3c4b7af6bf1a206cad198c63d890a93b5be72708 - Merge branch 'main' into jed/fluids-jacobian

Mon, 23 May 2022 04:40:50 +0000

Merge branch 'main' into jed/fluids-jacobian* main: Fluids - Add STG inflow (#868) ci - fix Nek5000 testing List of files: /libCEED/examples/fluids/STGRand.dat

ba6664ae303f5b2ef46b3df96973d9bdc665107c - Fluids - Add STG inflow (#868)

Sun, 22 May 2022 22:44:21 +0000

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 * 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 * examples/fluids: Minor bib citation edits Co-authored-by: Jed Brown * 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 List of files: /libCEED/examples/fluids/STGRand.dat

Changes in STGRand.dat

3c4b7af6bf1a206cad198c63d890a93b5be72708 - Merge branch 'main' into jed/fluids-jacobian

ba6664ae303f5b2ef46b3df96973d9bdc665107c - Fluids - Add STG inflow (#868)