deepmodeling · zhixchen · Sep 26, 2022 · Jun 16, 2022 · Jun 16, 2022 · Jun 16, 2022
diff --git a/Allwmake b/Allwmake
@@ -14,6 +14,7 @@ wmake src/TurbulenceModels/compressible
 wmake src/TurbulenceModels/turbulenceModels
 wmake src/regionModels/surfaceFilmModels
 src/lagrangian/Allwmake $targetType $*
+wmake src/dfCombustionModels
 wmake src/dynamicMesh
 wmake src/dynamicFvMesh
 

diff --git a/README.md b/README.md
@@ -1,10 +1,14 @@
-# DeepFlame v0.3.0
-DeepFlame is a computational fluid dynamics suite for single or multiphase, laminar or turbulent reacting flows at all speeds with machine learning capabilities. It aims to provide an open-source platform bringing together the individual strengths of [OpenFOAM](https://openfoam.org), [Cantera](https://cantera.org) and [pyTorch](https://pytorch.org/) libraries for machine learning assisted reacting flow simulations. It is also has the scope to incorporate next-generation heterogenous supercomputing and AI acceleration infrustructures such as GPU and FPGAs.  
+# DeepFlame v0.4.0
+DeepFlame is a computational fluid dynamics suite for single or multiphase, laminar or turbulent reacting flows at all speeds with machine learning capabilities. It aims to provide an open-source platform bringing together the individual strengths of [OpenFOAM](https://openfoam.org), [Cantera](https://cantera.org) and [pyTorch](https://pytorch.org/) libraries for machine learning assisted reacting flow simulations. It is also has the scope to incorporate next-generation heterogenous supercomputing and AI acceleration infrustructures such as GPU and FPGAs.
 
 ## Dependencies
 [OpenFOAM-7](https://openfoam.org/version/7), [Cantera C++ lib 2.6.0](https://anaconda.org/conda-forge/libcantera-devel), [Torch C++ lib 1.11.0](https://pytorch.org/)
 
 ## Features
+New in v0.4.0 (2022/09/26):
+- Adapt combustion library from OpenFOAM into DeepFlame
+- laminar; EDC; PaSR combustion models
+
 New in v0.3.0:
 - 1/2/3D adaptive mesh refinement
 - Add Sigma/dynSmag LES turbulence models
@@ -23,7 +27,7 @@ From v0.1.0:
 - Two-phase Lagrangian/Euler spray reacting flow solver `dfSprayFoam`
 - Cantera's native SUNDIALS CVODE solver for chemical reaction rate evaluation
 - Torch's tensor operation functionality for neutral network I/O and calculation
-- Interface for DNN model to obtain chemical reaction rates 
+- Interface for DNN model to obtain chemical reaction rates
 - Multiple example and tutorial cases with `Allrun` and `Allclean` scripts
   - 0D Perfectly Stirred Reactor
   - 1D Freely Propagating Premixed Flame
@@ -33,11 +37,11 @@ From v0.1.0:
   - 3D Aachen Bomb Spray Flame
 
 ## How to install
-The installation of DeepFlame is simple and requires [OpenFOAM-7](https://openfoam.org/version/7), [LibCantera](https://anaconda.org/conda-forge/libcantera-devel) and [LibTorch](https://pytorch.org/) . 
+The installation of DeepFlame is simple and requires [OpenFOAM-7](https://openfoam.org/version/7), [LibCantera](https://anaconda.org/conda-forge/libcantera-devel) and [LibTorch](https://pytorch.org/) .
 
 ### 1. Install [OpenFOAM-7](https://openfoam.org/version/7) (if not already installed)
-  
-  Quick install (for Ubuntu no later than 20.04): 
+
+  Quick install (for Ubuntu no later than 20.04):
 ```
 sudo sh -c "wget -O - https://dl.openfoam.org/gpg.key | apt-key add -"
 sudo add-apt-repository http://dl.openfoam.org/ubuntu
@@ -48,7 +52,7 @@ sudo apt-get -y install openfoam7
 
 ### 2. Source your OpenFOAM via the default path below (or your own path for OpenFOAM bashrc)
 ```
-source $HOME/OpenFOAM/OpenFOAM-7/etc/bashrc 
+source $HOME/OpenFOAM/OpenFOAM-7/etc/bashrc
 ```
 ### 3. Install [LibCantera](https://anaconda.org/conda-forge/libcantera-devel) via [conda](https://docs.conda.io/en/latest/miniconda.html#linux-installers)
 ```
@@ -66,7 +70,7 @@ git clone https://github.com/deepmodeling/deepflame-dev.git
 
 cd deepflame-dev
 ```
-### 5. Install precompiled [LibTorch](https://pytorch.org/) 
+### 5. Install precompiled [LibTorch](https://pytorch.org/)
 ```
 wget https://download.pytorch.org/libtorch/cpu/libtorch-cxx11-abi-shared-with-deps-1.11.0%2Bcpu.zip
 
@@ -81,7 +85,7 @@ Note: Some compiling issues may happen due to system compatability. Instead of u
 ## Running DeepFlame examples
 1. Source your OpenFOAM, for example (depends on your OpenFOAM path):
 ```
-source $HOME/OpenFOAM/OpenFOAM-7/etc/bashrc 
+source $HOME/OpenFOAM/OpenFOAM-7/etc/bashrc
 ```
 2. Source deepflame-dev/bashrc, for example (depends on your DeepFlame path):
 ```
@@ -94,11 +98,11 @@ cd $HOME/deepflame-dev/examples/df0DFoam/zeroD_cubicReactor/H2/cvodeSolver
 ./Allrun
 ```
 
-Note: For the example cases with torchSolver, an additional DNN model file in the `.pt` format is required. Please contact the developers if you would like a test run. 
+Note: For the example cases with torchSolver, an additional DNN model file in the `.pt` format is required. Please contact the developers if you would like a test run.
 
 
 ## Citing DeepFlame
-If you use DeepFlame for a publication, please use the citation: 
+If you use DeepFlame for a publication, please use the citation:
 
 DeepFlame: A computational fluid dynamics suite for multiphase turbulent reacting flows at all speeds with machine learning. URL:https://github.com/deepmodeling/deepflame-dev, 2022.
 

diff --git a/applications/solvers/df0DFoam/Make/options b/applications/solvers/df0DFoam/Make/options
@@ -9,7 +9,7 @@ EXE_INC = -std=c++14 \
     -I$(LIB_SRC)/sampling/lnInclude \
     -I$(LIB_SRC)/dynamicFvMesh/lnInclude \
     -I$(DF_SRC)/CanteraMixture/lnInclude \
-    -I$(DF_SRC)/dfChemistryModel \
+    -I$(DF_SRC)/dfChemistryModel/lnInclude \
     -I$(CANTERA_ROOT)/include \
     -I$(TORCH_ROOT)/include \
     -I$(TORCH_ROOT)/include/torch/csrc/api/include

diff --git a/applications/solvers/df0DFoam/YEqn.H b/applications/solvers/df0DFoam/YEqn.H
@@ -43,4 +43,4 @@ tmp<fv::convectionScheme<scalar>> mvConvection
 
     Y[inertIndex] = scalar(1) - Yt;
     Y[inertIndex].max(0.0);
-}
+}
diff --git a/applications/solvers/df0DFoam/df0DFoam.C b/applications/solvers/df0DFoam/df0DFoam.C
@@ -7,30 +7,23 @@
 -------------------------------------------------------------------------------
 License
     This file is part of OpenFOAM.
-
     OpenFOAM is free software: you can redistribute it and/or modify it
     under the terms of the GNU General Public License as published by
     the Free Software Foundation, either version 3 of the License, or
     (at your option) any later version.
-
     OpenFOAM is distributed in the hope that it will be useful, but WITHOUT
     ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
     FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License
     for more details.
-
     You should have received a copy of the GNU General Public License
     along with OpenFOAM.  If not, see <http://www.gnu.org/licenses/>.
-
 Application
     rhoPimpleFoam
-
 Description
     Transient solver for turbulent flow of compressible fluids for HVAC and
     similar applications, with optional mesh motion and mesh topology changes.
-
     Uses the flexible PIMPLE (PISO-SIMPLE) solution for time-resolved and
     pseudo-transient simulations.
-
 \*---------------------------------------------------------------------------*/
 #include "dfChemistryModel.H"
 #include "CanteraMixture.H"
@@ -106,4 +99,4 @@ int main(int argc, char *argv[])
 }
 
 
-// ************************************************************************* //
+// ************************************************************************* //
diff --git a/applications/solvers/dfHighSpeedFoam/Make/options b/applications/solvers/dfHighSpeedFoam/Make/options
@@ -14,7 +14,7 @@ EXE_INC = -std=c++14 \
     -I$(LIB_SRC)/Pstream/mpi \
     -I$(LIB_SRC)/meshTools/lnInclude \
     -I$(DF_SRC)/CanteraMixture/lnInclude \
-    -I$(DF_SRC)/dfChemistryModel \
+    -I$(DF_SRC)/dfChemistryModel/lnInclude \
     -I$(CANTERA_ROOT)/include \
     -I$(TORCH_ROOT)/include \
     -I$(TORCH_ROOT)/include/torch/csrc/api/include

diff --git a/applications/solvers/dfLowMachFoam/Make/options b/applications/solvers/dfLowMachFoam/Make/options
@@ -13,7 +13,8 @@ EXE_INC = -std=c++14 \
     -I$(LIB_SRC)/dynamicFvMesh/lnInclude \
     -I$(LIB_SRC)/Pstream/mpi \
     -I$(DF_SRC)/CanteraMixture/lnInclude \
-    -I$(DF_SRC)/dfChemistryModel \
+    -I$(DF_SRC)/dfChemistryModel/lnInclude \
+    -I$(DF_SRC)/dfCombustionModels/lnInclude \
     -I$(CANTERA_ROOT)/include \
     -I$(TORCH_ROOT)/include \
     -I$(TORCH_ROOT)/include/torch/csrc/api/include
@@ -29,6 +30,7 @@ EXE_LIBS = \
     -ldfCompressibleTurbulenceModels \
     -lCanteraMixture \
     -ldfChemistryModel \
+    -ldfCombustionModels  \
     $(CANTERA_ROOT)/lib/libcantera.so \
     $(TORCH_ROOT)/lib/libtorch.so \
     $(TORCH_ROOT)/lib/libc10.so \

diff --git a/applications/solvers/dfLowMachFoam/YEqn.H b/applications/solvers/dfLowMachFoam/YEqn.H
@@ -15,13 +15,13 @@ tmp<fv::convectionScheme<scalar>> mvConvection
 
 forAll(Y, i)
 {
-    sumYDiffError += chemistry.rhoD(i)*fvc::grad(Y[i]);
+    sumYDiffError += chemistry->rhoD(i)*fvc::grad(Y[i]);
 }
 const surfaceScalarField phiUc = linearInterpolate(sumYDiffError) & mesh.Sf();
 
 {
     start = std::clock();
-    chemistry.solve(mesh.time().deltaTValue());
+    combustion->correct();
     label flag_mpi_init;
     MPI_Initialized(&flag_mpi_init);
     if(flag_mpi_init) MPI_Barrier(PstreamGlobals::MPI_COMM_FOAM);
@@ -34,20 +34,20 @@ const surfaceScalarField phiUc = linearInterpolate(sumYDiffError) & mesh.Sf();
     forAll(Y, i)
     {
         volScalarField& Yi = Y[i];
-        hDiffCorrFlux += chemistry.hai(i)*(chemistry.rhoD(i)*fvc::grad(Yi) - Yi*sumYDiffError);
-        diffAlphaD += fvc::laplacian(thermo.alpha()*chemistry.hai(i), Yi);
+        hDiffCorrFlux += chemistry->hai(i)*(chemistry->rhoD(i)*fvc::grad(Yi) - Yi*sumYDiffError);
+        diffAlphaD += fvc::laplacian(thermo.alpha()*chemistry->hai(i), Yi);
 
         if (i != inertIndex)
         {
-            tmp<volScalarField> DEff = chemistry.rhoD(i) + turbulence->mut()/Sct;
+            tmp<volScalarField> DEff = chemistry->rhoD(i) + turbulence->mut()/Sct;
             fvScalarMatrix YiEqn
             (
                 fvm::ddt(rho, Yi)
               + mvConvection->fvmDiv(phi, Yi)
               - fvm::laplacian(DEff(), Yi)
               + mvConvection->fvmDiv(phiUc, Yi)
              ==
-                chemistry.RR(i)
+                combustion->R(Yi)
             );
 
             YiEqn.relax();

diff --git a/applications/solvers/dfLowMachFoam/createFields.H b/applications/solvers/dfLowMachFoam/createFields.H
@@ -22,14 +22,6 @@ volScalarField rho
     thermo.rho()
 );
 
-dfChemistryModel<basicThermo> chemistry(thermo);
-PtrList<volScalarField>& Y = chemistry.Y();
-const word inertSpecie(chemistry.lookup("inertSpecie"));
-const label inertIndex(chemistry.species()[inertSpecie]);
-
-chemistry.correctThermo();
-Info<< "At initial time, min/max(T) = " << min(T).value() << ", " << max(T).value() << endl;
-
 Info<< "Reading field U\n" << endl;
 volVectorField U
 (
@@ -62,6 +54,21 @@ autoPtr<compressible::turbulenceModel> turbulence
     )
 );
 
+Info<< "Creating reaction model\n" << endl;
+autoPtr<CombustionModel<basicThermo>> combustion
+(
+    CombustionModel<basicThermo>::New(thermo, turbulence())
+);
+Info<< "end Creating reaction model\n" << endl;
+dfChemistryModel<basicThermo>* chemistry = combustion->chemistry();
+PtrList<volScalarField>& Y = chemistry->Y();
+const word inertSpecie(chemistry->lookup("inertSpecie"));
+const label inertIndex(chemistry->species()[inertSpecie]);
+
+
+chemistry->correctThermo();
+Info<< "At initial time, min/max(T) = " << min(T).value() << ", " << max(T).value() << endl;
+
 Info<< "Creating field dpdt\n" << endl;
 volScalarField dpdt
 (
@@ -85,7 +92,7 @@ forAll(Y, i)
 }
 fields.add(thermo.he());
 
-const scalar Sct = chemistry.lookupOrDefault("Sct", 1.);
+const scalar Sct = chemistry->lookupOrDefault("Sct", 1.);
 volScalarField diffAlphaD
 (
     IOobject

diff --git a/applications/solvers/dfLowMachFoam/dfLowMachFoam.C b/applications/solvers/dfLowMachFoam/dfLowMachFoam.C
@@ -45,6 +45,8 @@ Description
 #include "localEulerDdtScheme.H"
 #include "fvcSmooth.H"
 #include "PstreamGlobals.H"
+#include "basicThermo.H"
+#include "CombustionModel.H"
 
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
 
@@ -128,7 +130,7 @@ int main(int argc, char *argv[])
             time_monitor_E += double(end - start) / double(CLOCKS_PER_SEC);
 
             start = std::clock();
-            chemistry.correctThermo();
+            chemistry->correctThermo();
             end = std::clock();
             time_monitor_corrThermo += double(end - start) / double(CLOCKS_PER_SEC);
 

diff --git a/applications/solvers/dfSprayFoam/Make/options b/applications/solvers/dfSprayFoam/Make/options
@@ -23,7 +23,8 @@ EXE_INC = -std=c++14 \
     -I$(LIB_SRC)/thermophysicalModels/thermophysicalProperties/lnInclude \
     -I$(DF_SRC)/thermophysicalModels/SLGThermo/lnInclude \
     -I$(DF_SRC)/CanteraMixture/lnInclude \
-    -I$(DF_SRC)/dfChemistryModel \
+    -I$(DF_SRC)/dfChemistryModel/lnInclude \
+    -I$(DF_SRC)/dfCombustionModels/lnInclude \
     -I$(CANTERA_ROOT)/include \
     -I$(TORCH_ROOT)/include \
     -I$(TORCH_ROOT)/include/torch/csrc/api/include
@@ -49,6 +50,7 @@ EXE_LIBS = \
     -ldfLagrangianSpray \
     -lCanteraMixture \
     -ldfChemistryModel \
+    -ldfCombustionModels  \
     $(CANTERA_ROOT)/lib/libcantera.so \
     $(TORCH_ROOT)/lib/libtorch.so \
     $(TORCH_ROOT)/lib/libc10.so \

diff --git a/applications/solvers/dfSprayFoam/YEqn.H b/applications/solvers/dfSprayFoam/YEqn.H
@@ -15,24 +15,23 @@ tmp<fv::convectionScheme<scalar>> mvConvection
 
 forAll(Y, i)
 {
-    sumYDiffError += chemistry.rhoD(i)*fvc::grad(Y[i]);
+    sumYDiffError += chemistry->rhoD(i)*fvc::grad(Y[i]);
 }
 const surfaceScalarField phiUc = linearInterpolate(sumYDiffError) & mesh.Sf();
 
 {
-    //combustion->correct();
-    chemistry.solve(mesh.time().deltaTValue());
+    combustion->correct();
     volScalarField Yt(0.0*Y[0]);
 
     forAll(Y, i)
     {
         volScalarField& Yi = Y[i];
-        hDiffCorrFlux += chemistry.hai(i)*(chemistry.rhoD(i)*fvc::grad(Yi) - Yi*sumYDiffError);
-        diffAlphaD += fvc::laplacian(thermo.alpha()*chemistry.hai(i), Yi);
+        hDiffCorrFlux += chemistry->hai(i)*(chemistry->rhoD(i)*fvc::grad(Yi) - Yi*sumYDiffError);
+        diffAlphaD += fvc::laplacian(thermo.alpha()*chemistry->hai(i), Yi);
 
         if (i != inertIndex)
         {
-            tmp<volScalarField> DEff = chemistry.rhoD(i) + turbulence->mut()/Sct;
+            tmp<volScalarField> DEff = chemistry->rhoD(i) + turbulence->mut()/Sct;
             fvScalarMatrix YEqn
             (
                 fvm::ddt(rho, Yi)
@@ -41,7 +40,7 @@ const surfaceScalarField phiUc = linearInterpolate(sumYDiffError) & mesh.Sf();
               + mvConvection->fvmDiv(phiUc, Yi)
              ==
                 parcels.SYi(i, Yi)
-              + chemistry.RR(i)
+              + combustion->R(Yi)
               //+ fvOptions(rho, Yi)
             );
 

diff --git a/applications/solvers/dfSprayFoam/createFields.H b/applications/solvers/dfSprayFoam/createFields.H
@@ -23,14 +23,6 @@ volScalarField rho
     thermo.rho()
 );
 
-dfChemistryModel<basicThermo> chemistry(thermo);
-PtrList<volScalarField>& Y = chemistry.Y();
-const word inertSpecie(chemistry.lookup("inertSpecie"));
-const label inertIndex(chemistry.species()[inertSpecie]);
-
-chemistry.correctThermo();
-Info<< "At initial time, min/max(T) = " << min(T).value() << ", " << max(T).value() << endl;
-
 Info<< "\nReading field U\n" << endl;
 volVectorField U
 (
@@ -83,6 +75,22 @@ autoPtr<compressible::turbulenceModel> turbulence
     )
 );
 
+Info<< "Creating reaction model\n" << endl;
+autoPtr<CombustionModel<basicThermo>> combustion
+(
+    CombustionModel<basicThermo>::New(thermo, turbulence())
+);
+Info<< "end Creating reaction model\n" << endl;
+dfChemistryModel<basicThermo>* chemistry = combustion->chemistry();
+PtrList<volScalarField>& Y = chemistry->Y();
+const word inertSpecie(chemistry->lookup("inertSpecie"));
+const label inertIndex(chemistry->species()[inertSpecie]);
+
+
+chemistry->correctThermo();
+Info<< "At initial time, min/max(T) = " << min(T).value() << ", " << max(T).value() << endl;
+
+
 Info<< "Creating field dpdt\n" << endl;
 volScalarField dpdt
 (
@@ -113,7 +121,7 @@ fields.add(thermo.he());
 
 // for diffusion velocity correction
 
-const scalar Sct = chemistry.lookupOrDefault("Sct", 1.);
+const scalar Sct = chemistry->lookupOrDefault("Sct", 1.);
 volScalarField diffAlphaD
 (
     IOobject

diff --git a/applications/solvers/dfSprayFoam/dfSprayFoam.C b/applications/solvers/dfSprayFoam/dfSprayFoam.C
@@ -43,6 +43,8 @@ Description
 #include "pimpleControl.H"
 #include "CorrectPhi.H"
 //#include "fvOptions.H"
+#include "basicThermo.H"
+#include "CombustionModel.H"
 
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
 
@@ -134,7 +136,7 @@ int main(int argc, char *argv[])
             #include "UEqn.H"
             #include "YEqn.H"
             #include "EEqn.H"
-            chemistry.correctThermo();
+            chemistry->correctThermo();
             Info<< "T gas min/max   " << min(T).value() << ", "
                 << max(T).value() << endl;
-Original file line number
+Diff line change
@@ Expand Up / @@ -43,4 +43,4 @@ tmp<fv::convectionScheme<scalar>> mvConvection @@
         Y[inertIndex] = scalar(1) - Yt;
         Y[inertIndex].max(0.0);
-    }
+    }