fluids: Solution component names CGNS compliant

- Note there isn't a CGNS name for our energy term (somehow...). The
standard uses "Density" to describe volume density rather than mass
density,

fluids: Solution component names CGNS compliant

- Note there isn't a CGNS name for our energy term (somehow...). The
standard uses "Density" to describe volume density rather than mass
density, so I've droppped that term here

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PetscFE determines basis for examples/fluids/navierstokes (#1264)

* breaking lots of DL stuff to test PetscFE

* fixed missing header

* fluids: Remove unused `Involute` function

* fluids: Se

PetscFE determines basis for examples/fluids/navierstokes (#1264)

* breaking lots of DL stuff to test PetscFE

* fixed missing header

* fluids: Remove unused `Involute` function

* fluids: Set quadrature points for PetscFE

* fluids: Fix GetRestrictionForDomain, Use CreateBasisFromPlex

* fluids: Remove Q_sur arg from SetupStrongBC_Ceed

* fluids: Remove extra SetClosurePermutationTensor

* fluids: Correct quadrature order to auxillary DMs

- Should factor in q_extra

* fluids: Fix parent Restriction creation for spanstats

* fluids: Correct qdata creation for strong bcs

* fluids: Set tensor closer only for tensor-product elements

Co-authored-by: Jeremy L Thompson <jeremy@jeremylt.org>

* fluids: Make shocktube test less brittle

- Small, insignificant changes to the coordinate locations make a
dramatic difference to the initial condition
- For the test case, there is a node right at the midpoint of the
domain. Adding the epsilon fudge factor makes the if statement more
stable

* fluids: Fix SGS test

- Change the test so that it passes on all hardware. It's a very
sentitive test and the changes to the basis creation changed the
initial conditions *just* enough to make the test not happy. Should
really try and make this more robust at some point...

* fluids: Address misc PR comments

* fluids: Remove quad_mode arg from CreateBasisFromPlex

---------

Co-authored-by: James Wright <james@jameswright.xyz>
Co-authored-by: Jeremy L Thompson <jeremy@jeremylt.org>

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Merge pull request #1234 from CEED/jrwrigh/fluids_64int

fluids: Compatability for PETSc w/ 64bit ints

fluids: Remove problem->bc function pointers

- Not needed, as essential boundary conditions go through
`DMPlexInsertBoundaryValues_NS` or
`DMPlexInsertBoundaryValues_StrongBC`

Merge pull request #1237 from CEED/jrwrigh/petsc-success

examples: Use PETSC_SUCCESS in PetscFunctionReturn

examples: Use PetscFunctionReturn in PETSC_SUCCESS

Merge pull request #1185 from CEED/jrwrigh/fluids-cleanup

fluids: Move to local Vec storage and 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

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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Lift, Drag, Heat Transfer (#1130)

* add functions for surface forces

* function for surface forces

* reaction forces

* add points to label

* WIP: examples/fluids: sketch surface force ca

Lift, Drag, Heat Transfer (#1130)

* add functions for surface forces

* function for surface forces

* reaction forces

* add points to label

* WIP: examples/fluids: sketch surface force calculations

* examples/fluids: fix for parallel, when there are no such points on a process

* add TSMonitor_FaceForce function

* update on TSMonitor FaceForce

* create .csv file

* cleanup TS Monitor FaceForce function

* include surface forces viewer to header file

* include ts monitor surface force viewer to cloptions

* update where TSMonitor FaceForce are called

* examples/fluids: update wall forces to write csv

mpiexec -n 5 build/fluids-navierstokes -options_file examples/fluids/vortexshedding.yaml -{ts,snes}_monitor -degree 1 -ts_monitor_wall_forces ascii:force.csv:ascii_csv

* update documentation

* reaction force data

* plotting script

* examples/fluids: seaborn plotting with twinx and colors

* delete data file

* tuck away csv file

* place python script in subdirectory

* examples/fluids/postprocess: put shedding period in title

* examples/fluids: document wall force and shedding postprocess

---------

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

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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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fluids: Switch to StateVar enum #1052

fluids: Switch to StateVar enum

fluids: Unify Newtonian Primitive functions #1035

Merge separate IFunction and IJacobian routines into a single helper function and
separate wrappers for each state variable option.

fluids: Rename primitive booleans, misc formatting

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

fluids: Make Strong STG compatible with primitive variables.

fluids: Make stg components dependent on primitive

Fluids - Newtonian with Primitive variables (#1011)

* Fluids - Initial commit for Newtonian primitive variables

* Fluids - include A0 (dU/dY) in the output

* Fluids - added ICs for IG in primi

Fluids - Newtonian with Primitive variables (#1011)

* Fluids - Initial commit for Newtonian primitive variables

* Fluids - include A0 (dU/dY) in the output

* Fluids - added ICs for IG in primitive variables

* Fluids - added Jacobean QFunction for primitive variables

* Fluids - added RHS QFunction for primitive variables

* Fluids - fixed compilation errors and warnings

* Fluids - added ICs for density_current with primitive variables

* Fluids - In/OutFlow BCs for channel in primitive variables

* Adding the missing parts after rebasing onto main

* Fluids - Use correct component names for primitive variables

* Fluids - Primitive variables supported only with implicit scheme

* Fluids - drop in/outflow for channel flow and call Exact_Channel_Prim() in Exact_Channel()

* Fluids - Set solver's QFunction data in an if-else statement

* Fluids - style

* Fluids - add a comment to explain why the the gravity body force is excluded from the potential energy.

* Fluids - Exact_Channel return State

* Fluids - density_current: some style and cleanup

* Fluids - DC: refactor & cleanup

* Fluids - Singel QFunction for prim&cons

* Fluids - Use absolute temperature

* Fluids - DC: Fix pressure

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Merge pull request #994 from CEED/fluids-block-diagonal

Fluids block diagonal

examples/fluids: skip legacy preallocation (we use COO)

When using -snes_fd_color or running a model that doesn't provide a
Jacobian (in which case coloring will be used automatically), we still
nee

examples/fluids: skip legacy preallocation (we use COO)

When using -snes_fd_color or running a model that doesn't provide a
Jacobian (in which case coloring will be used automatically), we still
need to preallocate.

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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 #980 from CEED/jrwrigh/fluids_tractionbc

examples/fluids: Move StrongSTGbcFunc to newtonian.h

- Requires significant changes to how the stg_context is passed to the
the strong bc

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

examples/fluids: add analytic Jacobian