doc - pin Altair <5.0 until Sphinx updates

examples/petsc: Remove unneeded PETSC_VERSION_LT

- We now require greater than 3.19 anyways

Co-authored-by: Jeremy L Thompson <jeremy@jeremylt.org>

fix: Update DMGetRegionDS calls in examples/petsc

- Also update minimum required PETSc version
- Update releasenotes with change to minimum PETSc version

Ken/idl (#1138)

* inflow sponge pushing p towards P0 compiles and runs but unknown yet whether it is effective or not

* looks like my first attempt at this is missing something as there is neglig

Ken/idl (#1138)

* inflow sponge pushing p towards P0 compiles and runs but unknown yet whether it is effective or not

* looks like my first attempt at this is missing something as there is negligible effect from Jacobian addition

* examples/fluids: IDL fixes and demo

* Fix IDL sign error and rename variables/clang-format
* Let newtonianwave.yaml use -reference_pressure and temperature
* Propagate P0 = reference.pressure

* Small tweak to add IDL to the 3 ramp parameters.

* fluids: Extract fluids binary vector load function

- Needs to be used in multiple places (for ICs and for testing data)

* fluids: Correct typo in previous commits

* fluids: Add IDL and newtonian wave test

* fluids: Rename Newtonian Wave --> Gaussian Wave

* fluids: Move RampCoefficient into utils

- Also change name to LinearRampCoefficient, as we may have different
kinds of ramps in the future

* fluids: Change IDL commandline options

* docs(fluids): Document internal damping layer

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

* fluids: Add ScaleN QF utility

* fluids: Extract InternalDampingLayer QFunction helper

---------

Co-authored-by: Jed Brown <jed@jedbrown.org>
Co-authored-by: KennethEJansen <jansenke@colorado.edu>
Co-authored-by: James Wright <james@jameswright.xyz>

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doc - update release notes

doc: upgrade versions and fix @param variables

doc: remove unnecessary breathe path hack

https://github.com/mcmtroffaes/sphinxcontrib-bibtex/issues/283#issuecomment-1028446347

doc: switch from sphinx-panels (deprecated) to sphinx-design (#1161)

operator: Get OperatorField by field name

Vortex shedding / flow past cylinder (#1082)

* add vortex shedding problem

* add file for the Qfunctions

* add yaml file

* update problem setup

* update IC qfunc

* update problem set

Vortex shedding / flow past cylinder (#1082)

* add vortex shedding problem

* add file for the Qfunctions

* add yaml file

* update problem setup

* update IC qfunc

* update problem setup

* update initial condition

* update yaml file

* add mesh file

* add vortexshedding to navierstokes.h

* register vortexshedding to cloptions.c

* update configuration/yaml file

* fix Min function

* examples/fluids: fix boundary condition labels for cylinder

$PhysicalNames
6
2 1 "inlet"
2 2 "outlet"
2 3 "top"
2 4 "bottom"
2 5 "cylinderwalls"
2 6 "frontandback"
$EndPhysicalNames

* update QFunctions in navierstokes.c

* update data and BC structs in navierstokes.h

* update vortexshedding.c

* update states

* update IC in vortexshedding.h

* add freestream BC to cloptions

* updates in setuplibceed.c

* include freestream BC in example

* cleanup duplicate variable names

* rename variables as freestream

* clean-up some warning messages

* clean up example

* add cylinder.geo

* label physical volume

* examples/fluids: fix cylinder mesh and add vortexshedding defaults

* update gravity vector

* examples/fluids: match domain to Shakib, get vortex street

* update to quadratic mesh

* clean up yaml file

* delete vortexshedding.c and vortexshedding.h

* remove vortexshedding from register

* update yaml file

* examples/fluids: Newtonian "still" initial condition

Reinstate outflow boundaries that were previously removed so that
existing tests can pass.

* examples/fluids: freestream inherits reference state

Fix freestream context reference counting bug.

* examples/fluids: avoid designated initializer in kernel code (breaks CUDA)

* add Shakib91 to references

* remove cylinder.geo and cylinder.msh

* wip:add documentation for vortex shedding

* update path to cylinder.msh

* add subdirectory for meshes

* parameterize cylinder.geo

* some fixes in cylinder.geo

* Fix cylinder.geo file

* examples/fluids: fix up mesh parametrization

Fix cylinder size (the function is Sqrt, not sqrt) and parametrize
resolution and aspect.

* examples/fluids: fix build after broken merge from main

* update Shakib1991 in references

* wip:docs for vortex shedding

* remove TODO comment

* reformulate docs

* fix docs

* delete cylinder.msh file

* work on documentation

* add vortex runtime options

* examples/fluids: update vortex shedding docs and mesh

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

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libCEED 0.11.0

doc: rename libCEED.svg to avoid latex build issue

sphinx/pandoc creates libCEED.pdf from libCEED.svg and places it in the
latex build directory where the manual, also named libCEED.pdf, needs to
go

doc: rename libCEED.svg to avoid latex build issue

sphinx/pandoc creates libCEED.pdf from libCEED.svg and places it in the
latex build directory where the manual, also named libCEED.pdf, needs to
go. Renaming avoids this conflict and circular include that breaks latex.

show more ...

doc: use lualatex and unicode-math for font consistency in pdf manual

Due to a mix of older packages, our math rendered with Computer Modern
rather than the intended TeX Gyre Pagella Math (a font ma

doc: use lualatex and unicode-math for font consistency in pdf manual

Due to a mix of older packages, our math rendered with Computer Modern
rather than the intended TeX Gyre Pagella Math (a font made to go with
our main text). The bm package does not work with unicode-math so we
provide a replacement for consistency with KaTeX.

show more ...

doc - add function rename/move to release notes

doc - fix myst_url_schemes type

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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doc(fluids): Add Newtonian Wave, bc_freestream

- Also fix citation in the Shock Tube documentation.

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

Update OCCA Backend (#1072)

* Update OCCA memory interop call.

* Removes deprecated kernelBuilder calls; builds directly from the device.

* Uses `std::memset` and `std:memcpy`.

* Uses `std:

Update OCCA Backend (#1072)

* Update OCCA memory interop call.

* Removes deprecated kernelBuilder calls; builds directly from the device.

* Uses `std::memset` and `std:memcpy`.

* Uses `std::to_string` instead of internal `occa::toString`.

* Uses `std::memcpy`.

* Sets kernel properties.

* Removes deprecated kernelBuilder calls; builds directly from the device.

* Removes deprecated kernelBuild call; builds directly from the device.

* Uses `std::memcpy`.

* Removes deprecated calls to `occa::linalg`.

* Add registration and device configuration for DPC++ and OpenCL backends.

* Add DPC++ and OpenCL backends to makefile.

* Spelling.

* Configure build flags for oneAPI compilers.

* Correctly set mode in `occa::json` object.

* Add missing functions to OCCA CeedVector implementation.

* Adds missing call to `setValueKernel` in OCCA CeedVector impl.

* Gets occa device function name from the CeedQFunction.

* Adds OpenCL and DPC++ to backends list.

* Uses unique kernel name for OCCA qFunction kernels.

* Adds a dummy `ceed.h` header in include in OCCA kernels.

* Rewrite arrays of structs in format that OCCA can handle.

* Adds stubs for missing functions in OCCA qfunctioncontext.

* Includes the cmath header when compiling C++ code.

* Add stubs for missing OCCA backend LinearAssembleXXX functions.

* Adds missing functions to OCCA implemenation of qFunctionContext.

* Removes math function headers which were causing OCCA JIT failures.

* Rewrite arrays of structs in format that OCCA can handle.

* Rewrites fluids example qfunctions to be compatible with OCCA.

* Fixes array dimensions in mass2dbuild.

* Rewrites advection problem kernels to work with OCCA.

* Rewrites blasius problem kernels to work with OCCA.

* Rewrites channel problem kernels to work with OCCA.

* Rewrites dirichlet bc kernels to work with OCCA.

* Rewrites newtonian kernels to work with OCCA.

* Rewrites setupgeo kernels to be compatible with OCCA.

* Rewrites stabilization kernels to be compatible with OCCA.

* Rewrites stg kernels to be compatible with OCCA.

* Adds occa backends to tests for the fluids example.

* doc - update OCCA info in release notes + README

* ci - run with OCCA v1.4

* occa - update copyright boilerplate

* occa - drop unused define

* ci - fix OCCA install

* wip

* ci - fix occa skip list

* make/ci - fix use of OCCA_DIR/bin/occa

* makefile - minor style

* ci - re-enable OCCA dir caching

* doc - update release notes to mention OCCA QF workarounds

Co-authored-by: Kris Rowe <kris.rowe@anl.gov>

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Refactor `cuda-gen` and `hip-gen` backends. (#1050)

* Add TODO items.

* rough, but something like this?

* wip - cleaning up some warnings, but more remain

* wip - reorganize

* wip - miss

Refactor `cuda-gen` and `hip-gen` backends. (#1050)

* Add TODO items.

* rough, but something like this?

* wip - cleaning up some warnings, but more remain

* wip - reorganize

* wip - missing kernels

* wip - replace t1d

* fix some kernels

* another typo

* more

* another one

* closer

* define T_1D

* typosgit add .!

* WIP: changes to cuda-shared framework for new kernels

* fix output writing

* buffer fix

* buffer sizes

* WIP: fixes for 2 and 3D basis kernels

* minor

* fix weight kernel for 3d

* remove debugging output

* minor reorg

* fix includes

* enable collo grad for cuda-shared

* move quoted kernels

* renaming

* missed a rename

* small fix

* more naming consistency

* faster 'useCollograd=false' path in *-gen

* more style

* one last style fix

* clearer collograd condition

* Add gen basis kernels to hip-shared

* Try some changes to hip-shared basis block sizes for new kernels

* cuda - drop extra kernel arg

* cuda - fix collograd check logic

* update gen comment about parallelization

* tidy up fields struct definition

* tidy up structs even more

* Update hip-gen basis templates use and move other hip-gen device functions to jit-source

* Finish hip-gen basis template update; small style updates to match CUDA

* missing isStrided

* Update block size used in 3D weight for new shared kernels

* update release notes

Co-authored-by: Jeremy L Thompson <jeremy@jeremylt.org>
Co-authored-by: nbeams <246972+nbeams@users.noreply.github.com>

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doc: Add CEED_QFUNCTION_ATTR to releasenotes

- Also add CEED_QFUNCTION_ATTR to the backend documentation

doc - fix ref warning for hoverxref_role_types

doc: fix warnings and malformed hyperlink target

doc: pin sphinxcontrib-bibtex==2.4.2

We can update to 2.5 when we upgrade to docutils-0.18 (which I think
needs sphinx-5).

doc: Update release notes

fmt - add CeedInt_FMT