rust: upgrade examples from structopt to clap-4

Structopt is deprecated because the functionality was merged into clap.

petsc - drop VecZero in diag assembly

some clean-up

fluids: Refactor STG wall distance variable

- Needless shortening.
- Confused me when debugging even though I wrote the code myself...

fluids: Fix STG Ek_tot calculation bug

When the spectrum is small enough, Ek_tot can be zero, causing a
divide-by-zero NaN, which then corrupts the calculation of the velocity
fluctuations later dow

fluids: Fix STG Ek_tot calculation bug

When the spectrum is small enough, Ek_tot can be zero, causing a
divide-by-zero NaN, which then corrupts the calculation of the velocity
fluctuations later down the line.

Originally found during OLCF Crusher Hackathon 4

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examples/petsc: fix missing PetscFunctionBegin

Fluids - Blasius: Some Minor Modifications (#1063)

* Fluids - blasius: default T_wall = T_inf = 288

* Fluids - blasius: break when Chebyshev solve diverges

* Fluids - blasius: add prefix for C

Fluids - Blasius: Some Minor Modifications (#1063)

* Fluids - blasius: default T_wall = T_inf = 288

* Fluids - blasius: break when Chebyshev solve diverges

* Fluids - blasius: add prefix for Chebyshev snes solve

* Fluids - blasius: N_Chebyshev -> n_chebyshev

* Update examples/fluids/tests-output/blasius_test.yaml

Co-authored-by: Jed Brown <jed@jedbrown.org>

* Fluids - blasius: Modify the parameters in the regression test

* examples/fluids: Blasius solution is variable density

We use the ideal gas relation that density ~ 1/enthalpy when held at
constant pressure.

* examples/fluids: Blasius slower growth factor

* examples/fluids: fix Chebyshev on GPU

and close memory leak

Co-authored-by: Jed Brown <jed@jedbrown.org>

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fluids: Fix time label for strong STG #1057

Fluids - fix blasius test

Fluids - Some fixes missing from #1039 (#1056)

* Fluids - Blasius: drop theta0, style, and update README

* Fluids - Add regression test for laminar blasius

fluids: Add STATIC and print-% to makefile

fluids: Set solution time label for strong stg

Fluids - Compressible Blasius boundary layer (#1039)

* Fluids - Compressible Blasius boundary layer solution

* Fluids - Blasius: default delta0 = 4.2e-3

* Fluids - Use the new helper functions

Fluids - Compressible Blasius boundary layer (#1039)

* Fluids - Compressible Blasius boundary layer solution

* Fluids - Blasius: default delta0 = 4.2e-3

* Fluids - Use the new helper functions in blasius

* Update examples/fluids/qfunctions/blasius_exact.h

Co-authored-by: Jed Brown <jed@jedbrown.org>

* Update examples/fluids/qfunctions/blasius_exact.h

Co-authored-by: Jed Brown <jed@jedbrown.org>

* Fluids - remove blasius_exact.h

* Fluids - N_Chebyshev: 10 -> 20

Co-authored-by: Jed Brown <jed@jedbrown.org>

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doc: Update fluids state_var option

fluids: Switch to StateVar enum

fluids: Use newtonian with StateFromQi*_t func pointers

This to "unify" the primitive and conservative formulations of the
newtonian solver. By passing function pointers to a helper function, the
co

fluids: Use newtonian with StateFromQi*_t func pointers

This to "unify" the primitive and conservative formulations of the
newtonian solver. By passing function pointers to a helper function, the
compiler can optimize for a given state function(s).

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fluids: Use StateFromQi* for newt boundary QFs

fluids: Add FluxTotal_Boundary, Refactor newt BI QFs

- Refactoring the newtonian boundary integral QFunctions

fluids: Rename primitive booleans, misc formatting

QF headers for typedefs and macros (#1036)

* jit - qf headers for typedefs and macros

* jit - smaller list of permitted files

* ceed - only include ceed.h in QF source

Fixed dXdx definition in setupgeo2d.h (#1034)

fluids: Fix for loop variable initialization

Fluids - Minor Refactor (#995)

* Fluids - remove *.bin* since it exists in libCEED/.gitignore

* cleanup

* WIP: Fluids - use FluxInviscid_fwd() for computing the flux jacobean

strong_conv is

Fluids - Minor Refactor (#995)

* Fluids - remove *.bin* since it exists in libCEED/.gitignore

* cleanup

* WIP: Fluids - use FluxInviscid_fwd() for computing the flux jacobean

strong_conv is not reproduced and stab is not computed correctly

* WIP: working on variational notation for stabilization

* Fluids - fix missing parts after rebasing onto main

* Fluids - fix SU in the IFunction

* Fluids - refactor stabilization

* Fluids - move stab helper functions to stabilization.h

* Fluids - minor style

* Fluids - minor refactor

* Fluids - add regression test for primitive variables

* Fluids - use UnpackState_*()

* Fluids - more refactoring of stabilization

* Fluids - DC: use utility functions

* Fluids - refactor total flux

* Fluids - minor cleanup

* Fluids - set x[0] = 0 for channel to exclude gravitational potential

* Fluids - updated stabilization.h

* Fluids - zero strong_conv before pass it to FluxInviscidStrong() to be safe

* Fluids - move switch-case for STAB to a helper function

* Fluids - rename Y -> R in Stabilization*()

* Fluids - fix stab sign in RHS

Co-authored-by: Jed Brown <jed@jedbrown.org>

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fluids: Use function pointers for StateFrom*, Misc fixes

- Fixes: I missed some StateFrom* functions that needed to be changed

doc: Document primitive variable options for newtonian solver