should only overwrite Inflow BCs.

* 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.

…-Combustion#12)

* first pass at documenting what multicomponent spray stuff would look like

* start to manifold Spray stuff

* Swap all \chi with X

* subtract 1 in sum indexing, add matrix L

* Remove sums to Npc, add comment about mixture vapor pres

* Remove remaining Npc, other minor changes

* Missed a couple Ng's

* Replace \forall var \in N, update rhoD

* Fix L^T indexing

* use \in instead of = in \forall statements

* define different species sets to simplify notation

* Update set notation, edits for consistency

* spray docs: conditioning on Y_vi>0 where appropriate

* fix spelling errors

* some progress on manifold docs

* Manifold documentation mostly finished

* document that cp in phi is cp of fuel, not skin mix (see PeleMP #12)

* Update link in docs, add fuel_names member to BaseLiqProps

* Add many-to-one mechanism

* Revert SprayProperties.H

* Replace all indx with dep_indx, add mapping matrix

* Add dynamically alocated pc_indx

* Make csr functions const.

* Progress. Works for WongLin but not Daif...

* Working many-to-one with Daif, needs cleaning/justification

* Rename some variables for better alignment with docs

* Update WallFilm.H for many-to-one (untested)

* Relax SPRAY_FUEL_NUM <= NUM_SPECIES

* Format

* remove many-to-one mechanism

* Enable many-to-one for PeleMP model

* Formatting...

* Remove full L matrix from testing

* Update docs for non-manifold case

* Fix clang-tidy errors

* Formatting

* Update notation for manifold in docs

* Remove duplicate array for gpv.mw, clean up comments

* Formatting........

* Bring back X_dn

* document temperature ref state changes for manifold properties

* Resolve downstream clang-tidy error

* Spelling error in docs

* Fix error in WallFilm.H

* Format and change conditional back to original

* Debugging w/liquid_fuels_nonreacting mech

* correct pc to pcspec

* Indexing for source terms

* Update print statements, add many-to-one test mechanism for debuggin

* Add some additional debug print statements to figure out Segfault. I think the issue should be resolved now.

* Format

* Progress toward Manifold w/o M21

* Hacky fix for Manifold. Need dep_indx to be same for both EOS

* Add dep_manifold_indx, rename indx to dep_indx in Manifold

* Format and remove many-to-one mech

* Fix bug

* Add oldY when SPRAY_FUEL_NUM = 1

* Fix spelling

* remove unused var

* Remove some debug print statements

* Add/remove some debug print statments

* More debugging...

* Add fix for Spray-A-WBreakup test PeleC

* Format

* First stab at many-to-one manifold

* Working many-to-one with Manifold

* Add mapping from phase-change species to manifold vars

* Remove debugging print statements

* Formatting

* Add loop over oldT in WallFilm.H

* Clang-tidy fix

* Minor docs update

* Add Manifold to all validation plots in docs

* Update user guide for Validate.py tests

* Update docs, initialize dep_manifold_indx and pc_manifold_indx with length 0 when no Manifold EOS

* print spray mappings only if verbose

* eliminate depricated liquid_spec_share_gas_dep variable

* simplify pc_index for GPU

* update many-to-one check in init_mw to compare SPRAY_FUEL_NUM to N_pc not NUM_SPECIES

* Fix spelling error

* update consistency checks for manifold cases

* remove redundant check

* Remove AMREX_GPU_HOST_DEVICE from init_mw

* Spelling and clang-tidy

* More GPU fixes

* minor cleanup

* for spray + manifold EOS, species in table are only spray species

* semi-working Many-to-one + Manifold

* Swap amrex::Warning with amrex::Print

Warnings are printed by every processor.

* Fix warnings

* clang-format

* slight update to yspec fluid indexing - maybe wrong

* remove extraneous comment in code

* clang-format

* some suggestions from copilot: check dep_manifold_names size

* fix indexing for source term deposition

* more minor fixes from copilot

* re-fix fuel indexing so it works for both manifold and nonmanifold

* Avoid division by zero in WallFilm.H

* fix error checking that applies for only manifold

* add versioning explainer to README

---------

Co-authored-by: Bruce Perry <[email protected]>