Adding new features to WRF scripting and tutorial

[braczka]

Description:

This adds several new important features when running WRF-DART. This imposes a mandatory fix which should improve forecasting skill, but also adds features requested by users regarding commonly used scientific setups and diagnostics.

1. Generalizes scripting to apply to multiple domain (nested) WRF DA setups.
2. Adds a new scientific tutorial example with nested setup (Kansas Derecho), which is also back-compatible with prior CONUS severe storm tutorial example. Tutorial designed to be less computationally expensive (than CONUS tutorial) for ease of use.
3. Imposes mandatory terrain-following atmospheric coordinate setup (opposed to default sigma-hybrid) to eliminate boundary condition bug during perturbation step. This fix has shown to improve forecasting skill.
4. Scripting includes built-in downscaling technique to pass perturbations from parent domain to nested domain.
5. Adds full work through of the generation of perturbations using WRFDA CV3. Prior tutorial skipped through this step and required the user to download perturbations manually.
6. Makes bash scripting the default scripting language. Prior csh language is limited in functionality and many users systems do not support csh (e.g. problems with loading modules etc.) This PR includes csh nested scripting as a backup reference.
7. Adds full description of switching between "assimilation mode" and "forecast mode" using namelist settings. Most WRF users apply forecasting after the assimilation period for scientific applications.

Fixes issue

Fixes issues #807 and imposes Kansas Derecho example as described in that issue.

Types of changes

• Bug fix (non-breaking change which fixes an issue)
• New feature (non-breaking change which adds functionality)
• Breaking change (fix or feature that would cause existing functionality to not work as expected)
• Documentation update

Documentation changes needed?

• My change requires a change to the documentation.
• I have updated the documentation accordingly.
  This change requires new documentation for the Kansas Derecho tutorial that supplants the prior CONUS tutorial example. The documentation parallels the prior documentation, but will add important new features such as 1) perturbation downscaling, 2) forecast mode, 3) expanded diagnostics.

Tests

I have tested the default bash scripting on the Kansas Derecho WRF-DART example. Completed example is located here: /glade/derecho/scratch/bmraczka/WRFv4.5_kansas.
I have tested csh nested scripting (backup) here: /glade/derecho/scratch/bmraczka/WRFv4.5_nested_hybridopt_0

Testing for backcompatibility of the CONUS tutorial example is here:

Checklist for merging

• Updated changelog entry
• Documentation updated
• Update conf.py

Checklist for release

• Merge into main
• Create release from the main branch with appropriate tag
• Delete feature-branch

Testing Datasets

• Dataset needed for testing available upon request
• Dataset download instructions included
• No dataset needed

The Kansas Derecho tutorial example requires NCEP observation (obs_seq) files for the application. For now these are located here: /glade/work/bmraczka/DART/observations/obs_converters/NCEP/ascii_to_obs/work Existing prep_bufr obs converter documentation was used to create these obs.

[braczka]

The bash and csh scripting designed for a nested WRF DA setup included in this PR seems robust as it has been tested for Kansas Derecho and CONUS examples. This PR still requires tutorial documentation for Kansas Derecho tutorial example. Seemed relevant to add this PR now as a draft considering the number of WRF-DART users who are converting csh to bash on their own, which could lead to problems. Better to provide a vetted bash scripting version now to help reduce support issues.

[braczka]

Backcompatiblity for the new multi-domain shell scripting tested for the original (old) CONUS single WRF domain setup here: /glade/derecho/scratch/bmraczka/WRFv4.5_conus/. Produces similar scientific results.