EB mask operations #21
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Set covered adv. fluxes/term.
esclapez
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Nov 4, 2021
* 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>
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Somewhat different approach than PeleLM: try to limit the number setCovered operations by instead checking the covered flag and skipping covered regions.