Merge remote-tracking branch 'origin/master' into develop

applications/solvers/heatTransfer/thermoFoam/EEqn.H

@@ -15,12 +15,16 @@
             )
           : -dpdt
         )
-      - fvm::laplacian(alphaEff, he)
      ==
         radiation->Sh(thermo, he)
       + fvOptions(rho, he)
     );
 
+    if (turbulence.valid())
+    {
+        EEqn -= fvm::laplacian(turbulence->alphaEff(), he);
+    }
+
     EEqn.relax();
 
     fvOptions.constrain(EEqn);

applications/solvers/heatTransfer/thermoFoam/createFields.H

@@ -35,7 +35,31 @@ volVectorField U
 
 #include "compressibleCreatePhi.H"
 
-#include "setAlphaEff.H"
+autoPtr<compressible::turbulenceModel> turbulence;
+
+IOobject turbulencePropertiesHeader
+(
+    "turbulenceProperties",
+    runTime.constant(),
+    mesh,
+    IOobject::MUST_READ_IF_MODIFIED,
+    IOobject::NO_WRITE,
+    false
+);
+
+if (turbulencePropertiesHeader.typeHeaderOk<IOdictionary>(false))
+{
+    Info<< "Creating turbulence model\n" << endl;
+
+    turbulence =
+        compressible::turbulenceModel::New
+        (
+            rho,
+            U,
+            phi,
+            thermo
+        );
+}
 
 #include "createDpdt.H"
 

applications/solvers/heatTransfer/thermoFoam/setAlphaEff.H

-Info<< "Creating turbulence model\n" << endl;
-tmp<volScalarField> talphaEff;
-
-IOobject turbulencePropertiesHeader
-(
-    "turbulenceProperties",
-    runTime.constant(),
-    mesh,
-    IOobject::MUST_READ_IF_MODIFIED,
-    IOobject::NO_WRITE,
-    false
-);
-
-if (turbulencePropertiesHeader.typeHeaderOk<IOdictionary>(true))
-{
-    autoPtr<compressible::turbulenceModel> turbulence
-    (
-        compressible::turbulenceModel::New
-        (
-            rho,
-            U,
-            phi,
-            thermo
-        )
-    );
-
-    talphaEff = turbulence->alphaEff();
-}
-else
-{
-    talphaEff = tmp<volScalarField>
-    (
-        new volScalarField
-        (
-            IOobject
-            (
-                "alphaEff",
-                runTime.timeName(),
-                mesh,
-                IOobject::NO_READ,
-                IOobject::NO_WRITE
-            ),
-            mesh,
-            dimensionedScalar("0", dimMass/dimLength/dimTime, 0.0)
-        )
-    );
-}

applications/solvers/heatTransfer/thermoFoam/thermoFoam.C

@@ -54,8 +54,6 @@ int main(int argc, char *argv[])
     #include "createFields.H"
     #include "createFvOptions.H"
 
-    const volScalarField& alphaEff = talphaEff();
-
     // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
 
     Info<< "\nEvolving thermodynamics\n" << endl;

src/TurbulenceModels/turbulenceModels/RAS/kOmegaSSTLM/kOmegaSSTLM.C

@@ -373,7 +373,8 @@ kOmegaSSTLM<BasicTurbulenceModel>::kOmegaSSTLM
         alphaRhoPhi,
         phi,
         transport,
-        propertiesName
+        propertiesName,
+        typeName
     ),
 
     ca1_
@@ -477,7 +478,12 @@ kOmegaSSTLM<BasicTurbulenceModel>::kOmegaSSTLM
         this->mesh_,
         dimensionedScalar("0", dimless, 0)
     )
-{}
+{
+    if (type == typeName)
+    {
+        this->printCoeffs(type);
+    }
+}
 
 
 // * * * * * * * * * * * * * * * Member Functions  * * * * * * * * * * * * * //

src/conversion/vtk/output/foamVtkPatchWriter.C

@@ -245,7 +245,7 @@ Foam::vtk::patchWriter::patchWriter
     nFaces_(0)
 {
     outputOptions opts(outOpts);
-    opts.append(false);  // No append
+    opts.append(false);  // No append supported
 
     os_.open((baseName + (legacy_ ? ".vtk" : ".vtp")).c_str());
     format_ = opts.newFormatter(os_);

src/conversion/vtk/output/foamVtkSurfaceMeshWriter.C

@@ -193,7 +193,7 @@ Foam::vtk::surfaceMeshWriter::surfaceMeshWriter
     os_()
 {
     outputOptions opts(outOpts);
-    opts.legacy(true);  // No append supported
+    opts.append(false);  // No append supported
 
     os_.open((baseName + (legacy_ ? ".vtk" : ".vtp")).c_str());
     format_ = opts.newFormatter(os_);

src/functionObjects/field/DESModelRegions/DESModelRegions.C

@@ -172,6 +172,8 @@ bool Foam::functionObjects::DESModelRegions::write()
         << "    writing field " << DESModelRegions.name() << nl
         << endl;
 
+    DESModelRegions.write();
+
     return true;
 }
 

src/meshTools/output/foamVtkWriteCellSetFaces.C

@@ -41,7 +41,7 @@ void Foam::vtk::writeCellSetFaces
 )
 {
     outputOptions opts(outOpts);
-    opts.legacy(true);  // Legacy only, no append
+    opts.legacy(true);  // Legacy only, no xml, no append
 
     const bool legacy_(opts.legacy());
 

src/meshTools/output/foamVtkWriteFaceSet.C

@@ -41,7 +41,7 @@ void Foam::vtk::writeFaceSet
 )
 {
     outputOptions opts(outOpts);
-    opts.legacy(true);  // Legacy only, no append
+    opts.legacy(true);  // Legacy only, no xml, no append
 
     const bool legacy_(opts.legacy());
 

src/meshTools/output/foamVtkWritePointSet.C

@@ -40,7 +40,7 @@ void Foam::vtk::writePointSet
 )
 {
     outputOptions opts(outOpts);
-    opts.legacy(true);  // Legacy only, no append
+    opts.legacy(true);  // Legacy only, no xml, no append
 
     const bool legacy_(opts.legacy());
 

src/parallel/decompose/decompositionMethods/multiLevelDecomp/multiLevelDecomp.C

@@ -3,7 +3,7 @@
   \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
    \\    /   O peration     |
     \\  /    A nd           | Copyright (C) 2011-2017 OpenFOAM Foundation
-     \\/     M anipulation  |
+     \\/     M anipulation  | Copyright (C) 2017 OpenCFD Ltd.
 -------------------------------------------------------------------------------
 License
     This file is part of OpenFOAM.
@@ -99,7 +99,7 @@ void Foam::multiLevelDecomp::subsetGlobalCellCells
         forAll(cCells, i)
         {
             // Get locally-compact cell index of neighbouring cell
-            label nbrCelli = oldToNew[cCells[i]];
+            const label nbrCelli = oldToNew[cCells[i]];
             if (nbrCelli == -1)
             {
                 cutConnections[allDist[cCells[i]]]++;
@@ -109,10 +109,10 @@ void Foam::multiLevelDecomp::subsetGlobalCellCells
                 // Reconvert local cell index into global one
 
                 // Get original neighbour
-                label celli = set[subCelli];
-                label oldNbrCelli = cellCells[celli][i];
+                const label celli = set[subCelli];
+                const label oldNbrCelli = cellCells[celli][i];
                 // Get processor from original neighbour
-                label proci = globalCells.whichProcID(oldNbrCelli);
+                const label proci = globalCells.whichProcID(oldNbrCelli);
                 // Convert into global compact numbering
                 cCells[newI++] = globalSubCells.toGlobal(proci, nbrCelli);
             }
@@ -127,15 +127,16 @@ void Foam::multiLevelDecomp::decompose
     const labelListList& pointPoints,
     const pointField& points,
     const scalarField& pointWeights,
-    const labelList& pointMap,      // map back to original points
-    const label levelI,
+    const labelUList& pointMap,     // map back to original points
+    const label currLevel,
+    const label leafOffset,
 
-    labelField& finalDecomp
+    labelList& finalDecomp
 )
 {
     labelList dist
     (
-        methods_[levelI].decompose
+        methods_[currLevel].decompose
         (
             pointPoints,
             points,
@@ -143,30 +144,62 @@ void Foam::multiLevelDecomp::decompose
         )
     );
 
+    // The next recursion level
+    const label nextLevel = currLevel+1;
+
+    // Number of domains at this current level
+    const label nCurrDomains = methods_[currLevel].nDomains();
+
+    // Calculate the domain remapping.
+    // The decompose() method delivers a distribution of [0..nDomains-1]
+    // which we map to the final location according to the decomposition
+    // leaf we are on.
+
+    labelList domainLookup(nCurrDomains);
+    {
+        label sizes = 1;  // Cumulative number of domains
+        for (label i = 0; i <= currLevel; ++i)
+        {
+            sizes *= methods_[i].nDomains();
+        }
+
+        // Distribution of domains at this level
+        sizes = this->nDomains() / sizes;
+
+        forAll(domainLookup, i)
+        {
+            domainLookup[i] = i * sizes + leafOffset;
+        }
+    }
+
+    if (debug)
+    {
+        Info<< "Distribute at level " << currLevel
+            << " to domains" << nl
+            << flatOutput(domainLookup) << endl;
+    }
+
+    // Extract processor+local index from point-point addressing
     forAll(pointMap, i)
     {
-        label orig = pointMap[i];
-        finalDecomp[orig] += dist[i];
+        const label orig = pointMap[i];
+        finalDecomp[orig] = domainLookup[dist[i]];
     }
 
-    if (levelI != methods_.size()-1)
+    if (nextLevel < methods_.size())
     {
         // Recurse
 
         // Determine points per domain
-        label n = methods_[levelI].nDomains();
-        labelListList domainToPoints(invertOneToMany(n, dist));
-
-        // 'Make space' for new levels of decomposition
-        finalDecomp *= methods_[levelI+1].nDomains();
+        labelListList domainToPoints(invertOneToMany(nCurrDomains, dist));
 
         // Extract processor+local index from point-point addressing
         if (debug && Pstream::master())
         {
-            Pout<< "Decomposition at level " << levelI << " :" << endl;
+            Pout<< "Decomposition at level " << currLevel << " :" << endl;
         }
 
-        for (label domainI = 0; domainI < n; domainI++)
+        for (label domainI = 0; domainI < nCurrDomains; domainI++)
         {
             // Extract elements for current domain
             const labelList domainPoints(findIndices(dist, domainI));
@@ -180,7 +213,7 @@ void Foam::multiLevelDecomp::decompose
             labelList nOutsideConnections;
             subsetGlobalCellCells
             (
-                n,
+                nCurrDomains,
                 domainI,
                 dist,
 
@@ -196,12 +229,12 @@ void Foam::multiLevelDecomp::decompose
             Pstream::listCombineScatter(nOutsideConnections);
             label nPatches = 0;
             label nFaces = 0;
-            forAll(nOutsideConnections, i)
+            for (const label nConnect : nOutsideConnections)
             {
-                if (nOutsideConnections[i] > 0)
+                if (nConnect > 0)
                 {
-                    nPatches++;
-                    nFaces += nOutsideConnections[i];
+                    ++nPatches;
+                    nFaces += nConnect;
                 }
             }
 
@@ -224,7 +257,8 @@ void Foam::multiLevelDecomp::decompose
                 subPoints,
                 subWeights,
                 subPointMap,
-                levelI+1,
+                nextLevel,
+                domainLookup[domainI], // The offset for this level and leaf
 
                 finalDecomp
             );
@@ -238,24 +272,30 @@ void Foam::multiLevelDecomp::decompose
         if (debug)
         {
             // Do straight decompose of two levels
-            label nNext = methods_[levelI+1].nDomains();
-            label nTotal = n*nNext;
+            const label nNext = methods_[nextLevel].nDomains();
+            const label nTotal = nCurrDomains * nNext;
 
-            // Retrieve original level0 dictionary and modify number of domains
-            dictionary::const_iterator iter =
-                decompositionDict_.optionalSubDict(typeName + "Coeffs").begin();
-            dictionary myDict = iter().dict();
-            myDict.set("numberOfSubdomains", nTotal);
+            // Get original level0 dictionary and modify numberOfSubdomains
+            dictionary level0Dict;
+            forAllConstIter(dictionary, methodsDict_, iter)
+            {
+                if (iter().isDict())
+                {
+                    level0Dict = iter().dict();
+                    break;
+                }
+            }
+            level0Dict.set("numberOfSubdomains", nTotal);
 
             if (debug && Pstream::master())
             {
-                Pout<< "Reference decomposition with " << myDict << " :"
+                Pout<< "Reference decomposition with " << level0Dict << " :"
                     << endl;
             }
 
             autoPtr<decompositionMethod> method0 = decompositionMethod::New
             (
-                myDict
+                level0Dict
             );
             labelList dist
             (
@@ -267,12 +307,12 @@ void Foam::multiLevelDecomp::decompose
                 )
             );
 
-            for (label blockI = 0; blockI < n; blockI++)
+            for (label blockI = 0; blockI < nCurrDomains; blockI++)
             {
                 // Count the number inbetween blocks of nNext size
 
                 label nPoints = 0;
-                labelList nOutsideConnections(n, 0);
+                labelList nOutsideConnections(nCurrDomains, 0);
                 forAll(pointPoints, pointi)
                 {
                     if ((dist[pointi] / nNext) == blockI)
@@ -283,7 +323,7 @@ void Foam::multiLevelDecomp::decompose
 
                         forAll(pPoints, i)
                         {
-                            label distBlockI = dist[pPoints[i]] / nNext;
+                            const label distBlockI = dist[pPoints[i]] / nNext;
                             if (distBlockI != blockI)
                             {
                                 nOutsideConnections[distBlockI]++;
@@ -301,12 +341,12 @@ void Foam::multiLevelDecomp::decompose
                 Pstream::listCombineScatter(nOutsideConnections);
                 label nPatches = 0;
                 label nFaces = 0;
-                forAll(nOutsideConnections, i)
+                for (const label nConnect : nOutsideConnections)
                 {
-                    if (nOutsideConnections[i] > 0)
+                    if (nConnect > 0)
                     {
-                        nPatches++;
-                        nFaces += nOutsideConnections[i];
+                        ++nPatches;
+                        nFaces += nConnect;
                     }
                 }
 
@@ -330,31 +370,37 @@ void Foam::multiLevelDecomp::decompose
 Foam::multiLevelDecomp::multiLevelDecomp(const dictionary& decompositionDict)
 :
     decompositionMethod(decompositionDict),
-    methodsDict_(decompositionDict_.optionalSubDict(typeName + "Coeffs"))
+    methodsDict_(decompositionDict_.subDict(typeName + "Coeffs"))
 {
     methods_.setSize(methodsDict_.size());
-    label i = 0;
+    label nLevels = 0;
     forAllConstIter(dictionary, methodsDict_, iter)
     {
-        methods_.set(i++, decompositionMethod::New(iter().dict()));
+        // Ignore primitive entries which may be there for additional control
+        if (iter().isDict())
+        {
+            methods_.set(nLevels++, decompositionMethod::New(iter().dict()));
+        }
     }
 
-    label n = 1;
+    methods_.setSize(nLevels);
+
+    label nTot = 1;
     Info<< "decompositionMethod " << type() << " :" << endl;
     forAll(methods_, i)
     {
         Info<< "    level " << i << " decomposing with " << methods_[i].type()
             << " into " << methods_[i].nDomains() << " subdomains." << endl;
 
-        n *= methods_[i].nDomains();
+        nTot *= methods_[i].nDomains();
     }
 
-    if (n != nDomains())
+    if (nTot != nDomains())
     {
         FatalErrorInFunction
             << "Top level decomposition specifies " << nDomains()
             << " domains which is not equal to the product of"
-            << " all sub domains " << n
+            << " all sub domains " << nTot
             << exit(FatalError);
     }
 }
@@ -385,7 +431,7 @@ Foam::labelList Foam::multiLevelDecomp::decompose
     CompactListList<label> cellCells;
     calcCellCells(mesh, identity(cc.size()), cc.size(), true, cellCells);
 
-    labelField finalDecomp(cc.size(), 0);
+    labelList finalDecomp(cc.size(), 0);
     labelList cellMap(identity(cc.size()));
 
     decompose
@@ -395,6 +441,7 @@ Foam::labelList Foam::multiLevelDecomp::decompose
         cWeights,
         cellMap,      // map back to original cells
         0,
+        0,
 
         finalDecomp
     );
@@ -410,7 +457,7 @@ Foam::labelList Foam::multiLevelDecomp::decompose
     const scalarField& pointWeights
 )
 {
-    labelField finalDecomp(points.size(), 0);
+    labelList finalDecomp(points.size(), 0);
     labelList pointMap(identity(points.size()));
 
     decompose
@@ -420,6 +467,7 @@ Foam::labelList Foam::multiLevelDecomp::decompose
         pointWeights,
         pointMap,       // map back to original points
         0,
+        0,
 
         finalDecomp
     );

src/parallel/decompose/decompositionMethods/multiLevelDecomp/multiLevelDecomp.H

@@ -3,7 +3,7 @@
   \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
    \\    /   O peration     |
     \\  /    A nd           | Copyright (C) 2011-2015 OpenFOAM Foundation
-     \\/     M anipulation  |
+     \\/     M anipulation  | Copyright (C) 2017 OpenCFD Ltd.
 -------------------------------------------------------------------------------
 License
     This file is part of OpenFOAM.
@@ -71,21 +71,22 @@ class multiLevelDecomp
             labelList& cutConnections
         ) const;
 
-        //- Decompose level methodI without addressing
+        //- Decompose at 'currLevel' without addressing
         void decompose
         (
             const labelListList& pointPoints,
             const pointField& points,
             const scalarField& pointWeights,
-            const labelList& pointMap,  // map back to original points
-            const label levelI,
+            const labelUList& pointMap,  // map back to original points
+            const label currLevel,
+            const label leafOffset,
 
-            labelField& finalDecomp
+            labelList& finalDecomp
         );
 
         //- Disallow default bitwise copy construct and assignment
-        void operator=(const multiLevelDecomp&);
-        multiLevelDecomp(const multiLevelDecomp&);
+        void operator=(const multiLevelDecomp&) = delete;
+        multiLevelDecomp(const multiLevelDecomp&) = delete;
 
 
 public: