @@ WARN_LOGFILE =
# spaces. See also FILE_PATTERNS and EXTENSION_MAPPING
# Note: If this tag is empty the current directory is searched.

INPUT = @abs_top_srcdir@/sorc/global_cycle.fd/docs/user_guide.md \
INPUT = @abs_top_srcdir@/sorc/global_cycle.fd/docs/global_cycle.md \
@abs_top_srcdir@/sorc/global_cycle.fd

# This tag can be used to specify the character encoding of the source files
Expand Down Expand Up @@ -1015,7 +1015,7 @@ FILTER_SOURCE_PATTERNS =
# (index.html). This can be useful if you have a project on for instance GitHub
# and want to reuse the introduction page also for the doxygen output.

USE_MDFILE_AS_MAINPAGE = user_guide.md
USE_MDFILE_AS_MAINPAGE = global_cycle.md

#---------------------------------------------------------------------------
# Configuration options related to source browsing
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5 changes: 5 additions & 0 deletions sorc/global_cycle.fd/docs/README.md
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This program updates the GFS surface conditions using
external snow and sea ice analyses. It updates monthly climatological
fields such as plant greenness fraction and albedo.

Documentation may be found at https://ufs-community.github.io/UFS_UTILS
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4 changes: 2 additions & 2 deletions sorc/grid_tools.fd/docs/Doxyfile.in
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Expand Up @@ -854,7 +854,7 @@ WARN_LOGFILE =
# spaces. See also FILE_PATTERNS and EXTENSION_MAPPING
# Note: If this tag is empty the current directory is searched.

INPUT = @abs_top_srcdir@/sorc/grid_tools.fd/docs/user_guide.md \
INPUT = @abs_top_srcdir@/sorc/grid_tools.fd/docs/grid_tools.md \
@abs_top_srcdir@/sorc/grid_tools.fd

# This tag can be used to specify the character encoding of the source files
Expand Down Expand Up @@ -1015,7 +1015,7 @@ FILTER_SOURCE_PATTERNS =
# (index.html). This can be useful if you have a project on for instance GitHub
# and want to reuse the introduction page also for the doxygen output.

USE_MDFILE_AS_MAINPAGE = user_guide.md
USE_MDFILE_AS_MAINPAGE = grid_tools.md

#---------------------------------------------------------------------------
# Configuration options related to source browsing
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3 changes: 3 additions & 0 deletions sorc/grid_tools.fd/docs/README.md
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@@ -0,0 +1,3 @@
Utility programs for creating model grids.

Documentation may be found at https://ufs-community.github.io/UFS_UTILS
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4 changes: 2 additions & 2 deletions sorc/lsm_routines.fd/docs/Doxyfile.in
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Expand Up @@ -854,7 +854,7 @@ WARN_LOGFILE =
# spaces. See also FILE_PATTERNS and EXTENSION_MAPPING
# Note: If this tag is empty the current directory is searched.

INPUT = @abs_top_srcdir@/sorc/lsm_routines.fd/docs/user_guide.md
INPUT = @abs_top_srcdir@/sorc/lsm_routines.fd/docs/lsm_routines.md

# This tag can be used to specify the character encoding of the source files
# that doxygen parses. Internally doxygen uses the UTF-8 encoding. Doxygen uses
Expand Down Expand Up @@ -1014,7 +1014,7 @@ FILTER_SOURCE_PATTERNS =
# (index.html). This can be useful if you have a project on for instance GitHub
# and want to reuse the introduction page also for the doxygen output.

USE_MDFILE_AS_MAINPAGE = user_guide.md
USE_MDFILE_AS_MAINPAGE = lsm_routines.md

#---------------------------------------------------------------------------
# Configuration options related to source browsing
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4 changes: 4 additions & 0 deletions sorc/lsm_routines.fd/docs/README.md
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This directory contains land surface model-specific routines that are
utilised elsewhere within UFS_UTILS.

Documentation may be found at https://ufs-community.github.io/UFS_UTILS
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4 changes: 2 additions & 2 deletions sorc/lsm_routines.fd/noah.fd/docs/Doxyfile.in
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Expand Up @@ -857,7 +857,7 @@ WARN_LOGFILE =
# spaces. See also FILE_PATTERNS and EXTENSION_MAPPING
# Note: If this tag is empty the current directory is searched.

INPUT = @abs_top_srcdir@/sorc/lsm_routines.fd/noah.fd/docs/user_guide.md \
INPUT = @abs_top_srcdir@/sorc/lsm_routines.fd/noah.fd/docs/noah.md \
@abs_top_srcdir@/sorc/lsm_routines.fd/noah.fd/

# This tag can be used to specify the character encoding of the source files
Expand Down Expand Up @@ -1018,7 +1018,7 @@ FILTER_SOURCE_PATTERNS =
# (index.html). This can be useful if you have a project on for instance GitHub
# and want to reuse the introduction page also for the doxygen output.

USE_MDFILE_AS_MAINPAGE = user_guide.md
USE_MDFILE_AS_MAINPAGE = noah.md

#---------------------------------------------------------------------------
# Configuration options related to source browsing
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Expand Up @@ -10,4 +10,4 @@ set_soilveg.f -> needed some changes for doxygen

sflx_snippet.f is a snippet of the file sflx.F, with minor changes to compil, and to enable frh2o routine to be called externally.


For complete documentation, see https://ufs-community.github.io/UFS_UTILS
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4 changes: 2 additions & 2 deletions sorc/orog_mask_tools.fd/docs/Doxyfile.in
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Expand Up @@ -854,7 +854,7 @@ WARN_LOGFILE =
# spaces. See also FILE_PATTERNS and EXTENSION_MAPPING
# Note: If this tag is empty the current directory is searched.

INPUT = @abs_top_srcdir@/sorc/orog_mask_tools.fd/docs/user_guide.md \
INPUT = @abs_top_srcdir@/sorc/orog_mask_tools.fd/docs/orog_mask_tools.md \
@abs_top_srcdir@/sorc/orog_mask_tools.fd

# This tag can be used to specify the character encoding of the source files
Expand Down Expand Up @@ -1015,7 +1015,7 @@ FILTER_SOURCE_PATTERNS =
# (index.html). This can be useful if you have a project on for instance GitHub
# and want to reuse the introduction page also for the doxygen output.

USE_MDFILE_AS_MAINPAGE = user_guide.md
USE_MDFILE_AS_MAINPAGE = orog_mask_tools.md

#---------------------------------------------------------------------------
# Configuration options related to source browsing
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4 changes: 4 additions & 0 deletions sorc/orog_mask_tools.fd/docs/README.md
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These programs are used in creating the terrain and land mask for
a model grid.

Documentation may be found at https://ufs-community.github.io/UFS_UTILS
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4 changes: 2 additions & 2 deletions sorc/sfc_climo_gen.fd/docs/Doxyfile.in
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Expand Up @@ -854,7 +854,7 @@ WARN_LOGFILE =
# spaces. See also FILE_PATTERNS and EXTENSION_MAPPING
# Note: If this tag is empty the current directory is searched.

INPUT = @abs_top_srcdir@/sorc/sfc_climo_gen.fd/docs/user_guide.md \
INPUT = @abs_top_srcdir@/sorc/sfc_climo_gen.fd/docs/sfc_climo_gen.md \
@abs_top_srcdir@/sorc/sfc_climo_gen.fd

# This tag can be used to specify the character encoding of the source files
Expand Down Expand Up @@ -1015,7 +1015,7 @@ FILTER_SOURCE_PATTERNS =
# (index.html). This can be useful if you have a project on for instance GitHub
# and want to reuse the introduction page also for the doxygen output.

USE_MDFILE_AS_MAINPAGE = user_guide.md
USE_MDFILE_AS_MAINPAGE = sfc_climo_gen.md

#---------------------------------------------------------------------------
# Configuration options related to source browsing
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4 changes: 4 additions & 0 deletions sorc/sfc_climo_gen.fd/docs/README.md
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This program creates climatological surface fields on the model grid,
such as soil type and albedo.

Documentation may be found at https://ufs-community.github.io/UFS_UTILS
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4 changes: 2 additions & 2 deletions sorc/vcoord_gen.fd/docs/Doxyfile.in
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Expand Up @@ -854,7 +854,7 @@ WARN_LOGFILE =
# spaces. See also FILE_PATTERNS and EXTENSION_MAPPING
# Note: If this tag is empty the current directory is searched.

INPUT = @abs_top_srcdir@/sorc/vcoord_gen.fd/docs/user_guide.md \
INPUT = @abs_top_srcdir@/sorc/vcoord_gen.fd/docs/vcoord_gen.md \
@abs_top_srcdir@/sorc/vcoord_gen.fd

# This tag can be used to specify the character encoding of the source files
Expand Down Expand Up @@ -1015,7 +1015,7 @@ FILTER_SOURCE_PATTERNS =
# (index.html). This can be useful if you have a project on for instance GitHub
# and want to reuse the introduction page also for the doxygen output.

USE_MDFILE_AS_MAINPAGE = user_guide.md
USE_MDFILE_AS_MAINPAGE = vcoord_gen.md

#---------------------------------------------------------------------------
# Configuration options related to source browsing
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4 changes: 4 additions & 0 deletions sorc/vcoord_gen.fd/docs/README.md
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This program generates the parameters needed to define
the forecast model's hybrid levels.

Documentation may be found at https://ufs-community.github.io/UFS_UTILS
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