fluids: Allow communication overlap in IFunction

fluids: Add MatShell generating code

fluids: Add CreateElemRestrColloc for statistics

- These CeedElemRestrictions are for storing the quadrature point data
at the child points and for their implementation into the parent
quadratur

fluids: Add CreateElemRestrColloc for statistics

- These CeedElemRestrictions are for storing the quadrature point data
at the child points and for their implementation into the parent
quadrature points.

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fluids: Mass QF for different number of components

- In order to avoid "Function defined, but not used" warnings, the
ReturnMassQFunction is used to return the correctly sized mass QF

fluids: Create SF for child->parent communication

fluids: Add CreateStatsDM using DMPlexFilter

- Use DMPlexFilter to extract target plane from the base mesh

fluids: Use CeedElemRestrictionCreateVector for qdata

examples/fluids TS: report converged/diverged reason with clean exit

The final state does not get written by the monitor with the default of
-ts_error_if_step_fails 1. Now we exit cleanly regardless

examples/fluids TS: report converged/diverged reason with clean exit

The final state does not get written by the monitor with the default of
-ts_error_if_step_fails 1. Now we exit cleanly regardless of reason,
ensuring that the final state checkpoint and monitor has been called.

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examples/fluids: write step and time to single binary checkpoint file

The -continue and -continue_time_filename arguments can be skipped when
reading new-style files, which include the step number.

examples/fluids: write step and time to single binary checkpoint file

The -continue and -continue_time_filename arguments can be skipped when
reading new-style files, which include the step number. When reading
legacy files, all three are necessary.

This deprecates the time file.

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fluids: Don't write output file when loading IC

- Stops overwriting of previous initial condition data

examples/fluids: deprecated output_freq for checkpoint_interval and fix numbering

examples/fluids: set step number after restart

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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fluids: default q_extra = 0

examples/fluids: eagerly initialize PETSc device

style: remove obsolete (with clang-format) INDENT comments

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: Make simulation continuation more flexible (#1086)

* fluids: Add options to continue from specific file

* fluids: Option to write out bins with step number

* doc(fluids): Document outp

fluids: Make simulation continuation more flexible (#1086)

* fluids: Add options to continue from specific file

* fluids: Option to write out bins with step number

* doc(fluids): Document output/continuation flags

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Merge pull request #1080 from CEED/ade/riemann-bcs

HLL Flux for Riemann BCs

fluids: Add newtonian_wave problem

- Mainly used to verify the HLL boundary condition.

fluids: Add STG fluctuations to initial condition

- Extrudes the STG fluctuations downstream of the inflow (using the STG
method's inherent dependence on streamwise distance)

fluids: Integrate freestream bc

fluids: Add SetupBCQFunctions to setuplibceed.c

- Condenses redundant code into a single function. Will be useful when
implementing the freestream bc

fluids: Create AddBCSubOperator in setuplibceed.c

- Condenses redundant code (and will help reduce redundancy when I add
in the freestream boundary conditions as well).

fluids: Fix time label for strong STG #1057