Fix or delete examples

[bendudson]

Work in progress.

Aiming to clean up the examples, to ensure that they all work. I think the number of examples should also be reduced, either by deleting them or moving them to a separate repository.

We should also have little test in each example, that at least ensures that the example builds and runs a short step.

• [x] 2Dturbulence_multigrid
• [x] 6field-simple
• [x] advdiff
• [x] advdiff2
• [x] backtrace
• [x] blob2d
• [ ] blob2d-laplacexz
• [ ] blob2d-outerloop
• [ ] boundary-conditions
• [x] boutcore
• [ ] boutpp
• [x] conducting-wall-mode
• [x] conduction
• [ ] conduction-snb
• [ ] constraints
• [x] dalf3
• [ ] eigen-box
• [ ] elm-pb
• [ ] elm-pb-outerloop
• [x] em-drift
• [ ] fci-wave
• [x] fci-wave-logn
• finite-volume
  • [ ] diffusion
  • [ ] fluid
  • [ ] test
• [x] gas-compress
• [x] gravity_reduced
• [ ] gyro-gem
• [x] hasegawa-wakatani
• [ ] hasegawa-wakatani-3d
• IMEX
  • [ ] advection-diffusion
  • [ ] advection-reaction
  • [ ] diffusion-nl
  • [ ] drift-wave
  • [ ] drift-wave-constraint
• [ ] invertable_operator
• [x] jorek-compare
• [x] lapd-drift
• [ ] laplace-petsc3d
• [ ] laplacexy
• [x] make-script
• [x] monitor
• [ ] monitor-newapi
• [x] orszag-tang
• performance
  • [ ] arithmetic
  • [ ] arithmetic_3d2d
  • [ ] bracket
  • [ ] communications
  • [ ] ddx
  • [ ] ddy
  • [ ] ddz
  • [ ] iterator
  • [ ] iterator-offsets
  • [ ] laplace
  • [ ] tuning_regionblocksize
• preconditioning
  • [ ] wave
• [x] reconnect-2field
• [x] shear-alfven-wave
• [ ] lstaggered_grid
• [ ] subsampling
• [x] tokamak-2fluid
• [x] uedge-benchmark
• [ ] wave-slab
• [x] zoidberg

[ZedThree]

Suggestions for deletion:

• 2Dturbulence_multigrid
  • Demonstrates a solver, could done with an input file for a different model
  • Move to separate repo?
• advdiff
  • I don't think this does what it says it does
• advdiff2
  • Same as advdiff but split over multiple files -- not necessarily a useful example?
• backtrace
  • Could just put the output in the docs?
• blob2d-laplacexz
  • Possibly squash into blob2d?
• ~~boutcore~~
  • ~~Think this has been replaced by boutpp? @dschwoerer ? edit: was incomplete move, resolved~~
• em-drift
  • Similar model to others?
• fci-wave-logn
  • Similar to fci-wave
• laplace-petsc3d
  • Is this maybe supposed to be a test?
• monitor
  • Old API -- should delete the API as well!
• staggered_grid
  • Maybe a test?
• subsampling
  • Maybe just documentation?
• zoidberg
  • Should be in zoidberg repo?

Move to separate repos?

• 6field-simple
• dalf3
• elm-pb[-outerloop]
• gravity_reduced
• gyro-gem
• hasegawa-wakatani-3d
• jorek-compare
• lapd-drift
• reconnect-2field
• tokamak-2fluid
• uedge-benchmark

[dschwoerer]

(sorry, I did a bad merge, and then a force push to fix it.)

[dschwoerer]

I have a fix for fci-wave in my db-outer branch, but that will require some of my other open PRs to work ... fci-wave has an example 'logn' - so I deleted fci-wave-logn ...