doc(fluids): Correct grammar in CLI descriptions

fluids: Move freestream bc setup to function

- This will allow it to be called from other problems more easily (ie.
for the Blasius problem)

doc(fluids): Add Newtonian Wave, bc_freestream

- Also fix citation in the Shock Tube documentation.

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

Merge pull request #1088 from CEED/jrwrigh/stg_fluctuating_IC

fluids: Add option for STG fluctuations in initial condition

fluids: Add STG fluctuations to initial condition

- Extrudes the STG fluctuations downstream of the inflow (using the STG
method's inherent dependence on streamwise distance)

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 - Some fixes missing from #1039 (#1056)

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

* Fluids - Add regression test for laminar blasius

fluids: Switch to StateVar enum #1052

doc: Update fluids state_var option

Merge pull request #1029 from CEED/jrwrigh/stg-primitive

fluids: Make Strong STG compatible with primitive variables.

doc: Document primitive variable options for newtonian solver

Merge pull request #1028 from CEED/jrwrigh/shrink-fluids-tests

doc: State output_freq=-1 -> output final state only

fluids: Skip I/O if output_freq == 0 (#1027)

Merge pull request #1008 from CEED/jeremy/doc-fixes

Small Doc Fixes

doc - update style since I'm touching the file

Merge pull request #962 from CEED/jed/fluids-jacobian

examples/fluids: add analytic Jacobian

examples/fluids: document developer options

Merge branch 'main' into jed/fluids-jacobian

* main: (24 commits)
op - more data in view
examples/fluids: Test for strong STG
examples/fluids: Add strong STG to documentation
examples/fluids

Merge branch 'main' into jed/fluids-jacobian

* main: (24 commits)
op - more data in view
examples/fluids: Test for strong STG
examples/fluids: Add strong STG to documentation
examples/fluids: Add option for BC from ICs
examples/fluids: Correct for non-origin domains
examples/fluids: Implement Strong STG BC
examples/fluids: Minor stg improvements/style
examples/fluids: Add Strong STG functions
examples/fluids: Fix memory leak in STG
GPU assembly: fix potential basis loading offset error
tests - more complex source include testing
pc - fix qf fallback cloning
restr - relax comp_stride check for num_comp == 1
make style
pc - avoid direct access of basis data in multigrid creation
ceed - refactor fallback Ceed creation into separate fn
minor - homogonize int vs CeedInt
basis - add input checks
restr - add input checks on element restrictions
examples/fluids: Update STG test for new mesh feats
...

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Merge pull request #967 from CEED/jrwrigh/strong-stg

Fluids: Strongly enforced STG

examples/fluids: Add strong STG to documentation

Merge pull request #964 from CEED/jrwrigh/mesh_from_file

examples/fluids: Create mesh from file distribution

examples/fluids: Update docs for meshing from file

Merge branch 'main' into jed/fluids-jacobian

* main:
Fluids - Add STG inflow (#868)
ci - fix Nek5000 testing

Fluids - Add STG inflow (#868)

* doc(fluids): Add STG equations

* doc(fluids): Add basic data flow for STG

* doc(fluids): Add Shur et al. 2014 STG paper to bib

* doc(fluids): Specify STG in

Fluids - Add STG inflow (#868)

* doc(fluids): Add STG equations

* doc(fluids): Add basic data flow for STG

* doc(fluids): Add Shur et al. 2014 STG paper to bib

* doc(fluids): Specify STG inputs files, misc additions

* doc(fluids): Add intro for STG section

* fix(fluids): Add #include ceed.h for qfunctions

- In the spirit of "include what you use"

* feat(fluids): Start work on stg_shur14.h

* doc-fix: Correct kappa_min definition

* Move STG setup functions to problems/stg_shur14

* feat: Add cholesky decomposition function

* fix: Correct stg_ctx malloc, reorganize creation

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

* fix(fluids): Correct return values of functions

* style: Fix up style

* feat(fluids): Get file paths from PetscOptions

- Also convert SetupSTGContext to return PetscErrorCode

* fix(fluids): Correct stg_ctx dereferencing

- Also move to size_t for type of the offsets

* feat(fluids): Add funcs for processing STG*.dat files

* feat(fluids): Move to PetscOptions* for STG flags

* feat: Use `PetscMax` instead of macro

* fix(fluids): Correct/Refactor file reading functions

- Move to `PetscSynchronizedFGets`
- Remove `inline`
- Pass `comm` between functions
- Add `OpenPHASTADatFile` to DRY

* docs(fluids): Fix equation typo

* fix(fluids): Correct calculation of kappa

* feat(fluids): Complete STGShur14_Calc

* feat(fluids): Add InterpolateProfile helper func

* feat(fluids): Add CalcSpectrum helper func

* feat(fluids): Add to STGShur14_Calc qfunction

* fix: Add M_PI, Update SETERRQ functions

- Also update style

* fix: Correct interpolation outside of datarange

* fix: Add missing definition for ke in CalcSpectrum

* feat: Migrate context and func signatures, Misc

- Create SetupSTGContext to be run in another Setup_____Context
function
- Migrate STGShur14Context, CreateSTGContext, and SetupSTGContext
signatures to navierstokes.h
- Add STG contexts to Physics and CeedData
- Add missing CHKERRQ to PetscFClose
- Move to SPDX license headers

* examples/fluids: Pass solution time via context label

* feat: Implement STG boundary integral

- Add theta0 and implicit members to STGShur14Context
- Tested via implementation to the blasius BL problem (though this will
probably go against the code history)

* feat: Fix STG Stuff

* feat: Implement STG inflow for blasius BL

- Note that fluctuations are turned off in this case

* examples/fluids: Add stg_mean_only flag

* examples/fluids: Check cholesky decomp for nans

- Also correct locaiton of cholesky decomposition in ReadSTGInflow()

* examples/fluids: Correct STG documentation

- Missing a 2 sqrt(3/2) factor and didn't take square root of q

* examples/fluids: Fix STGShur14_Calc

- Given the calculated spectrum, calculation of v' and u' verified
against python implementation (which was validated previously against
PHASTA)

* examples/fluids: Calc dXdx for boundary QFunctions

- Also calculate h from the dXdx in STGShur14_Inflow
- Replace h[0] result with constant dx spacing

* examples/fluids: Fix STG Spectra calcualtion

* examples/fluids: Fix build errors

- Ran into an include cycle collision that resulted in over-defining
SetupContext in advection.c
- newtonian_types.h (which has SetupContext defined) ->
stg_shur14_type.h -> navierstokes.h -> advection.c

* examples/fluids: Update and fix documentation

* examples/fluids: Correct dXdx comment, leave TODO

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

* examples/fluids: Minor bib citation edits

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

* examples/fluids: Add STGInflow.dat, fix blasius.yaml

* examples/fluids: int -> PetscInt | CeedInt

* examples/fluids: Style

* examples/fluids: Make Boolean names verb_noun format

- Also changes the stg flag to `-stg_use`

* examples/fluids: Add STG test

* examples/fluids: Style fix up

* examples/fluids: Update docs

* examples/fluids: Implement weakT option for STG

* examples/fluids: Fix casting for ROCm

* examples/fluids: avoid PETSc dependency in qfunctions

* examples/fluids: header cleanup

* backends/hip: avoid redundant inline

* examples/fluids: avoid VLA in qfunctions

GPUs don't like VLA and some compilers reject it when targeting GPUs.

* examples/fluids: Create STG_NMODES_MAX

* examples/fluids: Refactor stg setup out of blasius.c

* examples/fluids: Fix misc GPU bugs

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

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