diff --git a/applications/solvers/discreteMethods/dsmc/dsmcFoam/Make/files b/applications/solvers/discreteMethods/dsmc/dsmcFoam/Make/files
old mode 100755
new mode 100644
diff --git a/applications/solvers/discreteMethods/dsmc/dsmcFoam/Make/options b/applications/solvers/discreteMethods/dsmc/dsmcFoam/Make/options
old mode 100755
new mode 100644
diff --git a/applications/solvers/discreteMethods/molecularDynamics/mdEquilibrationFoam/Make/files b/applications/solvers/discreteMethods/molecularDynamics/mdEquilibrationFoam/Make/files
old mode 100755
new mode 100644
diff --git a/applications/solvers/discreteMethods/molecularDynamics/mdEquilibrationFoam/Make/options b/applications/solvers/discreteMethods/molecularDynamics/mdEquilibrationFoam/Make/options
old mode 100755
new mode 100644
diff --git a/applications/solvers/discreteMethods/molecularDynamics/mdFoam/Make/files b/applications/solvers/discreteMethods/molecularDynamics/mdFoam/Make/files
old mode 100755
new mode 100644
diff --git a/applications/solvers/discreteMethods/molecularDynamics/mdFoam/Make/options b/applications/solvers/discreteMethods/molecularDynamics/mdFoam/Make/options
old mode 100755
new mode 100644
diff --git a/applications/utilities/mesh/conversion/ideasUnvToFoam/Make/files b/applications/utilities/mesh/conversion/ideasUnvToFoam/Make/files
old mode 100755
new mode 100644
diff --git a/applications/utilities/mesh/conversion/ideasUnvToFoam/Make/options b/applications/utilities/mesh/conversion/ideasUnvToFoam/Make/options
old mode 100755
new mode 100644
diff --git a/applications/utilities/mesh/generation/extrudeMesh/extrudeMesh.C b/applications/utilities/mesh/generation/extrudeMesh/extrudeMesh.C
index 74e505394d..69dc36bccf 100644
--- a/applications/utilities/mesh/generation/extrudeMesh/extrudeMesh.C
+++ b/applications/utilities/mesh/generation/extrudeMesh/extrudeMesh.C
@@ -78,6 +78,7 @@ int main(int argc, char *argv[])
     if (sourceType == "patch")
     {
         fileName sourceCasePath(dict.lookup("sourceCase"));
+        sourceCasePath.expand();
         fileName sourceRootDir = sourceCasePath.path();
         fileName sourceCaseDir = sourceCasePath.name();
         word patchName(dict.lookup("sourcePatch"));
diff --git a/applications/utilities/mesh/generation/extrudeMesh/setRoots.H b/applications/utilities/mesh/generation/extrudeMesh/setRoots.H
deleted file mode 100644
index 9c13db28d1..0000000000
--- a/applications/utilities/mesh/generation/extrudeMesh/setRoots.H
+++ /dev/null
@@ -1,16 +0,0 @@
-    argList::validArgs.clear();
-    argList::noParallel();
-
-    argList::validOptions.insert("sourceCase", "source case");
-    argList::validOptions.insert("sourcePatch", "source patch");
-
-    argList::validOptions.insert("surface", "surface file");
-
-    argList::validOptions.insert("mergeFaces", "");
-
-    argList args(argc, argv);
-
-    if (!args.check())
-    {
-         FatalError.exit();
-    }
diff --git a/applications/utilities/postProcessing/miscellaneous/dsmcFieldsCalc/Make/files b/applications/utilities/postProcessing/miscellaneous/dsmcFieldsCalc/Make/files
old mode 100755
new mode 100644
diff --git a/applications/utilities/postProcessing/miscellaneous/dsmcFieldsCalc/Make/options b/applications/utilities/postProcessing/miscellaneous/dsmcFieldsCalc/Make/options
old mode 100755
new mode 100644
diff --git a/applications/utilities/preProcessing/dsmcInitialise/Make/files b/applications/utilities/preProcessing/dsmcInitialise/Make/files
old mode 100755
new mode 100644
diff --git a/applications/utilities/preProcessing/dsmcInitialise/Make/options b/applications/utilities/preProcessing/dsmcInitialise/Make/options
old mode 100755
new mode 100644
diff --git a/applications/utilities/preProcessing/mdInitialise/Make/files b/applications/utilities/preProcessing/mdInitialise/Make/files
old mode 100755
new mode 100644
diff --git a/applications/utilities/preProcessing/mdInitialise/Make/options b/applications/utilities/preProcessing/mdInitialise/Make/options
old mode 100755
new mode 100644
diff --git a/src/autoMesh/autoHexMesh/meshRefinement/meshRefinementBaffles.C b/src/autoMesh/autoHexMesh/meshRefinement/meshRefinementBaffles.C
index 0839e621cb..b5b4174fb3 100644
--- a/src/autoMesh/autoHexMesh/meshRefinement/meshRefinementBaffles.C
+++ b/src/autoMesh/autoHexMesh/meshRefinement/meshRefinementBaffles.C
@@ -113,7 +113,7 @@ Foam::label Foam::meshRefinement::createBaffle
                 true,                       // face flip
                 neiPatch,                   // patch for face
                 zoneID,                     // zone for face
-                zoneFlip                    // face flip in zone
+                !zoneFlip                   // face flip in zone
             )
         );
     }
diff --git a/src/autoMesh/autoHexMesh/trackedParticle/trackedParticle.C b/src/autoMesh/autoHexMesh/trackedParticle/trackedParticle.C
index 761ca5b447..7cd8fb9dd2 100644
--- a/src/autoMesh/autoHexMesh/trackedParticle/trackedParticle.C
+++ b/src/autoMesh/autoHexMesh/trackedParticle/trackedParticle.C
@@ -56,7 +56,7 @@ Foam::trackedParticle::trackedParticle
     bool readFields
 )
 :
-    ExactParticle<trackedParticle>(c, is)
+    ExactParticle<trackedParticle>(c, is, readFields)
 {
     if (readFields)
     {
diff --git a/src/lagrangian/basic/Cloud/Cloud.C b/src/lagrangian/basic/Cloud/Cloud.C
index 72e1b1f818..e3e0b4f63f 100644
--- a/src/lagrangian/basic/Cloud/Cloud.C
+++ b/src/lagrangian/basic/Cloud/Cloud.C
@@ -42,15 +42,12 @@ Foam::Cloud<ParticleType>::Cloud
 )
 :
     cloud(pMesh),
-    IDLList<ParticleType>(particles),
+    IDLList<ParticleType>(),
     polyMesh_(pMesh),
-    allFaces_(pMesh.faces()),
-    points_(pMesh.points()),
-    cellFaces_(pMesh.cells()),
-    allFaceCentres_(pMesh.faceCentres()),
-    owner_(pMesh.faceOwner()),
-    neighbour_(pMesh.faceNeighbour())
-{}
+    particleCount_(0)
+{
+    IDLList<ParticleType>::operator=(particles);
+}
 
 
 template<class ParticleType>
@@ -62,19 +59,31 @@ Foam::Cloud<ParticleType>::Cloud
 )
 :
     cloud(pMesh, cloudName),
-    IDLList<ParticleType>(particles),
+    IDLList<ParticleType>(),
     polyMesh_(pMesh),
-    allFaces_(pMesh.faces()),
-    points_(pMesh.points()),
-    cellFaces_(pMesh.cells()),
-    allFaceCentres_(pMesh.faceCentres()),
-    owner_(pMesh.faceOwner()),
-    neighbour_(pMesh.faceNeighbour())
-{}
+    particleCount_(0)
+{
+    IDLList<ParticleType>::operator=(particles);
+}
 
 
 // * * * * * * * * * * * * * * * Member Functions  * * * * * * * * * * * * * //
 
+template<class ParticleType>
+Foam::label Foam::Cloud<ParticleType>::getNewParticleID() const
+{
+    label id = particleCount_++;
+
+    if (id == labelMax)
+    {
+        WarningIn("Cloud<ParticleType>::getNewParticleID() const")
+            << "Particle counter has overflowed. This might cause problems"
+            << " when reconstructing particle tracks." << endl;
+    }
+    return id;
+}
+
+
 template<class ParticleType>
 void Foam::Cloud<ParticleType>::addParticle(ParticleType* pPtr)
 {
diff --git a/src/lagrangian/basic/Cloud/Cloud.H b/src/lagrangian/basic/Cloud/Cloud.H
index e298affe7d..626042e68a 100644
--- a/src/lagrangian/basic/Cloud/Cloud.H
+++ b/src/lagrangian/basic/Cloud/Cloud.H
@@ -50,6 +50,9 @@ namespace Foam
 template<class ParticleType>
 class Cloud;
 
+template<class ParticleType>
+class IOPosition;
+
 template<class ParticleType>
 Ostream& operator<<
 (
@@ -71,12 +74,9 @@ class Cloud
     // Private data
 
         const polyMesh& polyMesh_;
-        const faceList& allFaces_;
-        const vectorField& points_;
-        const cellList& cellFaces_;
-        const vectorField& allFaceCentres_;
-        const unallocLabelList& owner_;
-        const unallocLabelList& neighbour_;
+
+        //- Overall count of particles ever created. Never decreases.
+        mutable label particleCount_;
 
         //- Temporary storage for addressing. Used in findFaces.
         mutable DynamicList<label> labels_;
@@ -92,6 +92,8 @@ public:
 
     template<class ParticleT>
     friend class Particle;
+    template<class ParticleT>
+    friend class IOPosition;
 
     typedef ParticleType particleType;
 
@@ -218,6 +220,9 @@ public:
                 return IDLList<ParticleType>::clear();
             };
 
+            //- Get unique particle creation id
+            label getNewParticleID() const;
+
             //- Transfer particle to cloud
             void addParticle(ParticleType* pPtr);
 
@@ -251,13 +256,15 @@ public:
                 const IOField<DataType>& data
             ) const;
 
-            //- Read the field data for the cloud of particles
-            void readFields();
+            //- Read the field data for the cloud of particles. Dummy at
+            //  this level.
+            virtual void readFields();
 
 
         // Write
 
-            //- Write the field data for the cloud of particles
+            //- Write the field data for the cloud of particles Dummy at
+            //  this level.
             virtual void writeFields() const;
 
             //- Write using given format, version and compression.
diff --git a/src/lagrangian/basic/Cloud/CloudIO.C b/src/lagrangian/basic/Cloud/CloudIO.C
index 42c1a9317a..c1e4b30f80 100644
--- a/src/lagrangian/basic/Cloud/CloudIO.C
+++ b/src/lagrangian/basic/Cloud/CloudIO.C
@@ -67,12 +67,7 @@ Foam::Cloud<ParticleType>::Cloud
 :
     cloud(pMesh),
     polyMesh_(pMesh),
-    allFaces_(pMesh.faces()),
-    points_(pMesh.points()),
-    cellFaces_(pMesh.cells()),
-    allFaceCentres_(pMesh.faceCentres()),
-    owner_(pMesh.faceOwner()),
-    neighbour_(pMesh.faceNeighbour())
+    particleCount_(0)
 {
     initCloud(checkClass);
 }
@@ -88,12 +83,7 @@ Foam::Cloud<ParticleType>::Cloud
 :
     cloud(pMesh, cloudName),
     polyMesh_(pMesh),
-    allFaces_(pMesh.faces()),
-    points_(pMesh.points()),
-    cellFaces_(pMesh.cells()),
-    allFaceCentres_(pMesh.faceCentres()),
-    owner_(pMesh.faceOwner()),
-    neighbour_(pMesh.faceNeighbour())
+    particleCount_(0)
 {
     initCloud(checkClass);
 }
diff --git a/src/lagrangian/basic/IOPosition/IOPosition.C b/src/lagrangian/basic/IOPosition/IOPosition.C
index 810a9fbcf5..5f12742d8c 100644
--- a/src/lagrangian/basic/IOPosition/IOPosition.C
+++ b/src/lagrangian/basic/IOPosition/IOPosition.C
@@ -34,6 +34,7 @@ Foam::word Foam::IOPosition<ParticleType>::particlePropertiesName
     "particleProperties"
 );
 
+
 // * * * * * * * * * * * Private Member Functions  * * * * * * * * * * * * * //
 
 template<class ParticleType>
@@ -58,7 +59,7 @@ void Foam::IOPosition<ParticleType>::readParticleProperties()
         if (propsDict.found(procName))
         {
             propsDict.subDict(procName).lookup("particleCount")
-                >> Particle<ParticleType>::particleCount;
+                >> cloud_.particleCount_;
         }
     }
 }
@@ -83,11 +84,7 @@ void Foam::IOPosition<ParticleType>::writeParticleProperties() const
 
     word procName("processor" + Foam::name(Pstream::myProcNo()));
     propsDict.add(procName, dictionary());
-    propsDict.subDict(procName).add
-    (
-        "particleCount",
-        Particle<ParticleType>::particleCount
-    );
+    propsDict.subDict(procName).add("particleCount", cloud_.particleCount_);
 
     propsDict.regIOobject::write();
 }
@@ -135,13 +132,20 @@ bool Foam::IOPosition<ParticleType>::write() const
 template<class ParticleType>
 bool Foam::IOPosition<ParticleType>::writeData(Ostream& os) const
 {
+    // Write global cloud data
     writeParticleProperties();
 
     os<< cloud_.size() << nl << token::BEGIN_LIST << nl;
 
     forAllConstIter(typename Cloud<ParticleType>, cloud_, iter)
     {
-        os<< static_cast<const Particle<ParticleType>&>(iter()) << nl;
+        // Prevent writing additional fields
+        static_cast<const Particle<ParticleType>&>(iter()).write
+        (
+            os,
+            false
+        );
+        os  << nl;
     }
 
     os<< token::END_LIST << endl;
@@ -157,6 +161,7 @@ void Foam::IOPosition<ParticleType>::readData
     bool checkClass
 )
 {
+    // Read global cloud data. Resets count on cloud.
     readParticleProperties();
 
     Istream& is = readStream(checkClass ? typeName : "");
@@ -172,6 +177,7 @@ void Foam::IOPosition<ParticleType>::readData
 
         for (label i=0; i<s; i++)
         {
+            // Do not read any fields, position only
             c.append(new ParticleType(c, is, false));
         }
 
@@ -202,6 +208,7 @@ void Foam::IOPosition<ParticleType>::readData
         )
         {
             is.putBack(lastToken);
+            // Do not read any fields, position only
             c.append(new ParticleType(c, is, false));
             is >> lastToken;
         }
diff --git a/src/lagrangian/basic/IOPosition/IOPosition.H b/src/lagrangian/basic/IOPosition/IOPosition.H
index 069dc0135d..982416fdc8 100644
--- a/src/lagrangian/basic/IOPosition/IOPosition.H
+++ b/src/lagrangian/basic/IOPosition/IOPosition.H
@@ -26,7 +26,7 @@ Class
     Foam::IOPosition
 
 Description
-    Helper IO class to write particle positions
+    Helper IO class to read and write particle positions
 
 SourceFiles
     IOPosition.C
@@ -72,7 +72,7 @@ public:
 
     // Static data
 
-        //- Runtime type name information
+        //- Runtime type name information. Use cloud type.
         virtual const word& type() const
         {
             return cloud_.type();
@@ -90,11 +90,11 @@ public:
 
     // Member functions
 
-        void readData(Cloud<ParticleType>& c, bool checkClass);
+        virtual void readData(Cloud<ParticleType>& c, bool checkClass);
 
-        bool write() const;
+        virtual bool write() const;
 
-        bool writeData(Ostream& os) const;
+        virtual bool writeData(Ostream& os) const;
 };
 
 
diff --git a/src/lagrangian/basic/Particle/Particle.C b/src/lagrangian/basic/Particle/Particle.C
index 4b51b88a45..4838da0ad1 100644
--- a/src/lagrangian/basic/Particle/Particle.C
+++ b/src/lagrangian/basic/Particle/Particle.C
@@ -33,12 +33,6 @@ License
 #include "wallPolyPatch.H"
 #include "transform.H"
 
-// * * * * * * * * * * * * * * Static Data Members * * * * * * * * * * * * * //
-
-template<class ParticleType>
-Foam::label Foam::Particle<ParticleType>::particleCount = 0;
-
-
 // * * * * * * * * * * * * * Private Member Functions  * * * * * * * * * * * //
 
 template<class ParticleType>
@@ -75,7 +69,7 @@ void Foam::Particle<ParticleType>::findFaces
     DynamicList<label>& faceList
 ) const
 {
-    const polyMesh& mesh = cloud_.mesh();
+    const polyMesh& mesh = cloud_.pMesh();
     const labelList& faces = mesh.cells()[celli];
     const vector& C = mesh.cellCentres()[celli];
 
@@ -184,7 +178,7 @@ Foam::Particle<ParticleType>::Particle
     facei_(-1),
     stepFraction_(0.0),
     origProc_(Pstream::myProcNo()),
-    origId_(particleCount++)
+    origId_(cloud_.getNewParticleID())
 {}
 
 
@@ -313,13 +307,13 @@ Foam::scalar Foam::Particle<ParticleType>::trackToFace
         // change cell
         if (internalFace) // Internal face
         {
-            if (celli_ == cloud_.owner_[facei_])
+            if (celli_ == mesh.faceOwner()[facei_])
             {
-                celli_ = cloud_.neighbour_[facei_];
+                celli_ = mesh.faceNeighbour()[facei_];
             }
-            else if (celli_ == cloud_.neighbour_[facei_])
+            else if (celli_ == mesh.faceNeighbour()[facei_])
             {
-                celli_ = cloud_.owner_[facei_];
+                celli_ = mesh.faceOwner()[facei_];
             }
             else
             {
diff --git a/src/lagrangian/basic/Particle/Particle.H b/src/lagrangian/basic/Particle/Particle.H
index 71011d72a4..a1077a604e 100644
--- a/src/lagrangian/basic/Particle/Particle.H
+++ b/src/lagrangian/basic/Particle/Particle.H
@@ -279,9 +279,6 @@ public:
         //- String representation of properties
         static string propHeader;
 
-        //- Cumulative particle count used for particle id
-        static label particleCount;
-
 
     // Constructors
 
@@ -330,7 +327,15 @@ public:
 
             autoPtr<ParticleType> operator()(Istream& is) const
             {
-                return autoPtr<ParticleType>(new ParticleType(cloud_, is));
+                return autoPtr<ParticleType>
+                (
+                    new ParticleType
+                    (
+                        cloud_,
+                        is,
+                        true
+                    )
+                );
             }
         };
 
@@ -454,9 +459,14 @@ public:
 
     // I-O
 
+        //- Read the fields associated with the owner cloud
+        static void readFields(Cloud<ParticleType>& c);
+
         //- Write the fields associated with the owner cloud
         static void writeFields(const Cloud<ParticleType>& c);
 
+        //- Write the particle data
+        void write(Ostream& os, bool writeFields) const;
 
     // Ostream Operator
 
diff --git a/src/lagrangian/basic/Particle/ParticleIO.C b/src/lagrangian/basic/Particle/ParticleIO.C
index 5865cf5098..77774cf90b 100644
--- a/src/lagrangian/basic/Particle/ParticleIO.C
+++ b/src/lagrangian/basic/Particle/ParticleIO.C
@@ -50,23 +50,49 @@ Foam::Particle<ParticleType>::Particle
     origProc_(Pstream::myProcNo()),
     origId_(-1)
 {
+
+    // readFields : read additional data. Should be consistent with writeFields.
+
     if (is.format() == IOstream::ASCII)
     {
-        is >> position_ >> celli_ >> origProc_ >> origId_;
+        is >> position_ >> celli_;
+        if (readFields)
+        {
+            is >> origProc_ >> origId_;
+        }
+        else
+        {
+            origId_ = cloud_.getNewParticleID();
+        }
     }
     else
     {
         // In binary read all particle data - needed for parallel transfer
-        is.read
-        (
-            reinterpret_cast<char*>(&position_),
-            sizeof(position_)
-            + sizeof(celli_)
-            + sizeof(facei_)
-            + sizeof(stepFraction_)
-            + sizeof(origProc_)
-            + sizeof(origId_)
-        );
+        if (readFields)
+        {
+            is.read
+            (
+                reinterpret_cast<char*>(&position_),
+                sizeof(position_)
+              + sizeof(celli_)
+              + sizeof(facei_)
+              + sizeof(stepFraction_)
+              + sizeof(origProc_)
+              + sizeof(origId_)
+            );
+        }
+        else
+        {
+            is.read
+            (
+                reinterpret_cast<char*>(&position_),
+                sizeof(position_)
+              + sizeof(celli_)
+              + sizeof(facei_)
+              + sizeof(stepFraction_)
+            );
+            origId_ = cloud_.getNewParticleID();
+        }
     }
 
     if (celli_ == -1)
@@ -79,6 +105,38 @@ Foam::Particle<ParticleType>::Particle
 }
 
 
+template<class ParticleType>
+void Foam::Particle<ParticleType>::readFields
+(
+    Cloud<ParticleType>& c
+)
+{
+    if (!c.size())
+    {
+        return;
+    }
+
+    IOobject procIO(c.fieldIOobject("origProcId", IOobject::MUST_READ));
+    if (procIO.headerOk())
+    {
+        IOField<label> origProcId(procIO);
+        c.checkFieldIOobject(c, origProcId);
+        IOField<label> origId(c.fieldIOobject("origId", IOobject::MUST_READ));
+        c.checkFieldIOobject(c, origId);
+
+        label i = 0;
+        forAllIter(typename Cloud<ParticleType>, c, iter)
+        {
+            ParticleType& p = iter();
+
+            p.origProc_ = origProcId[i];
+            p.origId_ = origId[i];
+            i++;
+        }
+    }
+}
+
+
 template<class ParticleType>
 void Foam::Particle<ParticleType>::writeFields
 (
@@ -88,36 +146,91 @@ void Foam::Particle<ParticleType>::writeFields
     // Write the cloud position file
     IOPosition<ParticleType> ioP(c);
     ioP.write();
+
+    label np =  c.size();
+
+    IOField<label> origProc
+    (
+        c.fieldIOobject
+        (
+            "origProcId",
+            IOobject::NO_READ
+        ),
+        np
+    );
+    IOField<label> origId(c.fieldIOobject("origId", IOobject::NO_READ), np);
+
+    label i = 0;
+    forAllConstIter(typename Cloud<ParticleType>, c, iter)
+    {
+        origProc[i] = iter().origProc_;
+        origId[i] = iter().origId_;
+        i++;
+    }
+
+    origProc.write();
+    origId.write();
+}
+
+
+template<class ParticleType>
+void Foam::Particle<ParticleType>::write(Ostream& os, bool writeFields) const
+{
+    if (os.format() == IOstream::ASCII)
+    {
+        if (writeFields)
+        {
+            // Write the additional entries
+            os << position_
+               << token::SPACE << celli_
+               << token::SPACE << origProc_
+               << token::SPACE << origId_;
+        }
+        else
+        {
+            os << position_
+               << token::SPACE << celli_;
+        }
+    }
+    else
+    {
+        // In binary write both celli_ and facei_, needed for parallel transfer
+        if (writeFields)
+        {
+            os.write
+            (
+                reinterpret_cast<const char*>(&position_),
+                sizeof(position_)
+              + sizeof(celli_)
+              + sizeof(facei_)
+              + sizeof(stepFraction_)
+              + sizeof(origProc_)
+              + sizeof(origId_)
+            );
+        }
+        else
+        {
+            os.write
+            (
+                reinterpret_cast<const char*>(&position_),
+                sizeof(position_)
+              + sizeof(celli_)
+              + sizeof(facei_)
+              + sizeof(stepFraction_)
+            );
+        }
+    }
+
+    // Check state of Ostream
+    os.check("Particle<ParticleType>::write(Ostream& os, bool) const");
 }
 
 
 template<class ParticleType>
 Foam::Ostream& Foam::operator<<(Ostream& os, const Particle<ParticleType>& p)
 {
-    if (os.format() == IOstream::ASCII)
-    {
-        os << p.position_
-           << token::SPACE << p.celli_
-           << token::SPACE << p.origProc_
-           << token::SPACE << p.origId_;
-    }
-    else
-    {
-        // In binary write both celli_ and facei_, needed for parallel transfer
-        os.write
-        (
-            reinterpret_cast<const char*>(&p.position_),
-            sizeof(p.position_)
-          + sizeof(p.celli_)
-          + sizeof(p.facei_)
-          + sizeof(p.stepFraction_)
-          + sizeof(p.origProc_)
-          + sizeof(p.origId_)
-        );
-    }
-
-    // Check state of Ostream
-    os.check("Ostream& operator<<(Ostream&, const Particle<ParticleType>&)");
+    // Write all data
+    p.write(os, true);
 
     return os;
 }
diff --git a/src/lagrangian/basic/indexedParticle/indexedParticle.H b/src/lagrangian/basic/indexedParticle/indexedParticle.H
index fd20681a32..7023f0ba6d 100644
--- a/src/lagrangian/basic/indexedParticle/indexedParticle.H
+++ b/src/lagrangian/basic/indexedParticle/indexedParticle.H
@@ -84,7 +84,7 @@ public:
             bool readFields = true
         )
         :
-            Particle<indexedParticle>(c, is)
+            Particle<indexedParticle>(c, is, readFields)
         {}
 
         //- Construct as a copy
diff --git a/src/lagrangian/basic/indexedParticle/indexedParticleCloud.C b/src/lagrangian/basic/indexedParticle/indexedParticleCloud.C
index 52cf785b91..422661f76a 100644
--- a/src/lagrangian/basic/indexedParticle/indexedParticleCloud.C
+++ b/src/lagrangian/basic/indexedParticle/indexedParticleCloud.C
@@ -22,12 +22,9 @@ License
     along with OpenFOAM; if not, write to the Free Software Foundation,
     Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
 
-Description
-
 \*---------------------------------------------------------------------------*/
 
-#include "indexedParticle.H"
-#include "Cloud.H"
+#include "indexedParticleCloud.H"
 
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
 
@@ -43,4 +40,23 @@ defineTemplateTypeNameAndDebug(Cloud<indexedParticle>, 0);
 
 } // End namespace Foam
 
+// * * * * * * * * * * * * * * * * Constructors  * * * * * * * * * * * * * * //
+
+Foam::indexedParticleCloud::indexedParticleCloud
+(
+    const polyMesh& mesh,
+    const word& cloudName
+)
+:
+    Cloud<indexedParticle>(mesh, cloudName, false)
+{}
+
+
+// * * * * * * * * * * * * * * * Member Functions  * * * * * * * * * * * * * //
+
+void Foam::indexedParticleCloud::writeFields() const
+{
+    indexedParticle::writeFields(*this);
+}
+
 // ************************************************************************* //
diff --git a/src/lagrangian/basic/indexedParticle/indexedParticleCloud.H b/src/lagrangian/basic/indexedParticle/indexedParticleCloud.H
new file mode 100644
index 0000000000..65033e0a9d
--- /dev/null
+++ b/src/lagrangian/basic/indexedParticle/indexedParticleCloud.H
@@ -0,0 +1,91 @@
+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  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::indexedParticleCloud
+
+Description
+    A Cloud of particles carrying an additional index.
+
+SourceFiles
+    indexedParticleCloud.C
+
+\*---------------------------------------------------------------------------*/
+
+#ifndef indexedParticleCloud_H
+#define indexedParticleCloud_H
+
+#include "Cloud.H"
+#include "indexedParticle.H"
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+namespace Foam
+{
+
+/*---------------------------------------------------------------------------*\
+                           Class indexedParticleCloud Declaration
+\*---------------------------------------------------------------------------*/
+
+class indexedParticleCloud
+:
+    public Cloud<indexedParticle>
+{
+    // Private Member Functions
+
+        //- Disallow default bitwise copy construct
+        indexedParticleCloud(const indexedParticleCloud&);
+
+        //- Disallow default bitwise assignment
+        void operator=(const indexedParticleCloud&);
+
+
+public:
+
+    // Constructors
+
+        //- Construct given mesh
+        indexedParticleCloud
+        (
+            const polyMesh&,
+            const word& cloudName = "defaultCloud"
+        );
+
+
+    // Member Functions
+
+        //- Write fields
+        virtual void writeFields() const;
+};
+
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+} // End namespace Foam
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+#endif
+
+// ************************************************************************* //
diff --git a/src/lagrangian/basic/passiveParticle/passiveParticle.H b/src/lagrangian/basic/passiveParticle/passiveParticle.H
index ce4f7bfcad..c8d912ac76 100644
--- a/src/lagrangian/basic/passiveParticle/passiveParticle.H
+++ b/src/lagrangian/basic/passiveParticle/passiveParticle.H
@@ -28,9 +28,6 @@ Class
 Description
 
 SourceFiles
-    passiveParticleI.H
-    passiveParticle.C
-    passiveParticleIO.C
 
 \*---------------------------------------------------------------------------*/
 
@@ -78,7 +75,7 @@ public:
             bool readFields = true
         )
         :
-            Particle<passiveParticle>(c, is)
+            Particle<passiveParticle>(c, is, readFields)
         {}
 
         //- Construct as copy
diff --git a/src/lagrangian/basic/passiveParticle/passiveParticleCloud.C b/src/lagrangian/basic/passiveParticle/passiveParticleCloud.C
index 71af5dd82b..e60b691c1f 100644
--- a/src/lagrangian/basic/passiveParticle/passiveParticleCloud.C
+++ b/src/lagrangian/basic/passiveParticle/passiveParticleCloud.C
@@ -22,12 +22,9 @@ License
     along with OpenFOAM; if not, write to the Free Software Foundation,
     Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
 
-Description
-
 \*---------------------------------------------------------------------------*/
 
-#include "passiveParticle.H"
-#include "Cloud.H"
+#include "passiveParticleCloud.H"
 
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
 
@@ -39,8 +36,32 @@ namespace Foam
 defineParticleTypeNameAndDebug(passiveParticle, 0);
 defineTemplateTypeNameAndDebug(Cloud<passiveParticle>, 0);
 
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+};
+
+// * * * * * * * * * * * * * * * * Constructors  * * * * * * * * * * * * * * //
+
+Foam::passiveParticleCloud::passiveParticleCloud
+(
+    const polyMesh& mesh,
+    const word& cloudName
+)
+:
+    Cloud<passiveParticle>(mesh, cloudName, false)
+{}
+
+
+// * * * * * * * * * * * * * * * Member Functions  * * * * * * * * * * * * * //
+
+void Foam::passiveParticleCloud::readFields()
+{
+    passiveParticle::readFields(*this);
+}
+
+
+void Foam::passiveParticleCloud::writeFields() const
+{
+    passiveParticle::writeFields(*this);
+}
 
-} // End namespace Foam
 
 // ************************************************************************* //
diff --git a/src/lagrangian/basic/passiveParticle/passiveParticleCloud.H b/src/lagrangian/basic/passiveParticle/passiveParticleCloud.H
new file mode 100644
index 0000000000..b8faac8f43
--- /dev/null
+++ b/src/lagrangian/basic/passiveParticle/passiveParticleCloud.H
@@ -0,0 +1,94 @@
+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  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::passiveParticleCloud
+
+Description
+    A Cloud of passive particles
+
+SourceFiles
+    passiveParticleCloud.C
+
+\*---------------------------------------------------------------------------*/
+
+#ifndef passiveParticleCloud_H
+#define passiveParticleCloud_H
+
+#include "Cloud.H"
+#include "passiveParticle.H"
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+namespace Foam
+{
+
+/*---------------------------------------------------------------------------*\
+                           Class passiveParticleCloud Declaration
+\*---------------------------------------------------------------------------*/
+
+class passiveParticleCloud
+:
+    public Cloud<passiveParticle>
+{
+    // Private Member Functions
+
+        //- Disallow default bitwise copy construct
+        passiveParticleCloud(const passiveParticleCloud&);
+
+        //- Disallow default bitwise assignment
+        void operator=(const passiveParticleCloud&);
+
+
+public:
+
+    // Constructors
+
+        //- Construct given mesh
+        passiveParticleCloud
+        (
+            const polyMesh&,
+            const word& cloudName = "defaultCloud"
+        );
+
+
+    // Member Functions
+
+        //- Read fields
+        virtual void readFields();
+
+        //- Write fields
+        virtual void writeFields() const;
+};
+
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+} // End namespace Foam
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+#endif
+
+// ************************************************************************* //
diff --git a/src/lagrangian/coalCombustion/CoalCloud/CoalCloud.H b/src/lagrangian/coalCombustion/CoalCloud/CoalCloud.H
index 36e3b4e03e..d4d6c2bc94 100644
--- a/src/lagrangian/coalCombustion/CoalCloud/CoalCloud.H
+++ b/src/lagrangian/coalCombustion/CoalCloud/CoalCloud.H
@@ -87,7 +87,7 @@ public:
     // Member Functions
 
         //- Write fields
-        void writeFields() const;
+        virtual void writeFields() const;
 };
 
 
diff --git a/src/lagrangian/coalCombustion/Make/files b/src/lagrangian/coalCombustion/Make/files
old mode 100755
new mode 100644
diff --git a/src/lagrangian/coalCombustion/Make/options b/src/lagrangian/coalCombustion/Make/options
old mode 100755
new mode 100644
diff --git a/src/lagrangian/dieselSpray/parcel/parcelIO.C b/src/lagrangian/dieselSpray/parcel/parcelIO.C
index d84f2bb195..4ae7bbc90a 100644
--- a/src/lagrangian/dieselSpray/parcel/parcelIO.C
+++ b/src/lagrangian/dieselSpray/parcel/parcelIO.C
@@ -36,7 +36,7 @@ Foam::parcel::parcel
     bool readFields
 )
 :
-    Particle<parcel>(cloud, is),
+    Particle<parcel>(cloud, is, readFields),
 
     liquidComponents_
     (
diff --git a/src/lagrangian/dieselSpray/spray/spray.H b/src/lagrangian/dieselSpray/spray/spray.H
index f416e3cf4e..044423fc75 100644
--- a/src/lagrangian/dieselSpray/spray/spray.H
+++ b/src/lagrangian/dieselSpray/spray/spray.H
@@ -345,7 +345,7 @@ public:
     // I/O
 
             //- Write fields
-            void writeFields() const;
+            virtual void writeFields() const;
 };
 
 
diff --git a/src/lagrangian/dieselSpray/spraySubModels/wallModel/reflectParcel/reflectParcel.C2 b/src/lagrangian/dieselSpray/spraySubModels/wallModel/reflectParcel/reflectParcel.C2
deleted file mode 100755
index 7a209cc8e3..0000000000
--- a/src/lagrangian/dieselSpray/spraySubModels/wallModel/reflectParcel/reflectParcel.C2
+++ /dev/null
@@ -1,211 +0,0 @@
-// The FOAM Project // File: reflectParcel.C
-/*
--------------------------------------------------------------------------------
- =========         | Class Implementation
- \\      /         |
-  \\    /          | Name:   reflectParcel
-   \\  /           | Family: wallModel
-    \\/            |
-    F ield         | FOAM version: 2.3
-    O peration     |
-    A and          | Copyright (C) 1991-2009 OpenCFD Ltd.
-    M anipulation  |          All Rights Reserved.
--------------------------------------------------------------------------------
-DESCRIPTION
-
-AUTHOR
-    Henry G Weller.
-
--------------------------------------------------------------------------------
-*/
-
-#include "reflectParcel.H"
-#include "addToRunTimeSelectionTable.H"
-#include "wallPolyPatch.H"
-
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-namespace Foam
-{
-
-// * * * * * * * * * * * * * * Static Data Members * * * * * * * * * * * * * //
-
-defineTypeNameAndDebug(reflectParcel, 0);
-
-addToRunTimeSelectionTable
-(
-    wallModel,
-    reflectParcel,
-    dictionary
-);
-
-
-// * * * * * * * * * * * * * * * * Constructors  * * * * * * * * * * * * * * //
-
-// Construct from components
-reflectParcel::reflectParcel
-(
-    const dictionary& dict,
-    const fvMesh& mesh,
-    spray& sm
-)
-:
-    wallModel(dict, mesh, sm),
-    coeffsDict_(dict.subDict(typeName + "Coeffs")),
-    elasticity_(readScalar(coeffsDict_.lookup("elasticity")))
-{}
-
-
-// * * * * * * * * * * * * * * * * Destructor  * * * * * * * * * * * * * * * //
-
-reflectParcel::~reflectParcel()
-{}
-
-
-// * * * * * * * * * * * * * * * Member Functions  * * * * * * * * * * * * * //
-
-// Return 'keepParcel'
-bool reflectParcel::wallTreatment
-(
-    parcel& p
-) const
-{
-    label patchi = p.patch();
-    label facei = p.patchFace(patchi);
-
-    const polyMesh& mesh = spray_.mesh();
-
-    if (typeid(mesh_.boundaryMesh()[patchi]) == typeid(wallPolyPatch))
-    {
-        // wallNormal defined to point outwards of domain
-        vector Sf = mesh_.Sf().boundaryField()[patchi][facei];
-        Sf /= mag(Sf);
-
-        // adjust velocity when wall is moving
-        if (!mesh.moving())
-        {
-            scalar Un = p.U() & Sf;
-            
-            if (Un > 0)
-            {
-                p.U() -= (1.0 + elasticity_)*Un*Sf;
-            }
-
-        }
-        else
-        {
-            label facep = p.face();
-
-            scalar dt = spray_.runTime().deltaT().value();
-            scalar fraction = p.t0()/dt;
-            const vectorField& oldPoints = mesh.oldPoints();
-            const vector& Cf1 = mesh.faceCentres()[facep];
-
-            vector Cf0 = mesh.faces()[facep].centre(oldPoints);
-            vector Cf = Cf0 + fraction*(Cf1 - Cf0);
-            vector Sf0 = mesh.faces()[facep].normal(oldPoints);
-            Sf0 /= mag(Sf0);
-
-            scalar magSfDiff = mag(Sf - Sf0);
-
-            if (magSfDiff > SMALL)
-            {
-                bool pureRotation = false;
-
-                if (pureRotation)
-                {
-                    // rotation
-                    
-                    // find center of rotation
-                    vector omega = Sf0 ^ Sf;
-                    scalar magOmega = mag(omega);
-                    omega /= magOmega+SMALL;
-                    vector n0 = omega ^ Sf0;
-                    scalar lam = ((Cf1 - Cf0) & Sf)/(n0 & Sf);
-                    vector r0 = Cf0 + lam*n0;
-                    
-                    scalar phiVel = ::asin(magOmega)/dt;
-                    
-                    vector pos = p.position() - r0;
-                    vector v = phiVel*(omega ^ pos);
-
-                    vector Sfp = Sf0 + fraction*(Sf - Sf0);
-                    //vector Sfp = Sf;
-
-                    vector Ur = p.U() - v;
-                    scalar Urn = Ur & Sfp;
-                    /*
-                    scalar dd = (p.position() - r0) & Sfp;
-                    Info << "Urn = " << Urn
-                        << ", dd = " << dd
-                        << ", pos = " << p.position()
-                        << ", Sfp = " << Sfp
-                        << ", omega = " << omega
-                        << ", r0 = " << r0
-                        << endl;
-                        */
-                    if (Urn > 0.0)
-                    {
-                        p.U() -= (1.0 + elasticity_)*Urn*Sfp;
-                    }
-                }
-                else
-                {
-                    vector Sfp = Sf0 + fraction*(Sf - Sf0);
-                    //vector Sfp = Sf;
-                    vector omega = Sf0 ^ Sf;
-                    scalar magOmega = mag(omega);
-                    omega /= magOmega+SMALL;
-                    
-                    scalar phiVel = ::asin(magOmega)/dt;
-                    
-                    scalar dist = (p.position() - Cf) & Sfp;
-                    vector pos = p.position() - dist*Sfp;
-                    vector vrot = phiVel*(omega ^ (pos - Cf));
-                    vector vtrans = (Cf1 - Cf0)/dt;
-                    vector v = vtrans + vrot;
-
-                    scalar Un = ((p.U() - v) & Sfp);
-                    
-                    if (Un > 0.0)
-                    {
-                        p.U() -= (1.0 + elasticity_)*Un*Sfp;
-                    }
-                }
-            }
-            else
-            {
-                // translation
-
-                vector v = (Cf1 - Cf0)/dt;
-                vector Ur = p.U() - v;
-                scalar Urn = Ur & Sf;
-
-                if (Urn > 0.0)
-                {
-                    Ur -= (1.0 + elasticity_)*Urn*Sf;
-                    p.U() = Ur + v;
-                }
-
-
-            }
-        }
-
-    }
-    else
-    {
-        FatalError
-            << "bool reflectParcel::wallTreatment(parcel& parcel) const "
-                << " parcel has hit a boundary " 
-                << mesh_.boundary()[patchi].type()
-                << " which not yet has been implemented."
-            << abort(FatalError);
-    }
-    return true;
-}
-
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-} // End namespace Foam
-
-// ************************************************************************* //
diff --git a/src/lagrangian/dsmc/clouds/derived/dsmcCloud/dsmcCloud.H b/src/lagrangian/dsmc/clouds/derived/dsmcCloud/dsmcCloud.H
index d530205681..ad63aca9fc 100644
--- a/src/lagrangian/dsmc/clouds/derived/dsmcCloud/dsmcCloud.H
+++ b/src/lagrangian/dsmc/clouds/derived/dsmcCloud/dsmcCloud.H
@@ -91,7 +91,7 @@ public:
     // Member functions
 
         //- Write fields
-        void writeFields() const;
+        virtual void writeFields() const;
 };
 
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
diff --git a/src/lagrangian/intermediate/Make/files b/src/lagrangian/intermediate/Make/files
index c07a3a34fa..7911383146 100644
--- a/src/lagrangian/intermediate/Make/files
+++ b/src/lagrangian/intermediate/Make/files
@@ -59,6 +59,7 @@ submodels/addOns/radiation/scatter/cloudScatter/cloudScatter.C
 /* data entries */
 submodels/IO/DataEntry/makeDataEntries.C
 submodels/IO/DataEntry/polynomial/polynomial.C
+submodels/IO/DataEntry/polynomial/polynomialIO.C
 
 
 /* integration schemes */
diff --git a/src/lagrangian/intermediate/clouds/derived/BasicReactingCloud/BasicReactingCloud.H b/src/lagrangian/intermediate/clouds/derived/BasicReactingCloud/BasicReactingCloud.H
index 49a51a230e..0dea7344a6 100644
--- a/src/lagrangian/intermediate/clouds/derived/BasicReactingCloud/BasicReactingCloud.H
+++ b/src/lagrangian/intermediate/clouds/derived/BasicReactingCloud/BasicReactingCloud.H
@@ -92,7 +92,7 @@ public:
     // Member Functions
 
         //- Write fields
-        void writeFields() const;
+        virtual void writeFields() const;
 };
 
 
diff --git a/src/lagrangian/intermediate/clouds/derived/BasicReactingMultiphaseCloud/BasicReactingMultiphaseCloud.H b/src/lagrangian/intermediate/clouds/derived/BasicReactingMultiphaseCloud/BasicReactingMultiphaseCloud.H
index ac0853823f..11b6fb2378 100644
--- a/src/lagrangian/intermediate/clouds/derived/BasicReactingMultiphaseCloud/BasicReactingMultiphaseCloud.H
+++ b/src/lagrangian/intermediate/clouds/derived/BasicReactingMultiphaseCloud/BasicReactingMultiphaseCloud.H
@@ -92,7 +92,7 @@ public:
     // Member Functions
 
         //- Write fields
-        void writeFields() const;
+        virtual void writeFields() const;
 };
 
 
diff --git a/src/lagrangian/intermediate/clouds/derived/basicKinematicCloud/basicKinematicCloud.H b/src/lagrangian/intermediate/clouds/derived/basicKinematicCloud/basicKinematicCloud.H
index 91a8ae2e5b..9b2c6003d3 100644
--- a/src/lagrangian/intermediate/clouds/derived/basicKinematicCloud/basicKinematicCloud.H
+++ b/src/lagrangian/intermediate/clouds/derived/basicKinematicCloud/basicKinematicCloud.H
@@ -87,7 +87,7 @@ public:
     // Member functions
 
         //- Write fields
-        void writeFields() const;
+        virtual void writeFields() const;
 };
 
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
diff --git a/src/lagrangian/intermediate/clouds/derived/basicThermoCloud/basicThermoCloud.H b/src/lagrangian/intermediate/clouds/derived/basicThermoCloud/basicThermoCloud.H
index 5254fed8eb..cbe3695d5d 100644
--- a/src/lagrangian/intermediate/clouds/derived/basicThermoCloud/basicThermoCloud.H
+++ b/src/lagrangian/intermediate/clouds/derived/basicThermoCloud/basicThermoCloud.H
@@ -90,7 +90,7 @@ public:
     // Member Functions
 
         //- Write fields
-        void writeFields() const;
+        virtual void writeFields() const;
 };
 
 
diff --git a/src/lagrangian/intermediate/submodels/Kinematic/InjectionModel/InjectionModel/InjectionModel.C b/src/lagrangian/intermediate/submodels/Kinematic/InjectionModel/InjectionModel/InjectionModel.C
index fa48f4c28b..7c63f1c262 100644
--- a/src/lagrangian/intermediate/submodels/Kinematic/InjectionModel/InjectionModel/InjectionModel.C
+++ b/src/lagrangian/intermediate/submodels/Kinematic/InjectionModel/InjectionModel/InjectionModel.C
@@ -233,7 +233,8 @@ void Foam::InjectionModel<CloudType>::postInjectCheck(const label parcelsAdded)
 {
     if (parcelsAdded > 0)
     {
-        Pout<< "\n--> Cloud: " << owner_.name() << nl
+        Pout<< nl
+            << "--> Cloud: " << owner_.name() << nl
             << "    Added " << parcelsAdded
             << " new parcels" << nl << endl;
     }
diff --git a/src/lagrangian/molecularDynamics/molecule/Make/files b/src/lagrangian/molecularDynamics/molecule/Make/files
old mode 100755
new mode 100644
diff --git a/src/lagrangian/molecularDynamics/molecule/Make/options b/src/lagrangian/molecularDynamics/molecule/Make/options
old mode 100755
new mode 100644
diff --git a/src/lagrangian/solidParticle/solidParticleCloud.H b/src/lagrangian/solidParticle/solidParticleCloud.H
index 078594592d..f171007ce3 100644
--- a/src/lagrangian/solidParticle/solidParticleCloud.H
+++ b/src/lagrangian/solidParticle/solidParticleCloud.H
@@ -108,10 +108,10 @@ public:
             void move(const dimensionedVector& g);
 
 
-        // I-O
+        // Write
 
             //- Write fields
-            void writeFields() const;
+            virtual void writeFields() const;
 };
 
 
diff --git a/src/thermophysicalModels/radiation/radiationModel/fvDOM/interpolationLookUpTable/interpolationLookUpTable.C b/src/thermophysicalModels/radiation/radiationModel/fvDOM/interpolationLookUpTable/interpolationLookUpTable.C
old mode 100755
new mode 100644
diff --git a/src/thermophysicalModels/radiation/radiationModel/fvDOM/interpolationLookUpTable/interpolationLookUpTable.H b/src/thermophysicalModels/radiation/radiationModel/fvDOM/interpolationLookUpTable/interpolationLookUpTable.H
old mode 100755
new mode 100644
diff --git a/tutorials/lagrangian/coalChemistryFoam/simplifiedSiwek/system/fvSchemes b/tutorials/lagrangian/coalChemistryFoam/simplifiedSiwek/system/fvSchemes
old mode 100755
new mode 100644
diff --git a/tutorials/lagrangian/coalChemistryFoam/simplifiedSiwek/system/fvSolution b/tutorials/lagrangian/coalChemistryFoam/simplifiedSiwek/system/fvSolution
old mode 100755
new mode 100644
diff --git a/tutorials/lagrangian/porousExplicitSourceReactingParcelFoam/filter/Allclean b/tutorials/lagrangian/porousExplicitSourceReactingParcelFoam/filter/Allclean
index d8e9677f46..9ded4bdec6 100755
--- a/tutorials/lagrangian/porousExplicitSourceReactingParcelFoam/filter/Allclean
+++ b/tutorials/lagrangian/porousExplicitSourceReactingParcelFoam/filter/Allclean
@@ -3,6 +3,7 @@ set -x
 
 # remove old cell sets
 rm -rf constant/polyMesh/sets
+foamClearPolyMesh
 
 # remove old time folders
 rm -rf 0 *[1-9]*
diff --git a/tutorials/lagrangian/porousExplicitSourceReactingParcelFoam/filter/Allrun b/tutorials/lagrangian/porousExplicitSourceReactingParcelFoam/filter/Allrun
index 8378f1f44b..701d55dc28 100755
--- a/tutorials/lagrangian/porousExplicitSourceReactingParcelFoam/filter/Allrun
+++ b/tutorials/lagrangian/porousExplicitSourceReactingParcelFoam/filter/Allrun
@@ -15,6 +15,7 @@ setSet -batch system/sets.setSet >& log.setSet1
 setsToZones -noFlipMap >& log.setsToZones
 
 # create the first cyclic - lhs of porous zone
+unset FOAM_SETNAN
 createBaffles cycLeft cycLeft -overwrite >& log.createBaffles1
 
 # create the second cyclic - rhs of porous zone
diff --git a/tutorials/lagrangian/porousExplicitSourceReactingParcelFoam/filter/system/decomposeParDict b/tutorials/lagrangian/porousExplicitSourceReactingParcelFoam/filter/system/decomposeParDict
index 152e9d0528..c8ec739687 100644
--- a/tutorials/lagrangian/porousExplicitSourceReactingParcelFoam/filter/system/decomposeParDict
+++ b/tutorials/lagrangian/porousExplicitSourceReactingParcelFoam/filter/system/decomposeParDict
@@ -19,7 +19,7 @@ numberOfSubdomains 4;
 
 method          metis;
 
-preservePatches
+preserveFaceZones
 (
     cycLeft
     cycRight
@@ -39,9 +39,7 @@ hierarchicalCoeffs
 }
 
 metisCoeffs
-{
-    processorWeights ( 1 1 1 1 );
-}
+{}
 
 manualCoeffs
 {