Changed src/lagrangian/molecule folder to molecularDynamics and split off...

Changed src/lagrangian/molecule folder to molecularDynamics and split off separate potential library.

src/lagrangian/molecularDynamics/molecule/Make/files

+correlationFunction = correlationFunction
+
+distribution = distribution
+
+molecule = molecule
+moleculeCloud = moleculeCloud
+
+reducedUnits = reducedUnits
+
+referredMolecule = referredMolecule
+referredCellList = referredCellList
+referredCell = referredCell
+referralLists = referralLists
+
+tetherPotential = tetherPotential
+
+$(distribution)/distribution.C
+
+$(reducedUnits)/reducedUnits.C
+$(reducedUnits)/reducedUnitsIO.C
+
+$(molecule)/molecule.C
+$(molecule)/moleculeIO.C
+
+$(moleculeCloud)/moleculeCloud.C
+$(moleculeCloud)/moleculeCloudBuildCellOccupancy.C
+$(moleculeCloud)/moleculeCloudBuildCellInteractionLists.C
+$(moleculeCloud)/moleculeCloudBuildCellReferralLists.C
+
+$(moleculeCloud)/moleculeCloudTestEdgeEdgeDistance.C
+$(moleculeCloud)/moleculeCloudTestPointFaceDistance.C
+$(moleculeCloud)/moleculeCloudRealCellsInRangeOfSegment.C
+$(moleculeCloud)/moleculeCloudReferredCellsInRangeOfSegment.C
+
+$(moleculeCloud)/moleculeCloudCalculateForce.C
+$(moleculeCloud)/moleculeCloudCalculatePairForce.C
+$(moleculeCloud)/moleculeCloudCalculateTetherForce.C
+$(moleculeCloud)/moleculeCloudCalculateExternalForce.C
+$(moleculeCloud)/moleculeCloudIntegrateEquationsOfMotion.C
+$(moleculeCloud)/moleculeCloudRemoveHighEnergyOverlaps.C
+$(moleculeCloud)/moleculeCloudApplyConstraintsAndThermostats.C
+
+$(referralLists)/receivingReferralList.C
+$(referralLists)/sendingReferralList.C
+$(referredCellList)/referredCellList.C
+$(referredCell)/referredCell.C
+$(referredMolecule)/referredMolecule.C
+
+LIB = $(FOAM_LIBBIN)/libmolecule
+

src/lagrangian/molecularDynamics/molecule/Make/options

+EXE_INC = \
+    -I$(LIB_SRC)/finiteVolume/lnInclude \
+    -I$(LIB_SRC)/lagrangian/basic/lnInclude \
+    -I$(LIB_SRC)/lagrangian/molecularDynamics/potential/lnInclude
+
+EXE_LIBS = \
+    -lfiniteVolume \
+    -llagrangian \
+    -lpotential
+

src/lagrangian/molecularDynamics/molecule/correlationFunction/bufferedAccumulator/bufferedAccumulator.C

+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+   \\    /   O peration     |
+    \\  /    A nd           | Copyright (C) 1991-2007 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 "bufferedAccumulator.H"
+
+// * * * * * * * * * * * * * * Static Data Members * * * * * * * * * * * * * //
+
+template<class Type>
+const char* const
+    Foam::bufferedAccumulator<Type>::typeName("bufferedAccumulator");
+
+
+// * * * * * * * * * * * * * Private Member Functions  * * * * * * * * * * * //
+
+template<class Type>
+void Foam::bufferedAccumulator<Type>::accumulateAndResetBuffer(const label b)
+{
+    accumulationBuffer() += (*this)[b];
+
+    averagesTaken_++;
+
+    (*this)[b] = Field<Type>(bufferLength(), pTraits<Type>::zero);
+
+    bufferOffsets_[b] = 0;
+}
+
+
+// * * * * * * * * * * * * * * * * Constructors  * * * * * * * * * * * * * * //
+
+template<class Type>
+Foam::bufferedAccumulator<Type>::bufferedAccumulator()
+:
+    List< Field<Type> >(),
+    averagesTaken_(),
+    bufferOffsets_()
+{}
+
+
+template<class Type>
+Foam::bufferedAccumulator<Type>::bufferedAccumulator
+(
+    const label nBuffers,
+    const label bufferLength,
+    const label bufferingInterval
+)
+:
+    List< Field<Type> >(),
+    averagesTaken_(),
+    bufferOffsets_()
+{
+    setSizes
+    (
+        nBuffers,
+        bufferLength,
+        bufferingInterval
+    );
+}
+
+
+template<class Type>
+Foam::bufferedAccumulator<Type>::bufferedAccumulator
+(
+    const bufferedAccumulator<Type>& bA
+)
+:
+    List< Field<Type> >(static_cast< List< Field<Type> > >(bA)),
+    averagesTaken_(bA.averagesTaken()),
+    bufferOffsets_(bA.bufferOffsets())
+{}
+
+
+// * * * * * * * * * * * * * * * * Destructor  * * * * * * * * * * * * * * * //
+
+template<class Type>
+Foam::bufferedAccumulator<Type>::~bufferedAccumulator()
+{}
+
+
+// * * * * * * * * * * * * * * * Member Functions  * * * * * * * * * * * * * //
+
+template<class Type>
+void Foam::bufferedAccumulator<Type>::setSizes
+(
+    const label nBuffers,
+    const label bufferLength,
+    const label bufferingInterval
+)
+{
+    (*this).setSize(nBuffers + 1);
+
+    forAll((*this), b)
+    {
+        (*this)[b] = Field<Type>(bufferLength, pTraits<Type>::zero);
+    }
+
+    averagesTaken_ = 0;
+
+    bufferOffsets_.setSize(nBuffers);
+
+    forAll(bufferOffsets_, bO)
+    {
+        bufferOffsets_[bO] = -bufferingInterval * bO - 1;
+    }
+}
+
+template<class Type>
+Foam::label Foam::bufferedAccumulator<Type>::addToBuffers
+(
+    const List<Type>& valuesToAdd
+)
+{
+    label bufferToRefill = -1;
+
+    for (label b = 0; b < nBuffers(); b++)
+    {
+        Field<Type>& buf((*this)[b]);
+
+        label& bO = bufferOffsets_[b];
+
+        if (bO >= 0)
+        {
+            buf[bO] = valuesToAdd[b];
+        }
+
+        bO++;
+
+        if (bO == bufferLength())
+        {
+            accumulateAndResetBuffer(b);
+        }
+
+        if (bO == 0)
+        {
+            if (bufferToRefill != -1)
+            {
+                FatalErrorIn("bufferedAccumulator<Type>::addToBuffers ")
+                    << "More than one bufferedAccumulator accumulation "
+                    << "buffer filled at once, this is considered an error."
+                    << abort(FatalError);
+            }
+
+            bufferToRefill = b;
+        }
+    }
+
+    return bufferToRefill;
+}
+
+
+template<class Type>
+Foam::Field<Type> Foam::bufferedAccumulator<Type>::averaged() const
+{
+    if (averagesTaken_)
+    {
+        Field<Type> bA = accumulationBuffer()/averagesTaken_;
+
+        return bA;
+    }
+    else
+    {
+        WarningIn
+        (
+            "bufferedAccumulator<Type>::averagedbufferedAccumulator() const"
+        )
+        << "Averaged correlation function requested but averagesTaken = "
+        << averagesTaken_
+        << ". Returning empty field."
+        << endl;
+
+        return Field<Type>(bufferLength(), pTraits<Type>::zero);
+    }
+}
+
+
+template<class Type>
+void Foam::bufferedAccumulator<Type>::resetAveraging()
+{
+    accumulationBuffer() = Field<Type>(bufferLength(), pTraits<Type>::zero);
+
+    averagesTaken_ = 0;
+}
+
+
+// * * * * * * * * * * * * * * * Member Operators  * * * * * * * * * * * * * //
+
+template<class Type>
+void Foam::bufferedAccumulator<Type>::operator=
+(
+    const bufferedAccumulator<Type>& rhs
+)
+{
+    // Check for assignment to self
+    if (this == &rhs)
+    {
+        FatalErrorIn
+        (
+            "bufferedAccumulator<Type>::operator=(const bufferedAccumulator&)"
+        )
+            << "Attempted assignment to self"
+            << abort(FatalError);
+    }
+
+    List< Field<Type> >::operator=(rhs);
+
+    averagesTaken_ = rhs.averagesTaken();
+
+    bufferOffsets_ = rhs.bufferOffsets();
+}
+
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+#   include "bufferedAccumulatorIO.C"
+
+// ************************************************************************* //

src/lagrangian/molecularDynamics/molecule/correlationFunction/bufferedAccumulator/bufferedAccumulator.H

+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+   \\    /   O peration     |
+    \\  /    A nd           | Copyright (C) 1991-2007 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::bufferedAccumulator
+
+Description
+
+SourceFiles
+    bufferedAccumulatorI.H
+    bufferedAccumulator.C
+    bufferedAccumulatorIO.C
+
+\*---------------------------------------------------------------------------*/
+
+#ifndef bufferedAccumulator_H
+#define bufferedAccumulator_H
+
+#include "Field.H"
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+namespace Foam
+{
+
+template<class Type>
+class bufferedAccumulator;
+
+template<class Type>
+Ostream& operator<<
+(
+    Ostream&,
+    const bufferedAccumulator<Type>&
+);
+
+/*---------------------------------------------------------------------------*\
+                      Class bufferedAccumulator Declaration
+\*---------------------------------------------------------------------------*/
+
+template<class Type>
+class bufferedAccumulator
+:
+    public List< Field<Type> >
+{
+    // Private data
+
+        label averagesTaken_;
+
+        List<label> bufferOffsets_;
+
+
+    // Private Member Functions
+
+        inline Field<Type>& accumulationBuffer();
+
+        inline const Field<Type>& accumulationBuffer() const;
+
+        void accumulateAndResetBuffer(const label b);
+
+
+public:
+
+    //- Component type
+    typedef typename pTraits<Type>::cmptType cmptType;
+
+
+    // Static data members
+
+        static const char* const typeName;
+
+
+    // Constructors
+
+        //- Construct null
+        bufferedAccumulator();
+
+        //- Construct from components
+        bufferedAccumulator
+        (
+            const label nBuffers,
+            const label bufferLength,
+            const label bufferingInterval
+        );
+
+        //- Construct as copy
+        bufferedAccumulator(const bufferedAccumulator<Type>&);
+
+
+    // Destructor
+
+        ~bufferedAccumulator();
+
+
+    // Member Functions
+
+        label addToBuffers(const List<Type>& valuesToAdd);
+
+        Field<Type> averaged() const;
+
+        void resetAveraging();
+
+
+        // Access
+
+            inline label averagesTaken() const;
+
+            inline label nBuffers() const;
+
+            inline label bufferLength() const;
+
+            inline const List<label>& bufferOffsets() const;
+
+
+        // Edit
+
+            void setSizes
+            (
+                const label nBuffers,
+                const label bufferLength,
+                const label bufferingInterval
+            );
+
+
+    // Member Operators
+
+        void operator=(const bufferedAccumulator<Type>&);
+
+
+    // IOstream Operators
+
+        friend Ostream& operator<< <Type>
+        (
+            Ostream&,
+            const bufferedAccumulator<Type>&
+        );
+};
+
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+} // End namespace Foam
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+#include "bufferedAccumulatorI.H"
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+#ifdef NoRepository
+#   include "bufferedAccumulator.C"
+#endif
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+#endif
+
+// ************************************************************************* //

src/lagrangian/molecularDynamics/molecule/correlationFunction/bufferedAccumulator/bufferedAccumulatorI.H

+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+   \\    /   O peration     |
+    \\  /    A nd           | Copyright (C) 1991-2007 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
+
+\*---------------------------------------------------------------------------*/
+
+namespace Foam
+{
+
+// * * * * * * * * * * * * * Private Member Functions  * * * * * * * * * * * //
+
+template<class Type>
+inline Field<Type>& bufferedAccumulator<Type>::accumulationBuffer()
+{
+    return (*this)[nBuffers()];
+}
+
+
+template<class Type>
+inline const Field<Type>& bufferedAccumulator<Type>::accumulationBuffer() const
+{
+    return (*this)[nBuffers()];
+}
+
+
+// * * * * * * * * * * * * * * * Member Functions  * * * * * * * * * * * * * //
+
+template<class Type>
+inline label bufferedAccumulator<Type>::averagesTaken() const
+{
+    return averagesTaken_;
+}
+
+
+template<class Type>
+inline label bufferedAccumulator<Type>::nBuffers() const
+{
+    return bufferOffsets_.size();
+}
+
+
+template<class Type>
+inline label bufferedAccumulator<Type>::bufferLength() const
+{
+    return (*this)[0].size();
+}
+
+
+template<class Type>
+inline const List<label>& bufferedAccumulator<Type>::bufferOffsets() const
+{
+    return bufferOffsets_;
+}
+
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+} // End namespace Foam
+
+// ************************************************************************* //

src/lagrangian/molecularDynamics/molecule/correlationFunction/bufferedAccumulator/bufferedAccumulatorIO.C

+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  F ield         | OpenFOAM: The Open Source bAD Toolbox
+   \\    /   O peration     |
+    \\  /    A nd           | Copyright (C) 1991-2007 OpenbAD 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