fluids: Move RHSFunction to petsc-ops

fluids: Move setup function calls to better locations

- Move libCEED operator setup functions to SetupLibceed
- Rename turbulence statistics functions to match naming convention

fluids Move initial conditions -> petsc-ops

refactor(fluids): Dirichlet -> Strong BC

- Use "strong" and "dirichlet" to refer to the same thing
(hard-contrained degrees-of-freedom). Chose "strong", as dirichlet may
be enforced weakly.

Merge pull request #1149 from CEED/jrwrigh/newtonian_ddsgs

fluids: Data-driven SGS modeling

fluids: Add VecCopyP2C function

IWYU fixes (#1182)

* iwyu - include fixes

* iwyu - silence some iwyu output

* minor - clearer macro names

* iwyu - fix suggestion of "ceed/ceed.h" externally

* iwyu - lighter petsc heade

IWYU fixes (#1182)

* iwyu - include fixes

* iwyu - silence some iwyu output

* minor - clearer macro names

* iwyu - fix suggestion of "ceed/ceed.h" externally

* iwyu - lighter petsc headers

* iwyu - ceed/ceed.h -> ceed.h

* iwyu - cuda/hip include fixes

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Merge pull request #1174 from CEED/jeremy/operator-context

CeedOperatorContext* -> CeedOperator*Context*

style - rename CeedOperatorContext functions for consistency

fluids - fix QFunctionContext access errors

Merge pull request #1135 from CEED/jrwrigh/spanwise_stats

fluids: Use CeedElemRestrictionCreateVector for qdata

Vortex shedding / flow past cylinder (#1082)

* add vortex shedding problem

* add file for the Qfunctions

* add yaml file

* update problem setup

* update IC qfunc

* update problem set

Vortex shedding / flow past cylinder (#1082)

* add vortex shedding problem

* add file for the Qfunctions

* add yaml file

* update problem setup

* update IC qfunc

* update problem setup

* update initial condition

* update yaml file

* add mesh file

* add vortexshedding to navierstokes.h

* register vortexshedding to cloptions.c

* update configuration/yaml file

* fix Min function

* examples/fluids: fix boundary condition labels for cylinder

$PhysicalNames
6
2 1 "inlet"
2 2 "outlet"
2 3 "top"
2 4 "bottom"
2 5 "cylinderwalls"
2 6 "frontandback"
$EndPhysicalNames

* update QFunctions in navierstokes.c

* update data and BC structs in navierstokes.h

* update vortexshedding.c

* update states

* update IC in vortexshedding.h

* add freestream BC to cloptions

* updates in setuplibceed.c

* include freestream BC in example

* cleanup duplicate variable names

* rename variables as freestream

* clean-up some warning messages

* clean up example

* add cylinder.geo

* label physical volume

* examples/fluids: fix cylinder mesh and add vortexshedding defaults

* update gravity vector

* examples/fluids: match domain to Shakib, get vortex street

* update to quadratic mesh

* clean up yaml file

* delete vortexshedding.c and vortexshedding.h

* remove vortexshedding from register

* update yaml file

* examples/fluids: Newtonian "still" initial condition

Reinstate outflow boundaries that were previously removed so that
existing tests can pass.

* examples/fluids: freestream inherits reference state

Fix freestream context reference counting bug.

* examples/fluids: avoid designated initializer in kernel code (breaks CUDA)

* add Shakib91 to references

* remove cylinder.geo and cylinder.msh

* wip:add documentation for vortex shedding

* update path to cylinder.msh

* add subdirectory for meshes

* parameterize cylinder.geo

* some fixes in cylinder.geo

* Fix cylinder.geo file

* examples/fluids: fix up mesh parametrization

Fix cylinder size (the function is Sqrt, not sqrt) and parametrize
resolution and aspect.

* examples/fluids: fix build after broken merge from main

* update Shakib1991 in references

* wip:docs for vortex shedding

* remove TODO comment

* reformulate docs

* fix docs

* delete cylinder.msh file

* work on documentation

* add vortex runtime options

* examples/fluids: update vortex shedding docs and mesh

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

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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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Merge pull request #1080 from CEED/ade/riemann-bcs

HLL Flux for Riemann BCs

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: Integrate freestream bc

fluids: Add SetupBCQFunctions to setuplibceed.c

- Condenses redundant code into a single function. Will be useful when
implementing the freestream bc

fluids: Create AddBCSubOperator in setuplibceed.c

- Condenses redundant code (and will help reduce redundancy when I add
in the freestream boundary conditions as well).

Merge pull request #1016 from CEED/jed/plex-cell-coordinates

examples/fluids: use DMGetCellCoordinateDM to handle periodicity

examples/fluids: use DMGetCellCoordinateDM to handle periodicity

Note that without -dm_sparse_localize 0 (default=1), the cell DM will
only have cells with localized coordinates (and there is no vec

examples/fluids: use DMGetCellCoordinateDM to handle periodicity

Note that without -dm_sparse_localize 0 (default=1), the cell DM will
only have cells with localized coordinates (and there is no vector
representation that contains both).

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Merge pull request #1009 from CEED/jrwrigh/dirichlet_with_libceed

Fluids - Use libCEED to compute Dirichlet boundary conditions

fix(fluids): Create and use basis_xc_sur for dirichlet bcs