deepmodeling · OpenFOAMFans · Sep 26, 2022 · Jun 14, 2022 · Jun 15, 2022 · Jun 15, 2022
diff --git a/.gitattributes b/.gitattributes
@@ -0,0 +1,2 @@
+*.H linguist-language=C++
+*.C linguist-language=C++
diff --git a/.github/workflows/build_test.yml b/.github/workflows/build_test.yml
@@ -0,0 +1,67 @@
+name: building test for each PR
+on: 
+  push:
+  pull_request:
+
+jobs:
+  build_test:
+    runs-on: ubuntu-latest      
+    container: 
+      image: ubuntu:20.04
+    steps:
+     - name: Checkout
+       uses: actions/checkout@v3
+     - name: initialize
+       env:
+        DEBIAN_FRONTEND: noninteractive
+       run: |
+        apt install -y --no-install-recommends 
+        apt-get update 
+        apt-get install -y sudo
+        apt-get install -y wget
+        apt-get install -y unzip
+        apt-get install -y git
+        apt-get install -y software-properties-common
+
+
+     - name: openfoam7
+       env:
+        DEBIAN_FRONTEND: noninteractive
+       run: |
+        sudo sh -c "wget -O - https://dl.openfoam.org/gpg.key | apt-key add -" 
+        sudo add-apt-repository http://dl.openfoam.org/ubuntu
+        sudo apt-get update
+        export DEBIAN_FRONTEND=noninteractive 
+        apt-get -y install openfoam7  
+
+
+
+     - name: libtorch
+       run: |
+        wget https://download.pytorch.org/libtorch/cpu/libtorch-cxx11-abi-shared-with-deps-1.11.0%2Bcpu.zip
+        unzip libtorch-cxx11-abi-shared-with-deps-1.11.0+cpu.zip -d thirdParty 
+        rm libtorch-cxx11-abi-shared-with-deps-1.11.0+cpu.zip 
+
+
+     - name: clone
+       run: |
+        git clone https://github.com/deepmodeling/deepflame-dev.git
+        cd deepflame-dev
+
+
+
+
+     - name: cantera and build
+       run:  
+        /bin/bash -c "wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh && sh Miniconda3-latest-Linux-x86_64.sh -b && source ~/miniconda3/etc/profile.d/conda.sh && conda create -n libcantera && conda activate libcantera && conda install -c cantera libcantera-devel && source /opt/openfoam7/etc/bashrc &&  . install.sh "
+
+
+
+
+
+
+
+
+
+
+
diff --git a/.gitignore b/.gitignore
@@ -64,3 +64,4 @@ libtorch/
 polyMesh/
 thirdParty
 libtorch*.zip*
+.DS_Store
diff --git a/Allwmake b/Allwmake
@@ -6,13 +6,17 @@ cd ${0%/*} || exit 1    # Run from this directory
 
 wmake src/thermophysicalModels/thermophysicalProperties
 wmake src/thermophysicalModels/basic
+wmake src/functionObjects/field
 wmake src/CanteraMixture
 wmake src/thermophysicalModels/SLGThermo
 wmake src/dfChemistryModel
 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
 
 wmake applications/solvers/df0DFoam
 wmake applications/solvers/dfLowMachFoam

diff --git a/README.md b/README.md
@@ -1,19 +1,33 @@
-# DeepFlame v0.1.0
-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
-- Native Cantera reader for chemical mechanisms in `.cti`, `.xml` or `.ymal` formats
+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
+- Add functionObjects/field library
+- New example reactiveShockTube for dfHighSpeedFoam
+
+New in v0.2.0:
+- Dynamic load balancing for chemistry solver
+
+From v0.1.0:
+- Native Cantera reader for chemical mechanisms in `.cti`, `.xml` or `.yaml` formats
 - Full compatiblity with Cantera's `UnityLewis`, `Mix` and `Multi` transport models
 - Zero-dimensional constant pressure or constant volume reactor solver `df0DFoam`
 - Pressued-based low-Mach number reacting flow solver `dfLowMachFoam`
 - Density-based high-speed reacting flow solver `dfHighSpeedFoam`
 - 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
@@ -23,59 +37,74 @@ DeepFlame is a computational fluid dynamics suite for single or multiphase, lami
   - 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)
-2. Source your OpenFOAM via the default path below (or your own path for OpenFOAM bashrc)
+### 1. Install [OpenFOAM-7](https://openfoam.org/version/7) (if not already installed)
+
+  Quick install (for Ubuntu no later than 20.04):
 ```
-source $HOME/OpenFOAM/OpenFOAM-7/etc/bashrc 
+sudo sh -c "wget -O - https://dl.openfoam.org/gpg.key | apt-key add -"
+sudo add-apt-repository http://dl.openfoam.org/ubuntu
+sudo apt-get update
+sudo apt-get -y install openfoam7
 ```
-3. Install precompiled [LibCantera](https://anaconda.org/conda-forge/libcantera-devel) via [conda](https://docs.conda.io/en/latest/miniconda.html#linux-installers)
+  OpenFOAM 7 and ParaView 5.6.0 will be installed in the /opt directory.
+
+### 2. Source your OpenFOAM via the default path below (or your own path for OpenFOAM 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)
 ```
 conda create -n libcantera
 
 conda activate libcantera
 
-conda install -c conda-forge libcantera-devel
+conda install -c cantera libcantera-devel
 ```
-4. Clone the [DeepFlame repository](https://github.com/deepmodeling/deepflame-dev)
+Note: Check your Miniconda3/envs/libcantera directory and make sure the install was successful (lib/ include/ etc. exist).
+
+### 4. Clone the [DeepFlame repository](https://github.com/deepmodeling/deepflame-dev)
 ```
 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
 
 unzip libtorch-cxx11-abi-shared-with-deps-1.11.0+cpu.zip -d thirdParty
 ```
-6. Install DeepFlame
+### 6. Install DeepFlame
 ```
 . install.sh
 ```
-Some compiling issues may happen due to system compatability. Instead of using conda installed Cantera C++ lib and the downloaded Torch C++ lib, try to compile your own Cantera and Torch C++ libraries.
+Note: Some compiling issues may happen due to system compatability. Instead of using conda installed Cantera C++ lib and the downloaded Torch C++ lib, try to compile your own Cantera and Torch C++ libraries.
 
 ## 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):
 ```
 source $HOME/deepflame-dev/bashrc
 ```
 3. Go to an example case directory, for example:
 ```
-cd $HOME/deepflame-dev/examples/zeroD_cubicReactor/H2/cvodeSolver
+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.
+
+## Useful resources
+- First release v0.1.0 introduction talk (in Chinese) on [DeepModeling Community's official bilibili website](https://www.bilibili.com/video/BV1Vf4y1f7wB?vd_source=309a67109ca33c4ef79bf506f8ce70ab).
diff --git a/applications/solvers/df0DFoam/EEqn.H b/applications/solvers/df0DFoam/EEqn.H
@@ -1,5 +1,5 @@
 {
     volScalarField& he = thermo.he();
     if (constProp == "volume") he[0] = u0 + p[0]/rho[0];
-    chemistry->correctThermo();
+    chemistry.correctThermo();
 }
diff --git a/applications/solvers/df0DFoam/Make/options b/applications/solvers/df0DFoam/Make/options
@@ -10,7 +10,6 @@ EXE_INC = -std=c++14 \
     -I$(LIB_SRC)/dynamicFvMesh/lnInclude \
     -I$(DF_SRC)/CanteraMixture/lnInclude \
     -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
@@ -28,7 +27,6 @@ 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/df0DFoam/YEqn.H b/applications/solvers/df0DFoam/YEqn.H
@@ -10,8 +10,7 @@ tmp<fv::convectionScheme<scalar>> mvConvection
 );
 
 {
-    //chemistry.solve(mesh.time().deltaTValue());
-    combustion->correct();
+    chemistry.solve(mesh.time().deltaTValue());
 
     volScalarField Yt(0.0*Y[0]);
 
@@ -25,8 +24,7 @@ tmp<fv::convectionScheme<scalar>> mvConvection
             (
                 fvm::ddt(rho, Yi)
              ==
-                //chemistry.RR(i)
-                combustion->R(Yi)
+                chemistry.RR(i)
               //+ fvOptions(rho, Yi)
             );
 
@@ -45,4 +43,4 @@ tmp<fv::convectionScheme<scalar>> mvConvection
 
     Y[inertIndex] = scalar(1) - Yt;
     Y[inertIndex].max(0.0);
-}
+}
diff --git a/applications/solvers/df0DFoam/createFields.H b/applications/solvers/df0DFoam/createFields.H
@@ -87,16 +87,12 @@ multivariateSurfaceInterpolationScheme<scalar>::fieldTable fields;
 #include "createMRF.H"
 //#include "createFvOptions.H"
 
-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]);
+
+
+dfChemistryModel<basicThermo> chemistry(thermo);
+PtrList<volScalarField>& Y = chemistry.Y();
+const word inertSpecie(chemistry.lookup("inertSpecie"));
+const label inertIndex(chemistry.species()[inertSpecie]);
 
 forAll(Y, i)
 {
@@ -120,4 +116,4 @@ if
 }
 
 volScalarField& he = thermo.he();
-scalar u0 = he[0] - p[0]/rho[0];
+scalar u0 = he[0] - p[0]/rho[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"
@@ -46,8 +39,6 @@ Description
 //#include "fvOptions.H"
 #include "localEulerDdtScheme.H"
 #include "fvcSmooth.H"
-#include "basicThermo.H"
-#include "CombustionModel.H"
 
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
 
@@ -108,4 +99,4 @@ int main(int argc, char *argv[])
 }
 
 
-// ************************************************************************* //
+// ************************************************************************* //
diff --git a/applications/solvers/dfHighSpeedFoam/Make/options b/applications/solvers/dfHighSpeedFoam/Make/options
@@ -1,4 +1,7 @@
+-include $(GENERAL_RULES)/mplibType
+
 EXE_INC = -std=c++14 \
+    $(PFLAGS) $(PINC) \
     -I$(FOAM_APP)/solvers/compressible/rhoCentralFoam/BCs/lnInclude \
     -I$(LIB_SRC)/finiteVolume/cfdTools \
     -I$(LIB_SRC)/finiteVolume/lnInclude \
@@ -8,6 +11,7 @@ EXE_INC = -std=c++14 \
     -I$(LIB_SRC)/TurbulenceModels/compressible/lnInclude \
     -I$(LIB_SRC)/sampling/lnInclude \
     -I$(LIB_SRC)/dynamicFvMesh/lnInclude \
+    -I$(LIB_SRC)/Pstream/mpi \
     -I$(LIB_SRC)/meshTools/lnInclude \
     -I$(DF_SRC)/CanteraMixture/lnInclude \
     -I$(DF_SRC)/dfChemistryModel/lnInclude \
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1,2 @@
		*.H linguist-language=C++
		*.C linguist-language=C++