21.11 Release merge (#29)
* Move the CoveredMask reset flag out of the if statement.
* Add user-defined chemistry tolerances.
* Add a Triple flame in Exec/Cases/TripleFlame
* While making new level from coarse, get 1 ghost cell right so that
AmrNewTime data have one ghost cell properly set.
* Add a simple 2D CH4/Air premixed bunsen case. Tested up to 5 levels.
* Add a 3Dversion of the premixed bunsen flame.
* Need to reset the covered cell mask after restart in case regrid is not called right after.
* Add option to restart an efield simulation from a non-efield one.
* When restarting from non-efield chk, initialize electro-neutral nE
field.
* Fix PlotFile to plot I_R(nE) with efield and write/read in phiV/nE in
chk.
* Machinery to restart from non-efield chk.
* Update Precond operator to implement the second approximation of Stilda.
* Make use of the absolute tolerance in MLGMRES.
* Add fillpatch functions for the non-linear state components.
* Enable Schur complement approximation 2.
* Define and ParmParse m_ef_schur_approx.
* Floor nE along with species if required.
* Fix typos in PeleLMBC.cpp
* Update PeleLMeX header for new fillpatch functions.
* Replace mechanism.h by mechanism.H
* Setup gravity.
* Use gravity in velocity forces.
* Replace .copy by .ParallelCopy.
* Add a lifting hot bubble case in RegTests.
* Default the pprocConvOrder.py to CoVo inputs.
* Enable CoVo in all directions.
* Default input.2d_CoVo to diagonal direction.
* Update pprocConvOrder.py with version checking the convergence order.
* Init convergence testing CI.
* Fix convergence CI (#6)
* Fix deps in convergence CI.
* Update pprocConvOrder.py.
* Fix Pele Physics (#7)
* Update make system to catch up with PP.
* Update sources for latest PP.
* Fix parsing of constant transport parameters.
* Switch AMReX-Hydro (#8)
* Add AMReX-Hydro to deps and GMake.
* Remove LMX Godunov folder from listed sources.
* Fix AMReX-Hydro makefile again and need MOL.
* Swtich to HydroUtils to predict velocity and use
create_umac_grown_constrained.
* Remove stranded Godunov include.
* Add m_advection_type. Only Godunov in LMeX.
* Switch to HydroUtils::ComputeFluxesOnBoxFromState for advection fluxes.
* Remove Godunov from LMeX sources.
* Rewritte the advective flux divergence to comply with AMReX-Hydro way.
* Update CI.
* Feature balance (#9)
* Add kin. energy derive function.
* Add kin.energy derive and ParmParse temporals input.
* Start setting-up run-time diagnostics.
* Update MLNorm0 to not account for fine-covered cells.
* Setup mass balance in runtime diagnostics.
* Add temporal keys to FlameSheet regtests
* Git ignore
* Add gnuplot script for mass balance.
* Fix runtime selection of reactor. (#10)
* Missing AMReX-Hydro home in convergence testing.
* Update Make.PeleLMeX
* Update reactor in Sources.
* Remove one call too many to deallocate of transport.
* Update FlameSheet GMake
* Add CVODE input keys.
* Udpate GMake in Periodic and HotBubble
* Fix typo on ReactorNull default:
* Make LMeX GPU-compatible (#11)
* Remove device from lineaChmeForcing.
* Can't init capture in host_device functions.
* Fix call to host function on device lambdas.
* Change OMP.
* Should be the same, but make sure.
* Don't init transport for incompressible flows.
* Missing Gpu Managed. Will be updated later.
* Minor clean up in PeriodicCases.
* Fix parm in FLameSheet too.
* Restore FlameSheet 3D.
* Remove unused.
* Add Sundials memory helper.
* Remove auto-TPL. Recompile all the source each time. Need fix.
* Restore make TPL in GH workflow for now.
* Fix velocity ghost cells for Nodal projection. Function (#12)
should only overwrite Inflow BCs.
* Implement closed chamber algorithm. (#13)
* Add auto-detection of closed chamber and unable overwrite.
Add PPquery of linear solves tolerances.
* Add GammmaInv kernel.
* Move MFSum in Utils and initialize uncovered volume computation.
* MAC projection function handles closed chamber corrections.
* Nodal projection functions handle -/+ of Sbar in RHS.
* Remove TODO comment.
* Pass dp0dt in diffusion forcing.
* Pass dp0dt in Advection forcing.
* Add pOld <-> pNew in advance function.
* Add adjustPandDivU in Eos file.
* Add accessor to divU levels vector
* Add declarations.
* Add ambient pressure to checkpoint file header.
* Uses pNew to get dPdt.
* Fix BL_PROF in UMAC
* Add an enclosed flame test to test closed chamber.
* Add a CI testing closed chamber.
* Enable EB in LMeX (#16)
* Add missing EB sources to Make.
* Add volFrac to plotfile.
* Add PeleLM EB source file.
* Add a static_cast accessor to ebfactory.
* Update AMReX-Hydro calls to pass ebfactory in.
* Missing include for volfrac tagging.
* Update diffusion operator for EB.
* EB compiles and initialize properly.
* Make sure divTau has right Factory.
* Fix getDiffusivity to not set covered face to 0,0 but huge val.
* _OPENMP -> AMREX_USE_OMP
* Remove plot/abort after init.
* First pass at updating DiffusionOp for EB. Mostly done.
* Fix divergence of advective flux function for EB.
* Minor tweak in PeleLMDiffusion. FluxRedist still need to be implemented.
* Re-organive advection to get divergnce and then redistribute when EB.
fillBoundary in between req. a temporary.
* redistribute_AofS function.
* Add redist schemes for adv/diff, ensure enough ghost cells and declarations.
* Add ParmParse to control nodal solve MG depth.
* Enforce EB-covered to 0 for nodal projection.
* Add fluxdivegenceRD to handle diffusive flux redistribution. Fix MFSum
to exclude EB-covered regions.
* Diffusive flux redistribution function.
* Tedious switch between div/divRD for diffusiob fluxes. Might want to simplify later.
* Accessor to RhoH tower.
* Declarations.
* Add 3D case for EnclosedFlame and a thermo-diffusive CH4/H2 PMF.
* Number of ghost cells in EBFactory should be 6 because of StateRedist
* EBFlag test inst. reaction rate.
* Set covered to 0.0 in plotfiles.
* EBFlag in getHGivenT in enthalpy flux.
* Do initial redisitribution and get a covered state.
* Add initial redistribution machinery and first version of covered state. Need to improve !
* Less confusing message since we now have EB.
* StateRedist -> NewStateRedist default and EB-covered declaration.
* Add EB_FlowPastCylinder case, 2D/3D.
* Set EB-covered chi_incr to zero.
* Add FlowPastCylinder CI.
* A series of minor tweaks: (#17)
- git hash subrepo to screen
- TPROF region cleaned. Add /level chem VARS
- print to screen nCells/extend of each level during regridding
* Add typical value machinery (#18)
* Setup multi-level min/max excluding for EB/fine covered cells
and use that for typical values.
* Add typical values to chk.
* Reset typval at the beginning of advance when needed.
* ParmParse typval options.
* Typical value declarations & call during the initialization.
* Enable Hypre interface to Nodal/MAC linear solves (#19)
* Add Hypre interface ParmParse hook.
* Pass the right hypre_namespace to MacProj.
* MG depth for MAC solve.
* Pass hypre_namespace to nodal solve.
* Add examples of Nodal/MAC hypre options for FlowPastCylinder case.
* update README
* Add a few EB test cases (#20)
* Add an enclosed vortex, failing linear solves.
* Add an input file using Hypre for the Nodal solver
* Add an EB_EnclosedFlame case too.
* Add an Hypre input for the EB_EnclosedFlame case.
* Fix TypVal bug.
* Add the UserDefined hook to EB geom.
* Add Challenge problem. Something's up, not generating the EB geom
properly at this point.
* Error BC array sizes.
* Add commented out debug statement.
* Remove DEBUG and USE_HYPRE default.
* Restore complete PistonBowl geom.
* A bit more velocity.
* Update sample input file for GMG/Hypre nodal solves.
* EB mask operations (#21)
* Fix EB-covered test while building advective update.
* Check eb-covered while assembling divu
* Set covered diffusion term.
* Check EB-covered on advective face state reconstruction.
Set covered adv. fluxes/term.
* Add 3d input version of the enclosed vortex.
* Forgotten ANREX_USE_EB ifdef.
* Remove LMeX chem tol, now directly handled by the reactor.
Add flag to skip instantaneous RR when using ReactorNull.
* Reactor ini outside OMP region, turn ON skipInstantRR flag.
* Small rearrange of TPROF region for instantRR.
* Skip instantRR if triggered. Update the logic in divU calculation.
* Add a gaseous methane laminar counterflow diffusion flame. (#23)
* Update efield portions of the Sources/Exec (#24)
* Change compiler variable for Efield.
* Bring ABecCec operator up to date with some changes in GPU handling.
* Update Efield cases GNUMakefile
* Update input to FlameSheetIons
* Update Efield compiler check through the sources.
* Modify pltfile to include HRR and re-arrange a bit to not include I_R (#25)
in ReactorNull, drop rhoYs from pltfile by default for ligher plt.
* Update includes of Projector source location and names. (#26)
* Update includes of Projector source location and names.
* Update set typical values too.
* Update to catch up with new PelePhysics PMF (#27)
* Change PMF sources location.
* Update init and bc calls to updated PMF.
* Update the Cases files.
* Update PremBunsen3D input file.
* Update PeriodicCases
* Update EnclosedFlame
* Update EB_FlowPastCylinder
* Update FlameSheet
* Update HotBubble
* Update EB_EnclosedFlame
* Projector now moved to Hydro namespace
* Update input of EnclosedFlame
* update GNUmakefiles for templated PelePhysics (#28)
Co-authored-by: Bruce Perry <baperry@princeton.edu>
* Temporary test another branch of PP.
* Restore using PP development brqnch in CI.
Co-authored-by: Bruce Perry <53018946+baperry2@users.noreply.github.com>
Co-authored-by: Bruce Perry <baperry@princeton.edu>
Co-authored-by: nickwimer <nicholas.wimer@gmail.com>
Co-authored-by: Bruce Perry <53018946+baperry2@users.noreply.github.com>
Co-authored-by: Bruce Perry <baperry@princeton.edu>
