reactingMixture: Rationalised the reading of the species thermo and reactions

which are now read directly from the thermophysicalProperties dictionary for
consistency with non-reacting mixture thermodynamics.  The species thermo and
reactions lists can still be in separate files if convenient and included into
the thermophysicalProperties file using the standard dictionary #include.

applications/utilities/thermophysical/chemkinToFoam/chemkinToFoam.C

@@ -64,43 +64,47 @@ int main(int argc, char *argv[])
     bool newFormat = args.optionFound("newFormat");
 
     speciesTable species;
-
     chemkinReader cr(species, args[1], args[3], args[2], newFormat);
+    const HashPtrTable<gasHThermoPhysics>& speciesThermo = cr.speciesThermo();
 
-    OFstream reactionsFile(args[4]);
+    dictionary thermoDict;
-    writeEntry(reactionsFile, "elements", cr.elementNames());
+    thermoDict.add("species", cr.species());
-    reactionsFile << nl;
+
-    writeEntry(reactionsFile, "species", cr.species());
+    // Add the species thermo formatted entries
-    reactionsFile << nl;
+    {
-    cr.reactions().write(reactionsFile);
+        OStringStream os;
+        speciesThermo.write(os);
+        dictionary speciesThermoDict(IStringStream(os.str())());
+        thermoDict.merge(speciesThermoDict);
+    }
 
     // Temporary hack to splice the specie composition data into the thermo file
     // pending complete integration into the thermodynamics structure
 
-    OStringStream os;
-    cr.speciesThermo().write(os);
-    dictionary thermoDict(IStringStream(os.str())());
-
-    wordList speciesList(thermoDict.toc());
-
     // Add elements
-    forAll(speciesList, si)
+    forAllConstIter(HashPtrTable<gasHThermoPhysics>, speciesThermo, iter)
     {
+        const word specieName(iter.key());
+
         dictionary elementsDict("elements");
-        forAll(cr.specieComposition()[speciesList[si]], ei)
+        forAll(cr.specieComposition()[specieName], ei)
         {
             elementsDict.add
             (
-                cr.specieComposition()[speciesList[si]][ei].name(),
+                cr.specieComposition()[specieName][ei].name(),
-                cr.specieComposition()[speciesList[si]][ei].nAtoms()
+                cr.specieComposition()[specieName][ei].nAtoms()
             );
         }
 
-        thermoDict.subDict(speciesList[si]).add("elements", elementsDict);
+        thermoDict.subDict(specieName).add("elements", elementsDict);
     }
 
     thermoDict.write(OFstream(args[5])(), false);
 
+
+    OFstream reactionsFile(args[4]);
+    cr.reactions().write(reactionsFile);
+
     reactionsFile << nl;
 
     writeEntry

etc/caseDicts/annotated/collapseDict

@@ -72,7 +72,7 @@ controlMeshQualityCoeffs
 {
     // Name of the dictionary that has the mesh quality coefficients used
     // by motionSmoother::checkMesh
-    #include                    "meshQualityDict";
+    #include                    "meshQualityDict"
 
     // The amount that minimumEdgeLength will be reduced by for each
     // edge if that edge's collapse generates a poor quality face

etc/templates/singleFluidCHT/templates/0/fluid/T

@@ -14,7 +14,7 @@ FoamFile
 }
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
 
-#include "$FOAM_CASE/constant/initialConditions";
+#include "$FOAM_CASE/constant/initialConditions"
 
 dimensions      [0 0 0 1 0 0 0];
 

etc/templates/singleFluidCHT/templates/0/fluid/p

@@ -14,7 +14,7 @@ FoamFile
 }
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
 
-#include "$FOAM_CASE/constant/initialConditions";
+#include "$FOAM_CASE/constant/initialConditions"
 
 dimensions      [1 -1 -2 0 0 0 0];
 

etc/templates/singleFluidCHT/templates/0/fluid/p_rgh

@@ -14,7 +14,7 @@ FoamFile
 }
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
 
-#include "$FOAM_CASE/constant/initialConditions";
+#include "$FOAM_CASE/constant/initialConditions"
 
 dimensions      [ 1 -1 -2 0 0 0 0 ];
 

etc/templates/singleFluidCHT/templates/0/solid/T

@@ -14,7 +14,7 @@ FoamFile
 }
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
 
-#include "$FOAM_CASE/constant/initialConditions";
+#include "$FOAM_CASE/constant/initialConditions"
 
 dimensions      [ 0 0 0 1 0 0 0 ];
 

etc/templates/singleFluidCHT/templates/0/solid/p

@@ -14,7 +14,7 @@ FoamFile
 }
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
 
-#include "$FOAM_CASE/constant/initialConditions";
+#include "$FOAM_CASE/constant/initialConditions"
 
 dimensions      [1 -1 -2 0 0 0 0];
 

src/thermophysicalModels/reactionThermo/mixtures/multiComponentMixture/multiComponentMixture.C

@@ -2,7 +2,7 @@
   =========                 |
   \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
    \\    /   O peration     | Website:  https://openfoam.org
-    \\  /    A nd           | Copyright (C) 2011-2018 OpenFOAM Foundation
+    \\  /    A nd           | Copyright (C) 2011-2019 OpenFOAM Foundation
      \\/     M anipulation  |
 -------------------------------------------------------------------------------
 License
@@ -73,34 +73,6 @@ void Foam::multiComponentMixture<ThermoType>::correctMassFractions()
 
 // * * * * * * * * * * * * * * * * Constructors  * * * * * * * * * * * * * * //
 
-template<class ThermoType>
-Foam::multiComponentMixture<ThermoType>::multiComponentMixture
-(
-    const dictionary& thermoDict,
-    const wordList& specieNames,
-    const HashPtrTable<ThermoType>& thermoData,
-    const fvMesh& mesh,
-    const word& phaseName
-)
-:
-    basicSpecieMixture(thermoDict, specieNames, mesh, phaseName),
-    speciesData_(species_.size()),
-    mixture_("mixture", *thermoData[specieNames[0]]),
-    mixtureVol_("volMixture", *thermoData[specieNames[0]])
-{
-    forAll(species_, i)
-    {
-        speciesData_.set
-        (
-            i,
-            new ThermoType(*thermoData[species_[i]])
-        );
-    }
-
-    correctMassFractions();
-}
-
-
 template<class ThermoType>
 Foam::multiComponentMixture<ThermoType>::multiComponentMixture
 (

src/thermophysicalModels/reactionThermo/mixtures/multiComponentMixture/multiComponentMixture.H

@@ -86,17 +86,6 @@ public:
 
     // Constructors
 
-        //- Construct from dictionary, specie names, thermo database,
-        //  mesh and phase name
-        multiComponentMixture
-        (
-            const dictionary&,
-            const wordList& specieNames,
-            const HashPtrTable<ThermoType>& thermoData,
-            const fvMesh&,
-            const word&
-        );
-
         //- Construct from dictionary, mesh and phase name
         multiComponentMixture(const dictionary&, const fvMesh&, const word&);
 

src/thermophysicalModels/reactionThermo/mixtures/reactingMixture/foamChemistryReader/foamChemistryReader.C

@@ -1,185 +0,0 @@
-/*---------------------------------------------------------------------------*\
-  =========                 |
-  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
-   \\    /   O peration     | Website:  https://openfoam.org
-    \\  /    A nd           | Copyright (C) 2011-2019 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 "foamChemistryReader.H"
-#include "IFstream.H"
-#include "addToRunTimeSelectionTable.H"
-
-// * * * * * * * * * * * * * Private Member Functions  * * * * * * * * * * * //
-
-template<class ThermoType>
-Foam::speciesTable& Foam::foamChemistryReader<ThermoType>::setSpecies
-(
-    const dictionary& dict,
-    speciesTable& species
-)
-{
-    wordList s(dict.lookup("species"));
-    species.transfer(s);
-    return species;
-}
-
-
-template<class ThermoType>
-void Foam::foamChemistryReader<ThermoType>::readSpeciesComposition()
-{
-    if (!chemDict_.found("elements"))
-    {
-        Info<< "    elements not defined in " << chemDict_.name() << endl;
-        return;
-    }
-
-    wordList e(chemDict_.lookup("elements"));
-    label currentElementIndex(0);
-
-    DynamicList<word> elementNames_;
-    HashTable<label> elementIndices_;
-
-    forAll(e, ei)
-    {
-        if (!elementIndices_.found(e[ei]))
-        {
-            elementIndices_.insert(e[ei], currentElementIndex++);
-            elementNames_.append(e[ei]);
-        }
-        else
-        {
-            IOWarningInFunction(chemDict_)
-                << "element " << e[ei] << " already in table." << endl;
-        }
-    }
-
-    // Loop through all species in thermoDict to retrieve
-    // the species composition
-    forAll(speciesTable_, si)
-    {
-        if (thermoDict_.subDict(speciesTable_[si]).isDict("elements"))
-        {
-            dictionary currentElements
-            (
-                thermoDict_.subDict(speciesTable_[si]).subDict("elements")
-            );
-
-            wordList currentElementsName(currentElements.toc());
-            List<specieElement> currentComposition(currentElementsName.size());
-
-            forAll(currentElementsName, eni)
-            {
-                currentComposition[eni].name() = currentElementsName[eni];
-
-                currentComposition[eni].nAtoms() =
-                    currentElements.lookupOrDefault
-                    (
-                        currentElementsName[eni],
-                        0
-                    );
-            }
-
-            // Add current specie composition to the hash table
-            speciesCompositionTable::iterator specieCompositionIter
-            (
-                speciesComposition_.find(speciesTable_[si])
-            );
-
-            if (specieCompositionIter != speciesComposition_.end())
-            {
-                speciesComposition_.erase(specieCompositionIter);
-            }
-
-            speciesComposition_.insert(speciesTable_[si], currentComposition);
-        }
-        else
-        {
-            FatalIOErrorInFunction(thermoDict_)
-                << "Specie " << speciesTable_[si]
-                << " does not contain element description."
-                << exit(FatalIOError);
-        }
-    }
-}
-
-
-// * * * * * * * * * * * * * * * * Constructor * * * * * * * * * * * * * * * //
-
-template<class ThermoType>
-Foam::foamChemistryReader<ThermoType>::foamChemistryReader
-(
-    const fileName& reactionsFileName,
-    speciesTable& species,
-    const fileName& thermoFileName
-)
-:
-    chemDict_
-    (
-        IFstream
-        (
-            fileName(reactionsFileName).expand()
-        )()
-    ),
-    thermoDict_
-    (
-        IFstream
-        (
-            fileName(thermoFileName).expand()
-        )()
-    ),
-    speciesTable_(setSpecies(chemDict_, species)),
-    speciesThermo_(thermoDict_),
-    reactions_(speciesTable_, speciesThermo_, chemDict_)
-{
-    readSpeciesComposition();
-}
-
-
-template<class ThermoType>
-Foam::foamChemistryReader<ThermoType>::foamChemistryReader
-(
-    const dictionary& thermoDict,
-    speciesTable& species
-)
-:
-    chemDict_
-    (
-        IFstream
-        (
-            fileName(thermoDict.lookup("foamChemistryFile")).expand()
-        )()
-    ),
-    thermoDict_
-    (
-        IFstream
-        (
-            fileName(thermoDict.lookup("foamChemistryThermoFile")).expand()
-        )()
-    ),
-    speciesTable_(setSpecies(chemDict_, species)),
-    speciesThermo_(thermoDict_),
-    reactions_(speciesTable_, speciesThermo_, chemDict_)
-{
-    readSpeciesComposition();
-}
-
-
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //

src/thermophysicalModels/reactionThermo/mixtures/reactingMixture/foamChemistryReader/foamChemistryReader.H

@@ -1,178 +0,0 @@
-/*---------------------------------------------------------------------------*\
-  =========                 |
-  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
-   \\    /   O peration     | Website:  https://openfoam.org
-    \\  /    A nd           | Copyright (C) 2011-2019 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::foamChemistryReader
-
-Description
-    Chemistry reader for OpenFOAM format
-
-SourceFiles
-    foamChemistryReader.C
-
-\*---------------------------------------------------------------------------*/
-
-#ifndef foamChemistryReader_H
-#define foamChemistryReader_H
-
-#include "specieElement.H"
-#include "ReactionList.H"
-
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-namespace Foam
-{
-
-typedef HashTable<List<specieElement>> speciesCompositionTable;
-
-/*---------------------------------------------------------------------------*\
-                       Class foamChemistry Declaration
-\*---------------------------------------------------------------------------*/
-
-template<class ThermoType>
-class foamChemistryReader
-{
-        //- Chemistry/reactions dictionary
-        dictionary chemDict_;
-
-        //- Thermo properties dictionary
-        dictionary thermoDict_;
-
-        //- List of elements
-        DynamicList<word> elementNames_;
-
-        //- Element indices
-        HashTable<label> elementIndices_;
-
-        //- Table of species
-        speciesTable& speciesTable_;
-
-        //- Table of species composition
-        speciesCompositionTable speciesComposition_;
-
-        //- Table of the thermodynamic data given in the foamChemistry file
-        HashPtrTable<ThermoType> speciesThermo_;
-
-        //- List of the reactions
-        ReactionList<ThermoType> reactions_;
-
-
-    // Private Member Functions
-
-        //- Set the species list
-        speciesTable& setSpecies(const dictionary& dict, speciesTable& species);
-
-        //- Read the species composition
-        void readSpeciesComposition();
-
-
-public:
-
-    // Constructors
-
-        //- Construct from foamChemistry and thermodynamics file names
-        foamChemistryReader
-        (
-            const fileName& reactionsFileName,
-            speciesTable& species,
-            const fileName& thermoFileName
-        );
-
-        //- Construct by getting the foamChemistry and thermodynamics file names
-        //  from dictionary
-        foamChemistryReader
-        (
-            const dictionary& thermoDict,
-            speciesTable& species
-        );
-
-        //- Disallow default bitwise copy construction
-        foamChemistryReader(const foamChemistryReader&) = delete;
-
-
-    //- Destructor
-    virtual ~foamChemistryReader()
-    {}
-
-
-    // Member Functions
-
-        //- List of elements
-        const wordList& elementNames() const
-        {
-            return elementNames_;
-        }
-
-        //- Element indices
-        const HashTable<label>& elementIndices() const
-        {
-            return elementIndices_;
-        }
-
-        //- Table of species
-        const speciesTable& species() const
-        {
-            return speciesTable_;
-        }
-
-        //- Table of species composition
-        const speciesCompositionTable& specieComposition() const
-        {
-            return speciesComposition_;
-        }
-
-        //- Table of the thermodynamic data given in the foamChemistry file
-        const HashPtrTable<ThermoType>& speciesThermo() const
-        {
-            return speciesThermo_;
-        }
-
-        //- List of the reactions
-        const ReactionList<ThermoType>& reactions() const
-        {
-            return reactions_;
-        }
-
-
-    // Member Operators
-
-        //- Disallow default bitwise assignment
-        void operator=(const foamChemistryReader&) = delete;
-};
-
-
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-} // End namespace Foam
-
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-#ifdef NoRepository
-    #include "foamChemistryReader.C"
-#endif
-
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-#endif
-
-// ************************************************************************* //

src/thermophysicalModels/reactionThermo/mixtures/reactingMixture/reactingMixture.C

@@ -26,6 +26,63 @@ License
 #include "reactingMixture.H"
 #include "fvMesh.H"
 
+// * * * * * * * * * * * * * Private Member Functions  * * * * * * * * * * * //
+
+template<class ThermoType>
+Foam::speciesCompositionTable
+Foam::reactingMixture<ThermoType>::readSpeciesComposition
+(
+    const dictionary& thermoDict,
+    const speciesTable& species
+) const
+{
+    speciesCompositionTable speciesComposition_;
+
+    // Loop through all species in thermoDict to retrieve
+    // the species composition
+    forAll(species, si)
+    {
+        if (thermoDict.subDict(species[si]).isDict("elements"))
+        {
+            dictionary currentElements
+            (
+                thermoDict.subDict(species[si]).subDict("elements")
+            );
+
+            wordList currentElementsName(currentElements.toc());
+            List<specieElement> currentComposition(currentElementsName.size());
+
+            forAll(currentElementsName, eni)
+            {
+                currentComposition[eni].name() = currentElementsName[eni];
+
+                currentComposition[eni].nAtoms() =
+                    currentElements.lookupOrDefault
+                    (
+                        currentElementsName[eni],
+                        0
+                    );
+            }
+
+            // Add current specie composition to the hash table
+            speciesCompositionTable::iterator specieCompositionIter
+            (
+                speciesComposition_.find(species[si])
+            );
+
+            if (specieCompositionIter != speciesComposition_.end())
+            {
+                speciesComposition_.erase(specieCompositionIter);
+            }
+
+            speciesComposition_.insert(species[si], currentComposition);
+        }
+    }
+
+    return speciesComposition_;
+}
+
+
 // * * * * * * * * * * * * * * * * Constructors  * * * * * * * * * * * * * * //
 
 template<class ThermoType>
@@ -36,30 +93,35 @@ Foam::reactingMixture<ThermoType>::reactingMixture
     const word& phaseName
 )
 :
-    speciesTable(),
-    autoPtr<foamChemistryReader<ThermoType>>
-    (
-        new foamChemistryReader<ThermoType>(thermoDict, *this)
-    ),
     multiComponentMixture<ThermoType>
     (
         thermoDict,
-        *this,
-        autoPtr<foamChemistryReader<ThermoType>>::operator()().speciesThermo(),
         mesh,
         phaseName
     ),
-    reactions_
+    speciesComposition_(readSpeciesComposition(thermoDict, this->species()))
-    (
-        autoPtr<foamChemistryReader<ThermoType>>::operator()().reactions()
-    ),
-    speciesComposition_
-    (
-        autoPtr<foamChemistryReader<ThermoType>>::
-        operator()().specieComposition()
-    )
 {
-    autoPtr<foamChemistryReader<ThermoType>>::clear();
+    HashPtrTable<ThermoType> thermoDatabase;
+    const PtrList<ThermoType>& speciesData = this->speciesData();
+
+    forAll(speciesData, i)
+    {
+        thermoDatabase.insert
+        (
+            speciesData[i].name(),
+            speciesData[i].clone().ptr()
+        );
+    }
+
+    reactions_ = PtrList<Reaction<ThermoType>>
+    (
+        ReactionList<ThermoType>
+        (
+            this->species(),
+            thermoDatabase,
+            thermoDict
+        )
+    );
 }
 
 

src/thermophysicalModels/reactionThermo/mixtures/reactingMixture/reactingMixture.H

@@ -35,15 +35,17 @@ SourceFiles
 #ifndef reactingMixture_H
 #define reactingMixture_H
 
-#include "speciesTable.H"
-#include "foamChemistryReader.H"
 #include "multiComponentMixture.H"
+#include "ReactionList.H"
+#include "specieElement.H"
 
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
 
 namespace Foam
 {
 
+typedef HashTable<List<specieElement>> speciesCompositionTable;
+
 /*---------------------------------------------------------------------------*\
                       Class reactingMixture Declaration
 \*---------------------------------------------------------------------------*/
@@ -51,17 +53,21 @@ namespace Foam
 template<class ThermoType>
 class reactingMixture
 :
-    public speciesTable,
-    public autoPtr<foamChemistryReader<ThermoType>>,
     public multiComponentMixture<ThermoType>
 {
     // Private member data
 
-        PtrList<Reaction<ThermoType>> reactions_;
-
         //- Table of species composition
         speciesCompositionTable speciesComposition_;
 
+        PtrList<Reaction<ThermoType>> reactions_;
+
+        speciesCompositionTable readSpeciesComposition
+        (
+            const dictionary& thermoDict,
+            const speciesTable& speciesTable_
+        ) const;
+
 
 public:
 

src/thermophysicalModels/solidSpecie/transport/const/constAnIsoSolidTransport.H

@@ -96,6 +96,9 @@ public:
         //- Construct from dictionary
         constAnIsoSolidTransport(const dictionary&);
 
+        //- Construct and return a clone
+        inline autoPtr<constAnIsoSolidTransport> clone() const;
+
         // Selector from dictionary
         inline static autoPtr<constAnIsoSolidTransport> New
         (

src/thermophysicalModels/solidSpecie/transport/const/constAnIsoSolidTransportI.H

@@ -49,6 +49,17 @@ inline Foam::constAnIsoSolidTransport<Thermo>::constAnIsoSolidTransport
 {}
 
 
+template<class Thermo>
+inline Foam::autoPtr<Foam::constAnIsoSolidTransport<Thermo>>
+Foam::constAnIsoSolidTransport<Thermo>::clone() const
+{
+    return autoPtr<constAnIsoSolidTransport<Thermo>>
+    (
+        new constAnIsoSolidTransport<Thermo>(*this)
+    );
+}
+
+
 template<class Thermo>
 inline Foam::autoPtr<Foam::constAnIsoSolidTransport<Thermo>>
 Foam::constAnIsoSolidTransport<Thermo>::New

src/thermophysicalModels/solidSpecie/transport/const/constIsoSolidTransport.H

@@ -97,6 +97,9 @@ public:
         //- Construct from dictionary
         constIsoSolidTransport(const dictionary& dict);
 
+        //- Construct and return a clone
+        inline autoPtr<constIsoSolidTransport> clone() const;
+
         // Selector from dictionary
         inline static autoPtr<constIsoSolidTransport> New
         (

src/thermophysicalModels/solidSpecie/transport/const/constIsoSolidTransportI.H

@@ -25,30 +25,41 @@ License
 
 // * * * * * * * * * * * * * * * * Constructors  * * * * * * * * * * * * * * //
 
-template<class thermo>
+template<class Thermo>
-inline Foam::constIsoSolidTransport<thermo>::constIsoSolidTransport
+inline Foam::constIsoSolidTransport<Thermo>::constIsoSolidTransport
 (
-    const thermo& t,
+    const Thermo& t,
     const scalar kappa
 )
 :
-    thermo(t),
+    Thermo(t),
     kappa_(kappa)
 {}
 
 
-template<class thermo>
+template<class Thermo>
-inline Foam::constIsoSolidTransport<thermo>::constIsoSolidTransport
+inline Foam::constIsoSolidTransport<Thermo>::constIsoSolidTransport
 (
     const word& name,
     const constIsoSolidTransport& ct
 )
 :
-    thermo(name, ct),
+    Thermo(name, ct),
     kappa_(ct.kappa_)
 {}
 
 
+template<class Thermo>
+inline Foam::autoPtr<Foam::constIsoSolidTransport<Thermo>>
+Foam::constIsoSolidTransport<Thermo>::clone() const
+{
+    return autoPtr<constIsoSolidTransport<Thermo>>
+    (
+        new constIsoSolidTransport<Thermo>(*this)
+    );
+}
+
+
 template<class Thermo>
 inline Foam::autoPtr<Foam::constIsoSolidTransport<Thermo>>
 Foam::constIsoSolidTransport<Thermo>::New
@@ -62,25 +73,26 @@ Foam::constIsoSolidTransport<Thermo>::New
     );
 }
 
+
 // * * * * * * * * * * * * * * * Member Functions  * * * * * * * * * * * * * //
 
-template<class thermo>
+template<class Thermo>
-inline Foam::scalar Foam::constIsoSolidTransport<thermo>::
+inline Foam::scalar Foam::constIsoSolidTransport<Thermo>::
 kappa(const scalar p, const scalar T) const
 {
     return kappa_;
 }
 
-template<class thermo>
+template<class Thermo>
-inline Foam::vector Foam::constIsoSolidTransport<thermo>::
+inline Foam::vector Foam::constIsoSolidTransport<Thermo>::
 Kappa(const scalar p, const scalar T) const
 {
     return vector(kappa_, kappa_, kappa_);
 }
 
 
-template<class thermo>
+template<class Thermo>
-inline Foam::scalar Foam::constIsoSolidTransport<thermo>::
+inline Foam::scalar Foam::constIsoSolidTransport<Thermo>::
 mu(const scalar p, const scalar T) const
 {
     NotImplemented;
@@ -88,8 +100,8 @@ mu(const scalar p, const scalar T) const
 }
 
 
-template<class thermo>
+template<class Thermo>
-inline Foam::scalar Foam::constIsoSolidTransport<thermo>::
+inline Foam::scalar Foam::constIsoSolidTransport<Thermo>::
 alphah(const scalar p, const scalar T) const
 {
     return kappa_/this->Cp(p, T);
@@ -97,14 +109,14 @@ alphah(const scalar p, const scalar T) const
 
 // * * * * * * * * * * * * * * * Member Operators  * * * * * * * * * * * * * //
 
-template<class thermo>
+template<class Thermo>
-inline void Foam::constIsoSolidTransport<thermo>::operator+=
+inline void Foam::constIsoSolidTransport<Thermo>::operator+=
 (
-    const constIsoSolidTransport<thermo>& ct
+    const constIsoSolidTransport<Thermo>& ct
 )
 {
     scalar Y1 = this->Y();
-    thermo::operator+=(ct);
+    Thermo::operator+=(ct);
 
     Y1 /= this->Y();
     scalar Y2 = ct.Y()/this->Y();
@@ -116,16 +128,16 @@ inline void Foam::constIsoSolidTransport<thermo>::operator+=
 // * * * * * * * * * * * * * * * Friend Operators  * * * * * * * * * * * * * //
 
 
-template<class thermo>
+template<class Thermo>
-inline Foam::constIsoSolidTransport<thermo> Foam::operator*
+inline Foam::constIsoSolidTransport<Thermo> Foam::operator*
 (
     const scalar s,
-    const constIsoSolidTransport<thermo>& ct
+    const constIsoSolidTransport<Thermo>& ct
 )
 {
-    return constIsoSolidTransport<thermo>
+    return constIsoSolidTransport<Thermo>
     (
-        s*static_cast<const thermo&>(ct),
+        s*static_cast<const Thermo&>(ct),
         ct.kappa_
     );
 }

src/thermophysicalModels/solidSpecie/transport/exponential/exponentialSolidTransport.H

@@ -106,6 +106,9 @@ public:
         //- Construct from dictionary
         exponentialSolidTransport(const dictionary&);
 
+        //- Construct and return a clone
+        inline autoPtr<exponentialSolidTransport> clone() const;
+
         // Selector from dictionary
         inline static autoPtr<exponentialSolidTransport> New
         (

src/thermophysicalModels/solidSpecie/transport/exponential/exponentialSolidTransportI.H

@@ -55,6 +55,17 @@ inline Foam::exponentialSolidTransport<Thermo>::exponentialSolidTransport
 {}
 
 
+template<class Thermo>
+inline Foam::autoPtr<Foam::exponentialSolidTransport<Thermo>>
+Foam::exponentialSolidTransport<Thermo>::clone() const
+{
+    return autoPtr<exponentialSolidTransport<Thermo>>
+    (
+        new exponentialSolidTransport<Thermo>(*this)
+    );
+}
+
+
 template<class Thermo>
 inline Foam::autoPtr<Foam::exponentialSolidTransport<Thermo>>
 Foam::exponentialSolidTransport<Thermo>::New

src/thermophysicalModels/specie/reaction/Reactions/ReactionList/ReactionList.H

@@ -79,7 +79,7 @@ public:
             const HashPtrTable<ThermoType>& thermoDatabase
         );
 
-        //- Construct from dictionary
+        //- Construct from thermoDatabase and dictionary
         ReactionList
         (
             const speciesTable& species,
@@ -87,6 +87,14 @@ public:
             const dictionary& dict
         );
 
+        //- Construct from thermo list and dictionary
+        ReactionList
+        (
+            const speciesTable& species,
+            const PtrList<ThermoType>& thermoDatabase,
+            const dictionary& dict
+        );
+
         //- Construct copy
         ReactionList(const ReactionList<ThermoType>& reactions);
 

tutorials/combustion/chemFoam/gri/Allclean

@@ -6,7 +6,7 @@ cd ${0%/*} || exit 1    # Run from this directory
 
 cleanCase
 
-rm -rf 0 chemFoam.out constant/reactions constant/thermo \
+rm -rf 0 chemFoam.out constant/reactions constant/speciesThermo \
    validation/OF_vs_CHEMKINII.eps validation/chemkinII
 
 #------------------------------------------------------------------------------

tutorials/combustion/chemFoam/gri/Allrun

@@ -9,7 +9,7 @@ application=$(getApplication)
 
 runApplication chemkinToFoam \
                chemkin/chem.inp chemkin/therm.dat chemkin/transportProperties \
-               constant/reactions constant/thermo
+               constant/reactions constant/speciesThermo
 
 runApplication $application
 

tutorials/combustion/chemFoam/gri/constant/thermophysicalProperties

@@ -26,7 +26,7 @@ thermoType
     specie          specie;
 }
 
-foamChemistryFile "$FOAM_CASE/constant/reactions";
+#include "speciesThermo"
-foamChemistryThermoFile "$FOAM_CASE/constant/thermo";
+#include "reactions"
 
 // ************************************************************************* //

tutorials/combustion/chemFoam/h2/Allclean

@@ -6,7 +6,7 @@ cd ${0%/*} || exit 1    # Run from this directory
 
 cleanCase
 
-rm -rf 0 chemFoam.out constant/reactions constant/thermo \
+rm -rf 0 chemFoam.out constant/reactions constant/speciesThermo \
    validation/OF_vs_CHEMKINII.eps validation/chemkinII
 
 #------------------------------------------------------------------------------

tutorials/combustion/chemFoam/h2/Allrun

@@ -9,7 +9,7 @@ application=$(getApplication)
 
 runApplication chemkinToFoam \
                chemkin/chem.inp chemkin/therm.dat chemkin/transportProperties \
-               constant/reactions constant/thermo
+               constant/reactions constant/speciesThermo
 
 runApplication $application
 

tutorials/combustion/chemFoam/h2/constant/thermophysicalProperties

@@ -26,7 +26,7 @@ thermoType
     specie          specie;
 }
 
-foamChemistryFile "$FOAM_CASE/constant/reactions";
+#include "speciesThermo"
-foamChemistryThermoFile "$FOAM_CASE/constant/thermo";
+#include "reactions"
 
 // ************************************************************************* //

tutorials/combustion/chemFoam/ic8h18/Allclean

@@ -6,7 +6,7 @@ cd ${0%/*} || exit 1    # Run from this directory
 
 cleanCase
 
-rm -rf 0 chemFoam.out constant/reactions constant/thermo \
+rm -rf 0 chemFoam.out constant/reactions constant/speciesThermo \
    validation/OF_vs_CHEMKINII.eps validation/chemkinII
 
 #------------------------------------------------------------------------------

tutorials/combustion/chemFoam/ic8h18/Allrun

@@ -9,7 +9,7 @@ application=$(getApplication)
 
 runApplication chemkinToFoam \
                chemkin/chem.inp chemkin/therm.dat chemkin/transportProperties \
-               constant/reactions constant/thermo
+               constant/reactions constant/speciesThermo
 
 runApplication $application
 

tutorials/combustion/chemFoam/ic8h18/constant/thermophysicalProperties

@@ -26,7 +26,7 @@ thermoType
     specie          specie;
 }
 
-foamChemistryFile "$FOAM_CASE/constant/reactions";
+#include "speciesThermo"
-foamChemistryThermoFile "$FOAM_CASE/constant/thermo";
+#include "reactions"
 
 // ************************************************************************* //

tutorials/combustion/chemFoam/ic8h18_TDAC/Allclean

@@ -6,7 +6,7 @@ cd ${0%/*} || exit 1    # Run from this directory
 
 cleanCase
 
-rm -rf 0 chemFoam.out constant/reactions constant/thermo \
+rm -rf 0 chemFoam.out constant/reactions constant/speciesThermo \
    validation/OF_vs_CHEMKINII.eps validation/chemkinII
 
 #------------------------------------------------------------------------------

tutorials/combustion/chemFoam/ic8h18_TDAC/Allrun

@@ -9,7 +9,7 @@ application=$(getApplication)
 
 runApplication chemkinToFoam \
                chemkin/chem.inp chemkin/therm.dat chemkin/transportProperties \
-               constant/reactions constant/thermo
+               constant/reactions constant/speciesThermo
 
 runApplication $application
 

tutorials/combustion/chemFoam/ic8h18_TDAC/constant/thermophysicalProperties

@@ -26,7 +26,7 @@ thermoType
     specie          specie;
 }
 
-foamChemistryFile "$FOAM_CASE/constant/reactions";
+#include "speciesThermo"
-foamChemistryThermoFile "$FOAM_CASE/constant/thermo";
+#include "reactions"
 
 // ************************************************************************* //

tutorials/combustion/chemFoam/nc7h16/Allclean

@@ -6,7 +6,7 @@ cd ${0%/*} || exit 1    # Run from this directory
 
 cleanCase
 
-rm -rf 0 chemFoam.out constant/reactions constant/thermo \
+rm -rf 0 chemFoam.out constant/reactions constant/speciesThermo \
    validation/OF_vs_CHEMKINII.eps validation/chemkinII
 
 #------------------------------------------------------------------------------

tutorials/combustion/chemFoam/nc7h16/Allrun

@@ -9,7 +9,7 @@ application=$(getApplication)
 
 runApplication chemkinToFoam \
                chemkin/chem.inp chemkin/therm.dat chemkin/transportProperties \
-               constant/reactions constant/thermo
+               constant/reactions constant/speciesThermo
 
 runApplication $application
 

tutorials/combustion/chemFoam/nc7h16/constant/thermophysicalProperties

@@ -26,7 +26,7 @@ thermoType
     specie          specie;
 }
 
-foamChemistryFile "$FOAM_CASE/constant/reactions";
+#include "speciesThermo"
-foamChemistryThermoFile "$FOAM_CASE/constant/thermo";
+#include "reactions"
 
 // ************************************************************************* //

tutorials/combustion/coldEngineFoam/freePiston/constant/thermophysicalProperties

@@ -28,10 +28,7 @@ thermoType
 
 inertSpecie air;
 
-
+#include "include/thermo.air"
-foamChemistryFile "$FOAM_CASE/constant/include/reactions.air";
+#include "include/reactions.air"
-
-foamChemistryThermoFile "$FOAM_CASE/constant/include/thermo.air";
-
 
 // ************************************************************************* //

tutorials/combustion/fireFoam/LES/flameSpreadWaterSuppressionPanel/constant/pyrolysisRegion/thermophysicalProperties

@@ -25,12 +25,6 @@ thermoType
     energy          sensibleEnthalpy;
 }
 
-
-
-foamChemistryFile "$FOAM_CASE/constant/pyrolysisRegion/reactions";
-
-foamChemistryThermoFile "$FOAM_CASE/constant/pyrolysisRegion/thermo.solid";
-
 gasThermoType
 {
     transport       sutherland;
@@ -40,7 +34,6 @@ gasThermoType
     energy          sensibleEnthalpy;
 }
 
-
 gas
 {
     specie
@@ -62,5 +55,7 @@ gas
     }
 }
 
+#include "thermo.solid"
+#include "reactions"
 
 // ************************************************************************* //

tutorials/combustion/fireFoam/LES/flameSpreadWaterSuppressionPanel/constant/thermophysicalProperties

@@ -31,9 +31,9 @@ inertSpecie N2;
 fuel    C3H8;
 
 
-foamChemistryFile "$FOAM_CASE/constant/reactions";
+#include "reactions"
 
-foamChemistryThermoFile "$FOAM_CASE/constant/thermo.compressibleGas";
+#include "thermo.compressibleGas"
 
 liquids
 {

tutorials/combustion/fireFoam/LES/oppositeBurningPanels/constant/panelRegion/thermophysicalProperties

@@ -25,12 +25,6 @@ thermoType
     energy          sensibleEnthalpy;
 }
 
-
-
-foamChemistryFile "$FOAM_CASE/constant/panelRegion/reactions";
-
-foamChemistryThermoFile "$FOAM_CASE/constant/panelRegion/thermo.solid";
-
 gasThermoType
 {
     transport       sutherland;
@@ -62,5 +56,7 @@ gas
     }
 }
 
+#include "thermo.solid"
+#include "reactions"
 
 // ************************************************************************* //

tutorials/combustion/fireFoam/LES/oppositeBurningPanels/constant/thermophysicalProperties

@@ -31,9 +31,9 @@ inertSpecie N2;
 fuel        C3H8;
 
 
-foamChemistryFile "$FOAM_CASE/constant/reactions";
+#include "reactions"
 
-foamChemistryThermoFile "$FOAM_CASE/constant/thermo.compressibleGas";
+#include "thermo.compressibleGas"
 
 
 // ************************************************************************* //

tutorials/combustion/fireFoam/LES/smallPoolFire2D/constant/thermophysicalProperties

@@ -31,9 +31,9 @@ inertSpecie N2;
 fuel        CH4;
 
 
-foamChemistryFile "$FOAM_CASE/constant/reactions";
+#include "reactions"
 
-foamChemistryThermoFile "$FOAM_CASE/constant/thermo.compressibleGas";
+#include "thermo.compressibleGas"
 
 
 // ************************************************************************* //

tutorials/combustion/fireFoam/LES/smallPoolFire3D/constant/thermophysicalProperties

@@ -31,9 +31,9 @@ inertSpecie N2;
 fuel        CH4;
 
 
-foamChemistryFile "$FOAM_CASE/constant/reactions";
+#include "reactions"
 
-foamChemistryThermoFile "$FOAM_CASE/constant/thermo.compressibleGas";
+#include "thermo.compressibleGas"
 
 
 // ************************************************************************* //

tutorials/combustion/reactingFoam/RAS/DLR_A_LTS/constant/reactionsGRI

@@ -1,56 +1,3 @@
-elements        
-5
-(
-O
-H
-C
-N
-Ar
-)
-;
-
-species         
-36
-(
-H2
-H
-O
-O2
-OH
-H2O
-HO2
-H2O2
-C
-CH
-CH2
-CH2(S)
-CH3
-CH4
-CO
-CO2
-HCO
-CH2O
-CH2OH
-CH3O
-CH3OH
-C2H
-C2H2
-C2H3
-C2H4
-C2H5
-C2H6
-HCCO
-CH2CO
-HCCOH
-N2
-AR
-C3H7
-C3H8
-CH2CHO
-CH3CHO
-)
-;
-
 reactions
 {
     un-named-reaction-0
@@ -3611,4 +3558,3 @@ reactions
 
 Tlow            250;
 Thigh           5000;
-

tutorials/combustion/reactingFoam/RAS/DLR_A_LTS/constant/thermo.compressibleGasGRI

@@ -1,3 +1,5 @@
+species         36 ( H2 H O O2 OH H2O HO2 H2O2 C CH CH2 CH2(S) CH3 CH4 CO CO2 HCO CH2O CH2OH CH3O CH3OH C2H C2H2 C2H3 C2H4 C2H5 C2H6 HCCO CH2CO HCCOH N2 AR C3H7 C3H8 CH2CHO CH3CHO );
+
 OH
 {
     specie

tutorials/combustion/reactingFoam/RAS/DLR_A_LTS/constant/thermophysicalProperties

@@ -29,7 +29,7 @@ thermoType
 
 inertSpecie N2;
 
-foamChemistryFile "$FOAM_CASE/constant/reactionsGRI";
+#include "thermo.compressibleGasGRI"
-foamChemistryThermoFile "$FOAM_CASE/constant/thermo.compressibleGasGRI";
+#include "reactionsGRI"
 
 // ************************************************************************* //

tutorials/combustion/reactingFoam/RAS/SandiaD_LTS/constant/thermophysicalProperties

@@ -28,7 +28,7 @@ thermoType
 
 inertSpecie N2;
 
-foamChemistryFile "$FOAM_CASE/constant/reactionsGRI";
+#include "thermo.compressibleGasGRI"
-foamChemistryThermoFile "$FOAM_CASE/constant/thermo.compressibleGasGRI";
+#include "reactionsGRI"
 
 // ************************************************************************* //

tutorials/combustion/reactingFoam/RAS/membrane/constant/thermophysicalProperties

@@ -29,9 +29,9 @@ thermoType
 inertSpecie N2;
 
 
-foamChemistryFile "$FOAM_CASE/constant/reactions";
+#include "reactions"
 
-foamChemistryThermoFile "$FOAM_CASE/constant/thermo.compressibleGas";
+#include "thermo.compressibleGas"
 
 
 // ************************************************************************* //

tutorials/combustion/reactingFoam/laminar/counterFlowFlame2D/constant/thermophysicalProperties

@@ -29,9 +29,9 @@ thermoType
 inertSpecie N2;
 
 
-foamChemistryFile "$FOAM_CASE/constant/reactions";
+#include "reactions"
 
-foamChemistryThermoFile "$FOAM_CASE/constant/thermo.compressibleGas";
+#include "thermo.compressibleGas"
 
 
 // ************************************************************************* //

tutorials/combustion/reactingFoam/laminar/counterFlowFlame2DLTS/constant/thermophysicalProperties

@@ -29,9 +29,9 @@ thermoType
 inertSpecie N2;
 
 
-foamChemistryFile "$FOAM_CASE/constant/reactions";
+#include "reactions"
 
-foamChemistryThermoFile "$FOAM_CASE/constant/thermo.compressibleGas";
+#include "thermo.compressibleGas"
 
 
 // ************************************************************************* //

tutorials/combustion/reactingFoam/laminar/counterFlowFlame2DLTS_GRI_TDAC/constant/thermophysicalProperties

@@ -28,8 +28,8 @@ thermoType
 
 inertSpecie N2;
 
-foamChemistryFile "$FOAM_CASE/constant/reactionsGRI";
+#include "reactionsGRI"
-foamChemistryThermoFile "$FOAM_CASE/constant/thermo.compressibleGasGRI";
+#include "thermo.compressibleGasGRI"
 
 
 // ************************************************************************* //

tutorials/combustion/reactingFoam/laminar/counterFlowFlame2D_GRI/constant/thermophysicalProperties

@@ -28,8 +28,8 @@ thermoType
 
 inertSpecie N2;
 
-foamChemistryFile "$FOAM_CASE/constant/reactionsGRI";
+#include "reactionsGRI"
-foamChemistryThermoFile "$FOAM_CASE/constant/thermo.compressibleGasGRI";
+#include "thermo.compressibleGasGRI"
 
 
 // ************************************************************************* //

tutorials/combustion/reactingFoam/laminar/counterFlowFlame2D_GRI_TDAC/constant/thermophysicalProperties

@@ -28,8 +28,8 @@ thermoType
 
 inertSpecie N2;
 
-foamChemistryFile "$FOAM_CASE/constant/reactionsGRI";
+#include "reactionsGRI"
-foamChemistryThermoFile "$FOAM_CASE/constant/thermo.compressibleGasGRI";
+#include "thermo.compressibleGasGRI"
 
 
 // ************************************************************************* //

tutorials/heatTransfer/chtMultiRegionFoam/coolingSphere/templates/0/fluid/T

@@ -14,7 +14,7 @@ FoamFile
 }
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
 
-#include "$FOAM_CASE/constant/initialConditions";
+#include "$FOAM_CASE/constant/initialConditions"
 
 dimensions      [0 0 0 1 0 0 0];
 

tutorials/heatTransfer/chtMultiRegionFoam/coolingSphere/templates/0/fluid/p

@@ -14,7 +14,7 @@ FoamFile
 }
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
 
-#include "$FOAM_CASE/constant/initialConditions";
+#include "$FOAM_CASE/constant/initialConditions"
 
 dimensions      [1 -1 -2 0 0 0 0];
 

tutorials/heatTransfer/chtMultiRegionFoam/coolingSphere/templates/0/fluid/p_rgh

@@ -14,7 +14,7 @@ FoamFile
 }
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
 
-#include "$FOAM_CASE/constant/initialConditions";
+#include "$FOAM_CASE/constant/initialConditions"
 
 dimensions      [ 1 -1 -2 0 0 0 0 ];
 

tutorials/heatTransfer/chtMultiRegionFoam/coolingSphere/templates/0/solid/T

@@ -14,7 +14,7 @@ FoamFile
 }
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
 
-#include "$FOAM_CASE/constant/initialConditions";
+#include "$FOAM_CASE/constant/initialConditions"
 
 dimensions      [ 0 0 0 1 0 0 0 ];
 

tutorials/heatTransfer/chtMultiRegionFoam/coolingSphere/templates/0/solid/p

@@ -14,7 +14,7 @@ FoamFile
 }
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
 
-#include "$FOAM_CASE/constant/initialConditions";
+#include "$FOAM_CASE/constant/initialConditions"
 
 dimensions      [1 -1 -2 0 0 0 0];
 

tutorials/heatTransfer/chtMultiRegionFoam/reverseBurner/constant/gas/thermophysicalProperties

@@ -28,10 +28,7 @@ thermoType
 
 inertSpecie N2;
 
-
+#include "thermo.compressibleGas"
-foamChemistryFile "$FOAM_CASE/constant/gas/reactions";
+#include "reactions"
-
-foamChemistryThermoFile "$FOAM_CASE/constant/gas/thermo.compressibleGas";
-
 
 // ************************************************************************* //

tutorials/incompressible/porousSimpleFoam/straightDuctImplicit/system/collapseDict

@@ -63,7 +63,7 @@ controlMeshQualityCoeffs
 {
     // Name of the dictionary that has the mesh quality coefficients used
     // by motionSmoother::checkMesh
-    #include                    "meshQualityDict";
+    #include                    "meshQualityDict"
 
     // The amount that minimumEdgeLength will be reduced by for each
     // edge if that edge's collapse generates a poor quality face

tutorials/incompressible/porousSimpleFoam/straightDuctImplicit/system/collapseDict.collapseFaces

@@ -63,7 +63,7 @@ controlMeshQualityCoeffs
 {
     // Name of the dictionary that has the mesh quality coefficients used
     // by motionSmoother::checkMesh
-    #include                    "meshQualityDict";
+    #include                    "meshQualityDict"
 
     // The amount that minimumEdgeLength will be reduced by for each
     // edge if that edge's collapse generates a poor quality face

tutorials/incompressible/porousSimpleFoam/straightDuctImplicit/system/collapseDict.indirectPatchFaces

@@ -63,7 +63,7 @@ controlMeshQualityCoeffs
 {
     // Name of the dictionary that has the mesh quality coefficients used
     // by motionSmoother::checkMesh
-    #include                    "meshQualityDict";
+    #include                    "meshQualityDict"
 
     // The amount that minimumEdgeLength will be reduced by for each
     // edge if that edge's collapse generates a poor quality face

tutorials/lagrangian/coalChemistryFoam/simplifiedSiwek/constant/reactions

@@ -1,13 +1,3 @@
-species
-(
-    N2
-    O2
-    CH4
-    H2
-    CO2
-    H2O
-);
-
 reactions
 {
     methaneReaction

tutorials/lagrangian/coalChemistryFoam/simplifiedSiwek/constant/speciesThermo

@@ -1,19 +1,12 @@
-/*--------------------------------*- C++ -*----------------------------------*\
+species
-  =========                 |
+(
-  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+    N2
-   \\    /   O peration     | Website:  https://openfoam.org
+    O2
-    \\  /    A nd           | Version:  dev
+    CH4
-     \\/     M anipulation  |
+    H2
-\*---------------------------------------------------------------------------*/
+    CO2
-FoamFile
+    H2O
-{
+);
-    version     2.0;
-    format      ascii;
-    class       dictionary;
-    location    "constant";
-    object      foam.dat;
-}
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
 
 CO2
 {

tutorials/lagrangian/coalChemistryFoam/simplifiedSiwek/constant/thermophysicalProperties

@@ -27,9 +27,9 @@ thermoType
 }
 
 
-foamChemistryThermoFile "$FOAM_CASE/constant/foam.dat";
+#include "speciesThermo"
 
-foamChemistryFile "$FOAM_CASE/constant/foam.inp";
+#include "reactions"
 
 inertSpecie     N2;
 

tutorials/lagrangian/reactingParcelFoam/counterFlowFlame2DLTS/constant/thermophysicalProperties

@@ -29,9 +29,9 @@ thermoType
 inertSpecie N2;
 
 
-foamChemistryFile "$FOAM_CASE/constant/reactions";
+#include "reactions"
 
-foamChemistryThermoFile "$FOAM_CASE/constant/thermo.compressibleGas";
+#include "thermo.compressibleGas"
 
 
 // ************************************************************************* //

tutorials/lagrangian/reactingParcelFoam/cylinder/constant/foam.inp

@@ -1,10 +0,0 @@
-species
-(
-    O2
-    H2O
-    N2
-)
-;
-
-reactions
-{}

tutorials/lagrangian/reactingParcelFoam/cylinder/constant/reactions

@@ -0,0 +1,2 @@
+reactions
+{}

tutorials/lagrangian/reactingParcelFoam/cylinder/constant/speciesThermo

@@ -1,19 +1,9 @@
-/*--------------------------------*- C++ -*----------------------------------*\
+species
-  =========                 |
+(
-  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+    O2
-   \\    /   O peration     | Website:  https://openfoam.org
+    H2O
-    \\  /    A nd           | Version:  dev
+    N2
-     \\/     M anipulation  |
+);
-\*---------------------------------------------------------------------------*/
-FoamFile
-{
-    version     2.0;
-    format      ascii;
-    class       dictionary;
-    location    "constant";
-    object      foam.dat;
-}
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
 
 O2
 {

tutorials/lagrangian/reactingParcelFoam/cylinder/constant/thermophysicalProperties

@@ -27,9 +27,9 @@ thermoType
 }
 
 
-foamChemistryFile "$FOAM_CASE/constant/foam.inp";
+#include "reactions"
 
-foamChemistryThermoFile "$FOAM_CASE/constant/foam.dat";
+#include "speciesThermo"
 
 inertSpecie     N2;
 

tutorials/lagrangian/reactingParcelFoam/filter/constant/thermophysicalProperties

@@ -27,9 +27,9 @@ thermoType
 }
 
 
-foamChemistryFile "$FOAM_CASE/constant/reactions";
+#include "reactions"
 
-foamChemistryThermoFile "$FOAM_CASE/constant/thermo.incompressiblePoly";
+#include "thermo.incompressiblePoly"
 
 liquids
 {

tutorials/lagrangian/reactingParcelFoam/hotBoxes/constant/foam.inp

@@ -1,10 +0,0 @@
-species
-(
-    O2
-    H2O
-    N2
-)
-;
-
-reactions
-{}

tutorials/lagrangian/reactingParcelFoam/hotBoxes/constant/reactions

@@ -0,0 +1,2 @@
+reactions
+{}

tutorials/lagrangian/reactingParcelFoam/hotBoxes/constant/speciesThermo

@@ -1,19 +1,9 @@
-/*--------------------------------*- C++ -*----------------------------------*\
+species
-  =========                 |
+(
-  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+    O2
-   \\    /   O peration     | Website:  https://openfoam.org
+    H2O
-    \\  /    A nd           | Version:  dev
+    N2
-     \\/     M anipulation  |
+);
-\*---------------------------------------------------------------------------*/
-FoamFile
-{
-    version     2.0;
-    format      ascii;
-    class       dictionary;
-    location    "constant";
-    object      foam.dat;
-}
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
 
 O2
 {

tutorials/lagrangian/reactingParcelFoam/hotBoxes/constant/thermophysicalProperties

@@ -27,9 +27,9 @@ thermoType
 }
 
 
-foamChemistryFile "$FOAM_CASE/constant/foam.inp";
+#include "reactions"
 
-foamChemistryThermoFile "$FOAM_CASE/constant/foam.dat";
+#include "speciesThermo"
 
 inertSpecie     N2;
 

tutorials/lagrangian/reactingParcelFoam/parcelInBox/constant/thermophysicalProperties

@@ -27,9 +27,9 @@ thermoType
 }
 
 
-foamChemistryFile "$FOAM_CASE/constant/reactions";
+#include "reactions"
 
-foamChemistryThermoFile "$FOAM_CASE/constant/thermo.incompressiblePoly";
+#include "thermo.incompressiblePoly"
 
 inertSpecie     air;
 

tutorials/lagrangian/reactingParcelFoam/rivuletPanel/constant/foam.inp

@@ -1,10 +0,0 @@
-species
-(
-    O2
-    H2O
-    N2
-)
-;
-
-reactions
-{}

tutorials/lagrangian/reactingParcelFoam/rivuletPanel/constant/reactions

@@ -0,0 +1,2 @@
+reactions
+{}

tutorials/lagrangian/reactingParcelFoam/rivuletPanel/constant/speciesThermo

@@ -1,19 +1,9 @@
-/*--------------------------------*- C++ -*----------------------------------*\
+species
-  =========                 |
+(
-  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+    O2
-   \\    /   O peration     | Website:  https://openfoam.org
+    H2O
-    \\  /    A nd           | Version:  dev
+    N2
-     \\/     M anipulation  |
+);
-\*---------------------------------------------------------------------------*/
-FoamFile
-{
-    version     2.0;
-    format      ascii;
-    class       dictionary;
-    location    "constant";
-    object      foam.dat;
-}
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
 
 O2
 {

tutorials/lagrangian/reactingParcelFoam/rivuletPanel/constant/thermophysicalProperties

@@ -27,9 +27,9 @@ thermoType
 }
 
 
-foamChemistryFile "$FOAM_CASE/constant/foam.inp";
+#include "reactions"
 
-foamChemistryThermoFile "$FOAM_CASE/constant/foam.dat";
+#include "speciesThermo"
 
 inertSpecie     N2;
 

tutorials/lagrangian/reactingParcelFoam/splashPanel/constant/foam.inp

@@ -1,10 +0,0 @@
-species
-(
-    O2
-    H2O
-    N2
-)
-;
-
-reactions
-{}

tutorials/lagrangian/reactingParcelFoam/splashPanel/constant/reactions

@@ -0,0 +1,2 @@
+reactions
+{}

tutorials/lagrangian/reactingParcelFoam/splashPanel/constant/speciesThermo

@@ -1,19 +1,9 @@
-/*--------------------------------*- C++ -*----------------------------------*\
+species
-  =========                 |
+(
-  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+    O2
-   \\    /   O peration     | Website:  https://openfoam.org
+    H2O
-    \\  /    A nd           | Version:  dev
+    N2
-     \\/     M anipulation  |
+);
-\*---------------------------------------------------------------------------*/
-FoamFile
-{
-    version     2.0;
-    format      ascii;
-    class       dictionary;
-    location    "constant";
-    object      foam.dat;
-}
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
 
 O2
 {

tutorials/lagrangian/reactingParcelFoam/splashPanel/constant/thermophysicalProperties

@@ -27,9 +27,9 @@ thermoType
 }
 
 
-foamChemistryFile "$FOAM_CASE/constant/foam.inp";
+#include "reactions"
 
-foamChemistryThermoFile "$FOAM_CASE/constant/foam.dat";
+#include "speciesThermo"
 
 inertSpecie     N2;
 

tutorials/lagrangian/reactingParcelFoam/verticalChannel/constant/thermophysicalProperties

@@ -27,9 +27,9 @@ thermoType
 }
 
 
-foamChemistryFile "$FOAM_CASE/constant/reactions";
+#include "reactions"
 
-foamChemistryThermoFile "$FOAM_CASE/constant/thermo.incompressiblePoly";
+#include "thermo.incompressiblePoly"
 
 inertSpecie     air;
 

tutorials/lagrangian/reactingParcelFoam/verticalChannelLTS/constant/thermophysicalProperties

@@ -27,9 +27,9 @@ thermoType
 }
 
 
-foamChemistryFile "$FOAM_CASE/constant/reactions";
+#include "reactions"
 
-foamChemistryThermoFile "$FOAM_CASE/constant/thermo.incompressiblePoly";
+#include "thermo.incompressiblePoly"
 
 inertSpecie     air;
 

tutorials/lagrangian/simpleReactingParcelFoam/verticalChannel/constant/thermophysicalProperties

@@ -27,9 +27,9 @@ thermoType
 }
 
 
-foamChemistryFile "$FOAM_CASE/constant/reactions";
+#include "reactions"
 
-foamChemistryThermoFile "$FOAM_CASE/constant/thermo.incompressiblePoly";
+#include "thermo.incompressiblePoly"
 
 inertSpecie     air;
 

tutorials/lagrangian/sprayFoam/aachenBomb/Allclean

@@ -6,6 +6,6 @@ cd ${0%/*} || exit 1    # Run from this directory
 
 cleanCase
 
-rm -rf constant/reactions constant/thermo
+rm -rf constant/reactions constant/speciesThermo
 
 #------------------------------------------------------------------------------

tutorials/lagrangian/sprayFoam/aachenBomb/Allrun

@@ -9,7 +9,7 @@ application=$(getApplication)
 
 runApplication chemkinToFoam \
                chemkin/chem.inp chemkin/therm.dat chemkin/transportProperties \
-               constant/reactions constant/thermo
+               constant/reactions constant/speciesThermo
 
 runApplication blockMesh
 runApplication $application

tutorials/lagrangian/sprayFoam/aachenBomb/constant/thermophysicalProperties

@@ -26,8 +26,7 @@ thermoType
     specie          specie;
 }
 
-foamChemistryFile "$FOAM_CASE/constant/reactions";
+#include "speciesThermo"
-foamChemistryThermoFile "$FOAM_CASE/constant/thermo";
 
 newFormat       yes;
 
@@ -41,5 +40,6 @@ liquids
 solids
 {}
 
+#include "reactions"
 
 // ************************************************************************* //

tutorials/mesh/foamyHexMesh/blob/system/collapseDict

@@ -59,7 +59,7 @@ controlMeshQualityCoeffs
 {
     // Name of the dictionary that has the mesh quality coefficients used
     // by motionSmoother::checkMesh
-    #include                    "meshQualityDict";
+    #include                    "meshQualityDict"
 
     // The amount that minimumEdgeLength will be reduced by for each
     // edge if that edge's collapse generates a poor quality face

tutorials/mesh/foamyHexMesh/flange/system/collapseDict

@@ -59,7 +59,7 @@ controlMeshQualityCoeffs
 {
     // Name of the dictionary that has the mesh quality coefficients used
     // by motionSmoother::checkMesh
-    #include                    "meshQualityDict";
+    #include                    "meshQualityDict"
 
     // The amount that minimumEdgeLength will be reduced by for each
     // edge if that edge's collapse generates a poor quality face

tutorials/mesh/foamyHexMesh/mixerVessel/system/collapseDict.collapseFaces

@@ -63,7 +63,7 @@ controlMeshQualityCoeffs
 {
     // Name of the dictionary that has the mesh quality coefficients used
     // by motionSmoother::checkMesh
-    #include                    "meshQualityDict";
+    #include                    "meshQualityDict"
 
     // The amount that minimumEdgeLength will be reduced by for each
     // edge if that edge's collapse generates a poor quality face

tutorials/mesh/foamyHexMesh/mixerVessel/system/collapseDict.indirectPatchFaces

@@ -63,7 +63,7 @@ controlMeshQualityCoeffs
 {
     // Name of the dictionary that has the mesh quality coefficients used
     // by motionSmoother::checkMesh
-    #include                    "meshQualityDict";
+    #include                    "meshQualityDict"
 
     // The amount that minimumEdgeLength will be reduced by for each
     // edge if that edge's collapse generates a poor quality face

tutorials/mesh/foamyHexMesh/simpleShapes/system/collapseDict

@@ -60,7 +60,7 @@ controlMeshQualityCoeffs
 {
     // Name of the dictionary that has the mesh quality coefficients used
     // by motionSmoother::checkMesh
-    #include                    "meshQualityDict";
+    #include                    "meshQualityDict"
 
     // The amount that minimumEdgeLength will be reduced by for each
     // edge if that edge's collapse generates a poor quality face

tutorials/mesh/foamyQuadMesh/jaggedBoundary/system/foamyQuadMeshDict

@@ -141,7 +141,7 @@ shortEdgeFilter
 extrusion
 {
     extrude     off;
-    #include    "extrude2DMeshDict";
+    #include    "extrude2DMeshDict"
 }
 
 

tutorials/mesh/foamyQuadMesh/square/system/foamyQuadMeshDict

@@ -159,7 +159,7 @@ extrusion
 {
     extrude     off;
 
-    #include    "extrude2DMeshDict";
+    #include    "extrude2DMeshDict"
 }
 
 

tutorials/multiphase/interFoam/RAS/DTCHullWave/0/U.orig

@@ -15,7 +15,7 @@ FoamFile
 }
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
 
-#include        "$FOAM_CASE/constant/waveProperties";
+#include        "$FOAM_CASE/constant/waveProperties"
 
 dimensions      [0 1 -1 0 0 0 0];
 

tutorials/multiphase/reactingTwoPhaseEulerFoam/RAS/bubbleColumnEvaporatingReacting/constant/thermophysicalProperties.gas

@@ -28,10 +28,7 @@ thermoType
 
 inertSpecie AIR;
 
-
+#include "thermo.gas"
-foamChemistryFile "$FOAM_CASE/constant/reactions.gas";
+#include "reactions.gas"
-
-foamChemistryThermoFile "$FOAM_CASE/constant/thermo.gas";
-
 
 // ************************************************************************* //