Merge MR !90, 'jrwrigh/renaming', into 'main'

style: Refactor fluids -> HONEE

See merge request phypid/honee!90

style: Refactor fluids -> HONEE

Merge MR !72, 'jrwrigh/jit_changes', into 'main'

fix: Change QFunctions to account for libCEED#1696

See merge request phypid/honee!72

fix: Change QFunctions to account for libCEED#1696

Merge branch 'jrwrigh/refactor' into 'main'

refactor: Use utils in setupgeo helpers, other misc refactors

See merge request phypid/honee!37

refactor(qdata): SetupBoundaryGradient use helpers

Merge branch 'jrwrigh/diff_flux' into 'main'

feat: Add divergence of diffusive flux projection

See merge request phypid/honee!27

feat: Implement divergence of diffusive flux

Merge branch 'jrwrigh/license_changes' into 'main'

Update License post libCEED fork

See merge request phypid/honee!6

chore: Move to Apache-2.0 OR BSD-2-Clause

Drop JiT Guards in Most QF Source (#1540)

* backend - use pragma once

* gallery - drop source header guards

* ex - drop some qfunction source header guards

* fluids - drop guards on all sin

Drop JiT Guards in Most QF Source (#1540)

* backend - use pragma once

* gallery - drop source header guards

* ex - drop some qfunction source header guards

* fluids - drop guards on all singly included headers

* jit - drop most guards on backend JiT files

* sycl - drop extra header guards

* jit - enable #pragma once for QF source

* fluids - use #pragma once for util/helper qf source

* test - check different multiple includes

* fluids - fix odd include

* jit - update interface for building JiT string from multiple files

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Merge pull request #1537 from CEED/jeremy/pragma-once

Use #pragma once for non-JiT headers

minor - update copyright headers

fluids: Add QF value qdata packing/unpacking

fluids: Refactor setupgeo* functionality into helpers

- This allows for use of those helpers inside other qfunctions

Merge pull request #1104 from CEED/jeremy/formatting

Minor Formatting Fixes

minor - assorted formatting fixes

Merge pull request #1102 from CEED/jrwrigh/re-pretty_fluids

style: Prettyify fluids after clang-format switch

style: Prettyify fluids after clang-format switch

Mainly rearrange the input/output variable declarations for QFunctions

Merge pull request #1095 from CEED/jed/remove-stale-indent-comments

remove stale indent comments

style: remove obsolete (with clang-format) INDENT comments

Switch to clang-format (#1051)

* style - switch to clang-format

* ci - use newer libxsmm

* action - update format action

* format - consistent use of {} for multi-line if/for

* make - re

Switch to clang-format (#1051)

* style - switch to clang-format

* ci - use newer libxsmm

* action - update format action

* format - consistent use of {} for multi-line if/for

* make - remove stray newline

* make - simpler 'make format' target

* ci - use newer libxsmm

* doc - minor release note claification

* minor - minor fix

* minor - minor fix

* minor - minor fix

* minor - minor fix

* make format

* format - less aggressive alignment rules

* tidy - check for argument name mismatches

* fix newline

* format - mirror Ratel update to .clang-format

* fix merge error

* fix merge conflict

* fix merge error

* drop style in .phony list

* Update .clang-format

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

* apply updated format

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

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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

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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