style: Prettyify fluids after clang-format switch

Mainly rearrange the input/output variable declarations for QFunctions

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

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

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

fluids: Make Strong STG compatible with primitive variables.

fluids: Change newt->primitive to is_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 #1010 from CEED/jrwrigh/fluids_qfutils

fluids: Combine misc QF helpers into utils.h

Merge pull request #958 from CEED/jed/fluids-cleaning

examples/fluids cleaning

examples/fluids: make setup contexts independent

These are now private to each example and can be developed independently.

Shock Tube + YZB Discontinuity Capturing (#851)

* Implemented the Sod Shock Tube problem with YZB discontinuity capturing. for the explicit formulation. SU stabilization is also implemented for the

Shock Tube + YZB Discontinuity Capturing (#851)

* Implemented the Sod Shock Tube problem with YZB discontinuity capturing. for the explicit formulation. SU stabilization is also implemented for the explicit formulation.

* Changed variable name midpt to mid_point, removed redundant slip BC declarations.

* Fixed style error, made variable names clearer, and removed dead code.

* Missed a style fix

* Rebased with main

* Implemented the Sod Shock Tube problem with YZB discontinuity capturing. for the explicit formulation. SU stabilization is also implemented for the explicit formulation.

* Fixed style error, made variable names clearer, and removed dead code.

* Missed a style fix

* Implemented fixes to the flux jacobians

* Updated documentation, tau definition in SU, and recommended fixes to the flux Jacobian.

* Implemented the Sod Shock Tube problem with YZB discontinuity capturing. for the explicit formulation. SU stabilization is also implemented for the explicit formulation.

* Missed a style fix

* Implemented the Sod Shock Tube problem with YZB discontinuity capturing. for the explicit formulation. SU stabilization is also implemented for the explicit formulation.

* Fixes to style and documentation.

* Fixing unnecessary problem->dim declaration and missing field in comment describing initial condition density.

* Added warnings for incompatible user input combinations.

* Added comments on beta to documentation, fixed j_gradn style issues.

* Compilation errors on my end. Committing to see if it's local or not.

* Style fixes

* Implemented the Sod Shock Tube problem with YZB discontinuity capturing. for the explicit formulation. SU stabilization is also implemented for the explicit formulation.

* Changed variable name midpt to mid_point, removed redundant slip BC declarations.

* Fixed style error, made variable names clearer, and removed dead code.

* Missed a style fix

* Rebased with main

* Implemented the Sod Shock Tube problem with YZB discontinuity capturing. for the explicit formulation. SU stabilization is also implemented for the explicit formulation.

* Fixed style error, made variable names clearer, and removed dead code.

* Missed a style fix

* Implemented fixes to the flux jacobians

* Updated documentation, tau definition in SU, and recommended fixes to the flux Jacobian.

* Implemented the Sod Shock Tube problem with YZB discontinuity capturing. for the explicit formulation. SU stabilization is also implemented for the explicit formulation.

* Missed a style fix

* Implemented the Sod Shock Tube problem with YZB discontinuity capturing. for the explicit formulation. SU stabilization is also implemented for the explicit formulation.

* Fixes to style and documentation.

* Fixing unnecessary problem->dim declaration and missing field in comment describing initial condition density.

* Added warnings for incompatible user input combinations.

* Added comments on beta to documentation, fixed j_gradn style issues.

* Compilation errors on my end. Committing to see if it's local or not.

* Fluids: SETERRQ1 -> SETERRQ to be compatible with PETSc 3.17

* Fluids - Update shock-tube with #881

* Small fix to mid_point definition and removed repeat entries for Shock Tube problem in README.md.

* Including test output.

* Implemented the Sod Shock Tube problem with YZB discontinuity capturing. for the explicit formulation. SU stabilization is also implemented for the explicit formulation.

* Changed variable name midpt to mid_point, removed redundant slip BC declarations.

* Fixed style error, made variable names clearer, and removed dead code.

* Missed a style fix

* Rebased with main

* Implemented the Sod Shock Tube problem with YZB discontinuity capturing. for the explicit formulation. SU stabilization is also implemented for the explicit formulation.

* Fixed style error, made variable names clearer, and removed dead code.

* Missed a style fix

* Implemented fixes to the flux jacobians

* Updated documentation, tau definition in SU, and recommended fixes to the flux Jacobian.

* Implemented the Sod Shock Tube problem with YZB discontinuity capturing. for the explicit formulation. SU stabilization is also implemented for the explicit formulation.

* Missed a style fix

* Implemented the Sod Shock Tube problem with YZB discontinuity capturing. for the explicit formulation. SU stabilization is also implemented for the explicit formulation.

* Fixes to style and documentation.

* Fixing unnecessary problem->dim declaration and missing field in comment describing initial condition density.

* Added warnings for incompatible user input combinations.

* Added comments on beta to documentation, fixed j_gradn style issues.

* Compilation errors on my end. Committing to see if it's local or not.

* Fluids: SETERRQ1 -> SETERRQ to be compatible with PETSc 3.17

* Fluids - Update shock-tube with #881

* Fluids - added test output file for shocktube

* Small fix to mid_point definition and removed repeat entries for Shock Tube problem in README.md.

* Including test output.

* Update doc/sphinx/source/references.bib

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

* Update examples/fluids/README.md

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

* Update examples/fluids/index.md

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

* Update examples/fluids/navierstokes.h

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

* Update examples/fluids/problems/shocktube.c

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

* Update examples/fluids/qfunctions/shocktube.h

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

* Removed unused IFunction

* Added shocktube variables to SetupContext in advection.h, advection2d.h, and densitycurrent.h

* Missed some merge conflicts that have now been cleared up.

* Added helper function for covariant element length along a given vector.

* Added SetupContext to shocktube.h

* Fix to regression test path

* remove variable transpose of the Jacobian

* Fix index swap in implicit SUPG

* examples/fluids shocktube: fix stab summation and transpose

* delete IFunction

* example/fluids- updates reference solution

Co-authored-by: Timothy Aiken <timothyaiken@Timothys-MacBook-Pro.local>
Co-authored-by: Timothy Aiken <timothyaiken@cu-biot-10-10.203.167.69.int.colorado.edu>
Co-authored-by: Leila Ghaffari <Leila.Ghaffari@colorado.edu>
Co-authored-by: Jed Brown <jed@jedbrown.org>
Co-authored-by: Timothy Aiken <timothyaiken@cu-genvpn-tcom-10.180.164.177.int.colorado.edu>
Co-authored-by: AdelekeBankole <adeleke.bankole@colorado.edu>

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feat: Add blasius boundary layer and channel flow examples to examples/fluids (#942)

* examples/fluids: Upload current case for collaboration

* examples/fluids: Replace developing BL with duct

feat: Add blasius boundary layer and channel flow examples to examples/fluids (#942)

* examples/fluids: Upload current case for collaboration

* examples/fluids: Replace developing BL with duct

* examples/fluids: Allow density to "float" at inflow

* fix: Add u_normal

* examples/fluids: bug fix in density flux

* examples/fluids: implement "floating" pressure; prescribed u, T

* examples/fluids: fixing initialization

We need has_neumann=true to get the weak boundary integrals called. It
is initialized in problem->setup_ctx and used in SetupLibceed(). This is
a hack to always apply.

* examples/fluids: include kinetic energy in Blasius IC

* examples/fluids: Blasius quasi-2D (slip in z planes)

* feat: Add Exact_Channel function

* feat: Use Exact_Channel for IC and Inflow

* examples/fluids: Add channel example

* examples/fluids: Define mu in blasius.c, cleanup

* examples/fluid: Add Blasius solution calculator

* examples/fluids: Add blasius IC and BCs

* Convert to implicit TS

* examples/fluids: Update blasius.yaml

* Move to ChannelContext, refactor DC and newtonian

- Added a dedicated ChannelContext, which allows for user setting of
flow parameters and consistent sharing of parameters between
QFunctions (instead of hardcoding)
- Moved density current (DC) specific settings from newtonian.c
densitycurrent.c

* Make gravity into vector quantity

* Add in body force for channel

* examples/fluids: remove explicitly setting coordinate field

This is created automatically now by DMPlex and DMProjectCoordinates
breaks (localized) periodicity, resulting in a tangled mesh.

* examples/fluids: transpose flux Jacobian in SUPG stabilization

* examples/fluids: update docs commensurate with flux Jacobian transpose fix

* examples/fluids: work on docs for tau

* examples/fluids: Increase blasius Re, implement Xi to SUPG

- Increased the Uinf and mu by 4x for the blasius problem
- Implemented the calculation of Xi for the SUPG term in newtonian.h

* examples/fluids: Remove flux jacobian transpose

- Removed for both eulervortex.h and newtonian.h

* examples/fluids: Reset Newtonian unit scaling to neutral

- Note that this resets the scaling for the densitycurrent problem,
thus the examples (and possibly tests) will probably need to be
changed

* examples/fluids: fix PetscOptionsBegin for new PETSc

* feat: Add slanted domain top surface

* feat: Add graded mesh option for blasius

* fix: Correct inflow boundary condition handling

* feat: Move to blasius_context, add CLI options

* feat: Move Blasius to physical air properties

* fix: Blasius profile and mesh generation

- Add the correct float->int rounding
- Fix eta to a value after exceeding the table's bounds

fix: Add fix eta after exceeding table

* examples/fluids: Move to physical mu default, fix tests

* doc: Add minimum documentation for channel and blasius

* examples/fluids: Add primitive jacobian and tau

- Also add misc comments

* examples/fluids: propose alternative flux Jacobian via prim-to-conservative

* examples/fluids: Add PHASTA diagonal tau

* fix: Add back in timestep obtaining

* examples/fluids: Add analytic tractions to inflow and outflow

- This is a stop-gap until viscous flux can be computed properly on the
boundary from current solution.
- Tau constants in a state of flux still but this produced a decent v at
inflow and outflow, removing the steep dive caused by forcing
dv/dx=-du/dy from a zero traction of omission.

* examples/fluids: CLI options for diagonal c_tau's

* examples/fluids: Update dt via context labels

* feat: Add more blasius table points

* examples/fluids: Cleanup stab and adjust Ctau_E

* examples/fluids: Replace spatial tau with diagonal

* examples/fluids: Fix stab in Euler

- Initialize `stab` to zero, add sum over loop

* examples/fluids: Document diagonal tau formulation

* examples/fluids: Fix compiler warnings

* examples/fluids: check error codes and elide unused header

* examples/fluids: Correct blasius example CLI

- Also add mention of the `blasius.yaml` file

* examples/fluids: Add supg to default blasius.yaml

* examples/fluids: Use yaml for channel and blasius

- Instead of long CLI options
- Also cleaned up the yaml formatting
- Added Cartesian directions to the faceMarker names

* examples/fluids: Show example yamls in README

Co-authored-by: Jed Brown <jed@jedbrown.org>
Co-authored-by: Kenneth E. Jansen <Kenneth.Jansen@colorado.edu>

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Merge pull request #858 from CEED/jeremy/dump-copy-stuff

Strip redundant/outdated license info duplication

minor - update copyright headers

Extract generic Navier-Stokes code into 'newtonian.h' (#903)

* feat(fluids): Extract newtownian.h from DC problem

- Also trade out `int` for `StabilizationType` enum

* style: Fix parameter sp

Extract generic Navier-Stokes code into 'newtonian.h' (#903)

* feat(fluids): Extract newtownian.h from DC problem

- Also trade out `int` for `StabilizationType` enum

* style: Fix parameter spacing

* feat: Move generic setup from DC -> newtonian

- Includes moving from `DCContext` to `NewtonianIdealGasContext` at
appropriate locations

* feat: Add "still" IC for generic Newtonian IG problems

* feat: Move SetupContext from DC -> newtonian.c

* fix: Remove unused variables, general cleanup

* examples/fluids: remove unnecessary includes

* examples/fluids: copy declarations to make newtonian.h self-contained

* examples/fluids: full name for context

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

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Merge pull request #865 from CEED/leila/fluid-stab

Fluids - Fix bug in Stabilization (SU/SUPG)

examples/fluids: tau as spatial criterion 2 of hughesetal2010

Testing traveling vortex with

$ build/fluids-navierstokes -problem euler_vortex -ts_adapt_monitor -lx 1000 -ly 1000 -lz 50 -dm_plex_box

examples/fluids: tau as spatial criterion 2 of hughesetal2010

Testing traveling vortex with

$ build/fluids-navierstokes -problem euler_vortex -ts_adapt_monitor -lx 1000 -ly 1000 -lz 50 -dm_plex_box_faces 20,20,1 -ts_adapt_safety 0.8 -implicit -snes_atol 1e-3 -ksp_atol 1e-4 -ksp_rtol 1e-3 -ts_type alpha -ts_dt 0.1 -ksp_type bcgs -pc_type lu -log_view -snes_monitor -ksp_monitor -snes_converged_reason -output_freq 1 -degree 1 -ts_max_time 5. -stab supg -snes_lag_jacobian 30 -snes_lag_jacobian_persists -snes_mf_operator

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fluids - fix flux Jacobian and add su/supg to euler_vortex

Merge pull request #841 from CEED/jeremy/qf-multi-source

QFunction multi source support

qf - drop unneeded guards on math.h