Merge pull request #1443 from CEED/jrwrigh/riemann_slip

fluids: Change slip boundary condition formulation

test(fluids): Test bc_slip

fluids: Change -bc_slip_x -> -bc_symmetry_x

Merge pull request #1330 from CEED/jrwrigh/fluids_physical_grad

fluids: Add StatePhysicalGradientFromReference util

fluids: Add StatePhysicalGradientFromReference util

Merge pull request #1278 from CEED/jrwrigh/blasius-simplex

fluids: Fix STG and Blasius for non-box meshes

fluids: Use enum for mesh transformation flag

fluids: Explicit flag for blasius mesh modification

- So that blasius example can run using external meshes without any
attempt to modify them

Merge pull request #1222 from CEED/jrwrigh/fluids_typos

style(fluids): Misc typo fixes

style(fluids): Misc typo fixes

- Clean up blasius.yaml
- Typo fix to data-driven SGS setup
- Remove unneccessary CeedVector from SGS DD setup
- Fix STG error message to be more general

Merge pull request #1135 from CEED/jrwrigh/spanwise_stats

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.

show more ...

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

show more ...

Merge pull request #1131 from CEED/jed/checkpoint-interval

fluids: checkpoint interval

examples/fluids: deprecated output_freq for checkpoint_interval and fix numbering

Merge pull request #1096 from CEED/leila/fluids-stab-coef

Fluids-newtonian: Stabilization coefficients dependent on polynomial degree

fluids: default q_extra = 0

fluids/newtonian: automate Ctau_*

fluids/newtonian: automate Ctau_v

Merge branch 'main' into jed/fluids-jacobian

* main: (24 commits)
op - more data in view
examples/fluids: Test for strong STG
examples/fluids: Add strong STG to documentation
examples/fluids

Merge branch 'main' into jed/fluids-jacobian

* main: (24 commits)
op - more data in view
examples/fluids: Test for strong STG
examples/fluids: Add strong STG to documentation
examples/fluids: Add option for BC from ICs
examples/fluids: Correct for non-origin domains
examples/fluids: Implement Strong STG BC
examples/fluids: Minor stg improvements/style
examples/fluids: Add Strong STG functions
examples/fluids: Fix memory leak in STG
GPU assembly: fix potential basis loading offset error
tests - more complex source include testing
pc - fix qf fallback cloning
restr - relax comp_stride check for num_comp == 1
make style
pc - avoid direct access of basis data in multigrid creation
ceed - refactor fallback Ceed creation into separate fn
minor - homogonize int vs CeedInt
basis - add input checks
restr - add input checks on element restrictions
examples/fluids: Update STG test for new mesh feats
...

show more ...

Merge pull request #964 from CEED/jrwrigh/mesh_from_file

examples/fluids: Create mesh from file distribution

examples/fluids: Update docs for meshing from file

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 ...

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>

show more ...