21.10 Release merge (#14)
* 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.