fluids: Add nodal evaluation of SGS DD Model

fluids: Project grid anisotropy tensor

fluids: Add QF for velocity gradient L^2 projection

fluids: Add data-driven SGS evaluation QFunctions

- This includes transforming to/from the anisotropic physical-frame to
isotropic S-frame

fluids: Add rotation rate, velocity gradient helpers

- Also change KMStrainRate to KMStrainRate_State, leaving KMStrainRate
to be a generic interface to the velocity gradient

fluids: Add linear algebra tools to utils.h

fluids: Add symmetric eigensolver QF helper

- Adapted from https://github.com/jewettaij/jacobi_pd

fluids: Read in files for SGS Data-Driven Model

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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fluids: Misc doc fixes and code style changes

Merge pull request #1145 from prj-/jolivet/warnings

Fix -Wextra-semi -Wmissing-field-initializers

fluids: Stats collection weighted in QFunction

- Allows for only keeping one CeedVector for child statistics

fluids: Use enum for turbulence statistics components

- Also change the filenames to be more specific
- Define num_comp_stats via TURB_NUM_COMPONENTS

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

fluids: Change turb_spanstats CL option names

- Options controlling the actual TSMonitor are under
`ts_monitor_turbulence_spanstats_*`
- `stats_enable` removed in favor of
`ts_monitor_turbulence

fluids: Change turb_spanstats CL option names

- Options controlling the actual TSMonitor are under
`ts_monitor_turbulence_spanstats_*`
- `stats_enable` removed in favor of
`ts_monitor_turbulence_spanstats_viewer` being the statistics switch
- Related objects excluding the viewer (such as the dm and ksp) get the
prefix `turbulence_spanstats`
- Change the `stats_test` related functions and variables to use the
`mms` nomenclature, since they're method of manufactured solutions.

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fluids: Check result of statistics testing

fluids: Add stats collection QF

fluids: Add solution time to newtonian context

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

Fix -Wextra-semi -Wmissing-field-initializers

examples/fluids: Riemann outflow using pressure and temperature

* This allows stable sustained and transient recirculation.

* short-wake domain recirculation behind cylinder has sustained
rec

examples/fluids: Riemann outflow using pressure and temperature

* This allows stable sustained and transient recirculation.

* short-wake domain recirculation behind cylinder has sustained
recirculation. If the exterior temperature is different, the
recirculation will bring in the wrong temperature, but at least
it's stable.
* nwave with slow background causes transient flow reversal when
strong acoustic hits boundary.
* Clean outflow and lid for Blasius

* I tried the 2 P_ext - P_int strategy from Mengaldo (constant density)
and with specified exterior temperature, but they disrupted the interior
flow and were not significantly less reflective.

* The methods I tried for extrapolating interior temperature were not
stable. Simple extrapolation of velocity worked best, and did not show
signs of instability, perhaps because the neighboring flow and implicit
solve ties it together.

* This commit adds support for softmax control of recirculation, but the
parameters were finnicky, solver nonlinearity was a concern, and I'm not
convinced it's ever better than just allowing recirculation.

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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: remove C99 designated initializers for use with CUDA

nvrtc does not support this construct.

minor - assorted formatting fixes

style: Prettyify fluids after clang-format switch

Mainly rearrange the input/output variable declarations for QFunctions