Feature 1852 use case physics tendency

[bikegeek]

Pull Request Testing

• Describe testing already performed for these changes:
  

1. on host 'seneca', using met_test conda environment metplotpy.v5:

conda activate /home/met_test/.conda/envs/metplotpy.v5

2. Clone the METplus feature_1852_useCase_physics_tendency repo

3. Under the same 'base' directory as the METplus repo, clone the METplotpy 'develop' branch (METplus and METplotpy will be at the same directory level)

4. Obtain the short_range data tarball from host 'mohawk':
   /d2/www/dtcenter/dfiles/code/METplus/METplus_Data/v5.0/sample_data-short_range-5.0.tgz

5. Uncompress the tarball

6. Set the following environment variables on 'seneca' :

• MET_BUILD_BASE (set to /usr/local/met-10.0.0 for 'seneca')
• METPLUS_DATA (set to location of uncompressed data in step 5)
• METPLUS_BASE (set to location of the METplus source code)

7. Create user_system.conf file and set the:

• OUTPUT_BASE
• INPUT_BASE = {ENV[METPLUS_DATA]}
• MET_INSTALL_DIR = /usr/local/met-10.0.0

8. Generate the planview plot:
   python run_metplus.py
   path/to/parm/use_cases/model_applications/short_range/UserScript_fcstFV3_fcstOnly_PhysicsTendency_Planview.conf /your/path/to/user_system.conf

In the OUTPUT_BASE/plots directory, you will find the short_range-physics_tendency_planview.png

9. Repeat the above steps to generate the Vertical Profile plot, except use this conf file with the same user_system.conf file:
   UserScript_fcstFV3_fcstOnly_PhysicsTendency_VerticalProfile.conf

In the OUTPUT_BASE/plots directory, you will find the short_range-physics_tendency_vertical_profile.png

![Screen Shot 2022-10-20 at 10 28 02 AM](https://user-images.githubusercontent.com/3753118/197005904-07bb7c7c-c5f7-4941-8f68-4801dbc64209.png

10. Generate the Vertical Cross Section plots by repeating, except use this conf file:
    UserScript_fcstFV3_fcstOnly_PhysicsTendency_VerticalCrossSection.conf
    with the same user_system.conf file.

You will find the short_range-physics_tendency_vertical_cross_section.png in the OUTPUT_BASE/plots directory.

• Recommend testing for the reviewer(s) to perform, including the location of input datasets, and any additional instructions:
  
  Perform same steps as above

• Do these changes include sufficient documentation updates, ensuring that no errors or warnings exist in the build of the documentation? [Yes ]

• Do these changes include sufficient testing updates? [Yes]

• Will this PR result in changes to the test suite? [Yes]
  
  If yes, describe the new output and/or changes to the existing output:
  New data

• Please complete this pull request review by [Earliest convenience to meet beta4 release].
  

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[georgemccabe]

I am just reviewing the use case config format and execution in the automated tests. @fisherhucar will review the use case documentation.

I did not run the use cases on seneca, but I reviewed the use case runs in GitHub Actions and confirmed that they ran successfully. I downloaded the output data generated from the use cases and confirmed that the images look good. I confirmed that the only differences (besides other use case groups' output that were recently updated since this PR) are due to new output images created by the use cases, which is expected.

The use case config files are well organized based on the new ordering structure. My only suggestion would be to pull out arguments found in the USER_SCRIPT_COMMAND and values set in the YAML file that a user may want to adjust into variables in the METplus config file and reference those variables in the command and YAML. This is optional, but would be nice to add at some point so that it is easier for users to take this example and adjust it as needed.

For example, if fv3_history.nc file is an input to the script that a user may want to change, you could put that into a variable and reference it in the user script command. You could also pull out the pressure level (assuming -p 500 sets the pressure level to use?).

Before:

USER_SCRIPT_COMMAND = {PARM_BASE}/use_cases/model_applications/short_range/UserScript_fcstFV3_fcstOnly_PhysicsTendency_Planview/planview_plot.py {PARM_BASE}/use_cases/model_applications/short_range/UserScript_fcstFV3_fcstOnly_PhysicsTendency_Planview/physics_tendency_planview.yaml {INPUT_BASE}/model_applications/short_range/UserScript_fcstFV3_fcstOnly_PhysicsTendency/fv3_history.nc {INPUT_BASE}/model_applications/short_range/UserScript_fcstFV3_fcstOnly_PhysicsTendency/grid_spec.nc tmp pbl -p 500 -t 1 -v 20190504T14 -o {OUTPUT_BASE}/plots/short_range-physics_tendency_planview.png --nofineprint

After:

FV3_HISTORY_FILE = {INPUT_BASE}/model_applications/short_range/UserScript_fcstFV3_fcstOnly_PhysicsTendency/fv3_history.nc
PRESSURE_LEVEL = 500

USER_SCRIPT_COMMAND = {PARM_BASE}/use_cases/model_applications/short_range/UserScript_fcstFV3_fcstOnly_PhysicsTendency_Planview/planview_plot.py {PARM_BASE}/use_cases/model_applications/short_range/UserScript_fcstFV3_fcstOnly_PhysicsTendency_Planview/physics_tendency_planview.yaml {FV3_HISTORY_FILE} {INPUT_BASE}/model_applications/short_range/UserScript_fcstFV3_fcstOnly_PhysicsTendency/grid_spec.nc tmp pbl -p {PRESSURE_LEVEL} -t 1 -v 20190504T14 -o {OUTPUT_BASE}/plots/short_range-physics_tendency_planview.png --nofineprint

Again this is optional cleanup and isn't required for this PR. I approve.

[georgemccabe]

Note that after this PR is merged, we will need to update the develop-ref branch to include the new output that is generated by these 3 use cases.

[hankenstein2]

Everything looks good documentation wise.