MichaelisMentenReactionRate: Michaelis-Menten reaction rate for enzymatic reactions

Updated chemFoam to support liquid reactions

applications/solvers/combustion/chemFoam/chemFoam.C

@@ -41,6 +41,98 @@ Description
 #include "basicSpecieMixture.H"
 #include "cellModeller.H"
 
+
+template<class ThermoType>
+scalarList W(const rhoReactionThermo& thermo)
+{
+    const PtrList<ThermoType>& specieData =
+        dynamicCast<const reactingMixture<ThermoType>>(thermo)
+       .speciesData();
+
+    scalarList W(specieData.size());
+
+    forAll(specieData, i)
+    {
+        W[i] = specieData[i].W();
+    }
+
+    return W;
+}
+
+
+template<class ThermoType>
+scalar h0
+(
+    const rhoReactionThermo& thermo,
+    const scalarList& Y,
+    const scalar p,
+    const scalar T
+)
+{
+    const PtrList<ThermoType>& specieData =
+        dynamic_cast<const reactingMixture<ThermoType>&>(thermo)
+       .speciesData();
+
+    scalar h0 = 0;
+    forAll(Y, i)
+    {
+        h0 += Y[i]*specieData[i].Hs(p, T);
+    }
+
+    return h0;
+}
+
+
+scalarList W(const rhoReactionThermo& thermo)
+{
+    if (isA<reactingMixture<gasHThermoPhysics>>(thermo))
+    {
+        return W<gasHThermoPhysics>(thermo);
+    }
+    else if (isA<reactingMixture<constFluidHThermoPhysics>>(thermo))
+    {
+        return W<constFluidHThermoPhysics>(thermo);
+    }
+    else
+    {
+        FatalErrorInFunction
+            << "Thermodynamics type " << thermo.type()
+            << " not supported by chemFoam"
+            << exit(FatalError);
+
+        return scalarList::null();
+    }
+}
+
+
+scalar h0
+(
+    const rhoReactionThermo& thermo,
+    const scalarList& Y,
+    const scalar p,
+    const scalar T
+)
+{
+    if (isA<reactingMixture<gasHThermoPhysics>>(thermo))
+    {
+        return h0<gasHThermoPhysics>(thermo, Y, p, T);
+    }
+    else if (isA<reactingMixture<constFluidHThermoPhysics>>(thermo))
+    {
+        return h0<constFluidHThermoPhysics>(thermo, Y, p, T);
+    }
+    else
+    {
+        FatalErrorInFunction
+            << "Thermodynamics type " << thermo.type()
+            << " not supported by chemFoam"
+            << exit(FatalError);
+
+        return 0;
+    }
+}
+
+
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
 
 int main(int argc, char *argv[])

applications/solvers/combustion/chemFoam/pEqn.H

@@ -5,7 +5,7 @@
         scalar invW = 0.0;
         forAll(Y, i)
         {
-            invW += Y[i][0]/specieData[i].W();
+            invW += Y[i][0]/W[i];
         }
 
         Rspecific[0] = 1000.0*constant::physicoChemical::R.value()*invW;

applications/solvers/combustion/chemFoam/readInitialConditions.H

@@ -1,4 +1,4 @@
-    word constProp(initialConditions.lookup("constantProperty"));
+    const word constProp(initialConditions.lookup("constantProperty"));
     if ((constProp != "pressure") && (constProp != "volume"))
     {
         FatalError << "in initialConditions, unknown constantProperty type "
@@ -6,7 +6,7 @@
             << abort(FatalError);
     }
 
-    word fractionBasis(initialConditions.lookup("fractionBasis"));
+    const word fractionBasis(initialConditions.lookup("fractionBasis"));
     if ((fractionBasis != "mass") && (fractionBasis != "mole"))
     {
         FatalError << "in initialConditions, unknown fractionBasis type " << nl
@@ -14,20 +14,8 @@
             << fractionBasis << abort(FatalError);
     }
 
-    label nSpecie = Y.size();
-    PtrList<gasHThermoPhysics> specieData(Y.size());
-    forAll(specieData, i)
-    {
-        specieData.set
-        (
-            i,
-            new gasHThermoPhysics
-            (
-                dynamic_cast<const reactingMixture<gasHThermoPhysics>&>
-                    (thermo).speciesData()[i]
-            )
-        );
-    }
+    const label nSpecie = Y.size();
+    const scalarList W(::W(thermo));
 
     scalarList Y0(nSpecie, 0.0);
     scalarList X0(nSpecie, 0.0);
@@ -49,12 +37,12 @@
         forAll(Y, i)
         {
             X0[i] /= mTot;
-            mw += specieData[i].W()*X0[i];
+            mw += W[i]*X0[i];
         }
 
         forAll(Y, i)
         {
-            Y0[i] = X0[i]*specieData[i].W()/mw;
+            Y0[i] = X0[i]*W[i]/mw;
         }
     }
     else  // mass fraction
@@ -73,21 +61,21 @@
         forAll(Y, i)
         {
             Y0[i] /= mTot;
-            invW += Y0[i]/specieData[i].W();
+            invW += Y0[i]/W[i];
         }
         const scalar mw = 1.0/invW;
 
         forAll(Y, i)
         {
-            X0[i] = Y0[i]*mw/specieData[i].W();
+            X0[i] = Y0[i]*mw/W[i];
         }
     }
 
-    scalar h0 = 0.0;
+    const scalar h0 = ::h0(thermo, Y0, p[0], T0);
+
     forAll(Y, i)
     {
         Y[i] = Y0[i];
-        h0 += Y0[i]*specieData[i].Hs(p[0], T0);
     }
 
     thermo.he() = dimensionedScalar("h", dimEnergy/dimMass, h0);

src/thermophysicalModels/specie/Make/files

@@ -2,5 +2,6 @@ atomicWeights/atomicWeights.C
 specie/specie.C
 reaction/reactions/makeReactions.C
 reaction/reactions/makeLangmuirHinshelwoodReactions.C
+reaction/reactions/makeMichaelisMentenReactions.C
 
 LIB = $(FOAM_LIBBIN)/libspecie

src/thermophysicalModels/specie/reaction/Reactions/Reaction/Reaction.C

@@ -584,7 +584,6 @@ void Foam::Reaction<ReactionThermo>::dwdc
     const List<label>& c2s
 ) const
 {
-
     scalar pf, cf, pr, cr;
     label lRef, rRef;
 
@@ -706,7 +705,7 @@ void Foam::Reaction<ReactionThermo>::dwdc
         this->dcidc(p, T, c, dcidc);
         forAll(this->beta(), j)
         {
-            label sj = this-> beta()[j].first();
+            label sj = this->beta()[j].first();
             sj = reduced ? c2s[sj] : sj;
             if (sj != -1)
             {

src/thermophysicalModels/specie/reaction/reactionRate/MichaelisMenten/MichaelisMentenReactionRate.H

@@ -0,0 +1,165 @@
+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+   \\    /   O peration     |
+    \\  /    A nd           | Copyright (C) 2018 OpenFOAM Foundation
+     \\/     M anipulation  |
+-------------------------------------------------------------------------------
+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/>.
+
+Class
+    Foam::MichaelisMentenReactionRate
+
+Description
+    Michaelis-Menten reaction rate for enzymatic reactions.
+
+    Reference:
+    \verbatim
+        Michaelis, L., & Menten, M. L. (1913).
+        Die Kinetik der InwertinWirkung.
+        Biochem., (49), 333-369.
+    \endverbatim
+
+SourceFiles
+    MichaelisMentenReactionRateI.H
+
+\*---------------------------------------------------------------------------*/
+
+#ifndef MichaelisMentenReactionRate_H
+#define MichaelisMentenReactionRate_H
+
+#include "Reaction.H"
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+namespace Foam
+{
+
+// Forward declaration of friend functions and operators
+
+class MichaelisMentenReactionRate;
+
+Ostream& operator<<(Ostream&, const MichaelisMentenReactionRate&);
+
+
+/*---------------------------------------------------------------------------*\
+               Class MichaelisMentenReactionRate Declaration
+\*---------------------------------------------------------------------------*/
+
+class MichaelisMentenReactionRate
+{
+    // Private data
+
+        //- List of specie names present in reaction system
+        const speciesTable& species_;
+
+        //- The maximum reaction rate at saturating substrate concentration
+        scalar Vmax_;
+
+        //- The Michaelis constant
+        //  the substrate concentration at which the reaction rate is half Vmax_
+        scalar Km_;
+
+        //- The substrate specie index
+        label s_;
+
+        List<Tuple2<label, scalar>> beta_;
+
+
+public:
+
+    // Constructors
+
+        //- Construct from dictionary
+        inline MichaelisMentenReactionRate
+        (
+            const speciesTable& species,
+            const dictionary& dict
+        );
+
+
+    // Member Functions
+
+        //- Return the type name
+        static word type()
+        {
+            return "MichaelisMenten";
+        }
+
+        inline scalar operator()
+        (
+            const scalar p,
+            const scalar T,
+            const scalarField& c
+        ) const;
+
+        inline scalar ddT
+        (
+            const scalar p,
+            const scalar T,
+            const scalarField& c
+        ) const;
+
+        //- Third-body efficiencies (beta = 1-alpha)
+        //  non-empty only for third-body reactions
+        //  with enhanced molecularity (alpha != 1)
+        inline const List<Tuple2<label, scalar>>& beta() const;
+
+        //- Species concentration derivative of the pressure dependent term
+        inline void dcidc
+        (
+            const scalar p,
+            const scalar T,
+            const scalarField& c,
+            scalarField& dcidc
+        ) const;
+
+        //- Temperature derivative of the pressure dependent term
+        inline scalar dcidT
+        (
+            const scalar p,
+            const scalar T,
+            const scalarField& c
+        ) const;
+
+        //- Write to stream
+        inline void write(Ostream& os) const;
+
+
+    // Ostream Operator
+
+        inline friend Ostream& operator<<
+        (
+            Ostream&,
+            const MichaelisMentenReactionRate&
+        );
+};
+
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+} // End namespace Foam
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+#include "MichaelisMentenReactionRateI.H"
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+#endif
+
+// ************************************************************************* //

src/thermophysicalModels/specie/reaction/reactionRate/MichaelisMenten/MichaelisMentenReactionRateI.H

@@ -0,0 +1,116 @@
+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+   \\    /   O peration     |
+    \\  /    A nd           | Copyright (C) 2018 OpenFOAM Foundation
+     \\/     M anipulation  |
+-------------------------------------------------------------------------------
+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/>.
+
+\*---------------------------------------------------------------------------*/
+
+// * * * * * * * * * * * * * * * * Constructors  * * * * * * * * * * * * * * //
+
+inline Foam::MichaelisMentenReactionRate::MichaelisMentenReactionRate
+(
+    const speciesTable& st,
+    const dictionary& dict
+)
+:
+    species_(st),
+    Vmax_(readScalar(dict.lookup("Vmax"))),
+    Km_(readScalar(dict.lookup("Km"))),
+    s_(st[dict.lookup("S")])
+{
+    beta_.append(Tuple2<label, scalar>(s_, 1.0));
+}
+
+
+// * * * * * * * * * * * * * * * Member Functions  * * * * * * * * * * * * * //
+
+inline Foam::scalar Foam::MichaelisMentenReactionRate::operator()
+(
+    const scalar p,
+    const scalar T,
+    const scalarField& c
+) const
+{
+    return Vmax_/(Km_ + c[s_]);
+}
+
+
+inline Foam::scalar Foam::MichaelisMentenReactionRate::ddT
+(
+    const scalar p,
+    const scalar T,
+    const scalarField& c
+) const
+{
+    return 0;
+}
+
+
+inline const Foam::List<Foam::Tuple2<Foam::label, Foam::scalar>>&
+Foam::MichaelisMentenReactionRate::beta() const
+{
+    return beta_;
+}
+
+
+inline void Foam::MichaelisMentenReactionRate::dcidc
+(
+    const scalar p,
+    const scalar T,
+    const scalarField& c,
+    scalarField& dcidc
+) const
+{
+    dcidc[0] = -1.0/(Km_ + c[s_]);
+}
+
+
+inline Foam::scalar Foam::MichaelisMentenReactionRate::dcidT
+(
+    const scalar p,
+    const scalar T,
+    const scalarField& c
+) const
+{
+    return 0;
+}
+
+
+inline void Foam::MichaelisMentenReactionRate::write(Ostream& os) const
+{
+    os.writeKeyword("Vmax") << Vmax_ << token::END_STATEMENT << nl;
+    os.writeKeyword("Km") << Km_ << token::END_STATEMENT << nl;
+    os.writeKeyword("S") << species_[s_] << token::END_STATEMENT << nl;
+}
+
+
+inline Foam::Ostream& Foam::operator<<
+(
+    Ostream& os,
+    const MichaelisMentenReactionRate& mmrr
+)
+{
+    mmrr.write(os);
+    return os;
+}
+
+
+// ************************************************************************* //

src/thermophysicalModels/specie/reaction/reactions/makeMichaelisMentenReactions.C

@@ -0,0 +1,49 @@
+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+   \\    /   O peration     |
+    \\  /    A nd           | Copyright (C) 2018 OpenFOAM Foundation
+     \\/     M anipulation  |
+-------------------------------------------------------------------------------
+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/>.
+
+\*---------------------------------------------------------------------------*/
+
+#include "makeReaction.H"
+#include "reactionTypes.H"
+#include "MichaelisMentenReactionRate.H"
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+namespace Foam
+{
+    makeReaction
+    (
+        constFluidHThermoPhysics,
+        IrreversibleReaction,
+        MichaelisMentenReactionRate
+    )
+
+    makeReaction
+    (
+        constFluidEThermoPhysics,
+        IrreversibleReaction,
+        MichaelisMentenReactionRate
+    )
+}
+
+// ************************************************************************* //