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Update more documentation after move to ufs-community #597

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Nov 5, 2021
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Update more documentation after move to ufs-community #597

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a6e202d
Update doxygen for move to ufs-community.
GeorgeGayno-NOAA Nov 5, 2021
4cc6b7b
Merge branch 'develop' into feature/docs
GeorgeGayno-NOAA Nov 5, 2021
e589e9d
Minor updates to sorc/fvcom_tools.fd/docs/user_guide.md
GeorgeGayno-NOAA Nov 5, 2021
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4 changes: 2 additions & 2 deletions sorc/chgres_cube.fd/docs/user_guide.md
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Expand Up @@ -11,8 +11,8 @@ Common Data Form (NetCDF) data.
This document is part of the <a href="../index.html">UFS_UTILS
documentation</a>.

The chgres_cube program is part of the [NCEPLIBS
UFS_UTILS](https://github.com/NOAA-EMC/UFS_UTILS) project.
The chgres_cube program is part of the
[UFS_UTILS](https://github.com/ufs-community/UFS_UTILS) project.

## Where to find GFS GRIB2, NEMSIO and NetCDF data

Expand Down
8 changes: 2 additions & 6 deletions sorc/emcsfc_ice_blend.fd/docs/user_guide.md
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Expand Up @@ -10,9 +10,5 @@ analysis used to update the GFS once per day.
This document is part of the <a href="../index.html">UFS_UTILS
documentation</a>.

The emcsfc_ice_blend program is part of the [NCEPLIBS
UFS_UTILS](https://github.com/NOAA-EMC/UFS_UTILS) project.




The emcsfc_ice_blend program is part of the
[UFS_UTILS](https://github.com/ufs-community/UFS_UTILS) project.
6 changes: 2 additions & 4 deletions sorc/emcsfc_snow2mdl.fd/docs/user_guide.md
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Expand Up @@ -10,7 +10,5 @@ analysis used to update the GFS snow field once per day.
This document is part of the <a href="../index.html">UFS_UTILS
documentation</a>.

The emcsfc_snow2mdl program is part of the [NCEPLIBS
UFS_UTILS](https://github.com/NOAA-EMC/UFS_UTILS) project.


The emcsfc_snow2mdl program is part of the
[UFS_UTILS](https://github.com/ufs-community/UFS_UTILS) project.
84 changes: 46 additions & 38 deletions sorc/fvcom_tools.fd/docs/user_guide.md
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@brief replaces lake surface and lake ice temperature @anchor user_guide

**fvcom_to_FV3.exe**

**Introduction:**
This code replaces lake surface and lake ice temperature along
with aerial ice concentration generated from Great Lakes
Operational Forecast System (GLOFS), an FVCOM-based model, into
sfc_data.nc.
**NOTE** that the variables in the input files must reside on
the same grid. This means data from FVCOM must be horizontally
interpolated to the FV3 grid. This routine will also force a
minimum ice concentration of 15%. If ice concentration is less
than 15% in FVCOM, it will be set to 0% to avoid FV3 from
changing values less than 15% to 15% and generating unrealistic
lake ice temperatures.

**Library Dependencies:**
Installation depends on the netCDF library and cmake.

**Running:**
This routine will take four variables from the command line:
1. Name of FV3 sfc data file (e.g. sfc_data.tile7.halo0.nc)
# fvcom_tools

# Introduction

This code replaces lake surface and lake ice temperature along
with aerial ice concentration generated from Great Lakes
Operational Forecast System (GLOFS), an FVCOM-based model, into
sfc_data.nc.

This document is part of the <a href="../index.html">UFS_UTILS
documentation</a>.

The fvcom_tools program is part of the
[UFS_UTILS](https://github.com/ufs-community/UFS_UTILS) project.

## NOTE

The variables in the input files must reside on
the same grid. This means data from FVCOM must be horizontally
interpolated to the FV3 grid. This routine will also force a
minimum ice concentration of 15%. If ice concentration is less
than 15% in FVCOM, it will be set to 0% to avoid FV3 from
changing values less than 15% to 15% and generating unrealistic
lake ice temperatures.

## Library Dependencies:

Installation depends on the netCDF library and cmake.

## Running

This routine will take four variables from the command line:
1. Name of FV3 sfc data file (e.g. sfc_data.tile7.halo0.nc)
which is generated from chgres_cube.exe.
2. Name of FVCOM data file in netcdf format (e.g. fvcom.nc)
3. "warm" or "cold" start. "warm" start will read in
2. Name of FVCOM data file in netcdf format (e.g. fvcom.nc)
3. "warm" or "cold" start. "warm" start will read in
sfc_data.nc files generated from a restart of UFS-SRW.
"cold" start will read in sfc_data.nc files generated
from chgres_cube.
4. String of time slice to use in the fvcom.nc file. This string
4. String of time slice to use in the fvcom.nc file. This string
should match exactly what is in the Times variable of the .nc file.
To run the script, use the following example, modifying file
names as needed:
To run the script, use the following example, modifying file
names as needed:
./fvcom_to_FV3 sfc_data.tile7.halo0.nc fvcom.nc cold \
2020-01-31T18:00:00.000000
Output will be to the sfc data file and include lake surface
and lake ice temperature, and lake ice concentration from the
first time in the FVCOM file.

Output will be to the sfc data file and include lake surface
and lake ice temperature, and lake ice concentration from the
first time in the FVCOM file.

This routine is *strongly* based upon Eric James' (ESRL/GSL) work
to update HRRR/WRF Great Lakes' temperature data with FVCOM.
It also relies heavily on Ming Hu's (ESRL/GSL) ncio module.
to update HRRR/WRF Great Lakes' temperature data with FVCOM.
It also relies heavily on Ming Hu's (ESRL/GSL) ncio module.

## For more information, please contact:

**For more information, please contact:**
David Wright
University of Michigan and GLERL
dmwright@umich.edu
David Wright, University of Michigan and GLERL: dmwright@umich.edu
8 changes: 2 additions & 6 deletions sorc/gblevents.fd/docs/user_guide.md
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Expand Up @@ -8,9 +8,5 @@ The gblevents program performs pre and post processing of prepbufr events.
This document is part of the <a href="../index.html">UFS_UTILS
documentation</a>.

The gblevents program is part of the [NCEPLIBS
UFS_UTILS](https://github.com/NOAA-EMC/UFS_UTILS) project.




The gblevents program is part of the
[UFS_UTILS](https://github.com/ufs-community/UFS_UTILS) project.
4 changes: 2 additions & 2 deletions sorc/global_cycle.fd/docs/user_guide.md
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Expand Up @@ -11,5 +11,5 @@ the GFS and GDAS cycles.
This document is part of the <a href="../index.html">UFS_UTILS
documentation</a>.

The global_cycle program is part of the [NCEPLIBS
UFS_UTILS](https://github.com/NOAA-EMC/UFS_UTILS) project.
The global_cycle program is part of the
[UFS_UTILS](https://github.com/ufs-community/UFS_UTILS) project.
7 changes: 2 additions & 5 deletions sorc/grid_tools.fd/docs/user_guide.md
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Expand Up @@ -14,8 +14,5 @@ The grid_tools include:
This document is part of the <a href="../index.html">UFS_UTILS
documentation</a>.

The grid_tools programs are part of the [NCEPLIBS
UFS_UTILS](https://github.com/NOAA-EMC/UFS_UTILS) project.



The grid_tools programs are part of the
[UFS_UTILS](https://github.com/ufs-community/UFS_UTILS) project.
4 changes: 2 additions & 2 deletions sorc/lsm_routines.fd/docs/user_guide.md
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Expand Up @@ -13,5 +13,5 @@ The land models included are:
- <a href="../noah/index.html">Noah</a> - routines
for the Noah land surface model.

The lsm_routines libraries are used in the [NCEPLIBS
UFS_UTILS](https://github.com/NOAA-EMC/UFS_UTILS) project.
The lsm_routines libraries are used in the
[UFS_UTILS](https://github.com/ufs-community/UFS_UTILS) project.
4 changes: 2 additions & 2 deletions sorc/lsm_routines.fd/noah.fd/docs/user_guide.md
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Expand Up @@ -21,5 +21,5 @@ This document is part of the <a href="../index.html">UFS_UTILS documentation.</a

The NOAH routines are included in the <a href="../lsm_routines/index.html">lsm_routines directory.</a>

The NOAH library created here is used in the [NCEPLIBS
UFS_UTILS](https://github.com/NOAA-EMC/UFS_UTILS) project.
The NOAH library created here is used in the
[UFS_UTILS](https://github.com/ufs-community/UFS_UTILS) project.
6 changes: 2 additions & 4 deletions sorc/orog_mask_tools.fd/docs/user_guide.md
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Expand Up @@ -11,7 +11,5 @@ The orog_mask_tools include:
This document is part of the <a href="../index.html">UFS_UTILS
documentation</a>.

The orog_mask_tools programs are part of the [NCEPLIBS
UFS_UTILS](https://github.com/NOAA-EMC/UFS_UTILS) project.


The orog_mask_tools programs are part of the
[UFS_UTILS](https://github.com/ufs-community/UFS_UTILS) project.
6 changes: 2 additions & 4 deletions sorc/sfc_climo_gen.fd/docs/user_guide.md
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Expand Up @@ -9,7 +9,5 @@ fields, such as vegetation type and albedo, for an FV3 grid.
This document is part of the <a href="../index.html">UFS_UTILS
documentation</a>.

The orog_mask_tools programs are part of the [NCEPLIBS
UFS_UTILS](https://github.com/NOAA-EMC/UFS_UTILS) project.


The orog_mask_tools programs are part of the
[UFS_UTILS](https://github.com/ufs-community/UFS_UTILS) project.
6 changes: 2 additions & 4 deletions sorc/vcoord_gen.fd/docs/user_guide.md
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Expand Up @@ -11,7 +11,5 @@ by the forecast model to define the hybrid levels.
This document is part of the <a href="../index.html">UFS_UTILS
documentation</a>.

The vcoord_gen programs are part of the [NCEPLIBS
UFS_UTILS](https://github.com/NOAA-EMC/UFS_UTILS) project.


The vcoord_gen programs are part of the
[UFS_UTILS](https://github.com/ufs-community/UFS_UTILS) project.