fluids: Read in files for SGS Data-Driven Model

fluids: Move PHASTA file functions to misc.c

fluids: Refactor matops -> petsc_ops

Merge pull request #1191 from CEED/jrwrigh/fix_petsc_build

fix: Update DMGetRegionDS calls in examples/petsc

Update minimum petsc version for solids and fluids

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

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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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Merge pull request #1177 from CEED/jrwrigh/fluids-getcontextfield

fluids: Use ContextGetDouble for time and dt label updates

Merge pull request #1147 from CEED/jrwrigh/generic_l2_projection

fluids: Add generic L2 projection function

fluids: Remove unused spanstats lumped mass matrix

fluids: Add ComputeL2Projection function

Lift, Drag, Heat Transfer (#1130)

* add functions for surface forces

* function for surface forces

* reaction forces

* add points to label

* WIP: examples/fluids: sketch surface force ca

Lift, Drag, Heat Transfer (#1130)

* add functions for surface forces

* function for surface forces

* reaction forces

* add points to label

* WIP: examples/fluids: sketch surface force calculations

* examples/fluids: fix for parallel, when there are no such points on a process

* add TSMonitor_FaceForce function

* update on TSMonitor FaceForce

* create .csv file

* cleanup TS Monitor FaceForce function

* include surface forces viewer to header file

* include ts monitor surface force viewer to cloptions

* update where TSMonitor FaceForce are called

* examples/fluids: update wall forces to write csv

mpiexec -n 5 build/fluids-navierstokes -options_file examples/fluids/vortexshedding.yaml -{ts,snes}_monitor -degree 1 -ts_monitor_wall_forces ascii:force.csv:ascii_csv

* update documentation

* reaction force data

* plotting script

* examples/fluids: seaborn plotting with twinx and colors

* delete data file

* tuck away csv file

* place python script in subdirectory

* examples/fluids/postprocess: put shedding period in title

* examples/fluids: document wall force and shedding postprocess

---------

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

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Merge pull request #1135 from CEED/jrwrigh/spanwise_stats

refactor(fluids): Move stats ceed_data to SpanStatsSetupData

- Add create/destroy functions for SpanStatsSetupData
- Moved SF creation inside CreateStatsSF
- Removed unused members from user->spa

refactor(fluids): Move stats ceed_data to SpanStatsSetupData

- Add create/destroy functions for SpanStatsSetupData
- Moved SF creation inside CreateStatsSF
- Removed unused members from user->spanstats
- Added destroy of elem_restr_qx (a fix)
- Moved all parent L2 projection related operations into SetupL2ProjectionStats
- Removed QFunction members from SpanStatsSetupData (no need to keep
them beyond operator creation)

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fluids: Add MatopApplyContextDestroy

fluids: Stats collection weighted in QFunction

- Allows for only keeping one CeedVector for child statistics

fluids: Add turb spanstats test, change test option

- `-test` changed to `-test_type` enum to test different outputs

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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examples/fluids: fix stats after restart

* Switch from reweighted average to running sum of child stats
* Initialize sp_stats->prev_time after restart
* Use TS reason instead of extra flag
* Skip

examples/fluids: fix stats after restart

* Switch from reweighted average to running sum of child stats
* Initialize sp_stats->prev_time after restart
* Use TS reason instead of extra flag
* Skip redundant monitor call; monitors always get called after last step (converged or not)
* Close memory leak

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fluids: Create UpdateBoundaryValues, fix statistics

- Statistics would fail when non-zero strong bcs were used due to Q_loc
not containing those values. Instead, use user->Q_loc and call
UpdateB

fluids: Create UpdateBoundaryValues, fix statistics

- Statistics would fail when non-zero strong bcs were used due to Q_loc
not containing those values. Instead, use user->Q_loc and call
UpdateBoundaryValues to verify that the boundaries are set.

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fluids: Use persistent viewer for statistics

- Use prefix 'stats_viewer'
- Particularly useful for setting `stats_viewer_cgns_batch_size`

fluids: Remove StatsCollectFinalCall

- Effectively duplicate of TSMonitor_Statistics

fluids: Destory statistics objects at the end

fluids: Check result of statistics testing