Merge branch 'master' of ssh://noisy/home/noisy3/OpenFOAM/OpenFOAM-dev

applications/utilities/mesh/generation/extrudeMesh/extrudeMesh.C

@@ -23,8 +23,9 @@ License
     Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
 
 Description
-    Extrude mesh from existing patch (flipped so has inwards pointing
+    Extrude mesh from existing patch (by default outwards facing normals;
-    normals) or from patch read from file.
+    optional flips faces)
+    or from patch read from file.
     Note: Merges close points so be careful.
 
     Type of extrusion prescribed by run-time selectable model.
@@ -108,14 +109,11 @@ int main(int argc, char *argv[])
 
         const polyPatch& pp = mesh.boundaryMesh()[patchID];
         fMesh.reset(new faceMesh(pp.localFaces(), pp.localPoints()));
-        fMesh().flip();
 
         {
-            fileName surfName(patchName + ".sMesh");
+            fileName surfName(runTime.path()/patchName + ".sMesh");
-
+            Info<< "Writing patch as surfaceMesh to "
-            Info<< "Writing (flipped) patch as surfaceMesh to "
                 << surfName << nl << endl;
-
             OFstream os(surfName);
             os << fMesh() << nl;
         }
@@ -142,6 +140,20 @@ int main(int argc, char *argv[])
             << "patch or surface." << exit(FatalError);
     }
 
+    Switch flipNormals(dict.lookup("flipNormals"));
+
+    if (flipNormals)
+    {
+        Info<< "Flipping faces." << nl << endl;
+
+        faceList faces(fMesh().size());
+        forAll(faces, i)
+        {
+            faces[i] = fMesh()[i].reverseFace();
+        }
+        fMesh.reset(new faceMesh(faces, fMesh().localPoints()));
+    }
+
 
     Info<< "Extruding patch with :" << nl
             << "    points     : " << fMesh().points().size() << nl

applications/utilities/mesh/generation/extrudeMesh/extrudeModel/linearNormal/linearNormal.C

@@ -47,7 +47,14 @@ linearNormal::linearNormal(const dictionary& dict)
 :
     extrudeModel(typeName, dict),
     thickness_(readScalar(coeffDict_.lookup("thickness")))
-{}
+{
+    if (thickness_ <= 0)
+    {
+        FatalErrorIn("linearNormal(const dictionary&)")
+            << "thickness should be positive : " << thickness_
+            << exit(FatalError);
+    }
+}
 
 
 // * * * * * * * * * * * * * * * * Destructor  * * * * * * * * * * * * * * * //

applications/utilities/mesh/generation/extrudeMesh/extrudeProperties

@@ -19,31 +19,40 @@ FoamFile
 constructFrom patch;    //surface;
 
 // If construct from (flipped) patch
-sourceCase "../cavity";
+sourceCase "$FOAM_RUN/icoFoam/cavity";
 sourcePatch movingWall;
 
+// Flip surface normals before usage.
+flipNormals false;
+
 // If construct from surface
 surface "movingWall.sMesh";
 
 
-// Do front and back need to be merged?
+// Do front and back need to be merged? Usually only makes sense for 360
-mergeFaces false;
+// degree wedges.
+mergeFaces true;
+
 
 //- Linear extrusion in point-normal direction
 //extrudeModel        linearNormal;
+
 //- Wedge extrusion. If nLayers is 1 assumes symmetry around plane.
 extrudeModel        wedge;
+
 //- Extrudes into sphere around (0 0 0)
 //extrudeModel        linearRadial;
+
+//- Extrudes into sphere with grading according to pressure (atmospherics)
 //extrudeModel        sigmaRadial;
 
-nLayers             6;
+nLayers             20;
 
 wedgeCoeffs
 {
     axisPt      (0 0.1 0);
-    axis        (1 0 0);
+    axis        (-1 0 0);
-    angle       90.0;   // For nLayers=1 assume symmetry so angle/2 on each side
+    angle       360;  // For nLayers=1 assume symmetry so angle/2 on each side
 }
 
 linearNormalCoeffs

applications/utilities/mesh/generation/extrudeMesh/extrudedMesh/extrudedMesh.C

@@ -109,15 +109,33 @@ Foam::Xfer<Foam::faceList> Foam::extrudedMesh::extrudedFaces
         label currentLayerOffset = layer*surfacePoints.size();
         label nextLayerOffset = currentLayerOffset + surfacePoints.size();
 
-        // Side faces from layer to layer+1
+        // Vertical faces from layer to layer+1
-        for (label i=0; i<nInternalEdges; i++)
+        for (label edgeI=0; edgeI<nInternalEdges; edgeI++)
         {
-            quad[0] = surfaceEdges[i][1] + currentLayerOffset;
+            const edge& e = surfaceEdges[edgeI];
-            quad[1] = surfaceEdges[i][0] + currentLayerOffset;
+            const labelList& edgeFaces = extrudePatch.edgeFaces()[edgeI];
-            quad[2] = surfaceEdges[i][0] + nextLayerOffset;
-            quad[3] = surfaceEdges[i][1] + nextLayerOffset;
 
-            eFaces[facei++] = face(quad).reverseFace();
+            face& f = eFaces[facei++];
+            f.setSize(4);
+
+            if
+            (
+                (edgeFaces[0] < edgeFaces[1])
+             == sameOrder(surfaceFaces[edgeFaces[0]], e)
+            )
+            {
+                f[0] = e[0] + currentLayerOffset;
+                f[1] = e[1] + currentLayerOffset;
+                f[2] = e[1] + nextLayerOffset;
+                f[3] = e[0] + nextLayerOffset;
+            }
+            else
+            {
+                f[0] = e[1] + currentLayerOffset;
+                f[1] = e[0] + currentLayerOffset;
+                f[2] = e[0] + nextLayerOffset;
+                f[3] = e[1] + nextLayerOffset;
+            }
         }
 
         // Faces between layer and layer+1
@@ -128,9 +146,9 @@ Foam::Xfer<Foam::faceList> Foam::extrudedMesh::extrudedFaces
                 eFaces[facei++] =
                     face
                     (
-                        surfaceFaces[i].reverseFace()
+                        surfaceFaces[i] //.reverseFace()
                       + nextLayerOffset
-                    ).reverseFace();
+                    );
             }
         }
     }
@@ -142,40 +160,46 @@ Foam::Xfer<Foam::faceList> Foam::extrudedMesh::extrudedFaces
         label nextLayerOffset = currentLayerOffset + surfacePoints.size();
 
         // Side faces across layer
-        for (label i=nInternalEdges; i<surfaceEdges.size(); i++)
+        for (label edgeI=nInternalEdges; edgeI<surfaceEdges.size(); edgeI++)
         {
-            const edge& e = surfaceEdges[i];
+            const edge& e = surfaceEdges[edgeI];
-            quad[0] = e[1] + currentLayerOffset;
+            const labelList& edgeFaces = extrudePatch.edgeFaces()[edgeI];
-            quad[1] = e[0] + currentLayerOffset;
-            quad[2] = e[0] + nextLayerOffset;
-            quad[3] = e[1] + nextLayerOffset;
 
-            label ownerFace = extrudePatch.edgeFaces()[i][0];
+            face& f = eFaces[facei++];
+            f.setSize(4);
 
-            if (sameOrder(surfaceFaces[ownerFace], e))
+            if (sameOrder(surfaceFaces[edgeFaces[0]], e))
             {
-                reverse(quad);
+                f[0] = e[0] + currentLayerOffset;
+                f[1] = e[1] + currentLayerOffset;
+                f[2] = e[1] + nextLayerOffset;
+                f[3] = e[0] + nextLayerOffset;
+            }
+            else
+            {
+                f[0] = e[1] + currentLayerOffset;
+                f[1] = e[0] + currentLayerOffset;
+                f[2] = e[0] + nextLayerOffset;
+                f[3] = e[1] + nextLayerOffset;
             }
-
-            eFaces[facei++] = face(quad);
         }
     }
 
-    // Top faces
-    forAll(surfaceFaces, i)
-    {
-        eFaces[facei++] = face(surfaceFaces[i]).reverseFace();
-    }
-
     // Bottom faces
     forAll(surfaceFaces, i)
+    {
+        eFaces[facei++] = face(surfaceFaces[i]).reverseFace();
+    }
+
+    // Top faces
+    forAll(surfaceFaces, i)
     {
         eFaces[facei++] =
             face
             (
-                surfaceFaces[i].reverseFace()
+                surfaceFaces[i]
               + nLayers*surfacePoints.size()
-            ).reverseFace();
+            );
     }
 
     // return points for transferring

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

@@ -67,8 +67,13 @@ Foam::label Foam::checkTopology
     {
         forAll(mesh.faceZones(), zoneI)
         {
-            if (mesh.faceZones()[zoneI].checkParallelSync(true))
+            if (mesh.faceZones()[zoneI].checkParallelSync(false))
             {
+                Info<< " ***FaceZone " << mesh.faceZones()[zoneI].name()
+                    << " is not correctly synchronised"
+                    << " acrosss coupled boundaries."
+                    << " (coupled faces both"
+                    << " present in set but with opposite flipmap)" << endl;
                 noFailedChecks++;
             }
         }

bin/foamRunTutorials

@@ -50,7 +50,7 @@ elif [ -d "./system" ]
 then
     # Normal case.
     parentDir=`dirname $PWD`
-    application=`basename $parentDir`
+    application=`getApplication`
     runApplication blockMesh
     runApplication $application
 else

bin/tools/RunFunctions

@@ -29,6 +29,11 @@
 #
 #------------------------------------------------------------------------------
 
+getApplication ()
+{
+    grep application system/controlDict | sed "s/application *\([a-zA-Z]*\);/\1/"
+}
+
 runApplication ()
 {
     APP_RUN=$1; shift

src/OpenFOAM/fields/UniformDimensionedFields/UniformDimensionedField.H

@@ -60,7 +60,7 @@ class UniformDimensionedField
 public:
 
     //- Runtime type information
-    TypeName("DimensionedType");
+    TypeName("UniformDimensionedField");
 
 
     // Constructors

src/OpenFOAM/fields/UniformDimensionedFields/uniformDimensionedFields.H

@@ -28,7 +28,7 @@ InClass
 Description
 
 SourceFiles
-    UniformDimensionedFields.C
+    uniformDimensionedFields.C
 
 \*---------------------------------------------------------------------------*/
 

src/autoMesh/autoHexMesh/meshRefinement/meshRefinementBaffles.C

@@ -100,6 +100,12 @@ Foam::label Foam::meshRefinement::createBaffle
                 << " ownPatch:" << ownPatch << abort(FatalError);
         }
 
+        bool reverseFlip = false;
+        if (zoneID >= 0)
+        {
+            reverseFlip = !zoneFlip;
+        }
+
         dupFaceI = meshMod.setAction
         (
             polyAddFace
@@ -113,7 +119,7 @@ Foam::label Foam::meshRefinement::createBaffle
                 true,                       // face flip
                 neiPatch,                   // patch for face
                 zoneID,                     // zone for face
-                !zoneFlip                   // face flip in zone
+                reverseFlip                 // face flip in zone
             )
         );
     }

src/finiteVolume/Make/files

@@ -104,6 +104,7 @@ $(constraintFvPatchFields)/wedge/wedgeFvPatchFields.C
 $(constraintFvPatchFields)/wedge/wedgeFvPatchScalarField.C
 
 derivedFvPatchFields = $(fvPatchFields)/derived
+$(derivedFvPatchFields)/activeBaffleVelocity/activeBaffleVelocityFvPatchVectorField.C
 $(derivedFvPatchFields)/advective/advectiveFvPatchFields.C
 $(derivedFvPatchFields)/directMappedFixedValue/directMappedFixedValueFvPatchFields.C
 $(derivedFvPatchFields)/directMappedVelocityFluxFixedValue/directMappedVelocityFluxFixedValueFvPatchField.C

src/finiteVolume/fields/fvPatchFields/derived/activeBaffleVelocity/activeBaffleVelocityFvPatchVectorField.C

@@ -0,0 +1,274 @@
+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+   \\    /   O peration     |
+    \\  /    A nd           | Copyright (C) 1991-2009 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 2 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, write to the Free Software Foundation,
+    Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
+
+\*---------------------------------------------------------------------------*/
+
+#include "activeBaffleVelocityFvPatchVectorField.H"
+#include "addToRunTimeSelectionTable.H"
+#include "volFields.H"
+#include "surfaceFields.H"
+
+// * * * * * * * * * * * * * * * * Constructors  * * * * * * * * * * * * * * //
+
+Foam::activeBaffleVelocityFvPatchVectorField::
+activeBaffleVelocityFvPatchVectorField
+(
+    const fvPatch& p,
+    const DimensionedField<vector, volMesh>& iF
+)
+:
+    fixedValueFvPatchVectorField(p, iF),
+    pName_("p"),
+    cyclicPatchName_(),
+    cyclicPatchLabel_(-1),
+    orientation_(1),
+    initWallSf_(0),
+    initCyclicSf_(0),
+    openFraction_(0),
+    openingTime_(0),
+    maxOpenFractionDelta_(0),
+    curTimeIndex_(-1)
+{}
+
+
+Foam::activeBaffleVelocityFvPatchVectorField::
+activeBaffleVelocityFvPatchVectorField
+(
+    const activeBaffleVelocityFvPatchVectorField& ptf,
+    const fvPatch& p,
+    const DimensionedField<vector, volMesh>& iF,
+    const fvPatchFieldMapper& mapper
+)
+:
+    fixedValueFvPatchVectorField(ptf, p, iF, mapper),
+    pName_(ptf.pName_),
+    cyclicPatchName_(ptf.cyclicPatchName_),
+    cyclicPatchLabel_(ptf.cyclicPatchLabel_),
+    orientation_(ptf.orientation_),
+    initWallSf_(ptf.initWallSf_),
+    initCyclicSf_(ptf.initCyclicSf_),
+    openFraction_(ptf.openFraction_),
+    openingTime_(ptf.openingTime_),
+    maxOpenFractionDelta_(ptf.maxOpenFractionDelta_),
+    curTimeIndex_(-1)
+{}
+
+
+Foam::activeBaffleVelocityFvPatchVectorField::
+activeBaffleVelocityFvPatchVectorField
+(
+    const fvPatch& p,
+    const DimensionedField<vector, volMesh>& iF,
+    const dictionary& dict
+)
+:
+    fixedValueFvPatchVectorField(p, iF),
+    pName_("p"),
+    cyclicPatchName_(dict.lookup("cyclicPatch")),
+    cyclicPatchLabel_(p.patch().boundaryMesh().findPatchID(cyclicPatchName_)),
+    orientation_(readLabel(dict.lookup("orientation"))),
+    initWallSf_(p.Sf()),
+    initCyclicSf_(p.boundaryMesh()[cyclicPatchLabel_].Sf()),
+    openFraction_(readScalar(dict.lookup("openFraction"))),
+    openingTime_(readScalar(dict.lookup("openingTime"))),
+    maxOpenFractionDelta_(readScalar(dict.lookup("maxOpenFractionDelta"))),
+    curTimeIndex_(-1)
+{
+    fvPatchVectorField::operator=(vector::zero);
+
+    if (dict.found("p"))
+    {
+        dict.lookup("p") >> pName_;
+    }
+}
+
+
+Foam::activeBaffleVelocityFvPatchVectorField::
+activeBaffleVelocityFvPatchVectorField
+(
+    const activeBaffleVelocityFvPatchVectorField& ptf
+)
+:
+    fixedValueFvPatchVectorField(ptf),
+    pName_(ptf.pName_),
+    cyclicPatchName_(ptf.cyclicPatchName_),
+    cyclicPatchLabel_(ptf.cyclicPatchLabel_),
+    orientation_(ptf.orientation_),
+    initWallSf_(ptf.initWallSf_),
+    initCyclicSf_(ptf.initCyclicSf_),
+    openFraction_(ptf.openFraction_),
+    openingTime_(ptf.openingTime_),
+    maxOpenFractionDelta_(ptf.maxOpenFractionDelta_),
+    curTimeIndex_(-1)
+{}
+
+
+Foam::activeBaffleVelocityFvPatchVectorField::
+activeBaffleVelocityFvPatchVectorField
+(
+    const activeBaffleVelocityFvPatchVectorField& ptf,
+    const DimensionedField<vector, volMesh>& iF
+)
+:
+    fixedValueFvPatchVectorField(ptf, iF),
+    pName_(ptf.pName_),
+    cyclicPatchName_(ptf.cyclicPatchName_),
+    cyclicPatchLabel_(ptf.cyclicPatchLabel_),
+    orientation_(ptf.orientation_),
+    initWallSf_(ptf.initWallSf_),
+    initCyclicSf_(ptf.initCyclicSf_),
+    openFraction_(ptf.openFraction_),
+    openingTime_(ptf.openingTime_),
+    maxOpenFractionDelta_(ptf.maxOpenFractionDelta_),
+    curTimeIndex_(-1)
+{}
+
+
+// * * * * * * * * * * * * * * * Member Functions  * * * * * * * * * * * * * //
+
+void Foam::activeBaffleVelocityFvPatchVectorField::autoMap
+(
+    const fvPatchFieldMapper& m
+)
+{
+    fixedValueFvPatchVectorField::autoMap(m);
+
+    //- Note: cannot map field from cyclic patch anyway so just recalculate
+    //  Areas should be consistent when doing autoMap except in case of
+    //  topo changes.
+    initWallSf_ = patch().Sf();
+    initCyclicSf_ = patch().boundaryMesh()[cyclicPatchLabel_].Sf();
+}
+
+void Foam::activeBaffleVelocityFvPatchVectorField::rmap
+(
+    const fvPatchVectorField& ptf,
+    const labelList& addr
+)
+{
+    fixedValueFvPatchVectorField::rmap(ptf, addr);
+
+    //- Note: cannot map field from cyclic patch anyway so just recalculate
+    //  Areas should be consistent when doing rmap (mainly reconstructPar)
+    initWallSf_ = patch().Sf();
+    initCyclicSf_ = patch().boundaryMesh()[cyclicPatchLabel_].Sf();
+}
+
+
+void Foam::activeBaffleVelocityFvPatchVectorField::updateCoeffs()
+{
+    if (updated())
+    {
+        return;
+    }
+
+    // Execute the change to the openFraction only once per time-step
+    if (curTimeIndex_ != this->db().time().timeIndex())
+    {
+        const volScalarField& p = db().lookupObject<volScalarField>
+        (
+            pName_
+        );
+
+        const fvPatch& cyclicPatch = patch().boundaryMesh()[cyclicPatchLabel_];
+        const labelList& cyclicFaceCells = cyclicPatch.patch().faceCells();
+        label nCyclicFaces = cyclicFaceCells.size();
+        label nCyclicFacesPerSide = nCyclicFaces/2;
+
+        scalar forceDiff = 0;
+
+        for (label facei=0; facei<nCyclicFacesPerSide; facei++)
+        {
+            forceDiff += p[cyclicFaceCells[facei]]*mag(initCyclicSf_[facei]);
+        }
+
+        for (label facei=nCyclicFacesPerSide; facei<nCyclicFaces; facei++)
+        {
+            forceDiff -= p[cyclicFaceCells[facei]]*mag(initCyclicSf_[facei]);
+        }
+
+        openFraction_ =
+            max(min(
+                openFraction_
+              + max
+                (
+                    this->db().time().deltaT().value()/openingTime_,
+                    maxOpenFractionDelta_
+                )
+               *(orientation_*sign(forceDiff)),
+              1 - 1e-6), 1e-6);
+
+        Info<< "openFraction = " << openFraction_ << endl;
+
+        vectorField::subField Sfw = patch().patch().faceAreas();
+        vectorField newSfw = (1 - openFraction_)*initWallSf_;
+        forAll(Sfw, facei)
+        {
+            Sfw[facei] = newSfw[facei];
+        }
+        const_cast<scalarField&>(patch().magSf()) = mag(patch().Sf());
+
+        const_cast<vectorField&>(cyclicPatch.Sf()) =
+            openFraction_*initCyclicSf_;
+        const_cast<scalarField&>(cyclicPatch.magSf()) =
+            mag(cyclicPatch.Sf());
+
+        curTimeIndex_ = this->db().time().timeIndex();
+    }
+
+    fixedValueFvPatchVectorField::updateCoeffs();
+}
+
+
+void Foam::activeBaffleVelocityFvPatchVectorField::write(Ostream& os) const
+{
+    fvPatchVectorField::write(os);
+    os.writeKeyword("cyclicPatch")
+        << cyclicPatchName_ << token::END_STATEMENT << nl;
+    os.writeKeyword("orientation")
+        << orientation_ << token::END_STATEMENT << nl;
+    os.writeKeyword("openingTime")
+        << openingTime_ << token::END_STATEMENT << nl;
+    os.writeKeyword("maxOpenFractionDelta")
+        << maxOpenFractionDelta_ << token::END_STATEMENT << nl;
+    os.writeKeyword("openFraction")
+        << openFraction_ << token::END_STATEMENT << nl;
+    os.writeKeyword("p")
+        << pName_ << token::END_STATEMENT << nl;
+    writeEntry("value", os);
+}
+
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+namespace Foam
+{
+    makePatchTypeField
+    (
+        fvPatchVectorField,
+        activeBaffleVelocityFvPatchVectorField
+    );
+}
+
+// ************************************************************************* //

src/finiteVolume/fields/fvPatchFields/derived/activeBaffleVelocity/activeBaffleVelocityFvPatchVectorField.H

@@ -0,0 +1,193 @@
+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+   \\    /   O peration     |
+    \\  /    A nd           | Copyright (C) 1991-2009 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 2 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, write to the Free Software Foundation,
+    Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
+
+Class
+    Foam::activeBaffleVelocityFvPatchVectorField
+
+Description
+    Boundary condition that modifies mesh areas based on velocity.
+
+SourceFiles
+    activeBaffleVelocityFvPatchVectorField.C
+
+\*---------------------------------------------------------------------------*/
+
+#ifndef activeBaffleVelocityFvPatchVectorField_H
+#define activeBaffleVelocityFvPatchVectorField_H
+
+#include "fvPatchFields.H"
+#include "fixedValueFvPatchFields.H"
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+namespace Foam
+{
+
+/*---------------------------------------------------------------------------*\
+                 Class activeBaffleVelocityFvPatch Declaration
+\*---------------------------------------------------------------------------*/
+
+class activeBaffleVelocityFvPatchVectorField
+:
+    public fixedValueFvPatchVectorField
+{
+    // Private data
+
+        //- Name of the pressure field used to calculate the force
+        //  on the active baffle
+        word pName_;
+
+        //- Name of the cyclic patch used when the active baffle is open
+        word cyclicPatchName_;
+
+        //- Index of the cyclic patch used when the active baffle is open
+        label cyclicPatchLabel_;
+
+        //- Orientation (1 or -1) of the active baffle patch.
+        //  Used to change the direction of opening without the need for
+        //  reordering the patch faces
+        label orientation_;
+
+        //- Initial wall patch areas
+        vectorField initWallSf_;
+
+        //- Initial cyclic patch areas
+        vectorField initCyclicSf_;
+
+        //- Current fraction of the active baffle which is open
+        scalar openFraction_;
+
+        //- Time taken for the active baffle to open
+        scalar openingTime_;
+
+        //- Maximum fractional change to the active baffle openness
+        //  per time-step
+        scalar maxOpenFractionDelta_;
+
+        label curTimeIndex_;
+
+
+public:
+
+    //- Runtime type information
+    TypeName("activeBaffleVelocity");
+
+
+    // Constructors
+
+        //- Construct from patch and internal field
+        activeBaffleVelocityFvPatchVectorField
+        (
+            const fvPatch&,
+            const DimensionedField<vector, volMesh>&
+        );
+
+        //- Construct from patch, internal field and dictionary
+        activeBaffleVelocityFvPatchVectorField
+        (
+            const fvPatch&,
+            const DimensionedField<vector, volMesh>&,
+            const dictionary&
+        );
+
+        //- Construct by mapping given activeBaffleVelocityFvPatchVectorField
+        //  onto a new patch
+        activeBaffleVelocityFvPatchVectorField
+        (
+            const activeBaffleVelocityFvPatchVectorField&,
+            const fvPatch&,
+            const DimensionedField<vector, volMesh>&,
+            const fvPatchFieldMapper&
+        );
+
+        //- Construct as copy
+        activeBaffleVelocityFvPatchVectorField
+        (
+            const activeBaffleVelocityFvPatchVectorField&
+        );
+
+        //- Construct and return a clone
+        virtual tmp<fvPatchVectorField> clone() const
+        {
+            return tmp<fvPatchVectorField>
+            (
+                new activeBaffleVelocityFvPatchVectorField(*this)
+            );
+        }
+
+        //- Construct as copy setting internal field reference
+        activeBaffleVelocityFvPatchVectorField
+        (
+            const activeBaffleVelocityFvPatchVectorField&,
+            const DimensionedField<vector, volMesh>&
+        );
+
+        //- Construct and return a clone setting internal field reference
+        virtual tmp<fvPatchVectorField> clone
+        (
+            const DimensionedField<vector, volMesh>& iF
+        ) const
+        {
+            return tmp<fvPatchVectorField>
+            (
+                new activeBaffleVelocityFvPatchVectorField(*this, iF)
+            );
+        }
+
+
+    // Member functions
+
+        // Mapping functions
+
+            //- Map (and resize as needed) from self given a mapping object
+            virtual void autoMap
+            (
+                const fvPatchFieldMapper&
+            );
+
+            //- Reverse map the given fvPatchField onto this fvPatchField
+            virtual void rmap
+            (
+                const fvPatchVectorField&,
+                const labelList&
+            );
+
+
+        //- Update the coefficients associated with the patch field
+        virtual void updateCoeffs();
+
+        //- Write
+        virtual void write(Ostream&) const;
+};
+
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+} // End namespace Foam
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+#endif
+
+// ************************************************************************* //

src/lagrangian/molecularDynamics/molecule/molecule/moleculeIO.C

@@ -37,7 +37,7 @@ Foam::molecule::molecule
     bool readFields
 )
 :
-    Particle<molecule>(cloud, is, true),
+    Particle<molecule>(cloud, is, readFields),
     Q_(tensor::zero),
     v_(vector::zero),
     a_(vector::zero),

tutorials/DNS/dnsFoam/boxTurb16/Allrun

@@ -2,8 +2,8 @@
 # Source tutorial run functions
 . $WM_PROJECT_DIR/bin/tools/RunFunctions
 
-# Get application name from directory
+# Get application name
-application="dnsFoam"
+application=`getApplication`
 
 runApplication blockMesh
 runApplication boxTurb

tutorials/DNS/dnsFoam/boxTurb16/system/controlDict

@@ -15,6 +15,8 @@ FoamFile
 }
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
 
+application     dnsFoam;
+
 startFrom       startTime;
 
 startTime       0;

tutorials/basic/laplacianFoam/flange/Allrun

@@ -2,8 +2,8 @@
 # Source tutorial run functions
 . $WM_PROJECT_DIR/bin/tools/RunFunctions
 
-# Get application directory
+# Get application name
-application="laplacianFoam"
+application=`getApplication`
 
 runAnsysToFoam()
 {

tutorials/basic/laplacianFoam/flange/system/controlDict

@@ -15,6 +15,8 @@ FoamFile
 }
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
 
+application     laplacianFoam;
+
 startFrom       latestTime;
 
 startTime       0;

tutorials/basic/potentialFoam/cylinder/Allrun

@@ -2,7 +2,7 @@
 # Source tutorial run functions
 . $WM_PROJECT_DIR/bin/tools/RunFunctions
 
-application="potentialFoam"
+application=`getApplication`
 
 runApplication blockMesh
 runApplication $application

tutorials/basic/potentialFoam/cylinder/system/controlDict

@@ -15,6 +15,8 @@ FoamFile
 }
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
 
+application     potentialFoam;
+
 startFrom       startTime;
 
 startTime       0;

tutorials/basic/potentialFoam/pitzDaily/Allrun

@@ -2,7 +2,7 @@
 # Source tutorial run functions
 . $WM_PROJECT_DIR/bin/tools/RunFunctions
 
-application="potentialFoam"
+application=`getApplication`
 
 runApplication blockMesh
 runApplication $application

tutorials/basic/potentialFoam/pitzDaily/system/controlDict

@@ -15,6 +15,8 @@ FoamFile
 }
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
 
+application     potentialFoam;
+
 startFrom       startTime;
 
 startTime       0;

tutorials/basic/scalarTransportFoam/pitzDaily/system/controlDict

@@ -15,6 +15,8 @@ FoamFile
 }
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
 
+application     scalarTransportFoam;
+
 startFrom       startTime;
 
 startTime       0;

tutorials/combustion/XiFoam/les/pitzDaily/constant/g

@@ -9,7 +9,7 @@ FoamFile
 {
     version     2.0;
     format      ascii;
-    class       dictionary;
+    class       uniformDimensionedVectorField;
     location    "constant";
     object      g;
 }

tutorials/combustion/XiFoam/les/pitzDaily/system/controlDict

@@ -15,6 +15,8 @@ FoamFile
 }
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
 
+application     XiFoam;
+
 startFrom       startTime;
 
 startTime       0;

tutorials/combustion/XiFoam/les/pitzDaily3D/constant/g

@@ -9,7 +9,7 @@ FoamFile
 {
     version     2.0;
     format      ascii;
-    class       dictionary;
+    class       uniformDimensionedVectorField;
     location    "constant";
     object      g;
 }

tutorials/combustion/XiFoam/les/pitzDaily3D/system/controlDict

@@ -15,6 +15,8 @@ FoamFile
 }
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
 
+application     XiFoam;
+
 startFrom       startTime;
 
 startTime       0;

tutorials/combustion/XiFoam/ras/Allrun

@@ -2,7 +2,7 @@
 # Source tutorial run functions
 . $WM_PROJECT_DIR/bin/tools/RunFunctions
 
-# Get application name from directory
+# Set application name
 application="XiFoam"
 
 setControlDict () {

tutorials/combustion/XiFoam/ras/moriyoshiHomogeneous/constant/g

@@ -9,7 +9,7 @@ FoamFile
 {
     version     2.0;
     format      ascii;
-    class       dictionary;
+    class       uniformDimensionedVectorField;
     location    "constant";
     object      g;
 }

tutorials/combustion/XiFoam/ras/moriyoshiHomogeneous/system/controlDict

@@ -15,6 +15,8 @@ FoamFile
 }
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
 
+application     XiFoam;
+
 startFrom       latestTime;
 
 startTime       0;

tutorials/combustion/dieselFoam/aachenBomb/constant/g

@@ -9,7 +9,7 @@ FoamFile
 {
     version     2.0;
     format      binary;
-    class       dictionary;
+    class       uniformDimensionedVectorField;
     location    "constant";
     object      g;
 }

tutorials/combustion/dieselFoam/aachenBomb/system/controlDict

@@ -15,6 +15,8 @@ FoamFile
 }
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
 
+application     dieselFoam;
+
 startFrom       startTime;
 
 startTime       0;

tutorials/combustion/engineFoam/kivaTest/Allrun

@@ -2,8 +2,8 @@
 # Source tutorial run functions
 . $WM_PROJECT_DIR/bin/tools/RunFunctions
 
-# Get application name from directory
+# Get application name
-application="engineFoam"
+application=`getApplication`
 
 runKivaToFoam ()
 {

tutorials/combustion/engineFoam/kivaTest/constant/g

@@ -9,7 +9,7 @@ FoamFile
 {
     version     2.0;
     format      ascii;
-    class       dictionary;
+    class       uniformDimensionedVectorField;
     location    "constant";
     object      g;
 }

tutorials/combustion/engineFoam/kivaTest/system/controlDict

@@ -15,7 +15,7 @@ FoamFile
 }
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
 
-applicationClass engineFoam;
+application     engineFoam;
 
 startFrom       startTime;
 

tutorials/combustion/engineFoam/kivaTest/system/controlDict.1st

@@ -15,7 +15,7 @@ FoamFile
 }
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
 
-applicationClass engineFoam;
+application     engineFoam;
 
 startFrom       startTime;
 

tutorials/combustion/engineFoam/kivaTest/system/controlDict.2nd

@@ -15,7 +15,7 @@ FoamFile
 }
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
 
-applicationClass engineFoam;
+application     engineFoam;
 
 startFrom       startTime;
 

tutorials/compressible/rhoCentralFoam/Allrun

@@ -2,8 +2,8 @@
 # Source tutorial run functions
 . $WM_PROJECT_DIR/bin/tools/RunFunctions
 
-# Get application name from directory
+# Get application name
-application=${PWD##*/}
+application="rhoCentralFoam"
 
 cases=" \
 shockTube \

tutorials/compressible/rhoCentralFoam/LadenburgJet60psi/system/controlDict

@@ -15,6 +15,8 @@ FoamFile
 }
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
 
+application     rhoCentralFoam;
+
 startFrom       latestTime;
 
 startTime       0;

tutorials/compressible/rhoCentralFoam/biconic25-55Run35/system/controlDict

@@ -15,6 +15,8 @@ FoamFile
 }
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
 
+application     rhoCentralFoam;
+
 startFrom       latestTime;
 
 startTime       0.005;

tutorials/compressible/rhoCentralFoam/forwardStep/system/controlDict

@@ -15,6 +15,8 @@ FoamFile
 }
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
 
+application     rhoCentralFoam;
+
 startFrom       startTime;
 
 startTime       0;

tutorials/compressible/rhoCentralFoam/obliqueShock/system/controlDict

@@ -15,6 +15,8 @@ FoamFile
 }
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
 
+application     rhoCentralFoam;
+
 startFrom       startTime;
 
 startTime       0;

tutorials/compressible/rhoCentralFoam/shockTube/system/controlDict

@@ -15,6 +15,8 @@ FoamFile
 }
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
 
+application     rhoCentralFoam;
+
 startFrom       startTime;
 
 startTime       0;

tutorials/compressible/rhoCentralFoam/wedge15Ma5/system/controlDict

@@ -15,6 +15,8 @@ FoamFile
 }
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
 
+application     rhoCentralFoam;
+
 startFrom       startTime;
 
 startTime       0;

tutorials/compressible/rhoPimpleFoam/angledDuct/system/controlDict

@@ -15,6 +15,8 @@ FoamFile
 }
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
 
+application     rhoPimpleFoam;
+
 startFrom       startTime;
 
 startTime       0;

tutorials/compressible/rhoPisoFoam/les/pitzDaily/system/controlDict

@@ -15,6 +15,8 @@ FoamFile
 }
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
 
+application     rhoPisoFoam;
+
 startFrom       startTime;
 
 startTime       0;

tutorials/compressible/rhoPisoFoam/ras/cavity/system/controlDict

@@ -15,6 +15,8 @@ FoamFile
 }
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
 
+application     rhoPisoFoam;
+
 startFrom       startTime;
 
 startTime       0;

tutorials/compressible/rhoPorousSimpleFoam/angledDuctExplicit/system/controlDict

@@ -15,6 +15,8 @@ FoamFile
 }
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
 
+application     rhoPorousSimpleFoam;
+
 startFrom       startTime;
 
 startTime       0;

tutorials/compressible/rhoPorousSimpleFoam/angledDuctImplicit/system/controlDict

@@ -15,6 +15,8 @@ FoamFile
 }
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
 
+application     rhoPorousSimpleFoam;
+
 startFrom       startTime;
 
 startTime       0;

tutorials/compressible/rhoSonicFoam/forwardStep/system/controlDict

@@ -15,6 +15,8 @@ FoamFile
 }
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
 
+application     rhoSonicFoam;
+
 startFrom       latestTime;
 
 startTime       0;

tutorials/compressible/rhoSonicFoam/shockTube/Allrun

@@ -1,9 +1,10 @@
 #!/bin/sh
+
 # Source tutorial run functions
 . $WM_PROJECT_DIR/bin/tools/RunFunctions
 
-# Get application name from directory
+# Get application name
-application="rhoSonicFoam"
+application=`getApplication`
 
 runApplication blockMesh
 runApplication setFields

tutorials/compressible/rhoSonicFoam/shockTube/system/controlDict

@@ -15,6 +15,8 @@ FoamFile
 }
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
 
+application     rhoSonicFoam;
+
 startFrom       startTime;
 
 startTime       0;

tutorials/compressible/rhopSonicFoam/shockTube/Allrun

@@ -2,7 +2,7 @@
 # Source tutorial run functions
 . $WM_PROJECT_DIR/bin/tools/RunFunctions
 
-application="rhopSonicFoam"
+application=`getApplication`
 
 runApplication blockMesh
 runApplication setFields

tutorials/compressible/rhopSonicFoam/shockTube/system/controlDict

@@ -15,6 +15,8 @@ FoamFile
 }
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
 
+application     rhopSonicFoam;
+
 startFrom       startTime;
 
 startTime       0;

tutorials/compressible/rhopSonicFoam/wedge15Ma5/system/controlDict

@@ -15,6 +15,8 @@ FoamFile
 }
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
 
+application     rhopSonicFoam;
+
 startFrom       startTime;
 
 startTime       0;

tutorials/compressible/sonicFoam/Allrun

@@ -1,5 +0,0 @@
-#!/bin/sh
-set -x
-
-(cd laminar && ./Allrun)
-(cd ras && ./Allrun)

tutorials/compressible/sonicFoam/laminar/Allrun

@@ -1,22 +0,0 @@
-#!/bin/sh
-# Source tutorial run functions
-. $WM_PROJECT_DIR/bin/tools/RunFunctions
-
-# Get application name from directory
-application=sonicFoam
-
-cases=" \
-forwardStep \
-shockTube \
-"
-for case in $cases
-do
-    (cd $case && runApplication blockMesh)
-#
-    if [ "$case" = "shockTube" ] ; then
-        (cd $case && ./Allrun)
-    else
-        (cd $case && runApplication $application)
-    fi
-#
-done

tutorials/compressible/sonicFoam/laminar/forwardStep/system/controlDict

@@ -15,6 +15,8 @@ FoamFile
 }
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
 
+application     sonicFoam;
+
 startFrom       startTime;
 
 startTime       0;

tutorials/compressible/sonicFoam/laminar/shockTube/Allrun

@@ -2,7 +2,7 @@
 # Source tutorial run functions
 . $WM_PROJECT_DIR/bin/tools/RunFunctions
 
-application="sonicFoam"
+application=`getApplication`
 
 runApplication blockMesh
 runApplication setFields

tutorials/compressible/sonicFoam/laminar/shockTube/system/controlDict

@@ -15,6 +15,8 @@ FoamFile
 }
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
 
+application     sonicFoam;
+
 startFrom       startTime;
 
 startTime       0;

tutorials/compressible/sonicFoam/ras/Allrun

@@ -1,29 +0,0 @@
-#!/bin/sh
-# Source tutorial run functions
-. $WM_PROJECT_DIR/bin/tools/RunFunctions
-
-# Get application name from directory
-application=${PWD##*/}
-
-runStarToFoam ()
-{
-    if [ -f log.starToFoam ] ; then
-        echo "starToFoam already run on $PWD: remove log file to run"
-    else
-        echo "starToFoam: converting mesh $1"
-        starToFoam $1 > log.starToFoam 2>&1
-    fi
-}
-
-# Do prism
-(cd prism && foamRunTutorials)
-
-# Special handling for nacaAirfoil
-cd nacaAirfoil
-    runStarToFoam prostar/nacaAirfoil
-    mv constant/polyMesh/boundary temp
-    sed -e s/"\([\t ]*type[\t ]*\)symmetryPlane"/"\1empty"/g \
-        temp > constant/polyMesh/boundary
-    rm temp
-    runApplication $application
-cd ..

tutorials/compressible/sonicFoam/ras/nacaAirfoil/Allrun

@@ -0,0 +1,23 @@
+#!/bin/sh
+# Source tutorial run functions
+. $WM_PROJECT_DIR/bin/tools/RunFunctions
+
+# Get application name
+application=`getApplication`
+
+runStarToFoam ()
+{
+    if [ -f log.starToFoam ] ; then
+        echo "starToFoam already run on $PWD: remove log file to run"
+    else
+        echo "starToFoam: converting mesh $1"
+        starToFoam $1 > log.starToFoam 2>&1
+    fi
+}
+
+runStarToFoam prostar/nacaAirfoil
+mv constant/polyMesh/boundary temp
+sed -e s/"\([\t ]*type[\t ]*\)symmetryPlane"/"\1empty"/g \
+    temp > constant/polyMesh/boundary
+rm temp
+runApplication $application

tutorials/compressible/sonicFoam/ras/nacaAirfoil/Running_Notes

@@ -6,7 +6,3 @@ nacaAirfoil
 * limited 0.5 on all laplacianSchemes because the mesh is so poor
 * run to t = 0.02 with nextWrite; change to stopAt endTime to continue running
 * deltaT can be increased later in the run to 2e-07
-
-prism
-~~~~~
-* run to t = 0.0014 for convergence 

tutorials/compressible/sonicFoam/ras/nacaAirfoil/system/controlDict

@@ -15,6 +15,8 @@ FoamFile
 }
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
 
+application     sonicFoam;
+
 startFrom       latestTime;
 
 startTime       0;

tutorials/compressible/sonicFoam/ras/prism/system/controlDict

@@ -15,6 +15,8 @@ FoamFile
 }
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
 
+application     sonicFoam;
+
 startFrom       latestTime;
 
 startTime       0;

tutorials/compressible/sonicLiquidFoam/Allrun

@@ -2,8 +2,8 @@
 # Source tutorial run functions
 . $WM_PROJECT_DIR/bin/tools/RunFunctions
 
-# Get application name from directory
+# Set application name
-application=${PWD##*/}
+application="sonicLiquidFoam"
 
 setDecompressionTankFine ()
 {

tutorials/compressible/sonicLiquidFoam/decompressionTank/system/controlDict

@@ -15,6 +15,8 @@ FoamFile
 }
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
 
+application     sonicLiquidFoam;
+
 startFrom       startTime;
 
 startTime       0;

tutorials/discreteMethods/dsmcFoam/freeSpacePeriodic/system/controlDict

@@ -15,6 +15,8 @@ FoamFile
 }
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
 
+application     dsmcFoam;
+
 startFrom       startTime;
 
 startTime       0;