refactor: More consistent naming of qf context

Merge branch 'jrwrigh/license_changes' into 'main'

Update License post libCEED fork

See merge request phypid/honee!6

chore: Move to Apache-2.0 OR BSD-2-Clause

Merge branch 'jrwrigh/rearrange' into 'main'

Rearrange files into more future-oriented locations

See merge request phypid/honee!15

chore: Move navierstokes.* out of root directory

navierstokes.h to include and navierstokes.c into examples

Merge pull request #1562 from CEED/jrwrigh/fluids_problem_pointer

fluids: Make ProblemData a pointer to struct

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

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 ...

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: Switch to StateVar enum

fluids: Rename primitive booleans, misc formatting

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 #986 from CEED/leila/fluids-fix-memleak

Fluids - Fix memory leak

examples/fluids: minor - style

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

examples/fluids: add analytic Jacobian

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 ...

examples/fluids: fix sign and magnitude of channel flow body force

Add -body_force_scale, which can be -1 to test that a flow reversal
builds to the same steady profile with opposite sign.

I also c

examples/fluids: fix sign and magnitude of channel flow body force

Add -body_force_scale, which can be -1 to test that a flow reversal
builds to the same steady profile with opposite sign.

I also changed the domain size (reducing Reynolds number from 4500 to
45) so flow reversal can be observed reasonably quickly when desired.

show more ...

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

examples/fluids cleaning