From e4545b8be90cf42862fd0c118b11b23d5052f1b9 Mon Sep 17 00:00:00 2001
From: tlichtenegger <thomas.lichtenegger@jku.at>
Date: Mon, 4 Sep 2017 15:16:20 +0200
Subject: [PATCH 1/3] More info for debugging YEqn.

---
 applications/solvers/cfdemSolverRhoPimpleChem/debugYEqn.H | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/applications/solvers/cfdemSolverRhoPimpleChem/debugYEqn.H b/applications/solvers/cfdemSolverRhoPimpleChem/debugYEqn.H
index ea2c268c..2a475fd7 100644
--- a/applications/solvers/cfdemSolverRhoPimpleChem/debugYEqn.H
+++ b/applications/solvers/cfdemSolverRhoPimpleChem/debugYEqn.H
@@ -18,10 +18,10 @@
                     artMass[cellI] *=0.0;
                 }
             }
-            Info << "\nartificial mass of " << Y[i].name() << " per time step: "<< fvc::domainIntegrate(artMass) << endl;
+            Info << "\nartificial mass of species " << Y[i].name() << " per time step: "<< fvc::domainIntegrate(artMass) << endl;
             if(lVCell > -1)
             {
-                Info << "lowest value of " << lowestValue << " at cell " << lVCell << "with coordinates" << endl;
-                Info << "\t" << mesh.C()[lVCell].component(0) << "\t" << mesh.C()[lVCell].component(1)  << "\t" << mesh.C()[lVCell].component(2) << endl;
+                Pout << "lowest value of " << lowestValue << " at cell " << lVCell << " with coordinates" << endl;
+                Pout << "\t" << mesh.C()[lVCell].component(0) << "\t" << mesh.C()[lVCell].component(1)  << "\t" << mesh.C()[lVCell].component(2) << endl;
             }
 }

From be5b056d708d659e84463d629956cb60931b14fe Mon Sep 17 00:00:00 2001
From: tlichtenegger <thomas.lichtenegger@jku.at>
Date: Tue, 31 Oct 2017 13:32:42 +0100
Subject: [PATCH 2/3] Added functionality to communicate available gas volume
 per particle.

---
 .../solvers/cfdemSolverRhoPimpleChem/YEqn.H   |   2 +-
 src/lagrangian/cfdemParticle/Make/files       |   1 +
 .../reactantPerParticle/reactantPerParticle.C | 162 ++++++++++++++++++
 .../reactantPerParticle/reactantPerParticle.H | 105 ++++++++++++
 src/lagrangian/cfdemParticleComp/Make/files   |   1 +
 5 files changed, 270 insertions(+), 1 deletion(-)
 create mode 100644 src/lagrangian/cfdemParticle/subModels/chemistryModel/reactantPerParticle/reactantPerParticle.C
 create mode 100644 src/lagrangian/cfdemParticle/subModels/chemistryModel/reactantPerParticle/reactantPerParticle.H

diff --git a/applications/solvers/cfdemSolverRhoPimpleChem/YEqn.H b/applications/solvers/cfdemSolverRhoPimpleChem/YEqn.H
index e892eb48..b8af296d 100644
--- a/applications/solvers/cfdemSolverRhoPimpleChem/YEqn.H
+++ b/applications/solvers/cfdemSolverRhoPimpleChem/YEqn.H
@@ -42,7 +42,7 @@ tmp<fv::convectionScheme<scalar> > mvConvection
 
             fvOptions.correct(Yi);
 
-            // #include "debugYEqn.H"
+             #include "debugYEqn.H"
 
             Yi.max(0.0);
             Yt += Yi;
diff --git a/src/lagrangian/cfdemParticle/Make/files b/src/lagrangian/cfdemParticle/Make/files
index 48f76d0d..afe6512c 100644
--- a/src/lagrangian/cfdemParticle/Make/files
+++ b/src/lagrangian/cfdemParticle/Make/files
@@ -35,6 +35,7 @@ $(chemistryModels)/species/species.C
 $(chemistryModels)/noChemistry/noChemistry.C
 $(chemistryModels)/diffusionCoefficients/diffusionCoefficients.C
 $(chemistryModels)/massTransferCoeff/massTransferCoeff.C
+$(chemistryModels)/reactantPerParticle/reactantPerParticle.C
 
 $(energyModels)/energyModel/energyModel.C
 $(energyModels)/energyModel/newEnergyModel.C
diff --git a/src/lagrangian/cfdemParticle/subModels/chemistryModel/reactantPerParticle/reactantPerParticle.C b/src/lagrangian/cfdemParticle/subModels/chemistryModel/reactantPerParticle/reactantPerParticle.C
new file mode 100644
index 00000000..57a58f44
--- /dev/null
+++ b/src/lagrangian/cfdemParticle/subModels/chemistryModel/reactantPerParticle/reactantPerParticle.C
@@ -0,0 +1,162 @@
+/*---------------------------------------------------------------------------*\
+License
+
+    This 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.
+
+    This code 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 this code.  If not, see <http://www.gnu.org/licenses/>.
+
+    Copyright (C) 2015- Thomas Lichtenegger, JKU Linz, Austria
+                        M.Efe Kinaci, JKU Linz, Austria
+
+\*---------------------------------------------------------------------------*/
+
+#include "error.H"
+#include "reactantPerParticle.H"
+#include "addToRunTimeSelectionTable.H"
+
+#include "dataExchangeModel.H"
+#include "IFstream.H"
+
+
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+namespace Foam
+{
+
+// * * * * * * * * * * * * * * Static Data Members * * * * * * * * * * * * * //
+
+defineTypeNameAndDebug(reactantPerParticle, 0);
+
+addToRunTimeSelectionTable
+(
+        chemistryModel,
+        reactantPerParticle,
+        dictionary
+);
+
+// * * * * * * * * * * * * * * * * Constructors  * * * * * * * * * * * * * * //
+
+// Construct from components
+reactantPerParticle::reactantPerParticle
+(
+    const dictionary& dict,
+    cfdemCloudEnergy& sm
+)
+:
+    chemistryModel(dict,sm),
+    propsDict_(dict.subDict(typeName + "Props")),
+    mesh_(sm.mesh()),
+    reactantPerParticle_(NULL),
+    voidfractionFieldName_(propsDict_.lookupOrDefault<word>("voidfractionFieldName","voidfraction")),
+    voidfraction_(sm.mesh().lookupObject<volScalarField>(voidfractionFieldName_)),
+    particlesPerCell_
+    (   IOobject
+        (
+            "particlesPerCell",
+            sm.mesh().time().timeName(),
+            sm.mesh(),
+            IOobject::NO_READ,
+            IOobject::NO_WRITE
+        ),
+        sm.mesh(),
+        dimensionedScalar("zero", dimensionSet(0,0,0,0,0), 0)
+    ),
+    loopCounter_(-1),
+    Nevery_(propsDict_.lookupOrDefault<label>("Nevery",1))
+{
+    particleCloud_.checkCG(false);
+    allocateMyArrays();
+}
+
+// * * * * * * * * * * * * * * * * Destructor  * * * * * * * * * * * * * * * //
+
+reactantPerParticle::~reactantPerParticle()
+{
+    particleCloud_.dataExchangeM().destroy(reactantPerParticle_,1);
+}
+
+// * * * * * * * * * * * * * * * private Member Functions  * * * * * * * * * * * * * //
+void reactantPerParticle::allocateMyArrays() const
+{
+    double initVal=0.0;
+    if (particleCloud_.dataExchangeM().maxNumberOfParticles() > 0)
+    {
+        // get memory for 2d arrays
+        particleCloud_.dataExchangeM().allocateArray(reactantPerParticle_,initVal,1,"nparticles");
+    }
+}
+
+void reactantPerParticle::reAllocMyArrays() const
+{
+    if (particleCloud_.numberOfParticlesChanged())
+    {
+        double initVal=0.0;
+        particleCloud_.dataExchangeM().allocateArray(reactantPerParticle_,initVal,1);
+    }
+}
+
+// * * * * * * * * * * * * * * * * Member Fct  * * * * * * * * * * * * * * * //
+
+void reactantPerParticle::execute()
+{
+   
+    
+    loopCounter_++;
+    if (loopCounter_ % Nevery_ != 0)
+    {
+        return;
+    }
+    // realloc the arrays
+    reAllocMyArrays();
+
+    particlesPerCell_ *= 0.0;
+
+    label  cellI=0; 
+    scalar voidfraction(1);
+    scalar cellvolume(0.0);
+    scalar particlesPerCell(1.0);
+
+    // first create particles per cell field
+    for (int index=0; index<particleCloud_.numberOfParticles(); ++index)
+    {
+        cellI=particleCloud_.cellIDs()[index][0];
+        if (cellI >= 0)
+        {
+            particlesPerCell_[cellI] += 1.0;
+	}
+    }
+
+    // no fill array and communicate it
+    for (int index=0; index<particleCloud_.numberOfParticles(); ++index)
+    {
+        cellI=particleCloud_.cellIDs()[index][0];
+        if (cellI >= 0)
+        {
+            voidfraction    =   voidfraction_[cellI];
+            cellvolume      =   mesh_.V()[cellI];
+            particlesPerCell=   particlesPerCell_[cellI];
+            reactantPerParticle_[index][0] = voidfraction * cellvolume / particlesPerCell;
+        }
+    }
+
+        // give DEM data
+        particleCloud_.dataExchangeM().giveData("reactantPerParticle", "scalar-atom", reactantPerParticle_);
+       
+        Info << "give data done" << endl;
+}
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+} // End namespace Foam
+
+// ************************************************************************* //
diff --git a/src/lagrangian/cfdemParticle/subModels/chemistryModel/reactantPerParticle/reactantPerParticle.H b/src/lagrangian/cfdemParticle/subModels/chemistryModel/reactantPerParticle/reactantPerParticle.H
new file mode 100644
index 00000000..739ca5f6
--- /dev/null
+++ b/src/lagrangian/cfdemParticle/subModels/chemistryModel/reactantPerParticle/reactantPerParticle.H
@@ -0,0 +1,105 @@
+/*---------------------------------------------------------------------------*\
+License
+
+    This 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.
+
+    This code 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 this code.  If not, see <http://www.gnu.org/licenses/>.
+
+    Copyright (C) 2015- Thomas Lichtenegger, JKU Linz, Austria
+    
+    Description
+    Model to communicate available reactant per particle
+
+\*---------------------------------------------------------------------------*/
+
+#ifndef reactantPerParticle_H
+#define reactantPerParticle_H
+
+#include "fvCFD.H"
+#include "cfdemCloudEnergy.H"
+#include "chemistryModel.H"
+#include "diffusionCoefficients.H"
+
+#include "HashPtrTable.H"
+
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+namespace Foam
+{
+
+/*---------------------------------------------------------------------------*\
+                           Class reactantPerParticle Declaration
+\*---------------------------------------------------------------------------*/
+
+// for future use:
+// + communicate every N steps
+
+class reactantPerParticle
+:
+    public chemistryModel
+{
+private:
+
+    dictionary propsDict_;
+
+    const fvMesh& mesh_;
+
+    mutable double **reactantPerParticle_;
+    
+    word voidfractionFieldName_;
+
+    const volScalarField& voidfraction_;
+    
+    mutable volScalarField particlesPerCell_;
+
+    void allocateMyArrays() const;
+
+    label loopCounter_;
+    
+    label Nevery_;
+
+public:
+
+    //- Runtime type information
+    TypeName("reactantPerParticle");
+
+    // Constructors
+
+        //- Construct from components
+        reactantPerParticle
+        (
+            const dictionary& dict,
+            cfdemCloudEnergy& sm
+        );
+
+    // Destructor
+
+        virtual ~reactantPerParticle();
+
+    // Member Functions
+        void execute();
+
+        void reAllocMyArrays() const;
+
+};
+
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+} // End namespace Foam
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+#endif
+
+// ************************************************************************* //
diff --git a/src/lagrangian/cfdemParticleComp/Make/files b/src/lagrangian/cfdemParticleComp/Make/files
index 0684be77..230ab83a 100644
--- a/src/lagrangian/cfdemParticleComp/Make/files
+++ b/src/lagrangian/cfdemParticleComp/Make/files
@@ -34,6 +34,7 @@ $(chemistryModels)/species/species.C
 $(chemistryModels)/noChemistry/noChemistry.C
 $(chemistryModels)/diffusionCoefficients/diffusionCoefficients.C
 $(chemistryModels)/massTransferCoeff/massTransferCoeff.C
+$(chemistryModels)/reactantPerParticle/reactantPerParticle.C
 
 $(energyModels)/energyModel/energyModel.C
 $(energyModels)/energyModel/newEnergyModel.C

From 2cad403f20d66d300cdbfd06a1d557d165aa1812 Mon Sep 17 00:00:00 2001
From: tlichtenegger <thomas.lichtenegger@jku.at>
Date: Tue, 31 Oct 2017 13:33:43 +0100
Subject: [PATCH 3/3] Added setScalarSumCentre which always uses
 particle-center-based cells.

---
 .../averagingModel/averagingModel.C           | 25 +++++++++++++++++++
 .../averagingModel/averagingModel.H           |  8 ++++++
 .../chemistryModel/species/species.C          |  2 +-
 3 files changed, 34 insertions(+), 1 deletion(-)

diff --git a/src/lagrangian/cfdemParticle/subModels/averagingModel/averagingModel/averagingModel.C b/src/lagrangian/cfdemParticle/subModels/averagingModel/averagingModel/averagingModel.C
index 1f159643..d9201fcc 100644
--- a/src/lagrangian/cfdemParticle/subModels/averagingModel/averagingModel/averagingModel.C
+++ b/src/lagrangian/cfdemParticle/subModels/averagingModel/averagingModel/averagingModel.C
@@ -229,6 +229,31 @@ void averagingModel::setScalarSum
     field.correctBoundaryConditions();
 }
 
+void averagingModel::setScalarSumCentre
+(
+    volScalarField& field,
+    double**& value,
+    double**const& weight,
+    double**const& mask
+) const
+{
+    label cellI;
+    scalar valueScal;
+
+    for(int index=0; index< particleCloud_.numberOfParticles(); index++)
+    {
+        cellI = particleCloud_.cellIDs()[index][0];
+        if (cellI >= 0)
+        {
+            valueScal = value[index][0];
+            field[cellI] += valueScal;
+        }
+    }
+
+    // correct cell values to patches
+    field.correctBoundaryConditions();
+}
+
 void averagingModel::setDSauter
 (
     volScalarField& dSauter,
diff --git a/src/lagrangian/cfdemParticle/subModels/averagingModel/averagingModel/averagingModel.H b/src/lagrangian/cfdemParticle/subModels/averagingModel/averagingModel/averagingModel.H
index df1e2c58..1f46300e 100644
--- a/src/lagrangian/cfdemParticle/subModels/averagingModel/averagingModel/averagingModel.H
+++ b/src/lagrangian/cfdemParticle/subModels/averagingModel/averagingModel/averagingModel.H
@@ -175,6 +175,14 @@ public:
             double**const& weight,
             double**const& mask
         ) const;
+	
+	void setScalarSumCentre
+        (
+            volScalarField& field,
+            double**& value,
+            double**const& weight,
+            double**const& mask
+        ) const;
 
         void setDSauter
         (
diff --git a/src/lagrangian/cfdemParticle/subModels/chemistryModel/species/species.C b/src/lagrangian/cfdemParticle/subModels/chemistryModel/species/species.C
index 2386ed47..078f9299 100644
--- a/src/lagrangian/cfdemParticle/subModels/chemistryModel/species/species.C
+++ b/src/lagrangian/cfdemParticle/subModels/chemistryModel/species/species.C
@@ -317,7 +317,7 @@ void species::execute()
             particleCloud_.dataExchangeM().getData(mod_spec_names_[i],"scalar-atom",changeOfSpeciesMass_[i]);
             changeOfSpeciesMassFields_[i].primitiveFieldRef() = 0.0;
             changeOfSpeciesMassFields_[i].boundaryFieldRef() = 0.0;
-            particleCloud_.averagingM().setScalarSum
+            particleCloud_.averagingM().setScalarSumCentre
             (
                 changeOfSpeciesMassFields_[i],
                 changeOfSpeciesMass_[i],