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Update submods (#164)
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* Update submodules and keep compiling the AJac by default.

* Minor change to doc.
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@esclapez
esclapez authored Dec 30, 2022
1 parent ff1d044 commit 457a6e4
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4 changes: 2 additions & 2 deletions Docs/source/manual/Tutorials_FlowPastCyl.rst
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.. _sec:tutorialFlowPastCyl:

Tutorial - Non-reacting flow past a cylinder
============================================
Non-reacting flow past a cylinder
=================================

.. _sec:TUTO_FPC::Intro:

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2 changes: 1 addition & 1 deletion Submodules/AMReX-Hydro
Submodule AMReX-Hydro updated from cc9b82 to 5cb0f3
2 changes: 1 addition & 1 deletion Submodules/PeleMP
Submodule PeleMP updated 17 files
+1 −1 Exec/SprayTests/PeleC/jet_spray/SprayParticlesInitInsert.cpp
+3 −0 Exec/SprayTests/PeleC/jet_spray/prob.cpp
+47 −1 Exec/SprayTests/PeleLMeX/abramzon_test/SprayParticlesInitInsert.cpp
+0 −3 Exec/SprayTests/PeleLMeX/abramzon_test/initspraydata
+12 −39 Exec/SprayTests/PeleLMeX/abramzon_test/inputs_2d
+2 −2 Exec/SprayTests/PeleLMeX/abramzon_test/pelelm_prob.H
+55 −4 Exec/SprayTests/PeleLMeX/abramzon_test/pelelm_prob.cpp
+7 −1 Exec/SprayTests/PeleLMeX/abramzon_test/pelelm_prob_parm.H
+18 −20 Source/PP_Spray/Drag.H
+45 −52 Source/PP_Spray/SprayDerive.cpp
+5 −5 Source/PP_Spray/SprayFuelData.H
+24 −34 Source/PP_Spray/SprayInjection.H
+3 −1 Source/PP_Spray/SprayJet.H
+12 −2 Source/PP_Spray/SprayJet.cpp
+25 −32 Source/PP_Spray/SprayParticles.H
+126 −140 Source/PP_Spray/SprayParticles.cpp
+24 −24 Source/PP_Spray/WallFunctions.H
2 changes: 1 addition & 1 deletion Submodules/PelePhysics
Submodule PelePhysics updated 80 files
+6 −7 Eos/Fuego.H
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+0 −1 Reactions/ReactorArkode.cpp
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+0 −31 Reactions/ReactorCvodePreconditioner.cpp
+0 −27 Reactions/ReactorCvodeUtils.H
+10 −10 Reactions/ReactorRK64.cpp
+3 −2 Reactions/ReactorTypes.H
+235 −295 Support/Mechanism/Models/BurkeDryer/mechanism.H
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+253 −337 Support/Mechanism/Models/Davis/mechanism.H
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+248 −310 Support/Mechanism/Models/FFCM1_Red/mechanism.H
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+205 −232 Support/Mechanism/Models/Kolla/mechanism.H
+12 −15 Support/Mechanism/Models/Kolla/mechanism.cpp
+161 −131 Support/Mechanism/Models/LiDryer/mechanism.H
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+220 −247 Support/Mechanism/Models/LuDME/mechanism.H
+12 −15 Support/Mechanism/Models/LuDME/mechanism.cpp
+185 −155 Support/Mechanism/Models/LuEthylene/mechanism.H
+12 −15 Support/Mechanism/Models/LuEthylene/mechanism.cpp
+311 −373 Support/Mechanism/Models/NUIGalway/mechanism.H
+12 −15 Support/Mechanism/Models/NUIGalway/mechanism.cpp
+188 −158 Support/Mechanism/Models/SootReaction/mechanism.H
+12 −15 Support/Mechanism/Models/SootReaction/mechanism.cpp
+160 −278 Support/Mechanism/Models/air/mechanism.H
+13 −24 Support/Mechanism/Models/air/mechanism.cpp
+256 −285 Support/Mechanism/Models/alzeta/mechanism.H
+12 −15 Support/Mechanism/Models/alzeta/mechanism.cpp
+161 −131 Support/Mechanism/Models/chem-H/mechanism.H
+12 −15 Support/Mechanism/Models/chem-H/mechanism.cpp
+160 −276 Support/Mechanism/Models/decane_3sp/mechanism.H
+13 −24 Support/Mechanism/Models/decane_3sp/mechanism.cpp
+187 −157 Support/Mechanism/Models/dodecane_lu/mechanism.H
+12 −15 Support/Mechanism/Models/dodecane_lu/mechanism.cpp
+146 −123 Support/Mechanism/Models/dodecane_lu_qss/mechanism.H
+13 −15 Support/Mechanism/Models/dodecane_lu_qss/mechanism.cpp
+187 −157 Support/Mechanism/Models/dodecane_wang/mechanism.H
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+160 −276 Support/Mechanism/Models/dodmethair_4sp/mechanism.H
+13 −24 Support/Mechanism/Models/dodmethair_4sp/mechanism.cpp
+210 −239 Support/Mechanism/Models/drm19/mechanism.H
+12 −15 Support/Mechanism/Models/drm19/mechanism.cpp
+175 −145 Support/Mechanism/Models/ethylene_af/mechanism.H
+12 −15 Support/Mechanism/Models/ethylene_af/mechanism.cpp
+223 −252 Support/Mechanism/Models/grimech12/mechanism.H
+12 −15 Support/Mechanism/Models/grimech12/mechanism.cpp
+188 −158 Support/Mechanism/Models/grimech30-noArN/mechanism.H
+12 −15 Support/Mechanism/Models/grimech30-noArN/mechanism.cpp
+240 −269 Support/Mechanism/Models/grimech30/mechanism.H
+12 −15 Support/Mechanism/Models/grimech30/mechanism.cpp
+160 −276 Support/Mechanism/Models/heptane_3sp/mechanism.H
+13 −24 Support/Mechanism/Models/heptane_3sp/mechanism.cpp
+248 −275 Support/Mechanism/Models/heptane_fc/mechanism.H
+12 −15 Support/Mechanism/Models/heptane_fc/mechanism.cpp
+236 −206 Support/Mechanism/Models/heptane_lu_88sk/mechanism.H
+12 −15 Support/Mechanism/Models/heptane_lu_88sk/mechanism.cpp
+160 −276 Support/Mechanism/Models/nitrogens/mechanism.H
+13 −24 Support/Mechanism/Models/nitrogens/mechanism.cpp
+236 −263 Support/Mechanism/Models/propane_fc/mechanism.H
+12 −15 Support/Mechanism/Models/propane_fc/mechanism.cpp
+0 −47,672 Support/Mechanism/Models/propane_fc/propane_fc.cpp
+208 −235 Support/Mechanism/Models/sCO2/mechanism.H
+12 −15 Support/Mechanism/Models/sCO2/mechanism.cpp
+13 −0 Support/ceptr/ceptr/ceptr.py
+104 −105 Support/ceptr/ceptr/ck.py
+12 −1 Support/ceptr/ceptr/converter.py
+255 −190 Support/ceptr/ceptr/jacobian.py
+55 −32 Support/ceptr/ceptr/production.py
+1 −1 Support/ceptr/ceptr/qssa_converter.py
+15 −5 Support/ceptr/ceptr/reaction_info.py
+14 −8 Support/ceptr/ceptr/sparsity.py
+43 −29 Support/ceptr/ceptr/thermo.py
+18 −9 Support/ceptr/ceptr/transport.py
+1 −1 ThirdParty/GNUmakefile
+6 −9 Transport/Simple.H
+1 −1 Transport/Sutherland.H
+13 −1 Transport/TransportParams.H
+0 −1 Utility/TurbInflow/turbinflow.cpp
2 changes: 1 addition & 1 deletion Submodules/amrex
Submodule amrex updated 42 files
+35 −0 .github/workflows/ascent.yml
+62 −0 .github/workflows/codeql.yml
+32 −0 .github/workflows/petsc.yml
+1 −2 .github/workflows/sensei.yml
+26 −0 Docs/sphinx_documentation/source/AMReX_Profiling_Tools.rst
+2 −2 Src/Amr/AMReX_Derive.H
+81 −50 Src/AmrCore/AMReX_FillPatcher.H
+1 −5 Src/Base/AMReX_GpuAssert.H
+99 −1 Src/Base/AMReX_GpuContainers.H
+0 −14 Src/Base/AMReX_GpuDevice.cpp
+0 −19 Src/Base/AMReX_GpuLaunchFunctsG.H
+1 −5 Src/Base/AMReX_GpuPrint.H
+1 −5 Src/Base/AMReX_GpuQualifiers.H
+1 −5 Src/Base/AMReX_GpuTypes.H
+125 −5 Src/Base/AMReX_Math.H
+4 −1 Src/Base/AMReX_PlotFileDataImpl.cpp
+1 −5 Src/Base/AMReX_RandomEngine.H
+5 −1 Src/CMakeLists.txt
+24 −8 Src/LinearSolvers/MLMG/AMReX_MLCellABecLap.H
+5 −0 Src/LinearSolvers/MLMG/AMReX_MLLinOp.H
+246 −95 Src/LinearSolvers/MLMG/AMReX_MLPoisson.H
+39 −54 Src/LinearSolvers/MLMG/AMReX_MLPoisson_1D_K.H
+63 −84 Src/LinearSolvers/MLMG/AMReX_MLPoisson_2D_K.H
+49 −67 Src/LinearSolvers/MLMG/AMReX_MLPoisson_3D_K.H
+1 −1 Tools/CMake/AMReXParallelBackends.cmake
+0 −22 Tools/F_scripts/README.md
+0 −124 Tools/F_scripts/fcheck.py
+0 −31 Tools/F_scripts/findparams.py
+0 −380 Tools/F_scripts/makebuildinfo.py
+0 −510 Tools/F_scripts/write_probin.py
+1 −1 Tools/GNUMake/Make.machines
+1 −1 Tools/GNUMake/comps/hip.mak
+0 −92 Tools/Postprocessing/python/column_depth.py
+0 −109 Tools/Postprocessing/python/conv_slopes.py
+0 −27 Tools/Postprocessing/python/eos_data.txt
+0 −293 Tools/Postprocessing/python/helmeos.py
+0 −110 Tools/Postprocessing/python/test_helmeos.py
+0 −734 Tools/Py_util/plotsinglevar.py
+0 −8 Tools/Release/cleanWords.txt
+0 −202 Tools/Release/ppCleanup.py
+0 −54 Tools/Release/ppCleanupDir.py
+0 −251 Tools/Release/release.py
6 changes: 6 additions & 0 deletions Utils/Make.PeleLMeX
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Expand Up @@ -86,6 +86,12 @@ ifeq ($(PELE_USE_KLU), TRUE)
DEFINES += -DPELE_USE_KLU
endif

PELE_COMPILE_AJACOBIAN ?= TRUE

ifeq ($(PELE_COMPILE_AJACOBIAN), TRUE)
DEFINES += -DPELE_COMPILE_AJACOBIAN
endif

ChemDir = Support/Mechanism/Models/$(Chemistry_Model)

PPdirs := Utility/PMF Utility/TurbInflow Utility/PltFileManager Source $(ChemDir) Reactions Eos Transport
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