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Tuesday: Working with Models
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Today we will explore making changes to the yaml files that control the variational application. 

First download a fresh copy of the ``hyb-3dvar.yaml``

  ``wget http://academy.jcsda.org/june2019/hyb-3dvar.yaml``

This fixes one thing needed for the trajectory that was recently merged and updates the variables.

**Exercise 1: Run a hybrid-fgat assimilation**

- Copy the config files and rename ``hyb-3dvar`` to ``hyb-fgat``. This is the new experiment name.

- Update instances of experiment name in all the yaml files

- Background and ensemble time changes from 20180415 00z to 20180414 21z

- Add ``u`` and ``v`` to the background variables. They are needed to start the model.

- Change the time step from 3 hours to 1 hour. This is how often we analyze the observations.

- Cost function needs to change from 3D-Var in the yaml, can you find the cost function factories in oops/src/oops/assimilation/? Tip: you have to find the file that instantiates the cost factory. FGAT uses the 4DVar cost function so change to that in the yaml, the exact name comes from the factory file.

- Remove the second outer loop from variational: iteration: (Tip: the second outer loop has 5 inner loop iterations).

- ``./run.bash hyb-fgat``

- Plot the new increment with Panoply and check Jo/n in the log

**Exercise 2: Run a hybrid 4d-var**

Starting from the fgat run change the linear model to use the actual tlm and adjoint of fv3.

Tips:

1. The LinearModel is no longer named Id in the version or type and the VarChange is now Analysis2Model.
2. The variables for the LinearModel & traj are now: ``variables: ["ud","vd","T","delp","sphum","ice_wat","liq_wat","o3mr"]``
3. You'll need some more things in the configuration:

  ``lm_do_dyn: 1``

  ``lm_do_trb: 0``

  ``lm_do_mst: 0``

  ``nml_file: Data/fv3files/input_gfs_c12.nml``

  ``trc_file: Data/fv3files/field_table``

  ``nml_file_pert: Data/fv3files/inputpert_4dvar.nml``

- Plot increment and check Jo/n in the log

**Exercise 3: Examine BUMP dirac test output**

One of the regression tests run when building Jedi was a dirac test for GEOS.

  ``test_fv3jedi_dirac_geos``

It produced the output:

  ``build/fv3-jedi/test/Data/bump/dirac.loc.20180414_210000z.nc4``

Copy this file and open it with Panoply. The increment is at level 50 of ``ua``.

Now try modifying ``rh`` and ``rv`` in:

  ``build/fv3-jedi/test/testinput/bumpparameters_loc_geos.yaml``.

You can also modify ``build/fv3-jedi/test/testinput/dirac_geos.yaml`` - e.g. you can add more Dirac tests or change the variable and position.

Once you've modified rh and rv test by re-running 

  ``ctest -R test_fv3jedi_bumpparameters_loc``

  ``ctest -R test_fv3jedi_dirac_geos``

Plot the increment again and look at the impact of changing rh and rv.

**Exercise 4 (optional): Adapt the hyb-3dvar.yaml to run 4denvar.yaml**

Tip, there's an example here: ``oops/qg/test/testinput/4densvar_bump.yaml``