Merge remote branch 'OpenCFD/master' into olesenm

applications/solvers/combustion/chemFoam/Make/files

+chemFoam.C
+
+EXE = $(FOAM_APPBIN)/chemFoam

applications/solvers/combustion/chemFoam/Make/options

+EXE_INC = \
+    -I$(LIB_SRC)/finiteVolume/lnInclude \
+    -I$(LIB_SRC)/turbulenceModels/compressible/turbulenceModel \
+    -I$(LIB_SRC)/thermophysicalModels/specie/lnInclude \
+    -I$(LIB_SRC)/thermophysicalModels/thermophysicalFunctions/lnInclude \
+    -I$(LIB_SRC)/thermophysicalModels/reactionThermo/lnInclude \
+    -I$(LIB_SRC)/thermophysicalModels/basic/lnInclude \
+    -I$(LIB_SRC)/thermophysicalModels/laminarFlameSpeed/lnInclude \
+    -I$(LIB_SRC)/ODE/lnInclude\
+    -I$(LIB_SRC)/thermophysicalModels/chemistryModel/lnInclude \
+
+
+EXE_LIBS = \
+    -lfiniteVolume \
+    -lcompressibleRASModels \
+    -lreactionThermophysicalModels \
+    -lbasicThermophysicalModels \
+    -lchemistryModel \
+    -lODE \
+    -lthermophysicalFunctions \
+    -lspecie

applications/solvers/combustion/chemFoam/YEqn.H

+{
+    forAll(Y, specieI)
+    {
+        volScalarField& Yi = Y[specieI];
+
+        solve
+        (
+            fvm::ddt(rho, Yi) - chemistry.RR(specieI),
+            mesh.solver("Yi")
+        );
+    }
+}
\ No newline at end of file

applications/solvers/combustion/chemFoam/chemFoam.C

+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+   \\    /   O peration     |
+    \\  /    A nd           | Copyright (C) 2010-2010 OpenCFD Ltd.
+     \\/     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/>.
+
+Application
+    chemFoam
+
+Description
+    Solver for chemistry problems
+    - designed for use on single cell cases to provide comparison against
+      other chemistry solvers
+    - single cell mesh created on-the-fly
+    - fields created on the fly from the initial conditions
+
+\*---------------------------------------------------------------------------*/
+
+#include "fvCFD.H"
+#include "hCombustionThermo.H"
+#include "turbulenceModel.H"
+#include "psiChemistryModel.H"
+#include "chemistrySolver.H"
+#include "OFstream.H"
+#include "thermoPhysicsTypes.H"
+#include "basicMultiComponentMixture.H"
+#include "cellModeller.H"
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+int main(int argc, char *argv[])
+{
+    #include "setRootCase.H"
+    #include "createTime.H"
+    #include "createSingleCellMesh.H"
+    #include "createFields.H"
+    #include "readInitialConditions.H"
+
+    // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+    Info<< "\nStarting time loop\n" << endl;
+
+    while (runTime.run())
+    {
+        #include "readControls.H"
+
+        #include "setDeltaT.H"
+
+        runTime++;
+        Info<< "Time = " << runTime.timeName() << nl << endl;
+
+        #include "solveChemistry.H"
+
+        {
+            #include "YEqn.H"
+
+            #include "hEqn.H"
+
+            #include "pEqn.H"
+        }
+
+        #include "output.H"
+
+        Info<< "ExecutionTime = " << runTime.elapsedCpuTime() << " s"
+            << "  ClockTime = " << runTime.elapsedClockTime() << " s"
+            << nl << endl;
+    }
+
+    Info << "Number of steps = " << runTime.timeIndex() << endl;
+    Info << "End" << nl << endl;
+
+    return(0);
+}
+
+
+// ************************************************************************* //

applications/solvers/combustion/chemFoam/createBaseFields.H

+// write base thermo fields - not registered since will be re-read by
+// thermo package
+
+Info<< "Creating base fields for time " << runTime.timeName() << endl;
+{
+    volScalarField Ydefault
+    (
+        IOobject
+        (
+            "Ydefault",
+            runTime.timeName(),
+            mesh,
+            IOobject::READ_IF_PRESENT,
+            IOobject::NO_WRITE,
+            false
+        ),
+        mesh,
+        dimensionedScalar("Ydefault", dimless, 1)
+    );
+
+    Ydefault.write();
+
+    volScalarField p
+    (
+        IOobject
+        (
+            "p",
+            runTime.timeName(),
+            mesh,
+            IOobject::READ_IF_PRESENT,
+            IOobject::NO_WRITE,
+            false
+        ),
+        mesh,
+        dimensionedScalar("p", dimPressure, p0)
+    );
+
+    p.write();
+
+    volScalarField T
+    (
+        IOobject
+        (
+            "T",
+            runTime.timeName(),
+            mesh,
+            IOobject::READ_IF_PRESENT,
+            IOobject::NO_WRITE,
+            false
+        ),
+        mesh,
+        dimensionedScalar("T", dimTemperature, T0)
+    );
+
+    T.write();
+}
+

applications/solvers/combustion/chemFoam/createFields.H

+    if (mesh.nCells() != 1)
+    {
+        FatalErrorIn(args.executable())
+            << "Solver only applicable to single cell cases"
+            << exit(FatalError);
+    }
+
+    Info<< "Reading initial conditions.\n" << endl;
+    IOdictionary initialConditions
+    (
+        IOobject
+        (
+            "initialConditions",
+            runTime.constant(),
+            runTime,
+            IOobject::MUST_READ_IF_MODIFIED,
+            IOobject::NO_WRITE
+        )
+    );
+
+    scalar p0 = readScalar(initialConditions.lookup("p"));
+    scalar T0 = readScalar(initialConditions.lookup("T"));
+
+    #include "createBaseFields.H"
+
+    Info<< nl << "Reading thermophysicalProperties" << endl;
+    autoPtr<psiChemistryModel> pChemistry(psiChemistryModel::New(mesh));
+
+    psiChemistryModel& chemistry = pChemistry();
+    scalar dtChem = refCast<const psiChemistryModel>(chemistry).deltaTChem()[0];
+
+    hsCombustionThermo& thermo = chemistry.thermo();
+    basicMultiComponentMixture& composition = thermo.composition();
+    PtrList<volScalarField>& Y = composition.Y();
+
+    volScalarField rho
+    (
+        IOobject
+        (
+            "rho",
+            runTime.timeName(),
+            runTime,
+            IOobject::NO_READ,
+            IOobject::AUTO_WRITE
+        ),
+        thermo.rho()
+    );
+    volScalarField& p = thermo.p();
+    volScalarField& hs = thermo.hs();
+
+    volVectorField U
+    (
+        IOobject
+        (
+            "U",
+            runTime.timeName(),
+            runTime,
+            IOobject::NO_READ,
+            IOobject::NO_WRITE
+        ),
+        mesh,
+        dimensionedVector("zero", dimVelocity, vector::zero),
+        p.boundaryField().types()
+    );
+
+    #include "createPhi.H"
+
+    Info << "Creating turbulence model.\n" << endl;
+    autoPtr<compressible::turbulenceModel> turbulence
+    (
+        compressible::turbulenceModel::New
+        (
+            rho,
+            U,
+            phi,
+            thermo
+        )
+    );
+
+    OFstream post(args.path()/"chemFoam.out");
+    post<< "# Time" << token::TAB << "Temperature [K]" << token::TAB
+        << "Pressure [Pa]" << endl;
+
+

applications/solvers/combustion/chemFoam/createSingleCellMesh.H

+Info<< "Constructing single cell mesh" << nl << endl;
+
+labelList owner(6, 0);
+labelList neighbour(0);
+
+pointField points(8);
+points[0] = vector(0, 0, 0);
+points[1] = vector(1, 0, 0);
+points[2] = vector(1, 1, 0);
+points[3] = vector(0, 1, 0);
+points[4] = vector(0, 0, 1);
+points[5] = vector(1, 0, 1);
+points[6] = vector(1, 1, 1);
+points[7] = vector(0, 1, 1);
+
+const cellModel& hexa = *(cellModeller::lookup("hex"));
+faceList faces = hexa.modelFaces();
+
+fvMesh mesh
+(
+    IOobject
+    (
+        fvMesh::defaultRegion,
+        runTime.timeName(),
+        runTime,
+        IOobject::NO_READ
+    ),
+    xferMove<Field<vector> >(points),
+    faces.xfer(),
+    owner.xfer(),
+    neighbour.xfer()
+);
+
+List<polyPatch*> patches(1);
+
+patches[0] = new emptyPolyPatch("boundary", 6, 0, 0, mesh.boundaryMesh());
+
+mesh.addFvPatches(patches);

applications/solvers/combustion/chemFoam/hEqn.H

+{
+    if (constProp == "volume")
+    {
+        hs[0] = u0 + p[0]/rho[0] + integratedHeat;
+    }
+    else
+    {
+        hs[0] = hs0 + integratedHeat;
+    }
+}
\ No newline at end of file

applications/solvers/combustion/chemFoam/output.H

+    runTime.write();
+
+    Info<< "Sh = " << Sh
+        << ", T = " << thermo.T()[0]
+        << ", p = " << thermo.p()[0]
+        << ", " << Y[0].name() << " = " << Y[0][0]
+        << endl;
+
+    post<< runTime.value() << token::TAB << thermo.T()[0] << token::TAB
+        << thermo.p()[0] << endl;
+

applications/solvers/combustion/chemFoam/pEqn.H

+{
+    thermo.correct();
+    rho = thermo.rho();
+    if (constProp == "volume")
+    {
+        p[0] = rho0*R0*thermo.T()[0];
+        rho[0] = rho0;
+    }
+}
\ No newline at end of file

applications/solvers/combustion/chemFoam/readControls.H

+    if (runTime.controlDict().lookupOrDefault("suppressSolverInfo", false))
+    {
+        lduMatrix::debug = 0;
+    }
+
+    Switch adjustTimeStep(runTime.controlDict().lookup("adjustTimeStep"));
+
+    scalar maxDeltaT(readScalar(runTime.controlDict().lookup("maxDeltaT")));

applications/solvers/combustion/chemFoam/readInitialConditions.H

+    word constProp(initialConditions.lookup("constantProperty"));
+    if (constProp == "pressure" || constProp == "volume")
+    {
+        Info << constProp << " will be held constant." << nl
+            << " p   = " << p[0] << " [Pa]" << nl
+            << " T   = " << thermo.T()[0] << " [K] " << nl
+            << " rho = " << rho[0] << " [kg/m3]" << nl
+            << endl;
+    }
+    else
+    {
+        FatalError << "in initialConditions, unknown constantProperty type "
+            << constProp << nl << " Valid types are: pressure volume."
+            << abort(FatalError);
+    }
+
+    word fractionBasis(initialConditions.lookup("fractionBasis"));
+    if ((fractionBasis != "mass") && (fractionBasis != "mole"))
+    {
+        FatalError << "in initialConditions, unknown fractionBasis type " << nl
+            << "Valid types are: mass or mole."
+            << fractionBasis << abort(FatalError);
+    }
+
+    label nSpecie = Y.size();
+    PtrList<gasThermoPhysics> specieData(Y.size());
+    forAll(specieData, i)
+    {
+        specieData.set
+        (
+            i,
+            new gasThermoPhysics
+            (
+                dynamic_cast<const reactingMixture<gasThermoPhysics>&>
+                    (thermo).speciesData()[i]
+            )
+        );
+    }
+
+    scalarList Y0(nSpecie, 0.0);
+    scalarList X0(nSpecie, 0.0);
+
+    dictionary fractions(initialConditions.subDict("fractions"));
+    if (fractionBasis == "mole")
+    {
+        forAll(Y, i)
+        {
+            const word& name = Y[i].name();
+            if (fractions.found(name))
+            {
+                X0[i] = readScalar(fractions.lookup(name));
+            }
+        }
+
+        scalar mw = 0.0;
+        const scalar mTot = sum(X0);
+        forAll(Y, i)
+        {
+            X0[i] /= mTot;
+            mw += specieData[i].W()*X0[i];
+        }
+
+        forAll(Y, i)
+        {
+            Y0[i] = X0[i]*specieData[i].W()/mw;
+        }
+    }
+    else  // mass fraction
+    {
+        forAll(Y, i)
+        {
+            const word& name = Y[i].name();
+            if (fractions.found(name))
+            {
+                Y0[i] = readScalar(fractions.lookup(name));
+            }
+        }
+
+        scalar invW = 0.0;
+        const scalar mTot = sum(Y0);
+        forAll(Y, i)
+        {
+            Y0[i] /= mTot;
+            invW += Y0[i]/specieData[i].W();
+        }
+        const scalar mw = 1.0/invW;
+
+        forAll(Y, i)
+        {
+            X0[i] = Y0[i]*mw/specieData[i].W();
+        }
+    }
+
+    scalar hs0 = 0.0;
+    forAll(Y, i)
+    {
+        Y[i] = Y0[i];
+        hs0 += Y0[i]*specieData[i].Hs(T0);
+    }
+
+    hs = dimensionedScalar("hs", dimEnergy/dimMass, hs0);
+
+    thermo.correct();
+
+    rho = thermo.rho();
+    scalar rho0 = rho[0];
+    scalar u0 = hs0 - p0/rho0;
+    scalar R0 = p0/(rho0*T0);
+
+    scalar integratedHeat = 0.0;
+

applications/solvers/combustion/chemFoam/setDeltaT.H

+if (adjustTimeStep)
+{
+    runTime.setDeltaT(min(dtChem, maxDeltaT));
+    Info<< "deltaT = " <<  runTime.deltaT().value() << endl;
+}
+

applications/solvers/combustion/chemFoam/solveChemistry.H

+    dtChem = chemistry.solve
+    (
+        runTime.value() - runTime.deltaT().value(),
+        runTime.deltaT().value()
+    );
+    scalar Sh = chemistry.Sh()()[0]/rho[0];
+    integratedHeat += Sh*runTime.deltaT().value();

applications/test/nearWallDist-wave/Test-WallDist2.C

@@ -29,7 +29,7 @@ Description
 
 #include "fvCFD.H"
 #include "wallFvPatch.H"
-#include "MeshWave.H"
+#include "FaceCellWave.H"
 #include "wallPoint.H"
 
 
@@ -158,7 +158,7 @@ int main(int argc, char *argv[])
         forAll(allCellInfo, cellI)
         {
             scalar dist = allCellInfo[cellI].distSqr();
-            if (allCellInfo[cellI].valid())
+            if (allCellInfo[cellI].valid(wallDistCalc.data()))
             {
                 wallDistUncorrected[cellI] = Foam::sqrt(dist);
             }
@@ -180,7 +180,7 @@ int main(int argc, char *argv[])
                 const label meshFaceI = patchField.patch().start() + patchFaceI;
 
                 scalar dist = allFaceInfo[meshFaceI].distSqr();
-                if (allFaceInfo[meshFaceI].valid())
+                if (allFaceInfo[meshFaceI].valid(wallDistCalc.data()))
                 {
                     patchField[patchFaceI] = Foam::sqrt(dist);
                 }

applications/utilities/mesh/advanced/selectCells/selectCells.C

@@ -299,7 +299,7 @@ label selectOutsideCells
         mesh,
         outsideFaces.shrink(),
         outsideFacesInfo.shrink(),
-        mesh.globalData().nTotalCells()+1  // max iterations
+        mesh.globalData().nTotalCells()+1   // max iterations
     );
 
     // Now regionCalc should hold info on cells that are reachable from

applications/utilities/mesh/generation/blockMesh/blockMeshApp.C

@@ -158,7 +158,7 @@ int main(int argc, char *argv[])
     blockMesh::verbose(true);
 
     IOdictionary meshDict(meshDictIoPtr());
-    blockMesh blocks(meshDict);
+    blockMesh blocks(meshDict, regionName);
 
 
     if (args.optionFound("blockTopology"))

applications/utilities/mesh/manipulation/checkMesh/checkTopology.C

@@ -147,8 +147,8 @@ Foam::label Foam::checkTopology
             }
         }
 
-        faceSet oneCells(mesh, "oneInternalFaceCells", mesh.nCells()/100);
-        faceSet twoCells(mesh, "twoInternalFacesCells", mesh.nCells()/100);
+        cellSet oneCells(mesh, "oneInternalFaceCells", mesh.nCells()/100);
+        cellSet twoCells(mesh, "twoInternalFacesCells", mesh.nCells()/100);
 
         forAll(nInternalFaces, cellI)
         {

applications/utilities/postProcessing/graphics/PV3Readers/PV3blockMeshReader/vtkPV3blockMesh/vtkPV3blockMesh.C

@@ -321,7 +321,7 @@ void Foam::vtkPV3blockMesh::updateFoamMesh()
             )
         );
 
-        meshPtr_ = new blockMesh(meshDict);
+        meshPtr_ = new blockMesh(meshDict, polyMesh::defaultRegion);
     }
 
 

applications/utilities/postProcessing/lagrangian/steadyParticleTracks/steadyParticleTracksTemplates.C

@@ -83,7 +83,7 @@ PtrList<List<Type> > readFields
             {
                 Info<< "        reading field " << obj.name() << endl;
                 IOField<Type> newField(obj);
-                values.set(fieldI++, new List<Type>(newField.xferList()));
+                values.set(fieldI++, new List<Type>(newField.xfer()));
                 break;
             }
         }