examples/fluids: Update STG test for new mesh feats

Merge branch 'main' into jed/fluids-jacobian

* main:
Fluids - Add STG inflow (#868)
ci - fix Nek5000 testing

Fluids - Add STG inflow (#868)

* doc(fluids): Add STG equations

* doc(fluids): Add basic data flow for STG

* doc(fluids): Add Shur et al. 2014 STG paper to bib

* doc(fluids): Specify STG in

Fluids - Add STG inflow (#868)

* doc(fluids): Add STG equations

* doc(fluids): Add basic data flow for STG

* doc(fluids): Add Shur et al. 2014 STG paper to bib

* doc(fluids): Specify STG inputs files, misc additions

* doc(fluids): Add intro for STG section

* fix(fluids): Add #include ceed.h for qfunctions

- In the spirit of "include what you use"

* feat(fluids): Start work on stg_shur14.h

* doc-fix: Correct kappa_min definition

* Move STG setup functions to problems/stg_shur14

* feat: Add cholesky decomposition function

* fix: Correct stg_ctx malloc, reorganize creation

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

* fix(fluids): Correct return values of functions

* style: Fix up style

* feat(fluids): Get file paths from PetscOptions

- Also convert SetupSTGContext to return PetscErrorCode

* fix(fluids): Correct stg_ctx dereferencing

- Also move to size_t for type of the offsets

* feat(fluids): Add funcs for processing STG*.dat files

* feat(fluids): Move to PetscOptions* for STG flags

* feat: Use `PetscMax` instead of macro

* fix(fluids): Correct/Refactor file reading functions

- Move to `PetscSynchronizedFGets`
- Remove `inline`
- Pass `comm` between functions
- Add `OpenPHASTADatFile` to DRY

* docs(fluids): Fix equation typo

* fix(fluids): Correct calculation of kappa

* feat(fluids): Complete STGShur14_Calc

* feat(fluids): Add InterpolateProfile helper func

* feat(fluids): Add CalcSpectrum helper func

* feat(fluids): Add to STGShur14_Calc qfunction

* fix: Add M_PI, Update SETERRQ functions

- Also update style

* fix: Correct interpolation outside of datarange

* fix: Add missing definition for ke in CalcSpectrum

* feat: Migrate context and func signatures, Misc

- Create SetupSTGContext to be run in another Setup_____Context
function
- Migrate STGShur14Context, CreateSTGContext, and SetupSTGContext
signatures to navierstokes.h
- Add STG contexts to Physics and CeedData
- Add missing CHKERRQ to PetscFClose
- Move to SPDX license headers

* examples/fluids: Pass solution time via context label

* feat: Implement STG boundary integral

- Add theta0 and implicit members to STGShur14Context
- Tested via implementation to the blasius BL problem (though this will
probably go against the code history)

* feat: Fix STG Stuff

* feat: Implement STG inflow for blasius BL

- Note that fluctuations are turned off in this case

* examples/fluids: Add stg_mean_only flag

* examples/fluids: Check cholesky decomp for nans

- Also correct locaiton of cholesky decomposition in ReadSTGInflow()

* examples/fluids: Correct STG documentation

- Missing a 2 sqrt(3/2) factor and didn't take square root of q

* examples/fluids: Fix STGShur14_Calc

- Given the calculated spectrum, calculation of v' and u' verified
against python implementation (which was validated previously against
PHASTA)

* examples/fluids: Calc dXdx for boundary QFunctions

- Also calculate h from the dXdx in STGShur14_Inflow
- Replace h[0] result with constant dx spacing

* examples/fluids: Fix STG Spectra calcualtion

* examples/fluids: Fix build errors

- Ran into an include cycle collision that resulted in over-defining
SetupContext in advection.c
- newtonian_types.h (which has SetupContext defined) ->
stg_shur14_type.h -> navierstokes.h -> advection.c

* examples/fluids: Update and fix documentation

* examples/fluids: Correct dXdx comment, leave TODO

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

* examples/fluids: Minor bib citation edits

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

* examples/fluids: Add STGInflow.dat, fix blasius.yaml

* examples/fluids: int -> PetscInt | CeedInt

* examples/fluids: Style

* examples/fluids: Make Boolean names verb_noun format

- Also changes the stg flag to `-stg_use`

* examples/fluids: Add STG test

* examples/fluids: Style fix up

* examples/fluids: Update docs

* examples/fluids: Implement weakT option for STG

* examples/fluids: Fix casting for ROCm

* examples/fluids: avoid PETSc dependency in qfunctions

* examples/fluids: header cleanup

* backends/hip: avoid redundant inline

* examples/fluids: avoid VLA in qfunctions

GPUs don't like VLA and some compilers reject it when targeting GPUs.

* examples/fluids: Create STG_NMODES_MAX

* examples/fluids: Refactor stg setup out of blasius.c

* examples/fluids: Fix misc GPU bugs

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

show more ...

examples/fluids: fix sign and magnitude of channel flow body force

Add -body_force_scale, which can be -1 to test that a flow reversal
builds to the same steady profile with opposite sign.

I also c

examples/fluids: fix sign and magnitude of channel flow body force

Add -body_force_scale, which can be -1 to test that a flow reversal
builds to the same steady profile with opposite sign.

I also changed the domain size (reducing Reynolds number from 4500 to
45) so flow reversal can be observed reasonably quickly when desired.

show more ...

examples/fluids: add viscous channel flow test

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>

show more ...

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

show more ...

Fluids - Refactor and add GPU support (#754)

* Initial commit for using PetscFunctionList in fluids example

* WIP: debugging

* Debug: initialize PetscFunctionList with NULL

* allocate memor

Fluids - Refactor and add GPU support (#754)

* Initial commit for using PetscFunctionList in fluids example

* WIP: debugging

* Debug: initialize PetscFunctionList with NULL

* allocate memory for context problem

* freed allocated memory

* WIP: fluids: split density current into new compilation unit
I have dropped last changes before this commit so there might be some
bugs

* Fixed bugs after dropping the commit containing unnecessary changes

* NS: dropped unused variable from User struct

* WIP: factored out DMAddBoundary() for density_current

* split advection and advection2d into separate compilation units as well

* fluids: added *.o to make clean

* removed bc from problemData

* style

* commented the error handlers and moved petsc options regarding the boundary conditions to each compilation unit

* call bc functions inside SetUpDM()

* Moved all bc related statements from SetUpDM() to each compilation unit

* examples/fluids/advection.h: style

* WIP: modified CeedQFunctionContexts

* FFR: By creating a struct for DC context, one of the last test crushed so I had to reverse it. This should be investigated later.

* style

* examples/navierstokes: Use heap memory for ctxSetup

* examples/fluids: WIP - reading arrays through cl options for DC is enabled by using double pointers but there is still a problem with unit conversions and also need to fix other structs

* style

* WIP: Trying to assign values to context data in each problem function

* bug: there is a problem in pointer to struct

* WIP: Everything seems to be working but it breaks and I haven't figured out the reason ...

* fixed typo

* comment out stuff that have been moved to densitycurrent.c

* WIP: The first two regression test pass. There is a problem with stabilization.

* style

* Fluids: QFContext -> Physics

* WIP: passing StabilizationType to Physics (but PETSc is not happy and it diverges for SU and SUPG)

* Initial commit for refactoring advection(2d)

* WIP: Advection is set up except for wind_type

* WIP: refactored advection2d; need to fix the BCs for translation and also passing implicit to advection correctly

* WIP: pass wind_type to all functions correctly but there is still a problem with BCs in the case of translation (changes are not applied to advection yet)

* Apply the same fixes for BCs in advection

* Fluids - Refactor: Moved warnings to advection(2d)

* Fluids - Refactor: remove dead code

* Fluids - Refactor: Move *.h to /qfunctions and *.c to /src

* style

* Fluids - Refactor: drop the supg regression test for now

We need to debug SU/SUPG for density_current. The test does not work.

* Fluids - Refactor: Fixed the double-pointer issue

* Fluids - Refactor: Assign ctxSetup->time = 0 inside each problem's *.c

* Fluids - Refactor: make implicit a member of Physics

* Fluids - Refactor: Add warning for the usage of explicit and supg

* Some comments and naming

* Merge main after v0.8 (#723)

* Fluids - Five regression tests added for euler_vortex

* Fluids - Drop some of the regression tests for now (Needs to get fixed)

* Fluids - Moved all functions to their corresponding source files

* Fluids - move problem source files to /problems

* Fluids - drop dead regression test reference files

* Fluids - more consistent file names

* Fluids - drop dead code and comments

* Fluids - removed CreateVectorFromPetscVec() since it was only used once

* Fluids - created AppCtx for cl option variables and moved cl options to a cloption.c

* Fluids: change style of AppCtx

* style

* Fluids: /src -> /utils

* Created CreateDistributedDM() and some style

* Fluids - create RegisterProblem()

* style - minor

* style - minor

* Fluids - some more C style

* Fluids - /utils -> /src

* Fluids - create VizRefineDM() for viz_refine

* Fluids: some style and name change

* Fluids - style

* Fluids - remove the second ceed initialization

* Fluids - Created CeedData and SetupLibCEED()

* Fluids - create SetupContextForProblems()

* Fluids - Assign structs after they are created

* Fluids - style, minor

* Fluids - created RegressionTests_NS

* Fluids - created GetError_NS()

* Fluids - created PrintOutput_NS()

This processes bash output except for the problem summary which will be
included after mem_type is managed properly.

* Fluids - remove unused variables

* Fluids - created TSSolve_NS() which creates, sets up, and solves ts

* Fluids: Fixed a bug caused by merging#714

* Fluids - style

* Fluids - created SetupICsFromBinary() for case of -continue

* Fluids - create SetBCsFromICs_NS()

* Fluids - default degree had is 1 not 2

* Fluids: clean-up

* Fluids: style - minor

* Fluids - drop redundant operation

* Fluids: clean-up SetupLibCEED()

* Fluids: style - minor

* Fluids: WIP - C style

* Fluids: style - minor

* Fluids: move ceed vector creation to SetupLibCEED()

* Fluids: WIP - clean-up CreateOperatorForDomain()

* Fluids: major clean-up in CreateOperatorForDomain()

* Fluids: style - minor

* Fluids: drop VectorPlacePetscVec()

* Fluids: move ICs_FixMultiplicity() to misc.c

* Fluids: WIP - C style

* Fluids: fix merge conflict after d63eecaab22a26d3072677a1b66c0cf77aa9009d

* Fluids: drop unused function call DMLocalizeCoordinates()

* Fluids: replace user requested memType with MemTypeP2C()

* Fluids: C style

* Fluids: Q->num_Q (Q (# qpts) and Q (global state vector) were confusing my fresh petsc config)

* Fluids: WIP - add GPU vectors

* Fluids: Fixed the memory leak caused by Physics struct

* Fluids: style -minor

* Fluids: no need for casting

* Fluids: Fix mem leak (q0_ceed had to be destroyed at the end of navierstokes.c)

* Fluids: Fixed all mem leaks

* Fluids: Set VecType for dm_hierarchy

* Fluids/doc: fix style

* Fluids: fix missing VecRestoreArray()

* Fluids: clean-up ComputeLumpedMassMatrix()

* Fluids: Cleanup ICs_FixMultiplicity()

* Fluids: WIP - cleanup setupts.c

* Fluids: style - minor

* Fluids: Create element coord ceed vector locally and drop it from CeedData

* Fluids: fix some todos

* Fluids: drop unused code for EULER BCs

* Fluids: PetscMalloc1 -> PetscCalloc1

* Fluids - Define BCs for ADVECTION(2D) for all cases without having the user specify them and change the regressions accordingly

ToDo: For some reason I can't create new regression tests for explicit scheme.

* Fluids - Define problem->print_info() for each problem

* Fluids: Shorten some problem specific command line variables & style

* Fluids - Cleanup BCs in the translation mode

* Fluids - cleanup

* Fluids - more cleanup in BCs

* Fluids - Updated doc, README, and cleanup in the code and cl options

* Fluids - add more regression tests

* Fluids - Define tolerance for the convergence test

* Fluids: include x_coord in CeedData

* wip - gpu

Revert "Fluids: include x_coord in CeedData"

I had to revert this commit since it crashes DC

* style

* Fluids - remove unused variables

* Fluids - fix unused function warnings

* Fluids - fix the remaining warnings

* Fluids - style

* Fluids - add missing licence

* Fluids - bring back contexts to the QFunction header files

* Fluids - transfer QFunctions for boundary integral to their corresponding setupgeo(2d).h header files and add description for Setup2d

* fluids - fix context data sizes

* GPU - add helper function macro

* ex - use consistent MPI info output

* GPU - improve CEED_QFUNCTION_HELPER macro, more flexible

* Fluids - turn on some gpu tests

* Fluids - bring back element coordinate to CeedData

* Fluids - cleanup

* qfunction - clean up helper function macro

* Fixed the remaining conflicts from #769 (helped-by: @rezgarshakeri)

Co-authored-by: Jed Brown <jed@jedbrown.org>
Co-authored-by: jeremylt <thompson.jeremy.luke@gmail.com>

show more ...

examples/fluids: ETV - the convergence test comparison was failing since P_inlet is now hard-coded for each test and doesn't go through the scaling

examples/fluids: ETV - added reference csv file for the regression test

Fluids - More Regression Tests (#687)

* examples/fluids: Regression tests: Changed the reference files' names and
the flags to associate with the corresponding example (so far
density_current only

Fluids - More Regression Tests (#687)

* examples/fluids: Regression tests: Changed the reference files' names and
the flags to associate with the corresponding example (so far
density_current only)

Changed the files' names

Changed the flags

* examples/fluids: added new regression tests for advection(2d)

* examples/fluids: regression tests: removed the enums and passed defined command-line options for filepath and test tolerance.
Removed solver controls and assigned testtol=1E-11 for explicit cases.

style

examples/fluids: regression tests: fixed the pathfile issue (it needs to be relative)

examples/fluids: Specified a name for each test

examples/fluids: TESTARGS - trying absolute path for the test files

* tests/tap.sh: Print out test names for fluids examples

inspired-by: @jeremylt

tests/tap.sh: drop quotation marks from the printed test names

* tests: specify test name for ceed and nek examples and print the names when there are multiple test arguments

* examples/fluids: remove test_ from test names

* style

* tests/junit.py: Add name for tests with multiple test cases

* examples/ceed/ex1-volume.c: make the naming of the tests consistent

* tests/junit.py: a more compact if statement

helped-by: @jeremylt

* examples/fluids: drop the broken supg test of density_current for now

The stabilization enum is not passed to density_current QFunction hence
the test doesn't work. We need to create a new test when the code is
debugged.

show more ...

NS: Add data structures for different test types

NS: Check tests error by comparing with reference solutions from binary files