fluids: Change if...SETERRQ to PetscCheck

Merge pull request #1149 from CEED/jrwrigh/newtonian_ddsgs

fluids: Data-driven SGS modeling

fluids: Add flag for turning on SGS model

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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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

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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fluids: Use persistent viewer for statistics

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

fluids: Implement statistics collection

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

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

fluids: device bind petsc and fix HLLC for CUDA

examples/fluids: eagerly initialize PETSc device

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: Integrate freestream bc

examples/fluids: use shell for Amat, block diagonal aij* for Pmat

This adds two independent options for tuning solves.

-amat_type shell: causes Amat and Pmat to be different matrices, with shell
us

examples/fluids: use shell for Amat, block diagonal aij* for Pmat

This adds two independent options for tuning solves.

-amat_type shell: causes Amat and Pmat to be different matrices, with shell
used for Amat. It's technically possible to use other matrix formats
here.

-pmat_pbdiagonal: causes Pmat to be assembled as point-block diagonal.
Note that this usually only makes sense in addition to -amat_type shell
because otherwise your KSP is only working with the point-block diagonal.

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Shock Tube + YZB Discontinuity Capturing (#851)

* Implemented the Sod Shock Tube problem with YZB discontinuity capturing. for the explicit formulation. SU stabilization is also implemented for the

Shock Tube + YZB Discontinuity Capturing (#851)

* Implemented the Sod Shock Tube problem with YZB discontinuity capturing. for the explicit formulation. SU stabilization is also implemented for the explicit formulation.

* Changed variable name midpt to mid_point, removed redundant slip BC declarations.

* Fixed style error, made variable names clearer, and removed dead code.

* Missed a style fix

* Rebased with main

* Implemented the Sod Shock Tube problem with YZB discontinuity capturing. for the explicit formulation. SU stabilization is also implemented for the explicit formulation.

* Fixed style error, made variable names clearer, and removed dead code.

* Missed a style fix

* Implemented fixes to the flux jacobians

* Updated documentation, tau definition in SU, and recommended fixes to the flux Jacobian.

* Implemented the Sod Shock Tube problem with YZB discontinuity capturing. for the explicit formulation. SU stabilization is also implemented for the explicit formulation.

* Missed a style fix

* Implemented the Sod Shock Tube problem with YZB discontinuity capturing. for the explicit formulation. SU stabilization is also implemented for the explicit formulation.

* Fixes to style and documentation.

* Fixing unnecessary problem->dim declaration and missing field in comment describing initial condition density.

* Added warnings for incompatible user input combinations.

* Added comments on beta to documentation, fixed j_gradn style issues.

* Compilation errors on my end. Committing to see if it's local or not.

* Style fixes

* Implemented the Sod Shock Tube problem with YZB discontinuity capturing. for the explicit formulation. SU stabilization is also implemented for the explicit formulation.

* Changed variable name midpt to mid_point, removed redundant slip BC declarations.

* Fixed style error, made variable names clearer, and removed dead code.

* Missed a style fix

* Rebased with main

* Implemented the Sod Shock Tube problem with YZB discontinuity capturing. for the explicit formulation. SU stabilization is also implemented for the explicit formulation.

* Fixed style error, made variable names clearer, and removed dead code.

* Missed a style fix

* Implemented fixes to the flux jacobians

* Updated documentation, tau definition in SU, and recommended fixes to the flux Jacobian.

* Implemented the Sod Shock Tube problem with YZB discontinuity capturing. for the explicit formulation. SU stabilization is also implemented for the explicit formulation.

* Missed a style fix

* Implemented the Sod Shock Tube problem with YZB discontinuity capturing. for the explicit formulation. SU stabilization is also implemented for the explicit formulation.

* Fixes to style and documentation.

* Fixing unnecessary problem->dim declaration and missing field in comment describing initial condition density.

* Added warnings for incompatible user input combinations.

* Added comments on beta to documentation, fixed j_gradn style issues.

* Compilation errors on my end. Committing to see if it's local or not.

* Fluids: SETERRQ1 -> SETERRQ to be compatible with PETSc 3.17

* Fluids - Update shock-tube with #881

* Small fix to mid_point definition and removed repeat entries for Shock Tube problem in README.md.

* Including test output.

* Implemented the Sod Shock Tube problem with YZB discontinuity capturing. for the explicit formulation. SU stabilization is also implemented for the explicit formulation.

* Changed variable name midpt to mid_point, removed redundant slip BC declarations.

* Fixed style error, made variable names clearer, and removed dead code.

* Missed a style fix

* Rebased with main

* Implemented the Sod Shock Tube problem with YZB discontinuity capturing. for the explicit formulation. SU stabilization is also implemented for the explicit formulation.

* Fixed style error, made variable names clearer, and removed dead code.

* Missed a style fix

* Implemented fixes to the flux jacobians

* Updated documentation, tau definition in SU, and recommended fixes to the flux Jacobian.

* Implemented the Sod Shock Tube problem with YZB discontinuity capturing. for the explicit formulation. SU stabilization is also implemented for the explicit formulation.

* Missed a style fix

* Implemented the Sod Shock Tube problem with YZB discontinuity capturing. for the explicit formulation. SU stabilization is also implemented for the explicit formulation.

* Fixes to style and documentation.

* Fixing unnecessary problem->dim declaration and missing field in comment describing initial condition density.

* Added warnings for incompatible user input combinations.

* Added comments on beta to documentation, fixed j_gradn style issues.

* Compilation errors on my end. Committing to see if it's local or not.

* Fluids: SETERRQ1 -> SETERRQ to be compatible with PETSc 3.17

* Fluids - Update shock-tube with #881

* Fluids - added test output file for shocktube

* Small fix to mid_point definition and removed repeat entries for Shock Tube problem in README.md.

* Including test output.

* Update doc/sphinx/source/references.bib

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

* Update examples/fluids/README.md

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

* Update examples/fluids/index.md

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

* Update examples/fluids/navierstokes.h

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

* Update examples/fluids/problems/shocktube.c

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

* Update examples/fluids/qfunctions/shocktube.h

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

* Removed unused IFunction

* Added shocktube variables to SetupContext in advection.h, advection2d.h, and densitycurrent.h

* Missed some merge conflicts that have now been cleared up.

* Added helper function for covariant element length along a given vector.

* Added SetupContext to shocktube.h

* Fix to regression test path

* remove variable transpose of the Jacobian

* Fix index swap in implicit SUPG

* examples/fluids shocktube: fix stab summation and transpose

* delete IFunction

* example/fluids- updates reference solution

Co-authored-by: Timothy Aiken <timothyaiken@Timothys-MacBook-Pro.local>
Co-authored-by: Timothy Aiken <timothyaiken@cu-biot-10-10.203.167.69.int.colorado.edu>
Co-authored-by: Leila Ghaffari <Leila.Ghaffari@colorado.edu>
Co-authored-by: Jed Brown <jed@jedbrown.org>
Co-authored-by: Timothy Aiken <timothyaiken@cu-genvpn-tcom-10.180.164.177.int.colorado.edu>
Co-authored-by: AdelekeBankole <adeleke.bankole@colorado.edu>

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