* 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.

* 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.

Instead of evaluation T2= T*T and T3=T*T*T do T3=T2*T
Co-authored-by: Terence Lehmann <[email protected]>

)

* changed size of dbin

* adjusted the way COFD is saved in transport, and used in simple

* fixed my weird iterating and made it map vertically, not horizontaly

* changed the iteratios through dbin and calculations of Ddiag

* tweaked the calculations for the diffusivities

* adjusting the SRK diffusion

* adjusted the array size in TransportParams

* fixed an error with the implementation of the mole fraction within my equation

* added mechanism.* to branch

* ceptr:Improved T polynomial in mechanism.H(#13)

Instead of evaluation T2= T*T and T3=T*T*T do T3=T2*T
Co-authored-by: Terence Lehmann <[email protected]>

* ran some clang formatting on Simple.H

* ran clang format over transport.py

* more formatting

* remade almost all of the mechanisms

* cleaned up the code for the push

* Fix comments

* Fix comments 2

* changed size of dbin

* adjusted the way COFD is saved in transport, and used in simple

* fixed my weird iterating and made it map vertically, not horizontaly

* changed the iteratios through dbin and calculations of Ddiag

* tweaked the calculations for the diffusivities

* adjusting the SRK diffusion

* adjusted the array size in TransportParams

* fixed an error with the implementation of the mole fraction within my equation

* added mechanism.* to branch

* ran some clang formatting on Simple.H

* ran clang format over transport.py

* more formatting

* remade almost all of the mechanisms

* cleaned up the code for the push

* Adding the temperature change to the mechanism

* fixxed the logT Error

* Redo formating of comment

* Variable optimisation

* adjusted the SRK part of the equation as well

* formatting

* typo

* qss mechanism

* qss mech updates without extraneous changes

* fix sympy version more strictly in ceptr

---------

Co-authored-by: Justin Freiberger <[email protected]>
Co-authored-by: Terence Lehmann <[email protected]>
Co-authored-by: terence.lehmann <[email protected]>
Co-authored-by: Thomas Howarth <[email protected]>
Co-authored-by: Thomas Howarth <[email protected]>
Co-authored-by: Bruce Perry <[email protected]>