lagrangian: Improved handling of binary transfers

Now using memory offsets to calculate transfer block sizes rather than
sum of 'sizeof' to ensure word alignment is accounted for

src/lagrangian/DSMC/parcels/Templates/DSMCParcel/DSMCParcel.H

@@ -41,7 +41,6 @@ SourceFiles
 #include "IOstream.H"
 #include "autoPtr.H"
 #include "contiguous.H"
-
 #include "DSMCCloud.H"
 
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
@@ -70,6 +69,12 @@ class DSMCParcel
 :
     public ParcelType
 {
+    // Private member data
+
+        //- Size in bytes of the fields
+        static const std::size_t sizeofFields_;
+
+
 public:
 
     //- Class to hold DSMC particle constant properties
@@ -92,7 +97,7 @@ public:
 
     public:
 
-        // Constrcutors
+        // Constructors
 
             //- Null constructor, allows List of constantProperties to be
             //  created before the contents is initialised
@@ -104,10 +109,10 @@ public:
 
         // Member functions
 
-            //- Return const access to the particle density
+            //- Return const access to the particle mass [kg]
             inline scalar mass() const;
 
-            //- Return const access to the minimum particle mass
+            //- Return const access to the hard sphere diameter [m]
             inline scalar d() const;
 
             //- Return the reference total collision cross section
@@ -152,7 +157,7 @@ protected:
             vector U_;
 
             //- Internal energy of the Parcel, covering all non-translational
-            // degrees of freedom [J]
+            //  degrees of freedom [J]
             scalar Ei_;
 
             //- Parcel type id
@@ -196,7 +201,6 @@ public:
             return autoPtr<particle>(new DSMCParcel<ParcelType>(*this));
         }
 
-
         //- Factory class to read-construct particles used for
         //  parallel transfer
         class iNew
@@ -233,6 +237,7 @@ public:
             //- Return const access to internal energy
             inline scalar Ei() const;
 
+
         // Edit
 
             //- Return access to velocity

src/lagrangian/DSMC/parcels/Templates/DSMCParcel/DSMCParcelIO.C

@@ -28,6 +28,15 @@ License
 #include "IOField.H"
 #include "Cloud.H"
 
+// * * * * * * * * * * * * * * Static Data Members * * * * * * * * * * * * * //
+
+template<class ParcelType>
+const std::size_t Foam::DSMCParcel<ParcelType>::sizeofFields_
+(
+    sizeof(DSMCParcel<ParcelType>) - sizeof(ParcelType)
+);
+
+
 // * * * * * * * * * * * * * * * * Constructors  * * * * * * * * * * * * * * //
 
 template<class ParcelType>
@@ -53,13 +62,7 @@ Foam::DSMCParcel<ParcelType>::DSMCParcel
         }
         else
         {
-            is.read
-            (
-                reinterpret_cast<char*>(&U_),
-                sizeof(U_)
-              + sizeof(Ei_)
-              + sizeof(typeId_)
-            );
+            is.read(reinterpret_cast<char*>(&U_), sizeofFields_);
         }
     }
 
@@ -157,9 +160,7 @@ Foam::Ostream& Foam::operator<<
         os.write
         (
             reinterpret_cast<const char*>(&p.U_),
-            sizeof(p.U())
-          + sizeof(p.Ei())
-          + sizeof(p.typeId())
+            DSMCParcel<ParcelType>::sizeofFields_
         );
     }
 

src/lagrangian/basic/IOPosition/IOPosition.C

@@ -2,7 +2,7 @@
   =========                 |
   \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
    \\    /   O peration     |
-    \\  /    A nd           | Copyright (C) 2011 OpenFOAM Foundation
+    \\  /    A nd           | Copyright (C) 2011-2015 OpenFOAM Foundation
      \\/     M anipulation  |
 -------------------------------------------------------------------------------
 License
@@ -68,11 +68,7 @@ bool Foam::IOPosition<CloudType>::writeData(Ostream& os) const
 
     forAllConstIter(typename CloudType, cloud_, iter)
     {
-        const typename CloudType::particleType& p = iter();
-
-        // Prevent writing additional fields
-        p.write(os, false);
-
+        iter().writePosition(os);
         os  << nl;
     }
 
@@ -100,7 +96,7 @@ void Foam::IOPosition<CloudType>::readData(CloudType& c, bool checkClass)
 
         for (label i=0; i<s; i++)
         {
-            // Do not read any fields, position only
+            // Read position only
             c.append(new typename CloudType::particleType(mesh, is, false));
         }
 
@@ -129,7 +125,8 @@ void Foam::IOPosition<CloudType>::readData(CloudType& c, bool checkClass)
         )
         {
             is.putBack(lastToken);
-            // Do not read any fields, position only
+
+            // Write position only
             c.append(new typename CloudType::particleType(mesh, is, false));
             is  >> lastToken;
         }

src/lagrangian/basic/particle/particle.H

@@ -80,6 +80,15 @@ class particle
 :
     public IDLList<particle>::link
 {
+    // Private member data
+
+        //- Size in bytes of the position data
+        static const std::size_t sizeofPosition_;
+
+        //- Size in bytes of the fields
+        static const std::size_t sizeofFields_;
+
+
 public:
 
     template<class CloudType>
@@ -358,7 +367,6 @@ public:
             return autoPtr<particle>(new particle(*this));
         }
 
-
         //- Factory class to read-construct particles used for
         //  parallel transfer
         class iNew
@@ -556,8 +564,8 @@ public:
         template<class CloudType>
         static void writeFields(const CloudType& c);
 
-        //- Write the particle data
-        void write(Ostream& os, bool writeFields) const;
+        //- Write the particle position and cell
+        void writePosition(Ostream&) const;
 
 
     // Friend Operators

src/lagrangian/basic/particle/particleIO.C

@@ -2,7 +2,7 @@
   =========                 |
   \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
    \\    /   O peration     |
-    \\  /    A nd           | Copyright (C) 2011-2012 OpenFOAM Foundation
+    \\  /    A nd           | Copyright (C) 2011-2015 OpenFOAM Foundation
      \\/     M anipulation  |
 -------------------------------------------------------------------------------
 License
@@ -25,12 +25,21 @@ License
 
 #include "particle.H"
 #include "IOstreams.H"
-#include "IOPosition.H"
 
 // * * * * * * * * * * * * * * Static Data Members * * * * * * * * * * * * * //
 
 Foam::string Foam::particle::propertyList_ = Foam::particle::propertyList();
 
+const std::size_t Foam::particle::sizeofPosition_
+(
+    offsetof(particle, faceI_) - offsetof(particle, position_)
+);
+
+const std::size_t Foam::particle::sizeofFields_
+(
+    sizeof(particle) - offsetof(particle, position_)
+);
+
 
 // * * * * * * * * * * * * * * * * Constructors  * * * * * * * * * * * * * * //
 
@@ -46,45 +55,29 @@ Foam::particle::particle(const polyMesh& mesh, Istream& is, bool readFields)
     origProc_(Pstream::myProcNo()),
     origId_(-1)
 {
-    // readFields : read additional data. Should be consistent with writeFields.
-
     if (is.format() == IOstream::ASCII)
     {
         is  >> position_ >> cellI_;
 
         if (readFields)
         {
-            is  >> tetFaceI_ >> tetPtI_ >> origProc_ >> origId_;
+            is  >> faceI_
+                >> stepFraction_
+                >> tetFaceI_
+                >> tetPtI_
+                >> origProc_
+                >> origId_;
         }
     }
     else
     {
-        // In binary read all particle data - needed for parallel transfer
         if (readFields)
         {
-            is.read
-            (
-                reinterpret_cast<char*>(&position_),
-                sizeof(position_)
-              + sizeof(cellI_)
-              + sizeof(faceI_)
-              + sizeof(stepFraction_)
-              + sizeof(tetFaceI_)
-              + sizeof(tetPtI_)
-              + sizeof(origProc_)
-              + sizeof(origId_)
-            );
+            is.read(reinterpret_cast<char*>(&position_), sizeofFields_);
         }
         else
         {
-            is.read
-            (
-                reinterpret_cast<char*>(&position_),
-                sizeof(position_)
-              + sizeof(cellI_)
-              + sizeof(faceI_)
-              + sizeof(stepFraction_)
-            );
+            is.read(reinterpret_cast<char*>(&position_), sizeofPosition_);
         }
     }
 
@@ -93,66 +86,43 @@ Foam::particle::particle(const polyMesh& mesh, Istream& is, bool readFields)
 }
 
 
-void Foam::particle::write(Ostream& os, bool writeFields) const
+void Foam::particle::writePosition(Ostream& os) const
 {
     if (os.format() == IOstream::ASCII)
     {
-        if (writeFields)
-        {
-            // Write the additional entries
-            os  << position_
-                << token::SPACE << cellI_
-                << token::SPACE << tetFaceI_
-                << token::SPACE << tetPtI_
-                << token::SPACE << origProc_
-                << token::SPACE << origId_;
-        }
-        else
-        {
-            os  << position_
-                << token::SPACE << cellI_;
-        }
+        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(tetFaceI_)
-              + sizeof(tetPtI_)
-              + sizeof(origProc_)
-              + sizeof(origId_)
-            );
-        }
-        else
-        {
-            os.write
-            (
-                reinterpret_cast<const char*>(&position_),
-                sizeof(position_)
-              + sizeof(cellI_)
-              + sizeof(faceI_)
-              + sizeof(stepFraction_)
-            );
-        }
+        os.write(reinterpret_cast<const char*>(&position_), sizeofPosition_);
     }
 
     // Check state of Ostream
-    os.check("particle::write(Ostream& os, bool) const");
+    os.check("particle::writePosition(Ostream& os, bool) const");
 }
 
 
 Foam::Ostream& Foam::operator<<(Ostream& os, const particle& p)
 {
-    // Write all data
-    p.write(os, true);
+    if (os.format() == IOstream::ASCII)
+    {
+        os  << p.position_
+            << token::SPACE << p.cellI_
+            << token::SPACE << p.faceI_
+            << token::SPACE << p.stepFraction_
+            << token::SPACE << p.tetFaceI_
+            << token::SPACE << p.tetPtI_
+            << token::SPACE << p.origProc_
+            << token::SPACE << p.origId_;
+    }
+    else
+    {
+        os.write
+        (
+            reinterpret_cast<const char*>(&p.position_),
+            particle::sizeofFields_
+        );
+    }
 
     return os;
 }

src/lagrangian/intermediate/parcels/Templates/CollidingParcel/CollidingParcel.H

@@ -2,7 +2,7 @@
   =========                 |
   \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
    \\    /   O peration     |
-    \\  /    A nd           | Copyright (C) 2011-2013 OpenFOAM Foundation
+    \\  /    A nd           | Copyright (C) 2011-2015 OpenFOAM Foundation
      \\/     M anipulation  |
 -------------------------------------------------------------------------------
 License
@@ -38,12 +38,10 @@ SourceFiles
 #define CollidingParcel_H
 
 #include "particle.H"
-
 #include "CollisionRecordList.H"
 #include "labelFieldIOField.H"
 #include "vectorFieldIOField.H"
 
-
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
 
 namespace Foam
@@ -74,6 +72,12 @@ class CollidingParcel
 :
     public ParcelType
 {
+    // Private member data
+
+        //- Size in bytes of the fields
+        static const std::size_t sizeofFields_;
+
+
 public:
 
     //- Class to hold thermo particle constant properties

src/lagrangian/intermediate/parcels/Templates/CollidingParcel/CollidingParcelIO.C

@@ -2,7 +2,7 @@
   =========                 |
   \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
    \\    /   O peration     |
-    \\  /    A nd           | Copyright (C) 2011-2013 OpenFOAM Foundation
+    \\  /    A nd           | Copyright (C) 2011-2015 OpenFOAM Foundation
      \\/     M anipulation  |
 -------------------------------------------------------------------------------
 License
@@ -33,6 +33,13 @@ template<class ParcelType>
 Foam::string Foam::CollidingParcel<ParcelType>::propertyList_ =
     Foam::CollidingParcel<ParcelType>::propertyList();
 
+template<class ParcelType>
+const std::size_t Foam::CollidingParcel<ParcelType>::sizeofFields_
+(
+    offsetof(CollidingParcel<ParcelType>, collisionRecords_)
+  - offsetof(CollidingParcel<ParcelType>, f_)
+);
+
 
 // * * * * * * * * * * * * * * * * Constructors  * * * * * * * * * * * * * * //
 
@@ -60,13 +67,7 @@ Foam::CollidingParcel<ParcelType>::CollidingParcel
         }
         else
         {
-            is.read
-            (
-                reinterpret_cast<char*>(&f_),
-              + sizeof(f_)
-              + sizeof(angularMomentum_)
-              + sizeof(torque_)
-            );
+            is.read(reinterpret_cast<char*>(&f_), sizeofFields_);
         }
 
         is >> collisionRecords_;
@@ -285,10 +286,10 @@ Foam::Ostream& Foam::operator<<
     if (os.format() == IOstream::ASCII)
     {
         os  << static_cast<const ParcelType&>(p)
-            << token::SPACE << p.f()
-            << token::SPACE << p.angularMomentum()
-            << token::SPACE << p.torque()
-            << token::SPACE << p.collisionRecords();
+            << token::SPACE << p.f_
+            << token::SPACE << p.angularMomentum_
+            << token::SPACE << p.torque_
+            << token::SPACE << p.collisionRecords_;
     }
     else
     {
@@ -296,9 +297,7 @@ Foam::Ostream& Foam::operator<<
         os.write
         (
             reinterpret_cast<const char*>(&p.f_),
-          + sizeof(p.f())
-          + sizeof(p.angularMomentum())
-          + sizeof(p.torque())
+            CollidingParcel<ParcelType>::sizeofFields_
         );
         os  << p.collisionRecords();
     }

src/lagrangian/intermediate/parcels/Templates/KinematicParcel/KinematicParcel.H

@@ -2,7 +2,7 @@
   =========                 |
   \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
    \\    /   O peration     |
-    \\  /    A nd           | Copyright (C) 2011-2014 OpenFOAM Foundation
+    \\  /    A nd           | Copyright (C) 2011-2015 OpenFOAM Foundation
      \\/     M anipulation  |
 -------------------------------------------------------------------------------
 License
@@ -78,6 +78,15 @@ class KinematicParcel
 :
     public ParcelType
 {
+    // Private data
+
+        //- Size in bytes of the fields
+        static const std::size_t sizeofFields_;
+
+        //- Number of particle tracking attempts before we assume that it stalls
+        static label maxTrackAttempts;
+
+
 public:
 
     //- Class to hold kinematic particle constant properties
@@ -137,7 +146,7 @@ public:
             //- Return const access to the particle density
             inline scalar rho0() const;
 
-            //- Return const access to the minimum particle mass
+            //- Return const access to the minimum parcel mass
             inline scalar minParcelMass() const;
     };
 
@@ -218,10 +227,6 @@ public:
     };
 
 
-    //- Number of particle tracking attempts before we assume that it stalls
-    static label maxTrackAttempts;
-
-
 protected:
 
     // Protected data

src/lagrangian/intermediate/parcels/Templates/KinematicParcel/KinematicParcelIO.C

@@ -2,7 +2,7 @@
   =========                 |
   \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
    \\    /   O peration     |
-    \\  /    A nd           | Copyright (C) 2011-2014 OpenFOAM Foundation
+    \\  /    A nd           | Copyright (C) 2011-2015 OpenFOAM Foundation
      \\/     M anipulation  |
 -------------------------------------------------------------------------------
 License
@@ -34,6 +34,14 @@ template<class ParcelType>
 Foam::string Foam::KinematicParcel<ParcelType>::propertyList_ =
     Foam::KinematicParcel<ParcelType>::propertyList();
 
+template<class ParcelType>
+const std::size_t Foam::KinematicParcel<ParcelType>::sizeofFields_
+(
+    offsetof(KinematicParcel<ParcelType>, rhoc_)
+  - offsetof(KinematicParcel<ParcelType>, active_)
+);
+
+
 // * * * * * * * * * * * * * * * * Constructors  * * * * * * * * * * * * * * //
 
 template<class ParcelType>
@@ -76,8 +84,7 @@ Foam::KinematicParcel<ParcelType>::KinematicParcel
         }
         else
         {
-            label size = long(&UTurb_) - long(&active_) + sizeof(UTurb_);
-            is.read(reinterpret_cast<char*>(&active_), size);
+            is.read(reinterpret_cast<char*>(&active_), sizeofFields_);
         }
     }
 
@@ -236,9 +243,11 @@ Foam::Ostream& Foam::operator<<
     else
     {
         os  << static_cast<const ParcelType&>(p);
-
-        label size = long(&p.UTurb_) - long(&p.active_) + sizeof(p.UTurb_);
-        os.write(reinterpret_cast<const char*>(&p.active_), size);
+        os.write
+        (
+            reinterpret_cast<const char*>(&p.active_),
+            KinematicParcel<ParcelType>::sizeofFields_
+        );
     }
 
     // Check state of Ostream

src/lagrangian/intermediate/parcels/Templates/MPPICParcel/MPPICParcel.H

@@ -2,7 +2,7 @@
   =========                 |
   \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
    \\    /   O peration     |
-    \\  /    A nd           | Copyright (C) 2013 OpenFOAM Foundation
+    \\  /    A nd           | Copyright (C) 2013-2015 OpenFOAM Foundation
      \\/     M anipulation  |
 -------------------------------------------------------------------------------
 License
@@ -73,6 +73,12 @@ class MPPICParcel
 :
     public ParcelType
 {
+    // Private data
+
+        //- Size in bytes of the fields
+        static const std::size_t sizeofFields_;
+
+
 public:
 
     template<class CloudType>

src/lagrangian/intermediate/parcels/Templates/MPPICParcel/MPPICParcelIO.C

@@ -2,7 +2,7 @@
   =========                 |
   \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
    \\    /   O peration     |
-    \\  /    A nd           | Copyright (C) 2013 OpenFOAM Foundation
+    \\  /    A nd           | Copyright (C) 2013-2015 OpenFOAM Foundation
      \\/     M anipulation  |
 -------------------------------------------------------------------------------
 License
@@ -33,6 +33,12 @@ template<class ParcelType>
 Foam::string Foam::MPPICParcel<ParcelType>::propertyList_ =
     Foam::MPPICParcel<ParcelType>::propertyList();
 
+template<class ParcelType>
+const std::size_t Foam::MPPICParcel<ParcelType>::sizeofFields_
+(
+    sizeof(MPPICParcel<ParcelType>) - sizeof(ParcelType)
+);
+
 
 // * * * * * * * * * * * * * * * * Constructors  * * * * * * * * * * * * * * //
 
@@ -55,11 +61,7 @@ Foam::MPPICParcel<ParcelType>::MPPICParcel
         }
         else
         {
-            is.read
-            (
-                reinterpret_cast<char*>(&UCorrect_),
-              + sizeof(UCorrect_)
-            );
+            is.read(reinterpret_cast<char*>(&UCorrect_), sizeofFields_);
         }
     }
 
@@ -144,7 +146,7 @@ Foam::Ostream& Foam::operator<<
         os.write
         (
             reinterpret_cast<const char*>(&p.UCorrect_),
-          + sizeof(p.UCorrect())
+            MPPICParcel<ParcelType>::sizeofFields_
         );