fluids: Make ProblemData a pointer to struct

We basically use it as a pointer-to-struct type everywhere, so might as
well make it consistent with everything else

Merge pull request #1537 from CEED/jeremy/pragma-once

Use #pragma once for non-JiT headers

minor - update copyright headers

Merge pull request #1259 from CEED/jrwrigh/fluids-cleanup

fluids: Misc cleanup

fluids: Correct PetscFunction{Return,BeginUser} placement

- Respect the PETSc standard for style (https://petsc.org/release/developers/style/#coding-conventions-and-style)

fluids: Add PetscCallCeed

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

examples: Use PETSC_SUCCESS in PetscFunctionReturn

examples: Use PetscFunctionReturn in PETSC_SUCCESS

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

show more ...

Merge pull request #1104 from CEED/jeremy/formatting

Minor Formatting Fixes

minor - assorted formatting fixes

fluids: Add SimpleBC to problem setup function

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>

show more ...

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

show more ...

Merge pull request #991 from CEED/jeremy/memcheck-qf-ctx

Memcheck QFContext

fluids - fix setup context data misuse

Merge branch 'main' into jed/fluids-jacobian

* main:
Fluids - Add STG inflow (#868)
ci - fix Nek5000 testing

Fluids - Add STG inflow (#868)

* doc(fluids): Add STG equations

* doc(fluids): Add basic data flow for STG

* doc(fluids): Add Shur et al. 2014 STG paper to bib

* doc(fluids): Specify STG in

Fluids - Add STG inflow (#868)

* doc(fluids): Add STG equations

* doc(fluids): Add basic data flow for STG

* doc(fluids): Add Shur et al. 2014 STG paper to bib

* doc(fluids): Specify STG inputs files, misc additions

* doc(fluids): Add intro for STG section

* fix(fluids): Add #include ceed.h for qfunctions

- In the spirit of "include what you use"

* feat(fluids): Start work on stg_shur14.h

* doc-fix: Correct kappa_min definition

* Move STG setup functions to problems/stg_shur14

* feat: Add cholesky decomposition function

* fix: Correct stg_ctx malloc, reorganize creation

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

* fix(fluids): Correct return values of functions

* style: Fix up style

* feat(fluids): Get file paths from PetscOptions

- Also convert SetupSTGContext to return PetscErrorCode

* fix(fluids): Correct stg_ctx dereferencing

- Also move to size_t for type of the offsets

* feat(fluids): Add funcs for processing STG*.dat files

* feat(fluids): Move to PetscOptions* for STG flags

* feat: Use `PetscMax` instead of macro

* fix(fluids): Correct/Refactor file reading functions

- Move to `PetscSynchronizedFGets`
- Remove `inline`
- Pass `comm` between functions
- Add `OpenPHASTADatFile` to DRY

* docs(fluids): Fix equation typo

* fix(fluids): Correct calculation of kappa

* feat(fluids): Complete STGShur14_Calc

* feat(fluids): Add InterpolateProfile helper func

* feat(fluids): Add CalcSpectrum helper func

* feat(fluids): Add to STGShur14_Calc qfunction

* fix: Add M_PI, Update SETERRQ functions

- Also update style

* fix: Correct interpolation outside of datarange

* fix: Add missing definition for ke in CalcSpectrum

* feat: Migrate context and func signatures, Misc

- Create SetupSTGContext to be run in another Setup_____Context
function
- Migrate STGShur14Context, CreateSTGContext, and SetupSTGContext
signatures to navierstokes.h
- Add STG contexts to Physics and CeedData
- Add missing CHKERRQ to PetscFClose
- Move to SPDX license headers

* examples/fluids: Pass solution time via context label

* feat: Implement STG boundary integral

- Add theta0 and implicit members to STGShur14Context
- Tested via implementation to the blasius BL problem (though this will
probably go against the code history)

* feat: Fix STG Stuff

* feat: Implement STG inflow for blasius BL

- Note that fluctuations are turned off in this case

* examples/fluids: Add stg_mean_only flag

* examples/fluids: Check cholesky decomp for nans

- Also correct locaiton of cholesky decomposition in ReadSTGInflow()

* examples/fluids: Correct STG documentation

- Missing a 2 sqrt(3/2) factor and didn't take square root of q

* examples/fluids: Fix STGShur14_Calc

- Given the calculated spectrum, calculation of v' and u' verified
against python implementation (which was validated previously against
PHASTA)

* examples/fluids: Calc dXdx for boundary QFunctions

- Also calculate h from the dXdx in STGShur14_Inflow
- Replace h[0] result with constant dx spacing

* examples/fluids: Fix STG Spectra calcualtion

* examples/fluids: Fix build errors

- Ran into an include cycle collision that resulted in over-defining
SetupContext in advection.c
- newtonian_types.h (which has SetupContext defined) ->
stg_shur14_type.h -> navierstokes.h -> advection.c

* examples/fluids: Update and fix documentation

* examples/fluids: Correct dXdx comment, leave TODO

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

* examples/fluids: Minor bib citation edits

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

* examples/fluids: Add STGInflow.dat, fix blasius.yaml

* examples/fluids: int -> PetscInt | CeedInt

* examples/fluids: Style

* examples/fluids: Make Boolean names verb_noun format

- Also changes the stg flag to `-stg_use`

* examples/fluids: Add STG test

* examples/fluids: Style fix up

* examples/fluids: Update docs

* examples/fluids: Implement weakT option for STG

* examples/fluids: Fix casting for ROCm

* examples/fluids: avoid PETSc dependency in qfunctions

* examples/fluids: header cleanup

* backends/hip: avoid redundant inline

* examples/fluids: avoid VLA in qfunctions

GPUs don't like VLA and some compilers reject it when targeting GPUs.

* examples/fluids: Create STG_NMODES_MAX

* examples/fluids: Refactor stg setup out of blasius.c

* examples/fluids: Fix misc GPU bugs

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

show more ...

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.

examples/fluids: reduce prevalance of top-level setup_ctx

examples/fluids: consolidate two-step setup

Contexts are created in one place now and we have removed duplicate
struct definitions for physics.

examples/fluids: create struct in Problem for each qfunction + related

This is a cosmetic step toward better modularity.

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>

show more ...

Merge pull request #940 from CEED/jeremy/petsc-options

petsc - update for PetscOptionsBegin/End