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

fluids: Use standard boundary integrals for primitive

fluids: Make STG QFs primitive compatible

fluids: Make stg components dependent on primitive

fluids: Make newtonian boundary QFs primitive compatible

fluids: Change newt->primitive to is_primitive

fluids: Add missing \n to blasius warning message

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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tests: Shrink fluids test run time

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

fluids: Force final output except if output_freq=0

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

Merge pull request #1018 from CEED/jrwrigh/stg_precompute_ektot

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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examples/fluids: explicitly handle MFFD

examples/fluids: use shell for Amat, block diagonal aij* for Pmat

This adds two independent options for tuning solves.

-amat_type shell: causes Amat and Pmat to be different matrices, with shell
us

examples/fluids: use shell for Amat, block diagonal aij* for Pmat

This adds two independent options for tuning solves.

-amat_type shell: causes Amat and Pmat to be different matrices, with shell
used for Amat. It's technically possible to use other matrix formats
here.

-pmat_pbdiagonal: causes Pmat to be assembled as point-block diagonal.
Note that this usually only makes sense in addition to -amat_type shell
because otherwise your KSP is only working with the point-block diagonal.

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fluids: Store 1/Ektot

fluids: Implement stgdata for ektot

fluids: Add STG Preprocessing and Calc QFs