From ede8d064d0d1415cd5d1b19036361822405af185 Mon Sep 17 00:00:00 2001 From: Marc Henry de Frahan Date: Fri, 8 Dec 2023 12:21:55 -0700 Subject: [PATCH 01/21] Moved files around --- Eos/Make.package | 2 -- {Eos => Source/Eos}/EOS.H | 0 {Eos => Source/Eos}/EOS.cpp | 0 {Eos => Source/Eos}/Fuego.H | 0 {Eos => Source/Eos}/GammaLaw.H | 0 Source/Eos/Make.package | 5 +++++ {Eos => Source/Eos}/README | 0 {Eos => Source/Eos}/SRK.H | 0 {Reactions => Source/Reactions}/Make.package | 3 +++ {Reactions => Source/Reactions}/ReactorArkode.H | 0 .../Reactions}/ReactorArkode.cpp | 0 {Reactions => Source/Reactions}/ReactorBDF.H | 0 {Reactions => Source/Reactions}/ReactorBDF.cpp | 0 .../Reactions}/ReactorBDFsolver.H | 0 {Reactions => Source/Reactions}/ReactorBase.H | 0 {Reactions => Source/Reactions}/ReactorBase.cpp | 0 {Reactions => Source/Reactions}/ReactorCvode.H | 0 .../Reactions}/ReactorCvode.cpp | 0 .../Reactions}/ReactorCvodeCustomLinSolver.H | 0 .../Reactions}/ReactorCvodeCustomLinSolver.cpp | 0 .../Reactions}/ReactorCvodeJacobian.H | 0 .../Reactions}/ReactorCvodeJacobian.cpp | 0 .../Reactions}/ReactorCvodePreconditioner.H | 0 .../Reactions}/ReactorCvodePreconditioner.cpp | 0 .../Reactions}/ReactorCvodeUtils.H | 0 .../Reactions}/ReactorCvodeUtils.cpp | 0 {Reactions => Source/Reactions}/ReactorNull.H | 0 {Reactions => Source/Reactions}/ReactorNull.cpp | 0 {Reactions => Source/Reactions}/ReactorRK64.H | 0 {Reactions => Source/Reactions}/ReactorRK64.cpp | 0 {Reactions => Source/Reactions}/ReactorTypes.H | 0 {Reactions => Source/Reactions}/ReactorUtils.H | 0 .../Reactions}/ReactorUtils.cpp | 0 Source/Soot/Make.package | 3 +++ Source/Spray/Make.package | 3 +++ {Transport => Source/Transport}/Constant.H | 0 Source/Transport/Make.package | 5 +++++ {Transport => Source/Transport}/Simple.H | 0 {Transport => Source/Transport}/Sutherland.H | 0 {Transport => Source/Transport}/Transport.H | 0 {Transport => Source/Transport}/Transport.cpp | 0 .../Transport}/TransportParams.H | 0 .../Transport}/TransportTypes.H | 0 .../Utility}/Diagnostics/DiagBase.H | 0 .../Utility}/Diagnostics/DiagBase.cpp | 0 .../Utility}/Diagnostics/DiagConditional.H | 0 .../Utility}/Diagnostics/DiagConditional.cpp | 0 .../Utility}/Diagnostics/DiagFilter.H | 0 .../Utility}/Diagnostics/DiagFilter.cpp | 0 .../Utility}/Diagnostics/DiagFramePlane.H | 0 .../Utility}/Diagnostics/DiagFramePlane.cpp | 0 .../Utility}/Diagnostics/DiagPDF.H | 0 .../Utility}/Diagnostics/DiagPDF.cpp | 0 .../Utility}/Diagnostics/Make.package | 0 {Utility => Source/Utility}/Filter/Filter.H | 0 {Utility => Source/Utility}/Filter/Filter.cpp | 0 Source/Utility/Filter/Make.package | 5 +++++ Source/Utility/PMF/Make.package | 5 +++++ {Utility => Source/Utility}/PMF/PMF.H | 0 {Utility => Source/Utility}/PMF/PMFData.H | 0 {Utility => Source/Utility}/PMF/PMFData.cpp | 0 .../Utility}/PMF/cantera_pmf_generator.py | 0 {Utility => Source/Utility}/PMF/plotPMF.py | 0 Source/Utility/PltFileManager/Make.package | 5 +++++ .../Utility}/PltFileManager/PltFileManager.H | 0 .../Utility}/PltFileManager/PltFileManager.cpp | 0 .../PltFileManager/PltFileManagerBCFill.H | 0 .../Utility}/TurbInflow/Make.package | 0 .../Utility}/TurbInflow/turbinflow.H | 0 .../Utility}/TurbInflow/turbinflow.cpp | 0 Testing/Exec/Make.PelePhysics | 17 +++++++++++------ Transport/Make.package | 2 -- Utility/Filter/Make.package | 5 ----- Utility/PMF/Make.package | 5 ----- Utility/PltFileManager/Make.package | 5 ----- 75 files changed, 45 insertions(+), 25 deletions(-) delete mode 100644 Eos/Make.package rename {Eos => Source/Eos}/EOS.H (100%) rename {Eos => Source/Eos}/EOS.cpp (100%) rename {Eos => Source/Eos}/Fuego.H (100%) rename {Eos => Source/Eos}/GammaLaw.H (100%) create mode 100644 Source/Eos/Make.package rename {Eos => Source/Eos}/README (100%) rename {Eos => Source/Eos}/SRK.H (100%) rename {Reactions => Source/Reactions}/Make.package (80%) rename {Reactions => Source/Reactions}/ReactorArkode.H (100%) rename {Reactions => Source/Reactions}/ReactorArkode.cpp (100%) rename {Reactions => Source/Reactions}/ReactorBDF.H (100%) rename {Reactions => Source/Reactions}/ReactorBDF.cpp (100%) rename {Reactions => Source/Reactions}/ReactorBDFsolver.H (100%) rename {Reactions => Source/Reactions}/ReactorBase.H (100%) rename {Reactions => Source/Reactions}/ReactorBase.cpp (100%) rename {Reactions => Source/Reactions}/ReactorCvode.H (100%) rename {Reactions => Source/Reactions}/ReactorCvode.cpp (100%) rename {Reactions => Source/Reactions}/ReactorCvodeCustomLinSolver.H (100%) rename {Reactions => Source/Reactions}/ReactorCvodeCustomLinSolver.cpp (100%) rename {Reactions => Source/Reactions}/ReactorCvodeJacobian.H (100%) rename {Reactions => Source/Reactions}/ReactorCvodeJacobian.cpp (100%) rename {Reactions => Source/Reactions}/ReactorCvodePreconditioner.H (100%) rename {Reactions => Source/Reactions}/ReactorCvodePreconditioner.cpp (100%) rename {Reactions => Source/Reactions}/ReactorCvodeUtils.H (100%) rename {Reactions => Source/Reactions}/ReactorCvodeUtils.cpp (100%) rename {Reactions => Source/Reactions}/ReactorNull.H (100%) rename {Reactions => Source/Reactions}/ReactorNull.cpp (100%) rename {Reactions => Source/Reactions}/ReactorRK64.H (100%) rename {Reactions => Source/Reactions}/ReactorRK64.cpp (100%) rename {Reactions => Source/Reactions}/ReactorTypes.H (100%) rename {Reactions => Source/Reactions}/ReactorUtils.H (100%) rename {Reactions => Source/Reactions}/ReactorUtils.cpp (100%) rename {Transport => Source/Transport}/Constant.H (100%) create mode 100644 Source/Transport/Make.package rename {Transport => Source/Transport}/Simple.H (100%) rename {Transport => Source/Transport}/Sutherland.H (100%) rename {Transport => Source/Transport}/Transport.H (100%) rename {Transport => Source/Transport}/Transport.cpp (100%) rename {Transport => Source/Transport}/TransportParams.H (100%) rename {Transport => Source/Transport}/TransportTypes.H (100%) rename {Utility => Source/Utility}/Diagnostics/DiagBase.H (100%) rename {Utility => Source/Utility}/Diagnostics/DiagBase.cpp (100%) rename {Utility => Source/Utility}/Diagnostics/DiagConditional.H (100%) rename {Utility => Source/Utility}/Diagnostics/DiagConditional.cpp (100%) rename {Utility => Source/Utility}/Diagnostics/DiagFilter.H (100%) rename {Utility => Source/Utility}/Diagnostics/DiagFilter.cpp (100%) rename {Utility => Source/Utility}/Diagnostics/DiagFramePlane.H (100%) rename {Utility => Source/Utility}/Diagnostics/DiagFramePlane.cpp (100%) rename {Utility => Source/Utility}/Diagnostics/DiagPDF.H (100%) rename {Utility => Source/Utility}/Diagnostics/DiagPDF.cpp (100%) rename {Utility => Source/Utility}/Diagnostics/Make.package (100%) rename {Utility => Source/Utility}/Filter/Filter.H (100%) rename {Utility => Source/Utility}/Filter/Filter.cpp (100%) create mode 100644 Source/Utility/Filter/Make.package create mode 100644 Source/Utility/PMF/Make.package rename {Utility => Source/Utility}/PMF/PMF.H (100%) rename {Utility => Source/Utility}/PMF/PMFData.H (100%) rename {Utility => Source/Utility}/PMF/PMFData.cpp (100%) rename {Utility => Source/Utility}/PMF/cantera_pmf_generator.py (100%) rename {Utility => Source/Utility}/PMF/plotPMF.py (100%) create mode 100644 Source/Utility/PltFileManager/Make.package rename {Utility => Source/Utility}/PltFileManager/PltFileManager.H (100%) rename {Utility => Source/Utility}/PltFileManager/PltFileManager.cpp (100%) rename {Utility => Source/Utility}/PltFileManager/PltFileManagerBCFill.H (100%) rename {Utility => Source/Utility}/TurbInflow/Make.package (100%) rename {Utility => Source/Utility}/TurbInflow/turbinflow.H (100%) rename {Utility => Source/Utility}/TurbInflow/turbinflow.cpp (100%) delete mode 100644 Transport/Make.package delete mode 100644 Utility/Filter/Make.package delete mode 100644 Utility/PMF/Make.package delete mode 100644 Utility/PltFileManager/Make.package diff --git a/Eos/Make.package b/Eos/Make.package deleted file mode 100644 index ecea2eef1..000000000 --- a/Eos/Make.package +++ /dev/null @@ -1,2 +0,0 @@ -CEXE_headers += EOS.H GammaLaw.H Fuego.H SRK.H -CEXE_sources += EOS.cpp diff --git a/Eos/EOS.H b/Source/Eos/EOS.H similarity index 100% rename from Eos/EOS.H rename to Source/Eos/EOS.H diff --git a/Eos/EOS.cpp b/Source/Eos/EOS.cpp similarity index 100% rename from Eos/EOS.cpp rename to Source/Eos/EOS.cpp diff --git a/Eos/Fuego.H b/Source/Eos/Fuego.H similarity index 100% rename from Eos/Fuego.H rename to Source/Eos/Fuego.H diff --git a/Eos/GammaLaw.H b/Source/Eos/GammaLaw.H similarity index 100% rename from Eos/GammaLaw.H rename to Source/Eos/GammaLaw.H diff --git a/Source/Eos/Make.package b/Source/Eos/Make.package new file mode 100644 index 000000000..34456518e --- /dev/null +++ b/Source/Eos/Make.package @@ -0,0 +1,5 @@ +CEXE_headers += EOS.H GammaLaw.H Fuego.H SRK.H +CEXE_sources += EOS.cpp + +VPATH_LOCATIONS += $(PELE_PHYSICS_HOME)/Source/Eos +INCLUDE_LOCATIONS += $(PELE_PHYSICS_HOME)/Source/Eos \ No newline at end of file diff --git a/Eos/README b/Source/Eos/README similarity index 100% rename from Eos/README rename to Source/Eos/README diff --git a/Eos/SRK.H b/Source/Eos/SRK.H similarity index 100% rename from Eos/SRK.H rename to Source/Eos/SRK.H diff --git a/Reactions/Make.package b/Source/Reactions/Make.package similarity index 80% rename from Reactions/Make.package rename to Source/Reactions/Make.package index bcaee2f9e..78ff85528 100644 --- a/Reactions/Make.package +++ b/Source/Reactions/Make.package @@ -1,2 +1,5 @@ CEXE_headers += ReactorUtils.H ReactorTypes.H ReactorBase.H ReactorBDF.H ReactorBDFsolver.H ReactorRK64.H ReactorArkode.H ReactorNull.H ReactorCvode.H ReactorCvodeUtils.H ReactorCvodePreconditioner.H ReactorCvodeJacobian.H ReactorCvodeCustomLinSolver.H CEXE_sources += ReactorUtils.cpp ReactorBase.cpp ReactorBDF.cpp ReactorRK64.cpp ReactorArkode.cpp ReactorNull.cpp ReactorCvode.cpp ReactorCvodeUtils.cpp ReactorCvodePreconditioner.cpp ReactorCvodeJacobian.cpp ReactorCvodeCustomLinSolver.cpp + +VPATH_LOCATIONS += $(PELE_PHYSICS_HOME)/Source/Reactions +INCLUDE_LOCATIONS += $(PELE_PHYSICS_HOME)/Source/Reactions \ No newline at end of file diff --git a/Reactions/ReactorArkode.H b/Source/Reactions/ReactorArkode.H similarity index 100% rename from Reactions/ReactorArkode.H rename to Source/Reactions/ReactorArkode.H diff --git a/Reactions/ReactorArkode.cpp b/Source/Reactions/ReactorArkode.cpp similarity index 100% rename from Reactions/ReactorArkode.cpp rename to Source/Reactions/ReactorArkode.cpp diff --git a/Reactions/ReactorBDF.H b/Source/Reactions/ReactorBDF.H similarity index 100% rename from Reactions/ReactorBDF.H rename to Source/Reactions/ReactorBDF.H diff --git a/Reactions/ReactorBDF.cpp b/Source/Reactions/ReactorBDF.cpp similarity index 100% rename from Reactions/ReactorBDF.cpp rename to Source/Reactions/ReactorBDF.cpp diff --git a/Reactions/ReactorBDFsolver.H b/Source/Reactions/ReactorBDFsolver.H similarity index 100% rename from Reactions/ReactorBDFsolver.H rename to Source/Reactions/ReactorBDFsolver.H diff --git a/Reactions/ReactorBase.H b/Source/Reactions/ReactorBase.H similarity index 100% rename from Reactions/ReactorBase.H rename to Source/Reactions/ReactorBase.H diff --git a/Reactions/ReactorBase.cpp b/Source/Reactions/ReactorBase.cpp similarity index 100% rename from Reactions/ReactorBase.cpp rename to Source/Reactions/ReactorBase.cpp diff --git a/Reactions/ReactorCvode.H b/Source/Reactions/ReactorCvode.H similarity index 100% rename from Reactions/ReactorCvode.H rename to Source/Reactions/ReactorCvode.H diff --git a/Reactions/ReactorCvode.cpp b/Source/Reactions/ReactorCvode.cpp similarity index 100% rename from Reactions/ReactorCvode.cpp rename to Source/Reactions/ReactorCvode.cpp diff --git a/Reactions/ReactorCvodeCustomLinSolver.H b/Source/Reactions/ReactorCvodeCustomLinSolver.H similarity index 100% rename from Reactions/ReactorCvodeCustomLinSolver.H rename to Source/Reactions/ReactorCvodeCustomLinSolver.H diff --git a/Reactions/ReactorCvodeCustomLinSolver.cpp b/Source/Reactions/ReactorCvodeCustomLinSolver.cpp similarity index 100% rename from Reactions/ReactorCvodeCustomLinSolver.cpp rename to Source/Reactions/ReactorCvodeCustomLinSolver.cpp diff --git a/Reactions/ReactorCvodeJacobian.H b/Source/Reactions/ReactorCvodeJacobian.H similarity index 100% rename from Reactions/ReactorCvodeJacobian.H rename to Source/Reactions/ReactorCvodeJacobian.H diff --git a/Reactions/ReactorCvodeJacobian.cpp b/Source/Reactions/ReactorCvodeJacobian.cpp similarity index 100% rename from Reactions/ReactorCvodeJacobian.cpp rename to Source/Reactions/ReactorCvodeJacobian.cpp diff --git a/Reactions/ReactorCvodePreconditioner.H b/Source/Reactions/ReactorCvodePreconditioner.H similarity index 100% rename from Reactions/ReactorCvodePreconditioner.H rename to Source/Reactions/ReactorCvodePreconditioner.H diff --git a/Reactions/ReactorCvodePreconditioner.cpp b/Source/Reactions/ReactorCvodePreconditioner.cpp similarity index 100% rename from Reactions/ReactorCvodePreconditioner.cpp rename to Source/Reactions/ReactorCvodePreconditioner.cpp diff --git a/Reactions/ReactorCvodeUtils.H b/Source/Reactions/ReactorCvodeUtils.H similarity index 100% rename from Reactions/ReactorCvodeUtils.H rename to Source/Reactions/ReactorCvodeUtils.H diff --git a/Reactions/ReactorCvodeUtils.cpp b/Source/Reactions/ReactorCvodeUtils.cpp similarity index 100% rename from Reactions/ReactorCvodeUtils.cpp rename to Source/Reactions/ReactorCvodeUtils.cpp diff --git a/Reactions/ReactorNull.H b/Source/Reactions/ReactorNull.H similarity index 100% rename from Reactions/ReactorNull.H rename to Source/Reactions/ReactorNull.H diff --git a/Reactions/ReactorNull.cpp b/Source/Reactions/ReactorNull.cpp similarity index 100% rename from Reactions/ReactorNull.cpp rename to Source/Reactions/ReactorNull.cpp diff --git a/Reactions/ReactorRK64.H b/Source/Reactions/ReactorRK64.H similarity index 100% rename from Reactions/ReactorRK64.H rename to Source/Reactions/ReactorRK64.H diff --git a/Reactions/ReactorRK64.cpp b/Source/Reactions/ReactorRK64.cpp similarity index 100% rename from Reactions/ReactorRK64.cpp rename to Source/Reactions/ReactorRK64.cpp diff --git a/Reactions/ReactorTypes.H b/Source/Reactions/ReactorTypes.H similarity index 100% rename from Reactions/ReactorTypes.H rename to Source/Reactions/ReactorTypes.H diff --git a/Reactions/ReactorUtils.H b/Source/Reactions/ReactorUtils.H similarity index 100% rename from Reactions/ReactorUtils.H rename to Source/Reactions/ReactorUtils.H diff --git a/Reactions/ReactorUtils.cpp b/Source/Reactions/ReactorUtils.cpp similarity index 100% rename from Reactions/ReactorUtils.cpp rename to Source/Reactions/ReactorUtils.cpp diff --git a/Source/Soot/Make.package b/Source/Soot/Make.package index e030770b8..e43311df6 100644 --- a/Source/Soot/Make.package +++ b/Source/Soot/Make.package @@ -1,3 +1,6 @@ CEXE_headers += Constants_Soot.H SootData.H SootReactions.H SootModel.H SootModel_derive.H CEXE_sources += SootModel.cpp SootModel_react.cpp SootModel_derive.cpp + +VPATH_LOCATIONS += $(PELE_PHYSICS_HOME)/Source/Soot +INCLUDE_LOCATIONS += $(PELE_PHYSICS_HOME)/Source/Soot \ No newline at end of file diff --git a/Source/Spray/Make.package b/Source/Spray/Make.package index ba442c540..074d89f7b 100644 --- a/Source/Spray/Make.package +++ b/Source/Spray/Make.package @@ -15,3 +15,6 @@ CEXE_sources += SprayIO.cpp CEXE_headers += Drag.H CEXE_headers += WallFunctions.H + +VPATH_LOCATIONS += $(PELE_PHYSICS_HOME)/Source/Spray +INCLUDE_LOCATIONS += $(PELE_PHYSICS_HOME)/Source/Spray \ No newline at end of file diff --git a/Transport/Constant.H b/Source/Transport/Constant.H similarity index 100% rename from Transport/Constant.H rename to Source/Transport/Constant.H diff --git a/Source/Transport/Make.package b/Source/Transport/Make.package new file mode 100644 index 000000000..4af749035 --- /dev/null +++ b/Source/Transport/Make.package @@ -0,0 +1,5 @@ +CEXE_headers += Transport.H TransportTypes.H TransportParams.H Constant.H Simple.H Sutherland.H +CEXE_sources += Transport.cpp + +VPATH_LOCATIONS += $(PELE_PHYSICS_HOME)/Source/Transport +INCLUDE_LOCATIONS += $(PELE_PHYSICS_HOME)/Source/Transport \ No newline at end of file diff --git a/Transport/Simple.H b/Source/Transport/Simple.H similarity index 100% rename from Transport/Simple.H rename to Source/Transport/Simple.H diff --git a/Transport/Sutherland.H b/Source/Transport/Sutherland.H similarity index 100% rename from Transport/Sutherland.H rename to Source/Transport/Sutherland.H diff --git a/Transport/Transport.H b/Source/Transport/Transport.H similarity index 100% rename from Transport/Transport.H rename to Source/Transport/Transport.H diff --git a/Transport/Transport.cpp b/Source/Transport/Transport.cpp similarity index 100% rename from Transport/Transport.cpp rename to Source/Transport/Transport.cpp diff --git a/Transport/TransportParams.H b/Source/Transport/TransportParams.H similarity index 100% rename from Transport/TransportParams.H rename to Source/Transport/TransportParams.H diff --git a/Transport/TransportTypes.H b/Source/Transport/TransportTypes.H similarity index 100% rename from Transport/TransportTypes.H rename to Source/Transport/TransportTypes.H diff --git a/Utility/Diagnostics/DiagBase.H b/Source/Utility/Diagnostics/DiagBase.H similarity index 100% rename from Utility/Diagnostics/DiagBase.H rename to Source/Utility/Diagnostics/DiagBase.H diff --git a/Utility/Diagnostics/DiagBase.cpp b/Source/Utility/Diagnostics/DiagBase.cpp similarity index 100% rename from Utility/Diagnostics/DiagBase.cpp rename to Source/Utility/Diagnostics/DiagBase.cpp diff --git a/Utility/Diagnostics/DiagConditional.H b/Source/Utility/Diagnostics/DiagConditional.H similarity index 100% rename from Utility/Diagnostics/DiagConditional.H rename to Source/Utility/Diagnostics/DiagConditional.H diff --git a/Utility/Diagnostics/DiagConditional.cpp b/Source/Utility/Diagnostics/DiagConditional.cpp similarity index 100% rename from Utility/Diagnostics/DiagConditional.cpp rename to Source/Utility/Diagnostics/DiagConditional.cpp diff --git a/Utility/Diagnostics/DiagFilter.H b/Source/Utility/Diagnostics/DiagFilter.H similarity index 100% rename from Utility/Diagnostics/DiagFilter.H rename to Source/Utility/Diagnostics/DiagFilter.H diff --git a/Utility/Diagnostics/DiagFilter.cpp b/Source/Utility/Diagnostics/DiagFilter.cpp similarity index 100% rename from Utility/Diagnostics/DiagFilter.cpp rename to Source/Utility/Diagnostics/DiagFilter.cpp diff --git a/Utility/Diagnostics/DiagFramePlane.H b/Source/Utility/Diagnostics/DiagFramePlane.H similarity index 100% rename from Utility/Diagnostics/DiagFramePlane.H rename to Source/Utility/Diagnostics/DiagFramePlane.H diff --git a/Utility/Diagnostics/DiagFramePlane.cpp b/Source/Utility/Diagnostics/DiagFramePlane.cpp similarity index 100% rename from Utility/Diagnostics/DiagFramePlane.cpp rename to Source/Utility/Diagnostics/DiagFramePlane.cpp diff --git a/Utility/Diagnostics/DiagPDF.H b/Source/Utility/Diagnostics/DiagPDF.H similarity index 100% rename from Utility/Diagnostics/DiagPDF.H rename to Source/Utility/Diagnostics/DiagPDF.H diff --git a/Utility/Diagnostics/DiagPDF.cpp b/Source/Utility/Diagnostics/DiagPDF.cpp similarity index 100% rename from Utility/Diagnostics/DiagPDF.cpp rename to Source/Utility/Diagnostics/DiagPDF.cpp diff --git a/Utility/Diagnostics/Make.package b/Source/Utility/Diagnostics/Make.package similarity index 100% rename from Utility/Diagnostics/Make.package rename to Source/Utility/Diagnostics/Make.package diff --git a/Utility/Filter/Filter.H b/Source/Utility/Filter/Filter.H similarity index 100% rename from Utility/Filter/Filter.H rename to Source/Utility/Filter/Filter.H diff --git a/Utility/Filter/Filter.cpp b/Source/Utility/Filter/Filter.cpp similarity index 100% rename from Utility/Filter/Filter.cpp rename to Source/Utility/Filter/Filter.cpp diff --git a/Source/Utility/Filter/Make.package b/Source/Utility/Filter/Make.package new file mode 100644 index 000000000..0571d37b4 --- /dev/null +++ b/Source/Utility/Filter/Make.package @@ -0,0 +1,5 @@ +CEXE_sources += Filter.cpp +CEXE_headers += Filter.H + +VPATH_LOCATIONS += $(PELE_PHYSICS_HOME)/Source/Utility/Filter +INCLUDE_LOCATIONS += $(PELE_PHYSICS_HOME)/Source/Utility/Filter diff --git a/Source/Utility/PMF/Make.package b/Source/Utility/PMF/Make.package new file mode 100644 index 000000000..a94e2e6f4 --- /dev/null +++ b/Source/Utility/PMF/Make.package @@ -0,0 +1,5 @@ +CEXE_sources += PMFData.cpp +CEXE_headers += PMF.H PMFData.H + +VPATH_LOCATIONS += $(PELE_PHYSICS_HOME)/Source/Utility/PMF +INCLUDE_LOCATIONS += $(PELE_PHYSICS_HOME)/Source/Utility/PMF diff --git a/Utility/PMF/PMF.H b/Source/Utility/PMF/PMF.H similarity index 100% rename from Utility/PMF/PMF.H rename to Source/Utility/PMF/PMF.H diff --git a/Utility/PMF/PMFData.H b/Source/Utility/PMF/PMFData.H similarity index 100% rename from Utility/PMF/PMFData.H rename to Source/Utility/PMF/PMFData.H diff --git a/Utility/PMF/PMFData.cpp b/Source/Utility/PMF/PMFData.cpp similarity index 100% rename from Utility/PMF/PMFData.cpp rename to Source/Utility/PMF/PMFData.cpp diff --git a/Utility/PMF/cantera_pmf_generator.py b/Source/Utility/PMF/cantera_pmf_generator.py similarity index 100% rename from Utility/PMF/cantera_pmf_generator.py rename to Source/Utility/PMF/cantera_pmf_generator.py diff --git a/Utility/PMF/plotPMF.py b/Source/Utility/PMF/plotPMF.py similarity index 100% rename from Utility/PMF/plotPMF.py rename to Source/Utility/PMF/plotPMF.py diff --git a/Source/Utility/PltFileManager/Make.package b/Source/Utility/PltFileManager/Make.package new file mode 100644 index 000000000..4d3d87edb --- /dev/null +++ b/Source/Utility/PltFileManager/Make.package @@ -0,0 +1,5 @@ +CEXE_sources += PltFileManager.cpp +CEXE_headers += PltFileManager.H PltFileManagerBCfill.H + +VPATH_LOCATIONS += $(PELE_PHYSICS_HOME)/Source/Utility/PltFileManager +INCLUDE_LOCATIONS += $(PELE_PHYSICS_HOME)/Source/Utility/PltFileManager diff --git a/Utility/PltFileManager/PltFileManager.H b/Source/Utility/PltFileManager/PltFileManager.H similarity index 100% rename from Utility/PltFileManager/PltFileManager.H rename to Source/Utility/PltFileManager/PltFileManager.H diff --git a/Utility/PltFileManager/PltFileManager.cpp b/Source/Utility/PltFileManager/PltFileManager.cpp similarity index 100% rename from Utility/PltFileManager/PltFileManager.cpp rename to Source/Utility/PltFileManager/PltFileManager.cpp diff --git a/Utility/PltFileManager/PltFileManagerBCFill.H b/Source/Utility/PltFileManager/PltFileManagerBCFill.H similarity index 100% rename from Utility/PltFileManager/PltFileManagerBCFill.H rename to Source/Utility/PltFileManager/PltFileManagerBCFill.H diff --git a/Utility/TurbInflow/Make.package b/Source/Utility/TurbInflow/Make.package similarity index 100% rename from Utility/TurbInflow/Make.package rename to Source/Utility/TurbInflow/Make.package diff --git a/Utility/TurbInflow/turbinflow.H b/Source/Utility/TurbInflow/turbinflow.H similarity index 100% rename from Utility/TurbInflow/turbinflow.H rename to Source/Utility/TurbInflow/turbinflow.H diff --git a/Utility/TurbInflow/turbinflow.cpp b/Source/Utility/TurbInflow/turbinflow.cpp similarity index 100% rename from Utility/TurbInflow/turbinflow.cpp rename to Source/Utility/TurbInflow/turbinflow.cpp diff --git a/Testing/Exec/Make.PelePhysics b/Testing/Exec/Make.PelePhysics index 85ed2ae5d..fd29fae13 100644 --- a/Testing/Exec/Make.PelePhysics +++ b/Testing/Exec/Make.PelePhysics @@ -3,9 +3,10 @@ PELE_PHYSICS_HOME ?= $(abspath $(lastword $(PELE_HOME)/Submodules/PelePhysics)) AMREX_HOME ?= $(abspath $(lastword $(PELE_PHYSICS_HOME)/Submodules/amrex)) SUNDIALS_HOME ?= $(abspath $(lastword $(PELE_PHYSICS_HOME)/Submodules/sundials)) -EOS_HOME ?= $(PELE_PHYSICS_HOME)/Eos -REACTIONS_HOME ?= $(PELE_PHYSICS_HOME)/Reactions -TRAN_HOME ?= $(PELE_PHYSICS_HOME)/Transport +EOS_HOME ?= $(PELE_PHYSICS_HOME)/Source/Eos +REACTIONS_HOME ?= $(PELE_PHYSICS_HOME)/Source/Reactions +TRAN_HOME ?= $(PELE_PHYSICS_HOME)/Source/Transport +UTILITY_HOME ?= $(PELE_PHYSICS_HOME)/Source/Utility EBASE = Pele BL_NO_FORT = TRUE @@ -107,9 +108,13 @@ ifeq ($(Transport_Model), Sutherland) endif # Utilities -include $(PELE_PHYSICS_HOME)/Utility/PMF/Make.package -include $(PELE_PHYSICS_HOME)/Utility/PltFileManager/Make.package - +INCLUDE_LOCATIONS += $(UTILITY_HOME) +VPATH_LOCATIONS += $(UTILITY_HOME) +include $(UTILITY_HOME)/Diagnostics/Make.package +include $(UTILITY_HOME)/Filter/Make.package +include $(UTILITY_HOME)/PMF/Make.package +include $(UTILITY_HOME)/PltFileManager/Make.package +include $(UTILITY_HOME)/TurbInflow/Make.package Pdirs := Base Boundary AmrCore diff --git a/Transport/Make.package b/Transport/Make.package deleted file mode 100644 index 8e346880c..000000000 --- a/Transport/Make.package +++ /dev/null @@ -1,2 +0,0 @@ -CEXE_headers += Transport.H TransportTypes.H TransportParams.H Constant.H Simple.H Sutherland.H -CEXE_sources += Transport.cpp \ No newline at end of file diff --git a/Utility/Filter/Make.package b/Utility/Filter/Make.package deleted file mode 100644 index 147f76e85..000000000 --- a/Utility/Filter/Make.package +++ /dev/null @@ -1,5 +0,0 @@ -CEXE_sources += Filter.cpp -CEXE_headers += Filter.H - -VPATH_LOCATIONS += $(PELE_PHYSICS_HOME)/Utility/Filter -INCLUDE_LOCATIONS += $(PELE_PHYSICS_HOME)/Utility/Filter diff --git a/Utility/PMF/Make.package b/Utility/PMF/Make.package deleted file mode 100644 index 0c9f1a2f3..000000000 --- a/Utility/PMF/Make.package +++ /dev/null @@ -1,5 +0,0 @@ -CEXE_sources += PMFData.cpp -CEXE_headers += PMF.H PMFData.H - -VPATH_LOCATIONS += $(PELE_PHYSICS_HOME)/Utility/PMF -INCLUDE_LOCATIONS += $(PELE_PHYSICS_HOME)/Utility/PMF diff --git a/Utility/PltFileManager/Make.package b/Utility/PltFileManager/Make.package deleted file mode 100644 index f0584a4fe..000000000 --- a/Utility/PltFileManager/Make.package +++ /dev/null @@ -1,5 +0,0 @@ -CEXE_sources += PltFileManager.cpp -CEXE_headers += PltFileManager.H PltFileManagerBCfill.H - -VPATH_LOCATIONS += $(PELE_PHYSICS_HOME)/Utility/PltFileManager -INCLUDE_LOCATIONS += $(PELE_PHYSICS_HOME)/Utility/PltFileManager From 02638e52fb9f7f7bb93987ebeb8fafb47045b954 Mon Sep 17 00:00:00 2001 From: Marc Henry de Frahan Date: Fri, 8 Dec 2023 12:34:03 -0700 Subject: [PATCH 02/21] Fix clang format call in ci --- .github/workflows/ci.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index d159dc0cb..10b1cdc28 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -20,7 +20,7 @@ jobs: - name: Check formatting uses: DoozyX/clang-format-lint-action@v0.16.2 with: - source: './Eos ./Transport ./Reactions ./Source ./Utility ./Testing ./Support/Mechanism/Models' + source: './Source ./Testing ./Support/Mechanism/Models' exclude: '.' extensions: 'H,h,cpp' clangFormatVersion: 16 From 09735ea8d06fbda2f8791770e749b49689be19c6 Mon Sep 17 00:00:00 2001 From: Marc Henry de Frahan Date: Fri, 8 Dec 2023 12:44:35 -0700 Subject: [PATCH 03/21] Fix a path --- Source/Utility/Diagnostics/Make.package | 3 +++ Source/Utility/TurbInflow/Make.package | 2 ++ 2 files changed, 5 insertions(+) diff --git a/Source/Utility/Diagnostics/Make.package b/Source/Utility/Diagnostics/Make.package index e29bd45eb..7e642da98 100644 --- a/Source/Utility/Diagnostics/Make.package +++ b/Source/Utility/Diagnostics/Make.package @@ -9,3 +9,6 @@ CEXE_sources += DiagBase.cpp CEXE_sources += DiagFramePlane.cpp CEXE_sources += DiagPDF.cpp CEXE_sources += DiagConditional.cpp + +VPATH_LOCATIONS += $(PELE_PHYSICS_HOME)/Source/Utility/Diagnostics +INCLUDE_LOCATIONS += $(PELE_PHYSICS_HOME)/Source/Utility/Diagnostics diff --git a/Source/Utility/TurbInflow/Make.package b/Source/Utility/TurbInflow/Make.package index 2ca9e782d..09f78bb0f 100644 --- a/Source/Utility/TurbInflow/Make.package +++ b/Source/Utility/TurbInflow/Make.package @@ -1,3 +1,5 @@ CEXE_headers += turbinflow.H CEXE_sources += turbinflow.cpp +VPATH_LOCATIONS += $(PELE_PHYSICS_HOME)/Source/Utility/TurbInflow +INCLUDE_LOCATIONS += $(PELE_PHYSICS_HOME)/Source/Utility/TurbInflow From d2288c02bd01fc02a608e7414b2b6a899455ad7a Mon Sep 17 00:00:00 2001 From: Marc Henry de Frahan Date: Fri, 8 Dec 2023 13:03:18 -0700 Subject: [PATCH 04/21] Unifying some things --- Support/Mechanism/Models/Aromatic_KrNara/Make.package | 9 ++++----- Support/Mechanism/Models/FFCM1_Red/Make.package | 3 +-- Support/Mechanism/Models/H2-CO-CO2-3spec/Make.package | 3 ++- Support/Mechanism/Models/HP_DME/Make.package | 7 +++++++ Support/Mechanism/Models/IonizedAir/Make.package | 1 + Support/Mechanism/Models/LiDryer/Make.package | 3 ++- Support/Mechanism/Models/Null/Make.package | 3 ++- Support/Mechanism/Models/SootReaction/Make.package | 7 ++++++- Support/Mechanism/Models/air/Make.package | 3 ++- Support/Mechanism/Models/dodecane_wang/Make.package | 2 +- Support/Mechanism/Models/grimech30-noArN/Make.package | 1 + Support/Mechanism/Models/header/header.end | 2 -- Support/Mechanism/Models/header/header.mec | 6 ------ Support/Mechanism/Models/header/header.start | 8 -------- Support/Mechanism/Models/header/header.therm | 6 ------ Support/Mechanism/Models/header/header.trans | 6 ------ Support/Mechanism/Models/heptane_lu_88sk/Make.package | 2 +- .../Mechanism/Models/methaneIons_diRenzo/Make.package | 1 + Support/Mechanism/Models/ndodecane_35/Make.package | 2 +- Support/Mechanism/Models/nitrogens/Make.package | 3 ++- 20 files changed, 34 insertions(+), 44 deletions(-) delete mode 100644 Support/Mechanism/Models/header/header.end delete mode 100644 Support/Mechanism/Models/header/header.mec delete mode 100644 Support/Mechanism/Models/header/header.start delete mode 100644 Support/Mechanism/Models/header/header.therm delete mode 100644 Support/Mechanism/Models/header/header.trans diff --git a/Support/Mechanism/Models/Aromatic_KrNara/Make.package b/Support/Mechanism/Models/Aromatic_KrNara/Make.package index ddcc0b6a2..24c663c9a 100644 --- a/Support/Mechanism/Models/Aromatic_KrNara/Make.package +++ b/Support/Mechanism/Models/Aromatic_KrNara/Make.package @@ -1,10 +1,9 @@ -CEXE_headers+=chemistry_file.H +CEXE_headers+=mechanism.H -CEXE_sources+=mechanism.cpp mechanism_1.cpp mechanism_2.cpp +CEXE_sources+=mechanism.cpp -LIBRARIES += +LIBRARIES += -INCLUDE_LOCATIONS += $(CHEM_DIR) +INCLUDE_LOCATIONS += $(CHEM_DIR) VPATH_LOCATIONS += $(CHEM_DIR)/PMFs - diff --git a/Support/Mechanism/Models/FFCM1_Red/Make.package b/Support/Mechanism/Models/FFCM1_Red/Make.package index 2154d7164..24c663c9a 100644 --- a/Support/Mechanism/Models/FFCM1_Red/Make.package +++ b/Support/Mechanism/Models/FFCM1_Red/Make.package @@ -2,9 +2,8 @@ CEXE_headers+=mechanism.H CEXE_sources+=mechanism.cpp -LIBRARIES += +LIBRARIES += INCLUDE_LOCATIONS += $(CHEM_DIR) VPATH_LOCATIONS += $(CHEM_DIR)/PMFs - diff --git a/Support/Mechanism/Models/H2-CO-CO2-3spec/Make.package b/Support/Mechanism/Models/H2-CO-CO2-3spec/Make.package index 8a2397e5f..24c663c9a 100644 --- a/Support/Mechanism/Models/H2-CO-CO2-3spec/Make.package +++ b/Support/Mechanism/Models/H2-CO-CO2-3spec/Make.package @@ -1,6 +1,7 @@ -CEXE_sources+=mechanism.cpp CEXE_headers+=mechanism.H +CEXE_sources+=mechanism.cpp + LIBRARIES += INCLUDE_LOCATIONS += $(CHEM_DIR) diff --git a/Support/Mechanism/Models/HP_DME/Make.package b/Support/Mechanism/Models/HP_DME/Make.package index e4168f09c..24c663c9a 100644 --- a/Support/Mechanism/Models/HP_DME/Make.package +++ b/Support/Mechanism/Models/HP_DME/Make.package @@ -1,2 +1,9 @@ CEXE_headers+=mechanism.H + CEXE_sources+=mechanism.cpp + +LIBRARIES += + +INCLUDE_LOCATIONS += $(CHEM_DIR) + +VPATH_LOCATIONS += $(CHEM_DIR)/PMFs diff --git a/Support/Mechanism/Models/IonizedAir/Make.package b/Support/Mechanism/Models/IonizedAir/Make.package index 6b0fa8de5..24c663c9a 100644 --- a/Support/Mechanism/Models/IonizedAir/Make.package +++ b/Support/Mechanism/Models/IonizedAir/Make.package @@ -1,4 +1,5 @@ CEXE_headers+=mechanism.H + CEXE_sources+=mechanism.cpp LIBRARIES += diff --git a/Support/Mechanism/Models/LiDryer/Make.package b/Support/Mechanism/Models/LiDryer/Make.package index 8a2397e5f..24c663c9a 100644 --- a/Support/Mechanism/Models/LiDryer/Make.package +++ b/Support/Mechanism/Models/LiDryer/Make.package @@ -1,6 +1,7 @@ -CEXE_sources+=mechanism.cpp CEXE_headers+=mechanism.H +CEXE_sources+=mechanism.cpp + LIBRARIES += INCLUDE_LOCATIONS += $(CHEM_DIR) diff --git a/Support/Mechanism/Models/Null/Make.package b/Support/Mechanism/Models/Null/Make.package index 8a2397e5f..24c663c9a 100644 --- a/Support/Mechanism/Models/Null/Make.package +++ b/Support/Mechanism/Models/Null/Make.package @@ -1,6 +1,7 @@ -CEXE_sources+=mechanism.cpp CEXE_headers+=mechanism.H +CEXE_sources+=mechanism.cpp + LIBRARIES += INCLUDE_LOCATIONS += $(CHEM_DIR) diff --git a/Support/Mechanism/Models/SootReaction/Make.package b/Support/Mechanism/Models/SootReaction/Make.package index 0c7558a78..24c663c9a 100644 --- a/Support/Mechanism/Models/SootReaction/Make.package +++ b/Support/Mechanism/Models/SootReaction/Make.package @@ -1,4 +1,9 @@ +CEXE_headers+=mechanism.H + CEXE_sources+=mechanism.cpp -#VPATH_LOCATIONS += $(CHEM_DIR)/PMFs +LIBRARIES += + +INCLUDE_LOCATIONS += $(CHEM_DIR) +VPATH_LOCATIONS += $(CHEM_DIR)/PMFs diff --git a/Support/Mechanism/Models/air/Make.package b/Support/Mechanism/Models/air/Make.package index 8a2397e5f..24c663c9a 100644 --- a/Support/Mechanism/Models/air/Make.package +++ b/Support/Mechanism/Models/air/Make.package @@ -1,6 +1,7 @@ -CEXE_sources+=mechanism.cpp CEXE_headers+=mechanism.H +CEXE_sources+=mechanism.cpp + LIBRARIES += INCLUDE_LOCATIONS += $(CHEM_DIR) diff --git a/Support/Mechanism/Models/dodecane_wang/Make.package b/Support/Mechanism/Models/dodecane_wang/Make.package index 909eb2264..24c663c9a 100644 --- a/Support/Mechanism/Models/dodecane_wang/Make.package +++ b/Support/Mechanism/Models/dodecane_wang/Make.package @@ -1,6 +1,6 @@ CEXE_headers+=mechanism.H -CEXE_sources+=mechanism.cpp solver.cpp solver_simplified.cpp +CEXE_sources+=mechanism.cpp LIBRARIES += diff --git a/Support/Mechanism/Models/grimech30-noArN/Make.package b/Support/Mechanism/Models/grimech30-noArN/Make.package index 6b0fa8de5..24c663c9a 100644 --- a/Support/Mechanism/Models/grimech30-noArN/Make.package +++ b/Support/Mechanism/Models/grimech30-noArN/Make.package @@ -1,4 +1,5 @@ CEXE_headers+=mechanism.H + CEXE_sources+=mechanism.cpp LIBRARIES += diff --git a/Support/Mechanism/Models/header/header.end b/Support/Mechanism/Models/header/header.end deleted file mode 100644 index ddd5dae0d..000000000 --- a/Support/Mechanism/Models/header/header.end +++ /dev/null @@ -1,2 +0,0 @@ - -#endif diff --git a/Support/Mechanism/Models/header/header.mec b/Support/Mechanism/Models/header/header.mec deleted file mode 100644 index f2a227abf..000000000 --- a/Support/Mechanism/Models/header/header.mec +++ /dev/null @@ -1,6 +0,0 @@ - -\\ -\\ -\\ This is the mechanism file -\\ -\\ diff --git a/Support/Mechanism/Models/header/header.start b/Support/Mechanism/Models/header/header.start deleted file mode 100644 index 64b14978b..000000000 --- a/Support/Mechanism/Models/header/header.start +++ /dev/null @@ -1,8 +0,0 @@ - - - - -#if 0 - - - diff --git a/Support/Mechanism/Models/header/header.therm b/Support/Mechanism/Models/header/header.therm deleted file mode 100644 index 038e3ef28..000000000 --- a/Support/Mechanism/Models/header/header.therm +++ /dev/null @@ -1,6 +0,0 @@ - -\\ -\\ -\\ This is the therm file -\\ -\\ diff --git a/Support/Mechanism/Models/header/header.trans b/Support/Mechanism/Models/header/header.trans deleted file mode 100644 index a694754cf..000000000 --- a/Support/Mechanism/Models/header/header.trans +++ /dev/null @@ -1,6 +0,0 @@ - -\\ -\\ -\\ This is the tran file -\\ -\\ diff --git a/Support/Mechanism/Models/heptane_lu_88sk/Make.package b/Support/Mechanism/Models/heptane_lu_88sk/Make.package index 1ed6a7046..24c663c9a 100644 --- a/Support/Mechanism/Models/heptane_lu_88sk/Make.package +++ b/Support/Mechanism/Models/heptane_lu_88sk/Make.package @@ -1,4 +1,4 @@ -CEXE_headers+=chemistry_file.H +CEXE_headers+=mechanism.H CEXE_sources+=mechanism.cpp diff --git a/Support/Mechanism/Models/methaneIons_diRenzo/Make.package b/Support/Mechanism/Models/methaneIons_diRenzo/Make.package index 6b0fa8de5..24c663c9a 100644 --- a/Support/Mechanism/Models/methaneIons_diRenzo/Make.package +++ b/Support/Mechanism/Models/methaneIons_diRenzo/Make.package @@ -1,4 +1,5 @@ CEXE_headers+=mechanism.H + CEXE_sources+=mechanism.cpp LIBRARIES += diff --git a/Support/Mechanism/Models/ndodecane_35/Make.package b/Support/Mechanism/Models/ndodecane_35/Make.package index 1ed6a7046..24c663c9a 100644 --- a/Support/Mechanism/Models/ndodecane_35/Make.package +++ b/Support/Mechanism/Models/ndodecane_35/Make.package @@ -1,4 +1,4 @@ -CEXE_headers+=chemistry_file.H +CEXE_headers+=mechanism.H CEXE_sources+=mechanism.cpp diff --git a/Support/Mechanism/Models/nitrogens/Make.package b/Support/Mechanism/Models/nitrogens/Make.package index 8a2397e5f..24c663c9a 100644 --- a/Support/Mechanism/Models/nitrogens/Make.package +++ b/Support/Mechanism/Models/nitrogens/Make.package @@ -1,6 +1,7 @@ -CEXE_sources+=mechanism.cpp CEXE_headers+=mechanism.H +CEXE_sources+=mechanism.cpp + LIBRARIES += INCLUDE_LOCATIONS += $(CHEM_DIR) From d04c2b400068ec5c7488a24f87b4e0b8e0edc517 Mon Sep 17 00:00:00 2001 From: Marc Henry de Frahan Date: Fri, 8 Dec 2023 13:14:32 -0700 Subject: [PATCH 05/21] Move the mech files --- {Support/Mechanism/Models => Mechanisms}/Aromatic_KrNara/COFD.dat | 0 .../Mechanism/Models => Mechanisms}/Aromatic_KrNara/COFETA.dat | 0 .../Mechanism/Models => Mechanisms}/Aromatic_KrNara/COFLAM.dat | 0 .../Mechanism/Models => Mechanisms}/Aromatic_KrNara/COFTD.dat | 0 .../Mechanism/Models => Mechanisms}/Aromatic_KrNara/Make.package | 0 .../Models => Mechanisms}/Aromatic_KrNara/README_bigMech.md | 0 .../Mechanism/Models => Mechanisms}/Aromatic_KrNara/convert.sh | 0 .../Mechanism/Models => Mechanisms}/Aromatic_KrNara/mechanism.H | 0 .../Mechanism/Models => Mechanisms}/Aromatic_KrNara/mechanism.cpp | 0 .../Mechanism/Models => Mechanisms}/Aromatic_KrNara/mechanism.inp | 0 .../Models => Mechanisms}/Aromatic_KrNara/mechanism.yaml | 0 .../Mechanism/Models => Mechanisms}/Aromatic_KrNara/therm.dat | 0 {Support/Mechanism/Models => Mechanisms}/Aromatic_KrNara/tran.dat | 0 {Support/Mechanism/Models => Mechanisms}/BurkeDryer/Make.package | 0 {Support/Mechanism/Models => Mechanisms}/BurkeDryer/convert.sh | 0 {Support/Mechanism/Models => Mechanisms}/BurkeDryer/mechanism.H | 0 {Support/Mechanism/Models => Mechanisms}/BurkeDryer/mechanism.cpp | 0 {Support/Mechanism/Models => Mechanisms}/BurkeDryer/mechanism.inp | 0 .../Mechanism/Models => Mechanisms}/BurkeDryer/mechanism.yaml | 0 {Support/Mechanism/Models => Mechanisms}/BurkeDryer/therm.dat | 0 {Support/Mechanism/Models => Mechanisms}/BurkeDryer/tran.dat | 0 {Support/Mechanism/Models => Mechanisms}/C1-C2-NO/Make.package | 0 {Support/Mechanism/Models => Mechanisms}/C1-C2-NO/mechanism.H | 0 {Support/Mechanism/Models => Mechanisms}/C1-C2-NO/mechanism.cpp | 0 {Support/Mechanism/Models => Mechanisms}/C1-C2-NO/mechanism.inp | 0 {Support/Mechanism/Models => Mechanisms}/C1-C2-NO/mechanism.yaml | 0 {Support/Mechanism/Models => Mechanisms}/C1-C2-NO/therm.dat | 0 {Support/Mechanism/Models => Mechanisms}/C1-C2-NO/tran.dat | 0 .../Mechanism/Models => Mechanisms}/C1-C2-NO_qss/Make.package | 0 {Support/Mechanism/Models => Mechanisms}/C1-C2-NO_qss/mechanism.H | 0 .../Mechanism/Models => Mechanisms}/C1-C2-NO_qss/mechanism.cpp | 0 .../Models => Mechanisms}/C1-C2-NO_qss/non_qssa_list.yaml | 0 {Support/Mechanism/Models => Mechanisms}/C1-C2-NO_qss/qssa.yaml | 0 .../Mechanism/Models => Mechanisms}/C1-C2-NO_qss/qssa_input.toml | 0 .../Mechanism/Models => Mechanisms}/C1-C2-NO_qss/skeletal.inp | 0 .../Mechanism/Models => Mechanisms}/C1-C2-NO_qss/skeletal.yaml | 0 {Support/Mechanism/Models => Mechanisms}/C1-C2-NO_qss/therm.dat | 0 {Support/Mechanism/Models => Mechanisms}/C1-C2-NO_qss/tran.dat | 0 {Support/Mechanism/Models => Mechanisms}/CH4_lean/Make.package | 0 {Support/Mechanism/Models => Mechanisms}/CH4_lean/mechanism.H | 0 {Support/Mechanism/Models => Mechanisms}/CH4_lean/mechanism.cpp | 0 {Support/Mechanism/Models => Mechanisms}/CH4_lean/mechanism.inp | 0 {Support/Mechanism/Models => Mechanisms}/CH4_lean/mechanism.yaml | 0 {Support/Mechanism/Models => Mechanisms}/CH4_lean/therm.dat | 0 {Support/Mechanism/Models => Mechanisms}/CH4_lean/tran.dat | 0 .../Mechanism/Models => Mechanisms}/CH4_lean_qss/Make.package | 0 {Support/Mechanism/Models => Mechanisms}/CH4_lean_qss/mechanism.H | 0 .../Mechanism/Models => Mechanisms}/CH4_lean_qss/mechanism.cpp | 0 .../Models => Mechanisms}/CH4_lean_qss/non_qssa_list.yaml | 0 {Support/Mechanism/Models => Mechanisms}/CH4_lean_qss/qssa.yaml | 0 .../Mechanism/Models => Mechanisms}/CH4_lean_qss/qssa_input.toml | 0 .../Mechanism/Models => Mechanisms}/CH4_lean_qss/skeletal.yaml | 0 {Support/Mechanism/Models => Mechanisms}/CH4_lean_qss/therm.dat | 0 {Support/Mechanism/Models => Mechanisms}/CH4_lean_qss/tran.dat | 0 {Support/Mechanism/Models => Mechanisms}/Davis/Make.package | 0 {Support/Mechanism/Models => Mechanisms}/Davis/convert.sh | 0 {Support/Mechanism/Models => Mechanisms}/Davis/mechanism.H | 0 {Support/Mechanism/Models => Mechanisms}/Davis/mechanism.cpp | 0 {Support/Mechanism/Models => Mechanisms}/Davis/mechanism.inp | 0 {Support/Mechanism/Models => Mechanisms}/Davis/mechanism.yaml | 0 {Support/Mechanism/Models => Mechanisms}/Davis/therm.dat | 0 {Support/Mechanism/Models => 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a/Support/Mechanism/Models/propane_fc/Make.package b/Mechanisms/propane_fc/Make.package similarity index 100% rename from Support/Mechanism/Models/propane_fc/Make.package rename to Mechanisms/propane_fc/Make.package diff --git a/Support/Mechanism/Models/propane_fc/convert.sh b/Mechanisms/propane_fc/convert.sh similarity index 100% rename from Support/Mechanism/Models/propane_fc/convert.sh rename to Mechanisms/propane_fc/convert.sh diff --git a/Support/Mechanism/Models/propane_fc/mechanism.H b/Mechanisms/propane_fc/mechanism.H similarity index 100% rename from Support/Mechanism/Models/propane_fc/mechanism.H rename to Mechanisms/propane_fc/mechanism.H diff --git a/Support/Mechanism/Models/propane_fc/mechanism.cpp b/Mechanisms/propane_fc/mechanism.cpp similarity index 100% rename from Support/Mechanism/Models/propane_fc/mechanism.cpp rename to Mechanisms/propane_fc/mechanism.cpp diff --git a/Support/Mechanism/Models/propane_fc/mechanism.inp b/Mechanisms/propane_fc/mechanism.inp similarity index 100% rename from Support/Mechanism/Models/propane_fc/mechanism.inp rename to Mechanisms/propane_fc/mechanism.inp diff --git a/Support/Mechanism/Models/propane_fc/mechanism.yaml b/Mechanisms/propane_fc/mechanism.yaml similarity index 100% rename from Support/Mechanism/Models/propane_fc/mechanism.yaml rename to Mechanisms/propane_fc/mechanism.yaml diff --git a/Support/Mechanism/Models/propane_fc/therm.dat b/Mechanisms/propane_fc/therm.dat similarity index 100% rename from Support/Mechanism/Models/propane_fc/therm.dat rename to Mechanisms/propane_fc/therm.dat diff --git a/Support/Mechanism/Models/sCO2/Make.package b/Mechanisms/sCO2/Make.package similarity index 100% rename from Support/Mechanism/Models/sCO2/Make.package rename to Mechanisms/sCO2/Make.package diff --git a/Support/Mechanism/Models/sCO2/convert.sh b/Mechanisms/sCO2/convert.sh similarity index 100% rename from Support/Mechanism/Models/sCO2/convert.sh rename to Mechanisms/sCO2/convert.sh diff --git a/Support/Mechanism/Models/sCO2/mechanism.H b/Mechanisms/sCO2/mechanism.H similarity index 100% rename from Support/Mechanism/Models/sCO2/mechanism.H rename to Mechanisms/sCO2/mechanism.H diff --git a/Support/Mechanism/Models/sCO2/mechanism.cpp b/Mechanisms/sCO2/mechanism.cpp similarity index 100% rename from Support/Mechanism/Models/sCO2/mechanism.cpp rename to Mechanisms/sCO2/mechanism.cpp diff --git a/Support/Mechanism/Models/sCO2/mechanism.inp b/Mechanisms/sCO2/mechanism.inp similarity index 100% rename from Support/Mechanism/Models/sCO2/mechanism.inp rename to Mechanisms/sCO2/mechanism.inp diff --git a/Support/Mechanism/Models/sCO2/mechanism.yaml b/Mechanisms/sCO2/mechanism.yaml similarity index 100% rename from Support/Mechanism/Models/sCO2/mechanism.yaml rename to Mechanisms/sCO2/mechanism.yaml diff --git a/Support/Mechanism/Models/sCO2/therm.dat b/Mechanisms/sCO2/therm.dat similarity index 100% rename from Support/Mechanism/Models/sCO2/therm.dat rename to Mechanisms/sCO2/therm.dat diff --git a/Support/Mechanism/Models/sCO2/transport.txt b/Mechanisms/sCO2/transport.txt similarity index 100% rename from Support/Mechanism/Models/sCO2/transport.txt rename to Mechanisms/sCO2/transport.txt From 743d833626843be1948fa716e6d81cc96a984bca Mon Sep 17 00:00:00 2001 From: Marc Henry de Frahan Date: Fri, 8 Dec 2023 13:26:08 -0700 Subject: [PATCH 06/21] Update paths --- Testing/Exec/Make.PelePhysics | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/Testing/Exec/Make.PelePhysics b/Testing/Exec/Make.PelePhysics index fd29fae13..a7e07443f 100644 --- a/Testing/Exec/Make.PelePhysics +++ b/Testing/Exec/Make.PelePhysics @@ -77,13 +77,12 @@ ifeq ($(Eos_Model), GammaLaw) $(error Chemistry_Model definition not compatible with Eos_Model=GammaLaw) endif endif -CHEM_HOME = $(PELE_PHYSICS_HOME)/Support/Mechanism/Models/$(Chemistry_Model) -CHEM_ALL = $(PELE_PHYSICS_HOME)/Support/Mechanism/Models +CHEM_HOME = $(PELE_PHYSICS_HOME)/Mechanisms/$(Chemistry_Model) +CHEM_ALL = $(PELE_PHYSICS_HOME)/Mechanisms VPATH_LOCATIONS += $(CHEM_HOME) $(CHEM_ALL) Bpack += $(CHEM_HOME)/Make.package \ $(CHEM_ALL)/Make.package Blocs += $(CHEM_HOME) $(CHEM_ALL) -Blocs += $(PELE_PHYSICS_HOME)/Support/Evaluation # Transport include $(TRAN_HOME)/Make.package From 2f232f0915d605305a1a88e9d7998562edcaa2bf Mon Sep 17 00:00:00 2001 From: Marc Henry de Frahan Date: Fri, 8 Dec 2023 13:37:02 -0700 Subject: [PATCH 07/21] Update more paths --- .github/workflows/ci.yml | 10 +++++----- Docs/sphinx/Ceptr.rst | 16 ++++++++-------- Docs/sphinx/Tutorials.rst | 18 +++++++++--------- Mechanisms/converter.sh | 2 +- README.md | 4 ++-- Source/Eos/README | 2 +- Source/Utility/PMF/cantera_pmf_generator.py | 6 +++--- Support/ceptr/tests/test_ceptr.py | 2 +- Testing/Exec/Make.PelePhysics | 2 -- 9 files changed, 30 insertions(+), 32 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 10b1cdc28..e5d6bb1e4 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -20,7 +20,7 @@ jobs: - name: Check formatting uses: DoozyX/clang-format-lint-action@v0.16.2 with: - source: './Source ./Testing ./Support/Mechanism/Models' + source: './Source ./Testing ./Mechanism' exclude: '.' extensions: 'H,h,cpp' clangFormatVersion: 16 @@ -75,9 +75,9 @@ jobs: - name: Run tests run: poetry run pytest - name: Convert air mechanism - run: poetry run convert -f ${{github.workspace}}/Support/Mechanism/Models/air/mechanism.yaml + run: poetry run convert -f ${{github.workspace}}/Mechanisms/air/mechanism.yaml - name: Convert LiDryer mechanism - run: poetry run convert -f ${{github.workspace}}/Support/Mechanism/Models/LiDryer/mechanism.yaml + run: poetry run convert -f ${{github.workspace}}/Mechanisms/LiDryer/mechanism.yaml Transport-EOS-Reactions: needs: Formatting @@ -275,8 +275,8 @@ jobs: if [ "${{matrix.comp}}" == 'gnu' ] || [ "${{matrix.comp}}" == 'llvm' ]; then \ ccache -z cd ${{github.workspace}}/PelePhysics-${{matrix.comp}}/Support/ceptr - poetry run qssa -f ${{github.workspace}}/PelePhysics-${{matrix.comp}}/Support/Mechanism/Models/dodecane_lu_qss/skeletal.yaml -n ${{github.workspace}}/Support/Mechanism/Models/dodecane_lu_qss/non_qssa_list.yaml - poetry run convert -f ${{github.workspace}}/PelePhysics-${{matrix.comp}}/Support/Mechanism/Models/dodecane_lu_qss/qssa.yaml --qss_format_input ${{github.workspace}}/PelePhysics-${{matrix.comp}}/Support/Mechanism/Models/dodecane_lu_qss/qssa_input_non_optimized.toml --qss_symbolic_jacobian + poetry run qssa -f ${{github.workspace}}/PelePhysics-${{matrix.comp}}/Mechanisms/dodecane_lu_qss/skeletal.yaml -n ${{github.workspace}}/Mechanisms/dodecane_lu_qss/non_qssa_list.yaml + poetry run convert -f ${{github.workspace}}/PelePhysics-${{matrix.comp}}/Mechanisms/dodecane_lu_qss/qssa.yaml --qss_format_input ${{github.workspace}}/PelePhysics-${{matrix.comp}}/Mechanisms/dodecane_lu_qss/qssa_input_non_optimized.toml --qss_symbolic_jacobian cd ${{env.JAC_WORKING_DIRECTORY}} make -j ${{env.NPROCS}} Eos_Model=Fuego Chemistry_Model=dodecane_lu_qss DEBUG=TRUE TINY_PROFILE=TRUE USE_CCACHE=TRUE ${{matrix.amrex_build_args}} ./Pele3d.${{matrix.comp}}.DEBUG.TPROF.ex; \ diff --git a/Docs/sphinx/Ceptr.rst b/Docs/sphinx/Ceptr.rst index c7d77b682..49c99d061 100644 --- a/Docs/sphinx/Ceptr.rst +++ b/Docs/sphinx/Ceptr.rst @@ -30,7 +30,7 @@ There are three ways to use CEPTR to generate C++ mechanism files for a given ch 1. Using CEPTR directly:: $ cd ${PELE_PHYSICS_HOME}/Support/ceptr - $ poetry run convert -f ${PELE_PHYSICS_HOME}/Support/Mechanism/Models/LiDryer/mechanism.yaml + $ poetry run convert -f ${PELE_PHYSICS_HOME}/Mechanisms/LiDryer/mechanism.yaml 2. Using a helper script in the directory containing the ``mechanism.yaml`` file:: @@ -38,7 +38,7 @@ There are three ways to use CEPTR to generate C++ mechanism files for a given ch 3. Using a helper script in the ``Models`` directory:: - $ bash ${PELE_PHYSICS_HOME}/Support/Mechanism/Models/converter.sh -f ./LiDryer/mechanism.yaml + $ bash ${PELE_PHYSICS_HOME}/Mechanisms/converter.sh -f ./LiDryer/mechanism.yaml Batched generation @@ -52,23 +52,23 @@ Batched generation For non-reduced chemistries, CEPTR can take a file with a list of ``mechanism.yaml`` files to convert:: $ cd ${PELE_PHYSICS_HOME}/Support/ceptr - $ poetry run convert -l ${PELE_PHYSICS_HOME}/Support/Mechanism/Models/list_mech + $ poetry run convert -l ${PELE_PHYSICS_HOME}/Mechanisms/list_mech For reduced chemistries, CEPTR can take a file with a list of ``qssa.yaml`` and ``qssa_input.toml`` to convert:: $ cd ${PELE_PHYSICS_HOME}/Support/ceptr - $ poetry run convert -lq ${PELE_PHYSICS_HOME}/Support/Mechanism/Models/list_qss_mech + $ poetry run convert -lq ${PELE_PHYSICS_HOME}/Mechanisms/list_qss_mech For generating ``qssa.yaml`` for reduced chemistries, CEPTR can take a file with a list of ``skeletal.yaml`` and ``non_qssa_list.yaml``:: $ cd ${PELE_PHYSICS_HOME}/Support/ceptr - $ poetry run qssa -lq ${PELE_PHYSICS_HOME}/Support/Mechanism/Models/list_qss_mech + $ poetry run qssa -lq ${PELE_PHYSICS_HOME}/Mechanisms/list_qss_mech To generate all mechanisms:: - $ poetry run convert -l ${PELE_PHYSICS_HOME}/Support/Mechanism/Models/list_mech - $ poetry run qssa -lq ${PELE_PHYSICS_HOME}/Support/Mechanism/Models/list_qss_mech - $ poetry run convert -lq ${PELE_PHYSICS_HOME}/Support/Mechanism/Models/list_qss_mech + $ poetry run convert -l ${PELE_PHYSICS_HOME}/Mechanisms/list_mech + $ poetry run qssa -lq ${PELE_PHYSICS_HOME}/Mechanisms/list_qss_mech + $ poetry run convert -lq ${PELE_PHYSICS_HOME}/Mechanisms/list_qss_mech Converting CHEMKIN files diff --git a/Docs/sphinx/Tutorials.rst b/Docs/sphinx/Tutorials.rst index 6a14c2370..7bba5e199 100644 --- a/Docs/sphinx/Tutorials.rst +++ b/Docs/sphinx/Tutorials.rst @@ -18,21 +18,21 @@ Update ``poetry``:: $ cd ${PELE_PHYSICS_HOME}/Support/ceptr $ poetry update -Make sure the list of non-QSS species is correct in ``${PELE_PHYSICS_HOME}/Support/Mechanism/Models/dodecane_lu_qss/non_qssa_list.yaml`` +Make sure the list of non-QSS species is correct in ``${PELE_PHYSICS_HOME}/Mechanisms/dodecane_lu_qss/non_qssa_list.yaml`` -In the next step, ``skeletal.yaml`` is the ``mechanism.yaml`` of the skeletal version of the mechanism (here available under ``${PELE_PHYSICS_HOME}/Support/Mechanism/Models/dodecane_lu``). +In the next step, ``skeletal.yaml`` is the ``mechanism.yaml`` of the skeletal version of the mechanism (here available under ``${PELE_PHYSICS_HOME}/Mechanisms/dodecane_lu``). If only CHEMKIN files are available for the skeletal mechanism, see :ref:`Converting CHEMKIN files ` for generating ``skeletal.yaml``. Generate ``qssa.yaml`` from ``skeletal.yaml`` and ``non_qssa_list.yaml``:: $ cd ${PELE_PHYSICS_HOME}/Support/ceptr - $ poetry run qssa -f ${PELE_PHYSICS_HOME}/Support/Mechanism/Models/dodecane_lu_qss/skeletal.yaml -n ${PELE_PHYSICS_HOME}/Support/Mechanism/Models/dodecane_lu_qss/non_qssa_list.yaml + $ poetry run qssa -f ${PELE_PHYSICS_HOME}/Mechanisms/dodecane_lu_qss/skeletal.yaml -n ${PELE_PHYSICS_HOME}/Mechanisms/dodecane_lu_qss/non_qssa_list.yaml Generate ``mechanism.H`` and ``mechanism.cpp`` from ``qssa.yaml``:: $ cd ${PELE_PHYSICS_HOME}/Support/ceptr - $ poetry run convert -f ${PELE_PHYSICS_HOME}/Support/Mechanism/Models/dodecane_lu_qss/qssa.yaml --qss_format_input ${PELE_PHYSICS_HOME}/Support/Mechanism/Models/dodecane_lu_qss/qssa_input.toml --qss_symbolic_jacobian + $ poetry run convert -f ${PELE_PHYSICS_HOME}/Mechanisms/dodecane_lu_qss/qssa.yaml --qss_format_input ${PELE_PHYSICS_HOME}/Mechanisms/dodecane_lu_qss/qssa_input.toml --qss_symbolic_jacobian We recommend using the following ``qssa_input.toml``:: @@ -67,20 +67,20 @@ Update ``poetry``:: $ cd ${PELE_PHYSICS_HOME}/Support/ceptr $ poetry update -Make sure the list of non-QSS species is correct in ``Support/Mechanism/Models/dodecane_lu_qss/non_qssa_list.yaml`` +Make sure the list of non-QSS species is correct in ``Mechanisms/dodecane_lu_qss/non_qssa_list.yaml`` -In the next step, ``skeletal.yaml`` is the ``mechanism.yaml`` of the skeletal version of the mechanism (here available under ``${PELE_PHYSICS_HOME}/Support/Mechanism/Models/dodecane_lu``). +In the next step, ``skeletal.yaml`` is the ``mechanism.yaml`` of the skeletal version of the mechanism (here available under ``${PELE_PHYSICS_HOME}/Mechanisms/dodecane_lu``). If only CHEMKIN files are available for the skeletal mechanism, see :ref:`Converting CHEMKIN files ` for generating ``skeletal.yaml``. Generate ``qssa.yaml`` from ``skeletal.yaml`` and ``non_qssa_list.yaml``:: $ cd ${PELE_PHYSICS_HOME}/Support/ceptr - $ poetry run qssa -f ${PELE_PHYSICS_HOME}/Support/Mechanism/Models/dodecane_lu_qss/skeletal.yaml -n ${PELE_PHYSICS_HOME}/Support/Mechanism/Models/dodecane_lu_qss/non_qssa_list.yaml + $ poetry run qssa -f ${PELE_PHYSICS_HOME}/Mechanisms/dodecane_lu_qss/skeletal.yaml -n ${PELE_PHYSICS_HOME}/Mechanisms/dodecane_lu_qss/non_qssa_list.yaml Generate ``mechanism.H`` and ``mechanism.cpp`` from ``qssa.yaml``:: $ cd ${PELE_PHYSICS_HOME}/Support/ceptr - $ poetry run convert -f ${PELE_PHYSICS_HOME}/Support/Mechanism/Models/dodecane_lu_qss/qssa.yaml + $ poetry run convert -f ${PELE_PHYSICS_HOME}/Mechanisms/dodecane_lu_qss/qssa.yaml Tutorial 3 - Generating NC12H26 Skeletal mechanism -------------------------------------------------- @@ -97,5 +97,5 @@ If only CHEMKIN files are available, see :ref:`Converting CHEMKIN files /dev/null && pwd ) PELE_PHYSICS_HOME=${script_dir%%"${remove}"} echo "Using PELE_PHYSICS_HOME: ${PELE_PHYSICS_HOME}. Set PELE_PHYSICS_HOME you want a different one." diff --git a/README.md b/README.md index b379d2c88..1096e23ef 100644 --- a/README.md +++ b/README.md @@ -20,7 +20,7 @@ This information is read by the CEPTR tool, and source code files are generated * Mixture-averaged thermal diffusion coefficients are also available using the transport.use_soret flag (see PeleLMeX implementation for more information) * Utilization of auxiliary source files (C++) that follow the Cantera species production rate function interface (e.g., QSS approximations) -If the `Pele` codes are built with `Eos_dir = Fuego`, the make system variable `Chemistry_Model` must be set to one of the models (subfolders) that exist in the `${PELE_PHYSICS_HOME}/Support/Mechanism/Models` folder. The repository currently provides (multiple) models for each of the following mixtures: +If the `Pele` codes are built with `Eos_dir = Fuego`, the make system variable `Chemistry_Model` must be set to one of the models (subfolders) that exist in the `${PELE_PHYSICS_HOME}/Mechanisms` folder. The repository currently provides (multiple) models for each of the following mixtures: * air * hydrogen * methane @@ -35,4 +35,4 @@ If the `Pele` codes are built with `Eos_dir = Fuego`, the make system variable ` `PelePhysics` currently supports a cubic EOS model: `Soave-Redlich-Kwong`. It is built on top of the ideal gas models, and is selected by specifying its name as the `Eos_dir` during the build (the make system requires that both `Eos_dir` and `Chemistry_Model` be specified). Any additional parameters required for the EOS (e.g., attractions, repulsions, critical states) are either included in the underlying CEPTR database used to generate the source file model implementation, or else are inferred from the input model data. ## Model generation procedures -This repository provides the tools necessary for generating new Pele-compatible combustion mechanisms. Please refer to the `CEPTR documentation `_ for instructions on generating mechanism models. Make sure that you edit the `GNUmakefile` where you want to use this (in, e.g., `PeleC/Exec`) so that `Chemistry_Model` is `XXX`. In `PeleC/Exec/Make.PeleC`, the model is expected to be in the folder `${PELE_PHYSICS_HOME}/Support/Mechanism/Models/$(Chemistry_Model)`, and it is expected that the folder contains a `Make.package` file to include, so make sure things are where they need to be. Refer to other mechanisms for additional guidance. +This repository provides the tools necessary for generating new Pele-compatible combustion mechanisms. Please refer to the `CEPTR documentation `_ for instructions on generating mechanism models. Make sure that you edit the `GNUmakefile` where you want to use this (in, e.g., `PeleC/Exec`) so that `Chemistry_Model` is `XXX`. In `PeleC/Exec/Make.PeleC`, the model is expected to be in the folder `${PELE_PHYSICS_HOME}/Mechanisms/$(Chemistry_Model)`, and it is expected that the folder contains a `Make.package` file to include, so make sure things are where they need to be. Refer to other mechanisms for additional guidance. diff --git a/Source/Eos/README b/Source/Eos/README index 92231a9bd..44ae23a4c 100644 --- a/Source/Eos/README +++ b/Source/Eos/README @@ -14,7 +14,7 @@ Fuego: A mixture of ideal gases, computed using CEPTR-generated codes. The specific model is selected at compile time from the list in - ../Support/Mechanism/Models + ../Mechanisms Soave-Redlich-Kwong: diff --git a/Source/Utility/PMF/cantera_pmf_generator.py b/Source/Utility/PMF/cantera_pmf_generator.py index 1c2553a20..2677dc5fb 100644 --- a/Source/Utility/PMF/cantera_pmf_generator.py +++ b/Source/Utility/PMF/cantera_pmf_generator.py @@ -28,7 +28,7 @@ "-m", "--mechanism", default="drm19", - help="Name of PelePhysics mechanism from Support/Mechanism/Models", + help="Name of PelePhysics mechanism from Mechanisms", ) parser.add_argument( "-pp", "--pp_home", default="../../", help="Path to PelePhysics directory" @@ -60,7 +60,7 @@ "--output", default=None, help=( - "Path to directory where flames will be saved, if not specified files are saved to PelePhysics/Support/Mechanism/Models//PMFs/" + "Path to directory where flames will be saved, if not specified files are saved to PelePhysics/Mechanisms//PMFs/" ), ) args = parser.parse_args() @@ -99,7 +99,7 @@ ################# # Find mechanism in PelePhysics -pp_path = os.path.join(args.pp_home, "Support/Mechanism/Models") +pp_path = os.path.join(args.pp_home, "Mechanisms") if args.output is None: outdir = os.path.join(pp_path, mechanism, "PMFs") else: diff --git a/Support/ceptr/tests/test_ceptr.py b/Support/ceptr/tests/test_ceptr.py index 2c93c196a..c7f8784a1 100644 --- a/Support/ceptr/tests/test_ceptr.py +++ b/Support/ceptr/tests/test_ceptr.py @@ -11,7 +11,7 @@ def mechanism_path(mname): """Determine mechanism path.""" this_file_dir = pathlib.Path(__file__).parent.resolve() - model_path = "Mechanism/Models" + model_path = "Mechanism" return this_file_dir.parents[1] / model_path / mname diff --git a/Testing/Exec/Make.PelePhysics b/Testing/Exec/Make.PelePhysics index a7e07443f..777e8bd12 100644 --- a/Testing/Exec/Make.PelePhysics +++ b/Testing/Exec/Make.PelePhysics @@ -90,8 +90,6 @@ INCLUDE_LOCATIONS += $(TRAN_HOME) VPATH_LOCATIONS += $(TRAN_HOME) USE_FUEGO = FALSE -Blocs += $(PELE_PHYSICS_HOME)/Support/Mechanism - ifeq ($(Transport_Model), Simple) DEFINES += -DUSE_SIMPLE_TRANSPORT endif From c4c2c4768ffd0f9b565d6f897abeab0c076b8232 Mon Sep 17 00:00:00 2001 From: Marc Henry de Frahan Date: Fri, 8 Dec 2023 13:38:22 -0700 Subject: [PATCH 08/21] typo --- .github/workflows/ci.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index e5d6bb1e4..cc08a8096 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -20,7 +20,7 @@ jobs: - name: Check formatting uses: DoozyX/clang-format-lint-action@v0.16.2 with: - source: './Source ./Testing ./Mechanism' + source: './Source ./Testing ./Mechanisms' exclude: '.' extensions: 'H,h,cpp' clangFormatVersion: 16 From 18c5a0cddc0072b50c6793cd5bce673e1711d66b Mon Sep 17 00:00:00 2001 From: Marc Henry de Frahan Date: Fri, 8 Dec 2023 13:44:02 -0700 Subject: [PATCH 09/21] fix ceptr test --- Support/ceptr/tests/test_ceptr.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/Support/ceptr/tests/test_ceptr.py b/Support/ceptr/tests/test_ceptr.py index c7f8784a1..c005b6c73 100644 --- a/Support/ceptr/tests/test_ceptr.py +++ b/Support/ceptr/tests/test_ceptr.py @@ -11,8 +11,8 @@ def mechanism_path(mname): """Determine mechanism path.""" this_file_dir = pathlib.Path(__file__).parent.resolve() - model_path = "Mechanism" - return this_file_dir.parents[1] / model_path / mname + model_path = "Mechanisms" + return this_file_dir.parents[2] / model_path / mname def test_version(): From 5ae88714a0b2d09f11abd0c06300b4797d331a8c Mon Sep 17 00:00:00 2001 From: Marc Henry de Frahan Date: Fri, 8 Dec 2023 14:09:21 -0700 Subject: [PATCH 10/21] fix eos_dir usage --- README.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index 1096e23ef..d85409ec2 100644 --- a/README.md +++ b/README.md @@ -20,7 +20,7 @@ This information is read by the CEPTR tool, and source code files are generated * Mixture-averaged thermal diffusion coefficients are also available using the transport.use_soret flag (see PeleLMeX implementation for more information) * Utilization of auxiliary source files (C++) that follow the Cantera species production rate function interface (e.g., QSS approximations) -If the `Pele` codes are built with `Eos_dir = Fuego`, the make system variable `Chemistry_Model` must be set to one of the models (subfolders) that exist in the `${PELE_PHYSICS_HOME}/Mechanisms` folder. The repository currently provides (multiple) models for each of the following mixtures: +If the `Pele` codes are built with `Eos_Model = Fuego`, the make system variable `Chemistry_Model` must be set to one of the models (subfolders) that exist in the `${PELE_PHYSICS_HOME}/Mechanisms` folder. The repository currently provides (multiple) models for each of the following mixtures: * air * hydrogen * methane @@ -32,7 +32,7 @@ If the `Pele` codes are built with `Eos_dir = Fuego`, the make system variable ` ### NOTE: Non-ideal equations of state -`PelePhysics` currently supports a cubic EOS model: `Soave-Redlich-Kwong`. It is built on top of the ideal gas models, and is selected by specifying its name as the `Eos_dir` during the build (the make system requires that both `Eos_dir` and `Chemistry_Model` be specified). Any additional parameters required for the EOS (e.g., attractions, repulsions, critical states) are either included in the underlying CEPTR database used to generate the source file model implementation, or else are inferred from the input model data. +`PelePhysics` currently supports a cubic EOS model: `Soave-Redlich-Kwong`. It is built on top of the ideal gas models, and is selected by specifying its name as the `Eos_Model` during the build (the make system requires that both `Eos_Model` and `Chemistry_Model` be specified). Any additional parameters required for the EOS (e.g., attractions, repulsions, critical states) are either included in the underlying CEPTR database used to generate the source file model implementation, or else are inferred from the input model data. ## Model generation procedures This repository provides the tools necessary for generating new Pele-compatible combustion mechanisms. Please refer to the `CEPTR documentation `_ for instructions on generating mechanism models. Make sure that you edit the `GNUmakefile` where you want to use this (in, e.g., `PeleC/Exec`) so that `Chemistry_Model` is `XXX`. In `PeleC/Exec/Make.PeleC`, the model is expected to be in the folder `${PELE_PHYSICS_HOME}/Mechanisms/$(Chemistry_Model)`, and it is expected that the folder contains a `Make.package` file to include, so make sure things are where they need to be. Refer to other mechanisms for additional guidance. From d545f04494cdb351375a6dcdbfe53e847b307bf8 Mon Sep 17 00:00:00 2001 From: Marc Henry de Frahan Date: Fri, 8 Dec 2023 14:44:47 -0700 Subject: [PATCH 11/21] better make.package for spray --- Source/Spray/Distribution/Make.package | 3 +++ 1 file changed, 3 insertions(+) diff --git a/Source/Spray/Distribution/Make.package b/Source/Spray/Distribution/Make.package index b66e67f25..870e1be22 100644 --- a/Source/Spray/Distribution/Make.package +++ b/Source/Spray/Distribution/Make.package @@ -1,3 +1,6 @@ CEXE_headers += DistBase.H CEXE_headers += Distributions.H CEXE_sources += Distributions.cpp + +VPATH_LOCATIONS += $(PELE_PHYSICS_HOME)/Source/Spray/Distribution +INCLUDE_LOCATIONS += $(PELE_PHYSICS_HOME)/Source/Spray/Distribution \ No newline at end of file From cb62a2cde1956acae58ef960bb9f5023462e6360 Mon Sep 17 00:00:00 2001 From: Marc Henry de Frahan Date: Fri, 8 Dec 2023 14:46:36 -0700 Subject: [PATCH 12/21] another --- Source/Spray/BreakupSplash/Make.package | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/Source/Spray/BreakupSplash/Make.package b/Source/Spray/BreakupSplash/Make.package index d313c208a..c425ecdeb 100644 --- a/Source/Spray/BreakupSplash/Make.package +++ b/Source/Spray/BreakupSplash/Make.package @@ -1,6 +1,8 @@ - CEXE_headers += AhamedSplash.H CEXE_headers += TABBreakup.H CEXE_headers += ReitzKHRT.H CEXE_headers += SBData.H CEXE_headers += WallFilm.H + +VPATH_LOCATIONS += $(PELE_PHYSICS_HOME)/Source/Spray/BreakupSplash +INCLUDE_LOCATIONS += $(PELE_PHYSICS_HOME)/Source/Spray/BreakupSplash \ No newline at end of file From 819a1ea7fe5346e499a7fccb831502e1d9bd28ed Mon Sep 17 00:00:00 2001 From: Marc Henry de Frahan Date: Fri, 8 Dec 2023 15:14:27 -0700 Subject: [PATCH 13/21] remove refs to pelemp --- Source/Soot/SootModel.H | 2 +- Source/Soot/SootModel.cpp | 2 +- Source/Soot/SootModel_react.cpp | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/Source/Soot/SootModel.H b/Source/Soot/SootModel.H index ddc668e1d..9b83e66e2 100644 --- a/Source/Soot/SootModel.H +++ b/Source/Soot/SootModel.H @@ -5,7 +5,7 @@ // AMReX include statements #include -// PeleMP include statements +// Soot include statements #include "Constants_Soot.H" #include "SootData.H" #include "SootReactions.H" diff --git a/Source/Soot/SootModel.cpp b/Source/Soot/SootModel.cpp index 4b063cb20..6806618cf 100644 --- a/Source/Soot/SootModel.cpp +++ b/Source/Soot/SootModel.cpp @@ -5,7 +5,7 @@ // PelePhysics include statements #include "PelePhysics.H" -// PeleMP include statements +// Soot include statements #include "SootModel.H" using namespace amrex; diff --git a/Source/Soot/SootModel_react.cpp b/Source/Soot/SootModel_react.cpp index 36dc6c589..8a8396319 100644 --- a/Source/Soot/SootModel_react.cpp +++ b/Source/Soot/SootModel_react.cpp @@ -1,5 +1,5 @@ -// PeleMP include statements +// Soot include statements #include "SootModel.H" // PelePhysics include statements From 1f0bc08a871fd9e682065e8fa4a9000301fb0e11 Mon Sep 17 00:00:00 2001 From: Marc Henry de Frahan Date: Mon, 11 Dec 2023 09:14:41 -0700 Subject: [PATCH 14/21] Fix some unused vars --- Source/Spray/BreakupSplash/AhamedSplash.H | 4 ++-- Source/Spray/BreakupSplash/WallFilm.H | 2 +- Source/Spray/SprayInjection.H | 2 +- Source/Spray/SprayParticles.cpp | 2 +- Source/Spray/SpraySB.cpp | 10 +++++----- Source/Spray/WallFunctions.H | 8 ++++---- 6 files changed, 14 insertions(+), 14 deletions(-) diff --git a/Source/Spray/BreakupSplash/AhamedSplash.H b/Source/Spray/BreakupSplash/AhamedSplash.H index 2487a69af..88abf21ce 100644 --- a/Source/Spray/BreakupSplash/AhamedSplash.H +++ b/Source/Spray/BreakupSplash/AhamedSplash.H @@ -203,8 +203,8 @@ void droplet_splashing( SprayParticleContainer::ParticleType& p, int pid, - const amrex::RealVect& dx, - const amrex::RealVect& plo, + const amrex::RealVect& /*dx*/, + const amrex::RealVect& /*plo*/, const SprayData& fdat, const amrex::Real p_gas, const amrex::RealVect& vel_part, diff --git a/Source/Spray/BreakupSplash/WallFilm.H b/Source/Spray/BreakupSplash/WallFilm.H index 9d547cf15..83238f9d4 100644 --- a/Source/Spray/BreakupSplash/WallFilm.H +++ b/Source/Spray/BreakupSplash/WallFilm.H @@ -136,7 +136,7 @@ calculateFilmSource( // Species index const int fspec = fdat.indx[spf]; // Gas species index, might be the same - const int fdspec = fdat.dep_indx[spf]; + // const int fdspec = fdat.dep_indx[spf]; // Convert mass diffusion coefficient from mixture average // to binary for fuel only, not concerned with other species Ddiag[fspec] *= mw_skin / gpv.mw[fspec] * SPU.rhod_conv; diff --git a/Source/Spray/SprayInjection.H b/Source/Spray/SprayInjection.H index 37e05336b..585e4cf54 100644 --- a/Source/Spray/SprayInjection.H +++ b/Source/Spray/SprayInjection.H @@ -201,7 +201,7 @@ SprayParticleContainer::uniformSprayInit( const amrex::RealVect vel_part, const amrex::Real dia_part, const amrex::Real T_part, - const amrex::Real* Y_part, + const amrex::Real* /*Y_part*/, const int level, const int num_redist, const amrex::Real num_ppp) diff --git a/Source/Spray/SprayParticles.cpp b/Source/Spray/SprayParticles.cpp index b3a5e5156..36c366377 100644 --- a/Source/Spray/SprayParticles.cpp +++ b/Source/Spray/SprayParticles.cpp @@ -439,7 +439,7 @@ SprayParticleContainer::updateParticles( } Gpu::Atomic::Add( &engSrcarr(cur_indx), cur_coef * gpv.fluid_eng_src); - Real new_time = static_cast(cur_iter + 1) * sub_dt; + // Real new_time = static_cast(cur_iter + 1) * sub_dt; // Modify particle position by whole time step if (do_move && !fdat->fixed_parts && p.id() > 0 && !is_film) { for (int dir = 0; dir < AMREX_SPACEDIM; ++dir) { diff --git a/Source/Spray/SpraySB.cpp b/Source/Spray/SpraySB.cpp index 93d0d5412..3a89d8dea 100644 --- a/Source/Spray/SpraySB.cpp +++ b/Source/Spray/SpraySB.cpp @@ -60,10 +60,10 @@ SprayParticleContainer::CreateSBDroplets( rho_part = 1. / rho_part; #else Real rho_part = fdat->rhoL(T0, 0); - Real mu_part = fdat->muL(T0, 0); + // Real mu_part = fdat->muL(T0, 0); Y0[0] = 1.; #endif - Real pmass = M_PI / 6. * rho_part * std::pow(ref_dia, 3); + // Real pmass = M_PI / 6. * rho_part * std::pow(ref_dia, 3); Real U0mag = vel0.vectorLength(); // Splashing @@ -78,7 +78,7 @@ SprayParticleContainer::CreateSBDroplets( Real U0norm = normal.dotProduct(vel0); Real alpha = amrex::max(M_PI / 6., std::asin(amrex::Math::abs(U0norm) / U0mag)); - Real alpha_d = alpha * 180. / M_PI; + // Real alpha_d = alpha * 180. / M_PI; Real U0tan = std::sqrt(U0mag * U0mag - U0norm * U0norm); Real uBeta_0, uBeta_half, uBeta_pi, uPsi_coeff, usNorm; get_splash_vels( @@ -103,7 +103,7 @@ SprayParticleContainer::CreateSBDroplets( } else if (new_parts == 3) { utBeta = uBeta_pi; } - Real utPsi = uPsi_coeff * std::sin(psi); + // Real utPsi = uPsi_coeff * std::sin(psi); for (int dir = 0; dir < AMREX_SPACEDIM; ++dir) { Real pvel = AMREX_D_TERM( usNorm * normal[dir], +utBeta * tanBeta[dir], @@ -136,7 +136,7 @@ SprayParticleContainer::CreateSBDroplets( Real N_s = std::pow(num_dens0, m_breakupPPPFact); int N_d = amrex::max(1, static_cast(num_dens0 / N_s)); N_s = num_dens0 / static_cast(N_d); - Real new_mass = M_PI / 6. * rho_part * std::pow(dmean, 3); + // Real new_mass = M_PI / 6. * rho_part * std::pow(dmean, 3); #if AMREX_SPACEDIM == 3 RealVect testvec(1., 0., 0.); if (testvec.crossProduct(normal).vectorLength() < 1.E-5) { diff --git a/Source/Spray/WallFunctions.H b/Source/Spray/WallFunctions.H index ccb198675..c2499e1bd 100644 --- a/Source/Spray/WallFunctions.H +++ b/Source/Spray/WallFunctions.H @@ -96,7 +96,7 @@ check_wall( const amrex::IntVect& ijkc, #ifdef AMREX_USE_EB const amrex::IntVect& ijkc_prev, - const amrex::RealVect& vel_part, + const amrex::RealVect& /*vel_part*/, const bool use_EB, amrex::Array4 const& flags, amrex::Array4 const& bcent, @@ -185,7 +185,7 @@ impose_wall( const SprayData& fdat, const amrex::RealVect& dx, const amrex::RealVect& plo, - const amrex::RealVect& phi, + const amrex::RealVect& /*phi*/, amrex::IntVect& bflags, const amrex::Real* cBoilT, const amrex::Real p_fluid, @@ -215,8 +215,8 @@ impose_wall( ijkc_prev, vel_part, use_EB, flags, bcent, bnorm, #endif par_dot, normal); - amrex::IntVect refl_prev = ijkc; - bool do_deposit = false; + // amrex::IntVect refl_prev = ijkc; + // bool do_deposit = false; if (do_refl) { amrex::Real Nw_Vp = normal.dotProduct(vel_part); if (do_splash) { From 9cebdff66e0e9a0dcaf4d0a6a7fdde7b92b9575a Mon Sep 17 00:00:00 2001 From: Marc Henry de Frahan Date: Mon, 11 Dec 2023 09:20:34 -0700 Subject: [PATCH 15/21] Fix something --- Source/Spray/SprayParticles.H | 2 +- Source/Spray/SpraySB.cpp | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/Source/Spray/SprayParticles.H b/Source/Spray/SprayParticles.H index 679b05137..704b4bda0 100644 --- a/Source/Spray/SprayParticles.H +++ b/Source/Spray/SprayParticles.H @@ -20,7 +20,7 @@ #define NAI_SPR 0 // Forward declarations -class SBPtrs; +struct SBPtrs; class MyParIter : public amrex::ParIter { diff --git a/Source/Spray/SpraySB.cpp b/Source/Spray/SpraySB.cpp index 3a89d8dea..3ee8ceeeb 100644 --- a/Source/Spray/SpraySB.cpp +++ b/Source/Spray/SpraySB.cpp @@ -103,7 +103,7 @@ SprayParticleContainer::CreateSBDroplets( } else if (new_parts == 3) { utBeta = uBeta_pi; } - // Real utPsi = uPsi_coeff * std::sin(psi); + Real utPsi = uPsi_coeff * std::sin(psi); for (int dir = 0; dir < AMREX_SPACEDIM; ++dir) { Real pvel = AMREX_D_TERM( usNorm * normal[dir], +utBeta * tanBeta[dir], From df8d43bef10d545b596f712ecbcd8997ab4c30b9 Mon Sep 17 00:00:00 2001 From: Marc Henry de Frahan Date: Mon, 11 Dec 2023 11:59:44 -0700 Subject: [PATCH 16/21] fix unused --- Source/Spray/SpraySB.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Source/Spray/SpraySB.cpp b/Source/Spray/SpraySB.cpp index 3ee8ceeeb..105988cee 100644 --- a/Source/Spray/SpraySB.cpp +++ b/Source/Spray/SpraySB.cpp @@ -103,7 +103,7 @@ SprayParticleContainer::CreateSBDroplets( } else if (new_parts == 3) { utBeta = uBeta_pi; } - Real utPsi = uPsi_coeff * std::sin(psi); + AMREX_D_DECL(,,Real utPsi = uPsi_coeff * std::sin(psi);) for (int dir = 0; dir < AMREX_SPACEDIM; ++dir) { Real pvel = AMREX_D_TERM( usNorm * normal[dir], +utBeta * tanBeta[dir], From 5e8d58569f56dcf42ae0ac8e071167f5d26d069e Mon Sep 17 00:00:00 2001 From: Marc Henry de Frahan Date: Mon, 11 Dec 2023 12:49:52 -0700 Subject: [PATCH 17/21] better fix --- Source/Spray/SpraySB.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Source/Spray/SpraySB.cpp b/Source/Spray/SpraySB.cpp index 105988cee..8f5e766ba 100644 --- a/Source/Spray/SpraySB.cpp +++ b/Source/Spray/SpraySB.cpp @@ -103,7 +103,7 @@ SprayParticleContainer::CreateSBDroplets( } else if (new_parts == 3) { utBeta = uBeta_pi; } - AMREX_D_DECL(,,Real utPsi = uPsi_coeff * std::sin(psi);) + AMREX_D_PICK(,,Real utPsi = uPsi_coeff * std::sin(psi);) for (int dir = 0; dir < AMREX_SPACEDIM; ++dir) { Real pvel = AMREX_D_TERM( usNorm * normal[dir], +utBeta * tanBeta[dir], From 958ae46e7ea629db373af7cd6152ef6722c66b1e Mon Sep 17 00:00:00 2001 From: Marc Henry de Frahan Date: Mon, 11 Dec 2023 13:04:27 -0700 Subject: [PATCH 18/21] clang format --- Source/Spray/SpraySB.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Source/Spray/SpraySB.cpp b/Source/Spray/SpraySB.cpp index 8f5e766ba..c4b5b1f24 100644 --- a/Source/Spray/SpraySB.cpp +++ b/Source/Spray/SpraySB.cpp @@ -103,7 +103,7 @@ SprayParticleContainer::CreateSBDroplets( } else if (new_parts == 3) { utBeta = uBeta_pi; } - AMREX_D_PICK(,,Real utPsi = uPsi_coeff * std::sin(psi);) + AMREX_D_PICK(, , Real utPsi = uPsi_coeff * std::sin(psi);) for (int dir = 0; dir < AMREX_SPACEDIM; ++dir) { Real pvel = AMREX_D_TERM( usNorm * normal[dir], +utBeta * tanBeta[dir], From a09bde01e542e5039058c21c84dff9808f7c283b Mon Sep 17 00:00:00 2001 From: Marc Henry de Frahan Date: Mon, 11 Dec 2023 13:06:34 -0700 Subject: [PATCH 19/21] better format --- Source/Spray/SpraySB.cpp | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/Source/Spray/SpraySB.cpp b/Source/Spray/SpraySB.cpp index c4b5b1f24..8db55ea17 100644 --- a/Source/Spray/SpraySB.cpp +++ b/Source/Spray/SpraySB.cpp @@ -90,7 +90,6 @@ SprayParticleContainer::CreateSBDroplets( get_ms_theta(alpha, ms, del_film, ms_thetas); // Note: Must be -pi/2 < psi < pi, not 0 < psi < pi for symmetry for (int new_parts = 0; new_parts < Nsint; ++new_parts) { - Real psi = 0.5 * M_PI * (static_cast(new_parts) - 1.); ParticleType p; p.id() = ParticleType::NextID(); p.cpu() = ParallelDescriptor::MyProc(); @@ -103,7 +102,9 @@ SprayParticleContainer::CreateSBDroplets( } else if (new_parts == 3) { utBeta = uBeta_pi; } - AMREX_D_PICK(, , Real utPsi = uPsi_coeff * std::sin(psi);) + AMREX_D_PICK( + , , Real psi = 0.5 * M_PI * (static_cast(new_parts) - 1.); + Real utPsi = uPsi_coeff * std::sin(psi);) for (int dir = 0; dir < AMREX_SPACEDIM; ++dir) { Real pvel = AMREX_D_TERM( usNorm * normal[dir], +utBeta * tanBeta[dir], From 7593f845fd6cb7860e2280f39d0c9a39ce737a53 Mon Sep 17 00:00:00 2001 From: Marc Henry de Frahan Date: Tue, 12 Dec 2023 08:23:24 -0700 Subject: [PATCH 20/21] fix ceptr format --- Support/ceptr/ceptr/qssa.py | 6 ++--- Support/ceptr/ceptr/symbolic_math.py | 38 +++++++++++----------------- Support/ceptr/ceptr/utilities.py | 24 +++++++++--------- 3 files changed, 30 insertions(+), 38 deletions(-) diff --git a/Support/ceptr/ceptr/qssa.py b/Support/ceptr/ceptr/qssa.py index b1d821187..fdd0febc1 100644 --- a/Support/ceptr/ceptr/qssa.py +++ b/Support/ceptr/ceptr/qssa.py @@ -72,9 +72,9 @@ def process_qss(fname, nqssa, visualize, method): raise ValueError("Failure to generate QSSA mechanism.") qssa.update_user_header({"description": f"QSSA of {mechanism.name}"}) - qssa.update_user_data({ - "qssa_species": qssa_species, "n_qssa_species": len(qssa_species) - }) + qssa.update_user_data( + {"qssa_species": qssa_species, "n_qssa_species": len(qssa_species)} + ) forward_to_remove_idx = [] if forward_to_remove: for fr in forward_to_remove: diff --git a/Support/ceptr/ceptr/symbolic_math.py b/Support/ceptr/ceptr/symbolic_math.py index 740f12151..9c6d768b0 100644 --- a/Support/ceptr/ceptr/symbolic_math.py +++ b/Support/ceptr/ceptr/symbolic_math.py @@ -196,30 +196,22 @@ def convert_to_cpp(self, sym_smp): if self.remove_pow: # Positive exponents - user_functions["Pow"].append( - ( - lambda b, e: (e.is_Integer or e.is_Float) - and ( - abs(e - 1) < 1e-16 or abs(e - 2) < 1e-16 or abs(e - 3) < 1e-16 - ), - lambda b, e: "(" + "*".join(["(" + b + ")"] * int(float(e))) + ")", - ) - ) + user_functions["Pow"].append(( + lambda b, e: (e.is_Integer or e.is_Float) + and (abs(e - 1) < 1e-16 or abs(e - 2) < 1e-16 or abs(e - 3) < 1e-16), + lambda b, e: "(" + "*".join(["(" + b + ")"] * int(float(e))) + ")", + )) # Negative exponents - user_functions["Pow"].append( - ( - lambda b, e: (e.is_Integer or e.is_Float) - and ( - abs(e + 1) < 1e-16 or abs(e + 2) < 1e-16 or abs(e + 3) < 1e-16 - ), - lambda b, e: "(" - + "1.0/" - + "(" - + "*".join(["(" + b + ")"] * int(-float(e))) - + ")" - + ")", - ) - ) + user_functions["Pow"].append(( + lambda b, e: (e.is_Integer or e.is_Float) + and (abs(e + 1) < 1e-16 or abs(e + 2) < 1e-16 or abs(e + 3) < 1e-16), + lambda b, e: "(" + + "1.0/" + + "(" + + "*".join(["(" + b + ")"] * int(-float(e))) + + ")" + + ")", + )) if self.remove_pow10: user_functions["Pow"].append( diff --git a/Support/ceptr/ceptr/utilities.py b/Support/ceptr/ceptr/utilities.py index 829c93dd7..555dfab75 100644 --- a/Support/ceptr/ceptr/utilities.py +++ b/Support/ceptr/ceptr/utilities.py @@ -215,9 +215,9 @@ def fkc_conv_inv(self, mechanism, reaction, syms=None): if record_symbolic_operations: conversion_smp *= syms.refCinv_smp * syms.refCinv_smp else: - conversion = "*".join([ - f"pow(std::max(refCinv, {sc_cutoff(dim)}), {dim:f})" - ]) + conversion = "*".join( + [f"pow(std::max(refCinv, {sc_cutoff(dim)}), {dim:f})"] + ) if record_symbolic_operations: conversion_smp *= syms.refCinv_smp**dim else: @@ -229,9 +229,9 @@ def fkc_conv_inv(self, mechanism, reaction, syms=None): if dim.is_integer(): conversion = "*".join(["refC"] * int(dim)) else: - conversion = "*".join([ - f"pow(std::max(refC, {sc_cutoff(abs(dim))}), {abs(dim):f})" - ]) + conversion = "*".join( + [f"pow(std::max(refC, {sc_cutoff(abs(dim))}), {abs(dim):f})"] + ) if record_symbolic_operations: conversion_smp *= syms.refC_smp**dim @@ -263,9 +263,9 @@ def kc_conv(mechanism, reaction): if dim.is_integer(): conversion = "*".join(["refC"] * int(dim)) else: - conversion = "*".join([ - f"pow(std::max(refC, {sc_cutoff(dim)}),{dim:f})" - ]) + conversion = "*".join( + [f"pow(std::max(refC, {sc_cutoff(dim)}),{dim:f})"] + ) else: if dim == -1.0: conversion = "*".join(["refCinv"]) @@ -273,9 +273,9 @@ def kc_conv(mechanism, reaction): if dim.is_integer(): conversion = "*".join(["refCinv"] * int(dim)) else: - conversion = "*".join([ - f"pow(std::max(refCinv, {sc_cutoff(abs(dim))}),{abs(dim):f})" - ]) + conversion = "*".join( + [f"pow(std::max(refCinv, {sc_cutoff(abs(dim))}),{abs(dim):f})"] + ) return conversion From af0ed5433e4d922b1a86e09c5fc36c3e68f2c8f1 Mon Sep 17 00:00:00 2001 From: Bruce Perry Date: Tue, 12 Dec 2023 09:18:06 -0700 Subject: [PATCH 21/21] fix bug in spray injection --- Source/Spray/SprayInjection.H | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/Source/Spray/SprayInjection.H b/Source/Spray/SprayInjection.H index 585e4cf54..aeb2cb6dd 100644 --- a/Source/Spray/SprayInjection.H +++ b/Source/Spray/SprayInjection.H @@ -201,7 +201,7 @@ SprayParticleContainer::uniformSprayInit( const amrex::RealVect vel_part, const amrex::Real dia_part, const amrex::Real T_part, - const amrex::Real* /*Y_part*/, + const amrex::Real* Y_part, const int level, const int num_redist, const amrex::Real num_ppp) @@ -226,6 +226,9 @@ SprayParticleContainer::uniformSprayInit( } part_vals[SprayComps::pstateT] = T_part; part_vals[SprayComps::pstateDia] = dia_part; + for (int spf = 0; spf < SPRAY_FUEL_NUM; ++spf) { + part_vals[SprayComps::pstateY + spf] = Y_part[spf]; + } const SprayData* fdat = m_sprayData; amrex::Real initial_bm2 = 0.; if (fdat->do_breakup == 2) {