documentation updates

[DeniseWorthen]

PR Checklist

• Ths PR is up-to-date with the top of all sub-component repositories except for those sub-components which are the subject of this PR. Please consult the ufs-weather-model wiki if you are unsure how to do this.

• This PR has been tested using a branch which is up-to-date with the top of all sub-component repositories except for those sub-components which are the subject of this PR

• An Issue describing the work contained in this PR has been created either in the subcomponent(s) or in the ufs-weather-model. The Issue should be created in the repository that is most relevant to the changes in contained in the PR. The Issue and the dependent sub-component PR
  are specified below.

• If new or updated input data is required by this PR, it is clearly stated in the text of the PR.

Instructions: All subsequent sections of text should be filled in as appropriate.

The information provided below allows the code managers to understand the changes relevant to this PR, whether those changes are in the ufs-weather-model repository or in a subcomponent repository. Ufs-weather-model code managers will use the information provided to add any applicable labels, assign reviewers and place it in the Commit Queue. Once the PR is in the Commit Queue, it is the PR owner's responsiblity to keep the PR up-to-date with the develop branch of ufs-weather-model.

Description

Updates current ufs-weather-model documentation for additions of coupled components and applications.
RTD version can be viewed here

Issue(s) addressed

Fixes #464

Additional updates will still be required for the documentation, including a possible reorg now that we have so many components and applications

Testing

None required.

How were these changes tested? What compilers / HPCs was it tested with? Are the changes covered by regression tests? (If not, why? Do new tests need to be added?) Have regression tests and unit tests (utests) been run? On which platforms and with which compilers? (Note that unit tests can only be run on tier-1 platforms)

• hera.intel
• hera.gnu
• orion.intel
• cheyenne.intel
• cheyenne.gnu
• gaea.intel
• jet.intel
• wcoss_cray
• wcoss_dell_p3
• CI

Dependencies

None

Co-authors:

@binli2337
@jiandewang
@aliabdolali
@junwang-noaa
@MinsukJi-NOAA

[junwang-noaa]

Since it will be replaced by NG-GODAS, I think it is OK not including NG-GODAS-NEMSDATM until there is a request.

…

On Fri, Jul 30, 2021 at 11:37 AM BinLi-NOAA ***@***.***> wrote: ***@***.**** commented on this pull request. ------------------------------ In doc/UsersGuide/source/InputsOutputs.rst <#721 (comment)> : > + :widths: 10 70 + :header-rows: 1 + + * - App name + - Description + * - ATM + - Standalone UFSAtm + * - ATMW + - UFSAtm coupled to WW3 + * - ATMAERO + - UFSAtm coupled to GoCart + * - S2S + - Coupled UFSATM-MOM6-CICE6-CMEPS + * - S2SW + - Coupled UFSATM-MOM6-CICE6-WW3-CMEPS + * - DATM @junwang-noaa <https://github.com/junwang-noaa> @DeniseWorthen <https://github.com/DeniseWorthen> I think DATM should be changed to NG-GODAS. I am not sure whether we need to include NG-GODAS-NEMSDATM and related input files? — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#721 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AI7D6TNDACBKMMZXMFPFICDT2LBLRANCNFSM5BFD4CHA> .

[junwang-noaa]

How do we update the image file?

…

On Fri, Jul 30, 2021 at 11:45 AM Denise Worthen ***@***.***> wrote: ***@***.**** commented on this pull request. ------------------------------ In doc/UsersGuide/source/InputsOutputs.rst <#721 (comment)> : > @@ -685,7 +1385,7 @@ Note that the sfcf* and atmf* files are not output on the 6 tiles, but instead a The regional configuration will generate similar output files, but the *tile[1-6]* is not included in the filename. -Two files (*model_configure* and *diag_table*) control the output that is generated by the UFS Weather Model. The output files that contain the model variables are written to a file as shown in the figure below. The format of these output files is selected in *model_configure* as NetCDF or nemsio. The information in these files may be remapped, augmented with derived variables, and converted to GRIB2 by the Unified Post Processor (UPP). Model variables are listed in the *diag_table* in two groupings, *fv3_history* and *fv3_history2d*, as described in :numref:`Section %s <diag_tableFile>`. The names of the files that contain these model variables are specified in the *model_configure* file. When *quilting* is set to *.true.* for the write component, the variables listed in the groups *fv3_history* and *fv3_history2d* are converted into the two output files named in the *model_configure* file, e.g. *atmfHHH.* and *sfcfHHH.*. The bases of the file names (*atm* and *sfc*) are specified in the *model_configure* file, and *HHH* refers to the forecast hour. +Two files (*model_configure* and *diag_table*) control the output that is generated by the UFS Weather Model. The output files that contain the model variables are written to a file as shown in the figure below. The format of these output files is selected in *model_configure* as NetCDF. The information in these files may be remapped, augmented with derived variables, and converted to GRIB2 by the Unified Post Processor (UPP). Model variables are listed in the *diag_table* in two groupings, *fv3_history* and *fv3_history2d*, as described in :numref:`Section %s <diag_tableFile>`. The names of the files that contain these model variables are specified in the *model_configure* file. When *quilting* is set to *.true.* for the write component, the variables listed in the groups *fv3_history* and *fv3_history2d* are converted into the two output files named in the *model_configure* file, e.g. *atmfHHH.* and *sfcfHHH.*. The bases of the file names (*atm* and *sfc*) are specified in the *model_configure* file, and *HHH* refers to the forecast hour. .. image:: _static/fv3IO.png I can add a figure caption; I made a guess at a reasonable one. Also, I noticed the image file needs to be updated because we've renamed the output to atmf and sfcf instead of dynf and phyf. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#721 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AI7D6TJTQAVJBZND2FUKU2DT2LCIFANCNFSM5BFD4CHA> .

[DeniseWorthen]

There is a fv3IO.png file stored in UserGuide/source/_static that is used.

[junwang-noaa]

I think we can ask Laurie to update the fv3IO.png file later as we still have several tests using "dynf"/"phys" for history files.