Merge pull request #1226 from CEED/jed/fix-doc-math

doc: fix math in headers

doc: fix math in headers

There is a bad hyperref/unicode-math interaction apparently resulting
from how PDF bookmarks work. This replaces math in headers (section
titles) with unicode Greek letters

doc: fix math in headers

There is a bad hyperref/unicode-math interaction apparently resulting
from how PDF bookmarks work. This replaces math in headers (section
titles) with unicode Greek letters to fix doc-latexpdf.

https://tex.stackexchange.com/questions/570000/improper-alphabetic-constant-error-in-title-with-greek-bug-with-unicode-math-an

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Merge pull request #1189 from CEED/jrwrigh/differential_filter

fluids: Add differential filtering capability

doc(fluids): Add differential filtering

Merge pull request #1149 from CEED/jrwrigh/newtonian_ddsgs

fluids: Data-driven SGS modeling

doc(fluids): Document SGS, data-driven model

Merge pull request #1183 from CEED/leila/fluids-doc-fix

fluids/README: a small fix

fluids/README: a small fix

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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Fix for cubic elements in surface forces for lift/drag coefficients (#1158)

* update for surface forces to return dof

* update surface forces

* update on surface forces

* PetscCall section

Fix for cubic elements in surface forces for lift/drag coefficients (#1158)

* update for surface forces to return dof

* update surface forces

* update on surface forces

* PetscCall section get field components

* Update examples/fluids/src/setupts.c

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

* Update examples/fluids/src/setupts.c

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

* examples/fluids: lift query from inner loop

* examples/fluids: enable coarser meshes

* update yaml file

* fix path to creating figure

---------

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

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Merge pull request #1160 from CEED/jrwrigh/doc-fixes

fluids: Misc doc fixes and code style changes

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

doc(fluids): Document change in test flag

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: Use persistent viewer for statistics

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

doc(fluids): New spanwise statistics gathering flags

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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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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examples/fluids: deprecated output_freq for checkpoint_interval and fix numbering

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

fluids/newtonian: automate Ctau_v