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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Cleaner density inflow (#953)

* density weakly set on the inflow....also seems to have a commit intended for ken/primitiveSUPGterm OOOP

Merged onto main this density ONLY inflow step...fixed E_k

Cleaner density inflow (#953)

* density weakly set on the inflow....also seems to have a commit intended for ken/primitiveSUPGterm OOOP

Merged onto main this density ONLY inflow step...fixed E_kinitec bug along the way which used interior velocity.

* first cut at choose your weak inflow rho or T

* cleanup and a missing gamma

* dropped time step to 2e-6, added time limit of 0.001, added suggested parameters for tau constants for linear vs. quadratic. Note this is far from certain, expecially quadratic. Also left commented the required settings to forces SNES to do a fixed number of NL iterations. The current settings do 2 NL iterations for a while then drop to 1 which is ok for steady state but might not be good for SRS.

* potentially better Ctau_{C,M,E} that have much lower oscillations in the free stream even at large time steps like 3.2e-5

* examples/fluids: fix output_freq

* examples/fluids: use bool for weakT

Suggested-by: James Wright <james@jameswright.xyz>

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

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feat: Add blasius boundary layer and channel flow examples to examples/fluids (#942)

* examples/fluids: Upload current case for collaboration

* examples/fluids: Replace developing BL with duct

feat: Add blasius boundary layer and channel flow examples to examples/fluids (#942)

* examples/fluids: Upload current case for collaboration

* examples/fluids: Replace developing BL with duct

* examples/fluids: Allow density to "float" at inflow

* fix: Add u_normal

* examples/fluids: bug fix in density flux

* examples/fluids: implement "floating" pressure; prescribed u, T

* examples/fluids: fixing initialization

We need has_neumann=true to get the weak boundary integrals called. It
is initialized in problem->setup_ctx and used in SetupLibceed(). This is
a hack to always apply.

* examples/fluids: include kinetic energy in Blasius IC

* examples/fluids: Blasius quasi-2D (slip in z planes)

* feat: Add Exact_Channel function

* feat: Use Exact_Channel for IC and Inflow

* examples/fluids: Add channel example

* examples/fluids: Define mu in blasius.c, cleanup

* examples/fluid: Add Blasius solution calculator

* examples/fluids: Add blasius IC and BCs

* Convert to implicit TS

* examples/fluids: Update blasius.yaml

* Move to ChannelContext, refactor DC and newtonian

- Added a dedicated ChannelContext, which allows for user setting of
flow parameters and consistent sharing of parameters between
QFunctions (instead of hardcoding)
- Moved density current (DC) specific settings from newtonian.c
densitycurrent.c

* Make gravity into vector quantity

* Add in body force for channel

* examples/fluids: remove explicitly setting coordinate field

This is created automatically now by DMPlex and DMProjectCoordinates
breaks (localized) periodicity, resulting in a tangled mesh.

* examples/fluids: transpose flux Jacobian in SUPG stabilization

* examples/fluids: update docs commensurate with flux Jacobian transpose fix

* examples/fluids: work on docs for tau

* examples/fluids: Increase blasius Re, implement Xi to SUPG

- Increased the Uinf and mu by 4x for the blasius problem
- Implemented the calculation of Xi for the SUPG term in newtonian.h

* examples/fluids: Remove flux jacobian transpose

- Removed for both eulervortex.h and newtonian.h

* examples/fluids: Reset Newtonian unit scaling to neutral

- Note that this resets the scaling for the densitycurrent problem,
thus the examples (and possibly tests) will probably need to be
changed

* examples/fluids: fix PetscOptionsBegin for new PETSc

* feat: Add slanted domain top surface

* feat: Add graded mesh option for blasius

* fix: Correct inflow boundary condition handling

* feat: Move to blasius_context, add CLI options

* feat: Move Blasius to physical air properties

* fix: Blasius profile and mesh generation

- Add the correct float->int rounding
- Fix eta to a value after exceeding the table's bounds

fix: Add fix eta after exceeding table

* examples/fluids: Move to physical mu default, fix tests

* doc: Add minimum documentation for channel and blasius

* examples/fluids: Add primitive jacobian and tau

- Also add misc comments

* examples/fluids: propose alternative flux Jacobian via prim-to-conservative

* examples/fluids: Add PHASTA diagonal tau

* fix: Add back in timestep obtaining

* examples/fluids: Add analytic tractions to inflow and outflow

- This is a stop-gap until viscous flux can be computed properly on the
boundary from current solution.
- Tau constants in a state of flux still but this produced a decent v at
inflow and outflow, removing the steep dive caused by forcing
dv/dx=-du/dy from a zero traction of omission.

* examples/fluids: CLI options for diagonal c_tau's

* examples/fluids: Update dt via context labels

* feat: Add more blasius table points

* examples/fluids: Cleanup stab and adjust Ctau_E

* examples/fluids: Replace spatial tau with diagonal

* examples/fluids: Fix stab in Euler

- Initialize `stab` to zero, add sum over loop

* examples/fluids: Document diagonal tau formulation

* examples/fluids: Fix compiler warnings

* examples/fluids: check error codes and elide unused header

* examples/fluids: Correct blasius example CLI

- Also add mention of the `blasius.yaml` file

* examples/fluids: Add supg to default blasius.yaml

* examples/fluids: Use yaml for channel and blasius

- Instead of long CLI options
- Also cleaned up the yaml formatting
- Added Cartesian directions to the faceMarker names

* examples/fluids: Show example yamls in README

Co-authored-by: Jed Brown <jed@jedbrown.org>
Co-authored-by: Kenneth E. Jansen <Kenneth.Jansen@colorado.edu>

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Merge pull request #947 from CEED/jrwrigh/fluids-use_field_labels

examples/fluids: Set euler_context->curr_time via context fields

examples/fluids: Set ctx->time via context fields

Merge pull request #858 from CEED/jeremy/dump-copy-stuff

Strip redundant/outdated license info duplication

minor - update copyright headers

Extract generic Navier-Stokes code into 'newtonian.h' (#903)

* feat(fluids): Extract newtownian.h from DC problem

- Also trade out `int` for `StabilizationType` enum

* style: Fix parameter sp

Extract generic Navier-Stokes code into 'newtonian.h' (#903)

* feat(fluids): Extract newtownian.h from DC problem

- Also trade out `int` for `StabilizationType` enum

* style: Fix parameter spacing

* feat: Move generic setup from DC -> newtonian

- Includes moving from `DCContext` to `NewtonianIdealGasContext` at
appropriate locations

* feat: Add "still" IC for generic Newtonian IG problems

* feat: Move SetupContext from DC -> newtonian.c

* fix: Remove unused variables, general cleanup

* examples/fluids: remove unnecessary includes

* examples/fluids: copy declarations to make newtonian.h self-contained

* examples/fluids: full name for context

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

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Merge pull request #881 from CEED/leila/fluids-mesh

Fluids - Update mesh creating and remove problem-specific BCs

Set BCs in CL options

Factor out euler_outflow QFunction to be used in different problem cases

Use DMCreate() to create mesh instead of DMPlexCreateBoxMesh()

Merge pull request #886 from CEED/jeremy/min-petsc

ex - better namespacing of petsc ex headers

ex - better namespacing of petsc ex headers

Merge pull request #885 from CEED/jeremy/min-petsc

PETSc - set minimum version for examples

petsc - set minimum version for examples

Merge pull request #866 from CEED/jeremy/petsc-offsets

Use DMPlexGetLocalOffsets

petsc - use DMPlexGetLocalOffsets for building restrictions

Merge pull request #865 from CEED/leila/fluid-stab

Fluids - Fix bug in Stabilization (SU/SUPG)

eulervortex: add test_5 - non-smooth cylinder

examples/fluids: tau as spatial criterion 2 of hughesetal2010

Testing traveling vortex with

$ build/fluids-navierstokes -problem euler_vortex -ts_adapt_monitor -lx 1000 -ly 1000 -lz 50 -dm_plex_box

examples/fluids: tau as spatial criterion 2 of hughesetal2010

Testing traveling vortex with

$ build/fluids-navierstokes -problem euler_vortex -ts_adapt_monitor -lx 1000 -ly 1000 -lz 50 -dm_plex_box_faces 20,20,1 -ts_adapt_safety 0.8 -implicit -snes_atol 1e-3 -ksp_atol 1e-4 -ksp_rtol 1e-3 -ts_type alpha -ts_dt 0.1 -ksp_type bcgs -pc_type lu -log_view -snes_monitor -ksp_monitor -snes_converged_reason -output_freq 1 -degree 1 -ts_max_time 5. -stab supg -snes_lag_jacobian 30 -snes_lag_jacobian_persists -snes_mf_operator

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fluids - fix flux Jacobian and add su/supg to euler_vortex

Merge pull request #818 from CEED/leila/doc-fix

Examples - doc

examples/fluids: doc - include "running the mini-app"

EULER_VORTEX - removed debugging tests from the test suite

conv_test.sh: Drop the euler_test option and degree 3 as the results almost never ma

examples/fluids: doc - include "running the mini-app"

EULER_VORTEX - removed debugging tests from the test suite

conv_test.sh: Drop the euler_test option and degree 3 as the results almost never match with different PETSc configurations

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Merge pull request #800 from CEED/leila/fluids-small-refactor

Fluids - Small refactor

examples/fluids: Set up QFunction contexts in each compilation unit