Merge branch 'main' into jed/fluids-jacobian

* main: (24 commits)
op - more data in view
examples/fluids: Test for strong STG
examples/fluids: Add strong STG to documentation
examples/fluids

Merge branch 'main' into jed/fluids-jacobian

* main: (24 commits)
op - more data in view
examples/fluids: Test for strong STG
examples/fluids: Add strong STG to documentation
examples/fluids: Add option for BC from ICs
examples/fluids: Correct for non-origin domains
examples/fluids: Implement Strong STG BC
examples/fluids: Minor stg improvements/style
examples/fluids: Add Strong STG functions
examples/fluids: Fix memory leak in STG
GPU assembly: fix potential basis loading offset error
tests - more complex source include testing
pc - fix qf fallback cloning
restr - relax comp_stride check for num_comp == 1
make style
pc - avoid direct access of basis data in multigrid creation
ceed - refactor fallback Ceed creation into separate fn
minor - homogonize int vs CeedInt
basis - add input checks
restr - add input checks on element restrictions
examples/fluids: Update STG test for new mesh feats
...

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Merge pull request #967 from CEED/jrwrigh/strong-stg

Fluids: Strongly enforced STG

examples/fluids: Implement Strong STG BC

examples/fluids: add IJacobian for SUPG

I think this is exact for Galerkin on channel.yaml and blasius.yaml.
Specifically, SNES converges almost perfectly in this test than when
-snes_mf_operator is

examples/fluids: add IJacobian for SUPG

I think this is exact for Galerkin on channel.yaml and blasius.yaml.
Specifically, SNES converges almost perfectly in this test than when
-snes_mf_operator is added.

-options_file examples/fluids/channel.yaml -snes_monitor -ksp_converged_reason -stab none -ts_max_steps 3 -newtonian_unit_tests -ksp_rtol 1e-10 -order 2 -ts_dt 3e-6 -pc_type lu

I say "think" because something is fishy with the viscous energy term
velocity*stress. If I disable that term, then convergence is clearly
better with the analytic Jacobian (makes sense because it's accuracy is
machine epsilon) than with -snes_mf_operator. This is unexpected, but
the difference is near the limit of numerical stability so I'm not
confident it's wrong. Also, the term itself is so simple.

The Jacobian is inexact for SUPG in that Tau_d is frozen.

WIP: examples/fluids: support MatShell and Blasius_Inflow_Jacobian

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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 #947 from CEED/jrwrigh/fluids-use_field_labels

examples/fluids: Set euler_context->curr_time via context fields

examples/fluids: Set ctx->time via context fields

Merge pull request #943 from CEED/jed/petsc-format-string

examples: use PetscInt_FMT instead of %D

examples: use PetscInt_FMT instead of %D

This fixes many warnings now that PETSc uses printf format string
attribute checkers.

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

Strip redundant/outdated license info duplication

minor - update copyright headers

Merge pull request #877 from CEED/jeremy/field-names-for-people

Make qf/op field names human readable

style - make qf/op field names human readable

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

Fluids - Fix bug in Stabilization (SU/SUPG)

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

Fluids - Refactor and add GPU support (#754)

* Initial commit for using PetscFunctionList in fluids example

* WIP: debugging

* Debug: initialize PetscFunctionList with NULL

* allocate memor

Fluids - Refactor and add GPU support (#754)

* Initial commit for using PetscFunctionList in fluids example

* WIP: debugging

* Debug: initialize PetscFunctionList with NULL

* allocate memory for context problem

* freed allocated memory

* WIP: fluids: split density current into new compilation unit
I have dropped last changes before this commit so there might be some
bugs

* Fixed bugs after dropping the commit containing unnecessary changes

* NS: dropped unused variable from User struct

* WIP: factored out DMAddBoundary() for density_current

* split advection and advection2d into separate compilation units as well

* fluids: added *.o to make clean

* removed bc from problemData

* style

* commented the error handlers and moved petsc options regarding the boundary conditions to each compilation unit

* call bc functions inside SetUpDM()

* Moved all bc related statements from SetUpDM() to each compilation unit

* examples/fluids/advection.h: style

* WIP: modified CeedQFunctionContexts

* FFR: By creating a struct for DC context, one of the last test crushed so I had to reverse it. This should be investigated later.

* style

* examples/navierstokes: Use heap memory for ctxSetup

* examples/fluids: WIP - reading arrays through cl options for DC is enabled by using double pointers but there is still a problem with unit conversions and also need to fix other structs

* style

* WIP: Trying to assign values to context data in each problem function

* bug: there is a problem in pointer to struct

* WIP: Everything seems to be working but it breaks and I haven't figured out the reason ...

* fixed typo

* comment out stuff that have been moved to densitycurrent.c

* WIP: The first two regression test pass. There is a problem with stabilization.

* style

* Fluids: QFContext -> Physics

* WIP: passing StabilizationType to Physics (but PETSc is not happy and it diverges for SU and SUPG)

* Initial commit for refactoring advection(2d)

* WIP: Advection is set up except for wind_type

* WIP: refactored advection2d; need to fix the BCs for translation and also passing implicit to advection correctly

* WIP: pass wind_type to all functions correctly but there is still a problem with BCs in the case of translation (changes are not applied to advection yet)

* Apply the same fixes for BCs in advection

* Fluids - Refactor: Moved warnings to advection(2d)

* Fluids - Refactor: remove dead code

* Fluids - Refactor: Move *.h to /qfunctions and *.c to /src

* style

* Fluids - Refactor: drop the supg regression test for now

We need to debug SU/SUPG for density_current. The test does not work.

* Fluids - Refactor: Fixed the double-pointer issue

* Fluids - Refactor: Assign ctxSetup->time = 0 inside each problem's *.c

* Fluids - Refactor: make implicit a member of Physics

* Fluids - Refactor: Add warning for the usage of explicit and supg

* Some comments and naming

* Merge main after v0.8 (#723)

* Fluids - Five regression tests added for euler_vortex

* Fluids - Drop some of the regression tests for now (Needs to get fixed)

* Fluids - Moved all functions to their corresponding source files

* Fluids - move problem source files to /problems

* Fluids - drop dead regression test reference files

* Fluids - more consistent file names

* Fluids - drop dead code and comments

* Fluids - removed CreateVectorFromPetscVec() since it was only used once

* Fluids - created AppCtx for cl option variables and moved cl options to a cloption.c

* Fluids: change style of AppCtx

* style

* Fluids: /src -> /utils

* Created CreateDistributedDM() and some style

* Fluids - create RegisterProblem()

* style - minor

* style - minor

* Fluids - some more C style

* Fluids - /utils -> /src

* Fluids - create VizRefineDM() for viz_refine

* Fluids: some style and name change

* Fluids - style

* Fluids - remove the second ceed initialization

* Fluids - Created CeedData and SetupLibCEED()

* Fluids - create SetupContextForProblems()

* Fluids - Assign structs after they are created

* Fluids - style, minor

* Fluids - created RegressionTests_NS

* Fluids - created GetError_NS()

* Fluids - created PrintOutput_NS()

This processes bash output except for the problem summary which will be
included after mem_type is managed properly.

* Fluids - remove unused variables

* Fluids - created TSSolve_NS() which creates, sets up, and solves ts

* Fluids: Fixed a bug caused by merging#714

* Fluids - style

* Fluids - created SetupICsFromBinary() for case of -continue

* Fluids - create SetBCsFromICs_NS()

* Fluids - default degree had is 1 not 2

* Fluids: clean-up

* Fluids: style - minor

* Fluids - drop redundant operation

* Fluids: clean-up SetupLibCEED()

* Fluids: style - minor

* Fluids: WIP - C style

* Fluids: style - minor

* Fluids: move ceed vector creation to SetupLibCEED()

* Fluids: WIP - clean-up CreateOperatorForDomain()

* Fluids: major clean-up in CreateOperatorForDomain()

* Fluids: style - minor

* Fluids: drop VectorPlacePetscVec()

* Fluids: move ICs_FixMultiplicity() to misc.c

* Fluids: WIP - C style

* Fluids: fix merge conflict after d63eecaab22a26d3072677a1b66c0cf77aa9009d

* Fluids: drop unused function call DMLocalizeCoordinates()

* Fluids: replace user requested memType with MemTypeP2C()

* Fluids: C style

* Fluids: Q->num_Q (Q (# qpts) and Q (global state vector) were confusing my fresh petsc config)

* Fluids: WIP - add GPU vectors

* Fluids: Fixed the memory leak caused by Physics struct

* Fluids: style -minor

* Fluids: no need for casting

* Fluids: Fix mem leak (q0_ceed had to be destroyed at the end of navierstokes.c)

* Fluids: Fixed all mem leaks

* Fluids: Set VecType for dm_hierarchy

* Fluids/doc: fix style

* Fluids: fix missing VecRestoreArray()

* Fluids: clean-up ComputeLumpedMassMatrix()

* Fluids: Cleanup ICs_FixMultiplicity()

* Fluids: WIP - cleanup setupts.c

* Fluids: style - minor

* Fluids: Create element coord ceed vector locally and drop it from CeedData

* Fluids: fix some todos

* Fluids: drop unused code for EULER BCs

* Fluids: PetscMalloc1 -> PetscCalloc1

* Fluids - Define BCs for ADVECTION(2D) for all cases without having the user specify them and change the regressions accordingly

ToDo: For some reason I can't create new regression tests for explicit scheme.

* Fluids - Define problem->print_info() for each problem

* Fluids: Shorten some problem specific command line variables & style

* Fluids - Cleanup BCs in the translation mode

* Fluids - cleanup

* Fluids - more cleanup in BCs

* Fluids - Updated doc, README, and cleanup in the code and cl options

* Fluids - add more regression tests

* Fluids - Define tolerance for the convergence test

* Fluids: include x_coord in CeedData

* wip - gpu

Revert "Fluids: include x_coord in CeedData"

I had to revert this commit since it crashes DC

* style

* Fluids - remove unused variables

* Fluids - fix unused function warnings

* Fluids - fix the remaining warnings

* Fluids - style

* Fluids - add missing licence

* Fluids - bring back contexts to the QFunction header files

* Fluids - transfer QFunctions for boundary integral to their corresponding setupgeo(2d).h header files and add description for Setup2d

* fluids - fix context data sizes

* GPU - add helper function macro

* ex - use consistent MPI info output

* GPU - improve CEED_QFUNCTION_HELPER macro, more flexible

* Fluids - turn on some gpu tests

* Fluids - bring back element coordinate to CeedData

* Fluids - cleanup

* qfunction - clean up helper function macro

* Fixed the remaining conflicts from #769 (helped-by: @rezgarshakeri)

Co-authored-by: Jed Brown <jed@jedbrown.org>
Co-authored-by: jeremylt <thompson.jeremy.luke@gmail.com>

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