examples/fluids: summary report restart state/step/time

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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Merge pull request #1131 from CEED/jed/checkpoint-interval

fluids: checkpoint interval

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

Merge pull request #1129 from CEED/jed/fluids-restart

fluids restart: set step number

examples/fluids: set step number after restart

examples/fluids: remove duplicate typedef

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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examples/fluids doc: update description of SUPG

The old description is a relic from earlier comparisons of the GLS
versus VMS justifications. We now describe the version that is
implemented and work

examples/fluids doc: update description of SUPG

The old description is a relic from earlier comparisons of the GLS
versus VMS justifications. We now describe the version that is
implemented and works well.

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fluids: default q_extra = 0

fluids/newtonian: fix indexing of Ctau_v

fluids/newtonian: automate Ctau_*

fluids/newtonian: automate Ctau_v

fluids-newtonian: Stabilization coefficients dependent on polynomial degree

Merge pull request #1114 from CEED/jrwrigh/fix-ns-mesh-wording

fluids: Clarify definition of Global nodes

Merge pull request #1115 from CEED/jed/fluids-device-bind-petsc

fluids: device bind petsc and fix HLLC for CUDA

fix: Change "Owned Nodes" to "Local Nodes"

examples/fluids: remove C99 designated initializers for use with CUDA

nvrtc does not support this construct.

examples/fluids: eagerly initialize PETSc device

Merge pull request #1104 from CEED/jeremy/formatting

Minor Formatting Fixes

minor - assorted formatting fixes

Merge pull request #1102 from CEED/jrwrigh/re-pretty_fluids

style: Prettyify fluids after clang-format switch