From 328399998f3c2845389f5ee2629fe1ec414f5b3f Mon Sep 17 00:00:00 2001
From: graham <graham.macpherson@strath.ac.uk>
Date: Mon, 16 Jun 2008 18:05:19 +0100
Subject: [PATCH 1/5] Changed src/lagrangian/molecule folder to
 molecularDynamics and split off se parate potential library.

---
 src/lagrangian/molecule/Make/files            |   57 -
 src/lagrangian/molecule/Make/options          |    8 -
 .../bufferedAccumulator/bufferedAccumulator.C |  238 ---
 .../bufferedAccumulator/bufferedAccumulator.H |  178 ---
 .../bufferedAccumulatorI.H                    |   80 -
 .../bufferedAccumulatorIO.C                   |   52 -
 .../correlationFunction/correlationFunction.C |  224 ---
 .../correlationFunction/correlationFunction.H |  180 ---
 .../correlationFunctionI.H                    |   70 -
 .../correlationFunctionIO.C                   |   72 -
 .../molecule/distribution/distribution.C      |  449 ------
 .../molecule/distribution/distribution.H      |  133 --
 .../molecule/distribution/distributionI.H     |   42 -
 .../molecule/distribution/distributionIO.C    |   35 -
 .../molecule/mdTools/averageMDFields.H        |  227 ---
 .../calculateAutoCorrelationFunctions.H       |   83 --
 .../molecule/mdTools/calculateMDFields.H      |   23 -
 .../mdTools/calculateTransportProperties.H    |   65 -
 .../mdTools/createAutoCorrelationFunctions.H  |   99 --
 .../molecule/mdTools/createMDFields.H         |  306 ----
 .../molecule/mdTools/createRefUnits.H         |   22 -
 src/lagrangian/molecule/mdTools/md.H          |   11 -
 .../mdTools/meanMomentumEnergyAndNMols.H      |  130 --
 .../molecule/mdTools/resetMDFields.H          |   26 -
 .../molecule/mdTools/temperatureAndPressure.H |  114 --
 .../mdTools/temperatureAndPressureVariables.H |   59 -
 .../mdTools/temperatureEquilibration.H        |   43 -
 src/lagrangian/molecule/molecule/molecule.C   |  214 ---
 src/lagrangian/molecule/molecule/molecule.H   |  271 ----
 src/lagrangian/molecule/molecule/moleculeI.H  |  159 --
 src/lagrangian/molecule/molecule/moleculeIO.C |  208 ---
 .../molecule/moleculeCloud/moleculeCloud.C    |  135 --
 .../molecule/moleculeCloud/moleculeCloud.H    |  350 -----
 ...eculeCloudApplyConstraintsAndThermostats.C |   60 -
 .../moleculeCloudBuildCellInteractionLists.C  |   80 -
 .../moleculeCloudBuildCellOccupancy.C         |   54 -
 .../moleculeCloudBuildCellReferralLists.C     |  194 ---
 .../moleculeCloudBuildCellsFoundInRange.H     |   52 -
 .../moleculeCloudBuildDirectInteractionList.H |  188 ---
 ...oleculeCloudBuildReferredInteractionList.H | 1285 -----------------
 .../moleculeCloudCalculateExternalForce.C     |   42 -
 .../moleculeCloudCalculateForce.C             |   59 -
 .../moleculeCloudCalculatePairForce.C         |   41 -
 ...moleculeCloudCalculatePairForceRealCells.H |   49 -
 ...lculatePairForceRealCellsCalculationStep.H |   33 -
 ...culeCloudCalculatePairForceReferredCells.H |   59 -
 .../moleculeCloudCalculateTetherForce.C       |   69 -
 .../molecule/moleculeCloud/moleculeCloudI.H   |  184 ---
 .../moleculeCloudIntegrateEquationsOfMotion.C |   50 -
 .../moleculeCloudReadIdList.H                 |   14 -
 .../moleculeCloudReadMDParameters.H           |    6 -
 .../moleculeCloudReadMDSolution.H             |   27 -
 .../moleculeCloudReadPotentials.H             |  327 -----
 .../moleculeCloudRealCellsInRangeOfSegment.C  |  152 --
 ...leculeCloudReferredCellsInRangeOfSegment.C |  117 --
 .../moleculeCloudRemoveHighEnergyOverlaps.C   |   67 -
 ...leCloudRemoveHighEnergyOverlapsRealCells.H |   55 -
 ...ghEnergyOverlapsRealCellsCalculationStep.H |   70 -
 ...oudRemoveHighEnergyOverlapsReferredCells.H |  144 --
 .../moleculeCloudTestEdgeEdgeDistance.C       |   86 --
 .../moleculeCloudTestPointFaceDistance.C      |  235 ---
 .../pairPotential/basic/pairPotential.C       |  308 ----
 .../pairPotential/basic/pairPotential.H       |  196 ---
 .../pairPotential/basic/pairPotentialI.H      |  102 --
 .../pairPotential/basic/pairPotentialList.C   |  180 ---
 .../pairPotential/basic/pairPotentialList.H   |  169 ---
 .../pairPotential/basic/pairPotentialListI.H  |   59 -
 .../pairPotential/derived/lennardJones.C      |  132 --
 .../pairPotential/derived/lennardJones.H      |  148 --
 .../pairPotential/derived/lennardJonesI.H     |   69 -
 .../tetherPotential/tetherPotential.C         |   94 --
 .../tetherPotential/tetherPotential.H         |  125 --
 .../tetherPotential/tetherPotentialI.H        |   56 -
 .../tetherPotential/tetherPotentialList.C     |  146 --
 .../tetherPotential/tetherPotentialList.H     |  125 --
 .../tetherPotential/tetherPotentialListI.H    |   50 -
 .../molecule/reducedUnits/reducedUnits.C      |  165 ---
 .../molecule/reducedUnits/reducedUnits.H      |  184 ---
 .../molecule/reducedUnits/reducedUnitsI.H     |   95 --
 .../molecule/reducedUnits/reducedUnitsIO.C    |   61 -
 .../referralLists/receivingReferralList.C     |  181 ---
 .../referralLists/receivingReferralList.H     |  138 --
 .../referralLists/receivingReferralListI.H    |   56 -
 .../referralLists/sendingReferralList.C       |  178 ---
 .../referralLists/sendingReferralList.H       |  138 --
 .../referralLists/sendingReferralListI.H      |   56 -
 .../molecule/referredCell/referredCell.C      |  441 ------
 .../molecule/referredCell/referredCell.H      |  277 ----
 .../molecule/referredCell/referredCellI.H     |  127 --
 .../referredCellList/referredCellList.C       |  327 -----
 .../referredCellList/referredCellList.H       |  103 --
 .../referredCellList/referredCellListI.H      |   42 -
 .../referredMolecule/referredMolecule.C       |   89 --
 .../referredMolecule/referredMolecule.H       |  129 --
 .../referredMolecule/referredMoleculeI.H      |   75 -
 95 files changed, 12983 deletions(-)
 delete mode 100755 src/lagrangian/molecule/Make/files
 delete mode 100755 src/lagrangian/molecule/Make/options
 delete mode 100755 src/lagrangian/molecule/correlationFunction/bufferedAccumulator/bufferedAccumulator.C
 delete mode 100755 src/lagrangian/molecule/correlationFunction/bufferedAccumulator/bufferedAccumulator.H
 delete mode 100755 src/lagrangian/molecule/correlationFunction/bufferedAccumulator/bufferedAccumulatorI.H
 delete mode 100755 src/lagrangian/molecule/correlationFunction/bufferedAccumulator/bufferedAccumulatorIO.C
 delete mode 100644 src/lagrangian/molecule/correlationFunction/correlationFunction.C
 delete mode 100644 src/lagrangian/molecule/correlationFunction/correlationFunction.H
 delete mode 100644 src/lagrangian/molecule/correlationFunction/correlationFunctionI.H
 delete mode 100644 src/lagrangian/molecule/correlationFunction/correlationFunctionIO.C
 delete mode 100755 src/lagrangian/molecule/distribution/distribution.C
 delete mode 100755 src/lagrangian/molecule/distribution/distribution.H
 delete mode 100755 src/lagrangian/molecule/distribution/distributionI.H
 delete mode 100755 src/lagrangian/molecule/distribution/distributionIO.C
 delete mode 100755 src/lagrangian/molecule/mdTools/averageMDFields.H
 delete mode 100644 src/lagrangian/molecule/mdTools/calculateAutoCorrelationFunctions.H
 delete mode 100755 src/lagrangian/molecule/mdTools/calculateMDFields.H
 delete mode 100644 src/lagrangian/molecule/mdTools/calculateTransportProperties.H
 delete mode 100644 src/lagrangian/molecule/mdTools/createAutoCorrelationFunctions.H
 delete mode 100755 src/lagrangian/molecule/mdTools/createMDFields.H
 delete mode 100644 src/lagrangian/molecule/mdTools/createRefUnits.H
 delete mode 100755 src/lagrangian/molecule/mdTools/md.H
 delete mode 100755 src/lagrangian/molecule/mdTools/meanMomentumEnergyAndNMols.H
 delete mode 100755 src/lagrangian/molecule/mdTools/resetMDFields.H
 delete mode 100755 src/lagrangian/molecule/mdTools/temperatureAndPressure.H
 delete mode 100755 src/lagrangian/molecule/mdTools/temperatureAndPressureVariables.H
 delete mode 100755 src/lagrangian/molecule/mdTools/temperatureEquilibration.H
 delete mode 100755 src/lagrangian/molecule/molecule/molecule.C
 delete mode 100755 src/lagrangian/molecule/molecule/molecule.H
 delete mode 100755 src/lagrangian/molecule/molecule/moleculeI.H
 delete mode 100755 src/lagrangian/molecule/molecule/moleculeIO.C
 delete mode 100755 src/lagrangian/molecule/moleculeCloud/moleculeCloud.C
 delete mode 100755 src/lagrangian/molecule/moleculeCloud/moleculeCloud.H
 delete mode 100755 src/lagrangian/molecule/moleculeCloud/moleculeCloudApplyConstraintsAndThermostats.C
 delete mode 100755 src/lagrangian/molecule/moleculeCloud/moleculeCloudBuildCellInteractionLists.C
 delete mode 100755 src/lagrangian/molecule/moleculeCloud/moleculeCloudBuildCellOccupancy.C
 delete mode 100755 src/lagrangian/molecule/moleculeCloud/moleculeCloudBuildCellReferralLists.C
 delete mode 100755 src/lagrangian/molecule/moleculeCloud/moleculeCloudBuildCellsFoundInRange.H
 delete mode 100755 src/lagrangian/molecule/moleculeCloud/moleculeCloudBuildDirectInteractionList.H
 delete mode 100755 src/lagrangian/molecule/moleculeCloud/moleculeCloudBuildReferredInteractionList.H
 delete mode 100755 src/lagrangian/molecule/moleculeCloud/moleculeCloudCalculateExternalForce.C
 delete mode 100755 src/lagrangian/molecule/moleculeCloud/moleculeCloudCalculateForce.C
 delete mode 100755 src/lagrangian/molecule/moleculeCloud/moleculeCloudCalculatePairForce.C
 delete mode 100755 src/lagrangian/molecule/moleculeCloud/moleculeCloudCalculatePairForceRealCells.H
 delete mode 100755 src/lagrangian/molecule/moleculeCloud/moleculeCloudCalculatePairForceRealCellsCalculationStep.H
 delete mode 100755 src/lagrangian/molecule/moleculeCloud/moleculeCloudCalculatePairForceReferredCells.H
 delete mode 100755 src/lagrangian/molecule/moleculeCloud/moleculeCloudCalculateTetherForce.C
 delete mode 100755 src/lagrangian/molecule/moleculeCloud/moleculeCloudI.H
 delete mode 100755 src/lagrangian/molecule/moleculeCloud/moleculeCloudIntegrateEquationsOfMotion.C
 delete mode 100755 src/lagrangian/molecule/moleculeCloud/moleculeCloudReadMDParameters/moleculeCloudReadIdList.H
 delete mode 100755 src/lagrangian/molecule/moleculeCloud/moleculeCloudReadMDParameters/moleculeCloudReadMDParameters.H
 delete mode 100755 src/lagrangian/molecule/moleculeCloud/moleculeCloudReadMDParameters/moleculeCloudReadMDSolution.H
 delete mode 100755 src/lagrangian/molecule/moleculeCloud/moleculeCloudReadMDParameters/moleculeCloudReadPotentials.H
 delete mode 100755 src/lagrangian/molecule/moleculeCloud/moleculeCloudRealCellsInRangeOfSegment.C
 delete mode 100755 src/lagrangian/molecule/moleculeCloud/moleculeCloudReferredCellsInRangeOfSegment.C
 delete mode 100755 src/lagrangian/molecule/moleculeCloud/moleculeCloudRemoveHighEnergyOverlaps.C
 delete mode 100755 src/lagrangian/molecule/moleculeCloud/moleculeCloudRemoveHighEnergyOverlapsRealCells.H
 delete mode 100755 src/lagrangian/molecule/moleculeCloud/moleculeCloudRemoveHighEnergyOverlapsRealCellsCalculationStep.H
 delete mode 100755 src/lagrangian/molecule/moleculeCloud/moleculeCloudRemoveHighEnergyOverlapsReferredCells.H
 delete mode 100755 src/lagrangian/molecule/moleculeCloud/moleculeCloudTestEdgeEdgeDistance.C
 delete mode 100755 src/lagrangian/molecule/moleculeCloud/moleculeCloudTestPointFaceDistance.C
 delete mode 100755 src/lagrangian/molecule/potentials/pairPotential/basic/pairPotential.C
 delete mode 100755 src/lagrangian/molecule/potentials/pairPotential/basic/pairPotential.H
 delete mode 100755 src/lagrangian/molecule/potentials/pairPotential/basic/pairPotentialI.H
 delete mode 100755 src/lagrangian/molecule/potentials/pairPotential/basic/pairPotentialList.C
 delete mode 100755 src/lagrangian/molecule/potentials/pairPotential/basic/pairPotentialList.H
 delete mode 100755 src/lagrangian/molecule/potentials/pairPotential/basic/pairPotentialListI.H
 delete mode 100755 src/lagrangian/molecule/potentials/pairPotential/derived/lennardJones.C
 delete mode 100755 src/lagrangian/molecule/potentials/pairPotential/derived/lennardJones.H
 delete mode 100755 src/lagrangian/molecule/potentials/pairPotential/derived/lennardJonesI.H
 delete mode 100755 src/lagrangian/molecule/potentials/tetherPotential/tetherPotential.C
 delete mode 100755 src/lagrangian/molecule/potentials/tetherPotential/tetherPotential.H
 delete mode 100755 src/lagrangian/molecule/potentials/tetherPotential/tetherPotentialI.H
 delete mode 100755 src/lagrangian/molecule/potentials/tetherPotential/tetherPotentialList.C
 delete mode 100755 src/lagrangian/molecule/potentials/tetherPotential/tetherPotentialList.H
 delete mode 100755 src/lagrangian/molecule/potentials/tetherPotential/tetherPotentialListI.H
 delete mode 100644 src/lagrangian/molecule/reducedUnits/reducedUnits.C
 delete mode 100644 src/lagrangian/molecule/reducedUnits/reducedUnits.H
 delete mode 100644 src/lagrangian/molecule/reducedUnits/reducedUnitsI.H
 delete mode 100644 src/lagrangian/molecule/reducedUnits/reducedUnitsIO.C
 delete mode 100755 src/lagrangian/molecule/referralLists/receivingReferralList.C
 delete mode 100755 src/lagrangian/molecule/referralLists/receivingReferralList.H
 delete mode 100755 src/lagrangian/molecule/referralLists/receivingReferralListI.H
 delete mode 100755 src/lagrangian/molecule/referralLists/sendingReferralList.C
 delete mode 100755 src/lagrangian/molecule/referralLists/sendingReferralList.H
 delete mode 100755 src/lagrangian/molecule/referralLists/sendingReferralListI.H
 delete mode 100755 src/lagrangian/molecule/referredCell/referredCell.C
 delete mode 100755 src/lagrangian/molecule/referredCell/referredCell.H
 delete mode 100755 src/lagrangian/molecule/referredCell/referredCellI.H
 delete mode 100755 src/lagrangian/molecule/referredCellList/referredCellList.C
 delete mode 100755 src/lagrangian/molecule/referredCellList/referredCellList.H
 delete mode 100755 src/lagrangian/molecule/referredCellList/referredCellListI.H
 delete mode 100755 src/lagrangian/molecule/referredMolecule/referredMolecule.C
 delete mode 100755 src/lagrangian/molecule/referredMolecule/referredMolecule.H
 delete mode 100755 src/lagrangian/molecule/referredMolecule/referredMoleculeI.H

diff --git a/src/lagrangian/molecule/Make/files b/src/lagrangian/molecule/Make/files
deleted file mode 100755
index d8063d0974..0000000000
--- a/src/lagrangian/molecule/Make/files
+++ /dev/null
@@ -1,57 +0,0 @@
-correlationFunction = correlationFunction
-
-distribution = distribution
-
-molecule = molecule
-moleculeCloud = moleculeCloud
-
-reducedUnits = reducedUnits
-
-referredMolecule = referredMolecule
-referredCellList = referredCellList
-referredCell = referredCell
-referralLists = referralLists
-
-potentials = potentials
-pairPotential = $(potentials)/pairPotential
-tetherPotential = $(potentials)/tetherPotential
-
-$(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
-$(moleculeCloud)/moleculeCloudApplyConstraintsAndThermostats.C
-
-$(pairPotential)/basic/pairPotential.C
-$(pairPotential)/basic/pairPotentialList.C
-$(tetherPotential)/tetherPotential.C
-$(tetherPotential)/tetherPotentialList.C
-
-$(referralLists)/receivingReferralList.C
-$(referralLists)/sendingReferralList.C
-$(referredCellList)/referredCellList.C
-$(referredCell)/referredCell.C
-$(referredMolecule)/referredMolecule.C
-
-LIB = $(FOAM_LIBBIN)/libmolecule
-
diff --git a/src/lagrangian/molecule/Make/options b/src/lagrangian/molecule/Make/options
deleted file mode 100755
index a0fb316eec..0000000000
--- a/src/lagrangian/molecule/Make/options
+++ /dev/null
@@ -1,8 +0,0 @@
-EXE_INC = \
-    -I$(LIB_SRC)/finiteVolume/lnInclude \
-    -I$(LIB_SRC)/lagrangian/basic/lnInclude \
-
-EXE_LIBS = \
-    -lfiniteVolume \
-    -llagrangian
-
diff --git a/src/lagrangian/molecule/correlationFunction/bufferedAccumulator/bufferedAccumulator.C b/src/lagrangian/molecule/correlationFunction/bufferedAccumulator/bufferedAccumulator.C
deleted file mode 100755
index c8a5ca0f30..0000000000
--- a/src/lagrangian/molecule/correlationFunction/bufferedAccumulator/bufferedAccumulator.C
+++ /dev/null
@@ -1,238 +0,0 @@
-/*---------------------------------------------------------------------------*\
-  =========                 |
-  \\      /  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"
-
-// ************************************************************************* //
diff --git a/src/lagrangian/molecule/correlationFunction/bufferedAccumulator/bufferedAccumulator.H b/src/lagrangian/molecule/correlationFunction/bufferedAccumulator/bufferedAccumulator.H
deleted file mode 100755
index a42f75681d..0000000000
--- a/src/lagrangian/molecule/correlationFunction/bufferedAccumulator/bufferedAccumulator.H
+++ /dev/null
@@ -1,178 +0,0 @@
-/*---------------------------------------------------------------------------*\
-  =========                 |
-  \\      /  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 const 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
-
-// ************************************************************************* //
diff --git a/src/lagrangian/molecule/correlationFunction/bufferedAccumulator/bufferedAccumulatorI.H b/src/lagrangian/molecule/correlationFunction/bufferedAccumulator/bufferedAccumulatorI.H
deleted file mode 100755
index 7f27130f2b..0000000000
--- a/src/lagrangian/molecule/correlationFunction/bufferedAccumulator/bufferedAccumulatorI.H
+++ /dev/null
@@ -1,80 +0,0 @@
-/*---------------------------------------------------------------------------*\
-  =========                 |
-  \\      /  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 const 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
-
-// ************************************************************************* //
diff --git a/src/lagrangian/molecule/correlationFunction/bufferedAccumulator/bufferedAccumulatorIO.C b/src/lagrangian/molecule/correlationFunction/bufferedAccumulator/bufferedAccumulatorIO.C
deleted file mode 100755
index 5c6cf11da3..0000000000
--- a/src/lagrangian/molecule/correlationFunction/bufferedAccumulator/bufferedAccumulatorIO.C
+++ /dev/null
@@ -1,52 +0,0 @@
-/*---------------------------------------------------------------------------*\
-  =========                 |
-  \\      /  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
-    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"
-#include "IOstreams.H"
-
-// * * * * * * * * * * * * * * * IOstream Operators  * * * * * * * * * * * * //
-
-template<class Type>
-Foam::Ostream&
-    Foam::operator<<(Ostream& os, const bufferedAccumulator<Type>& bA)
-{
-
-    os<< bA.averagesTaken_
-      << static_cast<const List< Field<Type> >&>(bA)
-      << bA.bufferOffsets();
-
-    // Check state of Ostream
-    os.check
-    (
-        "Foam::Ostream& Foam::operator<<(Foam::Ostream&, "
-        "const Foam::bufferedAccumulator&)"
-    );
-
-    return os;
-}
-
-
-// ************************************************************************* //
diff --git a/src/lagrangian/molecule/correlationFunction/correlationFunction.C b/src/lagrangian/molecule/correlationFunction/correlationFunction.C
deleted file mode 100644
index ca63e1856c..0000000000
--- a/src/lagrangian/molecule/correlationFunction/correlationFunction.C
+++ /dev/null
@@ -1,224 +0,0 @@
-/*---------------------------------------------------------------------------*\
-  =========                 |
-  \\      /  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 "correlationFunction.H"
-
-// * * * * * * * * * * * * * * Static Data Members * * * * * * * * * * * * * //
-
-template<class Type>
-const char* const
-    Foam::correlationFunction<Type>::typeName("correlationFunction");
-
-
-// * * * * * * * * * * * * * Private Member Functions  * * * * * * * * * * * //
-
-template<class Type>
-void Foam::correlationFunction<Type>::setTimesAndSizes
-(
-    const label tZeroBufferSize
-)
-{
-    sampleSteps_  = ceil(sampleInterval_/mesh_.time().deltaT().value());
-
-    sampleInterval_ = sampleSteps_*mesh_.time().deltaT().value();
-
-    label bufferLength(ceil(duration_/sampleInterval_));
-
-    duration_ = bufferLength*sampleInterval_;
-
-    label bufferingInterval(ceil(averagingInterval_/sampleInterval_));
-
-    averagingInterval_ = bufferingInterval*sampleInterval_;
-
-    label nBuffers(ceil(duration_/averagingInterval_));
-
-    this->setSizes
-    (
-        nBuffers,
-        bufferLength,
-        bufferingInterval
-    );
-
-    tZeroBuffers_ =
-        Field< Field<Type> >
-        (
-            nBuffers,
-            Field<Type>
-            (
-                tZeroBufferSize,
-                pTraits<Type>::zero
-            )
-        );
-}
-
-
-// * * * * * * * * * * * * * * * * Constructors  * * * * * * * * * * * * * * //
-
-template<class Type>
-Foam::correlationFunction<Type>::correlationFunction
-(
-    const polyMesh& mesh,
-    const dictionary& cfDict,
-    const label tZeroBufferSize
-)
-:
-    bufferedAccumulator<scalar>(),
-    mesh_(mesh)
-{
-    duration_ = readScalar(cfDict.lookup("duration"));
-
-    sampleInterval_ = readScalar(cfDict.lookup("sampleInterval"));
-
-    averagingInterval_ = readScalar(cfDict.lookup("averagingInterval"));
-
-    setTimesAndSizes(tZeroBufferSize);
-}
-
-
-template<class Type>
-Foam::correlationFunction<Type>::correlationFunction
-(
-    const polyMesh& mesh,
-    const label tZeroBufferSize,
-    const scalar duration,
-    const scalar sampleInterval,
-    const scalar averagingInterval
-)
-:
-    bufferedAccumulator<scalar>(),
-    mesh_(mesh),
-    duration_(duration),
-    sampleInterval_(sampleInterval),
-    averagingInterval_(averagingInterval)
-{
-    setTimesAndSizes(tZeroBufferSize);
-}
-
-
-// * * * * * * * * * * * * * * * * Destructor  * * * * * * * * * * * * * * * //
-
-template<class Type>
-Foam::correlationFunction<Type>::~correlationFunction()
-{}
-
-
-// * * * * * * * * * * * * * * * Member Functions  * * * * * * * * * * * * * //
-
-template<class Type>
-void Foam::correlationFunction<Type>::calculateCorrelationFunction
-(
-    const Field<Type>& currentValues
-)
-{
-    if (measurandFieldSize() != currentValues.size())
-    {
-        FatalErrorIn("correlationFunction<Type>::calculateCorrelationFunction")
-            << "Trying to supply a Field of length"
-            << currentValues.size()
-            <<" to calculate the correlation function.  "
-            << "Expecting a Field of length "
-            << measurandFieldSize() << nl
-            << abort(FatalError);
-    }
-
-    List<scalar> cFSums(nBuffers(),0.0);
-
-    forAll(tZeroBuffers_, tZB)
-    {
-        scalar& cFSum = cFSums[tZB];
-
-        const Field<Type>& tZeroBuffer = tZeroBuffers_[tZB];
-
-        forAll(currentValues, cV)
-        {
-            const Type& tZeroBufferValue = tZeroBuffer[cV];
-
-            const Type& currentValue = currentValues[cV];
-
-            forAll(currentValue, component)
-            {
-                cFSum +=
-                (
-                    tZeroBufferValue[component]*currentValue[component]
-                );
-            }
-        }
-
-        cFSum /= (measurandFieldSize()*currentValues[0].size());
-    }
-
-    label bufferToRefill = addToBuffers(cFSums);
-
-    if (bufferToRefill != -1)
-    {
-        tZeroBuffers_[bufferToRefill] = currentValues;
-    }
-}
-
-
-template<class Type>
-void Foam::correlationFunction<Type>::calculateCorrelationFunction
-(
-    const Type& currentValue
-)
-{
-    if( measurandFieldSize() != 1)
-    {
-        FatalErrorIn("correlationFunction<Type>::calculateCorrelationFunction")
-            << "Trying to supply a single value to calculate the correlation "
-            << "function.  Expecting a Field of length "
-            << measurandFieldSize()
-            << abort(FatalError);
-    }
-
-    calculateCorrelationFunction(Field<Type>(1, currentValue));
-}
-
-
-template<class Type>
-Foam::scalar Foam::correlationFunction<Type>::integral() const
-{
-    Field<scalar> averageCF(averaged());
-
-    scalar cFIntegral = 0.0;
-
-    for(label v = 0; v < averageCF.size() - 1; v++)
-    {
-        cFIntegral +=
-            0.5
-           *sampleInterval_
-           *(averageCF[v+1] + averageCF[v]);
-    }
-
-    return cFIntegral;
-}
-
-
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-#   include "correlationFunctionIO.C"
-
-// ************************************************************************* //
diff --git a/src/lagrangian/molecule/correlationFunction/correlationFunction.H b/src/lagrangian/molecule/correlationFunction/correlationFunction.H
deleted file mode 100644
index f5fae016cd..0000000000
--- a/src/lagrangian/molecule/correlationFunction/correlationFunction.H
+++ /dev/null
@@ -1,180 +0,0 @@
-/*---------------------------------------------------------------------------*\
-  =========                 |
-  \\      /  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::correlationFunction
-
-Description
-
-SourceFiles
-    correlationFunctionI.H
-    correlationFunction.C
-    correlationFunctionIO.C
-
-\*---------------------------------------------------------------------------*/
-
-#ifndef correlationFunction_H
-#define correlationFunction_H
-
-#include "bufferedAccumulator.H"
-#include "dictionary.H"
-
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-namespace Foam
-{
-
-template<class Type>
-class correlationFunction;
-
-template<class Type>
-Ostream& operator<<
-(
-    Ostream&,
-    const correlationFunction<Type>&
-);
-
-/*---------------------------------------------------------------------------*\
-                    Class correlationFunction Declaration
-\*---------------------------------------------------------------------------*/
-
-template<class Type>
-class correlationFunction
-:
-    public bufferedAccumulator<scalar>
-{
-    // Private data
-
-        const polyMesh& mesh_;
-
-        Field< Field<Type> > tZeroBuffers_;
-
-        scalar duration_;
-        scalar sampleInterval_;
-        scalar averagingInterval_;
-
-        label sampleSteps_;
-
-
-    // Private Member Functions
-
-        void setTimesAndSizes(const label);
-
-        //- Disallow default bitwise copy construct
-        correlationFunction(const correlationFunction<Type>&);
-
-        //- Disallow default bitwise assignment
-        void operator=(const correlationFunction<Type>&);
-
-
-public:
-
-    //- Component type
-    typedef typename pTraits<Type>::cmptType cmptType;
-
-
-    // Static data members
-
-        static const char* const typeName;
-
-
-    // Constructors
-
-        //- Construct from dictionary
-        correlationFunction
-        (
-            const polyMesh&,
-            const dictionary&,
-            const label tZeroBufferSize
-        );
-
-        //- Construct from components
-        correlationFunction
-        (
-            const polyMesh&,
-            const label tZeroBufferSize,
-            const scalar duration,
-            const scalar sampleInterval,
-            const scalar averagingInterval
-
-        );
-
-
-    // Destructor
-
-        ~correlationFunction();
-
-
-    // Member Functions
-
-        void calculateCorrelationFunction(const Field<Type>&);
-
-        void calculateCorrelationFunction(const Type&);
-
-        scalar integral() const;
-
-        bool writeAveraged(Ostream&) const;
-
-
-    // Access
-
-        inline const Field< Field<Type> >& tZeroBuffers() const;
-
-        inline const scalar duration() const;
-
-        inline const scalar sampleInterval() const;
-
-        inline const scalar averagingInterval() const;
-
-        inline const label sampleSteps() const;
-
-        inline label measurandFieldSize() const;
-
-
-    // IOstream Operators
-
-        friend Ostream& operator<< <Type>
-        (Ostream&, const correlationFunction<Type>&);
-};
-
-
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-} // End namespace Foam
-
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-#include "correlationFunctionI.H"
-
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-#ifdef NoRepository
-#   include "correlationFunction.C"
-#endif
-
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-#endif
-
-// ************************************************************************* //
diff --git a/src/lagrangian/molecule/correlationFunction/correlationFunctionI.H b/src/lagrangian/molecule/correlationFunction/correlationFunctionI.H
deleted file mode 100644
index 2c2a3743c0..0000000000
--- a/src/lagrangian/molecule/correlationFunction/correlationFunctionI.H
+++ /dev/null
@@ -1,70 +0,0 @@
-/*---------------------------------------------------------------------------*\
-  =========                 |
-  \\      /  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
-
-\*---------------------------------------------------------------------------*/
-
-template<class Type>
-inline const Field< Field<Type> >& Foam::correlationFunction<Type>::
-tZeroBuffers() const
-{
-    return tZeroBuffers_;
-}
-
-
-template<class Type>
-inline const scalar Foam::correlationFunction<Type>::duration() const
-{
-    return duration_;
-}
-
-
-template<class Type>
-inline const scalar Foam::correlationFunction<Type>::sampleInterval() const
-{
-    return sampleInterval_;
-}
-
-
-template<class Type>
-inline const scalar Foam::correlationFunction<Type>::averagingInterval() const
-{
-    return averagingInterval_;
-}
-
-
-template<class Type>
-inline const label Foam::correlationFunction<Type>::sampleSteps() const
-{
-    return sampleSteps_;
-}
-
-
-template<class Type>
-inline label Foam::correlationFunction<Type>::measurandFieldSize() const
-{
-    return tZeroBuffers_[0].size();
-}
-
-
-// ************************************************************************* //
diff --git a/src/lagrangian/molecule/correlationFunction/correlationFunctionIO.C b/src/lagrangian/molecule/correlationFunction/correlationFunctionIO.C
deleted file mode 100644
index 0a080158ae..0000000000
--- a/src/lagrangian/molecule/correlationFunction/correlationFunctionIO.C
+++ /dev/null
@@ -1,72 +0,0 @@
-/*---------------------------------------------------------------------------*\
-  =========                 |
-  \\      /  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 "correlationFunction.H"
-#include "IOstreams.H"
-
-template<class Type>
-bool Foam::correlationFunction<Type>::writeAveraged(Ostream& os) const
-{
-    Field<scalar> averageCF(averaged());
-
-    forAll(averageCF, v)
-    {
-        os<< v*sampleInterval()
-          << token::SPACE
-          << averageCF[v]
-          << nl;
-    }
-
-    return os.good();
-}
-
-
-template<class Type>
-Foam::Ostream& Foam::operator<<
-(
-    Ostream& os,
-    const correlationFunction<Type>& cF
-)
-{
-    os<< cF.duration()
-      << nl << cF.sampleInterval()
-      << nl << cF.averagingInterval()
-      << nl << cF.sampleSteps()
-      << nl << cF.tZeroBuffers()
-      << nl << static_cast<const bufferedAccumulator<scalar>&>(cF);
-
-    // Check state of Ostream
-    os.check
-    (
-        "Foam::Ostream& Foam::operator<<"
-        "(Ostream&, const correlationFunction<Type>&)"
-    );
-
-    return os;
-}
-
-
-// ************************************************************************* //
diff --git a/src/lagrangian/molecule/distribution/distribution.C b/src/lagrangian/molecule/distribution/distribution.C
deleted file mode 100755
index 717929e5e4..0000000000
--- a/src/lagrangian/molecule/distribution/distribution.C
+++ /dev/null
@@ -1,449 +0,0 @@
-/*---------------------------------------------------------------------------*\
-  =========                 |
-  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
-   \\    /   O peration     |
-    \\  /    A nd           | Copyright (C) 1991-2005 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 "distribution.H"
-
-namespace Foam
-{
-
-// * * * * * * * * * * * * * * * * Constructors  * * * * * * * * * * * * * * //
-
-distribution::distribution()
-:
-    Map<label>(),
-    binWidth_(1)
-{}
-
-
-distribution::distribution(const scalar binWidth)
-:
-    Map<label>(),
-    binWidth_(binWidth)
-{}
-
-
-distribution::distribution(const distribution& d)
-:
-    Map<label>(static_cast< Map<label> >(d)),
-    binWidth_(d.binWidth())
-{}
-
-
-// * * * * * * * * * * * * * * * * Destructor  * * * * * * * * * * * * * * * //
-
-distribution::~distribution()
-{}
-
-
-// * * * * * * * * * * * * * * * Member Functions  * * * * * * * * * * * * * //
-
-label distribution::totalEntries() const
-{
-    label sumOfEntries = 0;
-
-    forAllConstIter(Map<label>, *this, iter)
-    {
-        sumOfEntries += iter();
-
-        if (sumOfEntries < 0)
-        {
-            WarningIn("label distribution::totalEntries()")
-                << "Accumulated distribution values total has become negative: "
-                << "sumOfEntries = " << sumOfEntries
-                << ". This is most likely to be because too many samples "
-                << "have been added to the bins and the label has 'rolled "
-                << "round'.  Try distribution::approxTotalEntries which "
-                << "returns a scalar." << endl;
-
-            sumOfEntries = -1;
-
-            break;
-        }
-    }
-
-    return sumOfEntries;
-}
-
-
-scalar distribution::approxTotalEntries() const
-{
-    scalar sumOfEntries = 0;
-
-    forAllConstIter(Map<label>, *this, iter)
-    {
-        sumOfEntries += scalar(iter());
-    }
-
-    return sumOfEntries;
-}
-
-
-scalar distribution::mean() const
-{
-    scalar runningSum = 0;
-
-    scalar totEnt = approxTotalEntries();
-
-    List<label> keys = toc();
-
-    forAll(keys,k)
-    {
-        label key = keys[k];
-
-        runningSum +=
-            (0.5 + scalar(key))
-           *binWidth_
-           *scalar((*this)[key])
-           /totEnt;
-    }
-
-    return runningSum;
-}
-
-
-scalar distribution::median()
-{
-    // From:
-    // http://mathworld.wolfram.com/StatisticalMedian.html
-    // The statistical median is the value of the distribution variable
-    // where the cumulative distribution = 0.5.
-
-    scalar median = 0.0;
-
-    scalar runningSum = 0.0;
-
-    List< Pair<scalar> > normDist(normalised());
-
-    if (normDist.size())
-    {
-        if (normDist.size() == 1)
-        {
-            median = normDist[0].first();
-        }
-        else if
-        (
-            normDist.size() > 1
-         && normDist[0].second()*binWidth_ > 0.5
-        )
-        {
-            scalar xk = normDist[1].first();
-            scalar xkm1 = normDist[0].first();
-            scalar Sk =
-                (normDist[0].second() + normDist[1].second())*binWidth_;
-            scalar Skm1 = normDist[0].second()*binWidth_;
-
-            median = (0.5 - Skm1)*(xk - xkm1)/(Sk - Skm1) + xkm1;
-        }
-        else
-        {
-            label lastNonZeroIndex = 0;
-
-            forAll(normDist,nD)
-            {
-                if (runningSum + (normDist[nD].second()*binWidth_) > 0.5)
-                {
-                    scalar xk = normDist[nD].first();
-                    scalar xkm1 = normDist[lastNonZeroIndex].first();
-                    scalar Sk = runningSum + (normDist[nD].second()*binWidth_);
-                    scalar Skm1 = runningSum;
-
-                    median = (0.5 - Skm1)*(xk - xkm1)/(Sk - Skm1) + xkm1;
-
-                    break;
-                }
-                else if (normDist[nD].second() > 0.0)
-                {
-                    runningSum += normDist[nD].second()*binWidth_;
-
-                    lastNonZeroIndex = nD;
-                }
-            }
-        }
-    }
-
-    return median;
-}
-
-
-void distribution::add(const scalar valueToAdd)
-{
-    iterator iter(this->begin());
-
-    label n = label(valueToAdd/binWidth_) - label(neg(valueToAdd/binWidth_));
-
-    iter = find(n);
-
-    if (iter == this->end())
-    {
-        this->insert(n,1);
-    }
-    else
-    {
-        (*this)[n]++;
-    }
-
-    if ((*this)[n] < 0)
-    {
-        FatalErrorIn("distribution::add(const scalar valueToAdd)")
-            << "Accumulated distribution value has become negative: "
-            << "bin = " << (0.5 + scalar(n)) * binWidth_
-            << ", value = " << (*this)[n]
-            << ". This is most likely to be because too many samples "
-            << "have been added to a bin and the label has 'rolled round'"
-            << abort(FatalError);
-    }
-}
-
-
-void distribution::add(const label valueToAdd)
-{
-    add(scalar(valueToAdd));
-}
-
-
-void distribution::insertMissingKeys()
-{
-    iterator iter(this->begin());
-
-    List<label> keys = toc();
-
-    sort(keys);
-
-    label k;
-
-    if (keys.size() > 0)
-    {
-        for (k = keys[0]; k < keys[keys.size()-1]; k++)
-        {
-            iter = find(k);
-
-            if (iter == this->end())
-            {
-                this->insert(k,0);
-            }
-        }
-    }
-}
-
-
-List< Pair<scalar> > distribution::normalised()
-{
-    scalar totEnt = approxTotalEntries();
-
-    insertMissingKeys();
-
-    List<label> keys = toc();
-
-    sort(keys);
-
-    List< Pair<scalar> > normDist(size());
-
-    forAll(keys,k)
-    {
-        label key = keys[k];
-
-        normDist[k].first() = (0.5 + scalar(key))*binWidth_;
-
-        normDist[k].second() = scalar((*this)[key])/totEnt/binWidth_;
-    }
-
-    return normDist;
-}
-
-
-List< Pair<scalar> > distribution::normalisedMinusMean()
-{
-    return normalisedShifted(mean());
-}
-
-
-List< Pair<scalar> > distribution::normalisedShifted(const scalar shiftValue)
-{
-    List< Pair<scalar> > oldDist(normalised());
-
-    List< Pair<scalar> > newDist(oldDist.size());
-
-    forAll(oldDist,u)
-    {
-        oldDist[u].first() -= shiftValue;
-    }
-
-    scalar lowestOldBin = oldDist[0].first()/binWidth_ - 0.5;
-
-    label lowestNewKey = label
-    (
-        lowestOldBin + 0.5*sign(lowestOldBin)
-    );
-
-    scalar interpolationStartDirection =
-        sign(scalar(lowestNewKey) - lowestOldBin);
-
-    label newKey = lowestNewKey;
-
-//     Info << shiftValue
-//         << nl << lowestOldBin
-//         << nl << lowestNewKey
-//         << nl << interpolationStartDirection
-//         << endl;
-
-//     scalar checkNormalisation = 0;
-
-//     forAll (oldDist, oD)
-//     {
-//         checkNormalisation += oldDist[oD].second()*binWidth_;
-//     }
-
-//     Info << "Initial normalisation = " << checkNormalisation << endl;
-
-    forAll(oldDist,u)
-    {
-        newDist[u].first() = (0.5 + scalar(newKey)) * binWidth_;
-
-        if (interpolationStartDirection < 0)
-        {
-            if (u == 0)
-            {
-                newDist[u].second() =
-                    (0.5 + scalar(newKey))*oldDist[u].second()
-                  - oldDist[u].second()
-                        *(oldDist[u].first() - binWidth_)/ binWidth_;
-            }
-            else
-            {
-                newDist[u].second() =
-                    (0.5 + scalar(newKey))
-                   *(oldDist[u].second() - oldDist[u-1].second())
-                  +
-                    (
-                        oldDist[u-1].second() * oldDist[u].first()
-                      - oldDist[u].second() * oldDist[u-1].first()
-                    )
-                    /binWidth_;
-            }
-        }
-        else
-        {
-            if (u == oldDist.size() - 1)
-            {
-                newDist[u].second() =
-                    (0.5 + scalar(newKey))*-oldDist[u].second()
-                  + oldDist[u].second() * (oldDist[u].first() + binWidth_)
-                   /binWidth_;
-            }
-            else
-            {
-                newDist[u].second() =
-                    (0.5 + scalar(newKey))
-                   *(oldDist[u+1].second() - oldDist[u].second())
-                  +
-                    (
-                        oldDist[u].second() * oldDist[u+1].first()
-                      - oldDist[u+1].second() * oldDist[u].first()
-                    )
-                   /binWidth_;
-            }
-        }
-
-        newKey++;
-    }
-
-//     checkNormalisation = 0;
-
-//     forAll (newDist, nD)
-//     {
-//         checkNormalisation += newDist[nD].second()*binWidth_;
-//     }
-
-//     Info << "Shifted normalisation = " << checkNormalisation << endl;
-
-    return newDist;
-}
-
-
-List< Pair<scalar> > distribution::raw()
-{
-    insertMissingKeys();
-
-    List<label> keys = toc();
-
-    sort(keys);
-
-    List< Pair<scalar> > rawDist(size());
-
-    forAll(keys,k)
-    {
-        label key = keys[k];
-
-        rawDist[k].first() = (0.5 + scalar(key)) * binWidth_;
-
-        rawDist[k].second() = scalar((*this)[key]);
-    }
-
-    return rawDist;
-}
-
-
-// * * * * * * * * * * * * * * * Member Operators  * * * * * * * * * * * * * //
-
-void distribution::operator=(const distribution& rhs)
-{
-    // Check for assignment to self
-    if (this == &rhs)
-    {
-        FatalErrorIn("distribution::operator=(const distribution&)")
-            << "Attempted assignment to self"
-            << abort(FatalError);
-    }
-
-    Map<label>::operator=(rhs);
-
-    binWidth_ = rhs.binWidth();
-}
-
-
-// * * * * * * * * * * * * * * * Friend Operators  * * * * * * * * * * * * * //
-
-Ostream& operator<<(Ostream& os, const distribution& d)
-{
-    os  << d.binWidth_
-        << static_cast<const Map<label>&>(d);
-
-    // Check state of Ostream
-    os.check
-    (
-        "Ostream& operator<<(Ostream&, "
-        "const distribution&)"
-    );
-
-    return os;
-}
-
-
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-} // End namespace Foam
-
-// ************************************************************************* //
diff --git a/src/lagrangian/molecule/distribution/distribution.H b/src/lagrangian/molecule/distribution/distribution.H
deleted file mode 100755
index 8cefd24a81..0000000000
--- a/src/lagrangian/molecule/distribution/distribution.H
+++ /dev/null
@@ -1,133 +0,0 @@
-/*---------------------------------------------------------------------------*\
-  =========                 |
-  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
-   \\    /   O peration     |
-    \\  /    A nd           | Copyright (C) 1991-2005 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::distribution
-
-Description
-
-SourceFiles
-    distributionI.H
-    distribution.C
-    distributionIO.C
-
-\*---------------------------------------------------------------------------*/
-
-#ifndef distribution_H
-#define distribution_H
-
-#include "Map.H"
-#include "Pair.H"
-
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-namespace Foam
-{
-
-/*---------------------------------------------------------------------------*\
-                           Class distribution Declaration
-\*---------------------------------------------------------------------------*/
-
-class distribution
-:
-    public Map<label>
-{
-    // Private data
-
-        scalar binWidth_;
-
-
-public:
-
-    // Constructors
-
-        //- Construct null
-        distribution();
-
-        //- Construct from binWidth
-        distribution(const scalar binWidth);
-
-        //- Construct as copy
-        distribution(const distribution&);
-
-
-    // Destructor
-
-        ~distribution();
-
-
-    // Member Functions
-
-        label totalEntries() const;
-
-        scalar approxTotalEntries() const;
-
-        scalar mean() const;
-
-        scalar median();
-
-        //- Add a value to the appropriate bin of the distribution.
-        void add(const scalar valueToAdd);
-
-        void add(const label valueToAdd);
-
-        void insertMissingKeys();
-
-        List< Pair<scalar> > normalised();
-
-        List< Pair<scalar> > normalisedMinusMean();
-
-        List< Pair<scalar> > normalisedShifted(const scalar shiftValue);
-
-        List< Pair<scalar> > raw();
-
-        // Access
-
-            inline const scalar binWidth() const;
-
-
-    // Member Operators
-
-        void operator=(const distribution&);
-
-
-    // IOstream Operators
-
-        friend Ostream& operator<<(Ostream&, const distribution&);
-};
-
-
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-} // End namespace Foam
-
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-#include "distributionI.H"
-
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-#endif
-
-// ************************************************************************* //
diff --git a/src/lagrangian/molecule/distribution/distributionI.H b/src/lagrangian/molecule/distribution/distributionI.H
deleted file mode 100755
index fed3118eb5..0000000000
--- a/src/lagrangian/molecule/distribution/distributionI.H
+++ /dev/null
@@ -1,42 +0,0 @@
-/*---------------------------------------------------------------------------*\
-  =========                 |
-  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
-   \\    /   O peration     |
-    \\  /    A nd           | Copyright (C) 1991-2005 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
-{
-
-// * * * * * * * * * * * * * * * Member Functions  * * * * * * * * * * * * * //
-
-inline const scalar distribution::binWidth() const
-{
-    return binWidth_;
-}
-
-
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-} // End namespace Foam
-
-// ************************************************************************* //
diff --git a/src/lagrangian/molecule/distribution/distributionIO.C b/src/lagrangian/molecule/distribution/distributionIO.C
deleted file mode 100755
index 57f6e774bb..0000000000
--- a/src/lagrangian/molecule/distribution/distributionIO.C
+++ /dev/null
@@ -1,35 +0,0 @@
-/*---------------------------------------------------------------------------*\
-  =========                 |
-  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
-   \\    /   O peration     |
-    \\  /    A nd           | Copyright (C) 1991-2005 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 "distribution.H"
-#include "IOstreams.H"
-
-// * * * * * * * * * * * * * * * * Constructors  * * * * * * * * * * * * * * //
-
-// construct from Istream
-
-
-// ************************************************************************* //
diff --git a/src/lagrangian/molecule/mdTools/averageMDFields.H b/src/lagrangian/molecule/mdTools/averageMDFields.H
deleted file mode 100755
index db0c24bc95..0000000000
--- a/src/lagrangian/molecule/mdTools/averageMDFields.H
+++ /dev/null
@@ -1,227 +0,0 @@
-if (runTime.outputTime())
-{
-    /*-----------------------------------------------------------------------*\
-        Number density
-    \*-----------------------------------------------------------------------*/
-
-    scalarField totalRhoN_sum(mesh.nCells(), 0.0);
-    
-    forAll (allSpeciesRhoN, rN)
-    {
-        allSpeciesRhoN[rN].internalField() =
-            allSpeciesN_RU[rN]
-            /mesh.cellVolumes()
-            /nAveragingSteps;
-            
-        totalRhoN_sum += allSpeciesRhoN[rN].internalField();
-    }
-    
-    totalRhoN.internalField() = totalRhoN_sum;
-    
-    
-    /*-----------------------------------------------------------------------*\
-        Mass density
-    \*-----------------------------------------------------------------------*/
-    
-    scalarField totalRhoM_sum(mesh.nCells(), 0.0);
-    
-    forAll (allSpeciesRhoM, rM)
-    {
-        allSpeciesRhoM[rM].internalField() =
-            allSpeciesM_RU[rM]
-            /mesh.cellVolumes()
-            /nAveragingSteps;
-            
-        totalRhoM_sum += allSpeciesRhoM[rM].internalField();
-    }
-    
-    totalRhoM.internalField() = totalRhoM_sum;
-    
-    /*-----------------------------------------------------------------------*\
-        Bulk velocity
-    \*-----------------------------------------------------------------------*/
-    
-    vectorField totalMomentum_sum(mesh.nCells(), vector::zero);
-    
-    scalarField totalMass_sum(mesh.nCells(), 0.0);
-    
-    forAll (allSpeciesVelocity, v)
-    {
-        // A check for 1/0 molecules is required.
-    
-        vectorField& singleSpeciesVelocity
-        (
-            allSpeciesVelocity[v].internalField()
-        );
-        
-        forAll(singleSpeciesVelocity, sSV)
-        {
-            if(allSpeciesN_RU[v][sSV])
-            {
-                singleSpeciesVelocity[sSV] = 
-                    allSpeciesVelocitySum_RU[v][sSV]
-                    /allSpeciesN_RU[v][sSV];
-                    
-                totalMomentum_sum[sSV] +=
-                    allSpeciesM_RU[v][sSV]
-                    /allSpeciesN_RU[v][sSV]
-                    *allSpeciesVelocitySum_RU[v][sSV];
-                    
-                totalMass_sum[sSV] += allSpeciesM_RU[v][sSV];
-            }
-            else
-            {
-                singleSpeciesVelocity[sSV] = vector::zero;
-            }
-        }
-    }
-    
-    forAll(totalVelocity.internalField(), tV)
-    {
-        if(totalMass_sum[tV] > VSMALL)
-        {
-            totalVelocity.internalField()[tV] =
-                totalMomentum_sum[tV]
-                /totalMass_sum[tV];
-        }
-        else
-        {
-            totalVelocity.internalField()[tV] =
-            vector::zero;
-        }
-    }
-    
-    /*-----------------------------------------------------------------------*\
-        Kinetic temperature
-    \*-----------------------------------------------------------------------*/
-    
-    scalarField totalTemperatureVTerms_sum(mesh.nCells(), 0.0);
-    
-    scalarField totalN_sum(mesh.nCells(), 0.0);
-    
-    forAll (allSpeciesTemperature, t)
-    {
-        // A check for 1/0 molecules is required.
-    
-        scalarField& singleSpeciesTemp
-        (
-            allSpeciesTemperature[t].internalField()
-        );
-        
-        forAll(singleSpeciesTemp, sST)
-        {
-            if(allSpeciesN_RU[t][sST])
-            {
-                singleSpeciesTemp[sST] = 
-                    allSpeciesM_RU[t][sST]
-                    /allSpeciesN_RU[t][sST]
-                    /(3.0 * moleculeCloud::kb * allSpeciesN_RU[t][sST])
-                    *
-                    (
-                        allSpeciesVelocityMagSquaredSum_RU[t][sST]
-                        -
-                        (
-                            allSpeciesVelocitySum_RU[t][sST]
-                            &
-                            allSpeciesVelocitySum_RU[t][sST]
-                        )
-                        /allSpeciesN_RU[t][sST]
-                    );
-                    
-                totalTemperatureVTerms_sum[sST] +=
-                    allSpeciesM_RU[t][sST]
-                    /allSpeciesN_RU[t][sST]
-                    *
-                    (
-                        allSpeciesVelocityMagSquaredSum_RU[t][sST]
-                        -
-                        (
-                            allSpeciesVelocitySum_RU[t][sST]
-                            &
-                            allSpeciesVelocitySum_RU[t][sST]
-                        )
-                        /allSpeciesN_RU[t][sST]
-                    );
-                    
-                totalN_sum[sST] += allSpeciesN_RU[t][sST];
-            }
-            else
-            {
-                singleSpeciesTemp[sST] = 0.0;
-            }
-        }
-    }
-    
-    forAll(totalTemperature.internalField(), tT)
-    {
-        if(totalN_sum[tT] > 0)
-        {
-            totalTemperature.internalField()[tT] =
-                totalTemperatureVTerms_sum[tT]
-                /(3.0 * moleculeCloud::kb * totalN_sum[tT]);
-        }
-        else
-        {
-            totalTemperature.internalField()[tT] = 0.0;
-        }
-    }
-    
-    /*-----------------------------------------------------------------------*\
-        Mean kinetic energy
-    \*-----------------------------------------------------------------------*/
-    
-    scalarField totalKE_sum(mesh.nCells(), 0.0);
-    
-    forAll (allSpeciesMeanKE, mKE)
-    {
-        // A check for 1/0 molecules is required.
-    
-        scalarField& singleSpeciesMeanKE
-        (
-            allSpeciesMeanKE[mKE].internalField()
-        );
-        
-        forAll(singleSpeciesMeanKE, sSMKE)
-        {
-            if(allSpeciesN_RU[mKE][sSMKE])
-            {
-                singleSpeciesMeanKE[sSMKE] = 
-                    allSpeciesM_RU[mKE][sSMKE]
-                    /allSpeciesN_RU[mKE][sSMKE]
-                    /(2.0 * allSpeciesN_RU[mKE][sSMKE])
-                    *
-                    (
-                        allSpeciesVelocityMagSquaredSum_RU[mKE][sSMKE]
-                    );
-                    
-                totalKE_sum[sSMKE] +=
-                    allSpeciesM_RU[mKE][sSMKE]
-                    /allSpeciesN_RU[mKE][sSMKE]
-                    /2.0
-                    *
-                    (
-                        allSpeciesVelocityMagSquaredSum_RU[mKE][sSMKE]
-                    );
-            }
-            else
-            {
-                singleSpeciesMeanKE[sSMKE] = 0.0;
-            }
-        }
-    }
-    
-    forAll(totalMeanKE.internalField(), tMKE)
-    {
-        if(totalN_sum[tMKE] > 0)
-        {
-            totalMeanKE.internalField()[tMKE] =
-                totalKE_sum[tMKE]
-                /totalN_sum[tMKE];
-        }
-        else
-        {
-            totalMeanKE.internalField()[tMKE] = 0.0;
-        }
-    }
-}
-
diff --git a/src/lagrangian/molecule/mdTools/calculateAutoCorrelationFunctions.H b/src/lagrangian/molecule/mdTools/calculateAutoCorrelationFunctions.H
deleted file mode 100644
index a7c4c326bb..0000000000
--- a/src/lagrangian/molecule/mdTools/calculateAutoCorrelationFunctions.H
+++ /dev/null
@@ -1,83 +0,0 @@
-/*---------------------------------------------------------------------------*\
-  =========                 |
-  \\      /  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
-
-\*---------------------------------------------------------------------------*/
-
-if (mesh.time().timeIndex() % vacf.sampleSteps() == 0)
-{
-    IDLList<molecule>::iterator mol(molecules.begin());
-
-    Field<vector> uVals(molecules.size());
-
-    label uV = 0;
-
-    for
-    (
-        mol = molecules.begin();
-        mol != molecules.end();
-        ++mol, uV++
-    )
-    {
-        uVals[uV] = mol().U();
-    }
-
-    vacf.calculateCorrelationFunction(uVals);
-}
-
-if (mesh.time().timeIndex() % pacf.sampleSteps() == 0)
-{
-    IDLList<molecule>::iterator mol(molecules.begin());
-
-    vector p = vector::zero;
-
-    for
-    (
-        mol = molecules.begin();
-        mol != molecules.end();
-        ++mol
-    )
-    {
-        p.x() +=
-            mol().mass() * mol().U().y() * mol().U().z()
-            +
-            0.5 * mol().rf().yz();
-
-        p.y() +=
-            mol().mass() * mol().U().z() * mol().U().x()
-            +
-            0.5 * mol().rf().zx();
-
-        p.z() +=
-            mol().mass() * mol().U().x() * mol().U().y()
-            +
-            0.5 * mol().rf().xy();
-    }
-
-    pacf.calculateCorrelationFunction(p);
-}
-
-if (mesh.time().timeIndex() % hfacf.sampleSteps() == 0)
-{
-//     hFacf.calculateCorrelationFunction();
-}
diff --git a/src/lagrangian/molecule/mdTools/calculateMDFields.H b/src/lagrangian/molecule/mdTools/calculateMDFields.H
deleted file mode 100755
index af5c938da4..0000000000
--- a/src/lagrangian/molecule/mdTools/calculateMDFields.H
+++ /dev/null
@@ -1,23 +0,0 @@
-const List<DynamicList<molecule*> >& cellOccupancy = molecules.cellOccupancy();
-
-forAll(cellOccupancy, cell)
-{
-    const List<molecule*>& molsInCell = cellOccupancy[cell];
-
-    forAll(molsInCell, mIC)
-    {
-        molecule* mol = molsInCell[mIC];
-
-        const label molId = mol->id();
-
-        const vector& molU = mol->U();
-
-        allSpeciesN_RU[molId][cell]++;
-
-        allSpeciesM_RU[molId][cell] += mol->mass();
-
-        allSpeciesVelocitySum_RU[molId][cell] += molU;
-
-        allSpeciesVelocityMagSquaredSum_RU[molId][cell] += molU & molU;
-    }
-}
diff --git a/src/lagrangian/molecule/mdTools/calculateTransportProperties.H b/src/lagrangian/molecule/mdTools/calculateTransportProperties.H
deleted file mode 100644
index 15e0dab7e3..0000000000
--- a/src/lagrangian/molecule/mdTools/calculateTransportProperties.H
+++ /dev/null
@@ -1,65 +0,0 @@
-/*---------------------------------------------------------------------------*\
-  =========                 |
-  \\      /  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
-
-\*---------------------------------------------------------------------------*/
-
-if (writeVacf)
-{
-    OFstream vacfFile(runTime.path()/"vacf");
-
-    if (!vacf.writeAveraged(vacfFile))
-    {
-        FatalErrorIn(args.executable())
-            << "Failed writing to "
-            << vacfFile.name()
-            << abort(FatalError);
-    }
-}
-
-Info << "Diffusion coefficient = "
-    << vacf.integral() << endl;
-
-if (writePacf)
-{
-    OFstream pacfFile(runTime.path()/"pacf");
-
-    if (!pacf.writeAveraged(pacfFile))
-    {
-        FatalErrorIn(args.executable())
-            << "Failed writing to "
-            << pacfFile.name()
-            << abort(FatalError);
-    }
-}
-
-Info<< "Viscosity = "
-    << pacf.integral()/averageTemperature/moleculeCloud::kb/meshVolume
-    << endl;
-
-if(writeHFacf)
-{
-
-}
-
-
diff --git a/src/lagrangian/molecule/mdTools/createAutoCorrelationFunctions.H b/src/lagrangian/molecule/mdTools/createAutoCorrelationFunctions.H
deleted file mode 100644
index 3bec4493dc..0000000000
--- a/src/lagrangian/molecule/mdTools/createAutoCorrelationFunctions.H
+++ /dev/null
@@ -1,99 +0,0 @@
-/*---------------------------------------------------------------------------*\
-  =========                 |
-  \\      /  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
-
-\*---------------------------------------------------------------------------*/
-
-Info << nl << "Creating autocorrelation functions." << endl;
-
-IOdictionary mdTransportProperitesDict
-(
-    IOobject
-    (
-        "mdTransportProperitesDict",
-        mesh.time().system(),
-        mesh,
-        IOobject::MUST_READ,
-        IOobject::NO_WRITE,
-        false
-    )
-);
-
-const dictionary& autocorrelationFunctionDict
-(
-    mdTransportProperitesDict.subDict("autocorrelationFunctions")
-);
-
-//- Velocity autocorrelation function
-
-Info << tab << "velocty" << endl;
-
-const dictionary& velocityACFDict
-(
-    autocorrelationFunctionDict.subDict("velocity")
-);
-
-correlationFunction<vector> vacf
-(
-    mesh,
-    velocityACFDict,
-    molecules.size()
-);
-
-bool writeVacf(Switch(velocityACFDict.lookup("writeFile")));
-
-//- Pressure autocorrelation function
-
-Info << tab << "pressure" << endl;
-
-const dictionary& pressureACFDict
-(
-    autocorrelationFunctionDict.subDict("pressure")
-);
-
-correlationFunction<vector> pacf
-(
-    mesh,
-    pressureACFDict,
-    1
-);
-
-bool writePacf(Switch(pressureACFDict.lookup("writeFile")));
-
-//- Heat flux autocorrelation function
-
-Info << tab << "heat flux" << endl;
-
-const dictionary& heatFluxACFDict
-(
-    autocorrelationFunctionDict.subDict("heatFlux")
-);
-
-correlationFunction<vector> hfacf
-(
-    mesh,
-    heatFluxACFDict,
-    1
-);
-
-bool writeHFacf(Switch(heatFluxACFDict.lookup("writeFile")));
diff --git a/src/lagrangian/molecule/mdTools/createMDFields.H b/src/lagrangian/molecule/mdTools/createMDFields.H
deleted file mode 100755
index f5742fd2c8..0000000000
--- a/src/lagrangian/molecule/mdTools/createMDFields.H
+++ /dev/null
@@ -1,306 +0,0 @@
-// Fields for data gathering
-
-List< scalarField > allSpeciesN_RU
-(
-    molecules.nIds(),
-    scalarField (mesh.nCells(), 0.0)
-);
-
-List< scalarField > allSpeciesM_RU
-(
-    molecules.nIds(),
-    scalarField (mesh.nCells(), 0.0)
-);
-
-List< vectorField > allSpeciesVelocitySum_RU
-(
-    molecules.nIds(),
-    vectorField (mesh.nCells(), vector::zero)
-);
-
-List< scalarField > allSpeciesVelocityMagSquaredSum_RU
-(
-    molecules.nIds(),
-    scalarField (mesh.nCells(), 0.0)
-);
-
-// Geometric Fields for IO
-
-Info << nl << "Creating fields." << endl;
-
-/*---------------------------------------------------------------------------*\
-    Number density
-\*---------------------------------------------------------------------------*/
-
-PtrList<volScalarField> allSpeciesRhoN
-(
-    molecules.nIds()
-);
-
-forAll (allSpeciesRhoN, rN)
-{
-    Info << "    Creating number density field for "
-        << molecules.idList()[rN] << endl;
-
-    allSpeciesRhoN.set
-    (
-        rN,
-        new volScalarField
-        (
-            IOobject
-            (
-                "rhoN_" + molecules.idList()[rN],
-                runTime.timeName(),
-                mesh,
-                IOobject::NO_READ,
-                IOobject::AUTO_WRITE
-            ),
-            mesh,
-            dimless/dimVolume,
-            "zeroGradient"
-        )
-    );
-    allSpeciesRhoN[rN].internalField() = scalarField (mesh.nCells(), 0.0);
-    allSpeciesRhoN[rN].correctBoundaryConditions();
-}
-
-Info << "    Creating total number density field" << endl;
-
-volScalarField totalRhoN
-(
-    IOobject
-    (
-        "rhoN_total",
-        runTime.timeName(),
-        mesh,
-        IOobject::NO_READ,
-        IOobject::AUTO_WRITE
-    ),
-    mesh,
-    dimless/dimVolume,
-    "zeroGradient"
-);
-totalRhoN.internalField() = scalarField (mesh.nCells(), 0.0);
-totalRhoN.correctBoundaryConditions();
-
-/*---------------------------------------------------------------------------*\
-    Mass density
-\*---------------------------------------------------------------------------*/
-
-PtrList<volScalarField> allSpeciesRhoM
-(
-    molecules.nIds()
-);
-
-forAll (allSpeciesRhoM, rM)
-{
-    Info << "    Creating mass density field for "
-        << molecules.idList()[rM] << endl;
-
-    allSpeciesRhoM.set
-    (
-        rM,
-        new volScalarField
-        (
-            IOobject
-            (
-                "rhoM_" + molecules.idList()[rM],
-                runTime.timeName(),
-                mesh,
-                IOobject::NO_READ,
-                IOobject::AUTO_WRITE
-            ),
-            mesh,
-            dimMass/dimVolume,
-            "zeroGradient"
-        )
-    );
-    allSpeciesRhoM[rM].internalField() = scalarField (mesh.nCells(), 0.0);
-    allSpeciesRhoM[rM].correctBoundaryConditions();
-}
-
-Info << "    Creating total mass density field" << endl;
-
-volScalarField totalRhoM
-(
-    IOobject
-    (
-        "rhoM_total",
-        runTime.timeName(),
-        mesh,
-        IOobject::NO_READ,
-        IOobject::AUTO_WRITE
-    ),
-    mesh,
-    dimMass/dimVolume,
-    "zeroGradient"
-);
-totalRhoM.internalField() = scalarField (mesh.nCells(), 0.0);
-totalRhoM.correctBoundaryConditions();
-
-/*---------------------------------------------------------------------------*\
-    Bulk velocity
-\*---------------------------------------------------------------------------*/
-
-PtrList<volVectorField> allSpeciesVelocity
-(
-    molecules.nIds()
-);
-
-forAll (allSpeciesVelocity, v)
-{
-    Info << "    Creating velocity field for "
-        << molecules.idList()[v] << endl;
-
-    allSpeciesVelocity.set
-    (
-        v,
-        new volVectorField
-        (
-            IOobject
-            (
-                "velocity_" + molecules.idList()[v],
-                runTime.timeName(),
-                mesh,
-                IOobject::NO_READ,
-                IOobject::AUTO_WRITE
-            ),
-            mesh,
-            dimVelocity,
-            "zeroGradient"
-        )
-    );
-    allSpeciesVelocity[v].internalField() =
-        vectorField (mesh.nCells(), vector::zero);
-    allSpeciesVelocity[v].correctBoundaryConditions();
-}
-
-Info << "    Creating total velocity field" << endl;
-
-volVectorField totalVelocity
-(
-    IOobject
-    (
-        "velocity_total",
-        runTime.timeName(),
-        mesh,
-        IOobject::NO_READ,
-        IOobject::AUTO_WRITE
-    ),
-    mesh,
-    dimVelocity,
-    "zeroGradient"
-);
-totalVelocity.internalField() = vectorField (mesh.nCells(), vector::zero);
-totalVelocity.correctBoundaryConditions();
-
-/*---------------------------------------------------------------------------*\
-    Kinetic temperature
-\*---------------------------------------------------------------------------*/
-
-PtrList<volScalarField> allSpeciesTemperature
-(
-    molecules.nIds()
-);
-
-forAll (allSpeciesTemperature, t)
-{
-    Info << "    Creating temperature field for "
-        << molecules.idList()[t] << endl;
-
-    allSpeciesTemperature.set
-    (
-        t,
-        new volScalarField
-        (
-            IOobject
-            (
-                "temperature_" + molecules.idList()[t],
-                runTime.timeName(),
-                mesh,
-                IOobject::NO_READ,
-                IOobject::AUTO_WRITE
-            ),
-            mesh,
-            dimTemperature,
-            "zeroGradient"
-        )
-    );
-    allSpeciesTemperature[t].internalField() = scalarField (mesh.nCells(), 0.0);
-    allSpeciesTemperature[t].correctBoundaryConditions();
-}
-
-Info << "    Creating total temperature field" << endl;
-
-volScalarField totalTemperature
-(
-    IOobject
-    (
-        "temperature_total",
-        runTime.timeName(),
-        mesh,
-        IOobject::NO_READ,
-        IOobject::AUTO_WRITE
-    ),
-    mesh,
-    dimTemperature,
-    "zeroGradient"
-);
-totalTemperature.internalField() = scalarField (mesh.nCells(), 0.0);
-totalTemperature.correctBoundaryConditions();
-
-/*---------------------------------------------------------------------------*\
-    Mean kinetic energy
-\*---------------------------------------------------------------------------*/
-
-
-PtrList<volScalarField> allSpeciesMeanKE
-(
-    molecules.nIds()
-);
-
-forAll (allSpeciesMeanKE, mKE)
-{
-    Info << "    Creating mean kinetic energy field for "
-        << molecules.idList()[mKE] << endl;
-
-    allSpeciesMeanKE.set
-    (
-        mKE,
-        new volScalarField
-        (
-            IOobject
-            (
-                "meanKE_" + molecules.idList()[mKE],
-                runTime.timeName(),
-                mesh,
-                IOobject::NO_READ,
-                IOobject::AUTO_WRITE
-            ),
-            mesh,
-            dimensionSet(1, 2, -2, 0, 0, 0, 0),
-            "zeroGradient"
-        )
-    );
-    allSpeciesMeanKE[mKE].internalField() = scalarField (mesh.nCells(), 0.0);
-    allSpeciesMeanKE[mKE].correctBoundaryConditions();
-}
-
-Info << "    Creating total mean kinetic energy field" << endl;
-
-volScalarField totalMeanKE
-(
-    IOobject
-    (
-        "meanKE_total",
-        runTime.timeName(),
-        mesh,
-        IOobject::NO_READ,
-        IOobject::AUTO_WRITE
-    ),
-    mesh,
-    dimensionSet(1, 2, -2, 0, 0, 0, 0),
-    "zeroGradient"
-);
-totalMeanKE.internalField() = scalarField (mesh.nCells(), 0.0);
-totalMeanKE.correctBoundaryConditions();
diff --git a/src/lagrangian/molecule/mdTools/createRefUnits.H b/src/lagrangian/molecule/mdTools/createRefUnits.H
deleted file mode 100644
index bbd6c6daf7..0000000000
--- a/src/lagrangian/molecule/mdTools/createRefUnits.H
+++ /dev/null
@@ -1,22 +0,0 @@
-reducedUnits refUnits;
-
-IOobject reducedUnitsDictIOobject
-(
-    "reducedUnitsDict",
-    runTime.system(),
-    mesh,
-    IOobject::READ_IF_PRESENT,
-    IOobject::NO_WRITE
-);
-
-if (reducedUnitsDictIOobject.headerOk())
-{
-    Info << nl
-        << "Reading reference quantities from reducedUnitsDict file." << endl;
-
-    IOdictionary reducedUnitsDict(reducedUnitsDictIOobject);
-
-    refUnits.setRefValues(reducedUnitsDict);
-}
-
-Info << refUnits << endl;
diff --git a/src/lagrangian/molecule/mdTools/md.H b/src/lagrangian/molecule/mdTools/md.H
deleted file mode 100755
index 5c018694bd..0000000000
--- a/src/lagrangian/molecule/mdTools/md.H
+++ /dev/null
@@ -1,11 +0,0 @@
-#ifndef md_H
-#define md_H
-
-#   include "moleculeCloud.H"
-
-#   include "correlationFunction.H"
-#   include "distribution.H"
-#   include "reducedUnits.H"
-
-#endif
-
diff --git a/src/lagrangian/molecule/mdTools/meanMomentumEnergyAndNMols.H b/src/lagrangian/molecule/mdTools/meanMomentumEnergyAndNMols.H
deleted file mode 100755
index 043e63c543..0000000000
--- a/src/lagrangian/molecule/mdTools/meanMomentumEnergyAndNMols.H
+++ /dev/null
@@ -1,130 +0,0 @@
-/*---------------------------------------------------------------------------*\
-  =========                 |
-  \\      /  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
-
-Global
-    meanMomentumEnergyAndNMols.H
-
-Description
-    Calculates and prints the mean momentum and energy in the system
-    and the number of molecules.
-
-\*---------------------------------------------------------------------------*/
-
-
-vector singleStepTotalMomentum(vector::zero);
-
-scalar singleStepMaxVelocityMag = 0.0;
-
-scalar singleStepTotalMass = 0.0;
-
-scalar singleStepTotalKE = 0.0;
-
-scalar singleStepTotalPE = 0.0;
-
-scalar singleStepTotalrDotf = 0.0;
-
-{
-    IDLList<molecule>::iterator mol(molecules.begin());
-
-    for
-    (
-        mol = molecules.begin();
-        mol != molecules.end();
-        ++mol
-    )
-    {
-        const scalar molM(mol().mass());
-
-        const vector& molU(mol().U());
-
-        singleStepTotalMomentum += molU * molM;
-
-        singleStepTotalMass += molM;
-
-        if(mag(molU) > singleStepMaxVelocityMag)
-        {
-            singleStepMaxVelocityMag = mag(molU);
-        }
-
-        singleStepTotalKE += 0.5*molM*magSqr(molU);
-
-        singleStepTotalPE += mol().potentialEnergy();
-
-        singleStepTotalrDotf += tr(mol().rf());
-    }
-}
-
-label singleStepNMols = molecules.size();
-
-if (Pstream::parRun())
-{
-    reduce(singleStepTotalMomentum, sumOp<vector>());
-
-    reduce(singleStepMaxVelocityMag, maxOp<scalar>());
-
-    reduce(singleStepTotalMass, sumOp<scalar>());
-
-    reduce(singleStepTotalKE, sumOp<scalar>());
-
-    reduce(singleStepTotalPE, sumOp<scalar>());
-
-    reduce(singleStepTotalrDotf, sumOp<scalar>());
-
-    reduce(singleStepNMols, sumOp<label>());
-}
-
-if (singleStepNMols)
-{
-    Info << "Number of mols in system = "
-            << singleStepNMols << nl
-        << "Overall number density = "
-            << singleStepNMols/meshVolume << " m^-3" << nl
-        << "Overall mass density = "
-            << singleStepTotalMass/meshVolume << " kg/m^3" << nl
-        << "Average velocity per mol = "
-            << singleStepTotalMomentum/singleStepTotalMass << " m/s" << nl
-        << "Maximum |velocity| = "
-            << singleStepMaxVelocityMag << " m/s" << nl
-        << "Average KE per mol = "
-            << singleStepTotalKE/singleStepNMols << " J" << nl
-        << "Average PE per mol = "
-            << singleStepTotalPE/singleStepNMols << " J" << nl
-        << "Average TE per mol = "
-            << (singleStepTotalKE + singleStepTotalPE)/singleStepNMols << " J"
-        << endl;
-
-//     Info << singleStepNMols << " "
-// //     << singleStepTotalMomentum/singleStepTotalMass << " "
-//     << singleStepMaxVelocityMag << " "
-//     << singleStepTotalKE/singleStepNMols << " "
-//     << singleStepTotalPE/singleStepNMols << " "
-//     << (singleStepTotalKE + singleStepTotalPE)/singleStepNMols << endl;
-}
-else
-{
-    Info << "No molecules in system" << endl;
-}
-
-
-// ************************************************************************* //
diff --git a/src/lagrangian/molecule/mdTools/resetMDFields.H b/src/lagrangian/molecule/mdTools/resetMDFields.H
deleted file mode 100755
index e5fdbbd8a4..0000000000
--- a/src/lagrangian/molecule/mdTools/resetMDFields.H
+++ /dev/null
@@ -1,26 +0,0 @@
-if (runTime.outputTime())
-{
-    allSpeciesN_RU = List< scalarField >
-    (
-        molecules.nIds(),
-        scalarField (mesh.nCells(), 0.0)
-    );
-
-    allSpeciesM_RU = List< scalarField >
-    (
-        molecules.nIds(),
-        scalarField (mesh.nCells(), 0.0)
-    );
-
-    allSpeciesVelocitySum_RU = List< vectorField >
-    (
-        molecules.nIds(),
-        vectorField (mesh.nCells(), vector::zero)
-    );
-
-    allSpeciesVelocityMagSquaredSum_RU = List< scalarField >
-    (
-        molecules.nIds(),
-        scalarField (mesh.nCells(), 0.0)
-    );
-}
diff --git a/src/lagrangian/molecule/mdTools/temperatureAndPressure.H b/src/lagrangian/molecule/mdTools/temperatureAndPressure.H
deleted file mode 100755
index 0563700cb7..0000000000
--- a/src/lagrangian/molecule/mdTools/temperatureAndPressure.H
+++ /dev/null
@@ -1,114 +0,0 @@
-/*---------------------------------------------------------------------------*\
-  =========                 |
-  \\      /  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
-
-Global
-    temperatureAndPressure.H
-
-Description
-    Accumulates values for temperature and pressure measurement, and
-    calculates and outputs the average values at output times.
-    Requires temperatureAndPressureVariables.H to be declared before the
-    timeloop.
-
-\*---------------------------------------------------------------------------*/
-
-accumulatedTotalMomentum += singleStepTotalMomentum;
-
-accumulatedTotalMass += singleStepTotalMass;
-
-accumulatedTotalKE += singleStepTotalKE;
-
-accumulatedTotalPE += singleStepTotalPE;
-
-accumulatedTotalrDotfSum += singleStepTotalrDotf;
-
-accumulatedNMols += singleStepNMols;
-
-if (runTime.outputTime())
-{
-    // calculate averages
-
-    if (accumulatedNMols)
-    {
-        Info << "calculating averages" << endl;
-
-        averageTemperature =
-        (
-            2.0/(3.0 * moleculeCloud::kb * accumulatedNMols)
-            *
-            (
-                accumulatedTotalKE
-                -
-                0.5*magSqr(accumulatedTotalMomentum)/accumulatedTotalMass
-            )
-        );
-
-        averagePressure =
-        (
-            (
-                (accumulatedNMols/nAveragingSteps)
-                *
-                moleculeCloud::kb * averageTemperature
-                +
-                accumulatedTotalrDotfSum/(6.0 * nAveragingSteps)
-            )
-            /
-            meshVolume
-        );
-
-        // output values
-
-        Info << "----------------------------------------" << nl
-            << "Averaged properties" << nl
-            << "Average |velocity| = "
-                << mag(accumulatedTotalMomentum)/accumulatedTotalMass
-                << " m/s" << nl
-            << "Average temperature = "
-                << averageTemperature << " K" << nl
-            << "Average pressure = "
-                << averagePressure << " N/m^2" << nl
-            << "----------------------------------------" << endl;
-    }
-    else
-    {
-        Info << "Not averaging temperature and pressure: "
-            << "no molecules in system" << endl;
-    }
-
-    // reset counters
-
-    accumulatedTotalMomentum = vector::zero;
-
-    accumulatedTotalMass = 0.0;
-
-    accumulatedTotalKE = 0.0;
-
-    accumulatedTotalPE = 0.0;
-
-    accumulatedTotalrDotfSum = 0.0;
-
-    accumulatedNMols = 0;
-}
-
-// ************************************************************************* //
diff --git a/src/lagrangian/molecule/mdTools/temperatureAndPressureVariables.H b/src/lagrangian/molecule/mdTools/temperatureAndPressureVariables.H
deleted file mode 100755
index 258cfac314..0000000000
--- a/src/lagrangian/molecule/mdTools/temperatureAndPressureVariables.H
+++ /dev/null
@@ -1,59 +0,0 @@
-/*---------------------------------------------------------------------------*\
-  =========                 |
-  \\      /  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
-
-Global
-    temperatureAndPressureVariables.H
-
-Description
-    Provides accumulation variables for temperatureAndPressure.H
-
-\*---------------------------------------------------------------------------*/
-
-vector accumulatedTotalMomentum(vector::zero);
-
-scalar accumulatedTotalMass = 0.0;
-
-scalar accumulatedTotalKE = 0.0;
-
-scalar accumulatedTotalPE = 0.0;
-
-scalar accumulatedTotalrDotfSum = 0.0;
-
-label accumulatedNMols = 0;
-
-scalar averageTemperature = 0.0;
-
-scalar averagePressure = 0.0;
-
-const scalarField& cellVols = mesh.cellVolumes();
-
-scalar meshVolume = sum(cellVols);
-
-if (Pstream::parRun())
-{
-    reduce(meshVolume, sumOp<scalar>());
-}
-
-
-// ************************************************************************* //
diff --git a/src/lagrangian/molecule/mdTools/temperatureEquilibration.H b/src/lagrangian/molecule/mdTools/temperatureEquilibration.H
deleted file mode 100755
index c640809cda..0000000000
--- a/src/lagrangian/molecule/mdTools/temperatureEquilibration.H
+++ /dev/null
@@ -1,43 +0,0 @@
-/*---------------------------------------------------------------------------*\
-  =========                 |
-  \\      /  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
-
-Global
-    temperatureEquilibration.H
-
-Description
-    Applies temperature control to molecules
-
-\*---------------------------------------------------------------------------*/
-
-if (runTime.outputTime())
-{
-    molecules.applyConstraintsAndThermostats
-    (
-        targetTemperature,
-        averageTemperature
-    );
-}
-
-
-// ************************************************************************* //
diff --git a/src/lagrangian/molecule/molecule/molecule.C b/src/lagrangian/molecule/molecule/molecule.C
deleted file mode 100755
index 0a46a0ca2c..0000000000
--- a/src/lagrangian/molecule/molecule/molecule.C
+++ /dev/null
@@ -1,214 +0,0 @@
-/*---------------------------------------------------------------------------*\
-  =========                 |
-  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
-   \\    /   O peration     |
-    \\  /    A nd           | Copyright (C) 1991-2005 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 "moleculeCloud.H"
-#include "Random.H"
-#include "Time.H"
-
-namespace Foam
-{
-
-// * * * * * * * * * * * * * * * Member Operators  * * * * * * * * * * * * * //
-
-bool molecule::move(molecule::trackData& td)
-{
-    td.switchProcessor = false;
-    td.keepParticle = true;
-
-    scalar deltaT = cloud().pMesh().time().deltaT().value();
-    scalar tEnd = (1.0 - stepFraction())*deltaT;
-    scalar dtMax = tEnd;
-
-    moleculeCloud::integrationMethods method
-            = td.molCloud().integrationMethod();
-
-    if (method == moleculeCloud::imVerletLeapfrog)
-    {
-        if (td.part() == 1)  // Leapfrog 1st Part
-        {
-            if (stepFraction() < VSMALL)
-            {
-                U_ += 0.5*deltaT*A_;
-            }
-
-            while (td.keepParticle && !td.switchProcessor && tEnd > SMALL)
-            {
-                // set the lagrangian time-step
-                scalar dt = min(dtMax, tEnd);
-
-                dt *= trackToFace(position() + dt*U_, td);
-
-                tEnd -= dt;
-                stepFraction() = 1.0 - tEnd/deltaT;
-            }
-        }
-        else if (td.part() == 2)  // Leapfrog 2nd Part
-        {
-            U_ += 0.5*deltaT*A_;
-        }
-        else
-        {
-            FatalErrorIn("molecule::move(molecule::trackData& td)") << nl
-                << td.part()
-                << " is an invalid part of integration method: "
-                << method << nl
-                << abort(FatalError);
-        }
-    }
-    else if (method == moleculeCloud::imPredictorCorrector)
-    {
-        if (td.part() == 1) // Predictor Part
-        {
-
-        }
-        else if (td.part() == 2) // Corrector Part
-        {
-
-        }
-        else
-        {
-            FatalErrorIn("molecule::move(molecule::trackData& td)") << nl
-                << td.part() << " is an invalid part of integration method: "
-                << method
-                << abort(FatalError);
-        }
-    }
-    else
-    {
-        FatalErrorIn("molecule::move(molecule::trackData& td)") << nl
-                << "Unknown integration method: "
-                << method
-                << abort(FatalError);
-    }
-
-    return td.keepParticle;
-}
-
-
-void molecule::transformProperties(const tensor& T)
-{}
-
-
-void molecule::transformProperties(const vector& separation)
-{
-    if (tethered_)
-    {
-        tetherPosition_ += separation;
-    }
-}
-
-
-void molecule::hitProcessorPatch
-(
-    const processorPolyPatch&,
-    molecule::trackData& td
-)
-{
-    td.switchProcessor = true;
-}
-
-
-void molecule::hitProcessorPatch
-(
-    const processorPolyPatch&,
-    int&
-)
-{}
-
-
-void molecule::hitWallPatch
-(
-    const wallPolyPatch& wpp,
-    molecule::trackData& td
-)
-{
-    vector nw = wpp.faceAreas()[wpp.whichFace(face())];
-    nw /= mag(nw);
-
-    scalar Un = U_ & nw;
-//     vector Ut = U_ - Un*nw;
-
-//     Random rand(clock::getTime());
-
-//     scalar tmac = 0.8;
-
-//     scalar wallTemp = 2.5;
-
-//     if (rand.scalar01() < tmac)
-//     {
-//         // Diffuse reflection
-//
-//         vector tw1 = Ut/mag(Ut);
-//
-//         vector tw2 = nw ^ tw1;
-//
-//         U_ = sqrt(wallTemp/mass_)*rand.GaussNormal()*tw1
-//                 + sqrt(wallTemp/mass_)*rand.GaussNormal()*tw2
-//                 - mag(sqrt(wallTemp/mass_)*rand.GaussNormal())*nw;
-//     }
-
-//     else
-//     {
-        // Specular reflection
-
-        if (Un > 0)
-        {
-            U_ -= 2*Un*nw;
-        }
-//     }
-
-}
-
-
-void molecule::hitWallPatch
-(
-    const wallPolyPatch&,
-    int&
-)
-{}
-
-
-void molecule::hitPatch
-(
-    const polyPatch&,
-    molecule::trackData& td
-)
-{
-    td.keepParticle = false;
-}
-
-
-void molecule::hitPatch
-(
-    const polyPatch&,
-    int&
-)
-{}
-
-} // End namespace Foam
-
-
-// ************************************************************************* //
diff --git a/src/lagrangian/molecule/molecule/molecule.H b/src/lagrangian/molecule/molecule/molecule.H
deleted file mode 100755
index 68cff646b1..0000000000
--- a/src/lagrangian/molecule/molecule/molecule.H
+++ /dev/null
@@ -1,271 +0,0 @@
-/*---------------------------------------------------------------------------*\
-  =========                 |
-  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
-   \\    /   O peration     |
-    \\  /    A nd           | Copyright (C) 1991-2005 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::molecule
-
-Description
-    Foam::molecule
-
-SourceFiles
-    moleculeI.H
-    molecule.C
-    moleculeIO.C
-
-\*---------------------------------------------------------------------------*/
-
-#ifndef molecule_H
-#define molecule_H
-
-#include "Particle.H"
-#include "IOstream.H"
-#include "autoPtr.H"
-
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-namespace Foam
-{
-
-// Class forward declarations
-class moleculeCloud;
-
-/*---------------------------------------------------------------------------*\
-                           Class molecule Declaration
-\*---------------------------------------------------------------------------*/
-
-class molecule
-:
-    public Particle<molecule>
-{
-    // Private data
-
-        //- Be careful with the ordering of data.  It has an impact on binary
-        //  transfer:
-        //  1) Put the largest data members 1st
-        //  2) Pair up labels,
-        //  3) Don't go scalar-label, scalar-label, becasue in 64bit mode,
-        //     the labels will be padded by 4bytes.
-
-        // - mass of molecule
-        scalar mass_;
-
-        // - Velocity of molecule
-        vector U_;
-
-        // - Acceleration of molecule
-        vector A_;
-
-        // - Tether position
-        vector tetherPosition_;
-
-        // - Potential energy that this molecules posseses
-        scalar potentialEnergy_;
-
-        // - r_ij f_ij, stress dyad
-        tensor rf_;
-
-        // - Is the molecule tethered?
-        label tethered_;
-
-        // - id (type) of molecule
-        label id_;
-
-
-public:
-
-    friend class Cloud<molecule>;
-
-    //- Class used to pass tracking data to the trackToFace function
-    class trackData
-    :
-        public Particle<molecule>::trackData
-    {
-        //- Reference to the cloud containing this particle
-        moleculeCloud& molCloud_;
-
-        // label specifying which part of the integration algorithm is taking
-        // place (i.e. leapfrog 1 or leapfrog 2. Predictor or Corrector)
-        label part_;
-
-
-    public:
-
-        // Constructors
-
-            inline trackData
-            (
-                moleculeCloud& molCloud,
-                label part
-            );
-
-        // Member functions
-
-            inline moleculeCloud& molCloud();
-
-            inline label part() const;
-    };
-
-    // Constructors
-
-        //- Construct from components
-        inline molecule
-        (
-            const Cloud<molecule>& c,
-            const vector& position,
-            const label celli,
-            const scalar mass,
-            const vector& U,
-            const vector& A,
-            const vector& tetherPosition,
-            const label tethered,
-            const label id
-        );
-
-        //- Construct from Istream
-        molecule
-        (
-            const Cloud<molecule>& c,
-            Istream& is,
-            bool readFields = true
-        );
-
-        //- Construct and return a clone
-        autoPtr<molecule> clone() const
-        {
-            return autoPtr<molecule>(new molecule(*this));
-        }
-
-
-    // Member Functions
-
-        void transformProperties(const tensor& T);
-
-        void transformProperties(const vector& separation);
-
-        // Access
-
-            //- Return id
-            inline const label id() const;
-
-            //- Return mass
-            inline const scalar mass() const;
-
-            //- Return velocity
-            inline const vector& U() const;
-            inline vector& U();
-
-            //- Return acceleration
-            inline const vector& A() const;
-            inline vector& A();
-
-            //- Return potential energy
-            inline const scalar potentialEnergy() const;
-            inline scalar& potentialEnergy();
-
-            //- Return stress contribution
-            inline const tensor& rf() const;
-            inline tensor& rf();
-
-            //- Return tethered
-            inline const label tethered() const;
-
-            //- Return tetherPosition
-            inline const vector& tetherPosition() const;
-
-
-        //- Tracking
-        bool move(trackData&);
-
-
-    // Member Operators
-
-        //- Overridable function to handle the particle hitting a
-        //  processorPatch
-        void hitProcessorPatch
-        (
-            const processorPolyPatch&,
-            molecule::trackData& td
-        );
-
-        //- Overridable function to handle the particle hitting a
-        //  processorPatch without trackData
-        void hitProcessorPatch
-        (
-            const processorPolyPatch&,
-            int&
-        );
-
-        //- Overridable function to handle the particle hitting a wallPatch
-        void hitWallPatch
-        (
-            const wallPolyPatch&,
-            molecule::trackData& td
-        );
-
-        //- Overridable function to handle the particle hitting a wallPatch
-        //- without trackData
-        void hitWallPatch
-        (
-            const wallPolyPatch&,
-            int&
-        );
-
-        //- Overridable function to handle the particle hitting a polyPatch
-        void hitPatch
-        (
-            const polyPatch&,
-            molecule::trackData& td
-        );
-
-        //- Overridable function to handle the particle hitting a polyPatch
-        //- without trackData
-        void hitPatch
-        (
-            const polyPatch&,
-            int&
-        );
-
-        static void readFields(moleculeCloud& mC);
-
-        static void writeFields(const moleculeCloud& mC);
-
-
-    // IOstream Operators
-
-        friend Ostream& operator<<(Ostream&, const molecule&);
-};
-
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-} // End namespace Foam
-
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-#include "moleculeI.H"
-
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-#endif
-
-// ************************************************************************* //
diff --git a/src/lagrangian/molecule/molecule/moleculeI.H b/src/lagrangian/molecule/molecule/moleculeI.H
deleted file mode 100755
index 6dd50e337e..0000000000
--- a/src/lagrangian/molecule/molecule/moleculeI.H
+++ /dev/null
@@ -1,159 +0,0 @@
-/*---------------------------------------------------------------------------*\
-  =========                 |
-  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
-   \\    /   O peration     |
-    \\  /    A nd           | Copyright (C) 1991-2005 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
-{
-
-// * * * * * * * * * * * * * * * * Constructors  * * * * * * * * * * * * * * //
-
-inline molecule::molecule
-(
-    const Cloud<molecule>& c,
-    const vector& position,
-    const label celli,
-    const scalar mass,
-    const vector& U,
-    const vector& A,
-    const vector& tetherPosition,
-    const label tethered,
-    const label id
-)
-:
-    Particle<molecule>(c, position, celli),
-    mass_(mass),
-    U_(U),
-    A_(A),
-    tetherPosition_(tetherPosition),
-    potentialEnergy_(0.0),
-    rf_(tensor::zero),
-    tethered_(tethered),
-    id_(id)
-{}
-
-
-inline molecule::trackData::trackData
-(
-    moleculeCloud& molCloud,
-    label part
-)
-:
-    Particle<molecule>::trackData(refCast<Cloud<molecule> >(molCloud)),
-    molCloud_(molCloud),
-    part_(part)
-{}
-
-
-// * * * * * * * * * * * * * * * Member Functions  * * * * * * * * * * * * * //
-
-inline const label molecule::id() const
-{
-    return id_;
-}
-
-
-inline const scalar molecule::mass() const
-{
-    return mass_;
-}
-
-
-inline const vector& molecule::U() const
-{
-    return U_;
-}
-
-
-inline vector& molecule::U()
-{
-    return U_;
-}
-
-
-inline const vector& molecule::A() const
-{
-    return A_;
-}
-
-
-inline vector& molecule::A()
-{
-    return A_;
-}
-
-
-inline const scalar molecule::potentialEnergy() const
-{
-    return potentialEnergy_;
-}
-
-
-inline scalar& molecule::potentialEnergy()
-{
-    return potentialEnergy_;
-}
-
-
-inline const tensor& molecule::rf() const
-{
-    return rf_;
-}
-
-
-inline tensor& molecule::rf()
-{
-    return rf_;
-}
-
-
-inline const label molecule::tethered() const
-{
-    return tethered_;
-}
-
-
-inline const vector& molecule::tetherPosition() const
-{
-    return tetherPosition_;
-}
-
-
-inline moleculeCloud& molecule::trackData::molCloud()
-{
-    return molCloud_;
-}
-
-
-inline label molecule::trackData::part() const
-{
-    return part_;
-}
-
-
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-} // End namespace Foam
-
-// ************************************************************************* //
diff --git a/src/lagrangian/molecule/molecule/moleculeIO.C b/src/lagrangian/molecule/molecule/moleculeIO.C
deleted file mode 100755
index f87b80cd46..0000000000
--- a/src/lagrangian/molecule/molecule/moleculeIO.C
+++ /dev/null
@@ -1,208 +0,0 @@
-/*---------------------------------------------------------------------------*\
-  =========                 |
-  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
-   \\    /   O peration     |
-    \\  /    A nd           | Copyright (C) 1991-2005 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 "molecule.H"
-#include "IOstreams.H"
-
-#include "moleculeCloud.H"
-
-// * * * * * * * * * * * * * * * * Constructors  * * * * * * * * * * * * * * //
-
-Foam::molecule::molecule
-(
-    const Cloud<molecule>& cloud,
-    Istream& is,
-    bool readFields
-)
-:
-    Particle<molecule>(cloud, is)
-{
-    if (readFields)
-    {
-        if (is.format() == IOstream::ASCII)
-        {
-            id_ = readLabel(is);
-            mass_ = readScalar(is);
-            is >> U_;
-            is >> A_;
-            is >> potentialEnergy_;
-            is >> rf_;
-            is >> tethered_;
-            is >> tetherPosition_;
-        }
-        else
-        {
-            is.read
-            (
-                reinterpret_cast<char*>(&mass_),
-                sizeof(mass_)
-                + sizeof(U_)
-                + sizeof(A_)
-                + sizeof(tetherPosition_)
-                + sizeof(potentialEnergy_)
-                + sizeof(rf_)
-                + sizeof(tethered_)
-                + sizeof(id_)
-            );
-        }
-    }
-
-    // Check state of Istream
-    is.check("Foam::molecule::molecule(Foam::Istream&)");
-}
-
-
-namespace Foam
-{
-
-void molecule::readFields(moleculeCloud& mC)
-{
-    if (!mC.size())
-    {
-        return;
-    }
-
-    IOField<label> id(mC.fieldIOobject("id"));
-    mC.checkFieldIOobject(mC, id);
-
-    IOField<scalar> mass(mC.fieldIOobject("mass"));
-    mC.checkFieldIOobject(mC, mass);
-
-    IOField<vector> U(mC.fieldIOobject("U"));
-    mC.checkFieldIOobject(mC, U);
-
-    IOField<vector> A(mC.fieldIOobject("A"));
-    mC.checkFieldIOobject(mC, A);
-
-    IOField<label> tethered(mC.fieldIOobject("tethered"));
-    mC.checkFieldIOobject(mC, tethered);
-
-    IOField<vector> tetherPositions(mC.fieldIOobject("tetherPositions"));
-    mC.checkFieldIOobject(mC, tetherPositions);
-
-    label i = 0;
-    forAllIter(moleculeCloud, mC, iter)
-    {
-        molecule& mol = iter();
-
-        mol.id_ = id[i];
-        mol.mass_ = mass[i];
-        mol.U_ = U[i];
-        mol.A_ = A[i];
-        mol.potentialEnergy_ = 0.0;
-        mol.rf_ = tensor::zero;
-        mol.tethered_ = tethered[i];
-        mol.tetherPosition_ = tetherPositions[i];
-        i++;
-    }
-}
-
-
-void molecule::writeFields(const moleculeCloud& mC)
-{
-    Particle<molecule>::writeFields(mC);
-
-    label np =  mC.size();
-
-    IOField<label> id(mC.fieldIOobject("id"), np);
-    IOField<scalar> mass(mC.fieldIOobject("mass"), np);
-    IOField<vector> U(mC.fieldIOobject("U"), np);
-    IOField<vector> A(mC.fieldIOobject("A"), np);
-    IOField<label> tethered(mC.fieldIOobject("tethered"), np);
-    IOField<vector> tetherPositions(mC.fieldIOobject("tetherPositions"), np);
-
-    label i = 0;
-    forAllConstIter(moleculeCloud, mC, iter)
-    {
-        const molecule& mol = iter();
-
-        id[i] = mol.id_;
-        mass[i] = mol.mass_;
-        U[i] = mol.U_;
-        A[i] = mol.A_;
-        tethered[i] = mol.tethered_;
-        tetherPositions[i] = mol.tetherPosition_;
-        i++;
-    }
-
-    id.write();
-    mass.write();
-    U.write();
-    A.write();
-    tethered.write();
-    tetherPositions.write();
-}
-
-};  // end of namespace Foam
-
-
-// * * * * * * * * * * * * * * * IOstream Operators  * * * * * * * * * * * * //
-
-Foam::Ostream& Foam::operator<<(Ostream& os, const molecule& mol)
-{
-    if (os.format() == IOstream::ASCII)
-    {
-        os  << mol.id_
-                << token::SPACE << mol.mass_
-                << token::SPACE << static_cast<const Particle<molecule>&>(mol)
-                << token::SPACE << mol.face()
-                << token::SPACE << mol.stepFraction()
-                << token::SPACE << mol.U_
-                << token::SPACE << mol.A_
-                << token::SPACE << mol.potentialEnergy_
-                << token::SPACE << mol.rf_
-                << token::SPACE << mol.tethered_
-                << token::SPACE << mol.tetherPosition_;
-    }
-    else
-    {
-        os  << static_cast<const Particle<molecule>&>(mol);
-        os.write
-        (
-            reinterpret_cast<const char*>(&mol.mass_),
-            sizeof(mol.mass_)
-            + sizeof(mol.U_)
-            + sizeof(mol.A_)
-            + sizeof(mol.tetherPosition_)
-            + sizeof(mol.potentialEnergy_)
-            + sizeof(mol.rf_)
-            + sizeof(mol.tethered_)
-            + sizeof(mol.id_)
-        );
-    }
-
-    // Check state of Ostream
-    os.check
-    (
-        "Foam::Ostream& Foam::operator<<"
-        "(Foam::Ostream&, const Foam::molecule&)"
-    );
-
-    return os;
-}
-
-
-// ************************************************************************* //
diff --git a/src/lagrangian/molecule/moleculeCloud/moleculeCloud.C b/src/lagrangian/molecule/moleculeCloud/moleculeCloud.C
deleted file mode 100755
index cf0ebebc7c..0000000000
--- a/src/lagrangian/molecule/moleculeCloud/moleculeCloud.C
+++ /dev/null
@@ -1,135 +0,0 @@
-/*---------------------------------------------------------------------------*\
-  =========                 |
-  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
-   \\    /   O peration     |
-    \\  /    A nd           | Copyright (C) 1991-2005 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 "moleculeCloud.H"
-#include "fvMesh.H"
-
-// * * * * * * * * * * * * * * Static Data Members * * * * * * * * * * * * * //
-
-namespace Foam
-{
-    defineParticleTypeNameAndDebug(molecule, 0);
-    defineTemplateTypeNameAndDebug(Cloud<molecule>, 0);
-};
-
-
-template<>
-const char* Foam::NamedEnum<Foam::moleculeCloud::
-integrationMethods, 2>::names[] =
-{
-    "verletLeapfrog",
-    "predictorCorrector"
-};
-
-const Foam::NamedEnum<Foam::moleculeCloud::integrationMethods, 2>
-        Foam::moleculeCloud::integrationMethodNames_;
-
-
-Foam::scalar Foam::moleculeCloud::transTol = 1e-12;
-
-Foam::scalar Foam::moleculeCloud::kb = 1.380650277e-23;
-
-
-// * * * * * * * * * * * * * * * * Constructors  * * * * * * * * * * * * * * //
-
-Foam::moleculeCloud::moleculeCloud(const polyMesh& mesh)
-:
-    Cloud<molecule>(mesh, "moleculeCloud", false),
-    mesh_(mesh),
-    referredInteractionList_(*this)
-{
-    molecule::readFields(*this);
-
-#   include "moleculeCloudReadMDParameters.H"
-
-    buildCellInteractionLists();
-
-    buildCellReferralLists();
-
-    buildCellOccupancy();
-}
-
-
-Foam::moleculeCloud::moleculeCloud
-(
-    const polyMesh& mesh,
-    label nMol,
-    const labelField& id,
-    const scalarField& mass,
-    const vectorField& positions,
-    const labelField& cells,
-    const vectorField& U,
-    const vectorField& A,
-    const labelField& tethered,
-    const vectorField& tetherPositions
-)
-:
-    Cloud<molecule>(mesh, "moleculeCloud", false),
-    mesh_(mesh),
-    referredInteractionList_(*this)
-{
-    molecule::readFields(*this);
-
-    clear();
-
-    // This clear ()is here for the moment to stop existing files
-    // being appended to, this would be better accomplished by getting
-    // mesh.removeFiles(mesh.instance()); (or equivalent) to work.
-
-    int i;
-
-    const Cloud<molecule>& cloud = *this;
-
-    for (i=0; i<nMol; i++)
-    {
-        addParticle
-        (
-            new molecule
-            (
-                cloud,
-                positions[i],
-                cells[i],
-                mass[i],
-                U[i],
-                A[i],
-                tetherPositions[i],
-                tethered[i],
-                id[i]
-            )
-        );
-    }
-};
-
-
-// * * * * * * * * * * * * * * * Member Functions  * * * * * * * * * * * * * //
-
-void Foam::moleculeCloud::writeFields() const
-{
-    molecule::writeFields(*this);
-}
-
-
-// ************************************************************************* //
diff --git a/src/lagrangian/molecule/moleculeCloud/moleculeCloud.H b/src/lagrangian/molecule/moleculeCloud/moleculeCloud.H
deleted file mode 100755
index 5175fdd0d8..0000000000
--- a/src/lagrangian/molecule/moleculeCloud/moleculeCloud.H
+++ /dev/null
@@ -1,350 +0,0 @@
-/*---------------------------------------------------------------------------*\
-  =========                 |
-  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
-   \\    /   O peration     |
-    \\  /    A nd           | Copyright (C) 1991-2005 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::moleculeCloud
-
-Description
-
-SourceFiles
-    moleculeCloudApplyConstraintsAndThermostats.C
-    moleculeCloudBuildCellInteractionLists.C
-    moleculeCloudBuildCellOccupancy.C
-    moleculeCloudBuildCellReferralLists.C
-    moleculeCloud.C
-    moleculeCloudCalculateAndAccumulateProperties.C
-    moleculeCloudCalculateExternalForce.C
-    moleculeCloudCalculateForce.C
-    moleculeCloudCalculatePairForce.C
-    moleculeCloudCalculateTetherForce.C
-    moleculeCloudIntegrateEquationsOfMotion.C
-    moleculeCloudRemoveHighEnergyOverlaps.C
-
-
-\*---------------------------------------------------------------------------*/
-
-#ifndef moleculeCloud_H
-#define moleculeCloud_H
-
-#include "Cloud.H"
-#include "molecule.H"
-#include "IOdictionary.H"
-#include "vector2D.H"
-
-#include "pairPotentialList.H"
-#include "tetherPotentialList.H"
-
-#include "receivingReferralList.H"
-#include "sendingReferralList.H"
-#include "referredCellList.H"
-
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-namespace Foam
-{
-
-/*---------------------------------------------------------------------------*\
-                           Class moleculeCloud Declaration
-\*---------------------------------------------------------------------------*/
-
-class moleculeCloud
-:
-    public Cloud<molecule>
-{
-
-public:
-
-    enum integrationMethods
-    {
-        imVerletLeapfrog,
-        imPredictorCorrector
-    };
-
-
-private:
-
-    // Private data
-
-        const polyMesh& mesh_;
-
-            // MD solution parameters
-
-            static const NamedEnum<integrationMethods, 2>
-                integrationMethodNames_;
-
-            integrationMethods integrationMethod_;
-
-            scalar potentialEnergyLimit_;
-
-            scalar guardRadius_;
-
-            scalar rCutMax_;
-
-            //- storing rCutMaxSqr in class as well as rCutMax to
-            //- avoid needing to calculate it often.
-            //- Possibilty of inconsistency if tinkered with.
-
-            scalar rCutMaxSqr_;
-
-            List<word> idList_;
-
-            labelList removalOrder_;
-
-            labelListList directInteractionList_;
-
-            referredCellList referredInteractionList_;
-
-            labelList realCellsWithinRCutMaxOfAnyReferringPatch_;
-
-            labelList realFacesWithinRCutMaxOfAnyReferringPatch_;
-
-            labelList realEdgesWithinRCutMaxOfAnyReferringPatch_;
-
-            labelList realPointsWithinRCutMaxOfAnyReferringPatch_;
-
-            List<sendingReferralList> cellSendingReferralLists_;
-
-            List<receivingReferralList> cellReceivingReferralLists_;
-
-            pairPotentialList pairPotentials_;
-
-            tetherPotentialList tetherPotentials_;
-
-            vector gravity_;
-
-            List< DynamicList<molecule*> > cellOccupancy_;
-
-
-        // Private Member Functions
-
-            //- Disallow default bitwise copy construct
-            moleculeCloud(const moleculeCloud&);
-
-            //- Disallow default bitwise assignment
-            void operator=(const moleculeCloud&);
-
-
-public:
-
-    // Static data members
-
-        //- Tolerance for checking that faces on a patch segment
-        static scalar transTol;
-
-        static scalar kb;
-
-
-    // Constructors
-
-        //- Construct given mesh
-        moleculeCloud(const polyMesh&);
-
-        //- Construct given polyMesh and fields of position, cell, mass,
-        //- id, U ands A.  Intended for use by the molConfig utility
-        moleculeCloud
-        (
-            const polyMesh& mesh,
-            label nMol,
-            const labelField& id,
-            const scalarField& mass,
-            const vectorField& positions,
-            const labelField& cells,
-            const vectorField& U,
-            const vectorField& A,
-            const labelField& tethered,
-            const vectorField& tetherPositions
-        );
-
-
-    // Member Functions
-
-        // Access
-
-            inline const polyMesh& mesh() const;
-
-        // MD solution parameters
-
-            inline const integrationMethods& integrationMethod() const;
-
-            inline scalar potentialEnergyLimit() const;
-
-            inline scalar guardRadius() const;
-
-            inline const scalar rCutMax() const;
-
-            inline const scalar rCutMaxSqr() const;
-
-            inline const List<word>& idList() const;
-
-            inline const labelList& removalOrder() const;
-
-            inline label nPairPotentials() const;
-
-            inline label nIds() const;
-
-            inline const labelListList& directInteractionList() const;
-
-            inline const referredCellList& referredInteractionList() const;
-
-            inline const labelList&
-                realCellsWithinRCutMaxOfAnyReferringPatch() const;
-
-            inline const labelList&
-                realFacesWithinRCutMaxOfAnyReferringPatch() const;
-
-            inline const labelList&
-                realEdgesWithinRCutMaxOfAnyReferringPatch() const;
-
-            inline const labelList&
-                realPointsWithinRCutMaxOfAnyReferringPatch() const;
-
-            inline const List<sendingReferralList>&
-                cellSendingReferralLists() const;
-
-            inline const List<receivingReferralList>&
-                cellReceivingReferralLists() const;
-
-            inline label nInteractingProcs() const;
-
-            inline const pairPotentialList& pairPotentials() const;
-
-            inline const tetherPotentialList& tetherPotentials() const;
-
-            inline const vector& gravity() const;
-
-            inline const List< DynamicList<molecule*> >& cellOccupancy() const;
-
-            void buildCellInteractionLists();
-
-            //- Build referralLists which define how to send information
-            // to referredCells to source cells
-            void buildCellReferralLists();
-
-            bool testPointFaceDistance
-            (
-                const label p,
-                const label faceNo
-            ) const;
-
-            bool testPointFaceDistance
-            (
-                const label p,
-                const referredCell& refCell
-            ) const;
-
-            bool testPointFaceDistance
-            (
-                const vectorList& pointsToTest,
-                const label faceNo
-            ) const;
-
-            bool testPointFaceDistance
-            (
-                const vector& p,
-                const label faceNo
-            ) const;
-
-            bool testPointFaceDistance
-            (
-                const vector& p,
-                const labelList& faceToTest,
-                const vectorList& points,
-                const vector& faceC,
-                const vector& faceA
-            ) const;
-
-            bool testEdgeEdgeDistance
-            (
-                const edge& eI,
-                const edge& eJ
-            ) const;
-
-            bool testEdgeEdgeDistance
-            (
-                const edge& eI,
-                const vector& eJs,
-                const vector& eJe
-            ) const;
-
-            const labelList realCellsInRangeOfSegment
-            (
-                const labelList& segmentFaces,
-                const labelList& segmentEdges,
-                const labelList& segmentPoints
-            ) const;
-
-            const labelList referredCellsInRangeOfSegment
-            (
-                const List<referredCell>& referredInteractionList,
-                const labelList& segmentFaces,
-                const labelList& segmentEdges,
-                const labelList& segmentPoints
-            ) const;
-
-            //- Determine which molecules are in which cells
-            void buildCellOccupancy();
-
-            //- Integrate the equations of motion using algorithm selected at
-            //  runtime from a dictionary. This will also call the function
-            //  to calculate the intermolecular forces (calculatePairForce()).
-
-            void integrateEquationsOfMotion();
-
-            void applyConstraintsAndThermostats
-            (
-                const scalar targetTemperature,
-                const scalar measuredTemperature
-            );
-
-            void calculateForce();
-
-            void calculatePairForce();
-
-            void calculateTetherForce();
-
-            void calculateExternalForce();
-
-            void removeHighEnergyOverlaps();
-
-
-    // Member Operators
-
-        //- Write fields
-        void writeFields() const;
-};
-
-
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-} // End namespace Foam
-
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-#include "moleculeCloudI.H"
-
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-#endif
-
-// ************************************************************************* //
diff --git a/src/lagrangian/molecule/moleculeCloud/moleculeCloudApplyConstraintsAndThermostats.C b/src/lagrangian/molecule/moleculeCloud/moleculeCloudApplyConstraintsAndThermostats.C
deleted file mode 100755
index d44b247d7b..0000000000
--- a/src/lagrangian/molecule/moleculeCloud/moleculeCloudApplyConstraintsAndThermostats.C
+++ /dev/null
@@ -1,60 +0,0 @@
-/*---------------------------------------------------------------------------*\
-  =========                 |
-  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
-   \\    /   O peration     |
-    \\  /    A nd           | Copyright (C) 1991-2005 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 "moleculeCloud.H"
-
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-void Foam::moleculeCloud::applyConstraintsAndThermostats
-(
-    const scalar targetTemperature,
-    const scalar measuredTemperature
-)
-{
-    scalar temperatureCorrectionFactor =
-        sqrt(targetTemperature/measuredTemperature);
-
-    Info<< "----------------------------------------" << nl
-        << "Temperature equilibration" << nl
-        << "Target temperature = "
-        << targetTemperature << nl
-        << "Measured temperature = "
-        << measuredTemperature << nl
-        << "Temperature correction factor ="
-        << temperatureCorrectionFactor << nl
-        << "----------------------------------------"
-        << endl;
-
-    iterator mol(this->begin());
-
-    for (mol = this->begin(); mol != this->end(); ++mol)
-    {
-        mol().U() *= temperatureCorrectionFactor;
-    }
-}
-
-
-// ************************************************************************* //
diff --git a/src/lagrangian/molecule/moleculeCloud/moleculeCloudBuildCellInteractionLists.C b/src/lagrangian/molecule/moleculeCloud/moleculeCloudBuildCellInteractionLists.C
deleted file mode 100755
index a8d9cc8db5..0000000000
--- a/src/lagrangian/molecule/moleculeCloud/moleculeCloudBuildCellInteractionLists.C
+++ /dev/null
@@ -1,80 +0,0 @@
-/*---------------------------------------------------------------------------*\
-  =========                 |
-  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
-   \\    /   O peration     |
-    \\  /    A nd           | Copyright (C) 1991-2005 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 "moleculeCloud.H"
-#include "polyBoundaryMeshEntries.H"
-#include "PstreamCombineReduceOps.H"
-
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-void Foam::moleculeCloud::buildCellInteractionLists()
-{
-// #       include "moleculeCloudCodeSnippets.H"
-
-    List<DynamicList<label> > directInteractionList(mesh_.nCells());
-
-#   include "moleculeCloudBuildDirectInteractionList.H"
-
-    directInteractionList_.setSize(mesh_.nCells());
-
-    forAll(directInteractionList, transDIL)
-    {
-        directInteractionList_[transDIL].transfer
-        (
-            directInteractionList[transDIL].shrink()
-        );
-    }
-
-//     for sorting DILs
-
-//     forAll(directInteractionList_, dIL)
-//     {
-//         sort(directInteractionList_[dIL]);
-//     }
-
-    cellOccupancy_.setSize(mesh_.nCells());
-
-    DynamicList<referredCell> referredInteractionList;
-
-#   include "moleculeCloudBuildReferredInteractionList.H"
-
-//#   include "moleculeCloudBuildReferredInteractionList_old.H"
-
-    referredInteractionList_.setSize
-    (
-        referredInteractionList.size()
-    );
-
-    forAll(referredInteractionList, rIL)
-    {
-        referredInteractionList_[rIL] = referredInteractionList[rIL];
-    }
-
-    referredInteractionList_.setRealCellsInRange();
-}
-
-
-// ************************************************************************* //
diff --git a/src/lagrangian/molecule/moleculeCloud/moleculeCloudBuildCellOccupancy.C b/src/lagrangian/molecule/moleculeCloud/moleculeCloudBuildCellOccupancy.C
deleted file mode 100755
index f02be61f7e..0000000000
--- a/src/lagrangian/molecule/moleculeCloud/moleculeCloudBuildCellOccupancy.C
+++ /dev/null
@@ -1,54 +0,0 @@
-/*---------------------------------------------------------------------------*\
-  =========                 |
-  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
-   \\    /   O peration     |
-    \\  /    A nd           | Copyright (C) 1991-2005 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 "moleculeCloud.H"
-
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-void Foam::moleculeCloud::buildCellOccupancy()
-{
-    forAll(cellOccupancy_, cO)
-    {
-        cellOccupancy_[cO].clear();
-    }
-
-    iterator mol(this->begin());
-
-    for (mol = this->begin(); mol != this->end(); ++mol)
-    {
-        cellOccupancy_[mol().cell()].append(&mol());
-    }
-
-    forAll(cellOccupancy_, cO)
-    {
-        cellOccupancy_[cO].shrink();
-    }
-
-    referredInteractionList_.referMolecules();
-}
-
-
-// ************************************************************************* //
diff --git a/src/lagrangian/molecule/moleculeCloud/moleculeCloudBuildCellReferralLists.C b/src/lagrangian/molecule/moleculeCloud/moleculeCloudBuildCellReferralLists.C
deleted file mode 100755
index ea1521800f..0000000000
--- a/src/lagrangian/molecule/moleculeCloud/moleculeCloudBuildCellReferralLists.C
+++ /dev/null
@@ -1,194 +0,0 @@
-/*---------------------------------------------------------------------------*\
-  =========                 |
-  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
-   \\    /   O peration     |
-    \\  /    A nd           | Copyright (C) 1991-2005 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 "moleculeCloud.H"
-
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-void Foam::moleculeCloud::buildCellReferralLists()
-{
-    Info<< nl << "Determining molecule referring schedule" << endl;
-
-    const referredCellList& refIntL(referredInteractionList());
-
-    DynamicList<label> referralProcs;
-
-    // Run through all referredCells to build list of interacting processors
-
-    forAll(refIntL, rIL)
-    {
-        const referredCell& rC(refIntL[rIL]);
-
-        if (findIndex(referralProcs, rC.sourceProc()) == -1)
-        {
-            referralProcs.append(rC.sourceProc());
-        }
-    }
-
-    referralProcs.shrink();
-
-//     Pout << "referralProcs: " << nl << referralProcs << endl;
-
-    List<DynamicList<label> > cellSendingReferralLists(referralProcs.size());
-
-    List<DynamicList<DynamicList<label> > >
-        cellReceivingReferralLists(referralProcs.size());
-
-    // Run through all referredCells again building up send and receive info
-
-    forAll(refIntL, rIL)
-    {
-        const referredCell& rC(refIntL[rIL]);
-
-        label rPI = findIndex(referralProcs, rC.sourceProc());
-
-        DynamicList<DynamicList<label> >& rRL(cellReceivingReferralLists[rPI]);
-
-        DynamicList<label>& sRL(cellSendingReferralLists[rPI]);
-
-        label existingSource = findIndex(sRL, rC.sourceCell());
-
-        // Check to see if this source cell has already been allocated to
-        // come to this processor.  If not, add the source cell to the sending
-        // list and add the current referred cell to the receiving list.
-
-        // It shouldn't be possible for the sending and receiving lists to be
-        // different lengths, because their append operations happen at the
-        // same time.
-
-        if (existingSource == -1)
-        {
-            sRL.append(rC.sourceCell());
-
-            rRL.append
-            (
-                DynamicList<label> (labelList(1,rIL))
-            );
-        }
-        else
-        {
-            rRL[existingSource].append(rIL);
-
-            rRL[existingSource].shrink();
-        }
-    }
-
-    forAll(referralProcs, rPI)
-    {
-        DynamicList<DynamicList<label> >& rRL(cellReceivingReferralLists[rPI]);
-
-        DynamicList<label>& sRL(cellSendingReferralLists[rPI]);
-
-        sRL.shrink();
-
-        rRL.shrink();
-    }
-
-    // It is assumed that cell exchange is reciprocal, if proc A has cells to
-    // send to proc B, then proc B must have some to send to proc A.
-
-    cellReceivingReferralLists_.setSize(referralProcs.size());
-
-    cellSendingReferralLists_.setSize(referralProcs.size());
-
-    forAll(referralProcs, rPI)
-    {
-        DynamicList<DynamicList<label> >& rRL(cellReceivingReferralLists[rPI]);
-
-        labelListList translLL(rRL.size());
-
-        forAll(rRL, rRLI)
-        {
-            translLL[rRLI] = rRL[rRLI];
-        }
-
-        cellReceivingReferralLists_[rPI] = receivingReferralList
-        (
-            referralProcs[rPI],
-            translLL
-        );
-    }
-
-    // Send sendingReferralLists to each interacting processor.
-
-    forAll(referralProcs, rPI)
-    {
-
-        DynamicList<label>& sRL(cellSendingReferralLists[rPI]);
-
-        if (referralProcs[rPI] != Pstream::myProcNo())
-        {
-            if (Pstream::parRun())
-            {
-                OPstream toInteractingProc
-                (
-                    Pstream::blocking,
-                    referralProcs[rPI]
-                );
-
-                toInteractingProc << sendingReferralList
-                (
-                    Pstream::myProcNo(),
-                    sRL
-                );
-            }
-        }
-    }
-
-    // Receive sendingReferralLists from each interacting processor.
-
-    forAll(referralProcs, rPI)
-    {
-        if (referralProcs[rPI] != Pstream::myProcNo())
-        {
-            if (Pstream::parRun())
-            {
-                IPstream fromInteractingProc
-                (
-                    Pstream::blocking,
-                    referralProcs[rPI]
-                );
-
-                fromInteractingProc >> cellSendingReferralLists_[rPI];
-            }
-        }
-        else
-        {
-            cellSendingReferralLists_[rPI] = sendingReferralList
-            (
-                Pstream::myProcNo(),
-                cellSendingReferralLists[rPI]
-            );
-        }
-    }
-
-//     Pout << "receiving list: " << nl << cellReceivingReferralLists_ << endl;
-
-//     Pout << "sending list: " << nl << cellSendingReferralLists_ << endl;
-}
-
-
-// ************************************************************************* //
diff --git a/src/lagrangian/molecule/moleculeCloud/moleculeCloudBuildCellsFoundInRange.H b/src/lagrangian/molecule/moleculeCloud/moleculeCloudBuildCellsFoundInRange.H
deleted file mode 100755
index 16c58efea3..0000000000
--- a/src/lagrangian/molecule/moleculeCloud/moleculeCloudBuildCellsFoundInRange.H
+++ /dev/null
@@ -1,52 +0,0 @@
-forAll (pointsOnThisSegment, pS)
-{
-    const point& ptP = mesh_.points()[pointsOnThisSegment[pS]];
-
-    // Assessing real cells in range is only required on the 1st iteration
-    // because they do not change from iteration to iteration.
-
-    if (iterationNo == 0)
-    {
-        forAll (mesh_.points(), pointIIndex)
-        {
-
-            // Compare separation of ptP to all other points in the mesh,
-            // add unique reference to cell with any point within rCutMax_
-            // to realCellsFoundInRange.
-
-            const point& ptI(mesh_.points()[pointIIndex]);
-
-            if (magSqr(ptP - ptI) <= rCutMaxSqr)
-            {
-                const labelList& ptICells(mesh_.pointCells()[pointIIndex]);
-
-                forAll(ptICells, pIC)
-                {
-                    const label cellI(ptICells[pIC]);
-
-                    if(findIndex(realCellsFoundInRange, cellI) == -1)
-                    {
-                        realCellsFoundInRange.append(cellI);
-                    }
-                }
-            }
-        }
-    }
-
-    forAll(referredInteractionList, rIL)
-    {
-        const vectorList& refCellPoints =
-            referredInteractionList[rIL].vertexPositions();
-
-        forAll(refCellPoints, rCP)
-        {
-            if (magSqr(ptP - refCellPoints[rCP]) <= rCutMaxSqr)
-            {
-                if(findIndex(referredCellsFoundInRange, rIL) == -1)
-                {
-                    referredCellsFoundInRange.append(rIL);
-                }
-            }
-        }
-    }
-}
diff --git a/src/lagrangian/molecule/moleculeCloud/moleculeCloudBuildDirectInteractionList.H b/src/lagrangian/molecule/moleculeCloud/moleculeCloudBuildDirectInteractionList.H
deleted file mode 100755
index c5f2d887bf..0000000000
--- a/src/lagrangian/molecule/moleculeCloud/moleculeCloudBuildDirectInteractionList.H
+++ /dev/null
@@ -1,188 +0,0 @@
-Info << nl << "Building list of direct interaction neighbours" << endl;
-
-forAll (mesh_.points(), p)
-{
-    forAll(mesh_.faces(), f)
-    {
-        if(testPointFaceDistance(p, f))
-        {
-            const labelList& pCells(mesh_.pointCells()[p]);
-
-            const label cellO(mesh_.faceOwner()[f]);
-
-            const label cellN(mesh_.faceNeighbour()[f]);
-
-            forAll(pCells, pC)
-            {
-                const label cellI(pCells[pC]);
-
-                // cells are not added to their own DIL
-
-                if (cellO > cellI)
-                {
-                    if (findIndex(directInteractionList[cellI], cellO) == -1)
-                    {
-                        directInteractionList[cellI].append(cellO);
-                    }
-                }
-
-                if (cellI > cellO)
-                {
-                    if (findIndex(directInteractionList[cellO], cellI) == -1)
-                    {
-                        directInteractionList[cellO].append(cellI);
-                    }
-                }
-
-                if (mesh_.isInternalFace(f))
-                {
-                    // boundary faces will not have neighbour information
-
-                    if (cellN > cellI)
-                    {
-                        if
-                        (
-                             findIndex(directInteractionList[cellI], cellN)
-                          == -1
-                        )
-                        {
-                            directInteractionList[cellI].append(cellN);
-                        }
-                    }
-
-                    if (cellI > cellN)
-                    {
-                        if
-                        (
-                            findIndex(directInteractionList[cellN], cellI)
-                         == -1
-                        )
-                        {
-                            directInteractionList[cellN].append(cellI);
-                        }
-                    }
-                }
-            }
-        }
-    }
-}
-
-label edgeJIndex;
-
-forAll (mesh_.edges(), edgeIIndex)
-{
-    const edge& eI(mesh_.edges()[edgeIIndex]);
-
-    for
-    (
-        edgeJIndex = edgeIIndex + 1;
-        edgeJIndex != mesh_.edges().size();
-        ++edgeJIndex
-    )
-    {
-        const edge& eJ(mesh_.edges()[edgeJIndex]);
-
-        if (testEdgeEdgeDistance(eI, eJ))
-        {
-            const labelList& eICells(mesh_.edgeCells()[edgeIIndex]);
-
-            const labelList& eJCells(mesh_.edgeCells()[edgeJIndex]);
-
-            forAll(eICells, eIC)
-            {
-                const label cellI(eICells[eIC]);
-
-                forAll(eJCells, eJC)
-                {
-                    const label cellJ(eJCells[eJC]);
-
-                    if (cellJ > cellI)
-                    {
-                        if
-                        (
-                            findIndex(directInteractionList[cellI], cellJ)
-                         == -1
-                        )
-                        {
-                            directInteractionList[cellI].append(cellJ);
-                        }
-                    }
-
-                    if (cellI > cellJ)
-                    {
-                        if
-                        (
-                            findIndex(directInteractionList[cellJ], cellI)
-                         == -1
-                        )
-                        {
-                            directInteractionList[cellJ].append(cellI);
-                        }
-                    }
-                }
-            }
-        }
-    }
-}
-
-// label pointJIndex;
-//
-// forAll (mesh_.points(), pointIIndex)
-// {
-//     const point& ptI
-//     (
-//         mesh_.points()[pointIIndex]
-//     );
-//
-//     for
-//     (
-//         pointJIndex = pointIIndex;
-//         pointJIndex != mesh_.points().size();
-//         ++pointJIndex
-//     )
-//     {
-//         const point& ptJ
-//         (
-//             mesh_.points()[pointJIndex]
-//         );
-//
-//         if (magSqr(ptI - ptJ) <= rCutMaxSqr)
-//         {
-//             const labelList& ptICells
-//             (
-//                 mesh_.pointCells()[pointIIndex]
-//             );
-//
-//             const labelList& ptJCells
-//             (
-//                 mesh_.pointCells()[pointJIndex]
-//             );
-//
-//             forAll(ptICells, pIC)
-//             {
-//                 const label cellI(ptICells[pIC]);
-//
-//                 forAll(ptJCells, pJC)
-//                 {
-//                     const label cellJ(ptJCells[pJC]);
-//
-//                     if (cellJ > cellI)
-//                     {
-//                         if(findIndex(directInteractionList[cellI], cellJ) == -1)
-//                         {
-//                             directInteractionList[cellI].append(cellJ);
-//                         }
-//                     }
-//
-//                     if (cellI > cellJ)
-//                     {
-//                         if(findIndex(directInteractionList[cellJ], cellI) == -1)
-//                         {
-//                             directInteractionList[cellJ].append(cellI);
-//                         }
-//                     }
-//                 }
-//             }
-//         }
-//     }
-// }
diff --git a/src/lagrangian/molecule/moleculeCloud/moleculeCloudBuildReferredInteractionList.H b/src/lagrangian/molecule/moleculeCloud/moleculeCloudBuildReferredInteractionList.H
deleted file mode 100755
index 5e1de72062..0000000000
--- a/src/lagrangian/molecule/moleculeCloud/moleculeCloudBuildReferredInteractionList.H
+++ /dev/null
@@ -1,1285 +0,0 @@
-Info << nl << "Building list of referred interaction neighbours" << endl;
-
-labelListList processorPatchSegmentMapping
-(
-    mesh_.globalData().processorPatches().size()
-);
-
-List<vectorList> allNeighbourFaceCentres
-(
-    mesh_.globalData().processorPatches().size()
-);
-
-List<vectorList> allNeighbourFaceAreas
-(
-    mesh_.globalData().processorPatches().size()
-);
-
-label nUndecomposedPatches = 0;
-
-if (Pstream::parRun())
-{
-    dictionary patchDictionary;
-
-    DynamicList<word> patchNames;
-
-//     IOobject undecomposedBoundaryHeader
-//     (
-//         "undecomposedBoundary",
-//         mesh_.time().constant(),
-//         polyMesh::meshSubDir,
-//         mesh_,
-//         IOobject::MUST_READ,
-//         IOobject::NO_WRITE,
-//         false
-//     );
-
-    Time undecomposedTime
-    (
-        Time::controlDictName,
-        mesh_.time().rootPath(),
-        mesh_.time().caseName().path()
-    );
-
-    IOobject undecomposedBoundaryHeader
-    (
-        "boundary",
-        undecomposedTime.constant(),
-        polyMesh::meshSubDir,
-        undecomposedTime,
-        IOobject::MUST_READ,
-        IOobject::NO_WRITE,
-        false
-    );
-
-    if (undecomposedBoundaryHeader.headerOk())
-    {
-        polyBoundaryMeshEntries undecomposedPatchEntries
-        (
-            undecomposedBoundaryHeader
-        );
-
-        forAll(undecomposedPatchEntries, patchi)
-        {
-            patchNames.append
-            (
-                undecomposedPatchEntries[patchi].keyword()
-            );
-
-            patchDictionary.add
-            (
-                undecomposedPatchEntries[patchi]
-            );
-        }
-    }
-    else
-    {
-        FatalErrorIn
-        (
-            "moleculeCloudBuildCellInteractionLists.C"
-        )
-            << nl << "unable to read undecomposed boundary file from "
-            "constant/polyMesh" << nl
-            << abort(FatalError);
-    }
-
-    labelIOList faceProcAddressing
-    (
-        IOobject
-        (
-            "faceProcAddressing",
-            mesh_.time().constant(),
-            polyMesh::meshSubDir,
-            mesh_,
-            IOobject::MUST_READ,
-            IOobject::NO_WRITE,
-            false
-        )
-    );
-
-    labelList procPatches(mesh_.globalData().processorPatches());
-
-    nUndecomposedPatches = patchNames.size();
-
-    // processorPatchSegmentMapping works by mapping the original patch
-    // and half that a face on a processor patch was on before decomposition.
-    // This creates a patch segment for each half of each original (cyclic)
-    // patch which can be assessed separately.
-    // There are n = patchNames.size() original patches, k = 0 to n-1.
-    // The mapping is:
-    // value = 0:  originally an internal face
-    // value = k, was originally on the on the patch k-1, 1st half
-    // value = -k, was originally on the on the patch k-1, 2nd half
-
-    forAll(procPatches,pP)
-    {
-        const processorPolyPatch& patch =
-            refCast<const processorPolyPatch>
-            (
-                mesh_.boundaryMesh()[procPatches[pP]]
-            );
-
-        labelList& procPatchSegMap = processorPatchSegmentMapping[pP];
-
-        procPatchSegMap.setSize(patch.size());
-
-        forAll (patch, pI)
-        {
-            label decomposedMeshFace = patch.start() + pI;
-
-            label faceProcAdd = faceProcAddressing[decomposedMeshFace];
-
-            label globalFace = abs(faceProcAdd)-1;
-
-//             Pout << "Patch index: " << pI
-//                     << " " << patch[pI]
-//                     << " Mesh index: " << decomposedMeshFace
-//                     << " faceProcAdd: " << faceProcAdd
-//                     << " globalFace:" << globalFace << endl;
-
-            label minStart = -1;
-
-            forAll(patchNames, pN)
-            {
-                if (patchDictionary.found(patchNames[pN]))
-                {
-                    const dictionary& patchDict =
-                        patchDictionary.subDict(patchNames[pN]);
-
-//                     word faceName(patchNames[pN]);
-                    label startFace(readLabel(patchDict.lookup("startFace")));
-                    label nFaces(readLabel(patchDict.lookup("nFaces")));
-
-                    if (minStart < 0 || startFace < minStart)
-                    {
-                        minStart = startFace;
-                    }
-
-                    if
-                    (
-                        globalFace >= startFace
-                     && globalFace < startFace + nFaces/2
-                    )
-                    {
-                        procPatchSegMap[pI] = pN + 1;
-                    }
-                    else if
-                    (
-                        globalFace >= startFace + nFaces/2
-                     && globalFace < startFace + nFaces
-                    )
-                    {
-                        procPatchSegMap[pI] = -(pN + 1);
-                    }
-                }
-            }
-
-            if (globalFace < minStart)
-            {
-                procPatchSegMap[pI] = 0;
-            }
-        }
-    }
-
-    forAll(procPatches,pP)
-    {
-        const processorPolyPatch& patch =
-            refCast<const processorPolyPatch>
-            (
-                mesh_.boundaryMesh()[procPatches[pP]]
-            );
-
-        {
-            OPstream toNeighbProc
-            (
-                Pstream::blocking,
-                patch.neighbProcNo(),
-                + 2*(sizeof(label) + patch.size()*sizeof(vector))
-            );
-
-            toNeighbProc
-                << patch.faceCentres()
-                << patch.faceAreas();
-
-//             Pout << "sending face info to processor "
-//                 << patch.neighbProcNo() << ", size = "
-//                 << patch.size() << endl;
-        }
-    }
-
-    forAll(procPatches,pP)
-    {
-        const processorPolyPatch& patch =
-            refCast<const processorPolyPatch>
-            (
-                mesh_.boundaryMesh()[procPatches[pP]]
-            );
-
-        vectorList& neighbFaceCentres = allNeighbourFaceCentres[pP];
-
-        neighbFaceCentres.setSize(patch.size());
-
-        vectorList& neighbFaceAreas = allNeighbourFaceAreas[pP];
-
-        neighbFaceAreas.setSize(patch.size());
-
-        {
-            IPstream fromNeighbProc
-            (
-                Pstream::blocking,
-                patch.neighbProcNo(),
-                2*(sizeof(label) + patch.size()*sizeof(vector))
-            );
-            fromNeighbProc
-                >> neighbFaceCentres
-                >> neighbFaceAreas;
-
-//             Pout << "receiving face info from processor "
-//                 << patch.neighbProcNo() << ", size = "
-//                 << patch.size() << endl;
-        }
-    }
-
-    // *************************************************************
-    // Tests that all processor patch segments from different
-    // original patches prior to decomposition produce the same
-    // transform. Check before 1st iteration.
-    // *************************************************************
-
-    forAll(procPatches,pP)
-    {
-        const processorPolyPatch& patch =
-            refCast<const processorPolyPatch>
-            (
-                mesh_.boundaryMesh()[procPatches[pP]]
-            );
-
-        const vectorList& neighbFaceCentres = allNeighbourFaceCentres[pP];
-
-        const vectorList& neighbFaceAreas = allNeighbourFaceAreas[pP];
-
-        label nUP;
-
-        for
-        (
-            nUP = -nUndecomposedPatches;
-            nUP <= nUndecomposedPatches;
-            nUP++
-        )
-        {
-            DynamicList<vector> refOff;
-
-            DynamicList<tensor> refTrans;
-
-            forAll (patch, faceI)
-            {
-                if (processorPatchSegmentMapping[pP][faceI] == nUP)
-                {
-                    referredCell testRefCell
-                    (
-                        mesh_,
-                        -1,
-                        -1,
-                        patch.faceCentres()[faceI],
-                        neighbFaceCentres[faceI],
-                        patch.faceNormals()[faceI],
-                        neighbFaceAreas[faceI]
-                       /(mag(neighbFaceAreas[faceI]) + VSMALL)
-                    );
-
-                    refOff.append(testRefCell.offset());
-
-                    refTrans.append(testRefCell.rotation());
-                }
-            }
-
-            refOff.shrink();
-
-            refTrans.shrink();
-
-            if (refOff.size())
-            {
-                if
-                (
-                    sum(mag(refOff-refOff[0]))/refOff.size() > transTol
-                 || sum(mag(refTrans-refTrans[0]))/refTrans.size() > transTol
-                )
-                {
-                    FatalErrorIn
-                    (
-                        "moleculeCloud::buildCellInteractionLists"
-                    )
-                        << nl << "Face pairs on patch "
-                        << patch.name()
-                        << ", segment " << patchNames[nUP]
-                        << " do not give the same referring "
-                        << " transformations to within tolerance of "
-                        << transTol << nl
-                        << " Referring offsets:" << refOff << nl
-                        << " Average sum of mag difference: "
-                        << sum(mag(refOff-refOff[0]))/refOff.size() << nl
-                        << " Referring transforms:" << refTrans << nl
-                        << " Average sum of mag difference: "
-                        << sum(mag(refTrans-refTrans[0]))/refTrans.size()
-                        << nl << abort(FatalError);
-                }
-            }
-        }
-    }
-}
-
-label cellsReferredThisIteration = 1;
-
-label iterationNo = 0;
-
-DynamicList<label> realCellsWithinRCutMaxOfAnyReferringPatch;
-
-while(cellsReferredThisIteration)
-{
-    label refIntListStartSize = referredInteractionList.size();
-
-    forAll (mesh_.boundaryMesh(), patchI)
-    {
-        // Treat local cyclics on each processor before processor boundaries.
-        // Separate treatment allows the serial version to run transparently.
-
-        if (mesh_.boundaryMesh()[patchI].type() == "cyclic")
-        {
-            const cyclicPolyPatch& patch =
-                    refCast<const cyclicPolyPatch>
-            (
-                mesh_.boundaryMesh()[patchI]
-            );
-
-            if(patch.size())
-            {
-    //             Pout << patch << endl;
-
-                if (iterationNo == 0)
-                {
-                    // Tests that all combinations of face pairs produce the
-                    // same transform.  Only check on 1st iteration.
-
-                    label faceL;
-                    // A face in the 1st half of the patch
-
-                    label faceM;
-                    // Face corresponding to faceL in the 2nd half of the
-                    // patch. Assumes correct face ordering.
-
-                    vectorList refOff(patch.size()/2);
-
-                    List<tensor> refTrans(patch.size()/2);
-
-                    for
-                    (
-                        faceL = 0, faceM = patch.size()/2;
-                        faceL < patch.size()/2;
-                        faceL++, faceM++
-                    )
-                    {
-                        referredCell testRefCell
-                        (
-                            mesh_,
-                            -1,
-                            -1,
-                            patch.faceCentres()[faceL],
-                            patch.faceCentres()[faceM],
-                            patch.faceNormals()[faceL],
-                            patch.faceNormals()[faceM]
-                        );
-
-                        refOff[faceL] = testRefCell.offset();
-
-                        refTrans[faceL] = testRefCell.rotation();
-                    }
-
-                    if
-                    (
-                        sum(mag(refOff - refOff[0]))/(patch.size()/2)
-                      > transTol
-                     || sum(mag(refTrans - refTrans[0]))/(patch.size()/2)
-                      > transTol
-                    )
-                    {
-                        FatalErrorIn
-                        (
-                            "moleculeCloud::buildCellInteractionLists"
-                        )
-                            << nl << "Face pairs on patch "
-                            << patch.name()
-                            << " do not give the same referring "
-                            << " transformations to within tolerance of "
-                            << transTol << nl
-                            << " Referring offsets:" << refOff << nl
-                            << " Average sum of mag difference: "
-                            << sum(mag(refOff-refOff[0]))/refOff.size() << nl
-                            << " Referring transforms:" << refTrans << nl
-                            << " Average sum of mag difference: "
-                            << sum(mag(refTrans-refTrans[0]))/refTrans.size()
-                            << nl << abort(FatalError);
-                    }
-                }
-
-                // ***********************************************************
-                // 1st half of face list - 1st side of boundary
-                // ***********************************************************
-
-                label faceI;
-
-                DynamicList<label> meshFacesOnThisSegment;
-
-                for (faceI = 0; faceI < patch.size()/2; faceI++)
-                {
-                    // unable to use the normal accessors for the polyPatch
-                    // because points on separate halves need used separately
-
-                    meshFacesOnThisSegment.append(faceI + patch.start());
-                }
-
-                meshFacesOnThisSegment.shrink();
-
-                DynamicList<label> meshEdgesOnThisSegment;
-
-                DynamicList<label> meshPointsOnThisSegment;
-
-                forAll(meshFacesOnThisSegment, mFOTS)
-                {
-                    const label segFace = meshFacesOnThisSegment[mFOTS];
-
-                    const labelList& faceEdges = mesh_.faceEdges()[segFace];
-
-                    forAll (faceEdges, fE)
-                    {
-                        const label faceEdge(faceEdges[fE]);
-
-                        if (findIndex(meshEdgesOnThisSegment, faceEdge) == -1)
-                        {
-                            meshEdgesOnThisSegment.append(faceEdge);
-                        }
-                    }
-
-                    const face& facePoints(mesh_.faces()[segFace]);
-
-                    forAll (facePoints, fP)
-                    {
-                        const label facePoint(facePoints[fP]);
-
-                        if
-                        (
-                            findIndex(meshPointsOnThisSegment, facePoint)
-                         == -1
-                        )
-                        {
-                            meshPointsOnThisSegment.append(facePoint);
-                        }
-                    }
-                }
-
-                meshEdgesOnThisSegment.shrink();
-
-                meshPointsOnThisSegment.shrink();
-
-                if (iterationNo == 0)
-                {
-                    // Assessing real cells in range is only required on
-                    // the 1st iteration because they do not change from
-                    // iteration to iteration.
-
-                    labelList realCellsFoundInRange
-                    (
-                        realCellsInRangeOfSegment
-                        (
-                            meshFacesOnThisSegment,
-                            meshEdgesOnThisSegment,
-                            meshPointsOnThisSegment
-                        )
-                    );
-
-                    forAll(realCellsFoundInRange,cFIR)
-                    {
-                        const label realCell = realCellsFoundInRange[cFIR];
-
-                        referredCell cellToRefer
-                        (
-                            mesh_,
-                            Pstream::myProcNo(),
-                            realCell,
-                            patch.faceCentres()[0],
-                            patch.faceCentres()[patch.size()/2],
-                            patch.faceNormals()[0],
-                            patch.faceNormals()[patch.size()/2]
-                        );
-
-                        // Test all existing referred and real cells to
-                        // check duplicates are not being made or cells
-                        // aren't being referred back onto themselves
-
-                        bool addCellToRefer = true;
-
-                        // Check if cellToRefer is an existing referred cell
-
-                        forAll(referredInteractionList, rIL)
-                        {
-                            if
-                            (
-                                cellToRefer.duplicate
-                                (
-                                    referredInteractionList[rIL]
-                                )
-                            )
-                            {
-                                addCellToRefer = false;
-
-                                break;
-                            }
-                        }
-
-                        // Check for cellToRefer being referred back
-                        // ontop of a real cell
-
-                        if
-                        (
-                            cellToRefer.duplicate
-                            (
-                                Pstream::myProcNo(),
-                                mesh_.nCells()
-                            )
-                        )
-                        {
-                            addCellToRefer = false;
-                        }
-
-                        if (addCellToRefer)
-                        {
-                            referredInteractionList.append(cellToRefer);
-                        }
-
-                        // add real cells found in range of cyclic patch
-                        // to whole mesh list
-
-                        if
-                        (
-                            findIndex
-                            (
-                                realCellsWithinRCutMaxOfAnyReferringPatch,
-                                realCell
-                            ) == -1
-                        )
-                        {
-                            realCellsWithinRCutMaxOfAnyReferringPatch.append
-                            (
-                                realCell
-                            );
-                        }
-                    }
-                }
-
-                referredInteractionList.shrink();
-
-                labelList referredCellsFoundInRange
-                (
-                    referredCellsInRangeOfSegment
-                    (
-                        referredInteractionList,
-                        meshFacesOnThisSegment,
-                        meshEdgesOnThisSegment,
-                        meshPointsOnThisSegment
-                    )
-                );
-
-                forAll(referredCellsFoundInRange,cFIR)
-                {
-                    referredCell& existingRefCell = referredInteractionList
-                    [
-                        referredCellsFoundInRange[cFIR]
-                    ];
-
-                    referredCell cellToReRefer = existingRefCell.reRefer
-                    (
-                        patch.faceCentres()[0],
-                        patch.faceCentres()[patch.size()/2],
-                        patch.faceNormals()[0],
-                        patch.faceNormals()[patch.size()/2]
-                    );
-
-                    // Test all existing referred and real cells to check
-                    // duplicates are not being made or cells aren't being
-                    // referred back onto themselves
-
-                    bool addCellToReRefer = true;
-
-                    // Check if cellToRefer is an existing referred cell
-
-                    forAll(referredInteractionList, rIL)
-                    {
-                        if
-                        (
-                            cellToReRefer.duplicate
-                            (
-                                referredInteractionList[rIL]
-                            )
-                        )
-                        {
-                            addCellToReRefer = false;
-
-                            break;
-                        }
-                    }
-
-                    // Check for cellToRefer being referred back
-                    // ontop of a real cell
-
-                    if
-                    (
-                        cellToReRefer.duplicate
-                        (
-                            Pstream::myProcNo(),
-                            mesh_.nCells()
-                        )
-                    )
-                    {
-                        addCellToReRefer = false;
-                    }
-
-                    if(addCellToReRefer)
-                    {
-                        referredInteractionList.append(cellToReRefer);
-                    }
-                }
-
-                // ***********************************************************
-                // 2nd half of face list - 2nd side of boundary
-                // ***********************************************************
-
-                meshFacesOnThisSegment.clear();
-
-                for (faceI = patch.size()/2; faceI < patch.size(); faceI++)
-                {
-                    // unable to use the normal accessors for the polyPatch
-                    // because points on separate halves need used separately
-
-                    meshFacesOnThisSegment.append(faceI + patch.start());
-                }
-
-                meshFacesOnThisSegment.shrink();
-
-                meshEdgesOnThisSegment.clear();
-
-                meshPointsOnThisSegment.clear();
-
-                forAll(meshFacesOnThisSegment, mFOTS)
-                {
-                    const label segFace = meshFacesOnThisSegment[mFOTS];
-
-                    const labelList& faceEdges = mesh_.faceEdges()[segFace];
-
-                    forAll (faceEdges, fE)
-                    {
-                        const label faceEdge(faceEdges[fE]);
-
-                        if(findIndex(meshEdgesOnThisSegment, faceEdge) == -1)
-                        {
-                            meshEdgesOnThisSegment.append(faceEdge);
-                        }
-                    }
-
-                    const face& facePoints(mesh_.faces()[segFace]);
-
-                    forAll (facePoints, fP)
-                    {
-                        const label facePoint(facePoints[fP]);
-
-                        if
-                        (
-                           findIndex(meshPointsOnThisSegment, facePoint)
-                         == -1
-                        )
-                        {
-                            meshPointsOnThisSegment.append(facePoint);
-                        }
-                    }
-                }
-
-                meshEdgesOnThisSegment.shrink();
-
-                meshPointsOnThisSegment.shrink();
-
-                if (iterationNo == 0)
-                {
-                    // Assessing real cells in range is only required on
-                    // the 1st iteration because they do not change from
-                    // iteration to iteration.
-
-                    labelList realCellsFoundInRange
-                    (
-                        realCellsInRangeOfSegment
-                        (
-                            meshFacesOnThisSegment,
-                            meshEdgesOnThisSegment,
-                            meshPointsOnThisSegment
-                        )
-                    );
-
-                    forAll(realCellsFoundInRange,cFIR)
-                    {
-                        const label realCell = realCellsFoundInRange[cFIR];
-
-                        referredCell cellToRefer
-                        (
-                            mesh_,
-                            Pstream::myProcNo(),
-                            realCell,
-                            patch.faceCentres()[patch.size()/2],
-                            patch.faceCentres()[0],
-                            patch.faceNormals()[patch.size()/2],
-                            patch.faceNormals()[0]
-                        );
-
-                        // Test all existing referred and real cells to
-                        // check duplicates are not being made or cells
-                        // aren't being referred back onto themselves
-
-                        bool addCellToRefer = true;
-
-                        // Check if cellToRefer is an existing referred cell
-
-                        forAll(referredInteractionList, rIL)
-                        {
-                            if
-                            (
-                                cellToRefer.duplicate
-                                (
-                                    referredInteractionList[rIL]
-                                )
-                            )
-                            {
-                                addCellToRefer = false;
-
-                                break;
-                            }
-                        }
-
-                        // Check for cellToRefer being referred back
-                        // ontop of a real cell
-
-                        if
-                        (
-                            cellToRefer.duplicate
-                            (
-                                Pstream::myProcNo(),
-                                mesh_.nCells()
-                            )
-                        )
-                        {
-                            addCellToRefer = false;
-                        }
-
-                        if (addCellToRefer)
-                        {
-                            referredInteractionList.append(cellToRefer);
-                        }
-
-                        // add real cells found in range of cyclic patch
-                        // to whole mesh list
-
-                        if
-                        (
-                            findIndex
-                            (
-                                realCellsWithinRCutMaxOfAnyReferringPatch,
-                                realCell
-                            ) == -1
-                        )
-                        {
-                            realCellsWithinRCutMaxOfAnyReferringPatch.append
-                            (
-                                realCell
-                            );
-                        }
-                    }
-                }
-
-                referredInteractionList.shrink();
-
-                referredCellsFoundInRange = referredCellsInRangeOfSegment
-                (
-                    referredInteractionList,
-                    meshFacesOnThisSegment,
-                    meshEdgesOnThisSegment,
-                    meshPointsOnThisSegment
-                );
-
-                forAll(referredCellsFoundInRange,cFIR)
-                {
-                    referredCell& existingRefCell = referredInteractionList
-                    [
-                        referredCellsFoundInRange[cFIR]
-                    ];
-
-                    referredCell cellToReRefer = existingRefCell.reRefer
-                    (
-                        patch.faceCentres()[patch.size()/2],
-                        patch.faceCentres()[0],
-                        patch.faceNormals()[patch.size()/2],
-                        patch.faceNormals()[0]
-                    );
-
-                    // Test all existing referred and real cells to check
-                    // duplicates are not being made or cells aren't being
-                    // referred back onto themselves
-
-                    bool addCellToReRefer = true;
-
-                    // Check if cellToRefer is an existing referred cell
-
-                    forAll(referredInteractionList, rIL)
-                    {
-                        if
-                        (
-                            cellToReRefer.duplicate
-                            (
-                                referredInteractionList[rIL]
-                            )
-                        )
-                        {
-                            addCellToReRefer = false;
-
-                            break;
-                        }
-                    }
-
-                    // Check for cellToRefer being referred back
-                    // ontop of a real cell
-
-                    if
-                    (
-                        cellToReRefer.duplicate
-                        (
-                            Pstream::myProcNo(),
-                            mesh_.nCells()
-                        )
-                    )
-                    {
-                        addCellToReRefer = false;
-                    }
-
-                    if (addCellToReRefer)
-                    {
-                        referredInteractionList.append(cellToReRefer);
-                    }
-                }
-            }
-        }
-    }
-
-    if (Pstream::parRun())
-    {
-        labelList procPatches(mesh_.globalData().processorPatches());
-
-        forAll(procPatches,pP)
-        {
-            const processorPolyPatch& patch =
-                refCast<const processorPolyPatch>
-                (
-                    mesh_.boundaryMesh()[procPatches[pP]]
-                );
-
-            DynamicList<referredCell> referredCellsToTransfer;
-
-            const vectorList& neighbFaceCentres = allNeighbourFaceCentres[pP];
-
-            const vectorList& neighbFaceAreas = allNeighbourFaceAreas[pP];
-
-            label nUP;
-
-            for
-            (
-                nUP = -nUndecomposedPatches;
-                nUP <= nUndecomposedPatches;
-                nUP++
-            )
-            {
-                // faceT is used to specify one face on this patch segment that
-                // will be used to calculate the transformation values.  All
-                // faces are guaranteed to produce the same transform because
-                // of the checks carried out at the start of the function.
-                // Setting to -1 until the 1st face on this segment is found.
-
-                label faceT = -1;
-
-                DynamicList<label> meshFacesOnThisSegment;
-
-                forAll (patch, faceI)
-                {
-                    if (processorPatchSegmentMapping[pP][faceI] == nUP)
-                    {
-                        if (faceT == -1)
-                        {
-                            faceT = faceI;
-                        }
-
-                        meshFacesOnThisSegment.append(faceI + patch.start());
-                    }
-                }
-
-                meshFacesOnThisSegment.shrink();
-
-                DynamicList<label> meshEdgesOnThisSegment;
-
-                DynamicList<label> meshPointsOnThisSegment;
-
-                forAll(meshFacesOnThisSegment, mFOTS)
-                {
-                    const label segFace = meshFacesOnThisSegment[mFOTS];
-
-                    const labelList& faceEdges = mesh_.faceEdges()[segFace];
-
-                    forAll (faceEdges, fE)
-                    {
-                        const label faceEdge(faceEdges[fE]);
-
-                        if(findIndex(meshEdgesOnThisSegment, faceEdge) == -1)
-                        {
-                            meshEdgesOnThisSegment.append(faceEdge);
-                        }
-                    }
-
-                    const face& facePoints(mesh_.faces()[segFace]);
-
-                    forAll (facePoints, fP)
-                    {
-                        const label facePoint(facePoints[fP]);
-
-                        if
-                        (
-                           findIndex(meshPointsOnThisSegment, facePoint)
-                         == -1
-                        )
-                        {
-                            meshPointsOnThisSegment.append(facePoint);
-                        }
-                    }
-                }
-
-                meshEdgesOnThisSegment.shrink();
-
-                meshPointsOnThisSegment.shrink();
-
-                if (meshFacesOnThisSegment.size())
-                {
-                    if (faceT == -1)
-                    {
-                        FatalErrorIn
-                        (
-                            "moleculeCloudBuildReferredInteractionList.H"
-                        )
-                        << nl << "faceT == -1 encountered but "
-                        << meshFacesOnThisSegment.size()
-                        << " faces found on patch segment."
-                        << abort(FatalError);
-                    }
-
-                    if (iterationNo == 0)
-                    {
-                        // Assessing real cells in range is only required on
-                        // the 1st iteration because they do not change from
-                        // iteration to iteration.
-
-                        labelList realCellsFoundInRange
-                        (
-                            realCellsInRangeOfSegment
-                            (
-                                meshFacesOnThisSegment,
-                                meshEdgesOnThisSegment,
-                                meshPointsOnThisSegment
-                            )
-                        );
-
-                        forAll(realCellsFoundInRange,cFIR)
-                        {
-                            const label realCell = realCellsFoundInRange[cFIR];
-
-                            referredCell cellToRefer
-                            (
-                                mesh_,
-                                Pstream::myProcNo(),
-                                realCell,
-                                patch.faceCentres()[faceT],
-                                neighbFaceCentres[faceT],
-                                patch.faceNormals()[faceT],
-                                neighbFaceAreas[faceT]
-                               /(mag(neighbFaceAreas[faceT]) + VSMALL)
-                            );
-
-                            referredCellsToTransfer.append(cellToRefer);
-
-                            // add real cells found in range of processor patch
-                            // to whole mesh list
-
-                            if
-                            (
-                                findIndex
-                                (
-                                    realCellsWithinRCutMaxOfAnyReferringPatch,
-                                    realCell
-                                )
-                             == -1
-                            )
-                            {
-                                realCellsWithinRCutMaxOfAnyReferringPatch.append
-                                (
-                                    realCell
-                                );
-                            }
-                        }
-                    }
-
-                    referredInteractionList.shrink();
-
-                    labelList referredCellsFoundInRange
-                    (
-                        referredCellsInRangeOfSegment
-                        (
-                            referredInteractionList,
-                            meshFacesOnThisSegment,
-                            meshEdgesOnThisSegment,
-                            meshPointsOnThisSegment
-                        )
-                    );
-
-                    forAll(referredCellsFoundInRange,cFIR)
-                    {
-                        referredCell& existingRefCell
-                            = referredInteractionList[referredCellsFoundInRange[cFIR]];
-
-                        referredCell cellToReRefer = existingRefCell.reRefer
-                        (
-                            patch.faceCentres()[faceT],
-                            neighbFaceCentres[faceT],
-                            patch.faceNormals()[faceT],
-                            neighbFaceAreas[faceT]
-                           /(mag(neighbFaceAreas[faceT]) + VSMALL)
-                        );
-
-                        referredCellsToTransfer.append(cellToReRefer);
-                    }
-                }
-            }
-
-            referredCellsToTransfer.shrink();
-
-            // Send these cells to the neighbouring processor.
-
-            {
-                OPstream toNeighbProc
-                (
-                    Pstream::blocking,
-                    patch.neighbProcNo()
-                );
-
-//                 Pout << "Processor " << Pstream::myProcNo()
-//                     << " sending to " << patch.neighbProcNo()
-//                     << nl << referredCellsToTransfer << endl;
-
-                toNeighbProc << referredCellsToTransfer;
-            }
-        }
-
-        forAll(procPatches,pP)
-        {
-            const processorPolyPatch& patch =
-                refCast<const processorPolyPatch>
-            (
-                mesh_.boundaryMesh()[procPatches[pP]]
-            );
-
-
-            // Receive the cells from neighbour
-
-            List<referredCell> referredCellsFromNeighbour(patch.size());
-
-            {
-                IPstream fromNeighbProc
-                (
-                    Pstream::blocking,
-                    patch.neighbProcNo()
-                );
-
-                fromNeighbProc >> referredCellsFromNeighbour;
-
-//                 Pout << "Processor " << Pstream::myProcNo()
-//                     << " receiving from " << patch.neighbProcNo()
-//                     << nl << referredCellsFromNeighbour << endl;
-            }
-
-            // Check to see if they are duplicates, if not append
-            // them to the referredInteractionList
-
-            forAll(referredCellsFromNeighbour,rCFN)
-            {
-                referredCell& cellToRefer
-                    = referredCellsFromNeighbour[rCFN];
-
-                // Test all existing referred and real cells to check duplicates
-                // are not being made or cells aren't being referred back onto
-                // themselves
-
-                bool addCellToRefer = true;
-
-                // Check if cellToRefer is an existing referred cell
-
-                forAll(referredInteractionList, rIL)
-                {
-                    if(cellToRefer.duplicate(referredInteractionList[rIL]))
-                    {
-                        addCellToRefer = false;
-
-                        break;
-                    }
-                }
-
-                // Check for cellToRefer being referred back ontop of a real cell
-
-                if
-                (
-                    cellToRefer.duplicate
-                    (
-                        Pstream::myProcNo(),
-                        mesh_.nCells()
-                    )
-                )
-                {
-                    addCellToRefer = false;
-                }
-
-                if (addCellToRefer)
-                {
-                    referredInteractionList.append(cellToRefer);
-                }
-            }
-        }
-    }
-
-    if (iterationNo == 0)
-    {
-        // record all real cells in range of any referring patch (cyclic or
-        // processor) on the first iteration when the real cells are evaluated.
-
-        realCellsWithinRCutMaxOfAnyReferringPatch_.transfer
-        (
-            realCellsWithinRCutMaxOfAnyReferringPatch.shrink()
-        );
-
-        // construct {faces, edges, points}WithinRCutMaxOfAnyReferringPatch_
-
-        DynamicList<label> realFacesWithinRCutMaxOfAnyReferringPatch;
-
-        DynamicList<label> realEdgesWithinRCutMaxOfAnyReferringPatch;
-
-        DynamicList<label> realPointsWithinRCutMaxOfAnyReferringPatch;
-
-        forAll(realCellsWithinRCutMaxOfAnyReferringPatch_, rCWR)
-        {
-            const label realCell
-            (
-                realCellsWithinRCutMaxOfAnyReferringPatch_[rCWR]
-            );
-
-            const labelList& rCFaces
-            (
-                mesh_.cells()[realCell]
-            );
-
-            forAll(rCFaces, rCF)
-            {
-                const label f(rCFaces[rCF]);
-
-                if
-                (
-                    findIndex(realFacesWithinRCutMaxOfAnyReferringPatch,f)
-                 == -1
-                )
-                {
-                    realFacesWithinRCutMaxOfAnyReferringPatch.append(f);
-                }
-            }
-
-            const labelList& rCEdges
-            (
-                mesh_.cellEdges()[realCell]
-            );
-
-            forAll(rCEdges, rCE)
-            {
-                const label e(rCEdges[rCE]);
-
-                if
-                (
-                    findIndex(realEdgesWithinRCutMaxOfAnyReferringPatch,e)
-                 == -1
-                )
-                {
-                    realEdgesWithinRCutMaxOfAnyReferringPatch.append(e);
-                }
-            }
-
-            const labelList& rCPoints
-            (
-                mesh_.cellPoints()[realCell]
-            );
-
-            forAll(rCPoints, rCP)
-            {
-                const label p(rCPoints[rCP]);
-
-                if
-                (
-                    findIndex(realPointsWithinRCutMaxOfAnyReferringPatch,p)
-                 == -1
-                )
-                {
-                    realPointsWithinRCutMaxOfAnyReferringPatch.append(p);
-                }
-            }
-        }
-
-        realFacesWithinRCutMaxOfAnyReferringPatch_.transfer
-        (
-            realFacesWithinRCutMaxOfAnyReferringPatch.shrink()
-        );
-
-        realEdgesWithinRCutMaxOfAnyReferringPatch_.transfer
-        (
-            realEdgesWithinRCutMaxOfAnyReferringPatch.shrink()
-        );
-
-        realPointsWithinRCutMaxOfAnyReferringPatch_.transfer
-        (
-            realPointsWithinRCutMaxOfAnyReferringPatch.shrink()
-        );
-    }
-
-    iterationNo++;
-
-    cellsReferredThisIteration =
-        referredInteractionList.size() - refIntListStartSize;
-
-//     Pout << tab << "Cells added this iteration: "
-//         << cellsReferredThisIteration << endl;
-
-    reduce(cellsReferredThisIteration, sumOp<label>());
-
-    Info << tab << "Cells added this iteration: "
-        << cellsReferredThisIteration << endl;
-}
-
-referredInteractionList.shrink();
-
-//     Info << "referredInteractionList.size() = "
-//         << referredInteractionList.size() << endl;
-
-//     forAll(referredInteractionList,rIL)
-//     {
-//         Info << referredInteractionList[rIL];
-//     }
diff --git a/src/lagrangian/molecule/moleculeCloud/moleculeCloudCalculateExternalForce.C b/src/lagrangian/molecule/moleculeCloud/moleculeCloudCalculateExternalForce.C
deleted file mode 100755
index ea6320ecb5..0000000000
--- a/src/lagrangian/molecule/moleculeCloud/moleculeCloudCalculateExternalForce.C
+++ /dev/null
@@ -1,42 +0,0 @@
-/*---------------------------------------------------------------------------*\
-  =========                 |
-  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
-   \\    /   O peration     |
-    \\  /    A nd           | Copyright (C) 1991-2005 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 "moleculeCloud.H"
-
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-void Foam::moleculeCloud::calculateExternalForce()
-{
-    iterator mol(this->begin());
-
-    for (mol = this->begin(); mol != this->end(); ++mol)
-    {
-        mol().A() += gravity_;
-    }
-}
-
-
-// ************************************************************************* //
diff --git a/src/lagrangian/molecule/moleculeCloud/moleculeCloudCalculateForce.C b/src/lagrangian/molecule/moleculeCloud/moleculeCloudCalculateForce.C
deleted file mode 100755
index 54aa9b1a42..0000000000
--- a/src/lagrangian/molecule/moleculeCloud/moleculeCloudCalculateForce.C
+++ /dev/null
@@ -1,59 +0,0 @@
-/*---------------------------------------------------------------------------*\
-  =========                 |
-  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
-   \\    /   O peration     |
-    \\  /    A nd           | Copyright (C) 1991-2005 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 "moleculeCloud.H"
-
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-void Foam::moleculeCloud::calculateForce()
-{
-    buildCellOccupancy();
-
-    iterator mol(this->begin());
-
-    // Set all accumulated quantities to zero
-    for (mol = this->begin(); mol != this->end(); ++mol)
-    {
-        mol().A() = vector::zero;
-
-        mol().potentialEnergy() = 0.0;
-
-        mol().rf() = tensor::zero;
-    }
-
-    calculatePairForce();
-
-    calculateTetherForce();
-
-    calculateExternalForce();
-}
-
-
-// ************************************************************************* //
-
-
-
-
diff --git a/src/lagrangian/molecule/moleculeCloud/moleculeCloudCalculatePairForce.C b/src/lagrangian/molecule/moleculeCloud/moleculeCloudCalculatePairForce.C
deleted file mode 100755
index 14b65c5a3c..0000000000
--- a/src/lagrangian/molecule/moleculeCloud/moleculeCloudCalculatePairForce.C
+++ /dev/null
@@ -1,41 +0,0 @@
-/*---------------------------------------------------------------------------*\
-  =========                 |
-  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
-   \\    /   O peration     |
-    \\  /    A nd           | Copyright (C) 1991-2005 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 "moleculeCloud.H"
-
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-void Foam::moleculeCloud::calculatePairForce()
-{
-    iterator mol(this->begin());
-
-#   include "moleculeCloudCalculatePairForceRealCells.H"
-
-#   include "moleculeCloudCalculatePairForceReferredCells.H"
-}
-
-
-// ************************************************************************* //
diff --git a/src/lagrangian/molecule/moleculeCloud/moleculeCloudCalculatePairForceRealCells.H b/src/lagrangian/molecule/moleculeCloud/moleculeCloudCalculatePairForceRealCells.H
deleted file mode 100755
index c3b3f1e7cc..0000000000
--- a/src/lagrangian/molecule/moleculeCloud/moleculeCloudCalculatePairForceRealCells.H
+++ /dev/null
@@ -1,49 +0,0 @@
-
-vector rIJ;
-
-scalar rIJMag;
-
-scalar rIJMagSq;
-
-vector fIJ;
-
-label idI;
-
-label idJ;
-
-mol = this->begin();
-
-molecule* molI = &mol();
-
-molecule* molJ = &mol();
-
-forAll(directInteractionList_, dIL)
-{
-    forAll(cellOccupancy_[dIL],cellIMols)
-    {
-        molI = cellOccupancy_[dIL][cellIMols];
-
-        forAll(directInteractionList_[dIL], interactingCells)
-        {
-            List< molecule* > cellJ =
-                cellOccupancy_[directInteractionList_[dIL][interactingCells]];
-
-            forAll(cellJ, cellJMols)
-            {
-                molJ = cellJ[cellJMols];
-
-#               include "moleculeCloudCalculatePairForceRealCellsCalculationStep.H"
-            }
-        }
-
-        forAll(cellOccupancy_[dIL],cellIOtherMols)
-        {
-            molJ = cellOccupancy_[dIL][cellIOtherMols];
-
-            if (molJ > molI)
-            {
-#                include "moleculeCloudCalculatePairForceRealCellsCalculationStep.H"
-            }
-        }
-    }
-}
diff --git a/src/lagrangian/molecule/moleculeCloud/moleculeCloudCalculatePairForceRealCellsCalculationStep.H b/src/lagrangian/molecule/moleculeCloud/moleculeCloudCalculatePairForceRealCellsCalculationStep.H
deleted file mode 100755
index 49e1e2d781..0000000000
--- a/src/lagrangian/molecule/moleculeCloud/moleculeCloudCalculatePairForceRealCellsCalculationStep.H
+++ /dev/null
@@ -1,33 +0,0 @@
-idI = molI->id();
-
-idJ = molJ->id();
-
-rIJ = molI->position() - molJ->position();
-
-rIJMagSq = magSqr(rIJ);
-
-if (pairPotentials_.rCutSqr(idI, idJ, rIJMagSq))
-{
-    rIJMag = mag(rIJ);
-
-    fIJ = (rIJ/rIJMag)*pairPotentials_.force(idI, idJ, rIJMag);
-
-    // Acceleration increment for molI
-    molI->A() += fIJ/(molI->mass());
-
-    // Acceleration increment for molJ
-    molJ->A() += -fIJ/(molJ->mass());
-
-    scalar potentialEnergy
-    (
-        pairPotentials_.energy(idI, idJ, rIJMag)
-    );
-
-    molI->potentialEnergy() += 0.5*potentialEnergy;
-
-    molJ->potentialEnergy() += 0.5*potentialEnergy;
-
-    molI->rf() += rIJ * fIJ;
-
-    molJ->rf() += rIJ * fIJ;
-}
diff --git a/src/lagrangian/molecule/moleculeCloud/moleculeCloudCalculatePairForceReferredCells.H b/src/lagrangian/molecule/moleculeCloud/moleculeCloudCalculatePairForceReferredCells.H
deleted file mode 100755
index c2fab2d10e..0000000000
--- a/src/lagrangian/molecule/moleculeCloud/moleculeCloudCalculatePairForceReferredCells.H
+++ /dev/null
@@ -1,59 +0,0 @@
-vector rKL;
-
-scalar rKLMag;
-
-scalar rKLMagSq;
-
-vector fKL;
-
-label idK;
-
-label idL;
-
-molecule* molK = &mol();
-
-forAll(referredInteractionList_, rIL)
-{
-    const List<label>& realCells =
-        referredInteractionList_[rIL].realCellsForInteraction();
-
-    forAll(referredInteractionList_[rIL], refMols)
-    {
-        referredMolecule* molL = &(referredInteractionList_[rIL][refMols]);
-
-        forAll(realCells, rC)
-        {
-            List<molecule*> cellK = cellOccupancy_[realCells[rC]];
-
-            forAll(cellK, cellKMols)
-            {
-                molK = cellK[cellKMols];
-
-                idK = molK->id();
-
-                idL = molL->id();
-
-                rKL = molK->position() - molL->position();
-
-                rKLMagSq = magSqr(rKL);
-
-                if (pairPotentials_.rCutSqr(idK, idL, rKLMagSq))
-                {
-                    rKLMag = mag(rKL);
-
-                    fKL = (rKL/rKLMag)*pairPotentials_.force(idK, idL, rKLMag);
-
-                    // Acceleration increment for molK
-                    molK->A() += fKL/(molK->mass());
-
-                    // Adding a contribution of 1/2 of the potential energy
-                    // from this interaction
-                    molK->potentialEnergy() +=
-                        0.5*pairPotentials_.energy(idK, idL, rKLMag);
-
-                    molK->rf() += rKL * fKL;
-                }
-            }
-        }
-    }
-}
diff --git a/src/lagrangian/molecule/moleculeCloud/moleculeCloudCalculateTetherForce.C b/src/lagrangian/molecule/moleculeCloud/moleculeCloudCalculateTetherForce.C
deleted file mode 100755
index 32b39a4089..0000000000
--- a/src/lagrangian/molecule/moleculeCloud/moleculeCloudCalculateTetherForce.C
+++ /dev/null
@@ -1,69 +0,0 @@
-/*---------------------------------------------------------------------------*\
-  =========                 |
-  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
-   \\    /   O peration     |
-    \\  /    A nd           | Copyright (C) 1991-2005 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 "moleculeCloud.H"
-
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-void Foam::moleculeCloud::calculateTetherForce()
-{
-    iterator mol(this->begin());
-
-    vector rIT;
-
-    scalar rITMag;
-
-    vector fIT;
-
-    for (mol = this->begin(); mol != this->end(); ++mol)
-    {
-        if (mol().tethered())
-        {
-            rIT = mol().position() - mol().tetherPosition();
-
-            rITMag = mag(rIT);
-
-            fIT = (rIT/rITMag) * tetherPotentials_.force
-            (
-                mol().id(),
-                rITMag
-            );
-
-            mol().A() += fIT/(mol().mass());
-
-            mol().potentialEnergy() += tetherPotentials_.energy
-            (
-                mol().id(),
-                rITMag
-            );
-
-            mol().rf() += rIT*fIT;
-        }
-    }
-}
-
-
-// ************************************************************************* //
diff --git a/src/lagrangian/molecule/moleculeCloud/moleculeCloudI.H b/src/lagrangian/molecule/moleculeCloud/moleculeCloudI.H
deleted file mode 100755
index 2d74b7b4b8..0000000000
--- a/src/lagrangian/molecule/moleculeCloud/moleculeCloudI.H
+++ /dev/null
@@ -1,184 +0,0 @@
-/*---------------------------------------------------------------------------*\
-  =========                 |
-  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
-   \\    /   O peration     |
-    \\  /    A nd           | Copyright (C) 1991-2005 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
-{
-
-// * * * * * * * * * * * * * * * Member Functions  * * * * * * * * * * * * * //
-
-inline const polyMesh& moleculeCloud::mesh() const
-{
-    return mesh_;
-}
-
-
-// MD solution parameters
-
-inline const moleculeCloud::integrationMethods&
-    moleculeCloud::integrationMethod() const
-{
-    return integrationMethod_;
-}
-
-
-inline scalar moleculeCloud::potentialEnergyLimit() const
-{
-    return potentialEnergyLimit_;
-}
-
-
-inline scalar moleculeCloud::guardRadius() const
-{
-    return guardRadius_;
-}
-
-
-inline const scalar moleculeCloud::rCutMax() const
-{
-    return rCutMax_;
-}
-
-
-inline const scalar moleculeCloud::rCutMaxSqr() const
-{
-    return rCutMaxSqr_;
-}
-
-
-inline const List<word>& moleculeCloud::idList() const
-{
-    return idList_;
-}
-
-
-inline label moleculeCloud::nPairPotentials() const
-{
-    return pairPotentials_.size();
-}
-
-
-inline label moleculeCloud::nIds() const
-{
-    return idList_.size();
-}
-
-
-inline const labelList& moleculeCloud::removalOrder() const
-{
-    return removalOrder_;
-}
-
-
-inline const labelListList& moleculeCloud::directInteractionList() const
-{
-    return directInteractionList_;
-}
-
-
-inline const referredCellList& moleculeCloud::referredInteractionList() const
-{
-    return referredInteractionList_;
-}
-
-
-inline const labelList&
-    moleculeCloud::realCellsWithinRCutMaxOfAnyReferringPatch() const
-{
-    return realCellsWithinRCutMaxOfAnyReferringPatch_;
-}
-
-
-inline const labelList&
-    moleculeCloud::realFacesWithinRCutMaxOfAnyReferringPatch() const
-{
-    return realFacesWithinRCutMaxOfAnyReferringPatch_;
-}
-
-
-inline const labelList&
-    moleculeCloud::realEdgesWithinRCutMaxOfAnyReferringPatch() const
-{
-    return realEdgesWithinRCutMaxOfAnyReferringPatch_;
-}
-
-
-inline const labelList&
-    moleculeCloud::realPointsWithinRCutMaxOfAnyReferringPatch() const
-{
-    return realPointsWithinRCutMaxOfAnyReferringPatch_;
-}
-
-
-inline const List<sendingReferralList>&
-    moleculeCloud::cellSendingReferralLists() const
-{
-    return cellSendingReferralLists_;
-}
-
-
-inline const List<receivingReferralList>&
-    moleculeCloud::cellReceivingReferralLists() const
-{
-    return cellReceivingReferralLists_;
-}
-
-
-inline label moleculeCloud::nInteractingProcs() const
-{
-    return cellReceivingReferralLists_.size();
-}
-
-
-inline const pairPotentialList& moleculeCloud::pairPotentials() const
-{
-    return pairPotentials_;
-}
-
-
-inline const tetherPotentialList& moleculeCloud::tetherPotentials() const
-{
-    return tetherPotentials_;
-}
-
-
-inline const vector& moleculeCloud::gravity() const
-{
-    return gravity_;
-}
-
-
-inline const List< DynamicList<molecule*> >&
-    moleculeCloud::cellOccupancy() const
-{
-    return cellOccupancy_;
-}
-
-
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-}  // End namespace Foam
-
-// ************************************************************************* //
diff --git a/src/lagrangian/molecule/moleculeCloud/moleculeCloudIntegrateEquationsOfMotion.C b/src/lagrangian/molecule/moleculeCloud/moleculeCloudIntegrateEquationsOfMotion.C
deleted file mode 100755
index dc2177d10b..0000000000
--- a/src/lagrangian/molecule/moleculeCloud/moleculeCloudIntegrateEquationsOfMotion.C
+++ /dev/null
@@ -1,50 +0,0 @@
-/*---------------------------------------------------------------------------*\
-  =========                 |
-  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
-   \\    /   O peration     |
-    \\  /    A nd           | Copyright (C) 1991-2005 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 "moleculeCloud.H"
-
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-void Foam::moleculeCloud::integrateEquationsOfMotion()
-{
-    // Supply trackData to the move method to tell it whether this is the
-    // leapfrog stage 1 or stage 2
-    // or whether it is the
-    // predictor or corrector step.
-
-    molecule::trackData td1(*this, 1);
-
-    Cloud<molecule>::move(td1);
-
-    calculateForce();
-
-    molecule::trackData td2(*this, 2);
-
-    Cloud<molecule>::move(td2);
-}
-
-
-// ************************************************************************* //
diff --git a/src/lagrangian/molecule/moleculeCloud/moleculeCloudReadMDParameters/moleculeCloudReadIdList.H b/src/lagrangian/molecule/moleculeCloud/moleculeCloudReadMDParameters/moleculeCloudReadIdList.H
deleted file mode 100755
index 8ddc55ed45..0000000000
--- a/src/lagrangian/molecule/moleculeCloud/moleculeCloudReadMDParameters/moleculeCloudReadIdList.H
+++ /dev/null
@@ -1,14 +0,0 @@
-IOdictionary idListDict
-(
-    IOobject
-    (
-        "idList",
-        mesh_.time().constant(),
-        mesh_,
-        IOobject::MUST_READ,
-        IOobject::NO_WRITE
-    )
-);
-
-idList_ = List<word>(idListDict.lookup("idList"));
-
diff --git a/src/lagrangian/molecule/moleculeCloud/moleculeCloudReadMDParameters/moleculeCloudReadMDParameters.H b/src/lagrangian/molecule/moleculeCloud/moleculeCloudReadMDParameters/moleculeCloudReadMDParameters.H
deleted file mode 100755
index f6d090bfb8..0000000000
--- a/src/lagrangian/molecule/moleculeCloud/moleculeCloudReadMDParameters/moleculeCloudReadMDParameters.H
+++ /dev/null
@@ -1,6 +0,0 @@
-
-#    include "moleculeCloudReadMDSolution.H"
-
-#    include "moleculeCloudReadIdList.H"
-
-#    include "moleculeCloudReadPotentials.H"
diff --git a/src/lagrangian/molecule/moleculeCloud/moleculeCloudReadMDParameters/moleculeCloudReadMDSolution.H b/src/lagrangian/molecule/moleculeCloud/moleculeCloudReadMDParameters/moleculeCloudReadMDSolution.H
deleted file mode 100755
index 07c6b30ff0..0000000000
--- a/src/lagrangian/molecule/moleculeCloud/moleculeCloudReadMDParameters/moleculeCloudReadMDSolution.H
+++ /dev/null
@@ -1,27 +0,0 @@
-Info<< nl <<  "Reading MD solution parameters:" << endl;
-
-IOdictionary mdSolution
-(
-    IOobject
-    (
-        "mdSolution",
-        mesh_.time().system(),
-        mesh_,
-        IOobject::MUST_READ,
-        IOobject::NO_WRITE
-    )
-);
-
-integrationMethod_ = integrationMethodNames_.read
-(
-    mdSolution.lookup("integrationMethod")
-);
-Info<< "integrationMethod =\t\t\t"
-    << integrationMethodNames_[integrationMethod_] << endl;
-
-potentialEnergyLimit_ = readScalar(mdSolution.lookup("potentialEnergyLimit"));
-Info<< "potentialEnergyLimit =\t\t\t" << potentialEnergyLimit_ << endl;
-
-guardRadius_ = readScalar(mdSolution.lookup("guardRadius"));
-Info<< "guardRadius =\t\t\t\t" << guardRadius_ << endl;
-
diff --git a/src/lagrangian/molecule/moleculeCloud/moleculeCloudReadMDParameters/moleculeCloudReadPotentials.H b/src/lagrangian/molecule/moleculeCloud/moleculeCloudReadMDParameters/moleculeCloudReadPotentials.H
deleted file mode 100755
index b1bdb2045c..0000000000
--- a/src/lagrangian/molecule/moleculeCloud/moleculeCloudReadMDParameters/moleculeCloudReadPotentials.H
+++ /dev/null
@@ -1,327 +0,0 @@
-IOdictionary potentialDict
-(
-    IOobject
-    (
-        "potentialDict",
-        mesh_.time().system(),
-        mesh_,
-        IOobject::MUST_READ,
-        IOobject::NO_WRITE
-    )
-);
-
-// ****************************************************************************
-// Pair potentials
-
-Info << nl << "Creating pair potentials:" << nl << endl;
-
-if (!potentialDict.found("pair"))
-{
-    FatalErrorIn("moleculeCloudReadPotentials.H") << nl
-            << "pair potential specification subDict not found"
-            << abort(FatalError);
-}
-
-const dictionary& pairDict = potentialDict.subDict("pair");
-
-pairPotentials_.setSizeAndNIds(nIds());
-
-label a;
-
-label b;
-
-rCutMax_ = 0.0;
-
-for
-(
-    a = 0;
-    a < idList_.size();
-    ++a
-)
-{
-    word idA = idList_[a];
-
-    for
-    (
-        b = a;
-        b < idList_.size();
-        ++b
-    )
-    {
-        word idB = idList_[b];
-
-        word pairPotentialName;
-
-        if (a==b)
-        {
-
-
-            if(pairDict.found(idA+"-"+idB))
-            {
-                pairPotentialName = idA+"-"+idB;
-            }
-
-            else
-            {
-                FatalErrorIn("moleculeCloudReadPotentials.H") << nl
-                        << "Pair pairPotential specification subDict "
-                        << idA+"-"+idB << " not found"
-                        << abort(FatalError);
-            }
-        }
-
-        else
-        {
-            if(pairDict.found(idA+"-"+idB))
-            {
-                pairPotentialName = idA+"-"+idB;
-            }
-
-            else if(pairDict.found(idB+"-"+idA))
-            {
-                pairPotentialName = idB+"-"+idA;
-            }
-
-            else
-            {
-                FatalErrorIn("moleculeCloudReadPotentials.H") << nl
-                        << "Pair pairPotential specification subDict "
-                        << idA+"-"+idB << " or " << idB+"-"+idA << " not found"
-                        << abort(FatalError);
-            }
-
-            if
-            (
-                pairDict.found(idA+"-"+idB)
-                && pairDict.found(idB+"-"+idA)
-            )
-            {
-                FatalErrorIn("moleculeCloudReadPotentials.H") << nl
-                        << "Pair pairPotential specification subDict "
-                        << idA+"-"+idB << " and "
-                        << idB+"-"+idA << " found - multiple definition"
-                        << abort(FatalError);
-            }
-        }
-
-        word pairPotentialType
-        (
-            pairDict.subDict(pairPotentialName).lookup("potentialType")
-        );
-
-        if
-        (
-            pairPotentialType == "maitlandSmithTabulated"
-        )
-        {
-            scalar rCut = readScalar
-            (
-                pairDict.subDict(pairPotentialName).lookup("rCut")
-            );
-
-            if(rCut > rCutMax_)
-            {
-                rCutMax_ = rCut;
-            }
-
-            pairPotentials_.addPotential
-            (
-                a,
-                b,
-                pairPotential
-                (
-                    pairDict.subDict(pairPotentialName)
-                )
-            );
-        }
-        else
-        {
-            FatalErrorIn("moleculeCloudReadPotentials.H") << nl
-                    << "pairPotentialType "<< pairPotentialType << " unknown"
-                    << abort(FatalError);
-        }
-
-        Info << pairPotentialName << ": "
-            << pairPotentials_.pairPotentialFunction(a,b) << endl;
-    }
-}
-
-rCutMax_ += guardRadius_;
-
-rCutMaxSqr_ = rCutMax_ * rCutMax_;
-
-Info << nl << "rCutMax + guardRadius = " << rCutMax_ << endl;
-
-if (potentialDict.found("removalOrder"))
-{
-    List<word> remOrd = potentialDict.lookup("removalOrder");
-
-    removalOrder_.setSize(remOrd.size());
-
-    forAll(removalOrder_, rO)
-    {
-        removalOrder_[rO] = findIndex(idList_, remOrd[rO]);
-    }
-}
-
-// ****************************************************************************
-// Tether potentials
-
-iterator mol(this->begin());
-
-DynamicList<label> tetherIds;
-
-for
-(
- mol = this->begin();
- mol != this->end();
- ++mol
-)
-{
-    if (mol().tethered())
-    {
-        if (findIndex(tetherIds, mol().id()) == -1)
-        {
-            tetherIds.append
-            (
-                mol().id()
-            );
-        }
-    }
-}
-
-if (Pstream::parRun())
-{
-    List< labelList > allTetherIds(Pstream::nProcs());
-
-    allTetherIds[Pstream::myProcNo()] = tetherIds;
-
-    Pstream::gatherList(allTetherIds);
-
-    if (Pstream::master())
-    {
-        DynamicList<label> globalTetherIds;
-
-        forAll(allTetherIds, procN)
-        {
-            const labelList& procNTetherIds = allTetherIds[procN];
-
-            forAll(procNTetherIds, id)
-            {
-                if (findIndex(globalTetherIds, procNTetherIds[id]) == -1)
-                {
-                    globalTetherIds.append
-                    (
-                        procNTetherIds[id]
-                    );
-                }
-            }
-        }
-
-        globalTetherIds.shrink();
-
-        tetherIds = globalTetherIds;
-    }
-
-    Pstream::scatter(tetherIds);
-}
-
-tetherIds.shrink();
-
-if (tetherIds.size())
-{
-    Info << nl << "Creating tether potentials:" << endl;
-
-    if (!potentialDict.found("tether"))
-    {
-        FatalErrorIn("moleculeCloudReadPotentials.H") << nl
-                << "tether potential specification subDict not found"
-                << abort(FatalError);
-    }
-
-    const dictionary& tetherDict = potentialDict.subDict("tether");
-
-    tetherPotentials_.setSizeAndTetherIds(tetherIds);
-
-    forAll (tetherIds, tid)
-    {
-        word tetherPotentialName = idList_[tetherIds[tid]];
-
-        if (!tetherDict.found(tetherPotentialName))
-        {
-            FatalErrorIn("moleculeCloudReadPotentials.H") << nl
-                    << "tether potential specification subDict "
-                    << tetherPotentialName << " not found"
-                    << abort(FatalError);
-        }
-
-        Info << nl << tetherPotentialName << endl;
-
-        word tetherPotentialType =
-            tetherDict.subDict(tetherPotentialName).lookup("potentialType");
-
-        if
-        (
-            tetherPotentialType == "harmonicSpring"
-        )
-        {
-
-            Info << "\tpotentialType = " << tetherPotentialType << endl;
-
-            scalar springConstant
-            (
-                readScalar
-                (
-                    tetherDict.subDict(tetherPotentialName).lookup
-                    (
-                        "springConstant"
-                    )
-                )
-            );
-
-            Info << "\tspringConstant = " << springConstant << endl;
-
-            tetherPotentials_.addPotential
-            (
-                tetherIds[tid],
-                tetherPotential
-                (
-                    tetherPotentialName,
-                    tetherPotentialType,
-                    springConstant
-                )
-            );
-        }
-
-        else
-        {
-            FatalErrorIn("moleculeCloudReadPotentials.H") << nl
-                    << "tetherPotentialType "
-                    << tetherPotentialType << " unknown"
-                    << abort(FatalError);
-        }
-    }
-}
-
-// ****************************************************************************
-// External Forces
-
-gravity_ = vector::zero;
-
-if (potentialDict.found("external"))
-{
-
-    Info << nl << "Reading external forces:" << endl;
-
-    const dictionary& externalDict = potentialDict.subDict("external");
-
-    // ************************************************************************
-    // gravity
-
-    if (externalDict.found("gravity"))
-    {
-        gravity_ = externalDict.lookup("gravity");
-    }
-}
-
-Info << nl << tab << "gravity = " << gravity_ << endl;
diff --git a/src/lagrangian/molecule/moleculeCloud/moleculeCloudRealCellsInRangeOfSegment.C b/src/lagrangian/molecule/moleculeCloud/moleculeCloudRealCellsInRangeOfSegment.C
deleted file mode 100755
index 03100cfd3b..0000000000
--- a/src/lagrangian/molecule/moleculeCloud/moleculeCloudRealCellsInRangeOfSegment.C
+++ /dev/null
@@ -1,152 +0,0 @@
-/*---------------------------------------------------------------------------*\
-  =========                 |
-  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
-   \\    /   O peration     |
-    \\  /    A nd           | Copyright (C) 1991-2005 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 "moleculeCloud.H"
-
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-const Foam::labelList Foam::moleculeCloud::realCellsInRangeOfSegment
-(
-    const labelList& segmentFaces,
-    const labelList& segmentEdges,
-    const labelList& segmentPoints
-) const
-{
-    DynamicList<label> realCellsFoundInRange;
-
-    forAll(segmentFaces, sF)
-    {
-        const label f = segmentFaces[sF];
-
-        forAll (mesh_.points(), p)
-        {
-            if (testPointFaceDistance(p, f))
-            {
-                const labelList& pCells(mesh_.pointCells()[p]);
-
-                forAll(pCells, pC)
-                {
-                    const label cellI(pCells[pC]);
-
-                    if (findIndex(realCellsFoundInRange, cellI) == -1)
-                    {
-                        realCellsFoundInRange.append(cellI);
-                    }
-                }
-            }
-        }
-    }
-
-    forAll(segmentPoints, sP)
-    {
-        const label p = segmentPoints[sP];
-
-        forAll(mesh_.faces(), f)
-        {
-            if (testPointFaceDistance(p, f))
-            {
-                const label cellO(mesh_.faceOwner()[f]);
-
-                if (findIndex(realCellsFoundInRange, cellO) == -1)
-                {
-                    realCellsFoundInRange.append(cellO);
-                }
-
-                if (mesh_.isInternalFace(f))
-                {
-                    // boundary faces will not have neighbour information
-
-                    const label cellN(mesh_.faceNeighbour()[f]);
-
-                    if (findIndex(realCellsFoundInRange, cellN) == -1)
-                    {
-                        realCellsFoundInRange.append(cellN);
-                    }
-                }
-            }
-        }
-    }
-
-    forAll(segmentEdges, sE)
-    {
-        const edge& eJ(mesh_.edges()[segmentEdges[sE]]);
-
-        forAll (mesh_.edges(), edgeIIndex)
-        {
-            const edge& eI(mesh_.edges()[edgeIIndex]);
-
-            if (testEdgeEdgeDistance(eI, eJ))
-            {
-                const labelList& eICells(mesh_.edgeCells()[edgeIIndex]);
-
-                forAll(eICells, eIC)
-                {
-                    const label cellI(eICells[eIC]);
-
-                    if (findIndex(realCellsFoundInRange, cellI) == -1)
-                    {
-                        realCellsFoundInRange.append(cellI);
-                    }
-                }
-            }
-        }
-    }
-
-//     forAll (points, p)
-//     {
-//         const point& ptI = mesh_.points()[points[p]];
-//
-//         forAll(mesh_.faces(), f)
-//         {
-//             if (testPointFaceDistance(ptI, f))
-//             {
-//                 const label cellO(mesh_.faceOwner()[f]);
-//
-//                 if (findIndex(realCellsFoundInRange, cellO) == -1)
-//                 {
-//                     realCellsFoundInRange.append(cellO);
-//                 }
-//
-//                 if (mesh_.isInternalFace(f))
-//                 {
-//                     // boundary faces will not have neighbour information
-//
-//                     const label cellN(mesh_.faceNeighbour()[f]);
-//
-//                     if (findIndex(realCellsFoundInRange, cellN) == -1)
-//                     {
-//                         realCellsFoundInRange.append(cellN);
-//                     }
-//                 }
-//             }
-//         }
-//     }
-//
-    return realCellsFoundInRange.shrink();
-}
-
-
-// ************************************************************************* //
diff --git a/src/lagrangian/molecule/moleculeCloud/moleculeCloudReferredCellsInRangeOfSegment.C b/src/lagrangian/molecule/moleculeCloud/moleculeCloudReferredCellsInRangeOfSegment.C
deleted file mode 100755
index f2e553a853..0000000000
--- a/src/lagrangian/molecule/moleculeCloud/moleculeCloudReferredCellsInRangeOfSegment.C
+++ /dev/null
@@ -1,117 +0,0 @@
-/*---------------------------------------------------------------------------*\
-  =========                 |
-  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
-   \\    /   O peration     |
-    \\  /    A nd           | Copyright (C) 1991-2005 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 "moleculeCloud.H"
-
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-const Foam::labelList Foam::moleculeCloud::referredCellsInRangeOfSegment
-(
-    const List<referredCell>& referredInteractionList,
-    const labelList& segmentFaces,
-    const labelList& segmentEdges,
-    const labelList& segmentPoints
-) const
-{
-    DynamicList<label> referredCellsFoundInRange;
-
-    forAll(segmentFaces, sF)
-    {
-        const label f = segmentFaces[sF];
-
-        forAll(referredInteractionList, rIL)
-        {
-            const vectorList& refCellPoints
-                = referredInteractionList[rIL].vertexPositions();
-
-            if (testPointFaceDistance(refCellPoints, f))
-            {
-                if (findIndex(referredCellsFoundInRange, rIL) == -1)
-                {
-                    referredCellsFoundInRange.append(rIL);
-                }
-            }
-        }
-    }
-
-    forAll(segmentPoints, sP)
-    {
-        const label p = segmentPoints[sP];
-
-        forAll(referredInteractionList, rIL)
-        {
-            const referredCell& refCell(referredInteractionList[rIL]);
-
-            if (testPointFaceDistance(p, refCell))
-            {
-                if (findIndex(referredCellsFoundInRange, rIL) == -1)
-                {
-                    referredCellsFoundInRange.append(rIL);
-                }
-            }
-        }
-    }
-
-    forAll(segmentEdges, sE)
-    {
-        const edge& eI(mesh_.edges()[segmentEdges[sE]]);
-
-        forAll(referredInteractionList, rIL)
-        {
-            const vectorList& refCellPoints
-                = referredInteractionList[rIL].vertexPositions();
-
-            const edgeList& refCellEdges
-                = referredInteractionList[rIL].edges();
-
-            forAll(refCellEdges, rCE)
-            {
-                const edge& eJ(refCellEdges[rCE]);
-
-                if
-                (
-                    testEdgeEdgeDistance
-                    (
-                        eI,
-                        refCellPoints[eJ.start()],
-                        refCellPoints[eJ.end()]
-                    )
-                )
-                {
-                    if(findIndex(referredCellsFoundInRange, rIL) == -1)
-                    {
-                        referredCellsFoundInRange.append(rIL);
-                    }
-                }
-            }
-        }
-    }
-
-    return referredCellsFoundInRange.shrink();
-}
-
-
-// ************************************************************************* //
diff --git a/src/lagrangian/molecule/moleculeCloud/moleculeCloudRemoveHighEnergyOverlaps.C b/src/lagrangian/molecule/moleculeCloud/moleculeCloudRemoveHighEnergyOverlaps.C
deleted file mode 100755
index ac4385574f..0000000000
--- a/src/lagrangian/molecule/moleculeCloud/moleculeCloudRemoveHighEnergyOverlaps.C
+++ /dev/null
@@ -1,67 +0,0 @@
-/*---------------------------------------------------------------------------*\
-  =========                 |
-  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
-   \\    /   O peration     |
-    \\  /    A nd           | Copyright (C) 1991-2005 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 "moleculeCloud.H"
-
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-void Foam::moleculeCloud::removeHighEnergyOverlaps()
-{
-    Info << nl << "Removing high energy overlaps, removal order:";
-
-    forAll(removalOrder_, rO)
-    {
-        Info << " " << idList_[removalOrder_[rO]];
-    }
-
-    Info << nl ;
-
-    label initialSize = this->size();
-
-    buildCellOccupancy();
-
-    iterator mol(this->begin());
-
-#   include "moleculeCloudRemoveHighEnergyOverlapsRealCells.H"
-
-    buildCellOccupancy();
-
-#   include "moleculeCloudRemoveHighEnergyOverlapsReferredCells.H"
-
-    buildCellOccupancy();
-
-    label molsRemoved = initialSize - this->size();
-
-    if (Pstream::parRun())
-    {
-        reduce(molsRemoved, sumOp<label>());
-    }
-
-    Info << tab << molsRemoved << " molecules removed" << endl;
-}
-
-
-// ************************************************************************* //
diff --git a/src/lagrangian/molecule/moleculeCloud/moleculeCloudRemoveHighEnergyOverlapsRealCells.H b/src/lagrangian/molecule/moleculeCloud/moleculeCloudRemoveHighEnergyOverlapsRealCells.H
deleted file mode 100755
index fe6d792842..0000000000
--- a/src/lagrangian/molecule/moleculeCloud/moleculeCloudRemoveHighEnergyOverlapsRealCells.H
+++ /dev/null
@@ -1,55 +0,0 @@
-{ 
-    vector rIJ;
-
-    scalar rIJMag;
-
-    scalar rIJMagSq;
-
-    label idI;
-
-    label idJ;
-
-    mol = this->begin();
-
-    molecule* molI = &mol();
-
-    molecule* molJ = &mol();
-
-    DynamicList<molecule*> molsToDelete;
-
-    forAll(directInteractionList_, dIL)
-    {
-        forAll(cellOccupancy_[dIL],cellIMols)
-        {
-            molI = cellOccupancy_[dIL][cellIMols];
-
-            forAll(directInteractionList_[dIL], interactingCells)
-            {
-                List< molecule* > cellJ =
-                    cellOccupancy_[directInteractionList_[dIL][interactingCells]];
-
-                forAll(cellJ, cellJMols)
-                {
-                    molJ = cellJ[cellJMols];
-
-#                   include "moleculeCloudRemoveHighEnergyOverlapsRealCellsCalculationStep.H"
-                }
-            }
-
-            forAll(cellOccupancy_[dIL],cellIOtherMols)
-            {
-                molJ = cellOccupancy_[dIL][cellIOtherMols];
-
-                if (molJ > molI)
-                {
-#                   include "moleculeCloudRemoveHighEnergyOverlapsRealCellsCalculationStep.H"
-                }
-            }
-        }
-    }
-
-    forAll (molsToDelete, mTD)
-    {
-        deleteParticle(*(molsToDelete[mTD]));
-    }
-}
diff --git a/src/lagrangian/molecule/moleculeCloud/moleculeCloudRemoveHighEnergyOverlapsRealCellsCalculationStep.H b/src/lagrangian/molecule/moleculeCloud/moleculeCloudRemoveHighEnergyOverlapsRealCellsCalculationStep.H
deleted file mode 100755
index bc36a60095..0000000000
--- a/src/lagrangian/molecule/moleculeCloud/moleculeCloudRemoveHighEnergyOverlapsRealCellsCalculationStep.H
+++ /dev/null
@@ -1,70 +0,0 @@
-idI = molI->id();
-
-idJ = molJ->id();
-
-rIJ = molI->position() - molJ->position();
-
-rIJMagSq = magSqr(rIJ);
-
-if (pairPotentials_.rCutSqr(idI, idJ, rIJMagSq))
-{
-    rIJMag = mag(rIJ);
-
-    bool remove = false;
-
-    if (rIJMag < SMALL)
-    {
-        WarningIn("moleculeCloud::removeHighEnergyOverlaps()")
-            << "Real molecule pair "
-            << " idI = " << idI
-            << " at position " << molI->position()
-            << " idJ = " << idJ
-            << " at position " << molJ->position()
-            << " are closer than " << SMALL
-            << ": mag separation = " << rIJMag
-            << ". These may have been placed on top of each"
-            << " other by a rounding error in molConfig in parallel"
-            << " or a block filled with molecules twice."
-            << " Removing one of the molecules."
-            << endl;
-
-        remove = true;
-    }
-
-    // Guard against pairPotentials_.energy being evaluated
-    // if rIJMag < SMALL. A floating point exception will
-    // happen otherwise.
-
-    if (!remove)
-    {
-        if
-        (
-            pairPotentials_.energy(idI, idJ, rIJMag) > potentialEnergyLimit_
-        )
-        {
-            remove = true;
-        }
-    }
-
-    if (remove)
-    {
-        if
-        (
-            idI == idJ
-         || findIndex(removalOrder_, idJ) < findIndex(removalOrder_, idI)
-        )
-        {
-            if (findIndex(molsToDelete, molJ) == -1)
-            {
-                molsToDelete.append(molJ);
-            }
-        }
-        else
-        {
-            if (findIndex(molsToDelete, molI) == -1)
-            {
-                molsToDelete.append(molI);
-            }
-        }
-    }
-}
diff --git a/src/lagrangian/molecule/moleculeCloud/moleculeCloudRemoveHighEnergyOverlapsReferredCells.H b/src/lagrangian/molecule/moleculeCloud/moleculeCloudRemoveHighEnergyOverlapsReferredCells.H
deleted file mode 100755
index 5b6b76135f..0000000000
--- a/src/lagrangian/molecule/moleculeCloud/moleculeCloudRemoveHighEnergyOverlapsReferredCells.H
+++ /dev/null
@@ -1,144 +0,0 @@
-{
-    vector rKL;
-
-    scalar rKLMag;
-
-    scalar rKLMagSq;
-
-    label idK;
-
-    label idL;
-
-    molecule* molK = &mol();
-
-    DynamicList<molecule*> molsToDelete;
-
-    forAll(referredInteractionList_, rIL)
-    {
-        referredCell& refCell = referredInteractionList_[rIL];
-
-        forAll(refCell, refMols)
-        {
-            referredMolecule* molL = &(refCell[refMols]);
-
-            List <label> realCells = refCell.realCellsForInteraction();
-
-            forAll(realCells, rC)
-            {
-                label cellK = realCells[rC];
-
-                List<molecule*> cellKMols = cellOccupancy_[cellK];
-
-                forAll(cellKMols, cKM)
-                {
-                    molK = cellKMols[cKM];
-
-                    idK = molK->id();
-
-                    idL = molL->id();
-
-                    rKL = molK->position() - molL->position();
-
-                    rKLMagSq = magSqr(rKL);
-
-                    if (pairPotentials_.rCutSqr(idK, idL, rKLMagSq))
-                    {
-                        rKLMag = mag(rKL);
-
-                        bool remove = false;
-
-                        if (rKLMag < SMALL)
-                        {
-                            WarningIn
-                            (
-                                "moleculeCloud::removeHighEnergyOverlaps()"
-                            )
-                                << "Real-referred molecule pair "
-                                << " idK = " << idK << " (real)"
-                                << " at position " << molK->position()
-                                << " idL = " << idL << " (referred)"
-                                << " at position " << molL->position()
-                                << " are closer than " << SMALL
-                                << ": mag separation = " << rKLMag
-                                << ". These may have been placed on top of each"
-                                << " other by a rounding error in molConfig in"
-                                << " parallel, a block filled with molecules"
-                                << " twice, or a lattice ending very close"
-                                << " to the edge of the mesh."
-                                << " Removing one of the molecules."
-                                << endl;
-
-                                remove = true;
-                        }
-
-                        // Guard against pairPotentials_.energy being evaluated
-                        // if rKLMag < SMALL. A floating point exception will
-                        // happen otherwise.
-
-                        if (!remove)
-                        {
-                            if
-                            (
-                                pairPotentials_.energy(idK, idL, rKLMag)
-                              > potentialEnergyLimit_
-                            )
-                            {
-                                remove = true;
-                            }
-                        }
-
-                        if (remove)
-                        {
-                            if
-                            (
-                                findIndex(removalOrder_, idK)
-                              < findIndex(removalOrder_, idL)
-                            )
-                            {
-                                if (findIndex(molsToDelete, molK) == -1)
-                                {
-                                    molsToDelete.append(molK);
-                                }
-                            }
-
-                            else if
-                            (
-                                findIndex(removalOrder_, idK)
-                             == findIndex(removalOrder_, idL)
-                            )
-                            {
-                                if
-                                (
-                                    Pstream::myProcNo() == refCell.sourceProc()
-                                 && cellK <= refCell.sourceCell()
-                                )
-                                {
-                                    if (findIndex(molsToDelete, molK) == -1)
-                                    {
-                                        molsToDelete.append(molK);
-                                    }
-                                }
-
-                                else if
-                                (
-                                    Pstream::myProcNo() < refCell.sourceProc()
-                                )
-                                {
-                                    if (findIndex(molsToDelete, molK) == -1)
-                                    {
-                                        molsToDelete.append(molK);
-                                    }
-                                }
-                            }
-                        }
-                    }
-                }
-            }
-        }
-    }
-
-    forAll (molsToDelete, mTD)
-    {
-        deleteParticle(*(molsToDelete[mTD]));
-    }
-}
diff --git a/src/lagrangian/molecule/moleculeCloud/moleculeCloudTestEdgeEdgeDistance.C b/src/lagrangian/molecule/moleculeCloud/moleculeCloudTestEdgeEdgeDistance.C
deleted file mode 100755
index 285447974c..0000000000
--- a/src/lagrangian/molecule/moleculeCloud/moleculeCloudTestEdgeEdgeDistance.C
+++ /dev/null
@@ -1,86 +0,0 @@
-/*---------------------------------------------------------------------------*\
-  =========                 |
-  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
-   \\    /   O peration     |
-    \\  /    A nd           | Copyright (C) 1991-2005 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 "moleculeCloud.H"
-
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-bool Foam::moleculeCloud::testEdgeEdgeDistance
-(
-    const edge& eI,
-    const edge& eJ
-) const
-{
-    const vector& eJs(mesh_.points()[eJ.start()]);
-    const vector& eJe(mesh_.points()[eJ.end()]);
-
-    return testEdgeEdgeDistance(eI, eJs, eJe);
-}
-
-bool Foam::moleculeCloud::testEdgeEdgeDistance
-(
-    const edge& eI,
-    const vector& eJs,
-    const vector& eJe
-) const
-{
-    vector a(eI.vec(mesh_.points()));
-    vector b(eJe - eJs);
-
-    const vector& eIs(mesh_.points()[eI.start()]);
-
-    vector c(eJs - eIs);
-
-    vector crossab = a ^ b;
-    scalar magCrossSqr = magSqr(crossab);
-
-    if (magCrossSqr > VSMALL)
-    {
-        // If the edges are parallel then a point-face
-        // search will pick them up
-
-        scalar s = ((c ^ b) & crossab)/magCrossSqr;
-        scalar t = ((c ^ a) & crossab)/magCrossSqr;
-
-        // Check for end points outside of range 0..1
-        // If the closest point is outside this range
-        // a point-face search will have found it.
-
-        return
-        (
-            s >= 0
-         && s <= 1
-         && t >= 0
-         && t <= 1
-         && magSqr(eIs + a*s - eJs - b*t) <= rCutMaxSqr()
-        );
-    }
-
-    return false;
-}
-
-
-// ************************************************************************* //
diff --git a/src/lagrangian/molecule/moleculeCloud/moleculeCloudTestPointFaceDistance.C b/src/lagrangian/molecule/moleculeCloud/moleculeCloudTestPointFaceDistance.C
deleted file mode 100755
index e01be86476..0000000000
--- a/src/lagrangian/molecule/moleculeCloud/moleculeCloudTestPointFaceDistance.C
+++ /dev/null
@@ -1,235 +0,0 @@
-/*---------------------------------------------------------------------------*\
-  =========                 |
-  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
-   \\    /   O peration     |
-    \\  /    A nd           | Copyright (C) 1991-2005 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 "moleculeCloud.H"
-
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-bool Foam::moleculeCloud::testPointFaceDistance
-(
-    const label p,
-    const label faceNo
-) const
-{
-    const vector& pointPosition(mesh_.points()[p]);
-
-    return testPointFaceDistance(pointPosition, faceNo);
-}
-
-bool Foam::moleculeCloud::testPointFaceDistance
-(
-    const label p,
-    const referredCell& refCell
-) const
-{
-    const vector& pointPosition(mesh_.points()[p]);
-
-    forAll (refCell.faces(), rCF)
-    {
-        if
-        (
-            testPointFaceDistance
-            (
-                pointPosition,
-                refCell.faces()[rCF],
-                refCell.vertexPositions(),
-                refCell.faceCentres()[rCF],
-                refCell.faceAreas()[rCF]
-            )
-        )
-        {
-            return true;
-        }
-    }
-
-    return false;
-}
-
-bool Foam::moleculeCloud::testPointFaceDistance
-(
-    const vectorList& pointsToTest,
-    const label faceNo
-) const
-{
-    forAll(pointsToTest, pTT)
-    {
-        const vector& p(pointsToTest[pTT]);
-
-        // if any point in the list is in range of the face
-        // then the rest do not need to be tested and
-        // true can be returned
-
-        if (testPointFaceDistance(p, faceNo))
-        {
-            return true;
-        }
-    }
-
-    return false;
-}
-
-bool Foam::moleculeCloud::testPointFaceDistance
-(
-    const vector& p,
-    const label faceNo
-) const
-{
-    const face& faceToTest(mesh_.faces()[faceNo]);
-
-    const vector& faceC(mesh_.faceCentres()[faceNo]);
-
-    const vector& faceA(mesh_.faceAreas()[faceNo]);
-
-    const vectorList& points(mesh_.points());
-
-    return testPointFaceDistance
-    (
-        p,
-        faceToTest,
-        points,
-        faceC,
-        faceA
-    );
-}
-
-bool Foam::moleculeCloud::testPointFaceDistance
-(
-    const vector& p,
-    const labelList& faceToTest,
-    const vectorList& points,
-    const vector& faceC,
-    const vector& faceA
-) const
-{
-    vector faceN(faceA/mag(faceA));
-
-    scalar perpDist((p - faceC) & faceN);
-
-    if (mag(perpDist) > rCutMax())
-    {
-        return false;
-    }
-
-    vector pointOnPlane = (p - faceN * perpDist);
-
-    if (magSqr(faceC - pointOnPlane) < rCutMaxSqr()*1e-8)
-    {
-        // If pointOnPlane is very close to the face centre
-        // then defining the local axes will be inaccurate
-        // and it is very likely that pointOnPlane will be
-        // inside the face, so return true if the points
-        // are in range to be safe
-
-        return (magSqr(pointOnPlane - p) <= rCutMaxSqr());
-    }
-
-    vector xAxis = (faceC - pointOnPlane)/mag(faceC - pointOnPlane);
-
-    vector yAxis =
-        ((faceC - pointOnPlane) ^ faceN)
-       /mag((faceC - pointOnPlane) ^ faceN);
-
-    List<vector2D> local2DVertices(faceToTest.size());
-
-    forAll(faceToTest, fTT)
-    {
-        const vector& V(points[faceToTest[fTT]]);
-
-        if (magSqr(V-p) <= rCutMaxSqr())
-        {
-            return true;
-        }
-
-        local2DVertices[fTT] = vector2D
-        (
-            ((V - pointOnPlane) & xAxis),
-            ((V - pointOnPlane) & yAxis)
-        );
-    }
-
-    scalar localFaceCx((faceC - pointOnPlane) & xAxis);
-
-    scalar la_valid = -1;
-
-    forAll(local2DVertices, fV)
-    {
-        const vector2D& va(local2DVertices[fV]);
-
-        const vector2D& vb
-        (
-            local2DVertices[(fV + 1) % local2DVertices.size()]
-        );
-
-        if (mag(vb.y()-va.y()) > SMALL)
-        {
-            scalar la =
-                (
-                    va.x() - va.y()*((vb.x() - va.x())/(vb.y() - va.y()))
-                )
-               /localFaceCx;
-
-            scalar lv = -va.y()/(vb.y() - va.y());
-
-
-            if (la >= 0 && la <= 1 && lv >= 0 && lv <= 1)
-            {
-                la_valid = la;
-
-                break;
-            }
-        }
-    }
-
-    if (la_valid < 0)
-    {
-        // perpendicular point inside face, nearest point is pointOnPlane;
-        return (magSqr(pointOnPlane-p) <= rCutMaxSqr());
-    }
-    else
-    {
-        // perpendicular point outside face, nearest point is
-        // on edge that generated la_valid;
-        return
-        (
-            magSqr(pointOnPlane + la_valid*(faceC - pointOnPlane) - p)
-         <= rCutMaxSqr()
-        );
-    }
-
-    // if the algorithm hasn't returned anything by now then something has
-    // gone wrong.
-
-    FatalErrorIn("moleculeCloudTestPointAndFaceDistance.C") << nl
-        << "point " << p << " to face " << faceToTest
-        << " comparison did not find a nearest point"
-        << " to be inside or outside face."
-        << abort(FatalError);
-
-    return false;
-}
-
-
-// ************************************************************************* //
diff --git a/src/lagrangian/molecule/potentials/pairPotential/basic/pairPotential.C b/src/lagrangian/molecule/potentials/pairPotential/basic/pairPotential.C
deleted file mode 100755
index f7c96414e4..0000000000
--- a/src/lagrangian/molecule/potentials/pairPotential/basic/pairPotential.C
+++ /dev/null
@@ -1,308 +0,0 @@
-/*---------------------------------------------------------------------------*\
-  =========                 |
-  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
-   \\    /   O peration     |
-    \\  /    A nd           | Copyright (C) 1991-2005 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 "pairPotential.H"
-
-// * * * * * * * * * * * * * Private Member Functions  * * * * * * * * * * * //
-
-void Foam::pairPotential::setLookupTables()
-{
-    label N = label((rCut_ - rMin_)/dr_) + 1;
-
-    forceLookup_.setSize(N);
-
-    energyLookup_.setSize(N);
-
-    forAll(forceLookup_, k)
-    {
-        forceLookup_[k] = force(k*dr_ + rMin_);
-
-        energyLookup_[k] = energy(k*dr_ + rMin_);
-    }
-
-    forceLookup_[N-1] = 0.0;
-    energyLookup_[N-1] = 0.0;
-}
-
-
-void Foam::pairPotential::setConstants()
-{
-    scalar nr = n(rCut_);
-
-    u_at_rCut_ =
-        epsilon_
-       *(
-            (6.0/(nr - 6.0))*Foam::pow( (rCut_/rm_), -nr)
-          - (nr/(nr - 6.0))*Foam::pow( (rCut_/rm_), -6)
-        );
-
-    du_by_dr_at_rCut_ =
-        -6.0 * epsilon_ * gamma_
-       *(
-            Foam::pow( (rCut_/rm_),-nr)
-           *(
-                (rCut_/rm_)
-               *(1.0 / (nr - 6.0) + log(rCut_ / rm_) + 1.0)
-              + (m_/gamma_)
-              - 1.0
-            )
-          - Foam::pow((rCut_/rm_),-6.0)
-            *(rCut_ / ( (nr - 6.0) * rm_) + (nr/gamma_))
-        )
-       /(rCut_*(nr - 6.0));
-}
-
-
-// * * * * * * * * * * * * * * * * Constructors  * * * * * * * * * * * * * * //
-
-Foam::pairPotential::pairPotential()
-{}
-
-
-Foam::pairPotential::pairPotential(const dictionary& pPDict)
-:
-    forceLookup_(),
-    energyLookup_(),
-    m_(),
-    gamma_(),
-    rm_(),
-    epsilon_(),
-    rCut_(),
-    rCutSqr_(),
-    u_at_rCut_(),
-    du_by_dr_at_rCut_(),
-    rMin_(),
-    dr_()
-{
-
-    m_ = readScalar(pPDict.lookup("m"));
-
-    gamma_ = readScalar(pPDict.lookup("gamma"));
-
-    rm_ = readScalar(pPDict.lookup("rm"));
-
-    epsilon_ = readScalar(pPDict.lookup("epsilon"));
-
-    rCut_ = readScalar(pPDict.lookup("rCut"));
-
-    rCutSqr_ = rCut_ * rCut_;
-
-    rMin_ = readScalar(pPDict.lookup("rMin"));
-
-    dr_ = readScalar(pPDict.lookup("dr"));
-
-    setConstants();
-
-    setLookupTables();
-}
-
-
-Foam::pairPotential::pairPotential
-(
-    const scalar m,
-    const scalar gamma,
-    const scalar rm,
-    const scalar epsilon,
-    const scalar rCut,
-    const scalar rMin,
-    const scalar dr
-)
-:
-    forceLookup_(),
-    energyLookup_(),
-    m_(m),
-    gamma_(gamma),
-    rm_(rm),
-    epsilon_(epsilon),
-    rCut_(rCut),
-    rCutSqr_(rCut*rCut),
-    u_at_rCut_(),
-    du_by_dr_at_rCut_(),
-    rMin_(rMin),
-    dr_(dr)
-{
-    setConstants();
-
-    setLookupTables();
-}
-
-
-// * * * * * * * * * * * * * * * * Destructor  * * * * * * * * * * * * * * * //
-
-Foam::pairPotential::~pairPotential()
-{}
-
-// * * * * * * * * * * * * * * * Member Functions  * * * * * * * * * * * * * //
-
-void Foam::pairPotential::write(Ostream& os) const
-{
-    os<< "Shifted force Maitland Smith pair potential."
-        << nl << tab << "m = " << m_
-        << nl << tab << "gamma = " << gamma_
-        << nl << tab << "rm = " << rm_
-        << nl << tab << "epsilon = " << epsilon_
-        << nl << tab << "rCut = " << rCut_
-        << nl << tab << "rMin = " << rMin_
-        << nl << tab << "dr = " << dr_
-        << endl;
-}
-
-
-Foam::scalar Foam::pairPotential::n(const scalar rIJMag) const
-{
-    return (m_ + gamma_*(rIJMag/rm_ - 1.0));
-}
-
-
-Foam::scalar Foam::pairPotential::force(const scalar rIJMag) const
-{
-    scalar nr(n(rIJMag));
-
-    scalar r = rIJMag/rm_;
-
-    scalar rN = Foam::pow(r,-nr);
-
-    scalar f =
-      - epsilon_
-       *(
-           - 6.0/(nr - 6.0)/(nr - 6.0)*(gamma_/rm_)*rN
-           + 6.0/(nr - 6.0)*rN
-             *((gamma_ - m_)/rIJMag - (gamma_/rm_)*(log(r) + 1.0))
-           + 6.0/(nr - 6.0)
-             *(1.0/(nr - 6.0)*(gamma_/rm_) + nr/rIJMag)*Foam::pow(r, -6)
-        )
-      + du_by_dr_at_rCut_;
-
-    return f;
-}
-
-
-Foam::scalar Foam::pairPotential::forceLookup(const scalar rIJMag) const
-{
-    scalar k_rIJ = (rIJMag - rMin_)/dr_;
-
-    label k(k_rIJ);
-
-    if (k < 0)
-    {
-        FatalErrorIn("pairPotential.C") << nl
-        << "rIJMag less than rMin" << nl
-        << abort(FatalError);
-    }
-
-    scalar f =
-        (k_rIJ - k)*forceLookup_[k+1]
-      + (k + 1 - k_rIJ)*forceLookup_[k];
-
-    return f;
-}
-
-
-Foam::List< Foam::Pair< Foam::scalar > >
-Foam::pairPotential::forceTable() const
-{
-    List< Pair<scalar> > forceTab(forceLookup_.size());
-
-    forAll(forceLookup_,k)
-    {
-        forceTab[k].first() = rMin_ + k*dr_;
-
-        forceTab[k].second() = forceLookup_[k];
-    }
-
-    return forceTab;
-}
-
-
-Foam::scalar Foam::pairPotential::energy(const scalar rIJMag) const
-{
-    scalar nr = n(rIJMag);
-
-    scalar e =
-        epsilon_
-       *(
-            (6.0 / (nr - 6.0))*Foam::pow( rIJMag/rm_, -nr)
-          - (nr / (nr - 6.0))*Foam::pow( rIJMag/rm_, -6)
-        )
-      - u_at_rCut_
-      - (rIJMag - rCut_)
-       *du_by_dr_at_rCut_;
-
-    return e;
-}
-
-
-Foam::scalar Foam::pairPotential::energyLookup(const scalar rIJMag) const
-{
-    scalar k_rIJ = (rIJMag - rMin_)/dr_;
-
-    label k(k_rIJ);
-
-    if (k < 0)
-    {
-        FatalErrorIn("pairPotential.C") << nl
-        << "rIJMag less than rMin" << nl
-        << abort(FatalError);
-    }
-
-    scalar e =
-        (k_rIJ - k)*energyLookup_[k+1]
-      + (k + 1 - k_rIJ)*energyLookup_[k];
-
-    return e;
-}
-
-
-Foam::List< Foam::Pair< Foam::scalar > >
-    Foam::pairPotential::energyTable() const
-{
-    List< Pair<scalar> > energyTab(energyLookup_.size());
-
-    forAll(energyLookup_,k)
-    {
-        energyTab[k].first() = rMin_ + k*dr_;
-
-        energyTab[k].second() = energyLookup_[k];
-    }
-
-    return energyTab;
-}
-
-
-// * * * * * * * * * * * * * * * Friend Functions  * * * * * * * * * * * * * //
-
-Foam::Ostream& Foam::operator<<(Ostream& os, const pairPotential& pot)
-{
-    pot.write(os);
-    os.check
-    (
-        "Foam::Ostream& Foam::pperator<<(Ostream& f, const pairPotential& pot"
-    );
-    return os;
-}
-
-
-// ************************************************************************* //
diff --git a/src/lagrangian/molecule/potentials/pairPotential/basic/pairPotential.H b/src/lagrangian/molecule/potentials/pairPotential/basic/pairPotential.H
deleted file mode 100755
index 7427f19331..0000000000
--- a/src/lagrangian/molecule/potentials/pairPotential/basic/pairPotential.H
+++ /dev/null
@@ -1,196 +0,0 @@
-/*---------------------------------------------------------------------------*\
-  =========                 |
-  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
-   \\    /   O peration     |
-    \\  /    A nd           | Copyright (C) 1991-2005 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::pairPotential
-
-Description
-
-    At the moment this is hard coded to be a shifted force
-    "maitlandSmith" potential.
-    In future use templated classes virtual functions,
-    function pointers and all kinds of good stuff to make
-    this a generic pair force,
-
-SourceFiles
-    pairPotentialI.H
-    pairPotential.C
-
-\*---------------------------------------------------------------------------*/
-
-#ifndef pairPotential_H
-#define pairPotential_H
-
-#include "vector.H"
-#include "dictionary.H"
-#include "List.H"
-#include "Pair.H"
-
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-namespace Foam
-{
-
-/*---------------------------------------------------------------------------*\
-                           Class pairPotential Declaration
-\*---------------------------------------------------------------------------*/
-
-class pairPotential
-{
-    // Private data
-
-        List<scalar> forceLookup_;
-
-        List<scalar> energyLookup_;
-
-        scalar m_;
-
-        scalar gamma_;
-
-        scalar rm_;
-
-        scalar epsilon_;
-
-        scalar rCut_;
-
-        scalar rCutSqr_;
-
-        scalar u_at_rCut_;
-
-        scalar du_by_dr_at_rCut_;
-
-        scalar rMin_;
-
-        scalar dr_;
-
-
-    // Private Member Functions
-
-        void setLookupTables();
-
-        void setConstants();
-
-
-public:
-
-    // Constructors
-
-        //- Construct null
-        pairPotential();
-
-        //- Construct from dictionary
-        pairPotential(const dictionary& pPDict);
-
-        //- Construct from components
-        pairPotential
-        (
-            const scalar m,
-            const scalar gamma,
-            const scalar rm,
-            const scalar epsilon,
-            const scalar rCut,
-            const scalar rMin,
-            const scalar dr
-        );
-
-
-    // Destructor
-
-        virtual ~pairPotential();
-
-
-    // Member Functions
-
-        // Access
-
-            inline const scalar m() const;
-
-            inline const scalar gamma() const ;
-
-            inline const scalar rm() const;
-
-            inline const scalar epsilon() const;
-
-            inline const scalar rCut() const;
-
-            inline const scalar rCutSqr() const;
-
-            inline const scalar rMin() const;
-
-            inline const scalar dr() const;
-
-
-        // Write
-
-            virtual void write(Ostream&) const;
-
-            scalar n(const scalar rIJMag) const;
-
-            scalar force(const scalar rIJMag) const;
-
-            scalar forceLookup(const scalar rIJMag) const;
-
-            List<Pair<scalar> > forceTable() const;
-
-            scalar energy(const scalar rIJMag) const;
-
-            scalar energyLookup(const scalar rIJMag) const;
-
-            List<Pair<scalar> > energyTable() const;
-
-
-    // Friend Operators
-
-        inline friend bool operator==
-        (
-            const pairPotential& a,
-            const pairPotential& b
-        );
-
-        inline friend bool operator!=
-        (
-            const pairPotential& a,
-            const pairPotential& b
-        );
-
-
-    // IOstream Operators
-
-        friend Ostream& operator<<(Ostream&, const pairPotential&);
-};
-
-
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-} // End namespace Foam
-
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-#include "pairPotentialI.H"
-
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-#endif
-
-// ************************************************************************* //
diff --git a/src/lagrangian/molecule/potentials/pairPotential/basic/pairPotentialI.H b/src/lagrangian/molecule/potentials/pairPotential/basic/pairPotentialI.H
deleted file mode 100755
index 71424d7403..0000000000
--- a/src/lagrangian/molecule/potentials/pairPotential/basic/pairPotentialI.H
+++ /dev/null
@@ -1,102 +0,0 @@
-/*---------------------------------------------------------------------------*\
-  =========                 |
-  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
-   \\    /   O peration     |
-    \\  /    A nd           | Copyright (C) 1991-2005 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
-
-\*---------------------------------------------------------------------------*/
-
-inline const Foam::scalar Foam::pairPotential::m() const
-{
-    return m_;
-}
-
-
-inline const Foam::scalar Foam::pairPotential::gamma() const
-{
-    return gamma_;
-}
-
-
-inline const Foam::scalar Foam::pairPotential::rm() const
-{
-    return rm_;
-}
-
-
-inline const Foam::scalar Foam::pairPotential::epsilon() const
-{
-    return epsilon_;
-}
-
-
-inline const Foam::scalar Foam::pairPotential::rCut() const
-{
-    return rCut_;
-}
-
-
-inline const Foam::scalar Foam::pairPotential::rCutSqr() const
-{
-    return rCutSqr_;
-}
-
-
-inline const Foam::scalar Foam::pairPotential::rMin() const
-{
-    return rMin_;
-}
-
-
-inline const Foam::scalar Foam::pairPotential::dr() const
-{
-    return dr_;
-}
-
-
-// * * * * * * * * * * * * * * * Friend Operators  * * * * * * * * * * * * * //
-
-inline bool Foam::operator==
-(
-    const pairPotential& a,
-    const pairPotential& b
-)
-{
-    return
-        (a.m() == b.m())
-     && (a.gamma() == b.gamma())
-     && (a.rm() == b.rm())
-     && (a.epsilon() == b.epsilon())
-     && (a.rCut() == b.rCut());
-}
-
-
-inline bool Foam::operator!=
-(
-    const pairPotential& a,
-    const pairPotential& b
-)
-{
-    return !(a == b);
-}
-
-
-// ************************************************************************* //
diff --git a/src/lagrangian/molecule/potentials/pairPotential/basic/pairPotentialList.C b/src/lagrangian/molecule/potentials/pairPotential/basic/pairPotentialList.C
deleted file mode 100755
index 7728490ee0..0000000000
--- a/src/lagrangian/molecule/potentials/pairPotential/basic/pairPotentialList.C
+++ /dev/null
@@ -1,180 +0,0 @@
-/*---------------------------------------------------------------------------*\
-  =========                 |
-  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
-   \\    /   O peration     |
-    \\  /    A nd           | Copyright (C) 1991-2005 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 "pairPotentialList.H"
-
-namespace Foam
-{
-
-// * * * * * * * * * * * * * * * * Constructors  * * * * * * * * * * * * * * //
-
-Foam::pairPotentialList::pairPotentialList()
-:
-    List<pairPotential> ()
-{}
-
-
-Foam::pairPotentialList::pairPotentialList
-(
-    const label nIds
-)
-:
-    List<pairPotential> ((nIds * (nIds + 1))/2),
-    nIds_(nIds)
-{}
-
-
-Foam::pairPotentialList::pairPotentialList
-(
-    const List<pairPotential>& pairPotentials,
-    const label nIds
-)
-:
-    List<pairPotential> (pairPotentials),
-    nIds_(nIds)
-{}
-
-
-// * * * * * * * * * * * * * * * * Destructor  * * * * * * * * * * * * * * * //
-
-pairPotentialList::~pairPotentialList()
-{}
-
-
-// * * * * * * * * * * * * * * * Member Functions  * * * * * * * * * * * * * //
-
-void pairPotentialList::setSizeAndNIds (const label nIds)
-{
-    nIds_ = nIds;
-    setSize((nIds * (nIds + 1))/2);
-}
-
-
-void pairPotentialList::addPotential
-(
-    const label a,
-    const label b,
-    const pairPotential& pot
-)
-{
-    if (pairPotentialIndex (a,b) > size()-1)
-    {
-        FatalErrorIn
-        (
-            "Foam::pairPotentialList::addPotential "
-            "(const label a, const label b, const pairPotential& pot)"
-        )<< "Attempting to add a pairPotential with too high an index"
-         << nl
-         << "Check if the pairPotentialList has been constructed "
-         << "with the number of ids to expect"
-         << nl << abort(FatalError);
-    }
-    else
-    {
-        (*this)[pairPotentialIndex (a,b)] = pot;
-    }
-}
-
-
-const pairPotential& pairPotentialList::pairPotentialFunction
-(
-    const label a,
-    const label b
-) const
-{
-    return (*this)[pairPotentialIndex (a,b)];
-}
-
-
-bool pairPotentialList::rCutSqr
-(
-    const label a,
-    const label b,
-    const scalar rIJMagSqr
-) const
-{
-    if(rIJMagSqr <= rCutSqr (a,b))
-    {
-        return true;
-    }
-    else
-    {
-        return false;
-    }
-}
-
-
-const scalar pairPotentialList::rCutSqr
-(
-    const label a,
-    const label b
-) const
-{
-    return (*this)[pairPotentialIndex (a,b)].rCutSqr();
-}
-
-
-const scalar pairPotentialList::rCut
-(
-    const label a,
-    const label b
-) const
-{
-    return (*this)[pairPotentialIndex (a,b)].rCut();
-}
-
-
-scalar pairPotentialList::force
-(
-    const label a,
-    const label b,
-    const scalar rIJMag
-) const
-{
-    scalar f = (*this)[pairPotentialIndex (a,b)].forceLookup(rIJMag);
-
-    return f;
-}
-
-
-scalar pairPotentialList::energy
-(
-    const label a,
-    const label b,
-    const scalar rIJMag
-) const
-{
-    scalar e = (*this)[pairPotentialIndex (a,b)].energyLookup(rIJMag);
-
-    return e;
-}
-
-
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-} // End namespace Foam
-
-// ************************************************************************* //
diff --git a/src/lagrangian/molecule/potentials/pairPotential/basic/pairPotentialList.H b/src/lagrangian/molecule/potentials/pairPotential/basic/pairPotentialList.H
deleted file mode 100755
index 26cbc0ca64..0000000000
--- a/src/lagrangian/molecule/potentials/pairPotential/basic/pairPotentialList.H
+++ /dev/null
@@ -1,169 +0,0 @@
-/*---------------------------------------------------------------------------*\
-  =========                 |
-  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
-   \\    /   O peration     |
-    \\  /    A nd           | Copyright (C) 1991-2005 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::pairPotentialList
-
-Description
-
-SourceFiles
-    pairPotentialListI.H
-    pairPotentialList.C
-
-\*---------------------------------------------------------------------------*/
-
-#ifndef pairPotentialList_H
-#define pairPotentialList_H
-
-#include "pairPotential.H"
-
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-namespace Foam
-{
-
-/*---------------------------------------------------------------------------*\
-                           Class pairPotentialList Declaration
-\*---------------------------------------------------------------------------*/
-
-class pairPotentialList
-:
-    public List<pairPotential>
-{
-    // Private data
-
-        label nIds_;
-
-
-    // Private Member Functions
-
-        inline label pairPotentialIndex
-        (
-            const label a,
-            const label b
-        ) const;
-
-        //- Disallow default bitwise assignment
-        void operator=(const pairPotentialList&);
-
-        //- Disallow default bitwise copy construct
-        pairPotentialList(const pairPotentialList&);
-
-
-public:
-
-    // Constructors
-
-        //- Construct null
-        pairPotentialList();
-
-        //- Construct from number of Ids
-        pairPotentialList
-        (
-            const label nIds
-        );
-
-        //- Construct from components
-        pairPotentialList
-        (
-            const List<pairPotential>& pairPotentials,
-            const label nIds
-        );
-
-
-    // Destructor
-
-        ~pairPotentialList();
-
-
-    // Member Functions
-
-        // Access
-
-            inline label nIds() const;
-
-            void setSizeAndNIds (const label);
-
-            void addPotential
-            (
-                const label a,
-                const label b,
-                const pairPotential& pot
-            );
-
-            const pairPotential& pairPotentialFunction
-            (
-                const label a,
-                const label b
-            ) const;
-
-            // Return true if rIJ is within rCut for this pair.
-            bool rCutSqr
-            (
-                const label a,
-                const label b,
-                const scalar rIJMagSqr
-            ) const;
-
-            const scalar rCutSqr
-            (
-                const label a,
-                const label b
-            ) const;
-
-            const scalar rCut
-            (
-                const label a,
-                const label b
-            ) const;
-
-            scalar force
-            (
-                const label a,
-                const label b,
-                const scalar rIJMag
-            ) const;
-
-            scalar energy
-            (
-                const label a,
-                const label b,
-                const scalar rIJMag
-            ) const;
-};
-
-
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-} // End namespace Foam
-
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-#include "pairPotentialListI.H"
-
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-#endif
-
-// ************************************************************************* //
diff --git a/src/lagrangian/molecule/potentials/pairPotential/basic/pairPotentialListI.H b/src/lagrangian/molecule/potentials/pairPotential/basic/pairPotentialListI.H
deleted file mode 100755
index d58fa545df..0000000000
--- a/src/lagrangian/molecule/potentials/pairPotential/basic/pairPotentialListI.H
+++ /dev/null
@@ -1,59 +0,0 @@
-/*---------------------------------------------------------------------------*\
-  =========                 |
-  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
-   \\    /   O peration     |
-    \\  /    A nd           | Copyright (C) 1991-2005 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
-
-\*---------------------------------------------------------------------------*/
-
-// * * * * * * * * * * * * * Private Member Functions  * * * * * * * * * * * //
-
-inline Foam::label Foam::pairPotentialList::pairPotentialIndex
-(
-    const label a,
-    const label b
-) const
-{
-    label index;
-
-    if (a < b)
-    {
-        index = a*(2*nIds_ - a - 1)/2 + b;
-    }
-
-    else
-    {
-        index = b*(2*nIds_ - b - 1)/2 + a;
-    }
-
-    return index;
-}
-
-
-// * * * * * * * * * * * * * * * Member Functions  * * * * * * * * * * * * * //
-
-inline Foam::label Foam::pairPotentialList::nIds() const
-{
-    return nIds_;
-}
-
-
-// ************************************************************************* //
diff --git a/src/lagrangian/molecule/potentials/pairPotential/derived/lennardJones.C b/src/lagrangian/molecule/potentials/pairPotential/derived/lennardJones.C
deleted file mode 100755
index 1eab1aa40a..0000000000
--- a/src/lagrangian/molecule/potentials/pairPotential/derived/lennardJones.C
+++ /dev/null
@@ -1,132 +0,0 @@
-/*---------------------------------------------------------------------------*\
-  =========                 |
-  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
-   \\    /   O peration     |
-    \\  /    A nd           | Copyright (C) 1991-2005 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 "pairPotential.H"
-
-namespace Foam
-{
-
-// * * * * * * * * * * * * * * * * Constructors  * * * * * * * * * * * * * * //
-
-pairPotential::pairPotential()
-{}
-
-
-// Construct from components
-pairPotential::pairPotential
-(
-    const word& pairPotentialName,
-    const word& pairPotentialType,
-    const scalar sigma,
-    const scalar epsilon,
-    const scalar rCut
-)
-:
-    pairPotentialName_(pairPotentialName),
-    pairPotentialType_(pairPotentialType),
-    sigma_(sigma),
-    epsilon_(epsilon),
-    rCut_(rCut),
-    rCutSqr_(rCut*rCut)
-{
-    // rCutShiftedForcePotentialConstTerm
-    rCutSFPotConst_ = (pow((rCut_/sigma_),-12) - pow((rCut_/sigma_),-6));
-
-    // rCutShiftedForceConstTerm
-    rCutSFConst_ =
-        (pow((rCut_/sigma_),-14) - 0.5*pow((rCut_/sigma_),-8))*rCut_;
-}
-
-
-// * * * * * * * * * * * * * * * * Destructor  * * * * * * * * * * * * * * * //
-
-pairPotential::~pairPotential()
-{}
-
-
-// * * * * * * * * * * * * * * * Member Functions  * * * * * * * * * * * * * //
-
-void pairPotential::write(Ostream& os) const
-{
-    os << pairPotentialName_
-       << nl << pairPotentialType_
-       << nl << sigma_
-       << nl << epsilon_
-       << nl << rCut_
-       << endl;
-}
-
-
-scalar pairPotential::force(const scalar rIJMag) const
-{
-    // (rIJ/sigma)^-2
-    scalar rIJoSMagSqInv = (sigma_/rIJMag)*(sigma_/rIJMag);
-
-    // (rIJ/sigma)^-6
-    scalar rIJoSMagSqInvCu = rIJoSMagSqInv*rIJoSMagSqInv*rIJoSMagSqInv;
-
-    scalar f = 48.0*epsilon_/(sigma_*sigma_)
-               *(rIJoSMagSqInvCu*(rIJoSMagSqInvCu - 0.5)*rIJoSMagSqInv
-             - rCutSFConst_/rIJMag);
-
-    return f;
-}
-
-
-scalar pairPotential::energy(const scalar rIJMag) const
-{
-    // (rIJ/sigma)^-2
-    scalar rIJoSMagSqInv = (sigma_/rIJMag)*(sigma_/rIJMag);
-
-    // (rIJ/sigma)^-6
-    scalar rIJoSMagSqInvCu = rIJoSMagSqInv*rIJoSMagSqInv*rIJoSMagSqInv;
-
-    scalar e = 4*epsilon_
-               *(
-                    rIJoSMagSqInvCu*(rIJoSMagSqInvCu - 1.0)
-                  - rCutSFPotConst_
-                  + 12*(rIJMag - rCut_)/(sigma_*sigma_)*rCutSFConst_
-                );
-
-    return e;
-}
-
-
-// * * * * * * * * * * * * * * * Friend Functions  * * * * * * * * * * * * * //
-
-Ostream& operator<<(Ostream& os, const pairPotential& pot)
-{
-    pot.write(os);
-    os.check("Ostream& operator<<(Ostream& f, const pairPotential& pot");
-    return os;
-}
-
-
-// * * * * * * * * * * * * * * * Friend Operators  * * * * * * * * * * * * * //
-
-} // End namespace Foam
-
-// ************************************************************************* //
diff --git a/src/lagrangian/molecule/potentials/pairPotential/derived/lennardJones.H b/src/lagrangian/molecule/potentials/pairPotential/derived/lennardJones.H
deleted file mode 100755
index 57dea3ab72..0000000000
--- a/src/lagrangian/molecule/potentials/pairPotential/derived/lennardJones.H
+++ /dev/null
@@ -1,148 +0,0 @@
-/*---------------------------------------------------------------------------*\
-  =========                 |
-  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
-   \\    /   O peration     |
-    \\  /    A nd           | Copyright (C) 1991-2005 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::pairPotential
-
-Description
-
-SourceFiles
-    pairPotentialI.H
-    pairPotential.C
-
-\*---------------------------------------------------------------------------*/
-
-#ifndef pairPotential_H
-#define pairPotential_H
-
-#include "vector.H"
-
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-namespace Foam
-{
-
-
-/*---------------------------------------------------------------------------*\
-                        Class pairPotential Declaration
-\*---------------------------------------------------------------------------*/
-
-class pairPotential
-{
-    // Private data
-
-        // At the moment this is hard coded to be a "shiftedLennardJones"
-        // potential.  In future use templated classes virtual functions,
-        // function pointers and all kinds of good stuff to make this a
-        // generic pair force,
-
-        // Not strictly necessary, but useful to keep track of what's what.
-        word pairPotentialName_;
-
-        // To be used when runTime selection of potential function is working.
-        word pairPotentialType_;
-
-        scalar sigma_;
-
-        scalar epsilon_;
-
-        scalar rCut_;
-
-        scalar rCutSqr_;
-
-        // rCutShiftedForcePotentialConstTerm
-        scalar rCutSFPotConst_;
-
-        // rCutShiftedForceConstTerm
-        scalar rCutSFConst_;
-
-
-public:
-
-    // Constructors
-
-        //- Construct null
-        pairPotential();
-
-        //- Construct from components
-        pairPotential
-        (
-            const word& pairPotentialName,
-            const word& pairPotentialType,
-            const scalar sigma,
-            const scalar epsilon,
-            const scalar rCut
-        );
-
-
-    // Destructor
-
-        virtual ~pairPotential();
-
-
-    // Member Functions
-
-        // Access
-
-            inline const word& pairPotentialName() const;
-
-            inline const word& pairPotentialType() const;
-
-            inline scalar sigma() const;
-
-            inline scalar epsilon() const;
-
-            inline scalar rCut() const;
-
-            inline scalar rCutSqr() const;
-
-
-        // Write
-
-            virtual void write(Ostream&) const;
-
-            scalar force(const scalar rIJMag) const;
-
-            scalar energy(const scalar rIJMag) const;
-
-
-    // IOstream Operators
-
-        friend Ostream& operator<<(Ostream&, const pairPotential&);
-};
-
-
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-} // End namespace Foam
-
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-#include "pairPotentialI.H"
-
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-#endif
-
-// ************************************************************************* //
diff --git a/src/lagrangian/molecule/potentials/pairPotential/derived/lennardJonesI.H b/src/lagrangian/molecule/potentials/pairPotential/derived/lennardJonesI.H
deleted file mode 100755
index 4e3a1a2f27..0000000000
--- a/src/lagrangian/molecule/potentials/pairPotential/derived/lennardJonesI.H
+++ /dev/null
@@ -1,69 +0,0 @@
-/*---------------------------------------------------------------------------*\
-  =========                 |
-  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
-   \\    /   O peration     |
-    \\  /    A nd           | Copyright (C) 1991-2005 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
-{
-
-// * * * * * * * * * * * * * * * Member Functions  * * * * * * * * * * * * * //
-
-inline const word& pairPotential::pairPotentialName() const
-{
-    return pairPotentialName_;
-}
-
-
-inline const word& pairPotential::pairPotentialType() const
-{
-    return pairPotentialType_;
-}
-
-
-inline scalar pairPotential::sigma() const
-{
-    return sigma_;
-}
-
-
-inline scalar pairPotential::epsilon() const
-{
-    return epsilon_;
-}
-
-
-inline scalar pairPotential::rCut() const
-{
-    return rCut_;
-}
-
-
-inline scalar pairPotential::rCutSqr() const
-{
-    return rCutSqr_;
-}
-
-} // End namespace Foam
-
-// ************************************************************************* //
diff --git a/src/lagrangian/molecule/potentials/tetherPotential/tetherPotential.C b/src/lagrangian/molecule/potentials/tetherPotential/tetherPotential.C
deleted file mode 100755
index 46c097b36d..0000000000
--- a/src/lagrangian/molecule/potentials/tetherPotential/tetherPotential.C
+++ /dev/null
@@ -1,94 +0,0 @@
-/*---------------------------------------------------------------------------*\
-  =========                 |
-  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
-   \\    /   O peration     |
-    \\  /    A nd           | Copyright (C) 1991-2005 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 "tetherPotential.H"
-
-namespace Foam
-{
-
-// * * * * * * * * * * * * * * * * Constructors  * * * * * * * * * * * * * * //
-
-tetherPotential::tetherPotential()
-{}
-
-
-tetherPotential::tetherPotential
-(
-    const word& tetherPotentialName,
-    const word& tetherPotentialType,
-    const scalar springConstant
-)
-:
-    tetherPotentialName_(tetherPotentialName),
-    tetherPotentialType_(tetherPotentialType),
-    springConstant_(springConstant)
-{}
-
-
-// * * * * * * * * * * * * * * * * Destructor  * * * * * * * * * * * * * * * //
-
-tetherPotential::~tetherPotential()
-{}
-
-
-// * * * * * * * * * * * * * * * Member Functions  * * * * * * * * * * * * * //
-
-void tetherPotential::write(Ostream& os) const
-{
-    os << tetherPotentialName_
-       << nl << tetherPotentialType_
-       << nl << springConstant_
-       << endl;
-}
-
-
-scalar tetherPotential::force(const scalar rITMag) const
-{
-    return -springConstant_ * rITMag;
-}
-
-
-scalar tetherPotential::energy(const scalar rITMag) const
-{
-    return 0.5*springConstant_*rITMag*rITMag;
-}
-
-
-// * * * * * * * * * * * * * * * Friend Functions  * * * * * * * * * * * * * //
-
-Ostream& operator<<(Ostream& os, const tetherPotential& pot)
-{
-    pot.write(os);
-    os.check("Ostream& operator<<(Ostream& f, const tetherPotential& pot");
-    return os;
-}
-
-
-// * * * * * * * * * * * * * * * Friend Operators  * * * * * * * * * * * * * //
-
-} // End namespace Foam
-
-// ************************************************************************* //
diff --git a/src/lagrangian/molecule/potentials/tetherPotential/tetherPotential.H b/src/lagrangian/molecule/potentials/tetherPotential/tetherPotential.H
deleted file mode 100755
index afa9a35e69..0000000000
--- a/src/lagrangian/molecule/potentials/tetherPotential/tetherPotential.H
+++ /dev/null
@@ -1,125 +0,0 @@
-/*---------------------------------------------------------------------------*\
-  =========                 |
-  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
-   \\    /   O peration     |
-    \\  /    A nd           | Copyright (C) 1991-2005 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::tetherPotential
-
-Description
-
-SourceFiles
-    tetherPotentialI.H
-    tetherPotential.C
-
-\*---------------------------------------------------------------------------*/
-
-#ifndef tetherPotential_H
-#define tetherPotential_H
-
-#include "vector.H"
-
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-namespace Foam
-{
-
-/*---------------------------------------------------------------------------*\
-                       Class tetherPotential Declaration
-\*---------------------------------------------------------------------------*/
-
-class tetherPotential
-{
-    // Private data
-
-        // At the moment this is hard coded to be a "harmonicSpring"
-        // potential.  In future use templated classes virtual functions,
-        // function pointers and all kinds of good stuff to make this a
-        // generic tether force,
-
-        word tetherPotentialName_;
-
-        word tetherPotentialType_;
-
-        scalar springConstant_;
-
-
-public:
-
-    // Constructors
-
-        //- Construct null
-        tetherPotential();
-
-        //- Construct from components
-        tetherPotential
-        (
-            const word& tetherPotentialName,
-            const word& tetherPotentialType,
-            const scalar springConstant_
-        );
-
-
-    // Destructor
-
-        virtual ~tetherPotential();
-
-
-    // Member Functions
-
-        // Access
-
-            inline const word& tetherPotentialName() const;
-
-            inline const word& tetherPotentialType() const;
-
-            inline scalar springConstant() const;
-
-            scalar force(const scalar rITMag) const;
-
-            scalar energy(const scalar rITMag) const;
-
-
-        // Write
-
-            virtual void write(Ostream&) const;
-
-
-    // IOstream Operators
-
-        friend Ostream& operator<<(Ostream&, const tetherPotential&);
-};
-
-
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-} // End namespace Foam
-
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-#include "tetherPotentialI.H"
-
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-#endif
-
-// ************************************************************************* //
diff --git a/src/lagrangian/molecule/potentials/tetherPotential/tetherPotentialI.H b/src/lagrangian/molecule/potentials/tetherPotential/tetherPotentialI.H
deleted file mode 100755
index d9ca0dae1a..0000000000
--- a/src/lagrangian/molecule/potentials/tetherPotential/tetherPotentialI.H
+++ /dev/null
@@ -1,56 +0,0 @@
-/*---------------------------------------------------------------------------*\
-  =========                 |
-  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
-   \\    /   O peration     |
-    \\  /    A nd           | Copyright (C) 1991-2005 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
-{
-
-// * * * * * * * * * * * * * * * Member Functions  * * * * * * * * * * * * * //
-
-inline const word& tetherPotential::tetherPotentialName() const
-{
-    return tetherPotentialName_;
-}
-
-
-inline const word& tetherPotential::tetherPotentialType() const
-{
-    return tetherPotentialType_;
-}
-
-
-inline scalar tetherPotential::springConstant() const
-{
-    return springConstant_;
-}
-
-
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-} // End namespace Foam
-
-// ************************************************************************* //
diff --git a/src/lagrangian/molecule/potentials/tetherPotential/tetherPotentialList.C b/src/lagrangian/molecule/potentials/tetherPotential/tetherPotentialList.C
deleted file mode 100755
index ac32daf60f..0000000000
--- a/src/lagrangian/molecule/potentials/tetherPotential/tetherPotentialList.C
+++ /dev/null
@@ -1,146 +0,0 @@
-/*---------------------------------------------------------------------------*\
-  =========                 |
-  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
-   \\    /   O peration     |
-    \\  /    A nd           | Copyright (C) 1991-2005 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 "tetherPotentialList.H"
-
-namespace Foam
-{
-
-// * * * * * * * * * * * * * Private Member Functions  * * * * * * * * * * * //
-
-label tetherPotentialList::tetherPotentialIndex(const label a)
-{
-    label index(findIndex(tetherIds_,a));
-
-    if (index == -1)
-    {
-        FatalErrorIn
-        (
-            "Foam::tetherPotentialList::tetherPotentialIndex(const label a)"
-        )
-            << "Attempting to access a tetherPotential with an unknown id"
-            << abort(FatalError);
-
-        return 0;
-    }
-    else
-    {
-        return index;
-    }
-}
-
-
-// * * * * * * * * * * * * * * * * Constructors  * * * * * * * * * * * * * * //
-
-Foam::tetherPotentialList::tetherPotentialList()
-:
-    List<tetherPotential> ()
-{}
-
-
-Foam::tetherPotentialList::tetherPotentialList
-(
-    const List<label> tetherIds
-)
-:
-    List<tetherPotential> (tetherIds.size()),
-    tetherIds_(tetherIds_)
-{}
-
-
-// * * * * * * * * * * * * * * * * Destructor  * * * * * * * * * * * * * * * //
-
-tetherPotentialList::~tetherPotentialList()
-{}
-
-
-// * * * * * * * * * * * * * * * Member Functions  * * * * * * * * * * * * * //
-
-void tetherPotentialList::setSizeAndTetherIds (const List<label>& tetherIds)
-{
-    tetherIds_ = tetherIds;
-    setSize(tetherIds.size());
-}
-
-
-void tetherPotentialList::addPotential
-(
-    const label a,
-    const tetherPotential& pot
-)
-{
-        (*this)[tetherPotentialIndex (a)] = pot;
-}
-
-
-tetherPotential& tetherPotentialList::tetherPotentialFunction (const label a)
-{
-    return (*this)[tetherPotentialIndex (a)];
-}
-
-
-scalar tetherPotentialList::force (const label a, const scalar rITMag)
-{
-    scalar f = (*this)[tetherPotentialIndex (a)].force(rITMag);
-
-    return f;
-}
-
-
-scalar tetherPotentialList::energy (const label a, const scalar rITMag)
-{
-    scalar e = (*this)[tetherPotentialIndex (a)].energy(rITMag);
-
-    return e;
-}
-
-
-// * * * * * * * * * * * * * * * Member Operators  * * * * * * * * * * * * * //
-
-void tetherPotentialList::operator=(const tetherPotentialList& rhs)
-{
-    // Check for assignment to self
-    if (this == &rhs)
-    {
-        FatalErrorIn
-        (
-            "Foam::tetherPotentialList::operator="
-            "(const Foam::tetherPotentialList&)"
-        )   << "Attempted assignment to self"
-            << abort(FatalError);
-    }
-
-    List<tetherPotential>::operator=(rhs);
-
-    tetherIds_ = rhs.tetherIds();
-}
-
-
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-} // End namespace Foam
-
-// ************************************************************************* //
diff --git a/src/lagrangian/molecule/potentials/tetherPotential/tetherPotentialList.H b/src/lagrangian/molecule/potentials/tetherPotential/tetherPotentialList.H
deleted file mode 100755
index ebd24e57f0..0000000000
--- a/src/lagrangian/molecule/potentials/tetherPotential/tetherPotentialList.H
+++ /dev/null
@@ -1,125 +0,0 @@
-/*---------------------------------------------------------------------------*\
-  =========                 |
-  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
-   \\    /   O peration     |
-    \\  /    A nd           | Copyright (C) 1991-2005 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::tetherPotentialList
-
-Description
-
-SourceFiles
-    tetherPotentialListI.H
-    tetherPotentialList.C
-
-\*---------------------------------------------------------------------------*/
-
-#ifndef tetherPotentialList_H
-#define tetherPotentialList_H
-
-#include "ListOps.H"
-#include "tetherPotential.H"
-
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-namespace Foam
-{
-
-/*---------------------------------------------------------------------------*\
-                      Class tetherPotentialList Declaration
-\*---------------------------------------------------------------------------*/
-
-class tetherPotentialList
-:
-    public List<tetherPotential>
-{
-    // Private data
-
-        List<label> tetherIds_;
-
-
-    // Private Member Functions
-
-        label tetherPotentialIndex(const label a);
-
-        //- Disallow default bitwise copy construct
-        tetherPotentialList(const tetherPotentialList&);
-
-
-public:
-
-    // Constructors
-
-        //- Construct null
-        tetherPotentialList();
-
-        //- Construct from list of tetherIDs
-        tetherPotentialList(const List<label> tetherIds);
-
-
-    // Destructor
-
-        ~tetherPotentialList();
-
-
-    // Member Functions
-
-        // Access
-
-            inline const List<label>& tetherIds() const;
-
-            inline label nTetherPotentials() const;
-
-            void setSizeAndTetherIds (const List<label>&);
-
-            void addPotential
-            (
-                const label a,
-                const tetherPotential& pot
-            );
-
-            tetherPotential& tetherPotentialFunction (const label a);
-
-            scalar force (const label a, const scalar rITMag);
-
-            scalar energy (const label a, const scalar rITMag);
-
-
-    // Member Operators
-
-        void operator=(const tetherPotentialList&);
-};
-
-
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-} // End namespace Foam
-
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-#include "tetherPotentialListI.H"
-
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-#endif
-
-// ************************************************************************* //
diff --git a/src/lagrangian/molecule/potentials/tetherPotential/tetherPotentialListI.H b/src/lagrangian/molecule/potentials/tetherPotential/tetherPotentialListI.H
deleted file mode 100755
index 4f89783918..0000000000
--- a/src/lagrangian/molecule/potentials/tetherPotential/tetherPotentialListI.H
+++ /dev/null
@@ -1,50 +0,0 @@
-/*---------------------------------------------------------------------------*\
-  =========                 |
-  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
-   \\    /   O peration     |
-    \\  /    A nd           | Copyright (C) 1991-2005 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
-{
-
-// * * * * * * * * * * * * * * * Member Functions  * * * * * * * * * * * * * //
-
-inline const List<label>& tetherPotentialList::tetherIds() const
-{
-    return tetherIds_;
-}
-
-
-inline label tetherPotentialList::nTetherPotentials() const
-{
-    return tetherIds_.size();
-}
-
-
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-} // End namespace Foam
-
-// ************************************************************************* //
diff --git a/src/lagrangian/molecule/reducedUnits/reducedUnits.C b/src/lagrangian/molecule/reducedUnits/reducedUnits.C
deleted file mode 100644
index 3536893f8e..0000000000
--- a/src/lagrangian/molecule/reducedUnits/reducedUnits.C
+++ /dev/null
@@ -1,165 +0,0 @@
-/*---------------------------------------------------------------------------*\
-  =========                 |
-  \\      /  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 "reducedUnits.H"
-
-// * * * * * * * * * * * * * * Static Data Members * * * * * * * * * * * * * //
-
-const  Foam::scalar Foam::reducedUnits::kb = 1.3806504e-23;
-
-
-// * * * * * * * * * * * * * Private Member Functions  * * * * * * * * * * * //
-
-void Foam::reducedUnits::calcRefValues()
-{
-    if
-    (
-        refTime_ < VSMALL
-     || refLength_ < VSMALL
-     || refMass_ < VSMALL
-    )
-    {
-        FatalErrorIn("Foam::reducedUnits::calcRefValues() ")
-            << "One of more referencence values too small for floating point "
-            << "calculation: "
-            << "refTime_ = " << refTime_
-            << ", refLength = " << refTemp_
-            << ", refMass = " << refMass_
-            << nl << abort(FatalError);
-    }
-
-    refEnergy_ = refLength_*refLength_*refMass_/(refTime_*refTime_);
-
-    refTemp_ = refEnergy_ / kb;
-
-    refForce_ = refEnergy_/refLength_;
-
-    refVelocity_ = Foam::sqrt(refEnergy_/refMass_);
-
-    refVolume_ = Foam::pow(refLength_,3.0);
-
-    refPressure_ = refEnergy_/refVolume_;
-
-    refMassDensity_ = refMass_/refVolume_;
-
-    refNumberDensity_ = 1.0/refVolume_;
-}
-
-
-// * * * * * * * * * * * * * * * * Constructors  * * * * * * * * * * * * * * //
-
-Foam::reducedUnits::reducedUnits()
-:
-    refLength_(1e-9),
-    refTime_(1e-12),
-    refMass_(1.660538782e-27)
-{
-    calcRefValues();
-}
-
-
-Foam::reducedUnits::reducedUnits
-(
-    scalar refLength,
-    scalar refTime,
-    scalar refMass
-)
-:
-    refLength_(refLength),
-    refTime_(refTime),
-    refMass_(refMass)
-{
-    calcRefValues();
-}
-
-
-Foam::reducedUnits::reducedUnits(const IOdictionary& reducedUnitsDict)
-:
-    refLength_(),
-    refTime_(),
-    refMass_()
-{
-    setRefValues(reducedUnitsDict);
-}
-
-
-// * * * * * * * * * * * * * * * * Destructor  * * * * * * * * * * * * * * * //
-
-Foam::reducedUnits::~reducedUnits()
-{}
-
-
-// * * * * * * * * * * * * * * * Member Functions  * * * * * * * * * * * * * //
-
-void Foam::reducedUnits::setRefValues
-(
-    scalar refLength,
-    scalar refTime,
-    scalar refMass
-)
-{
-    refLength_ = refLength;
-
-    refTime_ = refTime;
-
-    refMass_ = refMass;
-
-    calcRefValues();
-}
-
-
-void Foam::reducedUnits::setRefValues
-(
-    const IOdictionary& reducedUnitsDict
-)
-{
-    refLength_ = readScalar(reducedUnitsDict.lookup("refLength"));
-
-    refTime_ = readScalar(reducedUnitsDict.lookup("refTime"));
-
-    refMass_  = readScalar(reducedUnitsDict.lookup("refMass"));
-
-    calcRefValues();
-}
-
-
-// * * * * * * * * * * * * * * * Member Operators  * * * * * * * * * * * * * //
-
-void Foam::reducedUnits::operator=(const reducedUnits& rhs)
-{
-    // Check for assignment to self
-    if (this == &rhs)
-    {
-        FatalErrorIn
-        (
-            "Foam::reducedUnits::operator=(const Foam::reducedUnits&)"
-        )   << "Attempted assignment to self"
-            << abort(FatalError);
-    }
-}
-
-
-// ************************************************************************* //
diff --git a/src/lagrangian/molecule/reducedUnits/reducedUnits.H b/src/lagrangian/molecule/reducedUnits/reducedUnits.H
deleted file mode 100644
index 7adc1051fd..0000000000
--- a/src/lagrangian/molecule/reducedUnits/reducedUnits.H
+++ /dev/null
@@ -1,184 +0,0 @@
-/*---------------------------------------------------------------------------*\
-  =========                 |
-  \\      /  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::reducedUnits
-
-Description
-
-SourceFiles
-    reducedUnitsI.H
-    reducedUnits.C
-    reducedUnitsIO.C
-
-\*---------------------------------------------------------------------------*/
-
-#ifndef reducedUnits_H
-#define reducedUnits_H
-
-#include "scalar.H"
-#include "IOdictionary.H"
-
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-namespace Foam
-{
-
-/*---------------------------------------------------------------------------*\
-                           Class reducedUnits Declaration
-\*---------------------------------------------------------------------------*/
-
-class reducedUnits
-{
-    // Private data
-
-        // Reduced units
-
-            // Fundamental values
-
-                scalar refLength_;
-
-                scalar refTime_;
-
-                scalar refMass_;
-
-            // Derived values
-
-                scalar refEnergy_;
-
-                scalar refTemp_;
-
-                scalar refForce_;
-
-                scalar refVelocity_;
-
-                scalar refVolume_;
-
-                scalar refPressure_;
-
-               scalar refMassDensity_;
-
-                scalar refNumberDensity_;
-
-
-    // Private Member Functions
-
-        void calcRefValues();
-
-        //- Disallow default bitwise copy construct
-        reducedUnits(const reducedUnits&);
-
-        //- Disallow default bitwise assignment
-        void operator=(const reducedUnits&);
-
-
-public:
-
-    // Static data members
-
-        //- Static data someStaticData
-        static const scalar kb;
-
-
-    // Constructors
-
-        //- Construct with no argument, uses default values:
-        // length  = 1nm
-        // mass = 1.660538782e−27kg (unified atomic mass unit)
-        // temperature = 1K (therefore, energy = 1*kb)
-        reducedUnits();
-
-        //- Construct from components
-        reducedUnits
-        (
-            scalar refLength,
-            scalar refTime,
-            scalar refMass
-        );
-
-        //- Construct from dictionary
-        reducedUnits(const IOdictionary& reducedUnitsDict);
-
-
-    // Destructor
-
-        ~reducedUnits();
-
-
-    // Member Functions
-
-        void setRefValues
-        (
-            scalar refLength,
-            scalar refTime,
-            scalar refMass
-        );
-
-        void setRefValues(const IOdictionary& reducedUnitsDict);
-
-
-        // Access
-
-            inline scalar refLength() const;
-
-            inline scalar refTime() const;
-
-            inline scalar refMass() const;
-
-            inline scalar refTemp() const;
-
-            inline scalar refEnergy() const;
-
-            inline scalar refForce() const;
-
-            inline scalar refVelocity() const;
-
-            inline scalar refVolume() const;
-
-            inline scalar refPressure() const;
-
-            inline scalar refMassDensity() const;
-
-            inline scalar refNumberDensity() const;
-
-
-    // IOstream Operators
-
-        friend Ostream& operator<<(Ostream&, const reducedUnits&);
-};
-
-
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-} // End namespace Foam
-
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-#include "reducedUnitsI.H"
-
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-#endif
-
-// ************************************************************************* //
diff --git a/src/lagrangian/molecule/reducedUnits/reducedUnitsI.H b/src/lagrangian/molecule/reducedUnits/reducedUnitsI.H
deleted file mode 100644
index 8098885d68..0000000000
--- a/src/lagrangian/molecule/reducedUnits/reducedUnitsI.H
+++ /dev/null
@@ -1,95 +0,0 @@
-/*---------------------------------------------------------------------------*\
-  =========                 |
-  \\      /  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
-
-\*---------------------------------------------------------------------------*/
-
-// * * * * * * * * * * * * * * * Member Functions  * * * * * * * * * * * * * //
-
-inline Foam::scalar Foam::reducedUnits::refLength() const
-{
-    return refLength_;
-}
-
-
-inline Foam::scalar Foam::reducedUnits::refTime() const
-{
-    return refTime_;
-}
-
-
-inline Foam::scalar Foam::reducedUnits::refMass() const
-{
-    return refMass_;
-}
-
-
-inline Foam::scalar Foam::reducedUnits::refTemp() const
-{
-    return refTemp_;
-}
-
-
-inline Foam::scalar Foam::reducedUnits::refEnergy() const
-{
-    return refEnergy_;
-}
-
-
-inline Foam::scalar Foam::reducedUnits::refForce() const
-{
-    return refForce_;
-}
-
-
-inline Foam::scalar Foam::reducedUnits::refVelocity() const
-{
-    return refVelocity_;
-}
-
-
-inline Foam::scalar Foam::reducedUnits::refVolume() const
-{
-    return refVolume_;
-}
-
-
-inline Foam::scalar Foam::reducedUnits::refPressure() const
-{
-    return refPressure_;
-}
-
-
-inline Foam::scalar Foam::reducedUnits::refMassDensity() const
-{
-    return refMassDensity_;
-}
-
-
-inline Foam::scalar Foam::reducedUnits::refNumberDensity() const
-{
-    return refNumberDensity_;
-}
-
-
-// ************************************************************************* //
diff --git a/src/lagrangian/molecule/reducedUnits/reducedUnitsIO.C b/src/lagrangian/molecule/reducedUnits/reducedUnitsIO.C
deleted file mode 100644
index 88d110a5be..0000000000
--- a/src/lagrangian/molecule/reducedUnits/reducedUnitsIO.C
+++ /dev/null
@@ -1,61 +0,0 @@
-/*---------------------------------------------------------------------------*\
-  =========                 |
-  \\      /  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 "reducedUnits.H"
-#include "IOstreams.H"
-
-// * * * * * * * * * * * * * * * IOstream Operators  * * * * * * * * * * * * //
-
-Foam::Ostream& Foam::operator<<(Ostream& os, const reducedUnits& rU)
-{
-    os  << nl << "Defined: " << nl
-        << tab << "refLength = " << rU.refLength() << " m" << nl
-        << tab << "refTime = " << rU.refTime() << " s" << nl
-        << tab << "refMass = " << rU.refMass() << " kg" << nl
-        << tab << "Boltzmann constant, kb = " << reducedUnits::kb << " J/K"
-        << nl << "Calculated: " << nl
-        << tab << "refEnergy = " << rU.refEnergy() << " J" << nl
-        << tab << "refTemp = " << rU.refTemp() << " K" << nl
-        << tab << "refForce = " << rU.refForce() << " N" << nl
-        << tab << "refVelocity = " << rU.refVelocity() << " m/s" << nl
-        << tab << "refVolume = " << rU.refVolume() << " m^3" << nl
-        << tab << "refPressure = " << rU.refPressure() << " N/m^2" << nl
-        << tab << "refMassDensity = " << rU.refMassDensity() << " kg/m^3" << nl
-        << tab << "refNumberDensity = " << rU.refNumberDensity() << " m^-3"
-        << endl;
-
-    // Check state of Ostream
-    os.check
-    (
-        "Foam::Ostream& Foam::operator<<(Foam::Ostream&, "
-        "const Foam::reducedUnits&)"
-    );
-
-    return os;
-}
-
-
-// ************************************************************************* //
diff --git a/src/lagrangian/molecule/referralLists/receivingReferralList.C b/src/lagrangian/molecule/referralLists/receivingReferralList.C
deleted file mode 100755
index e35c660b74..0000000000
--- a/src/lagrangian/molecule/referralLists/receivingReferralList.C
+++ /dev/null
@@ -1,181 +0,0 @@
-/*---------------------------------------------------------------------------*\
-  =========                 |
-  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
-   \\    /   O peration     |
-    \\  /    A nd           | Copyright (C) 1991-2005 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 "receivingReferralList.H"
-
-namespace Foam
-{
-
-// * * * * * * * * * * * * * * * * Constructors  * * * * * * * * * * * * * * //
-
-receivingReferralList::receivingReferralList()
-:
-    labelListList(),
-    sourceProc_(-1)
-{}
-
-
-receivingReferralList::receivingReferralList
-(
-    const label sourceProc,
-    const labelListList& refCellsToSendTo
-)
-:
-    labelListList(refCellsToSendTo),
-    sourceProc_(sourceProc)
-{}
-
-
-receivingReferralList::receivingReferralList
-(
-    const receivingReferralList& rL
-)
-:
-    labelListList(rL),
-    sourceProc_(rL.sourceProc())
-{}
-
-
-// * * * * * * * * * * * * * * * * Destructor  * * * * * * * * * * * * * * * //
-
-receivingReferralList::~receivingReferralList()
-{}
-
-
-// * * * * * * * * * * * * * * * Member Operators  * * * * * * * * * * * * * //
-
-void receivingReferralList::operator=(const receivingReferralList& rhs)
-{
-    // Check for assignment to self
-    if (this == &rhs)
-    {
-        FatalErrorIn
-        (
-            "Foam::receivingReferralList::operator="
-            "(const Foam::receivingReferralList&)"
-        )
-            << "Attempted assignment to self"
-            << abort(FatalError);
-    }
-
-    labelListList::operator=(rhs);
-
-    sourceProc_ = rhs.sourceProc();
-}
-
-
-// * * * * * * * * * * * * * * * Friend Operators  * * * * * * * * * * * * * //
-
-bool operator==
-(
-    const receivingReferralList& a,
-    const receivingReferralList& b
-)
-{
-    // Trivial reject: lists are different size
-    if (a.size() != b.size())
-    {
-        return false;
-    }
-
-    // Or if source processors are not the same.
-    if (a.sourceProc() != b.sourceProc())
-    {
-        return false;
-    }
-
-    List<bool> fnd(a.size(), false);
-
-    forAll (b, bI)
-    {
-        labelList curLList = b[bI];
-
-        bool found = false;
-
-        forAll (a, aI)
-        {
-            if (a[aI] == curLList)
-            {
-                found = true;
-                fnd[aI] = true;
-                break;
-            }
-        }
-
-        if (!found)
-        {
-            return false;
-        }
-    }
-
-    // check if all LLists on a were marked
-    bool result = true;
-
-    forAll (fnd, aI)
-    {
-        result = (result && fnd[aI]);
-    }
-
-    return result;
-}
-
-
-Istream& operator>>(Istream& is, receivingReferralList& rRL)
-{
-    is >> rRL.sourceProc_ >> static_cast<labelListList&>(rRL);
-
-    is.check
-    (
-        "Istream& operator<<(Istream& f, const receivingReferralList& rRL"
-    );
-
-    return is;
-}
-
-
-Ostream& operator<<
-(
-    Ostream& os,
-    const receivingReferralList& rRL
-)
-{
-    os << rRL.sourceProc() << token::SPACE
-        << static_cast< const labelListList& >(rRL);
-
-    os.check
-    (
-        "Ostream& operator<<(Ostream& f, const receivingReferralList& rRL"
-    );
-
-    return os;
-}
-
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-} // End namespace Foam
-
-
-// ************************************************************************* //
diff --git a/src/lagrangian/molecule/referralLists/receivingReferralList.H b/src/lagrangian/molecule/referralLists/receivingReferralList.H
deleted file mode 100755
index e64a0836f8..0000000000
--- a/src/lagrangian/molecule/referralLists/receivingReferralList.H
+++ /dev/null
@@ -1,138 +0,0 @@
-/*---------------------------------------------------------------------------*\
-  =========                 |
-  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
-   \\    /   O peration     |
-    \\  /    A nd           | Copyright (C) 1991-2005 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::receivingReferralList
-
-Description
-
-SourceFiles
-    receivingReferralListI.H
-    receivingReferralList.C
-    receivingReferralListIO.C
-
-\*---------------------------------------------------------------------------*/
-
-#ifndef receivingReferralList_H
-#define receivingReferralList_H
-
-#include "labelList.H"
-
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-namespace Foam
-{
-
-/*---------------------------------------------------------------------------*\
-                    Class receivingReferralList Declaration
-\*---------------------------------------------------------------------------*/
-
-class receivingReferralList
-:
-    public labelListList
-{
-    // Private data
-
-        label sourceProc_;
-
-
-public:
-
-    // Constructors
-
-        //- Construct null
-        receivingReferralList();
-
-        //- Construct from components
-        receivingReferralList
-        (
-            const label sourceProc,
-            const labelListList& refCellsToSendTo
-        );
-
-        //- Construct as copy
-        receivingReferralList(const receivingReferralList&);
-
-
-    // Destructor
-
-        ~receivingReferralList();
-
-
-    // Member Functions
-
-        // Access
-
-            inline label sourceProc() const;
-
-
-    // Member Operators
-
-        void operator=(const receivingReferralList&);
-
-
-    // Friend Operators
-
-        friend bool operator==
-        (
-            const receivingReferralList& a,
-            const receivingReferralList& b
-        );
-
-        inline friend bool operator!=
-        (
-            const receivingReferralList& a,
-            const receivingReferralList& b
-        );
-
-
-    // IOstream Operators
-
-        friend Istream& operator>>
-        (
-            Istream&,
-            receivingReferralList&
-        );
-
-        friend Ostream& operator<<
-        (
-            Ostream&,
-            const receivingReferralList&
-        );
-};
-
-
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-} // End namespace Foam
-
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-#include "receivingReferralListI.H"
-
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-#endif
-
-// ************************************************************************* //
diff --git a/src/lagrangian/molecule/referralLists/receivingReferralListI.H b/src/lagrangian/molecule/referralLists/receivingReferralListI.H
deleted file mode 100755
index d91e01fe08..0000000000
--- a/src/lagrangian/molecule/referralLists/receivingReferralListI.H
+++ /dev/null
@@ -1,56 +0,0 @@
-/*---------------------------------------------------------------------------*\
-  =========                 |
-  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
-   \\    /   O peration     |
-    \\  /    A nd           | Copyright (C) 1991-2005 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
-{
-
-// * * * * * * * * * * * * * * * Member Functions  * * * * * * * * * * * * * //
-
-inline label receivingReferralList::sourceProc() const
-{
-    return sourceProc_;
-}
-
-
-// * * * * * * * * * * * * * * * Friend Operators  * * * * * * * * * * * * * //
-
-inline bool operator!=
-(
-    const receivingReferralList& a,
-    const receivingReferralList& b
-)
-{
-    return (!(a == b));
-}
-
-
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-} // End namespace Foam
-
-// ************************************************************************* //
diff --git a/src/lagrangian/molecule/referralLists/sendingReferralList.C b/src/lagrangian/molecule/referralLists/sendingReferralList.C
deleted file mode 100755
index 9065102193..0000000000
--- a/src/lagrangian/molecule/referralLists/sendingReferralList.C
+++ /dev/null
@@ -1,178 +0,0 @@
-/*---------------------------------------------------------------------------*\
-  =========                 |
-  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
-   \\    /   O peration     |
-    \\  /    A nd           | Copyright (C) 1991-2005 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 "sendingReferralList.H"
-
-namespace Foam
-{
-
-// * * * * * * * * * * * * * * * * Constructors  * * * * * * * * * * * * * * //
-
-sendingReferralList::sendingReferralList()
-:
-    labelList(),
-    destinationProc_(-1)
-{}
-
-
-sendingReferralList::sendingReferralList
-(
-    const label destinationProc,
-    const labelList& cellsToSend
-)
-:
-    labelList(cellsToSend),
-    destinationProc_(destinationProc)
-{}
-
-
-sendingReferralList::sendingReferralList
-(
-    const sendingReferralList& rL
-)
-:
-    labelList(rL),
-    destinationProc_(rL.destinationProc())
-{}
-
-
-// * * * * * * * * * * * * * * * * Destructor  * * * * * * * * * * * * * * * //
-
-sendingReferralList::~sendingReferralList()
-{}
-
-
-// * * * * * * * * * * * * * * * Member Operators  * * * * * * * * * * * * * //
-
-void sendingReferralList::operator=(const sendingReferralList& rhs)
-{
-    // Check for assignment to self
-    if (this == &rhs)
-    {
-        FatalErrorIn
-        (
-            "Foam::distribution::operator=(const Foam::distribution&)"
-        )
-            << "Attempted assignment to self"
-            << abort(FatalError);
-    }
-
-    labelList::operator=(rhs);
-
-    destinationProc_ = rhs.destinationProc();
-}
-
-
-// * * * * * * * * * * * * * * * Friend Operators  * * * * * * * * * * * * * //
-
-bool operator==
-(
-    const sendingReferralList& a,
-    const sendingReferralList& b
-)
-{
-    // Trivial reject: lists are different size
-    if (a.size() != b.size())
-    {
-        return false;
-    }
-
-    // Or if source processors are not the same.
-    if (a.destinationProc() != b.destinationProc())
-    {
-        return false;
-    }
-
-    List<bool> fnd(a.size(), false);
-
-    forAll (b, bI)
-    {
-        label curLabel = b[bI];
-
-        bool found = false;
-
-        forAll (a, aI)
-        {
-            if (a[aI] == curLabel)
-            {
-                found = true;
-                fnd[aI] = true;
-                break;
-            }
-        }
-
-        if (!found)
-        {
-            return false;
-        }
-    }
-
-    // check if all labels on a were marked
-    bool result = true;
-
-    forAll (fnd, aI)
-    {
-        result = (result && fnd[aI]);
-    }
-
-    return result;
-}
-
-
-Istream& operator>>
-(
-    Istream& is,
-    sendingReferralList& sRL
-)
-{
-    is >> sRL.destinationProc_ >> static_cast<labelList&>(sRL);
-
-    is.check("Istream& operator<<(Istream& f, const sendingReferralList& sRL");
-
-    return is;
-}
-
-
-Ostream& operator<<
-(
-    Ostream& os,
-    const sendingReferralList& rL
-)
-{
-    os << rL.destinationProc() << token::SPACE
-        << static_cast< const labelList& >(rL);
-
-    os.check("Ostream& operator<<(Ostream& f, const sendingReferralList& rL");
-
-    return os;
-}
-
-
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-} // End namespace Foam
-
-// ************************************************************************* //
diff --git a/src/lagrangian/molecule/referralLists/sendingReferralList.H b/src/lagrangian/molecule/referralLists/sendingReferralList.H
deleted file mode 100755
index 0d729e35be..0000000000
--- a/src/lagrangian/molecule/referralLists/sendingReferralList.H
+++ /dev/null
@@ -1,138 +0,0 @@
-/*---------------------------------------------------------------------------*\
-  =========                 |
-  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
-   \\    /   O peration     |
-    \\  /    A nd           | Copyright (C) 1991-2005 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::sendingReferralList
-
-Description
-
-SourceFiles
-    sendingReferralListI.H
-    sendingReferralList.C
-    sendingReferralListIO.C
-
-\*---------------------------------------------------------------------------*/
-
-#ifndef sendingReferralList_H
-#define sendingReferralList_H
-
-#include "labelList.H"
-
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-namespace Foam
-{
-
-/*---------------------------------------------------------------------------*\
-                      Class sendingReferralList Declaration
-\*---------------------------------------------------------------------------*/
-
-class sendingReferralList
-:
-    public labelList
-{
-    // Private data
-
-        label destinationProc_;
-
-
-public:
-
-    // Constructors
-
-        //- Construct null
-        sendingReferralList();
-
-        //- Construct from components
-        sendingReferralList
-        (
-            const label destinationProc,
-            const labelList& cellsToSend
-        );
-
-        //- Construct as copy
-        sendingReferralList(const sendingReferralList&);
-
-
-    // Destructor
-
-        ~sendingReferralList();
-
-
-    // Member Functions
-
-        // Access
-
-            inline label destinationProc() const;
-
-
-    // Member Operators
-
-        void operator=(const sendingReferralList&);
-
-
-    // Friend Operators
-
-        friend bool operator==
-        (
-            const sendingReferralList& a,
-            const sendingReferralList& b
-        );
-
-        inline friend bool operator!=
-        (
-            const sendingReferralList& a,
-            const sendingReferralList& b
-        );
-
-
-    // IOstream Operators
-
-        friend Istream& operator>>
-        (
-            Istream&,
-            sendingReferralList&
-        );
-
-        friend Ostream& operator<<
-        (
-            Ostream&,
-            const sendingReferralList&
-        );
-};
-
-
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-} // End namespace Foam
-
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-#include "sendingReferralListI.H"
-
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-#endif
-
-// ************************************************************************* //
diff --git a/src/lagrangian/molecule/referralLists/sendingReferralListI.H b/src/lagrangian/molecule/referralLists/sendingReferralListI.H
deleted file mode 100755
index d571962f5d..0000000000
--- a/src/lagrangian/molecule/referralLists/sendingReferralListI.H
+++ /dev/null
@@ -1,56 +0,0 @@
-/*---------------------------------------------------------------------------*\
-  =========                 |
-  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
-   \\    /   O peration     |
-    \\  /    A nd           | Copyright (C) 1991-2005 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
-{
-
-// * * * * * * * * * * * * * * * Member Functions  * * * * * * * * * * * * * //
-
-inline label sendingReferralList::destinationProc() const
-{
-    return destinationProc_;
-}
-
-
-// * * * * * * * * * * * * * * * Friend Operators  * * * * * * * * * * * * * //
-
-inline bool operator!=
-(
-    const sendingReferralList& a,
-    const sendingReferralList& b
-)
-{
-    return (!(a == b));
-}
-
-
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-} // End namespace Foam
-
-// ************************************************************************* //
diff --git a/src/lagrangian/molecule/referredCell/referredCell.C b/src/lagrangian/molecule/referredCell/referredCell.C
deleted file mode 100755
index c60ae69bf4..0000000000
--- a/src/lagrangian/molecule/referredCell/referredCell.C
+++ /dev/null
@@ -1,441 +0,0 @@
-/*---------------------------------------------------------------------------*\
-  =========                 |
-  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
-   \\    /   O peration     |
-    \\  /    A nd           | Copyright (C) 1991-2005 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 "referredCell.H"
-#include "moleculeCloud.H"
-
-namespace Foam
-{
-
-// * * * * * * * * * * * * * Private Member Functions  * * * * * * * * * * * //
-
-void referredCell::setConstructionData
-(
-    const polyMesh& mesh,
-    const label sourceCell
-)
-{
-    // * * * * * * * * * * * Points * * * * * * * * * * *
-
-    const labelList& points = mesh.cellPoints()[sourceCell];
-
-    vectorList sourceCellVertices(points.size());
-
-    forAll(sourceCellVertices, sCV)
-    {
-        sourceCellVertices[sCV] = mesh.points()[points[sCV]];
-    }
-
-    vertexPositions_ = referPositions(sourceCellVertices);
-
-    // * * * * * * * * * * * Edges * * * * * * * * * * *
-
-    const labelList& edges = mesh.cellEdges()[sourceCell];
-
-    edgeList sourceCellEdges(edges.size());
-
-    forAll(sourceCellEdges, sCE)
-    {
-        sourceCellEdges[sCE] = mesh.edges()[edges[sCE]];
-    }
-
-    locallyMapEdgeList(points, sourceCellEdges);
-
-    // * * * * * * * * * * * Faces * * * * * * * * * * *
-
-    labelList faces(mesh.cells()[sourceCell]);
-
-    vectorList sourceCellFaceCentres(faces.size());
-
-    vectorList sourceCellFaceAreas(faces.size());
-
-    labelListList sourceCellFaces(faces.size());
-
-    forAll(faces, f)
-    {
-        sourceCellFaces[f] = mesh.faces()[faces[f]];
-
-        sourceCellFaceCentres[f] = mesh.faceCentres()[faces[f]];
-
-        sourceCellFaceAreas[f] = mesh.faceAreas()[faces[f]];
-    }
-
-    locallyMapFaceList(points, sourceCellFaces);
-
-    faceCentres_ = referPositions(sourceCellFaceCentres);
-
-    faceAreas_ = rotateVectors(sourceCellFaceAreas);
-}
-
-
-void referredCell::locallyMapEdgeList
-(
-    const labelList& points,
-    const edgeList& sourceCellEdges
-)
-{
-    edges_.setSize(sourceCellEdges.size());
-
-    forAll(sourceCellEdges, sCE)
-    {
-        const edge& e(sourceCellEdges[sCE]);
-
-        edges_[sCE].start() = findIndex(points, e.start());
-
-        edges_[sCE].end() = findIndex(points, e.end());
-
-        if
-        (
-            edges_[sCE].start() == -1
-         || edges_[sCE].end() == -1
-        )
-        {
-            FatalErrorIn("Foam::referredCell::locallyMapEdgeList")
-                << "edgeList and points labelList for "
-                << "referred cell do not match: "
-                << nl << "points: " << points
-                << nl << "egdes: " << sourceCellEdges
-                << abort(FatalError);
-        }
-    }
-}
-
-
-void referredCell::locallyMapFaceList
-(
-    const labelList& points,
-    const labelListList& sourceCellFaces
-)
-{
-    faces_.setSize(sourceCellFaces.size());
-
-    forAll(sourceCellFaces, sCF)
-    {
-        const labelList& sourceCellFace(sourceCellFaces[sCF]);
-
-        labelList& localFace(faces_[sCF]);
-
-        localFace.setSize(sourceCellFace.size());
-
-        forAll(sourceCellFace, p)
-        {
-            localFace[p] = findIndex(points, sourceCellFace[p]);
-
-            if (localFace[p] == -1)
-            {
-                FatalErrorIn("Foam::referredCell::locallyMapEdgeList")
-                    << "edgeList and points labelList for "
-                    << "referred cell do not match: "
-                    << nl << "points: " << points
-                    << nl << "faces: " << sourceCellFaces
-                    << abort(FatalError);
-            }
-        }
-    }
-}
-
-
-vector referredCell::referPosition(const vector& positionToRefer)
-{
-    return offset_ + (rotation_ & positionToRefer);
-}
-
-
-vectorList referredCell::referPositions(const vectorList& positionsToRefer)
-{
-    return offset_ + (rotation_ & positionsToRefer);
-}
-
-
-vector referredCell::rotateVector(const vector& vectorToRotate)
-{
-    return rotation_ & vectorToRotate;
-}
-
-
-vectorList referredCell::rotateVectors(const vectorList& vectorsToRotate)
-{
-    return rotation_ & vectorsToRotate;
-}
-
-
-// * * * * * * * * * * * * * * * * Constructors  * * * * * * * * * * * * * * //
-
-referredCell::referredCell()
-:
-    DynamicList<referredMolecule>(),
-    sourceProc_(-1),
-    sourceCell_(-1),
-    vertexPositions_(),
-    offset_(vector::zero),
-    rotation_(I)
-{}
-
-
-referredCell::referredCell
-(
-    const polyMesh& mesh,
-    const label sourceProc,
-    const label sourceCell,
-    const vector& offset,
-    const tensor& rotation
-)
-:
-    DynamicList<referredMolecule>(),
-    sourceProc_(sourceProc),
-    sourceCell_(sourceCell),
-    offset_(offset),
-    rotation_(rotation)
-{
-    setConstructionData(mesh, sourceCell);
-}
-
-
-referredCell::referredCell
-(
-    const label sourceProc,
-    const label sourceCell,
-    const vectorList& vertexPositions,
-    const edgeList& localEdges,
-    const labelListList& localFaces,
-    const vectorList& faceCentres,
-    const vectorList& faceAreas,
-    const vector& offset,
-    const tensor& rotation
-)
-:
-    DynamicList<referredMolecule>(),
-    sourceProc_(sourceProc),
-    sourceCell_(sourceCell),
-    edges_(localEdges),
-    faces_(localFaces),
-    offset_(offset),
-    rotation_(rotation)
-{
-    // Supplied vertexPositions, faceCentres and faceAreas are of the
-    // "original" cell, and need to be transformed to the referred
-    // locations on construction
-
-    vertexPositions_ = referPositions(vertexPositions);
-
-    faceCentres_ = referPositions(faceCentres);
-
-    faceAreas_ = rotateVectors(faceAreas);
-}
-
-
-referredCell::referredCell
-(
-    const polyMesh& mesh,
-    const label sourceProc,
-    const label sourceCell,
-    const vector& cS,
-    const vector& cD,
-    const vector& nS,
-    const vector& nD
-)
-:
-    DynamicList<referredMolecule>(),
-    sourceProc_(sourceProc),
-    sourceCell_(sourceCell)
-{
-    // It is assumed that the vectors originating from the faces being referred
-    // here are correct periodic faces - i.e. they have the same area etc.
-
-    vector nA = -nS/mag(nS);
-    vector nB = nD/mag(nD);
-
-    rotation_ = rotationTensor(nA, nB);
-
-    offset_ = cD - (rotation_ & cS);
-
-    // Allow sourceCell = -1 to create a dummy referredCell
-    // to obtain the transformation
-
-    if(sourceCell >= 0)
-    {
-        setConstructionData(mesh, sourceCell);
-    }
-}
-
-
-// * * * * * * * * * * * * * * * * Destructor  * * * * * * * * * * * * * * * //
-
-referredCell::~referredCell()
-{}
-
-
-// * * * * * * * * * * * * * * * Member Functions  * * * * * * * * * * * * * //
-
-referredCell referredCell::reRefer
-(
-    const vector& cS,
-    const vector& cD,
-    const vector& nS,
-    const vector& nD
-)
-{
-    vector nA = -nS/mag(nS);
-    vector nB = nD/mag(nD);
-
-    tensor newRotation = rotationTensor(nA, nB);
-
-    vector newOffset = cD - (newRotation & cS);
-
-    tensor reReferredRotation = newRotation & rotation_;
-
-    vector reReferredOffset = newOffset + (newRotation & offset_);
-
-    return referredCell
-    (
-        sourceProc_,
-        sourceCell_,
-        rotation_.T() & (vertexPositions_ - offset_),
-        edges_,
-        faces_,
-        rotation_.T() & (faceCentres_ - offset_),
-        rotation_.T() & (faceAreas_),
-        reReferredOffset,
-        reReferredRotation
-    );
-}
-
-
-vector referredCell::referPosition(const vector& positionToRefer) const
-{
-    return offset_ + (rotation_ & positionToRefer);
-}
-
-
-vectorList referredCell::referPositions
-(
-    const vectorList& positionsToRefer
-) const
-{
-    return offset_ + (rotation_ & positionsToRefer);
-}
-
-
-vector referredCell::rotateVector(const vector& vectorToRotate) const
-{
-    return rotation_ & vectorToRotate;
-}
-
-
-vectorList referredCell::rotateVectors(const vectorList& vectorsToRotate) const
-{
-    return rotation_ & vectorsToRotate;
-}
-
-
-void referredCell::referInMols(const List<referredMolecule>& incomingMols)
-{
-    clear();
-
-    forAll(incomingMols, iM)
-    {
-        append
-        (
-            referredMolecule
-            (
-                incomingMols[iM].id(),
-                referPosition
-                (
-                    incomingMols[iM].position()
-                )
-            )
-        );
-    }
-}
-
-
-bool referredCell::duplicate(const referredCell& refCellDupl) const
-{
-    return
-    (
-        sourceProc_ == refCellDupl.sourceProc()
-        && sourceCell_ == refCellDupl.sourceCell()
-        && mag(offset_ - refCellDupl.offset()) < moleculeCloud::transTol
-    );
-}
-
-
-bool referredCell::duplicate(const label procNo,const label nCells) const
-{
-    return
-    (
-        sourceProc_ == procNo
-        && sourceCell_ < nCells
-        && mag(offset_) < moleculeCloud::transTol
-    );
-}
-
-
-// * * * * * * * * * * * * * * * Friend Functions  * * * * * * * * * * * * * //
-
-Istream& operator>>(Istream& is, referredCell& rC)
-{
-
-    is >> rC.sourceProc_
-        >> rC.sourceCell_
-        >> rC.vertexPositions_
-        >> rC.edges_
-        >> rC.faces_
-        >> rC.faceCentres_
-        >> rC.faceAreas_
-        >> rC.offset_
-        >> rC.rotation_;
-
-    is.check("Istream& operator<<(Istream& f, const referredCell& rC");
-
-    return is;
-}
-
-
-Ostream& operator<<(Ostream& os, const referredCell& rC)
-{
-
-    os << rC.sourceProc()
-        << token::SPACE << rC.sourceCell()
-        << token::SPACE << rC.vertexPositions()
-        << token::SPACE << rC.edges()
-        << token::SPACE << rC.faces()
-        << token::SPACE << rC.faceCentres()
-        << token::SPACE << rC.faceAreas()
-        << token::SPACE << rC.offset()
-        << token::SPACE << rC.rotation();
-
-    os.check("Ostream& operator<<(Ostream& f, const referredCell& rC");
-
-    return os;
-}
-
-
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-}  // End namespace Foam
-
-// ************************************************************************* //
diff --git a/src/lagrangian/molecule/referredCell/referredCell.H b/src/lagrangian/molecule/referredCell/referredCell.H
deleted file mode 100755
index 27aaf730fc..0000000000
--- a/src/lagrangian/molecule/referredCell/referredCell.H
+++ /dev/null
@@ -1,277 +0,0 @@
-/*---------------------------------------------------------------------------*\
-  =========                 |
-  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
-   \\    /   O peration     |
-    \\  /    A nd           | Copyright (C) 1991-2005 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::referredCell
-
-Description
-
-SourceFiles
-    referredCellI.H
-    referredCell.C
-
-\*---------------------------------------------------------------------------*/
-
-#ifndef referredCell_H
-#define referredCell_H
-
-#include "vector.H"
-#include "vectorList.H"
-#include "tensor.H"
-#include "transform.H"
-#include "DynamicList.H"
-#include "labelList.H"
-#include "edgeList.H"
-#include "polyMesh.H"
-
-#include "referredMolecule.H"
-
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-namespace Foam
-{
-
-/*---------------------------------------------------------------------------*\
-                           Class referredCell Declaration
-\*---------------------------------------------------------------------------*/
-
-class referredCell
-:
-    public DynamicList<referredMolecule>
-{
-    // Private data
-
-        label sourceProc_;
-
-        label sourceCell_;
-
-        //- Referred vertex positions
-        vectorList vertexPositions_;
-
-        edgeList edges_;
-
-        labelListList faces_;
-
-        vectorList faceCentres_;
-
-        vectorList faceAreas_;
-
-        labelList realCellsForInteraction_;
-
-        vector offset_;
-
-        tensor rotation_;
-
-
-    // Private Member Functions
-
-        void setConstructionData
-        (
-            const polyMesh& mesh,
-            const label sourceCell
-        );
-
-        void locallyMapEdgeList
-        (
-            const labelList& points,
-            const edgeList& sourceCellEdges
-        );
-
-        void locallyMapFaceList
-        (
-            const labelList& points,
-            const labelListList& sourceCellFaces
-        );
-
-        vector referPosition(const vector& positionToRefer);
-
-        vectorList referPositions(const vectorList& positionsToRefer);
-
-        vector rotateVector(const vector& vectorToRotate);
-
-        vectorList rotateVectors(const vectorList& vectorsToRotate);
-
-
-public:
-
-    // Constructors
-
-        //- Construct null
-
-        referredCell();
-
-        //- Construct from components with external edge information
-        referredCell
-        (
-            const polyMesh& mesh,
-            const label sourceProc,
-            const label sourceCell,
-            const vector& offset,
-            const tensor& rotation
-        );
-
-        //- Construct from components with existing local edge information
-        referredCell
-        (
-            const label sourceProc,
-            const label sourceCell,
-            const vectorList& vertexPositions,
-            const edgeList& localEdges,
-            const labelListList& localFaces,
-            const vectorList& faceCentres,
-            const vectorList& faceAreas,
-            const vector& offset,
-            const tensor& rotation
-        );
-
-        //- Construct from pair of face centers (c) and plain
-        //  face normals (n) (no need to make unit vectors or
-        //  reverse one direction)
-        //  Order of vectors important (S = source, D = Destination).
-        //  External edge information.
-
-        referredCell
-        (
-            const polyMesh& mesh,
-            const label sourceProc,
-            const label sourceCell,
-            const vector& cS,
-            const vector& cD,
-            const vector& nS,
-            const vector& nD
-        );
-
-
-    // Destructor
-
-        virtual ~referredCell();
-
-
-    // Member Functions
-
-        //- Take this referredCell object that has already had it's transform
-        //  calculated and refer it on again, retaining same source info.
-        referredCell reRefer
-        (
-            const vector& cS,
-            const vector& cD,
-            const vector& nS,
-            const vector& nD
-        );
-
-        //- Use internal transformatation values to transform the given
-        //  postion to its new location.
-        vector referPosition(const vector& positionToRefer) const;
-
-        //- Use internal transformatation values to transform the given
-        //  list of postions to their new locations.
-        vectorList referPositions(const vectorList& positionsToRefer) const;
-
-        //- Use internal transformatation values to rotate the given vector
-        vector rotateVector(const vector& vectorToRotate) const;
-
-        //- Use internal transformatation values to rotate the given
-        // list of vectors
-        vectorList rotateVectors(const vectorList& vectorsToRotate) const;
-
-        //- referInMols clears, the stored list of referred mols and takes
-        //  in a list of referred mols coming from a source processor,
-        //  transformingtheir positions
-        void referInMols(const List<referredMolecule>& incomingMols);
-
-        //- duplicate() function to test whether a referred or real cell
-        //  supplied by arguement is a duplicate of this referredCell.
-        //  Can be used bi-directionally - i.e. can be called on an existing
-        //  referred cell with a proposed referredCell as argument,
-        //  or vice versa.  Can only be called by a proposed referredCell with
-        //  a real cell index as arguement to test to see if the proposed
-        //  referredCell is a duplicate.
-        //  A duplicate cell is defined as one which has the same source
-        //  processor, source cell, and an equal offset. Real cells have zero
-        //  offset by definition.
-        bool duplicate(const referredCell& refCellDupl) const;
-
-        bool duplicate(const label procNo, const label nCells) const;
-
-
-        // Access
-
-            inline label sourceProc() const;
-
-            inline label sourceCell() const;
-
-            inline const vector& offset() const;
-
-            inline const tensor& rotation() const;
-
-            inline const vectorList& vertexPositions() const;
-
-            inline const edgeList& edges() const;
-
-            inline const labelListList& faces() const;
-
-            inline const vectorList& faceCentres() const;
-
-            inline const vectorList& faceAreas() const;
-
-            inline labelList& realCells();
-
-            inline const labelList& realCellsForInteraction() const;
-
-
-    // Friend Operators
-
-        inline friend bool operator==
-        (
-            const referredCell& a,
-            const referredCell& b
-        );
-
-        inline friend bool operator!=
-        (
-            const referredCell& a,
-            const referredCell& b
-        );
-
-
-    // IOstream Operators
-
-        friend Istream& operator>>(Istream&, referredCell&);
-        friend Ostream& operator<<(Ostream&, const referredCell&);
-};
-
-
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-} // End namespace Foam
-
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-#include "referredCellI.H"
-
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-#endif
-
-// ************************************************************************* //
diff --git a/src/lagrangian/molecule/referredCell/referredCellI.H b/src/lagrangian/molecule/referredCell/referredCellI.H
deleted file mode 100755
index 4135f7ff6e..0000000000
--- a/src/lagrangian/molecule/referredCell/referredCellI.H
+++ /dev/null
@@ -1,127 +0,0 @@
-/*---------------------------------------------------------------------------*\
-  =========                 |
-  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
-   \\    /   O peration     |
-    \\  /    A nd           | Copyright (C) 1991-2005 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
-{
-
-// * * * * * * * * * * * * * * * Member Functions  * * * * * * * * * * * * * //
-
-inline label referredCell::sourceProc() const
-{
-    return sourceProc_;
-}
-
-
-inline label referredCell::sourceCell() const
-{
-    return sourceCell_;
-}
-
-
-inline const vector& referredCell::offset() const
-{
-    return offset_;
-}
-
-
-inline const tensor& referredCell::rotation() const
-{
-    return rotation_;
-}
-
-
-inline const vectorList& referredCell::vertexPositions() const
-{
-    return vertexPositions_;
-}
-
-
-inline const edgeList& referredCell::edges() const
-{
-    return edges_;
-}
-
-
-inline const labelListList& referredCell::faces() const
-{
-    return faces_;
-}
-
-
-inline const vectorList& referredCell::faceCentres() const
-{
-    return faceCentres_;
-}
-
-
-inline const vectorList& referredCell::faceAreas() const
-{
-    return faceAreas_;
-}
-
-
-inline labelList& referredCell::realCells()
-{
-    return realCellsForInteraction_;
-}
-
-
-inline const labelList& referredCell::realCellsForInteraction() const
-{
-    return realCellsForInteraction_;
-}
-
-
-// * * * * * * * * * * * * * * * Friend Operators  * * * * * * * * * * * * * //
-
-inline bool operator==
-(
-    const referredCell& a,
-    const referredCell& b
-)
-{
-    return const_cast<referredCell&>(a).duplicate
-    (
-        const_cast<const referredCell&>(b)
-    );
-}
-
-
-inline bool operator!=
-(
-    const referredCell& a,
-    const referredCell& b
-)
-{
-    return !(a == b);
-}
-
-
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-} // End namespace Foam
-
-// ************************************************************************* //
diff --git a/src/lagrangian/molecule/referredCellList/referredCellList.C b/src/lagrangian/molecule/referredCellList/referredCellList.C
deleted file mode 100755
index cd69a1d9d4..0000000000
--- a/src/lagrangian/molecule/referredCellList/referredCellList.C
+++ /dev/null
@@ -1,327 +0,0 @@
-/*---------------------------------------------------------------------------*\
-  =========                 |
-  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
-   \\    /   O peration     |
-    \\  /    A nd           | Copyright (C) 1991-2005 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 "referredCellList.H"
-#include "moleculeCloud.H"
-
-namespace Foam
-{
-
-// * * * * * * * * * * * * * * * * Constructors  * * * * * * * * * * * * * * //
-
-referredCellList::referredCellList(moleculeCloud& molCloud)
-:
-    List<referredCell >(),
-    molCloud_(molCloud)
-{}
-
-
-referredCellList::referredCellList
-(
-    moleculeCloud& molCloud,
-    const List<referredCell>& referredCells,
-    const List<label>& realCells
-)
-:
-    List< referredCell >(referredCells),
-    molCloud_(molCloud)
-{}
-
-
-// * * * * * * * * * * * * * * * * Destructor  * * * * * * * * * * * * * * * //
-
-referredCellList::~referredCellList()
-{}
-
-
-// * * * * * * * * * * * * * * * Member Functions  * * * * * * * * * * * * * //
-
-void referredCellList::setRealCellsInRange()
-{
-    Info<< nl << "Finding real cells in range of referred cells" << endl;
-
-    forAll(*this, rC)
-    {
-        const polyMesh& mesh(molCloud_.mesh());
-
-        referredCell& refCell = (*this)[rC];
-
-        DynamicList<label> realCellsFoundInRange;
-
-        const vectorList& refCellPoints = refCell.vertexPositions();
-
-        forAll(molCloud_.realFacesWithinRCutMaxOfAnyReferringPatch(), rCF)
-        {
-            const label f
-            (
-                molCloud_.realFacesWithinRCutMaxOfAnyReferringPatch()[rCF]
-            );
-
-            if (molCloud_.testPointFaceDistance(refCellPoints,f))
-            {
-                const label cellO(mesh.faceOwner()[f]);
-
-                if (findIndex(realCellsFoundInRange, cellO) == -1)
-                {
-                    realCellsFoundInRange.append(cellO);
-                }
-
-                if (mesh.isInternalFace(f))
-                {
-                    // boundary faces will not have neighbour information
-
-                    const label cellN(mesh.faceNeighbour()[f]);
-
-                    if (findIndex(realCellsFoundInRange, cellN) == -1)
-                    {
-                        realCellsFoundInRange.append(cellN);
-                    }
-                }
-            }
-        }
-
-        forAll(molCloud_.realPointsWithinRCutMaxOfAnyReferringPatch(), rCP)
-        {
-            const label p
-            (
-                molCloud_.realPointsWithinRCutMaxOfAnyReferringPatch()[rCP]
-            );
-
-            if (molCloud_.testPointFaceDistance(p,refCell))
-            {
-                const labelList& pCells(mesh.pointCells()[p]);
-
-                forAll(pCells, pC)
-                {
-                    const label cellI(pCells[pC]);
-
-                    if (findIndex(realCellsFoundInRange, cellI) == -1)
-                    {
-                        realCellsFoundInRange.append(cellI);
-                    }
-                }
-            }
-        }
-
-
-        const edgeList& refCellEdges = refCell.edges();
-
-        forAll(molCloud_.realEdgesWithinRCutMaxOfAnyReferringPatch(), rCE)
-        {
-            const label edgeIIndex
-            (
-                molCloud_.realEdgesWithinRCutMaxOfAnyReferringPatch()[rCE]
-            );
-
-            const edge& eI(mesh.edges()[edgeIIndex]);
-
-            forAll(refCellEdges, rCE)
-            {
-                const edge& eJ(refCellEdges[rCE]);
-
-                if
-                (
-                    molCloud_.testEdgeEdgeDistance
-                    (
-                        eI,
-                        refCellPoints[eJ.start()],
-                        refCellPoints[eJ.end()]
-                    )
-                )
-                {
-                    const labelList& eICells(mesh.edgeCells()[edgeIIndex]);
-
-                    forAll(eICells, eIC)
-                    {
-                        const label cellI(eICells[eIC]);
-
-                        if (findIndex(realCellsFoundInRange, cellI) == -1)
-                        {
-                            realCellsFoundInRange.append(cellI);
-                        }
-                    }
-                }
-            }
-        }
-
-//         scalar rCutMaxSqr = molCloud_.rCutMax()*molCloud_.rCutMax();
-//
-//         forAll (molCloud_.mesh().points(), pointIIndex)
-//         {
-//             const point& ptI
-//             (
-//                 molCloud_.mesh().points()[pointIIndex]
-//             );
-//
-//             forAll(refCellPoints, rCP)
-//             {
-//                 if (magSqr(ptI - refCellPoints[rCP]) <= rCutMaxSqr)
-//                 {
-//                     const labelList& ptICells
-//                     (
-//                         molCloud_.mesh().pointCells()[pointIIndex]
-//                     );
-//
-//                     forAll(ptICells, pIC)
-//                     {
-//                         const label cellI(ptICells[pIC]);
-//
-//                         if(findIndex(realCellsFoundInRange, cellI) == -1)
-//                         {
-//                             realCellsFoundInRange.append(cellI);
-//                         }
-//                     }
-//                 }
-//             }
-//         }
-
-        refCell.realCells() = realCellsFoundInRange.shrink();
-    }
-}
-
-
-void referredCellList::referMolecules()
-{
-    // Create referred molecules for sending using cell occupancy and
-    // cellSendingReferralLists
-
-    const List<DynamicList<molecule*> >& cellOccupancy
-    (
-        molCloud_.cellOccupancy()
-    );
-
-    forAll(molCloud_.cellSendingReferralLists(), cSRL)
-    {
-        const sendingReferralList& sRL
-        (
-            molCloud_.cellSendingReferralLists()[cSRL]
-        );
-
-        List<DynamicList<referredMolecule> > molsToReferOut(sRL.size());
-
-        forAll(sRL, sRLI)
-        {
-            List<molecule*> realMols = cellOccupancy[sRL[sRLI]];
-
-            forAll (realMols, rM)
-            {
-                molecule* mol = realMols[rM];
-
-                molsToReferOut[sRLI].append
-                (
-                    referredMolecule
-                    (
-                        mol->id(),
-                        mol->position()
-                    )
-                );
-            }
-
-            molsToReferOut[sRLI].shrink();
-        }
-
-        // Send lists of referred molecules to other processors
-
-        if (sRL.destinationProc() != Pstream::myProcNo())
-        {
-            if (Pstream::parRun())
-            {
-                OPstream toInteractingProc
-                (
-                    Pstream::blocking,
-                    sRL.destinationProc()
-                );
-
-                toInteractingProc << molsToReferOut;
-            }
-        }
-        else
-        {
-            // Refer molecules directly for referred cells on the same
-            // processor.
-
-            const receivingReferralList& rRL
-            (
-                molCloud_.cellReceivingReferralLists()[cSRL]
-            );
-
-            forAll(rRL, rRLI)
-            {
-                forAll(rRL[rRLI], rC)
-                {
-                    referredCell& refCellToRefMolsTo = (*this)[rRL[rRLI][rC]];
-
-                    refCellToRefMolsTo.referInMols(molsToReferOut[rRLI]);
-                }
-            }
-        }
-    }
-
-    // Receive referred molecule lists to and distribute to referredCells
-    // according tocellReceivingReferralLists, referredCells deal with the
-    // transformations themselves
-
-    forAll(molCloud_.cellReceivingReferralLists(), cRRL)
-    {
-        const receivingReferralList& rRL
-        (
-            molCloud_.cellReceivingReferralLists()[cRRL]
-        );
-
-        List<List<referredMolecule> > molsToReferIn(rRL.size());
-
-        if (rRL.sourceProc() != Pstream::myProcNo())
-        {
-            if (Pstream::parRun())
-            {
-                IPstream fromInteractingProc
-                (
-                    Pstream::blocking,
-                    rRL.sourceProc()
-                );
-
-                fromInteractingProc >> molsToReferIn;
-            }
-
-            forAll(rRL, rRLI)
-            {
-                forAll(rRL[rRLI], rC)
-                {
-                    referredCell& refCellToRefMolsTo = (*this)[rRL[rRLI][rC]];
-
-                    refCellToRefMolsTo.referInMols(molsToReferIn[rRLI]);
-                }
-            }
-        }
-    }
-}
-
-
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-} // End namespace Foam
-
-// ************************************************************************* //
diff --git a/src/lagrangian/molecule/referredCellList/referredCellList.H b/src/lagrangian/molecule/referredCellList/referredCellList.H
deleted file mode 100755
index c025de52eb..0000000000
--- a/src/lagrangian/molecule/referredCellList/referredCellList.H
+++ /dev/null
@@ -1,103 +0,0 @@
-/*---------------------------------------------------------------------------*\
-  =========                 |
-  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
-   \\    /   O peration     |
-    \\  /    A nd           | Copyright (C) 1991-2005 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::referredCellList
-
-Description
-
-SourceFiles
-    referredCellListI.H
-    referredCellList.C
-
-\*---------------------------------------------------------------------------*/
-
-#ifndef referredCellList_H
-#define referredCellList_H
-
-#include "referredCell.H"
-#include "molecule.H"
-
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-namespace Foam
-{
-
-/*---------------------------------------------------------------------------*\
-                        Class referredCellList Declaration
-\*---------------------------------------------------------------------------*/
-
-class referredCellList
-:
-    public List< referredCell >
-{
-    // Private data
-
-        moleculeCloud& molCloud_;
-
-
-public:
-
-    // Constructors
-
-        //- Construct from moleculeCloud
-        referredCellList(moleculeCloud& molCloud);
-
-        //- Construct from components
-        referredCellList
-        (
-            moleculeCloud& molCloud,
-            const List<referredCell>& referredCells,
-            const List<label>& realCells
-        );
-
-
-    // Destructor
-
-        ~referredCellList();
-
-
-    // Member Functions
-
-        void setRealCellsInRange();
-
-        void referMolecules();
-
-        inline const moleculeCloud& molCloud();
-};
-
-
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-} // End namespace Foam
-
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-#include "referredCellListI.H"
-
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-#endif
-
-// ************************************************************************* //
diff --git a/src/lagrangian/molecule/referredCellList/referredCellListI.H b/src/lagrangian/molecule/referredCellList/referredCellListI.H
deleted file mode 100755
index 34767d88b6..0000000000
--- a/src/lagrangian/molecule/referredCellList/referredCellListI.H
+++ /dev/null
@@ -1,42 +0,0 @@
-/*---------------------------------------------------------------------------*\
-  =========                 |
-  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
-   \\    /   O peration     |
-    \\  /    A nd           | Copyright (C) 1991-2005 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
-{
-
-// * * * * * * * * * * * * * * * Member Operators  * * * * * * * * * * * * * //
-
-inline const Foam::moleculeCloud& Foam::referredCellList::molCloud()
-{
-    return molCloud_;
-}
-
-
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-} // End namespace Foam
-
-// ************************************************************************* //
diff --git a/src/lagrangian/molecule/referredMolecule/referredMolecule.C b/src/lagrangian/molecule/referredMolecule/referredMolecule.C
deleted file mode 100755
index 2453ca2f58..0000000000
--- a/src/lagrangian/molecule/referredMolecule/referredMolecule.C
+++ /dev/null
@@ -1,89 +0,0 @@
-/*---------------------------------------------------------------------------*\
-  =========                 |
-  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
-   \\    /   O peration     |
-    \\  /    A nd           | Copyright (C) 1991-2005 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 "referredMolecule.H"
-
-namespace Foam
-{
-
-// * * * * * * * * * * * * * * * * Constructors  * * * * * * * * * * * * * * //
-
-referredMolecule::referredMolecule()
-{}
-
-
-referredMolecule::referredMolecule
-(
-    const label id,
-    const vector& position
-)
-:
-    id_(id),
-    position_(position)
-{}
-
-
-// * * * * * * * * * * * * * * * * Destructor  * * * * * * * * * * * * * * * //
-
-referredMolecule::~referredMolecule()
-{}
-
-
-// * * * * * * * * * * * * * * * Friend Operators  * * * * * * * * * * * * * //
-
-Istream& operator>>
-(
-    Istream& is,
-    referredMolecule& rM
-)
-{
-    is >> rM.id_ >> rM.position_;
-
-    is.check("Istream& operator<<(Istream& f, const referredMolecule& sRL");
-
-    return is;
-}
-
-
-Ostream& operator<<
-(
-    Ostream& os,
-    const referredMolecule& rM
-)
-{
-    os << rM.id() << token::SPACE << rM.position();
-
-    os.check("Ostream& operator<<(Ostream& f, const referredMolecule& rM");
-
-    return os;
-}
-
-
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-} // End namespace Foam
-
-// ************************************************************************* //
diff --git a/src/lagrangian/molecule/referredMolecule/referredMolecule.H b/src/lagrangian/molecule/referredMolecule/referredMolecule.H
deleted file mode 100755
index fcac7925a9..0000000000
--- a/src/lagrangian/molecule/referredMolecule/referredMolecule.H
+++ /dev/null
@@ -1,129 +0,0 @@
-/*---------------------------------------------------------------------------*\
-  =========                 |
-  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
-   \\    /   O peration     |
-    \\  /    A nd           | Copyright (C) 1991-2005 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::referredMolecule
-
-Description
-
-SourceFiles
-    referredMoleculeI.H
-    referredMolecule.C
-
-\*---------------------------------------------------------------------------*/
-
-#ifndef referredMolecule_H
-#define referredMolecule_H
-
-#include "vector.H"
-
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-namespace Foam
-{
-/*---------------------------------------------------------------------------*\
-                           Class referredMolecule Declaration
-\*---------------------------------------------------------------------------*/
-
-class referredMolecule
-{
-    // Private data
-
-        label id_;
-
-        vector position_;
-
-
-public:
-
-    // Constructors
-
-        //- Construct null
-        referredMolecule();
-
-        //- Construct from components
-        referredMolecule
-        (
-            const label id,
-            const vector& position
-        );
-
-
-    // Destructor
-
-        virtual ~referredMolecule();
-
-
-    // Member Functions
-
-        // Access
-
-            inline label id() const;
-
-            inline const vector& position() const;
-
-
-    // Friend Operators
-
-        inline friend bool operator==
-        (
-            const referredMolecule& a,
-            const referredMolecule& b
-        );
-
-        inline friend bool operator!=
-        (
-            const referredMolecule& a,
-            const referredMolecule& b
-        );
-
-    // IOstream Operators
-
-        friend Istream& operator>>
-        (
-            Istream&,
-            referredMolecule&
-        );
-
-        friend Ostream& operator<<
-        (
-            Ostream&,
-            const referredMolecule&
-        );
-};
-
-
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-} // End namespace Foam
-
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-#include "referredMoleculeI.H"
-
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-#endif
-
-// ************************************************************************* //
diff --git a/src/lagrangian/molecule/referredMolecule/referredMoleculeI.H b/src/lagrangian/molecule/referredMolecule/referredMoleculeI.H
deleted file mode 100755
index b51b56035d..0000000000
--- a/src/lagrangian/molecule/referredMolecule/referredMoleculeI.H
+++ /dev/null
@@ -1,75 +0,0 @@
-/*---------------------------------------------------------------------------*\
-  =========                 |
-  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
-   \\    /   O peration     |
-    \\  /    A nd           | Copyright (C) 1991-2005 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
-{
-
-// * * * * * * * * * * * * * * * Member Functions  * * * * * * * * * * * * * //
-
-inline label referredMolecule::id() const
-{
-    return id_;
-}
-
-
-inline const vector& referredMolecule::position() const
-{
-    return position_;
-}
-
-
-// * * * * * * * * * * * * * * * Friend Operators  * * * * * * * * * * * * * //
-
-inline bool operator==
-(
-    const referredMolecule& a,
-    const referredMolecule& b
-)
-{
-    return
-    (
-        a.id() == b.id()
-     && a.position() == b.position()
-    );
-}
-
-
-inline bool operator!=
-(
-    const referredMolecule& a,
-    const referredMolecule& b
-)
-{
-    return !(a == b);
-}
-
-
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-} // End namespace Foam
-
-
-// ************************************************************************* //

From 5218b4f0ef3dc8aa2769e3b97be192c3f0f5aef9 Mon Sep 17 00:00:00 2001
From: graham <graham.macpherson@strath.ac.uk>
Date: Mon, 16 Jun 2008 18:06:28 +0100
Subject: [PATCH 2/5] Changed src/lagrangian/molecule folder to
 molecularDynamics and split off separate potential library.

---
 .../molecularDynamics/molecule/Make/files     |   50 +
 .../molecularDynamics/molecule/Make/options   |   10 +
 .../bufferedAccumulator/bufferedAccumulator.C |  238 +++
 .../bufferedAccumulator/bufferedAccumulator.H |  178 +++
 .../bufferedAccumulatorI.H                    |   80 +
 .../bufferedAccumulatorIO.C                   |   52 +
 .../correlationFunction/correlationFunction.C |  224 +++
 .../correlationFunction/correlationFunction.H |  180 +++
 .../correlationFunctionI.H                    |   70 +
 .../correlationFunctionIO.C                   |   72 +
 .../molecule/distribution/distribution.C      |  449 ++++++
 .../molecule/distribution/distribution.H      |  133 ++
 .../molecule/distribution/distributionI.H     |   42 +
 .../molecule/distribution/distributionIO.C    |   35 +
 .../molecule/mdTools/averageMDFields.H        |  227 +++
 .../calculateAutoCorrelationFunctions.H       |  105 ++
 .../molecule/mdTools/calculateMDFields.H      |   23 +
 .../mdTools/calculateTransportProperties.H    |   82 ++
 .../mdTools/createAutoCorrelationFunctions.H  |   99 ++
 .../molecule/mdTools/createMDFields.H         |  324 +++++
 .../molecule/mdTools/createRefUnits.H         |   22 +
 .../molecularDynamics/molecule/mdTools/md.H   |   11 +
 .../mdTools/meanMomentumEnergyAndNMols.H      |  130 ++
 .../molecule/mdTools/resetMDFields.H          |   26 +
 .../molecule/mdTools/temperatureAndPressure.H |  116 ++
 .../mdTools/temperatureAndPressureVariables.H |   59 +
 .../mdTools/temperatureEquilibration.H        |   43 +
 .../molecule/molecule/molecule.C              |  214 +++
 .../molecule/molecule/molecule.H              |  271 ++++
 .../molecule/molecule/moleculeI.H             |  165 +++
 .../molecule/molecule/moleculeIO.C            |  208 +++
 .../molecule/moleculeCloud/moleculeCloud.C    |  135 ++
 .../molecule/moleculeCloud/moleculeCloud.H    |  328 +++++
 ...eculeCloudApplyConstraintsAndThermostats.C |   60 +
 .../moleculeCloudBuildCellInteractionLists.C  |   80 +
 .../moleculeCloudBuildCellOccupancy.C         |   68 +
 .../moleculeCloudBuildCellReferralLists.C     |  194 +++
 .../moleculeCloudBuildDirectInteractionList.H |  188 +++
 ...oleculeCloudBuildReferredInteractionList.H | 1285 +++++++++++++++++
 .../moleculeCloudCalculateExternalForce.C     |   42 +
 .../moleculeCloudCalculateForce.C             |   59 +
 .../moleculeCloudCalculatePairForce.C         |   41 +
 ...moleculeCloudCalculatePairForceRealCells.H |   49 +
 ...lculatePairForceRealCellsCalculationStep.H |   33 +
 ...culeCloudCalculatePairForceReferredCells.H |   59 +
 .../moleculeCloudCalculateTetherForce.C       |   69 +
 .../moleculeCloud/moleculeCloudCodeSnippets.H |  193 +++
 .../molecule/moleculeCloud/moleculeCloudI.H   |  154 ++
 .../moleculeCloudIntegrateEquationsOfMotion.C |   50 +
 .../moleculeCloudReadMDParameters.H           |  177 +++
 .../moleculeCloudRealCellsInRangeOfSegment.C  |  152 ++
 ...leculeCloudReferredCellsInRangeOfSegment.C |  117 ++
 .../moleculeCloudRemoveHighEnergyOverlaps.C   |   67 +
 ...leCloudRemoveHighEnergyOverlapsRealCells.H |   55 +
 ...ghEnergyOverlapsRealCellsCalculationStep.H |   79 +
 ...oudRemoveHighEnergyOverlapsReferredCells.H |  152 ++
 .../moleculeCloudTestEdgeEdgeDistance.C       |   86 ++
 .../moleculeCloudTestPointFaceDistance.C      |  235 +++
 .../molecule/reducedUnits/reducedUnits.C      |  165 +++
 .../molecule/reducedUnits/reducedUnits.H      |  184 +++
 .../molecule/reducedUnits/reducedUnitsI.H     |   95 ++
 .../molecule/reducedUnits/reducedUnitsIO.C    |   61 +
 .../referralLists/receivingReferralList.C     |  181 +++
 .../referralLists/receivingReferralList.H     |  138 ++
 .../referralLists/receivingReferralListI.H    |   56 +
 .../referralLists/sendingReferralList.C       |  178 +++
 .../referralLists/sendingReferralList.H       |  138 ++
 .../referralLists/sendingReferralListI.H      |   56 +
 .../molecule/referredCell/referredCell.C      |  441 ++++++
 .../molecule/referredCell/referredCell.H      |  277 ++++
 .../molecule/referredCell/referredCellI.H     |  127 ++
 .../referredCellList/referredCellList.C       |  327 +++++
 .../referredCellList/referredCellList.H       |  103 ++
 .../referredCellList/referredCellListI.H      |   42 +
 .../referredMolecule/referredMolecule.C       |   89 ++
 .../referredMolecule/referredMolecule.H       |  129 ++
 .../referredMolecule/referredMoleculeI.H      |   75 +
 .../tetherPotential/tetherPotential.C         |   94 ++
 .../tetherPotential/tetherPotential.H         |  125 ++
 .../tetherPotential/tetherPotentialI.H        |   56 +
 .../tetherPotential/tetherPotentialList.C     |  146 ++
 .../tetherPotential/tetherPotentialList.H     |  125 ++
 .../tetherPotential/tetherPotentialListI.H    |   50 +
 .../molecularDynamics/potential/Make/files    |   35 +
 .../molecularDynamics/potential/Make/options  |    6 +
 .../basic/energyScalingFunction.C             |   76 +
 .../basic/energyScalingFunction.H             |  149 ++
 .../basic/newEnergyScalingFunction.C          |   79 +
 .../derived/doubleSigmoid/doubleSigmoid.C     |  104 ++
 .../derived/doubleSigmoid/doubleSigmoid.H     |  114 ++
 .../derived/noScaling/noScaling.C             |   81 ++
 .../derived/noScaling/noScaling.H             |   98 ++
 .../derived/shifted/shifted.C                 |   84 ++
 .../derived/shifted/shifted.H                 |  100 ++
 .../derived/shiftedForce/shiftedForce.C       |   86 ++
 .../derived/shiftedForce/shiftedForce.H       |  106 ++
 .../derived/sigmoid/sigmoid.C                 |  100 ++
 .../derived/sigmoid/sigmoid.H                 |  112 ++
 .../pairPotential/basic/newPairPotential.C    |   75 +
 .../pairPotential/basic/pairPotential.C       |  238 +++
 .../pairPotential/basic/pairPotential.H       |  195 +++
 .../pairPotential/basic/pairPotentialI.H      |   58 +
 .../pairPotential/basic/pairPotentialIO.C     |   53 +
 .../pairPotential/derived/azizChen/azizChen.C |  125 ++
 .../pairPotential/derived/azizChen/azizChen.H |  126 ++
 .../derived/lennardJones/lennardJones.C       |   99 ++
 .../derived/lennardJones/lennardJones.H       |  103 ++
 .../derived/maitlandSmith/maitlandSmith.C     |  103 ++
 .../derived/maitlandSmith/maitlandSmith.H     |  127 ++
 .../pairPotentialList/pairPotentialList.C     |  284 ++++
 .../pairPotentialList/pairPotentialList.H     |  172 +++
 .../pairPotentialList/pairPotentialListI.H    |   84 ++
 .../basic/newTetherPotential.C                |   75 +
 .../tetherPotential/basic/tetherPotential.C   |   71 +
 .../tetherPotential/basic/tetherPotential.H   |  143 ++
 .../derived/harmonicSpring/harmonicSpring.C   |   93 ++
 .../derived/harmonicSpring/harmonicSpring.H   |  104 ++
 .../restrainedHarmonicSpring.C                |  121 ++
 .../restrainedHarmonicSpring.H                |  106 ++
 .../tetherPotentialList/tetherPotentialList.C |  166 +++
 .../tetherPotentialList/tetherPotentialList.H |  141 ++
 .../tetherPotentialListI.H                    |   53 +
 122 files changed, 15848 insertions(+)
 create mode 100755 src/lagrangian/molecularDynamics/molecule/Make/files
 create mode 100755 src/lagrangian/molecularDynamics/molecule/Make/options
 create mode 100755 src/lagrangian/molecularDynamics/molecule/correlationFunction/bufferedAccumulator/bufferedAccumulator.C
 create mode 100755 src/lagrangian/molecularDynamics/molecule/correlationFunction/bufferedAccumulator/bufferedAccumulator.H
 create mode 100755 src/lagrangian/molecularDynamics/molecule/correlationFunction/bufferedAccumulator/bufferedAccumulatorI.H
 create mode 100755 src/lagrangian/molecularDynamics/molecule/correlationFunction/bufferedAccumulator/bufferedAccumulatorIO.C
 create mode 100644 src/lagrangian/molecularDynamics/molecule/correlationFunction/correlationFunction.C
 create mode 100644 src/lagrangian/molecularDynamics/molecule/correlationFunction/correlationFunction.H
 create mode 100644 src/lagrangian/molecularDynamics/molecule/correlationFunction/correlationFunctionI.H
 create mode 100644 src/lagrangian/molecularDynamics/molecule/correlationFunction/correlationFunctionIO.C
 create mode 100755 src/lagrangian/molecularDynamics/molecule/distribution/distribution.C
 create mode 100755 src/lagrangian/molecularDynamics/molecule/distribution/distribution.H
 create mode 100755 src/lagrangian/molecularDynamics/molecule/distribution/distributionI.H
 create mode 100755 src/lagrangian/molecularDynamics/molecule/distribution/distributionIO.C
 create mode 100755 src/lagrangian/molecularDynamics/molecule/mdTools/averageMDFields.H
 create mode 100644 src/lagrangian/molecularDynamics/molecule/mdTools/calculateAutoCorrelationFunctions.H
 create mode 100755 src/lagrangian/molecularDynamics/molecule/mdTools/calculateMDFields.H
 create mode 100644 src/lagrangian/molecularDynamics/molecule/mdTools/calculateTransportProperties.H
 create mode 100644 src/lagrangian/molecularDynamics/molecule/mdTools/createAutoCorrelationFunctions.H
 create mode 100755 src/lagrangian/molecularDynamics/molecule/mdTools/createMDFields.H
 create mode 100644 src/lagrangian/molecularDynamics/molecule/mdTools/createRefUnits.H
 create mode 100755 src/lagrangian/molecularDynamics/molecule/mdTools/md.H
 create mode 100755 src/lagrangian/molecularDynamics/molecule/mdTools/meanMomentumEnergyAndNMols.H
 create mode 100755 src/lagrangian/molecularDynamics/molecule/mdTools/resetMDFields.H
 create mode 100755 src/lagrangian/molecularDynamics/molecule/mdTools/temperatureAndPressure.H
 create mode 100755 src/lagrangian/molecularDynamics/molecule/mdTools/temperatureAndPressureVariables.H
 create mode 100755 src/lagrangian/molecularDynamics/molecule/mdTools/temperatureEquilibration.H
 create mode 100755 src/lagrangian/molecularDynamics/molecule/molecule/molecule.C
 create mode 100755 src/lagrangian/molecularDynamics/molecule/molecule/molecule.H
 create mode 100755 src/lagrangian/molecularDynamics/molecule/molecule/moleculeI.H
 create mode 100755 src/lagrangian/molecularDynamics/molecule/molecule/moleculeIO.C
 create mode 100755 src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloud.C
 create mode 100755 src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloud.H
 create mode 100755 src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudApplyConstraintsAndThermostats.C
 create mode 100755 src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudBuildCellInteractionLists.C
 create mode 100755 src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudBuildCellOccupancy.C
 create mode 100755 src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudBuildCellReferralLists.C
 create mode 100755 src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudBuildDirectInteractionList.H
 create mode 100755 src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudBuildReferredInteractionList.H
 create mode 100755 src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudCalculateExternalForce.C
 create mode 100755 src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudCalculateForce.C
 create mode 100755 src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudCalculatePairForce.C
 create mode 100755 src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudCalculatePairForceRealCells.H
 create mode 100755 src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudCalculatePairForceRealCellsCalculationStep.H
 create mode 100755 src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudCalculatePairForceReferredCells.H
 create mode 100755 src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudCalculateTetherForce.C
 create mode 100755 src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudCodeSnippets.H
 create mode 100755 src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudI.H
 create mode 100755 src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudIntegrateEquationsOfMotion.C
 create mode 100755 src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudReadMDParameters.H
 create mode 100755 src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudRealCellsInRangeOfSegment.C
 create mode 100755 src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudReferredCellsInRangeOfSegment.C
 create mode 100755 src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudRemoveHighEnergyOverlaps.C
 create mode 100755 src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudRemoveHighEnergyOverlapsRealCells.H
 create mode 100755 src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudRemoveHighEnergyOverlapsRealCellsCalculationStep.H
 create mode 100755 src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudRemoveHighEnergyOverlapsReferredCells.H
 create mode 100755 src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudTestEdgeEdgeDistance.C
 create mode 100755 src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudTestPointFaceDistance.C
 create mode 100644 src/lagrangian/molecularDynamics/molecule/reducedUnits/reducedUnits.C
 create mode 100644 src/lagrangian/molecularDynamics/molecule/reducedUnits/reducedUnits.H
 create mode 100644 src/lagrangian/molecularDynamics/molecule/reducedUnits/reducedUnitsI.H
 create mode 100644 src/lagrangian/molecularDynamics/molecule/reducedUnits/reducedUnitsIO.C
 create mode 100755 src/lagrangian/molecularDynamics/molecule/referralLists/receivingReferralList.C
 create mode 100755 src/lagrangian/molecularDynamics/molecule/referralLists/receivingReferralList.H
 create mode 100755 src/lagrangian/molecularDynamics/molecule/referralLists/receivingReferralListI.H
 create mode 100755 src/lagrangian/molecularDynamics/molecule/referralLists/sendingReferralList.C
 create mode 100755 src/lagrangian/molecularDynamics/molecule/referralLists/sendingReferralList.H
 create mode 100755 src/lagrangian/molecularDynamics/molecule/referralLists/sendingReferralListI.H
 create mode 100755 src/lagrangian/molecularDynamics/molecule/referredCell/referredCell.C
 create mode 100755 src/lagrangian/molecularDynamics/molecule/referredCell/referredCell.H
 create mode 100755 src/lagrangian/molecularDynamics/molecule/referredCell/referredCellI.H
 create mode 100755 src/lagrangian/molecularDynamics/molecule/referredCellList/referredCellList.C
 create mode 100755 src/lagrangian/molecularDynamics/molecule/referredCellList/referredCellList.H
 create mode 100755 src/lagrangian/molecularDynamics/molecule/referredCellList/referredCellListI.H
 create mode 100755 src/lagrangian/molecularDynamics/molecule/referredMolecule/referredMolecule.C
 create mode 100755 src/lagrangian/molecularDynamics/molecule/referredMolecule/referredMolecule.H
 create mode 100755 src/lagrangian/molecularDynamics/molecule/referredMolecule/referredMoleculeI.H
 create mode 100755 src/lagrangian/molecularDynamics/molecule/tetherPotential/tetherPotential.C
 create mode 100755 src/lagrangian/molecularDynamics/molecule/tetherPotential/tetherPotential.H
 create mode 100755 src/lagrangian/molecularDynamics/molecule/tetherPotential/tetherPotentialI.H
 create mode 100755 src/lagrangian/molecularDynamics/molecule/tetherPotential/tetherPotentialList.C
 create mode 100755 src/lagrangian/molecularDynamics/molecule/tetherPotential/tetherPotentialList.H
 create mode 100755 src/lagrangian/molecularDynamics/molecule/tetherPotential/tetherPotentialListI.H
 create mode 100644 src/lagrangian/molecularDynamics/potential/Make/files
 create mode 100644 src/lagrangian/molecularDynamics/potential/Make/options
 create mode 100644 src/lagrangian/molecularDynamics/potential/energyScalingFunction/basic/energyScalingFunction.C
 create mode 100644 src/lagrangian/molecularDynamics/potential/energyScalingFunction/basic/energyScalingFunction.H
 create mode 100644 src/lagrangian/molecularDynamics/potential/energyScalingFunction/basic/newEnergyScalingFunction.C
 create mode 100644 src/lagrangian/molecularDynamics/potential/energyScalingFunction/derived/doubleSigmoid/doubleSigmoid.C
 create mode 100644 src/lagrangian/molecularDynamics/potential/energyScalingFunction/derived/doubleSigmoid/doubleSigmoid.H
 create mode 100644 src/lagrangian/molecularDynamics/potential/energyScalingFunction/derived/noScaling/noScaling.C
 create mode 100644 src/lagrangian/molecularDynamics/potential/energyScalingFunction/derived/noScaling/noScaling.H
 create mode 100644 src/lagrangian/molecularDynamics/potential/energyScalingFunction/derived/shifted/shifted.C
 create mode 100644 src/lagrangian/molecularDynamics/potential/energyScalingFunction/derived/shifted/shifted.H
 create mode 100644 src/lagrangian/molecularDynamics/potential/energyScalingFunction/derived/shiftedForce/shiftedForce.C
 create mode 100644 src/lagrangian/molecularDynamics/potential/energyScalingFunction/derived/shiftedForce/shiftedForce.H
 create mode 100644 src/lagrangian/molecularDynamics/potential/energyScalingFunction/derived/sigmoid/sigmoid.C
 create mode 100644 src/lagrangian/molecularDynamics/potential/energyScalingFunction/derived/sigmoid/sigmoid.H
 create mode 100644 src/lagrangian/molecularDynamics/potential/pairPotential/basic/newPairPotential.C
 create mode 100644 src/lagrangian/molecularDynamics/potential/pairPotential/basic/pairPotential.C
 create mode 100644 src/lagrangian/molecularDynamics/potential/pairPotential/basic/pairPotential.H
 create mode 100755 src/lagrangian/molecularDynamics/potential/pairPotential/basic/pairPotentialI.H
 create mode 100644 src/lagrangian/molecularDynamics/potential/pairPotential/basic/pairPotentialIO.C
 create mode 100644 src/lagrangian/molecularDynamics/potential/pairPotential/derived/azizChen/azizChen.C
 create mode 100644 src/lagrangian/molecularDynamics/potential/pairPotential/derived/azizChen/azizChen.H
 create mode 100644 src/lagrangian/molecularDynamics/potential/pairPotential/derived/lennardJones/lennardJones.C
 create mode 100644 src/lagrangian/molecularDynamics/potential/pairPotential/derived/lennardJones/lennardJones.H
 create mode 100644 src/lagrangian/molecularDynamics/potential/pairPotential/derived/maitlandSmith/maitlandSmith.C
 create mode 100644 src/lagrangian/molecularDynamics/potential/pairPotential/derived/maitlandSmith/maitlandSmith.H
 create mode 100755 src/lagrangian/molecularDynamics/potential/pairPotential/pairPotentialList/pairPotentialList.C
 create mode 100755 src/lagrangian/molecularDynamics/potential/pairPotential/pairPotentialList/pairPotentialList.H
 create mode 100755 src/lagrangian/molecularDynamics/potential/pairPotential/pairPotentialList/pairPotentialListI.H
 create mode 100644 src/lagrangian/molecularDynamics/potential/tetherPotential/basic/newTetherPotential.C
 create mode 100644 src/lagrangian/molecularDynamics/potential/tetherPotential/basic/tetherPotential.C
 create mode 100644 src/lagrangian/molecularDynamics/potential/tetherPotential/basic/tetherPotential.H
 create mode 100644 src/lagrangian/molecularDynamics/potential/tetherPotential/derived/harmonicSpring/harmonicSpring.C
 create mode 100644 src/lagrangian/molecularDynamics/potential/tetherPotential/derived/harmonicSpring/harmonicSpring.H
 create mode 100644 src/lagrangian/molecularDynamics/potential/tetherPotential/derived/restrainedHarmonicSpring/restrainedHarmonicSpring.C
 create mode 100644 src/lagrangian/molecularDynamics/potential/tetherPotential/derived/restrainedHarmonicSpring/restrainedHarmonicSpring.H
 create mode 100755 src/lagrangian/molecularDynamics/potential/tetherPotential/tetherPotentialList/tetherPotentialList.C
 create mode 100755 src/lagrangian/molecularDynamics/potential/tetherPotential/tetherPotentialList/tetherPotentialList.H
 create mode 100755 src/lagrangian/molecularDynamics/potential/tetherPotential/tetherPotentialList/tetherPotentialListI.H

diff --git a/src/lagrangian/molecularDynamics/molecule/Make/files b/src/lagrangian/molecularDynamics/molecule/Make/files
new file mode 100755
index 0000000000..a490edafe1
--- /dev/null
+++ b/src/lagrangian/molecularDynamics/molecule/Make/files
@@ -0,0 +1,50 @@
+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 = $(FOAM_LIBBIN)/libmolecule
+
diff --git a/src/lagrangian/molecularDynamics/molecule/Make/options b/src/lagrangian/molecularDynamics/molecule/Make/options
new file mode 100755
index 0000000000..cc91fd4bbe
--- /dev/null
+++ b/src/lagrangian/molecularDynamics/molecule/Make/options
@@ -0,0 +1,10 @@
+EXE_INC = \
+    -I$(LIB_SRC)/finiteVolume/lnInclude \
+    -I$(LIB_SRC)/lagrangian/basic/lnInclude \
+    -I$(LIB_SRC)/lagrangian/molecularDynamics/potential/lnInclude
+
+EXE_LIBS = \
+    -lfiniteVolume \
+    -llagrangian \
+    -lpotential
+
diff --git a/src/lagrangian/molecularDynamics/molecule/correlationFunction/bufferedAccumulator/bufferedAccumulator.C b/src/lagrangian/molecularDynamics/molecule/correlationFunction/bufferedAccumulator/bufferedAccumulator.C
new file mode 100755
index 0000000000..c8a5ca0f30
--- /dev/null
+++ b/src/lagrangian/molecularDynamics/molecule/correlationFunction/bufferedAccumulator/bufferedAccumulator.C
@@ -0,0 +1,238 @@
+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  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"
+
+// ************************************************************************* //
diff --git a/src/lagrangian/molecularDynamics/molecule/correlationFunction/bufferedAccumulator/bufferedAccumulator.H b/src/lagrangian/molecularDynamics/molecule/correlationFunction/bufferedAccumulator/bufferedAccumulator.H
new file mode 100755
index 0000000000..27bd52771c
--- /dev/null
+++ b/src/lagrangian/molecularDynamics/molecule/correlationFunction/bufferedAccumulator/bufferedAccumulator.H
@@ -0,0 +1,178 @@
+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  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
+
+// ************************************************************************* //
diff --git a/src/lagrangian/molecularDynamics/molecule/correlationFunction/bufferedAccumulator/bufferedAccumulatorI.H b/src/lagrangian/molecularDynamics/molecule/correlationFunction/bufferedAccumulator/bufferedAccumulatorI.H
new file mode 100755
index 0000000000..cb3bcc617e
--- /dev/null
+++ b/src/lagrangian/molecularDynamics/molecule/correlationFunction/bufferedAccumulator/bufferedAccumulatorI.H
@@ -0,0 +1,80 @@
+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  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
+
+// ************************************************************************* //
diff --git a/src/lagrangian/molecularDynamics/molecule/correlationFunction/bufferedAccumulator/bufferedAccumulatorIO.C b/src/lagrangian/molecularDynamics/molecule/correlationFunction/bufferedAccumulator/bufferedAccumulatorIO.C
new file mode 100755
index 0000000000..5c6cf11da3
--- /dev/null
+++ b/src/lagrangian/molecularDynamics/molecule/correlationFunction/bufferedAccumulator/bufferedAccumulatorIO.C
@@ -0,0 +1,52 @@
+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  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
+    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"
+#include "IOstreams.H"
+
+// * * * * * * * * * * * * * * * IOstream Operators  * * * * * * * * * * * * //
+
+template<class Type>
+Foam::Ostream&
+    Foam::operator<<(Ostream& os, const bufferedAccumulator<Type>& bA)
+{
+
+    os<< bA.averagesTaken_
+      << static_cast<const List< Field<Type> >&>(bA)
+      << bA.bufferOffsets();
+
+    // Check state of Ostream
+    os.check
+    (
+        "Foam::Ostream& Foam::operator<<(Foam::Ostream&, "
+        "const Foam::bufferedAccumulator&)"
+    );
+
+    return os;
+}
+
+
+// ************************************************************************* //
diff --git a/src/lagrangian/molecularDynamics/molecule/correlationFunction/correlationFunction.C b/src/lagrangian/molecularDynamics/molecule/correlationFunction/correlationFunction.C
new file mode 100644
index 0000000000..ca63e1856c
--- /dev/null
+++ b/src/lagrangian/molecularDynamics/molecule/correlationFunction/correlationFunction.C
@@ -0,0 +1,224 @@
+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  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 "correlationFunction.H"
+
+// * * * * * * * * * * * * * * Static Data Members * * * * * * * * * * * * * //
+
+template<class Type>
+const char* const
+    Foam::correlationFunction<Type>::typeName("correlationFunction");
+
+
+// * * * * * * * * * * * * * Private Member Functions  * * * * * * * * * * * //
+
+template<class Type>
+void Foam::correlationFunction<Type>::setTimesAndSizes
+(
+    const label tZeroBufferSize
+)
+{
+    sampleSteps_  = ceil(sampleInterval_/mesh_.time().deltaT().value());
+
+    sampleInterval_ = sampleSteps_*mesh_.time().deltaT().value();
+
+    label bufferLength(ceil(duration_/sampleInterval_));
+
+    duration_ = bufferLength*sampleInterval_;
+
+    label bufferingInterval(ceil(averagingInterval_/sampleInterval_));
+
+    averagingInterval_ = bufferingInterval*sampleInterval_;
+
+    label nBuffers(ceil(duration_/averagingInterval_));
+
+    this->setSizes
+    (
+        nBuffers,
+        bufferLength,
+        bufferingInterval
+    );
+
+    tZeroBuffers_ =
+        Field< Field<Type> >
+        (
+            nBuffers,
+            Field<Type>
+            (
+                tZeroBufferSize,
+                pTraits<Type>::zero
+            )
+        );
+}
+
+
+// * * * * * * * * * * * * * * * * Constructors  * * * * * * * * * * * * * * //
+
+template<class Type>
+Foam::correlationFunction<Type>::correlationFunction
+(
+    const polyMesh& mesh,
+    const dictionary& cfDict,
+    const label tZeroBufferSize
+)
+:
+    bufferedAccumulator<scalar>(),
+    mesh_(mesh)
+{
+    duration_ = readScalar(cfDict.lookup("duration"));
+
+    sampleInterval_ = readScalar(cfDict.lookup("sampleInterval"));
+
+    averagingInterval_ = readScalar(cfDict.lookup("averagingInterval"));
+
+    setTimesAndSizes(tZeroBufferSize);
+}
+
+
+template<class Type>
+Foam::correlationFunction<Type>::correlationFunction
+(
+    const polyMesh& mesh,
+    const label tZeroBufferSize,
+    const scalar duration,
+    const scalar sampleInterval,
+    const scalar averagingInterval
+)
+:
+    bufferedAccumulator<scalar>(),
+    mesh_(mesh),
+    duration_(duration),
+    sampleInterval_(sampleInterval),
+    averagingInterval_(averagingInterval)
+{
+    setTimesAndSizes(tZeroBufferSize);
+}
+
+
+// * * * * * * * * * * * * * * * * Destructor  * * * * * * * * * * * * * * * //
+
+template<class Type>
+Foam::correlationFunction<Type>::~correlationFunction()
+{}
+
+
+// * * * * * * * * * * * * * * * Member Functions  * * * * * * * * * * * * * //
+
+template<class Type>
+void Foam::correlationFunction<Type>::calculateCorrelationFunction
+(
+    const Field<Type>& currentValues
+)
+{
+    if (measurandFieldSize() != currentValues.size())
+    {
+        FatalErrorIn("correlationFunction<Type>::calculateCorrelationFunction")
+            << "Trying to supply a Field of length"
+            << currentValues.size()
+            <<" to calculate the correlation function.  "
+            << "Expecting a Field of length "
+            << measurandFieldSize() << nl
+            << abort(FatalError);
+    }
+
+    List<scalar> cFSums(nBuffers(),0.0);
+
+    forAll(tZeroBuffers_, tZB)
+    {
+        scalar& cFSum = cFSums[tZB];
+
+        const Field<Type>& tZeroBuffer = tZeroBuffers_[tZB];
+
+        forAll(currentValues, cV)
+        {
+            const Type& tZeroBufferValue = tZeroBuffer[cV];
+
+            const Type& currentValue = currentValues[cV];
+
+            forAll(currentValue, component)
+            {
+                cFSum +=
+                (
+                    tZeroBufferValue[component]*currentValue[component]
+                );
+            }
+        }
+
+        cFSum /= (measurandFieldSize()*currentValues[0].size());
+    }
+
+    label bufferToRefill = addToBuffers(cFSums);
+
+    if (bufferToRefill != -1)
+    {
+        tZeroBuffers_[bufferToRefill] = currentValues;
+    }
+}
+
+
+template<class Type>
+void Foam::correlationFunction<Type>::calculateCorrelationFunction
+(
+    const Type& currentValue
+)
+{
+    if( measurandFieldSize() != 1)
+    {
+        FatalErrorIn("correlationFunction<Type>::calculateCorrelationFunction")
+            << "Trying to supply a single value to calculate the correlation "
+            << "function.  Expecting a Field of length "
+            << measurandFieldSize()
+            << abort(FatalError);
+    }
+
+    calculateCorrelationFunction(Field<Type>(1, currentValue));
+}
+
+
+template<class Type>
+Foam::scalar Foam::correlationFunction<Type>::integral() const
+{
+    Field<scalar> averageCF(averaged());
+
+    scalar cFIntegral = 0.0;
+
+    for(label v = 0; v < averageCF.size() - 1; v++)
+    {
+        cFIntegral +=
+            0.5
+           *sampleInterval_
+           *(averageCF[v+1] + averageCF[v]);
+    }
+
+    return cFIntegral;
+}
+
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+#   include "correlationFunctionIO.C"
+
+// ************************************************************************* //
diff --git a/src/lagrangian/molecularDynamics/molecule/correlationFunction/correlationFunction.H b/src/lagrangian/molecularDynamics/molecule/correlationFunction/correlationFunction.H
new file mode 100644
index 0000000000..fcd023e363
--- /dev/null
+++ b/src/lagrangian/molecularDynamics/molecule/correlationFunction/correlationFunction.H
@@ -0,0 +1,180 @@
+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  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::correlationFunction
+
+Description
+
+SourceFiles
+    correlationFunctionI.H
+    correlationFunction.C
+    correlationFunctionIO.C
+
+\*---------------------------------------------------------------------------*/
+
+#ifndef correlationFunction_H
+#define correlationFunction_H
+
+#include "bufferedAccumulator.H"
+#include "dictionary.H"
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+namespace Foam
+{
+
+template<class Type>
+class correlationFunction;
+
+template<class Type>
+Ostream& operator<<
+(
+    Ostream&,
+    const correlationFunction<Type>&
+);
+
+/*---------------------------------------------------------------------------*\
+                    Class correlationFunction Declaration
+\*---------------------------------------------------------------------------*/
+
+template<class Type>
+class correlationFunction
+:
+    public bufferedAccumulator<scalar>
+{
+    // Private data
+
+        const polyMesh& mesh_;
+
+        Field< Field<Type> > tZeroBuffers_;
+
+        scalar duration_;
+        scalar sampleInterval_;
+        scalar averagingInterval_;
+
+        label sampleSteps_;
+
+
+    // Private Member Functions
+
+        void setTimesAndSizes(const label);
+
+        //- Disallow default bitwise copy construct
+        correlationFunction(const correlationFunction<Type>&);
+
+        //- Disallow default bitwise assignment
+        void operator=(const correlationFunction<Type>&);
+
+
+public:
+
+    //- Component type
+    typedef typename pTraits<Type>::cmptType cmptType;
+
+
+    // Static data members
+
+        static const char* const typeName;
+
+
+    // Constructors
+
+        //- Construct from dictionary
+        correlationFunction
+        (
+            const polyMesh&,
+            const dictionary&,
+            const label tZeroBufferSize
+        );
+
+        //- Construct from components
+        correlationFunction
+        (
+            const polyMesh&,
+            const label tZeroBufferSize,
+            const scalar duration,
+            const scalar sampleInterval,
+            const scalar averagingInterval
+
+        );
+
+
+    // Destructor
+
+        ~correlationFunction();
+
+
+    // Member Functions
+
+        void calculateCorrelationFunction(const Field<Type>&);
+
+        void calculateCorrelationFunction(const Type&);
+
+        scalar integral() const;
+
+        bool writeAveraged(Ostream&) const;
+
+
+    // Access
+
+        inline const Field< Field<Type> >& tZeroBuffers() const;
+
+        inline scalar duration() const;
+
+        inline scalar sampleInterval() const;
+
+        inline scalar averagingInterval() const;
+
+        inline label sampleSteps() const;
+
+        inline label measurandFieldSize() const;
+
+
+    // IOstream Operators
+
+        friend Ostream& operator<< <Type>
+        (Ostream&, const correlationFunction<Type>&);
+};
+
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+} // End namespace Foam
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+#include "correlationFunctionI.H"
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+#ifdef NoRepository
+#   include "correlationFunction.C"
+#endif
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+#endif
+
+// ************************************************************************* //
diff --git a/src/lagrangian/molecularDynamics/molecule/correlationFunction/correlationFunctionI.H b/src/lagrangian/molecularDynamics/molecule/correlationFunction/correlationFunctionI.H
new file mode 100644
index 0000000000..6858f647a6
--- /dev/null
+++ b/src/lagrangian/molecularDynamics/molecule/correlationFunction/correlationFunctionI.H
@@ -0,0 +1,70 @@
+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  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
+
+\*---------------------------------------------------------------------------*/
+
+template<class Type>
+inline const Field< Field<Type> >& Foam::correlationFunction<Type>::
+tZeroBuffers() const
+{
+    return tZeroBuffers_;
+}
+
+
+template<class Type>
+inline scalar Foam::correlationFunction<Type>::duration() const
+{
+    return duration_;
+}
+
+
+template<class Type>
+inline scalar Foam::correlationFunction<Type>::sampleInterval() const
+{
+    return sampleInterval_;
+}
+
+
+template<class Type>
+inline scalar Foam::correlationFunction<Type>::averagingInterval() const
+{
+    return averagingInterval_;
+}
+
+
+template<class Type>
+inline label Foam::correlationFunction<Type>::sampleSteps() const
+{
+    return sampleSteps_;
+}
+
+
+template<class Type>
+inline label Foam::correlationFunction<Type>::measurandFieldSize() const
+{
+    return tZeroBuffers_[0].size();
+}
+
+
+// ************************************************************************* //
diff --git a/src/lagrangian/molecularDynamics/molecule/correlationFunction/correlationFunctionIO.C b/src/lagrangian/molecularDynamics/molecule/correlationFunction/correlationFunctionIO.C
new file mode 100644
index 0000000000..0a080158ae
--- /dev/null
+++ b/src/lagrangian/molecularDynamics/molecule/correlationFunction/correlationFunctionIO.C
@@ -0,0 +1,72 @@
+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  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 "correlationFunction.H"
+#include "IOstreams.H"
+
+template<class Type>
+bool Foam::correlationFunction<Type>::writeAveraged(Ostream& os) const
+{
+    Field<scalar> averageCF(averaged());
+
+    forAll(averageCF, v)
+    {
+        os<< v*sampleInterval()
+          << token::SPACE
+          << averageCF[v]
+          << nl;
+    }
+
+    return os.good();
+}
+
+
+template<class Type>
+Foam::Ostream& Foam::operator<<
+(
+    Ostream& os,
+    const correlationFunction<Type>& cF
+)
+{
+    os<< cF.duration()
+      << nl << cF.sampleInterval()
+      << nl << cF.averagingInterval()
+      << nl << cF.sampleSteps()
+      << nl << cF.tZeroBuffers()
+      << nl << static_cast<const bufferedAccumulator<scalar>&>(cF);
+
+    // Check state of Ostream
+    os.check
+    (
+        "Foam::Ostream& Foam::operator<<"
+        "(Ostream&, const correlationFunction<Type>&)"
+    );
+
+    return os;
+}
+
+
+// ************************************************************************* //
diff --git a/src/lagrangian/molecularDynamics/molecule/distribution/distribution.C b/src/lagrangian/molecularDynamics/molecule/distribution/distribution.C
new file mode 100755
index 0000000000..717929e5e4
--- /dev/null
+++ b/src/lagrangian/molecularDynamics/molecule/distribution/distribution.C
@@ -0,0 +1,449 @@
+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+   \\    /   O peration     |
+    \\  /    A nd           | Copyright (C) 1991-2005 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 "distribution.H"
+
+namespace Foam
+{
+
+// * * * * * * * * * * * * * * * * Constructors  * * * * * * * * * * * * * * //
+
+distribution::distribution()
+:
+    Map<label>(),
+    binWidth_(1)
+{}
+
+
+distribution::distribution(const scalar binWidth)
+:
+    Map<label>(),
+    binWidth_(binWidth)
+{}
+
+
+distribution::distribution(const distribution& d)
+:
+    Map<label>(static_cast< Map<label> >(d)),
+    binWidth_(d.binWidth())
+{}
+
+
+// * * * * * * * * * * * * * * * * Destructor  * * * * * * * * * * * * * * * //
+
+distribution::~distribution()
+{}
+
+
+// * * * * * * * * * * * * * * * Member Functions  * * * * * * * * * * * * * //
+
+label distribution::totalEntries() const
+{
+    label sumOfEntries = 0;
+
+    forAllConstIter(Map<label>, *this, iter)
+    {
+        sumOfEntries += iter();
+
+        if (sumOfEntries < 0)
+        {
+            WarningIn("label distribution::totalEntries()")
+                << "Accumulated distribution values total has become negative: "
+                << "sumOfEntries = " << sumOfEntries
+                << ". This is most likely to be because too many samples "
+                << "have been added to the bins and the label has 'rolled "
+                << "round'.  Try distribution::approxTotalEntries which "
+                << "returns a scalar." << endl;
+
+            sumOfEntries = -1;
+
+            break;
+        }
+    }
+
+    return sumOfEntries;
+}
+
+
+scalar distribution::approxTotalEntries() const
+{
+    scalar sumOfEntries = 0;
+
+    forAllConstIter(Map<label>, *this, iter)
+    {
+        sumOfEntries += scalar(iter());
+    }
+
+    return sumOfEntries;
+}
+
+
+scalar distribution::mean() const
+{
+    scalar runningSum = 0;
+
+    scalar totEnt = approxTotalEntries();
+
+    List<label> keys = toc();
+
+    forAll(keys,k)
+    {
+        label key = keys[k];
+
+        runningSum +=
+            (0.5 + scalar(key))
+           *binWidth_
+           *scalar((*this)[key])
+           /totEnt;
+    }
+
+    return runningSum;
+}
+
+
+scalar distribution::median()
+{
+    // From:
+    // http://mathworld.wolfram.com/StatisticalMedian.html
+    // The statistical median is the value of the distribution variable
+    // where the cumulative distribution = 0.5.
+
+    scalar median = 0.0;
+
+    scalar runningSum = 0.0;
+
+    List< Pair<scalar> > normDist(normalised());
+
+    if (normDist.size())
+    {
+        if (normDist.size() == 1)
+        {
+            median = normDist[0].first();
+        }
+        else if
+        (
+            normDist.size() > 1
+         && normDist[0].second()*binWidth_ > 0.5
+        )
+        {
+            scalar xk = normDist[1].first();
+            scalar xkm1 = normDist[0].first();
+            scalar Sk =
+                (normDist[0].second() + normDist[1].second())*binWidth_;
+            scalar Skm1 = normDist[0].second()*binWidth_;
+
+            median = (0.5 - Skm1)*(xk - xkm1)/(Sk - Skm1) + xkm1;
+        }
+        else
+        {
+            label lastNonZeroIndex = 0;
+
+            forAll(normDist,nD)
+            {
+                if (runningSum + (normDist[nD].second()*binWidth_) > 0.5)
+                {
+                    scalar xk = normDist[nD].first();
+                    scalar xkm1 = normDist[lastNonZeroIndex].first();
+                    scalar Sk = runningSum + (normDist[nD].second()*binWidth_);
+                    scalar Skm1 = runningSum;
+
+                    median = (0.5 - Skm1)*(xk - xkm1)/(Sk - Skm1) + xkm1;
+
+                    break;
+                }
+                else if (normDist[nD].second() > 0.0)
+                {
+                    runningSum += normDist[nD].second()*binWidth_;
+
+                    lastNonZeroIndex = nD;
+                }
+            }
+        }
+    }
+
+    return median;
+}
+
+
+void distribution::add(const scalar valueToAdd)
+{
+    iterator iter(this->begin());
+
+    label n = label(valueToAdd/binWidth_) - label(neg(valueToAdd/binWidth_));
+
+    iter = find(n);
+
+    if (iter == this->end())
+    {
+        this->insert(n,1);
+    }
+    else
+    {
+        (*this)[n]++;
+    }
+
+    if ((*this)[n] < 0)
+    {
+        FatalErrorIn("distribution::add(const scalar valueToAdd)")
+            << "Accumulated distribution value has become negative: "
+            << "bin = " << (0.5 + scalar(n)) * binWidth_
+            << ", value = " << (*this)[n]
+            << ". This is most likely to be because too many samples "
+            << "have been added to a bin and the label has 'rolled round'"
+            << abort(FatalError);
+    }
+}
+
+
+void distribution::add(const label valueToAdd)
+{
+    add(scalar(valueToAdd));
+}
+
+
+void distribution::insertMissingKeys()
+{
+    iterator iter(this->begin());
+
+    List<label> keys = toc();
+
+    sort(keys);
+
+    label k;
+
+    if (keys.size() > 0)
+    {
+        for (k = keys[0]; k < keys[keys.size()-1]; k++)
+        {
+            iter = find(k);
+
+            if (iter == this->end())
+            {
+                this->insert(k,0);
+            }
+        }
+    }
+}
+
+
+List< Pair<scalar> > distribution::normalised()
+{
+    scalar totEnt = approxTotalEntries();
+
+    insertMissingKeys();
+
+    List<label> keys = toc();
+
+    sort(keys);
+
+    List< Pair<scalar> > normDist(size());
+
+    forAll(keys,k)
+    {
+        label key = keys[k];
+
+        normDist[k].first() = (0.5 + scalar(key))*binWidth_;
+
+        normDist[k].second() = scalar((*this)[key])/totEnt/binWidth_;
+    }
+
+    return normDist;
+}
+
+
+List< Pair<scalar> > distribution::normalisedMinusMean()
+{
+    return normalisedShifted(mean());
+}
+
+
+List< Pair<scalar> > distribution::normalisedShifted(const scalar shiftValue)
+{
+    List< Pair<scalar> > oldDist(normalised());
+
+    List< Pair<scalar> > newDist(oldDist.size());
+
+    forAll(oldDist,u)
+    {
+        oldDist[u].first() -= shiftValue;
+    }
+
+    scalar lowestOldBin = oldDist[0].first()/binWidth_ - 0.5;
+
+    label lowestNewKey = label
+    (
+        lowestOldBin + 0.5*sign(lowestOldBin)
+    );
+
+    scalar interpolationStartDirection =
+        sign(scalar(lowestNewKey) - lowestOldBin);
+
+    label newKey = lowestNewKey;
+
+//     Info << shiftValue
+//         << nl << lowestOldBin
+//         << nl << lowestNewKey
+//         << nl << interpolationStartDirection
+//         << endl;
+
+//     scalar checkNormalisation = 0;
+
+//     forAll (oldDist, oD)
+//     {
+//         checkNormalisation += oldDist[oD].second()*binWidth_;
+//     }
+
+//     Info << "Initial normalisation = " << checkNormalisation << endl;
+
+    forAll(oldDist,u)
+    {
+        newDist[u].first() = (0.5 + scalar(newKey)) * binWidth_;
+
+        if (interpolationStartDirection < 0)
+        {
+            if (u == 0)
+            {
+                newDist[u].second() =
+                    (0.5 + scalar(newKey))*oldDist[u].second()
+                  - oldDist[u].second()
+                        *(oldDist[u].first() - binWidth_)/ binWidth_;
+            }
+            else
+            {
+                newDist[u].second() =
+                    (0.5 + scalar(newKey))
+                   *(oldDist[u].second() - oldDist[u-1].second())
+                  +
+                    (
+                        oldDist[u-1].second() * oldDist[u].first()
+                      - oldDist[u].second() * oldDist[u-1].first()
+                    )
+                    /binWidth_;
+            }
+        }
+        else
+        {
+            if (u == oldDist.size() - 1)
+            {
+                newDist[u].second() =
+                    (0.5 + scalar(newKey))*-oldDist[u].second()
+                  + oldDist[u].second() * (oldDist[u].first() + binWidth_)
+                   /binWidth_;
+            }
+            else
+            {
+                newDist[u].second() =
+                    (0.5 + scalar(newKey))
+                   *(oldDist[u+1].second() - oldDist[u].second())
+                  +
+                    (
+                        oldDist[u].second() * oldDist[u+1].first()
+                      - oldDist[u+1].second() * oldDist[u].first()
+                    )
+                   /binWidth_;
+            }
+        }
+
+        newKey++;
+    }
+
+//     checkNormalisation = 0;
+
+//     forAll (newDist, nD)
+//     {
+//         checkNormalisation += newDist[nD].second()*binWidth_;
+//     }
+
+//     Info << "Shifted normalisation = " << checkNormalisation << endl;
+
+    return newDist;
+}
+
+
+List< Pair<scalar> > distribution::raw()
+{
+    insertMissingKeys();
+
+    List<label> keys = toc();
+
+    sort(keys);
+
+    List< Pair<scalar> > rawDist(size());
+
+    forAll(keys,k)
+    {
+        label key = keys[k];
+
+        rawDist[k].first() = (0.5 + scalar(key)) * binWidth_;
+
+        rawDist[k].second() = scalar((*this)[key]);
+    }
+
+    return rawDist;
+}
+
+
+// * * * * * * * * * * * * * * * Member Operators  * * * * * * * * * * * * * //
+
+void distribution::operator=(const distribution& rhs)
+{
+    // Check for assignment to self
+    if (this == &rhs)
+    {
+        FatalErrorIn("distribution::operator=(const distribution&)")
+            << "Attempted assignment to self"
+            << abort(FatalError);
+    }
+
+    Map<label>::operator=(rhs);
+
+    binWidth_ = rhs.binWidth();
+}
+
+
+// * * * * * * * * * * * * * * * Friend Operators  * * * * * * * * * * * * * //
+
+Ostream& operator<<(Ostream& os, const distribution& d)
+{
+    os  << d.binWidth_
+        << static_cast<const Map<label>&>(d);
+
+    // Check state of Ostream
+    os.check
+    (
+        "Ostream& operator<<(Ostream&, "
+        "const distribution&)"
+    );
+
+    return os;
+}
+
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+} // End namespace Foam
+
+// ************************************************************************* //
diff --git a/src/lagrangian/molecularDynamics/molecule/distribution/distribution.H b/src/lagrangian/molecularDynamics/molecule/distribution/distribution.H
new file mode 100755
index 0000000000..e9bfdfccf8
--- /dev/null
+++ b/src/lagrangian/molecularDynamics/molecule/distribution/distribution.H
@@ -0,0 +1,133 @@
+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+   \\    /   O peration     |
+    \\  /    A nd           | Copyright (C) 1991-2005 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::distribution
+
+Description
+
+SourceFiles
+    distributionI.H
+    distribution.C
+    distributionIO.C
+
+\*---------------------------------------------------------------------------*/
+
+#ifndef distribution_H
+#define distribution_H
+
+#include "Map.H"
+#include "Pair.H"
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+namespace Foam
+{
+
+/*---------------------------------------------------------------------------*\
+                           Class distribution Declaration
+\*---------------------------------------------------------------------------*/
+
+class distribution
+:
+    public Map<label>
+{
+    // Private data
+
+        scalar binWidth_;
+
+
+public:
+
+    // Constructors
+
+        //- Construct null
+        distribution();
+
+        //- Construct from binWidth
+        distribution(const scalar binWidth);
+
+        //- Construct as copy
+        distribution(const distribution&);
+
+
+    // Destructor
+
+        ~distribution();
+
+
+    // Member Functions
+
+        label totalEntries() const;
+
+        scalar approxTotalEntries() const;
+
+        scalar mean() const;
+
+        scalar median();
+
+        //- Add a value to the appropriate bin of the distribution.
+        void add(const scalar valueToAdd);
+
+        void add(const label valueToAdd);
+
+        void insertMissingKeys();
+
+        List< Pair<scalar> > normalised();
+
+        List< Pair<scalar> > normalisedMinusMean();
+
+        List< Pair<scalar> > normalisedShifted(const scalar shiftValue);
+
+        List< Pair<scalar> > raw();
+
+        // Access
+
+            inline scalar binWidth() const;
+
+
+    // Member Operators
+
+        void operator=(const distribution&);
+
+
+    // IOstream Operators
+
+        friend Ostream& operator<<(Ostream&, const distribution&);
+};
+
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+} // End namespace Foam
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+#include "distributionI.H"
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+#endif
+
+// ************************************************************************* //
diff --git a/src/lagrangian/molecularDynamics/molecule/distribution/distributionI.H b/src/lagrangian/molecularDynamics/molecule/distribution/distributionI.H
new file mode 100755
index 0000000000..85d5934da0
--- /dev/null
+++ b/src/lagrangian/molecularDynamics/molecule/distribution/distributionI.H
@@ -0,0 +1,42 @@
+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+   \\    /   O peration     |
+    \\  /    A nd           | Copyright (C) 1991-2005 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
+{
+
+// * * * * * * * * * * * * * * * Member Functions  * * * * * * * * * * * * * //
+
+inline scalar distribution::binWidth() const
+{
+    return binWidth_;
+}
+
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+} // End namespace Foam
+
+// ************************************************************************* //
diff --git a/src/lagrangian/molecularDynamics/molecule/distribution/distributionIO.C b/src/lagrangian/molecularDynamics/molecule/distribution/distributionIO.C
new file mode 100755
index 0000000000..57f6e774bb
--- /dev/null
+++ b/src/lagrangian/molecularDynamics/molecule/distribution/distributionIO.C
@@ -0,0 +1,35 @@
+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+   \\    /   O peration     |
+    \\  /    A nd           | Copyright (C) 1991-2005 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 "distribution.H"
+#include "IOstreams.H"
+
+// * * * * * * * * * * * * * * * * Constructors  * * * * * * * * * * * * * * //
+
+// construct from Istream
+
+
+// ************************************************************************* //
diff --git a/src/lagrangian/molecularDynamics/molecule/mdTools/averageMDFields.H b/src/lagrangian/molecularDynamics/molecule/mdTools/averageMDFields.H
new file mode 100755
index 0000000000..db0c24bc95
--- /dev/null
+++ b/src/lagrangian/molecularDynamics/molecule/mdTools/averageMDFields.H
@@ -0,0 +1,227 @@
+if (runTime.outputTime())
+{
+    /*-----------------------------------------------------------------------*\
+        Number density
+    \*-----------------------------------------------------------------------*/
+
+    scalarField totalRhoN_sum(mesh.nCells(), 0.0);
+    
+    forAll (allSpeciesRhoN, rN)
+    {
+        allSpeciesRhoN[rN].internalField() =
+            allSpeciesN_RU[rN]
+            /mesh.cellVolumes()
+            /nAveragingSteps;
+            
+        totalRhoN_sum += allSpeciesRhoN[rN].internalField();
+    }
+    
+    totalRhoN.internalField() = totalRhoN_sum;
+    
+    
+    /*-----------------------------------------------------------------------*\
+        Mass density
+    \*-----------------------------------------------------------------------*/
+    
+    scalarField totalRhoM_sum(mesh.nCells(), 0.0);
+    
+    forAll (allSpeciesRhoM, rM)
+    {
+        allSpeciesRhoM[rM].internalField() =
+            allSpeciesM_RU[rM]
+            /mesh.cellVolumes()
+            /nAveragingSteps;
+            
+        totalRhoM_sum += allSpeciesRhoM[rM].internalField();
+    }
+    
+    totalRhoM.internalField() = totalRhoM_sum;
+    
+    /*-----------------------------------------------------------------------*\
+        Bulk velocity
+    \*-----------------------------------------------------------------------*/
+    
+    vectorField totalMomentum_sum(mesh.nCells(), vector::zero);
+    
+    scalarField totalMass_sum(mesh.nCells(), 0.0);
+    
+    forAll (allSpeciesVelocity, v)
+    {
+        // A check for 1/0 molecules is required.
+    
+        vectorField& singleSpeciesVelocity
+        (
+            allSpeciesVelocity[v].internalField()
+        );
+        
+        forAll(singleSpeciesVelocity, sSV)
+        {
+            if(allSpeciesN_RU[v][sSV])
+            {
+                singleSpeciesVelocity[sSV] = 
+                    allSpeciesVelocitySum_RU[v][sSV]
+                    /allSpeciesN_RU[v][sSV];
+                    
+                totalMomentum_sum[sSV] +=
+                    allSpeciesM_RU[v][sSV]
+                    /allSpeciesN_RU[v][sSV]
+                    *allSpeciesVelocitySum_RU[v][sSV];
+                    
+                totalMass_sum[sSV] += allSpeciesM_RU[v][sSV];
+            }
+            else
+            {
+                singleSpeciesVelocity[sSV] = vector::zero;
+            }
+        }
+    }
+    
+    forAll(totalVelocity.internalField(), tV)
+    {
+        if(totalMass_sum[tV] > VSMALL)
+        {
+            totalVelocity.internalField()[tV] =
+                totalMomentum_sum[tV]
+                /totalMass_sum[tV];
+        }
+        else
+        {
+            totalVelocity.internalField()[tV] =
+            vector::zero;
+        }
+    }
+    
+    /*-----------------------------------------------------------------------*\
+        Kinetic temperature
+    \*-----------------------------------------------------------------------*/
+    
+    scalarField totalTemperatureVTerms_sum(mesh.nCells(), 0.0);
+    
+    scalarField totalN_sum(mesh.nCells(), 0.0);
+    
+    forAll (allSpeciesTemperature, t)
+    {
+        // A check for 1/0 molecules is required.
+    
+        scalarField& singleSpeciesTemp
+        (
+            allSpeciesTemperature[t].internalField()
+        );
+        
+        forAll(singleSpeciesTemp, sST)
+        {
+            if(allSpeciesN_RU[t][sST])
+            {
+                singleSpeciesTemp[sST] = 
+                    allSpeciesM_RU[t][sST]
+                    /allSpeciesN_RU[t][sST]
+                    /(3.0 * moleculeCloud::kb * allSpeciesN_RU[t][sST])
+                    *
+                    (
+                        allSpeciesVelocityMagSquaredSum_RU[t][sST]
+                        -
+                        (
+                            allSpeciesVelocitySum_RU[t][sST]
+                            &
+                            allSpeciesVelocitySum_RU[t][sST]
+                        )
+                        /allSpeciesN_RU[t][sST]
+                    );
+                    
+                totalTemperatureVTerms_sum[sST] +=
+                    allSpeciesM_RU[t][sST]
+                    /allSpeciesN_RU[t][sST]
+                    *
+                    (
+                        allSpeciesVelocityMagSquaredSum_RU[t][sST]
+                        -
+                        (
+                            allSpeciesVelocitySum_RU[t][sST]
+                            &
+                            allSpeciesVelocitySum_RU[t][sST]
+                        )
+                        /allSpeciesN_RU[t][sST]
+                    );
+                    
+                totalN_sum[sST] += allSpeciesN_RU[t][sST];
+            }
+            else
+            {
+                singleSpeciesTemp[sST] = 0.0;
+            }
+        }
+    }
+    
+    forAll(totalTemperature.internalField(), tT)
+    {
+        if(totalN_sum[tT] > 0)
+        {
+            totalTemperature.internalField()[tT] =
+                totalTemperatureVTerms_sum[tT]
+                /(3.0 * moleculeCloud::kb * totalN_sum[tT]);
+        }
+        else
+        {
+            totalTemperature.internalField()[tT] = 0.0;
+        }
+    }
+    
+    /*-----------------------------------------------------------------------*\
+        Mean kinetic energy
+    \*-----------------------------------------------------------------------*/
+    
+    scalarField totalKE_sum(mesh.nCells(), 0.0);
+    
+    forAll (allSpeciesMeanKE, mKE)
+    {
+        // A check for 1/0 molecules is required.
+    
+        scalarField& singleSpeciesMeanKE
+        (
+            allSpeciesMeanKE[mKE].internalField()
+        );
+        
+        forAll(singleSpeciesMeanKE, sSMKE)
+        {
+            if(allSpeciesN_RU[mKE][sSMKE])
+            {
+                singleSpeciesMeanKE[sSMKE] = 
+                    allSpeciesM_RU[mKE][sSMKE]
+                    /allSpeciesN_RU[mKE][sSMKE]
+                    /(2.0 * allSpeciesN_RU[mKE][sSMKE])
+                    *
+                    (
+                        allSpeciesVelocityMagSquaredSum_RU[mKE][sSMKE]
+                    );
+                    
+                totalKE_sum[sSMKE] +=
+                    allSpeciesM_RU[mKE][sSMKE]
+                    /allSpeciesN_RU[mKE][sSMKE]
+                    /2.0
+                    *
+                    (
+                        allSpeciesVelocityMagSquaredSum_RU[mKE][sSMKE]
+                    );
+            }
+            else
+            {
+                singleSpeciesMeanKE[sSMKE] = 0.0;
+            }
+        }
+    }
+    
+    forAll(totalMeanKE.internalField(), tMKE)
+    {
+        if(totalN_sum[tMKE] > 0)
+        {
+            totalMeanKE.internalField()[tMKE] =
+                totalKE_sum[tMKE]
+                /totalN_sum[tMKE];
+        }
+        else
+        {
+            totalMeanKE.internalField()[tMKE] = 0.0;
+        }
+    }
+}
+
diff --git a/src/lagrangian/molecularDynamics/molecule/mdTools/calculateAutoCorrelationFunctions.H b/src/lagrangian/molecularDynamics/molecule/mdTools/calculateAutoCorrelationFunctions.H
new file mode 100644
index 0000000000..8f7574a077
--- /dev/null
+++ b/src/lagrangian/molecularDynamics/molecule/mdTools/calculateAutoCorrelationFunctions.H
@@ -0,0 +1,105 @@
+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  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
+
+\*---------------------------------------------------------------------------*/
+
+if (mesh.time().timeIndex() % vacf.sampleSteps() == 0)
+{
+    IDLList<molecule>::iterator mol(molecules.begin());
+
+    Field<vector> uVals(molecules.size());
+
+    label uV = 0;
+
+    for
+    (
+        mol = molecules.begin();
+        mol != molecules.end();
+        ++mol, uV++
+    )
+    {
+        uVals[uV] = mol().U();
+    }
+
+    vacf.calculateCorrelationFunction(uVals);
+}
+
+if (mesh.time().timeIndex() % pacf.sampleSteps() == 0)
+{
+    IDLList<molecule>::iterator mol(molecules.begin());
+
+    vector p = vector::zero;
+
+    for
+    (
+        mol = molecules.begin();
+        mol != molecules.end();
+        ++mol
+    )
+    {
+        p.x() +=
+            mol().mass() * mol().U().y() * mol().U().z()
+            +
+            0.5 * mol().rf().yz();
+
+        p.y() +=
+            mol().mass() * mol().U().z() * mol().U().x()
+            +
+            0.5 * mol().rf().zx();
+
+        p.z() +=
+            mol().mass() * mol().U().x() * mol().U().y()
+            +
+            0.5 * mol().rf().xy();
+    }
+
+    pacf.calculateCorrelationFunction(p);
+}
+
+if (mesh.time().timeIndex() % hfacf.sampleSteps() == 0)
+{
+
+    IDLList<molecule>::iterator mol(molecules.begin());
+
+    vector s = vector::zero;
+
+    for
+    (
+        mol = molecules.begin();
+        mol != molecules.end();
+        ++mol
+    )
+    {
+        s +=
+        (
+            0.5 * mol().mass() * magSqr(mol().U())
+            +
+            mol().potentialEnergy()
+        ) * mol().U()
+        +
+        0.5 * ( mol().rf() & mol().U() );
+    }
+
+    hfacf.calculateCorrelationFunction(s);
+}
diff --git a/src/lagrangian/molecularDynamics/molecule/mdTools/calculateMDFields.H b/src/lagrangian/molecularDynamics/molecule/mdTools/calculateMDFields.H
new file mode 100755
index 0000000000..af5c938da4
--- /dev/null
+++ b/src/lagrangian/molecularDynamics/molecule/mdTools/calculateMDFields.H
@@ -0,0 +1,23 @@
+const List<DynamicList<molecule*> >& cellOccupancy = molecules.cellOccupancy();
+
+forAll(cellOccupancy, cell)
+{
+    const List<molecule*>& molsInCell = cellOccupancy[cell];
+
+    forAll(molsInCell, mIC)
+    {
+        molecule* mol = molsInCell[mIC];
+
+        const label molId = mol->id();
+
+        const vector& molU = mol->U();
+
+        allSpeciesN_RU[molId][cell]++;
+
+        allSpeciesM_RU[molId][cell] += mol->mass();
+
+        allSpeciesVelocitySum_RU[molId][cell] += molU;
+
+        allSpeciesVelocityMagSquaredSum_RU[molId][cell] += molU & molU;
+    }
+}
diff --git a/src/lagrangian/molecularDynamics/molecule/mdTools/calculateTransportProperties.H b/src/lagrangian/molecularDynamics/molecule/mdTools/calculateTransportProperties.H
new file mode 100644
index 0000000000..b0923c42db
--- /dev/null
+++ b/src/lagrangian/molecularDynamics/molecule/mdTools/calculateTransportProperties.H
@@ -0,0 +1,82 @@
+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  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
+
+\*---------------------------------------------------------------------------*/
+
+if (writeVacf)
+{
+    OFstream vacfFile(runTime.path()/"vacf");
+
+    if (!vacf.writeAveraged(vacfFile))
+    {
+        FatalErrorIn(args.executable())
+            << "Failed writing to "
+            << vacfFile.name()
+            << abort(FatalError);
+    }
+}
+
+Info << "Diffusion coefficient = "
+    << vacf.integral() << endl;
+
+if (writePacf)
+{
+    OFstream pacfFile(runTime.path()/"pacf");
+
+    if (!pacf.writeAveraged(pacfFile))
+    {
+        FatalErrorIn(args.executable())
+            << "Failed writing to "
+            << pacfFile.name()
+            << abort(FatalError);
+    }
+}
+
+Info<< "Viscosity = "
+    << pacf.integral()/averageTemperature/moleculeCloud::kb/meshVolume
+    << endl;
+
+if(writeHFacf)
+{
+    OFstream hfacfFile
+    (
+        runTime.path()/ + "hfacf"
+    );
+    
+    if (!hfacf.writeAveraged(hfacfFile))
+    {
+        FatalErrorIn(args.executable())
+            << "Failed writing to "
+            << hfacfFile.name()
+            << abort(FatalError);
+    }
+}
+
+Info << "Thermal conductivity = "
+    << hfacf.integral()
+        /averageTemperature
+        /averageTemperature
+        /moleculeCloud::kb
+        / meshVolume
+    << endl;
diff --git a/src/lagrangian/molecularDynamics/molecule/mdTools/createAutoCorrelationFunctions.H b/src/lagrangian/molecularDynamics/molecule/mdTools/createAutoCorrelationFunctions.H
new file mode 100644
index 0000000000..3bec4493dc
--- /dev/null
+++ b/src/lagrangian/molecularDynamics/molecule/mdTools/createAutoCorrelationFunctions.H
@@ -0,0 +1,99 @@
+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  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
+
+\*---------------------------------------------------------------------------*/
+
+Info << nl << "Creating autocorrelation functions." << endl;
+
+IOdictionary mdTransportProperitesDict
+(
+    IOobject
+    (
+        "mdTransportProperitesDict",
+        mesh.time().system(),
+        mesh,
+        IOobject::MUST_READ,
+        IOobject::NO_WRITE,
+        false
+    )
+);
+
+const dictionary& autocorrelationFunctionDict
+(
+    mdTransportProperitesDict.subDict("autocorrelationFunctions")
+);
+
+//- Velocity autocorrelation function
+
+Info << tab << "velocty" << endl;
+
+const dictionary& velocityACFDict
+(
+    autocorrelationFunctionDict.subDict("velocity")
+);
+
+correlationFunction<vector> vacf
+(
+    mesh,
+    velocityACFDict,
+    molecules.size()
+);
+
+bool writeVacf(Switch(velocityACFDict.lookup("writeFile")));
+
+//- Pressure autocorrelation function
+
+Info << tab << "pressure" << endl;
+
+const dictionary& pressureACFDict
+(
+    autocorrelationFunctionDict.subDict("pressure")
+);
+
+correlationFunction<vector> pacf
+(
+    mesh,
+    pressureACFDict,
+    1
+);
+
+bool writePacf(Switch(pressureACFDict.lookup("writeFile")));
+
+//- Heat flux autocorrelation function
+
+Info << tab << "heat flux" << endl;
+
+const dictionary& heatFluxACFDict
+(
+    autocorrelationFunctionDict.subDict("heatFlux")
+);
+
+correlationFunction<vector> hfacf
+(
+    mesh,
+    heatFluxACFDict,
+    1
+);
+
+bool writeHFacf(Switch(heatFluxACFDict.lookup("writeFile")));
diff --git a/src/lagrangian/molecularDynamics/molecule/mdTools/createMDFields.H b/src/lagrangian/molecularDynamics/molecule/mdTools/createMDFields.H
new file mode 100755
index 0000000000..dccd1891a7
--- /dev/null
+++ b/src/lagrangian/molecularDynamics/molecule/mdTools/createMDFields.H
@@ -0,0 +1,324 @@
+// Fields for data gathering
+
+List< scalarField > allSpeciesN_RU
+(
+    molecules.pairPotentials().nIds(),
+    scalarField (mesh.nCells(), 0.0)
+);
+
+List< scalarField > allSpeciesM_RU
+(
+    molecules.pairPotentials().nIds(),
+    scalarField (mesh.nCells(), 0.0)
+);
+
+List< vectorField > allSpeciesVelocitySum_RU
+(
+    molecules.pairPotentials().nIds(),
+    vectorField (mesh.nCells(), vector::zero)
+);
+
+List< scalarField > allSpeciesVelocityMagSquaredSum_RU
+(
+    molecules.pairPotentials().nIds(),
+    scalarField (mesh.nCells(), 0.0)
+);
+
+// Geometric Fields for IO
+
+Info << nl << "Creating fields." << endl;
+
+/*---------------------------------------------------------------------------*\
+    Number density
+\*---------------------------------------------------------------------------*/
+
+PtrList<volScalarField> allSpeciesRhoN
+(
+    molecules.pairPotentials().nIds()
+);
+
+forAll (allSpeciesRhoN, rN)
+{
+    Info << "    Creating number density field for "
+        << molecules.pairPotentials().idList()[rN] << endl;
+
+    allSpeciesRhoN.set
+    (
+        rN,
+        new volScalarField
+        (
+            IOobject
+            (
+                "rhoN_" + molecules.pairPotentials().idList()[rN],
+                runTime.timeName(),
+                mesh,
+                IOobject::NO_READ,
+                IOobject::AUTO_WRITE
+            ),
+            mesh,
+            dimless/dimVolume,
+            "zeroGradient"
+        )
+    );
+    allSpeciesRhoN[rN].internalField() = scalarField (mesh.nCells(), 0.0);
+    allSpeciesRhoN[rN].correctBoundaryConditions();
+}
+
+Info << "    Creating total number density field" << endl;
+
+volScalarField totalRhoN
+(
+    IOobject
+    (
+        "rhoN_total",
+        runTime.timeName(),
+        mesh,
+        IOobject::NO_READ,
+        IOobject::AUTO_WRITE
+    ),
+    mesh,
+    dimless/dimVolume,
+    "zeroGradient"
+);
+totalRhoN.internalField() = scalarField (mesh.nCells(), 0.0);
+totalRhoN.correctBoundaryConditions();
+
+/*---------------------------------------------------------------------------*\
+    Mass density
+\*---------------------------------------------------------------------------*/
+
+PtrList<volScalarField> allSpeciesRhoM
+(
+    molecules.pairPotentials().nIds()
+);
+
+forAll (allSpeciesRhoM, rM)
+{
+    Info << "    Creating mass density field for "
+        << molecules.pairPotentials().idList()[rM] << endl;
+
+    allSpeciesRhoM.set
+    (
+        rM,
+        new volScalarField
+        (
+            IOobject
+            (
+                "rhoM_" + molecules.pairPotentials().idList()[rM],
+                runTime.timeName(),
+                mesh,
+                IOobject::NO_READ,
+                IOobject::AUTO_WRITE
+            ),
+            mesh,
+            dimMass/dimVolume,
+            "zeroGradient"
+        )
+    );
+    allSpeciesRhoM[rM].internalField() = scalarField (mesh.nCells(), 0.0);
+    allSpeciesRhoM[rM].correctBoundaryConditions();
+}
+
+Info << "    Creating total mass density field" << endl;
+
+volScalarField totalRhoM
+(
+    IOobject
+    (
+        "rhoM_total",
+        runTime.timeName(),
+        mesh,
+        IOobject::NO_READ,
+        IOobject::AUTO_WRITE
+    ),
+    mesh,
+    dimMass/dimVolume,
+    "zeroGradient"
+);
+totalRhoM.internalField() = scalarField (mesh.nCells(), 0.0);
+totalRhoM.correctBoundaryConditions();
+
+/*---------------------------------------------------------------------------*\
+    Bulk velocity
+\*---------------------------------------------------------------------------*/
+
+PtrList<volVectorField> allSpeciesVelocity
+(
+    molecules.pairPotentials().nIds()
+);
+
+forAll (allSpeciesVelocity, v)
+{
+    Info << "    Creating velocity field for "
+        << molecules.pairPotentials().idList()[v] << endl;
+
+    allSpeciesVelocity.set
+    (
+        v,
+        new volVectorField
+        (
+            IOobject
+            (
+                "velocity_" + molecules.pairPotentials().idList()[v],
+                runTime.timeName(),
+                mesh,
+                IOobject::NO_READ,
+                IOobject::AUTO_WRITE
+            ),
+            mesh,
+            dimVelocity,
+            "zeroGradient"
+        )
+    );
+    allSpeciesVelocity[v].internalField() =
+        vectorField (mesh.nCells(), vector::zero);
+    allSpeciesVelocity[v].correctBoundaryConditions();
+}
+
+Info << "    Creating total velocity field" << endl;
+
+// volVectorField totalVelocity
+// (
+//     IOobject
+//     (
+//         "velocity_total",
+//         runTime.timeName(),
+//         mesh,
+//         IOobject::NO_READ,
+//         IOobject::AUTO_WRITE
+//     ),
+//     mesh,
+//     dimVelocity,
+//     "zeroGradient"
+// );
+// totalVelocity.internalField() = vectorField (mesh.nCells(), vector::zero);
+// totalVelocity.correctBoundaryConditions();
+
+
+volVectorField totalVelocity
+
+(
+    IOobject
+    (
+
+    "velocity_total",
+    runTime.timeName(),
+    mesh,
+    IOobject::NO_READ,
+    IOobject::AUTO_WRITE
+
+    ),
+    mesh,
+    dimensionedVector("zero", dimVelocity, vector::zero)
+);
+
+/*---------------------------------------------------------------------------*\
+    Kinetic temperature
+\*---------------------------------------------------------------------------*/
+
+PtrList<volScalarField> allSpeciesTemperature
+(
+    molecules.pairPotentials().nIds()
+);
+
+forAll (allSpeciesTemperature, t)
+{
+    Info << "    Creating temperature field for "
+        << molecules.pairPotentials().idList()[t] << endl;
+
+    allSpeciesTemperature.set
+    (
+        t,
+        new volScalarField
+        (
+            IOobject
+            (
+                "temperature_" + molecules.pairPotentials().idList()[t],
+                runTime.timeName(),
+                mesh,
+                IOobject::NO_READ,
+                IOobject::AUTO_WRITE
+            ),
+            mesh,
+            dimTemperature,
+            "zeroGradient"
+        )
+    );
+    allSpeciesTemperature[t].internalField() = scalarField (mesh.nCells(), 0.0);
+    allSpeciesTemperature[t].correctBoundaryConditions();
+}
+
+Info << "    Creating total temperature field" << endl;
+
+volScalarField totalTemperature
+(
+    IOobject
+    (
+        "temperature_total",
+        runTime.timeName(),
+        mesh,
+        IOobject::NO_READ,
+        IOobject::AUTO_WRITE
+    ),
+    mesh,
+    dimTemperature,
+    "zeroGradient"
+);
+totalTemperature.internalField() = scalarField (mesh.nCells(), 0.0);
+totalTemperature.correctBoundaryConditions();
+
+/*---------------------------------------------------------------------------*\
+    Mean kinetic energy
+\*---------------------------------------------------------------------------*/
+
+
+PtrList<volScalarField> allSpeciesMeanKE
+(
+    molecules.pairPotentials().nIds()
+);
+
+forAll (allSpeciesMeanKE, mKE)
+{
+    Info << "    Creating mean kinetic energy field for "
+        << molecules.pairPotentials().idList()[mKE] << endl;
+
+    allSpeciesMeanKE.set
+    (
+        mKE,
+        new volScalarField
+        (
+            IOobject
+            (
+                "meanKE_" + molecules.pairPotentials().idList()[mKE],
+                runTime.timeName(),
+                mesh,
+                IOobject::NO_READ,
+                IOobject::AUTO_WRITE
+            ),
+            mesh,
+            dimensionSet(1, 2, -2, 0, 0, 0, 0),
+            "zeroGradient"
+        )
+    );
+    allSpeciesMeanKE[mKE].internalField() = scalarField (mesh.nCells(), 0.0);
+    allSpeciesMeanKE[mKE].correctBoundaryConditions();
+}
+
+Info << "    Creating total mean kinetic energy field" << endl;
+
+volScalarField totalMeanKE
+(
+    IOobject
+    (
+        "meanKE_total",
+        runTime.timeName(),
+        mesh,
+        IOobject::NO_READ,
+        IOobject::AUTO_WRITE
+    ),
+    mesh,
+    dimensionSet(1, 2, -2, 0, 0, 0, 0),
+    "zeroGradient"
+);
+totalMeanKE.internalField() = scalarField (mesh.nCells(), 0.0);
+totalMeanKE.correctBoundaryConditions();
diff --git a/src/lagrangian/molecularDynamics/molecule/mdTools/createRefUnits.H b/src/lagrangian/molecularDynamics/molecule/mdTools/createRefUnits.H
new file mode 100644
index 0000000000..bbd6c6daf7
--- /dev/null
+++ b/src/lagrangian/molecularDynamics/molecule/mdTools/createRefUnits.H
@@ -0,0 +1,22 @@
+reducedUnits refUnits;
+
+IOobject reducedUnitsDictIOobject
+(
+    "reducedUnitsDict",
+    runTime.system(),
+    mesh,
+    IOobject::READ_IF_PRESENT,
+    IOobject::NO_WRITE
+);
+
+if (reducedUnitsDictIOobject.headerOk())
+{
+    Info << nl
+        << "Reading reference quantities from reducedUnitsDict file." << endl;
+
+    IOdictionary reducedUnitsDict(reducedUnitsDictIOobject);
+
+    refUnits.setRefValues(reducedUnitsDict);
+}
+
+Info << refUnits << endl;
diff --git a/src/lagrangian/molecularDynamics/molecule/mdTools/md.H b/src/lagrangian/molecularDynamics/molecule/mdTools/md.H
new file mode 100755
index 0000000000..5c018694bd
--- /dev/null
+++ b/src/lagrangian/molecularDynamics/molecule/mdTools/md.H
@@ -0,0 +1,11 @@
+#ifndef md_H
+#define md_H
+
+#   include "moleculeCloud.H"
+
+#   include "correlationFunction.H"
+#   include "distribution.H"
+#   include "reducedUnits.H"
+
+#endif
+
diff --git a/src/lagrangian/molecularDynamics/molecule/mdTools/meanMomentumEnergyAndNMols.H b/src/lagrangian/molecularDynamics/molecule/mdTools/meanMomentumEnergyAndNMols.H
new file mode 100755
index 0000000000..043e63c543
--- /dev/null
+++ b/src/lagrangian/molecularDynamics/molecule/mdTools/meanMomentumEnergyAndNMols.H
@@ -0,0 +1,130 @@
+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  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
+
+Global
+    meanMomentumEnergyAndNMols.H
+
+Description
+    Calculates and prints the mean momentum and energy in the system
+    and the number of molecules.
+
+\*---------------------------------------------------------------------------*/
+
+
+vector singleStepTotalMomentum(vector::zero);
+
+scalar singleStepMaxVelocityMag = 0.0;
+
+scalar singleStepTotalMass = 0.0;
+
+scalar singleStepTotalKE = 0.0;
+
+scalar singleStepTotalPE = 0.0;
+
+scalar singleStepTotalrDotf = 0.0;
+
+{
+    IDLList<molecule>::iterator mol(molecules.begin());
+
+    for
+    (
+        mol = molecules.begin();
+        mol != molecules.end();
+        ++mol
+    )
+    {
+        const scalar molM(mol().mass());
+
+        const vector& molU(mol().U());
+
+        singleStepTotalMomentum += molU * molM;
+
+        singleStepTotalMass += molM;
+
+        if(mag(molU) > singleStepMaxVelocityMag)
+        {
+            singleStepMaxVelocityMag = mag(molU);
+        }
+
+        singleStepTotalKE += 0.5*molM*magSqr(molU);
+
+        singleStepTotalPE += mol().potentialEnergy();
+
+        singleStepTotalrDotf += tr(mol().rf());
+    }
+}
+
+label singleStepNMols = molecules.size();
+
+if (Pstream::parRun())
+{
+    reduce(singleStepTotalMomentum, sumOp<vector>());
+
+    reduce(singleStepMaxVelocityMag, maxOp<scalar>());
+
+    reduce(singleStepTotalMass, sumOp<scalar>());
+
+    reduce(singleStepTotalKE, sumOp<scalar>());
+
+    reduce(singleStepTotalPE, sumOp<scalar>());
+
+    reduce(singleStepTotalrDotf, sumOp<scalar>());
+
+    reduce(singleStepNMols, sumOp<label>());
+}
+
+if (singleStepNMols)
+{
+    Info << "Number of mols in system = "
+            << singleStepNMols << nl
+        << "Overall number density = "
+            << singleStepNMols/meshVolume << " m^-3" << nl
+        << "Overall mass density = "
+            << singleStepTotalMass/meshVolume << " kg/m^3" << nl
+        << "Average velocity per mol = "
+            << singleStepTotalMomentum/singleStepTotalMass << " m/s" << nl
+        << "Maximum |velocity| = "
+            << singleStepMaxVelocityMag << " m/s" << nl
+        << "Average KE per mol = "
+            << singleStepTotalKE/singleStepNMols << " J" << nl
+        << "Average PE per mol = "
+            << singleStepTotalPE/singleStepNMols << " J" << nl
+        << "Average TE per mol = "
+            << (singleStepTotalKE + singleStepTotalPE)/singleStepNMols << " J"
+        << endl;
+
+//     Info << singleStepNMols << " "
+// //     << singleStepTotalMomentum/singleStepTotalMass << " "
+//     << singleStepMaxVelocityMag << " "
+//     << singleStepTotalKE/singleStepNMols << " "
+//     << singleStepTotalPE/singleStepNMols << " "
+//     << (singleStepTotalKE + singleStepTotalPE)/singleStepNMols << endl;
+}
+else
+{
+    Info << "No molecules in system" << endl;
+}
+
+
+// ************************************************************************* //
diff --git a/src/lagrangian/molecularDynamics/molecule/mdTools/resetMDFields.H b/src/lagrangian/molecularDynamics/molecule/mdTools/resetMDFields.H
new file mode 100755
index 0000000000..337647ec02
--- /dev/null
+++ b/src/lagrangian/molecularDynamics/molecule/mdTools/resetMDFields.H
@@ -0,0 +1,26 @@
+if (runTime.outputTime())
+{
+    allSpeciesN_RU = List< scalarField >
+    (
+        molecules.pairPotentials().nIds(),
+        scalarField (mesh.nCells(), 0.0)
+    );
+
+    allSpeciesM_RU = List< scalarField >
+    (
+        molecules.pairPotentials().nIds(),
+        scalarField (mesh.nCells(), 0.0)
+    );
+
+    allSpeciesVelocitySum_RU = List< vectorField >
+    (
+        molecules.pairPotentials().nIds(),
+        vectorField (mesh.nCells(), vector::zero)
+    );
+
+    allSpeciesVelocityMagSquaredSum_RU = List< scalarField >
+    (
+        molecules.pairPotentials().nIds(),
+        scalarField (mesh.nCells(), 0.0)
+    );
+}
diff --git a/src/lagrangian/molecularDynamics/molecule/mdTools/temperatureAndPressure.H b/src/lagrangian/molecularDynamics/molecule/mdTools/temperatureAndPressure.H
new file mode 100755
index 0000000000..0ae8b5d1ea
--- /dev/null
+++ b/src/lagrangian/molecularDynamics/molecule/mdTools/temperatureAndPressure.H
@@ -0,0 +1,116 @@
+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  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
+
+Global
+    temperatureAndPressure.H
+
+Description
+    Accumulates values for temperature and pressure measurement, and
+    calculates and outputs the average values at output times.
+    Requires temperatureAndPressureVariables.H to be declared before the
+    timeloop.
+
+\*---------------------------------------------------------------------------*/
+
+accumulatedTotalMomentum += singleStepTotalMomentum;
+
+accumulatedTotalMass += singleStepTotalMass;
+
+accumulatedTotalKE += singleStepTotalKE;
+
+accumulatedTotalPE += singleStepTotalPE;
+
+accumulatedTotalrDotfSum += singleStepTotalrDotf;
+
+accumulatedNMols += singleStepNMols;
+
+if (runTime.outputTime())
+{
+    // calculate averages
+
+    if (accumulatedNMols)
+    {
+        Info << "calculating averages" << endl;
+
+        averageTemperature =
+        (
+            2.0/(3.0 * moleculeCloud::kb * accumulatedNMols)
+            *
+            (
+                accumulatedTotalKE
+                -
+                0.5*magSqr(accumulatedTotalMomentum)/accumulatedTotalMass
+            )
+        );
+
+        averagePressure =
+        (
+            (
+                (accumulatedNMols/nAveragingSteps)
+                *
+                moleculeCloud::kb * averageTemperature
+                +
+                accumulatedTotalrDotfSum/(6.0 * nAveragingSteps)
+            )
+            /
+            meshVolume
+        );
+
+        // output values
+
+        Info << "----------------------------------------" << nl
+            << "Averaged properties" << nl
+            << "Average |velocity| = "
+                << mag(accumulatedTotalMomentum)/accumulatedTotalMass
+                << " m/s" << nl
+            << "Average temperature = "
+                << averageTemperature << " K" << nl
+            << "accumulatedTotalrDotfSum = "
+                << accumulatedTotalrDotfSum << nl
+            << "Average pressure = "
+                << averagePressure << " N/m^2" << nl
+            << "----------------------------------------" << endl;
+    }
+    else
+    {
+        Info << "Not averaging temperature and pressure: "
+            << "no molecules in system" << endl;
+    }
+
+    // reset counters
+
+    accumulatedTotalMomentum = vector::zero;
+
+    accumulatedTotalMass = 0.0;
+
+    accumulatedTotalKE = 0.0;
+
+    accumulatedTotalPE = 0.0;
+
+    accumulatedTotalrDotfSum = 0.0;
+
+    accumulatedNMols = 0;
+}
+
+// ************************************************************************* //
diff --git a/src/lagrangian/molecularDynamics/molecule/mdTools/temperatureAndPressureVariables.H b/src/lagrangian/molecularDynamics/molecule/mdTools/temperatureAndPressureVariables.H
new file mode 100755
index 0000000000..258cfac314
--- /dev/null
+++ b/src/lagrangian/molecularDynamics/molecule/mdTools/temperatureAndPressureVariables.H
@@ -0,0 +1,59 @@
+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  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
+
+Global
+    temperatureAndPressureVariables.H
+
+Description
+    Provides accumulation variables for temperatureAndPressure.H
+
+\*---------------------------------------------------------------------------*/
+
+vector accumulatedTotalMomentum(vector::zero);
+
+scalar accumulatedTotalMass = 0.0;
+
+scalar accumulatedTotalKE = 0.0;
+
+scalar accumulatedTotalPE = 0.0;
+
+scalar accumulatedTotalrDotfSum = 0.0;
+
+label accumulatedNMols = 0;
+
+scalar averageTemperature = 0.0;
+
+scalar averagePressure = 0.0;
+
+const scalarField& cellVols = mesh.cellVolumes();
+
+scalar meshVolume = sum(cellVols);
+
+if (Pstream::parRun())
+{
+    reduce(meshVolume, sumOp<scalar>());
+}
+
+
+// ************************************************************************* //
diff --git a/src/lagrangian/molecularDynamics/molecule/mdTools/temperatureEquilibration.H b/src/lagrangian/molecularDynamics/molecule/mdTools/temperatureEquilibration.H
new file mode 100755
index 0000000000..c640809cda
--- /dev/null
+++ b/src/lagrangian/molecularDynamics/molecule/mdTools/temperatureEquilibration.H
@@ -0,0 +1,43 @@
+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  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
+
+Global
+    temperatureEquilibration.H
+
+Description
+    Applies temperature control to molecules
+
+\*---------------------------------------------------------------------------*/
+
+if (runTime.outputTime())
+{
+    molecules.applyConstraintsAndThermostats
+    (
+        targetTemperature,
+        averageTemperature
+    );
+}
+
+
+// ************************************************************************* //
diff --git a/src/lagrangian/molecularDynamics/molecule/molecule/molecule.C b/src/lagrangian/molecularDynamics/molecule/molecule/molecule.C
new file mode 100755
index 0000000000..0a46a0ca2c
--- /dev/null
+++ b/src/lagrangian/molecularDynamics/molecule/molecule/molecule.C
@@ -0,0 +1,214 @@
+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+   \\    /   O peration     |
+    \\  /    A nd           | Copyright (C) 1991-2005 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 "moleculeCloud.H"
+#include "Random.H"
+#include "Time.H"
+
+namespace Foam
+{
+
+// * * * * * * * * * * * * * * * Member Operators  * * * * * * * * * * * * * //
+
+bool molecule::move(molecule::trackData& td)
+{
+    td.switchProcessor = false;
+    td.keepParticle = true;
+
+    scalar deltaT = cloud().pMesh().time().deltaT().value();
+    scalar tEnd = (1.0 - stepFraction())*deltaT;
+    scalar dtMax = tEnd;
+
+    moleculeCloud::integrationMethods method
+            = td.molCloud().integrationMethod();
+
+    if (method == moleculeCloud::imVerletLeapfrog)
+    {
+        if (td.part() == 1)  // Leapfrog 1st Part
+        {
+            if (stepFraction() < VSMALL)
+            {
+                U_ += 0.5*deltaT*A_;
+            }
+
+            while (td.keepParticle && !td.switchProcessor && tEnd > SMALL)
+            {
+                // set the lagrangian time-step
+                scalar dt = min(dtMax, tEnd);
+
+                dt *= trackToFace(position() + dt*U_, td);
+
+                tEnd -= dt;
+                stepFraction() = 1.0 - tEnd/deltaT;
+            }
+        }
+        else if (td.part() == 2)  // Leapfrog 2nd Part
+        {
+            U_ += 0.5*deltaT*A_;
+        }
+        else
+        {
+            FatalErrorIn("molecule::move(molecule::trackData& td)") << nl
+                << td.part()
+                << " is an invalid part of integration method: "
+                << method << nl
+                << abort(FatalError);
+        }
+    }
+    else if (method == moleculeCloud::imPredictorCorrector)
+    {
+        if (td.part() == 1) // Predictor Part
+        {
+
+        }
+        else if (td.part() == 2) // Corrector Part
+        {
+
+        }
+        else
+        {
+            FatalErrorIn("molecule::move(molecule::trackData& td)") << nl
+                << td.part() << " is an invalid part of integration method: "
+                << method
+                << abort(FatalError);
+        }
+    }
+    else
+    {
+        FatalErrorIn("molecule::move(molecule::trackData& td)") << nl
+                << "Unknown integration method: "
+                << method
+                << abort(FatalError);
+    }
+
+    return td.keepParticle;
+}
+
+
+void molecule::transformProperties(const tensor& T)
+{}
+
+
+void molecule::transformProperties(const vector& separation)
+{
+    if (tethered_)
+    {
+        tetherPosition_ += separation;
+    }
+}
+
+
+void molecule::hitProcessorPatch
+(
+    const processorPolyPatch&,
+    molecule::trackData& td
+)
+{
+    td.switchProcessor = true;
+}
+
+
+void molecule::hitProcessorPatch
+(
+    const processorPolyPatch&,
+    int&
+)
+{}
+
+
+void molecule::hitWallPatch
+(
+    const wallPolyPatch& wpp,
+    molecule::trackData& td
+)
+{
+    vector nw = wpp.faceAreas()[wpp.whichFace(face())];
+    nw /= mag(nw);
+
+    scalar Un = U_ & nw;
+//     vector Ut = U_ - Un*nw;
+
+//     Random rand(clock::getTime());
+
+//     scalar tmac = 0.8;
+
+//     scalar wallTemp = 2.5;
+
+//     if (rand.scalar01() < tmac)
+//     {
+//         // Diffuse reflection
+//
+//         vector tw1 = Ut/mag(Ut);
+//
+//         vector tw2 = nw ^ tw1;
+//
+//         U_ = sqrt(wallTemp/mass_)*rand.GaussNormal()*tw1
+//                 + sqrt(wallTemp/mass_)*rand.GaussNormal()*tw2
+//                 - mag(sqrt(wallTemp/mass_)*rand.GaussNormal())*nw;
+//     }
+
+//     else
+//     {
+        // Specular reflection
+
+        if (Un > 0)
+        {
+            U_ -= 2*Un*nw;
+        }
+//     }
+
+}
+
+
+void molecule::hitWallPatch
+(
+    const wallPolyPatch&,
+    int&
+)
+{}
+
+
+void molecule::hitPatch
+(
+    const polyPatch&,
+    molecule::trackData& td
+)
+{
+    td.keepParticle = false;
+}
+
+
+void molecule::hitPatch
+(
+    const polyPatch&,
+    int&
+)
+{}
+
+} // End namespace Foam
+
+
+// ************************************************************************* //
diff --git a/src/lagrangian/molecularDynamics/molecule/molecule/molecule.H b/src/lagrangian/molecularDynamics/molecule/molecule/molecule.H
new file mode 100755
index 0000000000..cbc0a7a134
--- /dev/null
+++ b/src/lagrangian/molecularDynamics/molecule/molecule/molecule.H
@@ -0,0 +1,271 @@
+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+   \\    /   O peration     |
+    \\  /    A nd           | Copyright (C) 1991-2005 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
+    molecule
+
+Description
+
+SourceFiles
+    moleculeI.H
+    molecule.C
+    moleculeIO.C
+
+\*---------------------------------------------------------------------------*/
+
+#ifndef molecule_H
+#define molecule_H
+
+#include "Particle.H"
+#include "IOstream.H"
+#include "autoPtr.H"
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+namespace Foam
+{
+
+// Class forward declarations
+class moleculeCloud;
+
+/*---------------------------------------------------------------------------*\
+                           Class molecule Declaration
+\*---------------------------------------------------------------------------*/
+
+class molecule
+:
+    public Particle<molecule>
+{
+    // Private data
+
+        //- Be careful with the ordering of data.  It has an impact on binary
+        //  transfer:
+        //  1) Put the largest data members 1st
+        //  2) Pair up labels,
+        //  3) Don't go scalar-label, scalar-label, becasue in 64bit mode,
+        //     the labels will be padded by 4bytes.
+
+        // - mass of molecule
+        scalar mass_;
+
+        // - Velocity of molecule
+        vector U_;
+
+        // - Acceleration of molecule
+        vector A_;
+
+        // - Tether position
+        vector tetherPosition_;
+
+        // - Potential energy that this molecules posseses
+        scalar potentialEnergy_;
+
+        // - r_ij f_ij, stress dyad
+        tensor rf_;
+
+        // - Is the molecule tethered?
+        label tethered_;
+
+        // - id (type) of molecule
+        label id_;
+
+
+public:
+
+    friend class Cloud<molecule>;
+
+    //- Class used to pass tracking data to the trackToFace function
+    class trackData
+    :
+        public Particle<molecule>::trackData
+    {
+        //- Reference to the cloud containing this particle
+        moleculeCloud& molCloud_;
+
+        // label specifying which part of the integration algorithm is taking
+        // place (i.e. leapfrog 1 or leapfrog 2. Predictor or Corrector)
+        label part_;
+
+
+    public:
+
+        // Constructors
+
+            inline trackData
+            (
+                moleculeCloud& molCloud,
+                label part
+            );
+
+        // Member functions
+
+            inline moleculeCloud& molCloud();
+
+            inline label part() const;
+    };
+
+    // Constructors
+
+        //- Construct from components
+        inline molecule
+        (
+            const Cloud<molecule>& c,
+            const vector& position,
+            const label celli,
+            const scalar mass,
+            const vector& U,
+            const vector& A,
+            const vector& tetherPosition,
+            const label tethered,
+            const label id
+        );
+
+        //- Construct from Istream
+        molecule
+        (
+            const Cloud<molecule>& c,
+            Istream& is,
+            bool readFields = true
+        );
+
+        //- Construct and return a clone
+        autoPtr<molecule> clone() const
+        {
+            return autoPtr<molecule>(new molecule(*this));
+        }
+
+
+    // Member Functions
+
+        void transformProperties(const tensor& T);
+
+        void transformProperties(const vector& separation);
+
+        // Access
+
+            //- Return id
+            inline label id() const;
+
+            //- Return mass
+            inline scalar mass() const;
+
+            //- Return velocity
+            inline const vector& U() const;
+            inline vector& U();
+
+            //- Return acceleration
+            inline const vector& A() const;
+            inline vector& A();
+
+            //- Return potential energy
+            inline scalar potentialEnergy() const;
+            inline scalar& potentialEnergy();
+
+            //- Return stress contribution
+            inline const tensor& rf() const;
+            inline tensor& rf();
+
+            //- Return tethered
+            inline label tethered() const;
+
+            //- Return tetherPosition
+            inline const vector& tetherPosition() const;
+            inline vector& tetherPosition();
+
+
+        //- Tracking
+        bool move(trackData&);
+
+
+    // Member Operators
+
+        //- Overridable function to handle the particle hitting a
+        //  processorPatch
+        void hitProcessorPatch
+        (
+            const processorPolyPatch&,
+            molecule::trackData& td
+        );
+
+        //- Overridable function to handle the particle hitting a
+        //  processorPatch without trackData
+        void hitProcessorPatch
+        (
+            const processorPolyPatch&,
+            int&
+        );
+
+        //- Overridable function to handle the particle hitting a wallPatch
+        void hitWallPatch
+        (
+            const wallPolyPatch&,
+            molecule::trackData& td
+        );
+
+        //- Overridable function to handle the particle hitting a wallPatch
+        //- without trackData
+        void hitWallPatch
+        (
+            const wallPolyPatch&,
+            int&
+        );
+
+        //- Overridable function to handle the particle hitting a polyPatch
+        void hitPatch
+        (
+            const polyPatch&,
+            molecule::trackData& td
+        );
+
+        //- Overridable function to handle the particle hitting a polyPatch
+        //- without trackData
+        void hitPatch
+        (
+            const polyPatch&,
+            int&
+        );
+
+        static void readFields(moleculeCloud& mC);
+
+        static void writeFields(const moleculeCloud& mC);
+
+
+    // IOstream Operators
+
+        friend Ostream& operator<<(Ostream&, const molecule&);
+};
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+} // End namespace Foam
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+#include "moleculeI.H"
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+#endif
+
+// ************************************************************************* //
diff --git a/src/lagrangian/molecularDynamics/molecule/molecule/moleculeI.H b/src/lagrangian/molecularDynamics/molecule/molecule/moleculeI.H
new file mode 100755
index 0000000000..c9f1b9eb73
--- /dev/null
+++ b/src/lagrangian/molecularDynamics/molecule/molecule/moleculeI.H
@@ -0,0 +1,165 @@
+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+   \\    /   O peration     |
+    \\  /    A nd           | Copyright (C) 1991-2005 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
+{
+
+// * * * * * * * * * * * * * * * * Constructors  * * * * * * * * * * * * * * //
+
+inline molecule::molecule
+(
+    const Cloud<molecule>& c,
+    const vector& position,
+    const label celli,
+    const scalar mass,
+    const vector& U,
+    const vector& A,
+    const vector& tetherPosition,
+    const label tethered,
+    const label id
+)
+:
+    Particle<molecule>(c, position, celli),
+    mass_(mass),
+    U_(U),
+    A_(A),
+    tetherPosition_(tetherPosition),
+    potentialEnergy_(0.0),
+    rf_(tensor::zero),
+    tethered_(tethered),
+    id_(id)
+{}
+
+
+inline molecule::trackData::trackData
+(
+    moleculeCloud& molCloud,
+    label part
+)
+:
+    Particle<molecule>::trackData(refCast<Cloud<molecule> >(molCloud)),
+    molCloud_(molCloud),
+    part_(part)
+{}
+
+
+// * * * * * * * * * * * * * * * Member Functions  * * * * * * * * * * * * * //
+
+inline label molecule::id() const
+{
+    return id_;
+}
+
+
+inline scalar molecule::mass() const
+{
+    return mass_;
+}
+
+
+inline const vector& molecule::U() const
+{
+    return U_;
+}
+
+
+inline vector& molecule::U()
+{
+    return U_;
+}
+
+
+inline const vector& molecule::A() const
+{
+    return A_;
+}
+
+
+inline vector& molecule::A()
+{
+    return A_;
+}
+
+
+inline scalar molecule::potentialEnergy() const
+{
+    return potentialEnergy_;
+}
+
+
+inline scalar& molecule::potentialEnergy()
+{
+    return potentialEnergy_;
+}
+
+
+inline const tensor& molecule::rf() const
+{
+    return rf_;
+}
+
+
+inline tensor& molecule::rf()
+{
+    return rf_;
+}
+
+
+inline label molecule::tethered() const
+{
+    return tethered_;
+}
+
+
+inline const vector& molecule::tetherPosition() const
+{
+    return tetherPosition_;
+}
+
+
+inline vector& molecule::tetherPosition()
+{
+    return tetherPosition_;
+}
+
+
+inline moleculeCloud& molecule::trackData::molCloud()
+{
+    return molCloud_;
+}
+
+
+inline label molecule::trackData::part() const
+{
+    return part_;
+}
+
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+} // End namespace Foam
+
+// ************************************************************************* //
diff --git a/src/lagrangian/molecularDynamics/molecule/molecule/moleculeIO.C b/src/lagrangian/molecularDynamics/molecule/molecule/moleculeIO.C
new file mode 100755
index 0000000000..f87b80cd46
--- /dev/null
+++ b/src/lagrangian/molecularDynamics/molecule/molecule/moleculeIO.C
@@ -0,0 +1,208 @@
+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+   \\    /   O peration     |
+    \\  /    A nd           | Copyright (C) 1991-2005 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 "molecule.H"
+#include "IOstreams.H"
+
+#include "moleculeCloud.H"
+
+// * * * * * * * * * * * * * * * * Constructors  * * * * * * * * * * * * * * //
+
+Foam::molecule::molecule
+(
+    const Cloud<molecule>& cloud,
+    Istream& is,
+    bool readFields
+)
+:
+    Particle<molecule>(cloud, is)
+{
+    if (readFields)
+    {
+        if (is.format() == IOstream::ASCII)
+        {
+            id_ = readLabel(is);
+            mass_ = readScalar(is);
+            is >> U_;
+            is >> A_;
+            is >> potentialEnergy_;
+            is >> rf_;
+            is >> tethered_;
+            is >> tetherPosition_;
+        }
+        else
+        {
+            is.read
+            (
+                reinterpret_cast<char*>(&mass_),
+                sizeof(mass_)
+                + sizeof(U_)
+                + sizeof(A_)
+                + sizeof(tetherPosition_)
+                + sizeof(potentialEnergy_)
+                + sizeof(rf_)
+                + sizeof(tethered_)
+                + sizeof(id_)
+            );
+        }
+    }
+
+    // Check state of Istream
+    is.check("Foam::molecule::molecule(Foam::Istream&)");
+}
+
+
+namespace Foam
+{
+
+void molecule::readFields(moleculeCloud& mC)
+{
+    if (!mC.size())
+    {
+        return;
+    }
+
+    IOField<label> id(mC.fieldIOobject("id"));
+    mC.checkFieldIOobject(mC, id);
+
+    IOField<scalar> mass(mC.fieldIOobject("mass"));
+    mC.checkFieldIOobject(mC, mass);
+
+    IOField<vector> U(mC.fieldIOobject("U"));
+    mC.checkFieldIOobject(mC, U);
+
+    IOField<vector> A(mC.fieldIOobject("A"));
+    mC.checkFieldIOobject(mC, A);
+
+    IOField<label> tethered(mC.fieldIOobject("tethered"));
+    mC.checkFieldIOobject(mC, tethered);
+
+    IOField<vector> tetherPositions(mC.fieldIOobject("tetherPositions"));
+    mC.checkFieldIOobject(mC, tetherPositions);
+
+    label i = 0;
+    forAllIter(moleculeCloud, mC, iter)
+    {
+        molecule& mol = iter();
+
+        mol.id_ = id[i];
+        mol.mass_ = mass[i];
+        mol.U_ = U[i];
+        mol.A_ = A[i];
+        mol.potentialEnergy_ = 0.0;
+        mol.rf_ = tensor::zero;
+        mol.tethered_ = tethered[i];
+        mol.tetherPosition_ = tetherPositions[i];
+        i++;
+    }
+}
+
+
+void molecule::writeFields(const moleculeCloud& mC)
+{
+    Particle<molecule>::writeFields(mC);
+
+    label np =  mC.size();
+
+    IOField<label> id(mC.fieldIOobject("id"), np);
+    IOField<scalar> mass(mC.fieldIOobject("mass"), np);
+    IOField<vector> U(mC.fieldIOobject("U"), np);
+    IOField<vector> A(mC.fieldIOobject("A"), np);
+    IOField<label> tethered(mC.fieldIOobject("tethered"), np);
+    IOField<vector> tetherPositions(mC.fieldIOobject("tetherPositions"), np);
+
+    label i = 0;
+    forAllConstIter(moleculeCloud, mC, iter)
+    {
+        const molecule& mol = iter();
+
+        id[i] = mol.id_;
+        mass[i] = mol.mass_;
+        U[i] = mol.U_;
+        A[i] = mol.A_;
+        tethered[i] = mol.tethered_;
+        tetherPositions[i] = mol.tetherPosition_;
+        i++;
+    }
+
+    id.write();
+    mass.write();
+    U.write();
+    A.write();
+    tethered.write();
+    tetherPositions.write();
+}
+
+};  // end of namespace Foam
+
+
+// * * * * * * * * * * * * * * * IOstream Operators  * * * * * * * * * * * * //
+
+Foam::Ostream& Foam::operator<<(Ostream& os, const molecule& mol)
+{
+    if (os.format() == IOstream::ASCII)
+    {
+        os  << mol.id_
+                << token::SPACE << mol.mass_
+                << token::SPACE << static_cast<const Particle<molecule>&>(mol)
+                << token::SPACE << mol.face()
+                << token::SPACE << mol.stepFraction()
+                << token::SPACE << mol.U_
+                << token::SPACE << mol.A_
+                << token::SPACE << mol.potentialEnergy_
+                << token::SPACE << mol.rf_
+                << token::SPACE << mol.tethered_
+                << token::SPACE << mol.tetherPosition_;
+    }
+    else
+    {
+        os  << static_cast<const Particle<molecule>&>(mol);
+        os.write
+        (
+            reinterpret_cast<const char*>(&mol.mass_),
+            sizeof(mol.mass_)
+            + sizeof(mol.U_)
+            + sizeof(mol.A_)
+            + sizeof(mol.tetherPosition_)
+            + sizeof(mol.potentialEnergy_)
+            + sizeof(mol.rf_)
+            + sizeof(mol.tethered_)
+            + sizeof(mol.id_)
+        );
+    }
+
+    // Check state of Ostream
+    os.check
+    (
+        "Foam::Ostream& Foam::operator<<"
+        "(Foam::Ostream&, const Foam::molecule&)"
+    );
+
+    return os;
+}
+
+
+// ************************************************************************* //
diff --git a/src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloud.C b/src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloud.C
new file mode 100755
index 0000000000..cf0ebebc7c
--- /dev/null
+++ b/src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloud.C
@@ -0,0 +1,135 @@
+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+   \\    /   O peration     |
+    \\  /    A nd           | Copyright (C) 1991-2005 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 "moleculeCloud.H"
+#include "fvMesh.H"
+
+// * * * * * * * * * * * * * * Static Data Members * * * * * * * * * * * * * //
+
+namespace Foam
+{
+    defineParticleTypeNameAndDebug(molecule, 0);
+    defineTemplateTypeNameAndDebug(Cloud<molecule>, 0);
+};
+
+
+template<>
+const char* Foam::NamedEnum<Foam::moleculeCloud::
+integrationMethods, 2>::names[] =
+{
+    "verletLeapfrog",
+    "predictorCorrector"
+};
+
+const Foam::NamedEnum<Foam::moleculeCloud::integrationMethods, 2>
+        Foam::moleculeCloud::integrationMethodNames_;
+
+
+Foam::scalar Foam::moleculeCloud::transTol = 1e-12;
+
+Foam::scalar Foam::moleculeCloud::kb = 1.380650277e-23;
+
+
+// * * * * * * * * * * * * * * * * Constructors  * * * * * * * * * * * * * * //
+
+Foam::moleculeCloud::moleculeCloud(const polyMesh& mesh)
+:
+    Cloud<molecule>(mesh, "moleculeCloud", false),
+    mesh_(mesh),
+    referredInteractionList_(*this)
+{
+    molecule::readFields(*this);
+
+#   include "moleculeCloudReadMDParameters.H"
+
+    buildCellInteractionLists();
+
+    buildCellReferralLists();
+
+    buildCellOccupancy();
+}
+
+
+Foam::moleculeCloud::moleculeCloud
+(
+    const polyMesh& mesh,
+    label nMol,
+    const labelField& id,
+    const scalarField& mass,
+    const vectorField& positions,
+    const labelField& cells,
+    const vectorField& U,
+    const vectorField& A,
+    const labelField& tethered,
+    const vectorField& tetherPositions
+)
+:
+    Cloud<molecule>(mesh, "moleculeCloud", false),
+    mesh_(mesh),
+    referredInteractionList_(*this)
+{
+    molecule::readFields(*this);
+
+    clear();
+
+    // This clear ()is here for the moment to stop existing files
+    // being appended to, this would be better accomplished by getting
+    // mesh.removeFiles(mesh.instance()); (or equivalent) to work.
+
+    int i;
+
+    const Cloud<molecule>& cloud = *this;
+
+    for (i=0; i<nMol; i++)
+    {
+        addParticle
+        (
+            new molecule
+            (
+                cloud,
+                positions[i],
+                cells[i],
+                mass[i],
+                U[i],
+                A[i],
+                tetherPositions[i],
+                tethered[i],
+                id[i]
+            )
+        );
+    }
+};
+
+
+// * * * * * * * * * * * * * * * Member Functions  * * * * * * * * * * * * * //
+
+void Foam::moleculeCloud::writeFields() const
+{
+    molecule::writeFields(*this);
+}
+
+
+// ************************************************************************* //
diff --git a/src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloud.H b/src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloud.H
new file mode 100755
index 0000000000..600c874346
--- /dev/null
+++ b/src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloud.H
@@ -0,0 +1,328 @@
+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+   \\    /   O peration     |
+    \\  /    A nd           | Copyright (C) 1991-2005 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::moleculeCloud
+
+Description
+
+SourceFiles
+    moleculeCloudApplyConstraintsAndThermostats.C
+    moleculeCloudBuildCellInteractionLists.C
+    moleculeCloudBuildCellOccupancy.C
+    moleculeCloudBuildCellReferralLists.C
+    moleculeCloud.C
+    moleculeCloudCalculateAndAccumulateProperties.C
+    moleculeCloudCalculateExternalForce.C
+    moleculeCloudCalculateForce.C
+    moleculeCloudCalculatePairForce.C
+    moleculeCloudCalculateTetherForce.C
+    moleculeCloudIntegrateEquationsOfMotion.C
+    moleculeCloudRemoveHighEnergyOverlaps.C
+
+
+\*---------------------------------------------------------------------------*/
+
+#ifndef moleculeCloud_H
+#define moleculeCloud_H
+
+#include "Cloud.H"
+#include "molecule.H"
+#include "IOdictionary.H"
+#include "vector2D.H"
+
+#include "pairPotentialList.H"
+#include "tetherPotentialList.H"
+
+#include "receivingReferralList.H"
+#include "sendingReferralList.H"
+#include "referredCellList.H"
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+namespace Foam
+{
+
+/*---------------------------------------------------------------------------*\
+                           Class moleculeCloud Declaration
+\*---------------------------------------------------------------------------*/
+
+class moleculeCloud
+:
+    public Cloud<molecule>
+{
+
+public:
+
+    enum integrationMethods
+    {
+        imVerletLeapfrog,
+        imPredictorCorrector
+    };
+
+
+private:
+
+    // Private data
+
+        const polyMesh& mesh_;
+
+            // MD solution parameters
+
+            static const NamedEnum<integrationMethods, 2>
+                integrationMethodNames_;
+
+            integrationMethods integrationMethod_;
+
+            scalar potentialEnergyLimit_;
+
+            labelList removalOrder_;
+
+            labelListList directInteractionList_;
+
+            referredCellList referredInteractionList_;
+
+            labelList realCellsWithinRCutMaxOfAnyReferringPatch_;
+
+            labelList realFacesWithinRCutMaxOfAnyReferringPatch_;
+
+            labelList realEdgesWithinRCutMaxOfAnyReferringPatch_;
+
+            labelList realPointsWithinRCutMaxOfAnyReferringPatch_;
+
+            List<sendingReferralList> cellSendingReferralLists_;
+
+            List<receivingReferralList> cellReceivingReferralLists_;
+
+            pairPotentialList pairPotentials_;
+
+            tetherPotentialList tetherPotentials_;
+
+            vector gravity_;
+
+            List< DynamicList<molecule*> > cellOccupancy_;
+
+
+        // Private Member Functions
+
+            //- Disallow default bitwise copy construct
+            moleculeCloud(const moleculeCloud&);
+
+            //- Disallow default bitwise assignment
+            void operator=(const moleculeCloud&);
+
+
+public:
+
+    // Static data members
+
+        //- Tolerance for checking that faces on a patch segment
+        static scalar transTol;
+
+        static scalar kb;
+
+
+    // Constructors
+
+        //- Construct given mesh
+        moleculeCloud(const polyMesh&);
+
+        //- Construct given polyMesh and fields of position, cell, mass,
+        //- id, U ands A.  Intended for use by the molConfig utility
+        moleculeCloud
+        (
+            const polyMesh& mesh,
+            label nMol,
+            const labelField& id,
+            const scalarField& mass,
+            const vectorField& positions,
+            const labelField& cells,
+            const vectorField& U,
+            const vectorField& A,
+            const labelField& tethered,
+            const vectorField& tetherPositions
+        );
+
+
+    // Member Functions
+
+        // Access
+
+            inline const polyMesh& mesh() const;
+
+        // MD solution parameters
+
+            inline const integrationMethods& integrationMethod() const;
+
+            inline scalar potentialEnergyLimit() const;
+
+            inline const labelList& removalOrder() const;
+
+            inline label nPairPotentials() const;
+
+            inline const labelListList& directInteractionList() const;
+
+            inline const referredCellList& referredInteractionList() const;
+
+            inline const labelList&
+                realCellsWithinRCutMaxOfAnyReferringPatch() const;
+
+            inline const labelList&
+                realFacesWithinRCutMaxOfAnyReferringPatch() const;
+
+            inline const labelList&
+                realEdgesWithinRCutMaxOfAnyReferringPatch() const;
+
+            inline const labelList&
+                realPointsWithinRCutMaxOfAnyReferringPatch() const;
+
+            inline const List<sendingReferralList>&
+                cellSendingReferralLists() const;
+
+            inline const List<receivingReferralList>&
+                cellReceivingReferralLists() const;
+
+            inline label nInteractingProcs() const;
+
+            inline const pairPotentialList& pairPotentials() const;
+
+            inline const tetherPotentialList& tetherPotentials() const;
+
+            inline const vector& gravity() const;
+
+            inline const List< DynamicList<molecule*> >& cellOccupancy() const;
+
+            void buildCellInteractionLists();
+
+            //- Build referralLists which define how to send information
+            // to referredCells to source cells
+            void buildCellReferralLists();
+
+            bool testPointFaceDistance
+            (
+                const label p,
+                const label faceNo
+            ) const;
+
+            bool testPointFaceDistance
+            (
+                const label p,
+                const referredCell& refCell
+            ) const;
+
+            bool testPointFaceDistance
+            (
+                const vectorList& pointsToTest,
+                const label faceNo
+            ) const;
+
+            bool testPointFaceDistance
+            (
+                const vector& p,
+                const label faceNo
+            ) const;
+
+            bool testPointFaceDistance
+            (
+                const vector& p,
+                const labelList& faceToTest,
+                const vectorList& points,
+                const vector& faceC,
+                const vector& faceA
+            ) const;
+
+            bool testEdgeEdgeDistance
+            (
+                const edge& eI,
+                const edge& eJ
+            ) const;
+
+            bool testEdgeEdgeDistance
+            (
+                const edge& eI,
+                const vector& eJs,
+                const vector& eJe
+            ) const;
+
+            const labelList realCellsInRangeOfSegment
+            (
+                const labelList& segmentFaces,
+                const labelList& segmentEdges,
+                const labelList& segmentPoints
+            ) const;
+
+            const labelList referredCellsInRangeOfSegment
+            (
+                const List<referredCell>& referredInteractionList,
+                const labelList& segmentFaces,
+                const labelList& segmentEdges,
+                const labelList& segmentPoints
+            ) const;
+
+            //- Determine which molecules are in which cells
+            void buildCellOccupancy();
+
+            //- Integrate the equations of motion using algorithm selected at
+            //  runtime from a dictionary. This will also call the function
+            //  to calculate the intermolecular forces (calculatePairForce()).
+
+            void integrateEquationsOfMotion();
+
+            void applyConstraintsAndThermostats
+            (
+                const scalar targetTemperature,
+                const scalar measuredTemperature
+            );
+
+            void calculateForce();
+
+            void calculatePairForce();
+
+            void calculateTetherForce();
+
+            void calculateExternalForce();
+
+            void removeHighEnergyOverlaps();
+
+
+    // Member Operators
+
+        //- Write fields
+        void writeFields() const;
+};
+
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+} // End namespace Foam
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+#include "moleculeCloudI.H"
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+#endif
+
+// ************************************************************************* //
diff --git a/src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudApplyConstraintsAndThermostats.C b/src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudApplyConstraintsAndThermostats.C
new file mode 100755
index 0000000000..d44b247d7b
--- /dev/null
+++ b/src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudApplyConstraintsAndThermostats.C
@@ -0,0 +1,60 @@
+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+   \\    /   O peration     |
+    \\  /    A nd           | Copyright (C) 1991-2005 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 "moleculeCloud.H"
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+void Foam::moleculeCloud::applyConstraintsAndThermostats
+(
+    const scalar targetTemperature,
+    const scalar measuredTemperature
+)
+{
+    scalar temperatureCorrectionFactor =
+        sqrt(targetTemperature/measuredTemperature);
+
+    Info<< "----------------------------------------" << nl
+        << "Temperature equilibration" << nl
+        << "Target temperature = "
+        << targetTemperature << nl
+        << "Measured temperature = "
+        << measuredTemperature << nl
+        << "Temperature correction factor ="
+        << temperatureCorrectionFactor << nl
+        << "----------------------------------------"
+        << endl;
+
+    iterator mol(this->begin());
+
+    for (mol = this->begin(); mol != this->end(); ++mol)
+    {
+        mol().U() *= temperatureCorrectionFactor;
+    }
+}
+
+
+// ************************************************************************* //
diff --git a/src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudBuildCellInteractionLists.C b/src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudBuildCellInteractionLists.C
new file mode 100755
index 0000000000..a8d9cc8db5
--- /dev/null
+++ b/src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudBuildCellInteractionLists.C
@@ -0,0 +1,80 @@
+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+   \\    /   O peration     |
+    \\  /    A nd           | Copyright (C) 1991-2005 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 "moleculeCloud.H"
+#include "polyBoundaryMeshEntries.H"
+#include "PstreamCombineReduceOps.H"
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+void Foam::moleculeCloud::buildCellInteractionLists()
+{
+// #       include "moleculeCloudCodeSnippets.H"
+
+    List<DynamicList<label> > directInteractionList(mesh_.nCells());
+
+#   include "moleculeCloudBuildDirectInteractionList.H"
+
+    directInteractionList_.setSize(mesh_.nCells());
+
+    forAll(directInteractionList, transDIL)
+    {
+        directInteractionList_[transDIL].transfer
+        (
+            directInteractionList[transDIL].shrink()
+        );
+    }
+
+//     for sorting DILs
+
+//     forAll(directInteractionList_, dIL)
+//     {
+//         sort(directInteractionList_[dIL]);
+//     }
+
+    cellOccupancy_.setSize(mesh_.nCells());
+
+    DynamicList<referredCell> referredInteractionList;
+
+#   include "moleculeCloudBuildReferredInteractionList.H"
+
+//#   include "moleculeCloudBuildReferredInteractionList_old.H"
+
+    referredInteractionList_.setSize
+    (
+        referredInteractionList.size()
+    );
+
+    forAll(referredInteractionList, rIL)
+    {
+        referredInteractionList_[rIL] = referredInteractionList[rIL];
+    }
+
+    referredInteractionList_.setRealCellsInRange();
+}
+
+
+// ************************************************************************* //
diff --git a/src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudBuildCellOccupancy.C b/src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudBuildCellOccupancy.C
new file mode 100755
index 0000000000..89ad6cd3e6
--- /dev/null
+++ b/src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudBuildCellOccupancy.C
@@ -0,0 +1,68 @@
+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+   \\    /   O peration     |
+    \\  /    A nd           | Copyright (C) 1991-2005 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
+    moleculeCloud
+
+Description
+
+\*----------------------------------------------------------------------------*/
+
+#include "moleculeCloud.H"
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+namespace Foam
+{
+
+void moleculeCloud::buildCellOccupancy()
+{
+    forAll(cellOccupancy_, cO)
+    {
+        cellOccupancy_[cO].clear();
+    }
+
+    iterator mol(this->begin());
+
+    for
+    (
+        mol = this->begin();
+        mol != this->end();
+        ++mol
+    )
+    {
+        cellOccupancy_[mol().cell()].append(&mol());
+    }
+
+    forAll(cellOccupancy_, cO)
+    {
+        cellOccupancy_[cO].shrink();
+    }
+
+    referredInteractionList_.referMolecules();
+}
+
+} // End namespace Foam
+
+// ************************************************************************* //
diff --git a/src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudBuildCellReferralLists.C b/src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudBuildCellReferralLists.C
new file mode 100755
index 0000000000..ea1521800f
--- /dev/null
+++ b/src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudBuildCellReferralLists.C
@@ -0,0 +1,194 @@
+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+   \\    /   O peration     |
+    \\  /    A nd           | Copyright (C) 1991-2005 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 "moleculeCloud.H"
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+void Foam::moleculeCloud::buildCellReferralLists()
+{
+    Info<< nl << "Determining molecule referring schedule" << endl;
+
+    const referredCellList& refIntL(referredInteractionList());
+
+    DynamicList<label> referralProcs;
+
+    // Run through all referredCells to build list of interacting processors
+
+    forAll(refIntL, rIL)
+    {
+        const referredCell& rC(refIntL[rIL]);
+
+        if (findIndex(referralProcs, rC.sourceProc()) == -1)
+        {
+            referralProcs.append(rC.sourceProc());
+        }
+    }
+
+    referralProcs.shrink();
+
+//     Pout << "referralProcs: " << nl << referralProcs << endl;
+
+    List<DynamicList<label> > cellSendingReferralLists(referralProcs.size());
+
+    List<DynamicList<DynamicList<label> > >
+        cellReceivingReferralLists(referralProcs.size());
+
+    // Run through all referredCells again building up send and receive info
+
+    forAll(refIntL, rIL)
+    {
+        const referredCell& rC(refIntL[rIL]);
+
+        label rPI = findIndex(referralProcs, rC.sourceProc());
+
+        DynamicList<DynamicList<label> >& rRL(cellReceivingReferralLists[rPI]);
+
+        DynamicList<label>& sRL(cellSendingReferralLists[rPI]);
+
+        label existingSource = findIndex(sRL, rC.sourceCell());
+
+        // Check to see if this source cell has already been allocated to
+        // come to this processor.  If not, add the source cell to the sending
+        // list and add the current referred cell to the receiving list.
+
+        // It shouldn't be possible for the sending and receiving lists to be
+        // different lengths, because their append operations happen at the
+        // same time.
+
+        if (existingSource == -1)
+        {
+            sRL.append(rC.sourceCell());
+
+            rRL.append
+            (
+                DynamicList<label> (labelList(1,rIL))
+            );
+        }
+        else
+        {
+            rRL[existingSource].append(rIL);
+
+            rRL[existingSource].shrink();
+        }
+    }
+
+    forAll(referralProcs, rPI)
+    {
+        DynamicList<DynamicList<label> >& rRL(cellReceivingReferralLists[rPI]);
+
+        DynamicList<label>& sRL(cellSendingReferralLists[rPI]);
+
+        sRL.shrink();
+
+        rRL.shrink();
+    }
+
+    // It is assumed that cell exchange is reciprocal, if proc A has cells to
+    // send to proc B, then proc B must have some to send to proc A.
+
+    cellReceivingReferralLists_.setSize(referralProcs.size());
+
+    cellSendingReferralLists_.setSize(referralProcs.size());
+
+    forAll(referralProcs, rPI)
+    {
+        DynamicList<DynamicList<label> >& rRL(cellReceivingReferralLists[rPI]);
+
+        labelListList translLL(rRL.size());
+
+        forAll(rRL, rRLI)
+        {
+            translLL[rRLI] = rRL[rRLI];
+        }
+
+        cellReceivingReferralLists_[rPI] = receivingReferralList
+        (
+            referralProcs[rPI],
+            translLL
+        );
+    }
+
+    // Send sendingReferralLists to each interacting processor.
+
+    forAll(referralProcs, rPI)
+    {
+
+        DynamicList<label>& sRL(cellSendingReferralLists[rPI]);
+
+        if (referralProcs[rPI] != Pstream::myProcNo())
+        {
+            if (Pstream::parRun())
+            {
+                OPstream toInteractingProc
+                (
+                    Pstream::blocking,
+                    referralProcs[rPI]
+                );
+
+                toInteractingProc << sendingReferralList
+                (
+                    Pstream::myProcNo(),
+                    sRL
+                );
+            }
+        }
+    }
+
+    // Receive sendingReferralLists from each interacting processor.
+
+    forAll(referralProcs, rPI)
+    {
+        if (referralProcs[rPI] != Pstream::myProcNo())
+        {
+            if (Pstream::parRun())
+            {
+                IPstream fromInteractingProc
+                (
+                    Pstream::blocking,
+                    referralProcs[rPI]
+                );
+
+                fromInteractingProc >> cellSendingReferralLists_[rPI];
+            }
+        }
+        else
+        {
+            cellSendingReferralLists_[rPI] = sendingReferralList
+            (
+                Pstream::myProcNo(),
+                cellSendingReferralLists[rPI]
+            );
+        }
+    }
+
+//     Pout << "receiving list: " << nl << cellReceivingReferralLists_ << endl;
+
+//     Pout << "sending list: " << nl << cellSendingReferralLists_ << endl;
+}
+
+
+// ************************************************************************* //
diff --git a/src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudBuildDirectInteractionList.H b/src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudBuildDirectInteractionList.H
new file mode 100755
index 0000000000..c5f2d887bf
--- /dev/null
+++ b/src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudBuildDirectInteractionList.H
@@ -0,0 +1,188 @@
+Info << nl << "Building list of direct interaction neighbours" << endl;
+
+forAll (mesh_.points(), p)
+{
+    forAll(mesh_.faces(), f)
+    {
+        if(testPointFaceDistance(p, f))
+        {
+            const labelList& pCells(mesh_.pointCells()[p]);
+
+            const label cellO(mesh_.faceOwner()[f]);
+
+            const label cellN(mesh_.faceNeighbour()[f]);
+
+            forAll(pCells, pC)
+            {
+                const label cellI(pCells[pC]);
+
+                // cells are not added to their own DIL
+
+                if (cellO > cellI)
+                {
+                    if (findIndex(directInteractionList[cellI], cellO) == -1)
+                    {
+                        directInteractionList[cellI].append(cellO);
+                    }
+                }
+
+                if (cellI > cellO)
+                {
+                    if (findIndex(directInteractionList[cellO], cellI) == -1)
+                    {
+                        directInteractionList[cellO].append(cellI);
+                    }
+                }
+
+                if (mesh_.isInternalFace(f))
+                {
+                    // boundary faces will not have neighbour information
+
+                    if (cellN > cellI)
+                    {
+                        if
+                        (
+                             findIndex(directInteractionList[cellI], cellN)
+                          == -1
+                        )
+                        {
+                            directInteractionList[cellI].append(cellN);
+                        }
+                    }
+
+                    if (cellI > cellN)
+                    {
+                        if
+                        (
+                            findIndex(directInteractionList[cellN], cellI)
+                         == -1
+                        )
+                        {
+                            directInteractionList[cellN].append(cellI);
+                        }
+                    }
+                }
+            }
+        }
+    }
+}
+
+label edgeJIndex;
+
+forAll (mesh_.edges(), edgeIIndex)
+{
+    const edge& eI(mesh_.edges()[edgeIIndex]);
+
+    for
+    (
+        edgeJIndex = edgeIIndex + 1;
+        edgeJIndex != mesh_.edges().size();
+        ++edgeJIndex
+    )
+    {
+        const edge& eJ(mesh_.edges()[edgeJIndex]);
+
+        if (testEdgeEdgeDistance(eI, eJ))
+        {
+            const labelList& eICells(mesh_.edgeCells()[edgeIIndex]);
+
+            const labelList& eJCells(mesh_.edgeCells()[edgeJIndex]);
+
+            forAll(eICells, eIC)
+            {
+                const label cellI(eICells[eIC]);
+
+                forAll(eJCells, eJC)
+                {
+                    const label cellJ(eJCells[eJC]);
+
+                    if (cellJ > cellI)
+                    {
+                        if
+                        (
+                            findIndex(directInteractionList[cellI], cellJ)
+                         == -1
+                        )
+                        {
+                            directInteractionList[cellI].append(cellJ);
+                        }
+                    }
+
+                    if (cellI > cellJ)
+                    {
+                        if
+                        (
+                            findIndex(directInteractionList[cellJ], cellI)
+                         == -1
+                        )
+                        {
+                            directInteractionList[cellJ].append(cellI);
+                        }
+                    }
+                }
+            }
+        }
+    }
+}
+
+// label pointJIndex;
+//
+// forAll (mesh_.points(), pointIIndex)
+// {
+//     const point& ptI
+//     (
+//         mesh_.points()[pointIIndex]
+//     );
+//
+//     for
+//     (
+//         pointJIndex = pointIIndex;
+//         pointJIndex != mesh_.points().size();
+//         ++pointJIndex
+//     )
+//     {
+//         const point& ptJ
+//         (
+//             mesh_.points()[pointJIndex]
+//         );
+//
+//         if (magSqr(ptI - ptJ) <= rCutMaxSqr)
+//         {
+//             const labelList& ptICells
+//             (
+//                 mesh_.pointCells()[pointIIndex]
+//             );
+//
+//             const labelList& ptJCells
+//             (
+//                 mesh_.pointCells()[pointJIndex]
+//             );
+//
+//             forAll(ptICells, pIC)
+//             {
+//                 const label cellI(ptICells[pIC]);
+//
+//                 forAll(ptJCells, pJC)
+//                 {
+//                     const label cellJ(ptJCells[pJC]);
+//
+//                     if (cellJ > cellI)
+//                     {
+//                         if(findIndex(directInteractionList[cellI], cellJ) == -1)
+//                         {
+//                             directInteractionList[cellI].append(cellJ);
+//                         }
+//                     }
+//
+//                     if (cellI > cellJ)
+//                     {
+//                         if(findIndex(directInteractionList[cellJ], cellI) == -1)
+//                         {
+//                             directInteractionList[cellJ].append(cellI);
+//                         }
+//                     }
+//                 }
+//             }
+//         }
+//     }
+// }
diff --git a/src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudBuildReferredInteractionList.H b/src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudBuildReferredInteractionList.H
new file mode 100755
index 0000000000..5e1de72062
--- /dev/null
+++ b/src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudBuildReferredInteractionList.H
@@ -0,0 +1,1285 @@
+Info << nl << "Building list of referred interaction neighbours" << endl;
+
+labelListList processorPatchSegmentMapping
+(
+    mesh_.globalData().processorPatches().size()
+);
+
+List<vectorList> allNeighbourFaceCentres
+(
+    mesh_.globalData().processorPatches().size()
+);
+
+List<vectorList> allNeighbourFaceAreas
+(
+    mesh_.globalData().processorPatches().size()
+);
+
+label nUndecomposedPatches = 0;
+
+if (Pstream::parRun())
+{
+    dictionary patchDictionary;
+
+    DynamicList<word> patchNames;
+
+//     IOobject undecomposedBoundaryHeader
+//     (
+//         "undecomposedBoundary",
+//         mesh_.time().constant(),
+//         polyMesh::meshSubDir,
+//         mesh_,
+//         IOobject::MUST_READ,
+//         IOobject::NO_WRITE,
+//         false
+//     );
+
+    Time undecomposedTime
+    (
+        Time::controlDictName,
+        mesh_.time().rootPath(),
+        mesh_.time().caseName().path()
+    );
+
+    IOobject undecomposedBoundaryHeader
+    (
+        "boundary",
+        undecomposedTime.constant(),
+        polyMesh::meshSubDir,
+        undecomposedTime,
+        IOobject::MUST_READ,
+        IOobject::NO_WRITE,
+        false
+    );
+
+    if (undecomposedBoundaryHeader.headerOk())
+    {
+        polyBoundaryMeshEntries undecomposedPatchEntries
+        (
+            undecomposedBoundaryHeader
+        );
+
+        forAll(undecomposedPatchEntries, patchi)
+        {
+            patchNames.append
+            (
+                undecomposedPatchEntries[patchi].keyword()
+            );
+
+            patchDictionary.add
+            (
+                undecomposedPatchEntries[patchi]
+            );
+        }
+    }
+    else
+    {
+        FatalErrorIn
+        (
+            "moleculeCloudBuildCellInteractionLists.C"
+        )
+            << nl << "unable to read undecomposed boundary file from "
+            "constant/polyMesh" << nl
+            << abort(FatalError);
+    }
+
+    labelIOList faceProcAddressing
+    (
+        IOobject
+        (
+            "faceProcAddressing",
+            mesh_.time().constant(),
+            polyMesh::meshSubDir,
+            mesh_,
+            IOobject::MUST_READ,
+            IOobject::NO_WRITE,
+            false
+        )
+    );
+
+    labelList procPatches(mesh_.globalData().processorPatches());
+
+    nUndecomposedPatches = patchNames.size();
+
+    // processorPatchSegmentMapping works by mapping the original patch
+    // and half that a face on a processor patch was on before decomposition.
+    // This creates a patch segment for each half of each original (cyclic)
+    // patch which can be assessed separately.
+    // There are n = patchNames.size() original patches, k = 0 to n-1.
+    // The mapping is:
+    // value = 0:  originally an internal face
+    // value = k, was originally on the on the patch k-1, 1st half
+    // value = -k, was originally on the on the patch k-1, 2nd half
+
+    forAll(procPatches,pP)
+    {
+        const processorPolyPatch& patch =
+            refCast<const processorPolyPatch>
+            (
+                mesh_.boundaryMesh()[procPatches[pP]]
+            );
+
+        labelList& procPatchSegMap = processorPatchSegmentMapping[pP];
+
+        procPatchSegMap.setSize(patch.size());
+
+        forAll (patch, pI)
+        {
+            label decomposedMeshFace = patch.start() + pI;
+
+            label faceProcAdd = faceProcAddressing[decomposedMeshFace];
+
+            label globalFace = abs(faceProcAdd)-1;
+
+//             Pout << "Patch index: " << pI
+//                     << " " << patch[pI]
+//                     << " Mesh index: " << decomposedMeshFace
+//                     << " faceProcAdd: " << faceProcAdd
+//                     << " globalFace:" << globalFace << endl;
+
+            label minStart = -1;
+
+            forAll(patchNames, pN)
+            {
+                if (patchDictionary.found(patchNames[pN]))
+                {
+                    const dictionary& patchDict =
+                        patchDictionary.subDict(patchNames[pN]);
+
+//                     word faceName(patchNames[pN]);
+                    label startFace(readLabel(patchDict.lookup("startFace")));
+                    label nFaces(readLabel(patchDict.lookup("nFaces")));
+
+                    if (minStart < 0 || startFace < minStart)
+                    {
+                        minStart = startFace;
+                    }
+
+                    if
+                    (
+                        globalFace >= startFace
+                     && globalFace < startFace + nFaces/2
+                    )
+                    {
+                        procPatchSegMap[pI] = pN + 1;
+                    }
+                    else if
+                    (
+                        globalFace >= startFace + nFaces/2
+                     && globalFace < startFace + nFaces
+                    )
+                    {
+                        procPatchSegMap[pI] = -(pN + 1);
+                    }
+                }
+            }
+
+            if (globalFace < minStart)
+            {
+                procPatchSegMap[pI] = 0;
+            }
+        }
+    }
+
+    forAll(procPatches,pP)
+    {
+        const processorPolyPatch& patch =
+            refCast<const processorPolyPatch>
+            (
+                mesh_.boundaryMesh()[procPatches[pP]]
+            );
+
+        {
+            OPstream toNeighbProc
+            (
+                Pstream::blocking,
+                patch.neighbProcNo(),
+                + 2*(sizeof(label) + patch.size()*sizeof(vector))
+            );
+
+            toNeighbProc
+                << patch.faceCentres()
+                << patch.faceAreas();
+
+//             Pout << "sending face info to processor "
+//                 << patch.neighbProcNo() << ", size = "
+//                 << patch.size() << endl;
+        }
+    }
+
+    forAll(procPatches,pP)
+    {
+        const processorPolyPatch& patch =
+            refCast<const processorPolyPatch>
+            (
+                mesh_.boundaryMesh()[procPatches[pP]]
+            );
+
+        vectorList& neighbFaceCentres = allNeighbourFaceCentres[pP];
+
+        neighbFaceCentres.setSize(patch.size());
+
+        vectorList& neighbFaceAreas = allNeighbourFaceAreas[pP];
+
+        neighbFaceAreas.setSize(patch.size());
+
+        {
+            IPstream fromNeighbProc
+            (
+                Pstream::blocking,
+                patch.neighbProcNo(),
+                2*(sizeof(label) + patch.size()*sizeof(vector))
+            );
+            fromNeighbProc
+                >> neighbFaceCentres
+                >> neighbFaceAreas;
+
+//             Pout << "receiving face info from processor "
+//                 << patch.neighbProcNo() << ", size = "
+//                 << patch.size() << endl;
+        }
+    }
+
+    // *************************************************************
+    // Tests that all processor patch segments from different
+    // original patches prior to decomposition produce the same
+    // transform. Check before 1st iteration.
+    // *************************************************************
+
+    forAll(procPatches,pP)
+    {
+        const processorPolyPatch& patch =
+            refCast<const processorPolyPatch>
+            (
+                mesh_.boundaryMesh()[procPatches[pP]]
+            );
+
+        const vectorList& neighbFaceCentres = allNeighbourFaceCentres[pP];
+
+        const vectorList& neighbFaceAreas = allNeighbourFaceAreas[pP];
+
+        label nUP;
+
+        for
+        (
+            nUP = -nUndecomposedPatches;
+            nUP <= nUndecomposedPatches;
+            nUP++
+        )
+        {
+            DynamicList<vector> refOff;
+
+            DynamicList<tensor> refTrans;
+
+            forAll (patch, faceI)
+            {
+                if (processorPatchSegmentMapping[pP][faceI] == nUP)
+                {
+                    referredCell testRefCell
+                    (
+                        mesh_,
+                        -1,
+                        -1,
+                        patch.faceCentres()[faceI],
+                        neighbFaceCentres[faceI],
+                        patch.faceNormals()[faceI],
+                        neighbFaceAreas[faceI]
+                       /(mag(neighbFaceAreas[faceI]) + VSMALL)
+                    );
+
+                    refOff.append(testRefCell.offset());
+
+                    refTrans.append(testRefCell.rotation());
+                }
+            }
+
+            refOff.shrink();
+
+            refTrans.shrink();
+
+            if (refOff.size())
+            {
+                if
+                (
+                    sum(mag(refOff-refOff[0]))/refOff.size() > transTol
+                 || sum(mag(refTrans-refTrans[0]))/refTrans.size() > transTol
+                )
+                {
+                    FatalErrorIn
+                    (
+                        "moleculeCloud::buildCellInteractionLists"
+                    )
+                        << nl << "Face pairs on patch "
+                        << patch.name()
+                        << ", segment " << patchNames[nUP]
+                        << " do not give the same referring "
+                        << " transformations to within tolerance of "
+                        << transTol << nl
+                        << " Referring offsets:" << refOff << nl
+                        << " Average sum of mag difference: "
+                        << sum(mag(refOff-refOff[0]))/refOff.size() << nl
+                        << " Referring transforms:" << refTrans << nl
+                        << " Average sum of mag difference: "
+                        << sum(mag(refTrans-refTrans[0]))/refTrans.size()
+                        << nl << abort(FatalError);
+                }
+            }
+        }
+    }
+}
+
+label cellsReferredThisIteration = 1;
+
+label iterationNo = 0;
+
+DynamicList<label> realCellsWithinRCutMaxOfAnyReferringPatch;
+
+while(cellsReferredThisIteration)
+{
+    label refIntListStartSize = referredInteractionList.size();
+
+    forAll (mesh_.boundaryMesh(), patchI)
+    {
+        // Treat local cyclics on each processor before processor boundaries.
+        // Separate treatment allows the serial version to run transparently.
+
+        if (mesh_.boundaryMesh()[patchI].type() == "cyclic")
+        {
+            const cyclicPolyPatch& patch =
+                    refCast<const cyclicPolyPatch>
+            (
+                mesh_.boundaryMesh()[patchI]
+            );
+
+            if(patch.size())
+            {
+    //             Pout << patch << endl;
+
+                if (iterationNo == 0)
+                {
+                    // Tests that all combinations of face pairs produce the
+                    // same transform.  Only check on 1st iteration.
+
+                    label faceL;
+                    // A face in the 1st half of the patch
+
+                    label faceM;
+                    // Face corresponding to faceL in the 2nd half of the
+                    // patch. Assumes correct face ordering.
+
+                    vectorList refOff(patch.size()/2);
+
+                    List<tensor> refTrans(patch.size()/2);
+
+                    for
+                    (
+                        faceL = 0, faceM = patch.size()/2;
+                        faceL < patch.size()/2;
+                        faceL++, faceM++
+                    )
+                    {
+                        referredCell testRefCell
+                        (
+                            mesh_,
+                            -1,
+                            -1,
+                            patch.faceCentres()[faceL],
+                            patch.faceCentres()[faceM],
+                            patch.faceNormals()[faceL],
+                            patch.faceNormals()[faceM]
+                        );
+
+                        refOff[faceL] = testRefCell.offset();
+
+                        refTrans[faceL] = testRefCell.rotation();
+                    }
+
+                    if
+                    (
+                        sum(mag(refOff - refOff[0]))/(patch.size()/2)
+                      > transTol
+                     || sum(mag(refTrans - refTrans[0]))/(patch.size()/2)
+                      > transTol
+                    )
+                    {
+                        FatalErrorIn
+                        (
+                            "moleculeCloud::buildCellInteractionLists"
+                        )
+                            << nl << "Face pairs on patch "
+                            << patch.name()
+                            << " do not give the same referring "
+                            << " transformations to within tolerance of "
+                            << transTol << nl
+                            << " Referring offsets:" << refOff << nl
+                            << " Average sum of mag difference: "
+                            << sum(mag(refOff-refOff[0]))/refOff.size() << nl
+                            << " Referring transforms:" << refTrans << nl
+                            << " Average sum of mag difference: "
+                            << sum(mag(refTrans-refTrans[0]))/refTrans.size()
+                            << nl << abort(FatalError);
+                    }
+                }
+
+                // ***********************************************************
+                // 1st half of face list - 1st side of boundary
+                // ***********************************************************
+
+                label faceI;
+
+                DynamicList<label> meshFacesOnThisSegment;
+
+                for (faceI = 0; faceI < patch.size()/2; faceI++)
+                {
+                    // unable to use the normal accessors for the polyPatch
+                    // because points on separate halves need used separately
+
+                    meshFacesOnThisSegment.append(faceI + patch.start());
+                }
+
+                meshFacesOnThisSegment.shrink();
+
+                DynamicList<label> meshEdgesOnThisSegment;
+
+                DynamicList<label> meshPointsOnThisSegment;
+
+                forAll(meshFacesOnThisSegment, mFOTS)
+                {
+                    const label segFace = meshFacesOnThisSegment[mFOTS];
+
+                    const labelList& faceEdges = mesh_.faceEdges()[segFace];
+
+                    forAll (faceEdges, fE)
+                    {
+                        const label faceEdge(faceEdges[fE]);
+
+                        if (findIndex(meshEdgesOnThisSegment, faceEdge) == -1)
+                        {
+                            meshEdgesOnThisSegment.append(faceEdge);
+                        }
+                    }
+
+                    const face& facePoints(mesh_.faces()[segFace]);
+
+                    forAll (facePoints, fP)
+                    {
+                        const label facePoint(facePoints[fP]);
+
+                        if
+                        (
+                            findIndex(meshPointsOnThisSegment, facePoint)
+                         == -1
+                        )
+                        {
+                            meshPointsOnThisSegment.append(facePoint);
+                        }
+                    }
+                }
+
+                meshEdgesOnThisSegment.shrink();
+
+                meshPointsOnThisSegment.shrink();
+
+                if (iterationNo == 0)
+                {
+                    // Assessing real cells in range is only required on
+                    // the 1st iteration because they do not change from
+                    // iteration to iteration.
+
+                    labelList realCellsFoundInRange
+                    (
+                        realCellsInRangeOfSegment
+                        (
+                            meshFacesOnThisSegment,
+                            meshEdgesOnThisSegment,
+                            meshPointsOnThisSegment
+                        )
+                    );
+
+                    forAll(realCellsFoundInRange,cFIR)
+                    {
+                        const label realCell = realCellsFoundInRange[cFIR];
+
+                        referredCell cellToRefer
+                        (
+                            mesh_,
+                            Pstream::myProcNo(),
+                            realCell,
+                            patch.faceCentres()[0],
+                            patch.faceCentres()[patch.size()/2],
+                            patch.faceNormals()[0],
+                            patch.faceNormals()[patch.size()/2]
+                        );
+
+                        // Test all existing referred and real cells to
+                        // check duplicates are not being made or cells
+                        // aren't being referred back onto themselves
+
+                        bool addCellToRefer = true;
+
+                        // Check if cellToRefer is an existing referred cell
+
+                        forAll(referredInteractionList, rIL)
+                        {
+                            if
+                            (
+                                cellToRefer.duplicate
+                                (
+                                    referredInteractionList[rIL]
+                                )
+                            )
+                            {
+                                addCellToRefer = false;
+
+                                break;
+                            }
+                        }
+
+                        // Check for cellToRefer being referred back
+                        // ontop of a real cell
+
+                        if
+                        (
+                            cellToRefer.duplicate
+                            (
+                                Pstream::myProcNo(),
+                                mesh_.nCells()
+                            )
+                        )
+                        {
+                            addCellToRefer = false;
+                        }
+
+                        if (addCellToRefer)
+                        {
+                            referredInteractionList.append(cellToRefer);
+                        }
+
+                        // add real cells found in range of cyclic patch
+                        // to whole mesh list
+
+                        if
+                        (
+                            findIndex
+                            (
+                                realCellsWithinRCutMaxOfAnyReferringPatch,
+                                realCell
+                            ) == -1
+                        )
+                        {
+                            realCellsWithinRCutMaxOfAnyReferringPatch.append
+                            (
+                                realCell
+                            );
+                        }
+                    }
+                }
+
+                referredInteractionList.shrink();
+
+                labelList referredCellsFoundInRange
+                (
+                    referredCellsInRangeOfSegment
+                    (
+                        referredInteractionList,
+                        meshFacesOnThisSegment,
+                        meshEdgesOnThisSegment,
+                        meshPointsOnThisSegment
+                    )
+                );
+
+                forAll(referredCellsFoundInRange,cFIR)
+                {
+                    referredCell& existingRefCell = referredInteractionList
+                    [
+                        referredCellsFoundInRange[cFIR]
+                    ];
+
+                    referredCell cellToReRefer = existingRefCell.reRefer
+                    (
+                        patch.faceCentres()[0],
+                        patch.faceCentres()[patch.size()/2],
+                        patch.faceNormals()[0],
+                        patch.faceNormals()[patch.size()/2]
+                    );
+
+                    // Test all existing referred and real cells to check
+                    // duplicates are not being made or cells aren't being
+                    // referred back onto themselves
+
+                    bool addCellToReRefer = true;
+
+                    // Check if cellToRefer is an existing referred cell
+
+                    forAll(referredInteractionList, rIL)
+                    {
+                        if
+                        (
+                            cellToReRefer.duplicate
+                            (
+                                referredInteractionList[rIL]
+                            )
+                        )
+                        {
+                            addCellToReRefer = false;
+
+                            break;
+                        }
+                    }
+
+                    // Check for cellToRefer being referred back
+                    // ontop of a real cell
+
+                    if
+                    (
+                        cellToReRefer.duplicate
+                        (
+                            Pstream::myProcNo(),
+                            mesh_.nCells()
+                        )
+                    )
+                    {
+                        addCellToReRefer = false;
+                    }
+
+                    if(addCellToReRefer)
+                    {
+                        referredInteractionList.append(cellToReRefer);
+                    }
+                }
+
+                // ***********************************************************
+                // 2nd half of face list - 2nd side of boundary
+                // ***********************************************************
+
+                meshFacesOnThisSegment.clear();
+
+                for (faceI = patch.size()/2; faceI < patch.size(); faceI++)
+                {
+                    // unable to use the normal accessors for the polyPatch
+                    // because points on separate halves need used separately
+
+                    meshFacesOnThisSegment.append(faceI + patch.start());
+                }
+
+                meshFacesOnThisSegment.shrink();
+
+                meshEdgesOnThisSegment.clear();
+
+                meshPointsOnThisSegment.clear();
+
+                forAll(meshFacesOnThisSegment, mFOTS)
+                {
+                    const label segFace = meshFacesOnThisSegment[mFOTS];
+
+                    const labelList& faceEdges = mesh_.faceEdges()[segFace];
+
+                    forAll (faceEdges, fE)
+                    {
+                        const label faceEdge(faceEdges[fE]);
+
+                        if(findIndex(meshEdgesOnThisSegment, faceEdge) == -1)
+                        {
+                            meshEdgesOnThisSegment.append(faceEdge);
+                        }
+                    }
+
+                    const face& facePoints(mesh_.faces()[segFace]);
+
+                    forAll (facePoints, fP)
+                    {
+                        const label facePoint(facePoints[fP]);
+
+                        if
+                        (
+                           findIndex(meshPointsOnThisSegment, facePoint)
+                         == -1
+                        )
+                        {
+                            meshPointsOnThisSegment.append(facePoint);
+                        }
+                    }
+                }
+
+                meshEdgesOnThisSegment.shrink();
+
+                meshPointsOnThisSegment.shrink();
+
+                if (iterationNo == 0)
+                {
+                    // Assessing real cells in range is only required on
+                    // the 1st iteration because they do not change from
+                    // iteration to iteration.
+
+                    labelList realCellsFoundInRange
+                    (
+                        realCellsInRangeOfSegment
+                        (
+                            meshFacesOnThisSegment,
+                            meshEdgesOnThisSegment,
+                            meshPointsOnThisSegment
+                        )
+                    );
+
+                    forAll(realCellsFoundInRange,cFIR)
+                    {
+                        const label realCell = realCellsFoundInRange[cFIR];
+
+                        referredCell cellToRefer
+                        (
+                            mesh_,
+                            Pstream::myProcNo(),
+                            realCell,
+                            patch.faceCentres()[patch.size()/2],
+                            patch.faceCentres()[0],
+                            patch.faceNormals()[patch.size()/2],
+                            patch.faceNormals()[0]
+                        );
+
+                        // Test all existing referred and real cells to
+                        // check duplicates are not being made or cells
+                        // aren't being referred back onto themselves
+
+                        bool addCellToRefer = true;
+
+                        // Check if cellToRefer is an existing referred cell
+
+                        forAll(referredInteractionList, rIL)
+                        {
+                            if
+                            (
+                                cellToRefer.duplicate
+                                (
+                                    referredInteractionList[rIL]
+                                )
+                            )
+                            {
+                                addCellToRefer = false;
+
+                                break;
+                            }
+                        }
+
+                        // Check for cellToRefer being referred back
+                        // ontop of a real cell
+
+                        if
+                        (
+                            cellToRefer.duplicate
+                            (
+                                Pstream::myProcNo(),
+                                mesh_.nCells()
+                            )
+                        )
+                        {
+                            addCellToRefer = false;
+                        }
+
+                        if (addCellToRefer)
+                        {
+                            referredInteractionList.append(cellToRefer);
+                        }
+
+                        // add real cells found in range of cyclic patch
+                        // to whole mesh list
+
+                        if
+                        (
+                            findIndex
+                            (
+                                realCellsWithinRCutMaxOfAnyReferringPatch,
+                                realCell
+                            ) == -1
+                        )
+                        {
+                            realCellsWithinRCutMaxOfAnyReferringPatch.append
+                            (
+                                realCell
+                            );
+                        }
+                    }
+                }
+
+                referredInteractionList.shrink();
+
+                referredCellsFoundInRange = referredCellsInRangeOfSegment
+                (
+                    referredInteractionList,
+                    meshFacesOnThisSegment,
+                    meshEdgesOnThisSegment,
+                    meshPointsOnThisSegment
+                );
+
+                forAll(referredCellsFoundInRange,cFIR)
+                {
+                    referredCell& existingRefCell = referredInteractionList
+                    [
+                        referredCellsFoundInRange[cFIR]
+                    ];
+
+                    referredCell cellToReRefer = existingRefCell.reRefer
+                    (
+                        patch.faceCentres()[patch.size()/2],
+                        patch.faceCentres()[0],
+                        patch.faceNormals()[patch.size()/2],
+                        patch.faceNormals()[0]
+                    );
+
+                    // Test all existing referred and real cells to check
+                    // duplicates are not being made or cells aren't being
+                    // referred back onto themselves
+
+                    bool addCellToReRefer = true;
+
+                    // Check if cellToRefer is an existing referred cell
+
+                    forAll(referredInteractionList, rIL)
+                    {
+                        if
+                        (
+                            cellToReRefer.duplicate
+                            (
+                                referredInteractionList[rIL]
+                            )
+                        )
+                        {
+                            addCellToReRefer = false;
+
+                            break;
+                        }
+                    }
+
+                    // Check for cellToRefer being referred back
+                    // ontop of a real cell
+
+                    if
+                    (
+                        cellToReRefer.duplicate
+                        (
+                            Pstream::myProcNo(),
+                            mesh_.nCells()
+                        )
+                    )
+                    {
+                        addCellToReRefer = false;
+                    }
+
+                    if (addCellToReRefer)
+                    {
+                        referredInteractionList.append(cellToReRefer);
+                    }
+                }
+            }
+        }
+    }
+
+    if (Pstream::parRun())
+    {
+        labelList procPatches(mesh_.globalData().processorPatches());
+
+        forAll(procPatches,pP)
+        {
+            const processorPolyPatch& patch =
+                refCast<const processorPolyPatch>
+                (
+                    mesh_.boundaryMesh()[procPatches[pP]]
+                );
+
+            DynamicList<referredCell> referredCellsToTransfer;
+
+            const vectorList& neighbFaceCentres = allNeighbourFaceCentres[pP];
+
+            const vectorList& neighbFaceAreas = allNeighbourFaceAreas[pP];
+
+            label nUP;
+
+            for
+            (
+                nUP = -nUndecomposedPatches;
+                nUP <= nUndecomposedPatches;
+                nUP++
+            )
+            {
+                // faceT is used to specify one face on this patch segment that
+                // will be used to calculate the transformation values.  All
+                // faces are guaranteed to produce the same transform because
+                // of the checks carried out at the start of the function.
+                // Setting to -1 until the 1st face on this segment is found.
+
+                label faceT = -1;
+
+                DynamicList<label> meshFacesOnThisSegment;
+
+                forAll (patch, faceI)
+                {
+                    if (processorPatchSegmentMapping[pP][faceI] == nUP)
+                    {
+                        if (faceT == -1)
+                        {
+                            faceT = faceI;
+                        }
+
+                        meshFacesOnThisSegment.append(faceI + patch.start());
+                    }
+                }
+
+                meshFacesOnThisSegment.shrink();
+
+                DynamicList<label> meshEdgesOnThisSegment;
+
+                DynamicList<label> meshPointsOnThisSegment;
+
+                forAll(meshFacesOnThisSegment, mFOTS)
+                {
+                    const label segFace = meshFacesOnThisSegment[mFOTS];
+
+                    const labelList& faceEdges = mesh_.faceEdges()[segFace];
+
+                    forAll (faceEdges, fE)
+                    {
+                        const label faceEdge(faceEdges[fE]);
+
+                        if(findIndex(meshEdgesOnThisSegment, faceEdge) == -1)
+                        {
+                            meshEdgesOnThisSegment.append(faceEdge);
+                        }
+                    }
+
+                    const face& facePoints(mesh_.faces()[segFace]);
+
+                    forAll (facePoints, fP)
+                    {
+                        const label facePoint(facePoints[fP]);
+
+                        if
+                        (
+                           findIndex(meshPointsOnThisSegment, facePoint)
+                         == -1
+                        )
+                        {
+                            meshPointsOnThisSegment.append(facePoint);
+                        }
+                    }
+                }
+
+                meshEdgesOnThisSegment.shrink();
+
+                meshPointsOnThisSegment.shrink();
+
+                if (meshFacesOnThisSegment.size())
+                {
+                    if (faceT == -1)
+                    {
+                        FatalErrorIn
+                        (
+                            "moleculeCloudBuildReferredInteractionList.H"
+                        )
+                        << nl << "faceT == -1 encountered but "
+                        << meshFacesOnThisSegment.size()
+                        << " faces found on patch segment."
+                        << abort(FatalError);
+                    }
+
+                    if (iterationNo == 0)
+                    {
+                        // Assessing real cells in range is only required on
+                        // the 1st iteration because they do not change from
+                        // iteration to iteration.
+
+                        labelList realCellsFoundInRange
+                        (
+                            realCellsInRangeOfSegment
+                            (
+                                meshFacesOnThisSegment,
+                                meshEdgesOnThisSegment,
+                                meshPointsOnThisSegment
+                            )
+                        );
+
+                        forAll(realCellsFoundInRange,cFIR)
+                        {
+                            const label realCell = realCellsFoundInRange[cFIR];
+
+                            referredCell cellToRefer
+                            (
+                                mesh_,
+                                Pstream::myProcNo(),
+                                realCell,
+                                patch.faceCentres()[faceT],
+                                neighbFaceCentres[faceT],
+                                patch.faceNormals()[faceT],
+                                neighbFaceAreas[faceT]
+                               /(mag(neighbFaceAreas[faceT]) + VSMALL)
+                            );
+
+                            referredCellsToTransfer.append(cellToRefer);
+
+                            // add real cells found in range of processor patch
+                            // to whole mesh list
+
+                            if
+                            (
+                                findIndex
+                                (
+                                    realCellsWithinRCutMaxOfAnyReferringPatch,
+                                    realCell
+                                )
+                             == -1
+                            )
+                            {
+                                realCellsWithinRCutMaxOfAnyReferringPatch.append
+                                (
+                                    realCell
+                                );
+                            }
+                        }
+                    }
+
+                    referredInteractionList.shrink();
+
+                    labelList referredCellsFoundInRange
+                    (
+                        referredCellsInRangeOfSegment
+                        (
+                            referredInteractionList,
+                            meshFacesOnThisSegment,
+                            meshEdgesOnThisSegment,
+                            meshPointsOnThisSegment
+                        )
+                    );
+
+                    forAll(referredCellsFoundInRange,cFIR)
+                    {
+                        referredCell& existingRefCell
+                            = referredInteractionList[referredCellsFoundInRange[cFIR]];
+
+                        referredCell cellToReRefer = existingRefCell.reRefer
+                        (
+                            patch.faceCentres()[faceT],
+                            neighbFaceCentres[faceT],
+                            patch.faceNormals()[faceT],
+                            neighbFaceAreas[faceT]
+                           /(mag(neighbFaceAreas[faceT]) + VSMALL)
+                        );
+
+                        referredCellsToTransfer.append(cellToReRefer);
+                    }
+                }
+            }
+
+            referredCellsToTransfer.shrink();
+
+            // Send these cells to the neighbouring processor.
+
+            {
+                OPstream toNeighbProc
+                (
+                    Pstream::blocking,
+                    patch.neighbProcNo()
+                );
+
+//                 Pout << "Processor " << Pstream::myProcNo()
+//                     << " sending to " << patch.neighbProcNo()
+//                     << nl << referredCellsToTransfer << endl;
+
+                toNeighbProc << referredCellsToTransfer;
+            }
+        }
+
+        forAll(procPatches,pP)
+        {
+            const processorPolyPatch& patch =
+                refCast<const processorPolyPatch>
+            (
+                mesh_.boundaryMesh()[procPatches[pP]]
+            );
+
+
+            // Receive the cells from neighbour
+
+            List<referredCell> referredCellsFromNeighbour(patch.size());
+
+            {
+                IPstream fromNeighbProc
+                (
+                    Pstream::blocking,
+                    patch.neighbProcNo()
+                );
+
+                fromNeighbProc >> referredCellsFromNeighbour;
+
+//                 Pout << "Processor " << Pstream::myProcNo()
+//                     << " receiving from " << patch.neighbProcNo()
+//                     << nl << referredCellsFromNeighbour << endl;
+            }
+
+            // Check to see if they are duplicates, if not append
+            // them to the referredInteractionList
+
+            forAll(referredCellsFromNeighbour,rCFN)
+            {
+                referredCell& cellToRefer
+                    = referredCellsFromNeighbour[rCFN];
+
+                // Test all existing referred and real cells to check duplicates
+                // are not being made or cells aren't being referred back onto
+                // themselves
+
+                bool addCellToRefer = true;
+
+                // Check if cellToRefer is an existing referred cell
+
+                forAll(referredInteractionList, rIL)
+                {
+                    if(cellToRefer.duplicate(referredInteractionList[rIL]))
+                    {
+                        addCellToRefer = false;
+
+                        break;
+                    }
+                }
+
+                // Check for cellToRefer being referred back ontop of a real cell
+
+                if
+                (
+                    cellToRefer.duplicate
+                    (
+                        Pstream::myProcNo(),
+                        mesh_.nCells()
+                    )
+                )
+                {
+                    addCellToRefer = false;
+                }
+
+                if (addCellToRefer)
+                {
+                    referredInteractionList.append(cellToRefer);
+                }
+            }
+        }
+    }
+
+    if (iterationNo == 0)
+    {
+        // record all real cells in range of any referring patch (cyclic or
+        // processor) on the first iteration when the real cells are evaluated.
+
+        realCellsWithinRCutMaxOfAnyReferringPatch_.transfer
+        (
+            realCellsWithinRCutMaxOfAnyReferringPatch.shrink()
+        );
+
+        // construct {faces, edges, points}WithinRCutMaxOfAnyReferringPatch_
+
+        DynamicList<label> realFacesWithinRCutMaxOfAnyReferringPatch;
+
+        DynamicList<label> realEdgesWithinRCutMaxOfAnyReferringPatch;
+
+        DynamicList<label> realPointsWithinRCutMaxOfAnyReferringPatch;
+
+        forAll(realCellsWithinRCutMaxOfAnyReferringPatch_, rCWR)
+        {
+            const label realCell
+            (
+                realCellsWithinRCutMaxOfAnyReferringPatch_[rCWR]
+            );
+
+            const labelList& rCFaces
+            (
+                mesh_.cells()[realCell]
+            );
+
+            forAll(rCFaces, rCF)
+            {
+                const label f(rCFaces[rCF]);
+
+                if
+                (
+                    findIndex(realFacesWithinRCutMaxOfAnyReferringPatch,f)
+                 == -1
+                )
+                {
+                    realFacesWithinRCutMaxOfAnyReferringPatch.append(f);
+                }
+            }
+
+            const labelList& rCEdges
+            (
+                mesh_.cellEdges()[realCell]
+            );
+
+            forAll(rCEdges, rCE)
+            {
+                const label e(rCEdges[rCE]);
+
+                if
+                (
+                    findIndex(realEdgesWithinRCutMaxOfAnyReferringPatch,e)
+                 == -1
+                )
+                {
+                    realEdgesWithinRCutMaxOfAnyReferringPatch.append(e);
+                }
+            }
+
+            const labelList& rCPoints
+            (
+                mesh_.cellPoints()[realCell]
+            );
+
+            forAll(rCPoints, rCP)
+            {
+                const label p(rCPoints[rCP]);
+
+                if
+                (
+                    findIndex(realPointsWithinRCutMaxOfAnyReferringPatch,p)
+                 == -1
+                )
+                {
+                    realPointsWithinRCutMaxOfAnyReferringPatch.append(p);
+                }
+            }
+        }
+
+        realFacesWithinRCutMaxOfAnyReferringPatch_.transfer
+        (
+            realFacesWithinRCutMaxOfAnyReferringPatch.shrink()
+        );
+
+        realEdgesWithinRCutMaxOfAnyReferringPatch_.transfer
+        (
+            realEdgesWithinRCutMaxOfAnyReferringPatch.shrink()
+        );
+
+        realPointsWithinRCutMaxOfAnyReferringPatch_.transfer
+        (
+            realPointsWithinRCutMaxOfAnyReferringPatch.shrink()
+        );
+    }
+
+    iterationNo++;
+
+    cellsReferredThisIteration =
+        referredInteractionList.size() - refIntListStartSize;
+
+//     Pout << tab << "Cells added this iteration: "
+//         << cellsReferredThisIteration << endl;
+
+    reduce(cellsReferredThisIteration, sumOp<label>());
+
+    Info << tab << "Cells added this iteration: "
+        << cellsReferredThisIteration << endl;
+}
+
+referredInteractionList.shrink();
+
+//     Info << "referredInteractionList.size() = "
+//         << referredInteractionList.size() << endl;
+
+//     forAll(referredInteractionList,rIL)
+//     {
+//         Info << referredInteractionList[rIL];
+//     }
diff --git a/src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudCalculateExternalForce.C b/src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudCalculateExternalForce.C
new file mode 100755
index 0000000000..ea6320ecb5
--- /dev/null
+++ b/src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudCalculateExternalForce.C
@@ -0,0 +1,42 @@
+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+   \\    /   O peration     |
+    \\  /    A nd           | Copyright (C) 1991-2005 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 "moleculeCloud.H"
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+void Foam::moleculeCloud::calculateExternalForce()
+{
+    iterator mol(this->begin());
+
+    for (mol = this->begin(); mol != this->end(); ++mol)
+    {
+        mol().A() += gravity_;
+    }
+}
+
+
+// ************************************************************************* //
diff --git a/src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudCalculateForce.C b/src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudCalculateForce.C
new file mode 100755
index 0000000000..54aa9b1a42
--- /dev/null
+++ b/src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudCalculateForce.C
@@ -0,0 +1,59 @@
+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+   \\    /   O peration     |
+    \\  /    A nd           | Copyright (C) 1991-2005 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 "moleculeCloud.H"
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+void Foam::moleculeCloud::calculateForce()
+{
+    buildCellOccupancy();
+
+    iterator mol(this->begin());
+
+    // Set all accumulated quantities to zero
+    for (mol = this->begin(); mol != this->end(); ++mol)
+    {
+        mol().A() = vector::zero;
+
+        mol().potentialEnergy() = 0.0;
+
+        mol().rf() = tensor::zero;
+    }
+
+    calculatePairForce();
+
+    calculateTetherForce();
+
+    calculateExternalForce();
+}
+
+
+// ************************************************************************* //
+
+
+
+
diff --git a/src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudCalculatePairForce.C b/src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudCalculatePairForce.C
new file mode 100755
index 0000000000..14b65c5a3c
--- /dev/null
+++ b/src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudCalculatePairForce.C
@@ -0,0 +1,41 @@
+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+   \\    /   O peration     |
+    \\  /    A nd           | Copyright (C) 1991-2005 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 "moleculeCloud.H"
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+void Foam::moleculeCloud::calculatePairForce()
+{
+    iterator mol(this->begin());
+
+#   include "moleculeCloudCalculatePairForceRealCells.H"
+
+#   include "moleculeCloudCalculatePairForceReferredCells.H"
+}
+
+
+// ************************************************************************* //
diff --git a/src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudCalculatePairForceRealCells.H b/src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudCalculatePairForceRealCells.H
new file mode 100755
index 0000000000..c3b3f1e7cc
--- /dev/null
+++ b/src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudCalculatePairForceRealCells.H
@@ -0,0 +1,49 @@
+
+vector rIJ;
+
+scalar rIJMag;
+
+scalar rIJMagSq;
+
+vector fIJ;
+
+label idI;
+
+label idJ;
+
+mol = this->begin();
+
+molecule* molI = &mol();
+
+molecule* molJ = &mol();
+
+forAll(directInteractionList_, dIL)
+{
+    forAll(cellOccupancy_[dIL],cellIMols)
+    {
+        molI = cellOccupancy_[dIL][cellIMols];
+
+        forAll(directInteractionList_[dIL], interactingCells)
+        {
+            List< molecule* > cellJ =
+                cellOccupancy_[directInteractionList_[dIL][interactingCells]];
+
+            forAll(cellJ, cellJMols)
+            {
+                molJ = cellJ[cellJMols];
+
+#               include "moleculeCloudCalculatePairForceRealCellsCalculationStep.H"
+            }
+        }
+
+        forAll(cellOccupancy_[dIL],cellIOtherMols)
+        {
+            molJ = cellOccupancy_[dIL][cellIOtherMols];
+
+            if (molJ > molI)
+            {
+#                include "moleculeCloudCalculatePairForceRealCellsCalculationStep.H"
+            }
+        }
+    }
+}
diff --git a/src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudCalculatePairForceRealCellsCalculationStep.H b/src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudCalculatePairForceRealCellsCalculationStep.H
new file mode 100755
index 0000000000..9f2080d02e
--- /dev/null
+++ b/src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudCalculatePairForceRealCellsCalculationStep.H
@@ -0,0 +1,33 @@
+idI = molI->id();
+
+idJ = molJ->id();
+
+rIJ = molI->position() - molJ->position();
+
+rIJMagSq = magSqr(rIJ);
+
+if(pairPotentials_.rCutSqr(idI, idJ, rIJMagSq))
+{
+    rIJMag = mag(rIJ);
+
+    fIJ = (rIJ/rIJMag)*pairPotentials_.force(idI, idJ, rIJMag);
+
+    // Acceleration increment for molI
+    molI->A() += fIJ/(molI->mass());
+
+    // Acceleration increment for molJ
+    molJ->A() += -fIJ/(molJ->mass());
+
+    scalar potentialEnergy
+    (
+        pairPotentials_.energy(idI, idJ, rIJMag)
+    );
+
+    molI->potentialEnergy() += 0.5*potentialEnergy;
+
+    molJ->potentialEnergy() += 0.5*potentialEnergy;
+
+    molI->rf() += rIJ * fIJ;
+
+    molJ->rf() += rIJ * fIJ;
+}
diff --git a/src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudCalculatePairForceReferredCells.H b/src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudCalculatePairForceReferredCells.H
new file mode 100755
index 0000000000..c2fab2d10e
--- /dev/null
+++ b/src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudCalculatePairForceReferredCells.H
@@ -0,0 +1,59 @@
+vector rKL;
+
+scalar rKLMag;
+
+scalar rKLMagSq;
+
+vector fKL;
+
+label idK;
+
+label idL;
+
+molecule* molK = &mol();
+
+forAll(referredInteractionList_, rIL)
+{
+    const List<label>& realCells =
+        referredInteractionList_[rIL].realCellsForInteraction();
+
+    forAll(referredInteractionList_[rIL], refMols)
+    {
+        referredMolecule* molL = &(referredInteractionList_[rIL][refMols]);
+
+        forAll(realCells, rC)
+        {
+            List<molecule*> cellK = cellOccupancy_[realCells[rC]];
+
+            forAll(cellK, cellKMols)
+            {
+                molK = cellK[cellKMols];
+
+                idK = molK->id();
+
+                idL = molL->id();
+
+                rKL = molK->position() - molL->position();
+
+                rKLMagSq = magSqr(rKL);
+
+                if (pairPotentials_.rCutSqr(idK, idL, rKLMagSq))
+                {
+                    rKLMag = mag(rKL);
+
+                    fKL = (rKL/rKLMag)*pairPotentials_.force(idK, idL, rKLMag);
+
+                    // Acceleration increment for molK
+                    molK->A() += fKL/(molK->mass());
+
+                    // Adding a contribution of 1/2 of the potential energy
+                    // from this interaction
+                    molK->potentialEnergy() +=
+                        0.5*pairPotentials_.energy(idK, idL, rKLMag);
+
+                    molK->rf() += rKL * fKL;
+                }
+            }
+        }
+    }
+}
diff --git a/src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudCalculateTetherForce.C b/src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudCalculateTetherForce.C
new file mode 100755
index 0000000000..32b39a4089
--- /dev/null
+++ b/src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudCalculateTetherForce.C
@@ -0,0 +1,69 @@
+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+   \\    /   O peration     |
+    \\  /    A nd           | Copyright (C) 1991-2005 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 "moleculeCloud.H"
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+void Foam::moleculeCloud::calculateTetherForce()
+{
+    iterator mol(this->begin());
+
+    vector rIT;
+
+    scalar rITMag;
+
+    vector fIT;
+
+    for (mol = this->begin(); mol != this->end(); ++mol)
+    {
+        if (mol().tethered())
+        {
+            rIT = mol().position() - mol().tetherPosition();
+
+            rITMag = mag(rIT);
+
+            fIT = (rIT/rITMag) * tetherPotentials_.force
+            (
+                mol().id(),
+                rITMag
+            );
+
+            mol().A() += fIT/(mol().mass());
+
+            mol().potentialEnergy() += tetherPotentials_.energy
+            (
+                mol().id(),
+                rITMag
+            );
+
+            mol().rf() += rIT*fIT;
+        }
+    }
+}
+
+
+// ************************************************************************* //
diff --git a/src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudCodeSnippets.H b/src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudCodeSnippets.H
new file mode 100755
index 0000000000..a66b409b45
--- /dev/null
+++ b/src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudCodeSnippets.H
@@ -0,0 +1,193 @@
+// Parallel coding to access boundary information to build up interaction cell info
+
+// See preservePatchTypes for how to read the boundary file.
+
+// Read faceProcAddressing, as per reconstructPar, to get hold of the original,
+// undecomposed face label from a face on a processor mesh.  See email from Mattijs:
+
+// > Is it a case of reading the faceProcAddressing file, in the same way as
+// > something like reconstructPar?
+//         Correct.
+// 
+//         Note that faceProcAddressing is a bit weird since it also includes which side 
+// of an internal face we have. If I remember correctly:
+// 
+//         faceI == 0 illegal
+//         faceI > 0 we have the original owner of  faceI-1 i.e. we have the face in the 
+//         original order.
+//         faceI < 0 we have the original neighbour of -faceI-1 so the face is flipped.
+
+// Use the same functionality as
+// label polyBoundaryMesh::whichPatch(const label faceIndex) const
+// To determine which patch a face was on originally.
+
+if (Pstream::parRun())
+{
+//     if (Pstream::myProcNo() == Pstream::masterNo())
+// //     {
+//         dictionary patchDictionary;
+// 
+//         DynamicList<word> patchNames;
+// 
+//         {
+//             IOobject undecomposedBoundaryHeader
+//             (
+//                 "undecomposedBoundary",
+//                 mesh_.time().constant(),
+//                 polyMesh::meshSubDir,
+//                 mesh_,
+//                 IOobject::MUST_READ,
+//                 IOobject::NO_WRITE,
+//                 false
+//             );
+// 
+//             if (undecomposedBoundaryHeader.headerOk())
+//             {
+//                 polyBoundaryMeshEntries undecomposedPatchEntries
+//                 (
+//                     undecomposedBoundaryHeader
+//                 );
+// 
+//                 forAll(undecomposedPatchEntries, patchi)
+//                 {
+//                     patchNames.append
+//                     (
+//                         undecomposedPatchEntries[patchi].keyword()
+//                     );
+// 
+//                     patchDictionary.add
+//                     (
+//                         undecomposedPatchEntries[patchi]
+//                     );
+//                 }
+//             }
+//             else
+//             {
+//                 FatalErrorIn
+//                 (
+//                     "moleculeCloudBuildCellInteractionLists.C\n"
+//                 )
+//                     << "undecomposedBoundary file not found in "
+//                         "constant/polyMesh"
+//                     << abort(FatalError);
+//             }
+//         }
+// 
+//         labelIOList faceProcAddressing
+//         (
+//             IOobject
+//             (
+//                 "faceProcAddressing",
+//                 mesh_.time().constant(),
+//                 polyMesh::meshSubDir,
+//                 mesh_,
+//                 IOobject::MUST_READ,
+//                 IOobject::NO_WRITE,
+//                 false
+//             )
+//         );
+
+        labelList procPatches(mesh_.globalData().processorPatches());
+
+        forAll(procPatches,pP)
+        {
+            const processorPolyPatch& patch =
+                refCast<const processorPolyPatch>
+            (
+                mesh_.boundaryMesh()[procPatches[pP]]
+            );
+// 
+//             Pout << nl << "name: " << patch.name() << nl
+//                     << "start: " << patch.start() << nl
+//                     << "size: " << patch.size() << nl
+//                     << "separated: " << Switch(patch.separated()) << nl
+//                     << "parallel: " << Switch(patch.parallel()) << nl << endl;
+// 
+//             forAll (patch, pI)
+//             {
+//                 label decomposedMeshFace = patch.start() + pI;
+// 
+//                 label faceProcAdd = faceProcAddressing[decomposedMeshFace];
+// 
+//                 label globalFace = abs(faceProcAdd)-1;
+// 
+//                 Pout << "Patch index: " << pI
+//                         << " " << patch[pI]
+//                         << " Mesh index: " << decomposedMeshFace
+//                         << " faceProcAdd: " << faceProcAdd
+//                         << " globalFace:" << globalFace;
+// 
+//                 label minStart = -1;
+// 
+//                 // Scanning the dictionary each time is a very ugly way of
+//                 // finding out what patch a face originally belonged to, but
+//                 // it proves the concept.  Read the patch info a container
+//                 // class and have a neat way of tell which patch a face is from
+//                 // embedded in that.  Split each processor face down into
+//                 // separate lists for each different originiating patch.
+// 
+//                 forAll(patchNames, patchi)
+//                 {
+//                     if (patchDictionary.found(patchNames[patchi]))
+//                     {
+//                         const dictionary& patchDict = 
+//                                 patchDictionary.subDict(patchNames[patchi]);
+// 
+//                         word faceName(patchNames[patchi]);
+//                         label startFace(readLabel(patchDict.lookup("startFace")));
+//                         label nFaces(readLabel(patchDict.lookup("nFaces")));
+// 
+//                         if
+//                         (
+//                             minStart < 0
+//                          || startFace < minStart
+//                         )
+//                         {
+//                             minStart = startFace;
+//                         }
+// 
+//                         if
+//                         (
+//                             globalFace >= startFace
+//                          && globalFace < startFace + nFaces
+//                         )
+//                         {
+//                             Pout << " original patch: " << faceName  << endl;
+//                         }
+//                     }
+//                 }
+// 
+//                 if (globalFace < minStart)
+//                 {
+//                     Pout << " originally an internal face" << endl;
+//                 }
+//             }
+// 
+            if (patch.separated())
+            {
+                 Pout << patch.separation();
+            }
+
+            if (!patch.parallel())
+            {
+                 Pout << patch.forwardT();
+            }
+        }
+//     }
+//     else
+//     {
+// 
+//     }
+
+        // Get coords of my shared points
+//     vector sharedPoints(vector::one*(Pstream::myProcNo()+1));
+//     label testRedLab(Pstream::myProcNo()+1);
+    
+//     Pout << testRedLab << endl;
+
+        // Append from all processors
+//     combineReduce(sharedPoints, plusEqOp<vector>());
+//     reduce(testRedLab, plusOp<label>());
+
+//     Pout << testRedLab << endl;
+}
diff --git a/src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudI.H b/src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudI.H
new file mode 100755
index 0000000000..215f59d309
--- /dev/null
+++ b/src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudI.H
@@ -0,0 +1,154 @@
+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+   \\    /   O peration     |
+    \\  /    A nd           | Copyright (C) 1991-2005 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
+{
+
+// * * * * * * * * * * * * * * * Member Functions  * * * * * * * * * * * * * //
+
+inline const polyMesh& moleculeCloud::mesh() const
+{
+    return mesh_;
+}
+
+
+// MD solution parameters
+
+inline const moleculeCloud::integrationMethods&
+    moleculeCloud::integrationMethod() const
+{
+    return integrationMethod_;
+}
+
+
+inline scalar moleculeCloud::potentialEnergyLimit() const
+{
+    return potentialEnergyLimit_;
+}
+
+
+inline label moleculeCloud::nPairPotentials() const
+{
+    return pairPotentials_.size();
+}
+
+
+inline const labelList& moleculeCloud::removalOrder() const
+{
+    return removalOrder_;
+}
+
+
+inline const labelListList& moleculeCloud::directInteractionList() const
+{
+    return directInteractionList_;
+}
+
+
+inline const referredCellList& moleculeCloud::referredInteractionList() const
+{
+    return referredInteractionList_;
+}
+
+
+inline const labelList&
+    moleculeCloud::realCellsWithinRCutMaxOfAnyReferringPatch() const
+{
+    return realCellsWithinRCutMaxOfAnyReferringPatch_;
+}
+
+
+inline const labelList&
+    moleculeCloud::realFacesWithinRCutMaxOfAnyReferringPatch() const
+{
+    return realFacesWithinRCutMaxOfAnyReferringPatch_;
+}
+
+
+inline const labelList&
+    moleculeCloud::realEdgesWithinRCutMaxOfAnyReferringPatch() const
+{
+    return realEdgesWithinRCutMaxOfAnyReferringPatch_;
+}
+
+
+inline const labelList&
+    moleculeCloud::realPointsWithinRCutMaxOfAnyReferringPatch() const
+{
+    return realPointsWithinRCutMaxOfAnyReferringPatch_;
+}
+
+
+inline const List<sendingReferralList>&
+    moleculeCloud::cellSendingReferralLists() const
+{
+    return cellSendingReferralLists_;
+}
+
+
+inline const List<receivingReferralList>&
+    moleculeCloud::cellReceivingReferralLists() const
+{
+    return cellReceivingReferralLists_;
+}
+
+
+inline label moleculeCloud::nInteractingProcs() const
+{
+    return cellReceivingReferralLists_.size();
+}
+
+
+inline const pairPotentialList& moleculeCloud::pairPotentials() const
+{
+    return pairPotentials_;
+}
+
+
+inline const tetherPotentialList& moleculeCloud::tetherPotentials() const
+{
+    return tetherPotentials_;
+}
+
+
+inline const vector& moleculeCloud::gravity() const
+{
+    return gravity_;
+}
+
+
+inline const List< DynamicList<molecule*> >&
+    moleculeCloud::cellOccupancy() const
+{
+    return cellOccupancy_;
+}
+
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+}  // End namespace Foam
+
+// ************************************************************************* //
diff --git a/src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudIntegrateEquationsOfMotion.C b/src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudIntegrateEquationsOfMotion.C
new file mode 100755
index 0000000000..dc2177d10b
--- /dev/null
+++ b/src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudIntegrateEquationsOfMotion.C
@@ -0,0 +1,50 @@
+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+   \\    /   O peration     |
+    \\  /    A nd           | Copyright (C) 1991-2005 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 "moleculeCloud.H"
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+void Foam::moleculeCloud::integrateEquationsOfMotion()
+{
+    // Supply trackData to the move method to tell it whether this is the
+    // leapfrog stage 1 or stage 2
+    // or whether it is the
+    // predictor or corrector step.
+
+    molecule::trackData td1(*this, 1);
+
+    Cloud<molecule>::move(td1);
+
+    calculateForce();
+
+    molecule::trackData td2(*this, 2);
+
+    Cloud<molecule>::move(td2);
+}
+
+
+// ************************************************************************* //
diff --git a/src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudReadMDParameters.H b/src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudReadMDParameters.H
new file mode 100755
index 0000000000..b74f9c5abf
--- /dev/null
+++ b/src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudReadMDParameters.H
@@ -0,0 +1,177 @@
+Info<< nl <<  "Reading MD solution parameters:" << endl;
+
+IOdictionary mdSolution
+(
+    IOobject
+    (
+        "mdSolution",
+        mesh_.time().system(),
+        mesh_,
+        IOobject::MUST_READ,
+        IOobject::NO_WRITE
+    )
+);
+
+integrationMethod_ = integrationMethodNames_.read
+(
+    mdSolution.lookup("integrationMethod")
+);
+
+potentialEnergyLimit_ = readScalar
+(
+    mdSolution.lookup("potentialEnergyLimit")
+);
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+IOdictionary potentialDict
+(
+    IOobject
+    (
+        "potentialDict",
+        mesh_.time().system(),
+        mesh_,
+        IOobject::MUST_READ,
+        IOobject::NO_WRITE
+    )
+);
+
+IOdictionary idListDict
+(
+    IOobject
+    (
+        "idList",
+        mesh_.time().constant(),
+        mesh_,
+        IOobject::MUST_READ,
+        IOobject::NO_WRITE
+    )
+);
+
+// ****************************************************************************
+// Pair potentials
+
+if (!potentialDict.found("pair"))
+{
+    FatalErrorIn("moleculeCloudReadPotentials.H") << nl
+            << "pair potential specification subDict not found"
+            << abort(FatalError);
+}
+
+const dictionary& pairDict = potentialDict.subDict("pair");
+
+pairPotentials_.buildPotentials(idListDict, pairDict, mesh_);
+
+if (potentialDict.found("removalOrder"))
+{
+    List<word> remOrd = potentialDict.lookup("removalOrder");
+
+    removalOrder_.setSize(remOrd.size());
+
+    forAll(removalOrder_, rO)
+    {
+        removalOrder_[rO] = findIndex(pairPotentials_.idList(), remOrd[rO]);
+    }
+}
+
+// ****************************************************************************
+// Tether potentials
+
+iterator mol(this->begin());
+
+DynamicList<label> tetherIds;
+
+for
+(
+ mol = this->begin();
+ mol != this->end();
+ ++mol
+)
+{
+    if (mol().tethered())
+    {
+        if (findIndex(tetherIds, mol().id()) == -1)
+        {
+            tetherIds.append
+            (
+                mol().id()
+            );
+        }
+    }
+}
+
+if (Pstream::parRun())
+{
+    List< labelList > allTetherIds(Pstream::nProcs());
+
+    allTetherIds[Pstream::myProcNo()] = tetherIds;
+
+    Pstream::gatherList(allTetherIds);
+
+    if (Pstream::master())
+    {
+        DynamicList<label> globalTetherIds;
+
+        forAll(allTetherIds, procN)
+        {
+            const labelList& procNTetherIds = allTetherIds[procN];
+
+            forAll(procNTetherIds, id)
+            {
+                if (findIndex(globalTetherIds, procNTetherIds[id]) == -1)
+                {
+                    globalTetherIds.append
+                    (
+                        procNTetherIds[id]
+                    );
+                }
+            }
+        }
+
+        globalTetherIds.shrink();
+
+        tetherIds = globalTetherIds;
+    }
+
+    Pstream::scatter(tetherIds);
+}
+
+tetherIds.shrink();
+
+if (tetherIds.size())
+{
+    if (!potentialDict.found("tether"))
+    {
+        FatalErrorIn("moleculeCloudReadPotentials.H") << nl
+                << "tether potential specification subDict not found"
+                << abort(FatalError);
+    }
+
+    const dictionary& tetherDict = potentialDict.subDict("tether");
+
+    tetherPotentials_.buildPotentials(idListDict, tetherDict, tetherIds);
+}
+
+// ****************************************************************************
+// External Forces
+
+gravity_ = vector::zero;
+
+if (potentialDict.found("external"))
+{
+
+    Info << nl << "Reading external forces:" << endl;
+
+    const dictionary& externalDict = potentialDict.subDict("external");
+
+    // ************************************************************************
+    // gravity
+
+    if (externalDict.found("gravity"))
+    {
+        gravity_ = externalDict.lookup("gravity");
+    }
+}
+
+Info << nl << tab << "gravity = " << gravity_ << endl;
+
diff --git a/src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudRealCellsInRangeOfSegment.C b/src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudRealCellsInRangeOfSegment.C
new file mode 100755
index 0000000000..03100cfd3b
--- /dev/null
+++ b/src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudRealCellsInRangeOfSegment.C
@@ -0,0 +1,152 @@
+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+   \\    /   O peration     |
+    \\  /    A nd           | Copyright (C) 1991-2005 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 "moleculeCloud.H"
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+const Foam::labelList Foam::moleculeCloud::realCellsInRangeOfSegment
+(
+    const labelList& segmentFaces,
+    const labelList& segmentEdges,
+    const labelList& segmentPoints
+) const
+{
+    DynamicList<label> realCellsFoundInRange;
+
+    forAll(segmentFaces, sF)
+    {
+        const label f = segmentFaces[sF];
+
+        forAll (mesh_.points(), p)
+        {
+            if (testPointFaceDistance(p, f))
+            {
+                const labelList& pCells(mesh_.pointCells()[p]);
+
+                forAll(pCells, pC)
+                {
+                    const label cellI(pCells[pC]);
+
+                    if (findIndex(realCellsFoundInRange, cellI) == -1)
+                    {
+                        realCellsFoundInRange.append(cellI);
+                    }
+                }
+            }
+        }
+    }
+
+    forAll(segmentPoints, sP)
+    {
+        const label p = segmentPoints[sP];
+
+        forAll(mesh_.faces(), f)
+        {
+            if (testPointFaceDistance(p, f))
+            {
+                const label cellO(mesh_.faceOwner()[f]);
+
+                if (findIndex(realCellsFoundInRange, cellO) == -1)
+                {
+                    realCellsFoundInRange.append(cellO);
+                }
+
+                if (mesh_.isInternalFace(f))
+                {
+                    // boundary faces will not have neighbour information
+
+                    const label cellN(mesh_.faceNeighbour()[f]);
+
+                    if (findIndex(realCellsFoundInRange, cellN) == -1)
+                    {
+                        realCellsFoundInRange.append(cellN);
+                    }
+                }
+            }
+        }
+    }
+
+    forAll(segmentEdges, sE)
+    {
+        const edge& eJ(mesh_.edges()[segmentEdges[sE]]);
+
+        forAll (mesh_.edges(), edgeIIndex)
+        {
+            const edge& eI(mesh_.edges()[edgeIIndex]);
+
+            if (testEdgeEdgeDistance(eI, eJ))
+            {
+                const labelList& eICells(mesh_.edgeCells()[edgeIIndex]);
+
+                forAll(eICells, eIC)
+                {
+                    const label cellI(eICells[eIC]);
+
+                    if (findIndex(realCellsFoundInRange, cellI) == -1)
+                    {
+                        realCellsFoundInRange.append(cellI);
+                    }
+                }
+            }
+        }
+    }
+
+//     forAll (points, p)
+//     {
+//         const point& ptI = mesh_.points()[points[p]];
+//
+//         forAll(mesh_.faces(), f)
+//         {
+//             if (testPointFaceDistance(ptI, f))
+//             {
+//                 const label cellO(mesh_.faceOwner()[f]);
+//
+//                 if (findIndex(realCellsFoundInRange, cellO) == -1)
+//                 {
+//                     realCellsFoundInRange.append(cellO);
+//                 }
+//
+//                 if (mesh_.isInternalFace(f))
+//                 {
+//                     // boundary faces will not have neighbour information
+//
+//                     const label cellN(mesh_.faceNeighbour()[f]);
+//
+//                     if (findIndex(realCellsFoundInRange, cellN) == -1)
+//                     {
+//                         realCellsFoundInRange.append(cellN);
+//                     }
+//                 }
+//             }
+//         }
+//     }
+//
+    return realCellsFoundInRange.shrink();
+}
+
+
+// ************************************************************************* //
diff --git a/src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudReferredCellsInRangeOfSegment.C b/src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudReferredCellsInRangeOfSegment.C
new file mode 100755
index 0000000000..f2e553a853
--- /dev/null
+++ b/src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudReferredCellsInRangeOfSegment.C
@@ -0,0 +1,117 @@
+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+   \\    /   O peration     |
+    \\  /    A nd           | Copyright (C) 1991-2005 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 "moleculeCloud.H"
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+const Foam::labelList Foam::moleculeCloud::referredCellsInRangeOfSegment
+(
+    const List<referredCell>& referredInteractionList,
+    const labelList& segmentFaces,
+    const labelList& segmentEdges,
+    const labelList& segmentPoints
+) const
+{
+    DynamicList<label> referredCellsFoundInRange;
+
+    forAll(segmentFaces, sF)
+    {
+        const label f = segmentFaces[sF];
+
+        forAll(referredInteractionList, rIL)
+        {
+            const vectorList& refCellPoints
+                = referredInteractionList[rIL].vertexPositions();
+
+            if (testPointFaceDistance(refCellPoints, f))
+            {
+                if (findIndex(referredCellsFoundInRange, rIL) == -1)
+                {
+                    referredCellsFoundInRange.append(rIL);
+                }
+            }
+        }
+    }
+
+    forAll(segmentPoints, sP)
+    {
+        const label p = segmentPoints[sP];
+
+        forAll(referredInteractionList, rIL)
+        {
+            const referredCell& refCell(referredInteractionList[rIL]);
+
+            if (testPointFaceDistance(p, refCell))
+            {
+                if (findIndex(referredCellsFoundInRange, rIL) == -1)
+                {
+                    referredCellsFoundInRange.append(rIL);
+                }
+            }
+        }
+    }
+
+    forAll(segmentEdges, sE)
+    {
+        const edge& eI(mesh_.edges()[segmentEdges[sE]]);
+
+        forAll(referredInteractionList, rIL)
+        {
+            const vectorList& refCellPoints
+                = referredInteractionList[rIL].vertexPositions();
+
+            const edgeList& refCellEdges
+                = referredInteractionList[rIL].edges();
+
+            forAll(refCellEdges, rCE)
+            {
+                const edge& eJ(refCellEdges[rCE]);
+
+                if
+                (
+                    testEdgeEdgeDistance
+                    (
+                        eI,
+                        refCellPoints[eJ.start()],
+                        refCellPoints[eJ.end()]
+                    )
+                )
+                {
+                    if(findIndex(referredCellsFoundInRange, rIL) == -1)
+                    {
+                        referredCellsFoundInRange.append(rIL);
+                    }
+                }
+            }
+        }
+    }
+
+    return referredCellsFoundInRange.shrink();
+}
+
+
+// ************************************************************************* //
diff --git a/src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudRemoveHighEnergyOverlaps.C b/src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudRemoveHighEnergyOverlaps.C
new file mode 100755
index 0000000000..e12ea9dbce
--- /dev/null
+++ b/src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudRemoveHighEnergyOverlaps.C
@@ -0,0 +1,67 @@
+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+   \\    /   O peration     |
+    \\  /    A nd           | Copyright (C) 1991-2005 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 "moleculeCloud.H"
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+void Foam::moleculeCloud::removeHighEnergyOverlaps()
+{
+    Info << nl << "Removing high energy overlaps, removal order:";
+
+    forAll(removalOrder_, rO)
+    {
+        Info << " " << pairPotentials_.idList()[removalOrder_[rO]];
+    }
+
+    Info << nl ;
+
+    label initialSize = this->size();
+
+    buildCellOccupancy();
+
+    iterator mol(this->begin());
+
+#   include "moleculeCloudRemoveHighEnergyOverlapsRealCells.H"
+
+    buildCellOccupancy();
+
+#   include "moleculeCloudRemoveHighEnergyOverlapsReferredCells.H"
+
+    buildCellOccupancy();
+
+    label molsRemoved = initialSize - this->size();
+
+    if (Pstream::parRun())
+    {
+        reduce(molsRemoved, sumOp<label>());
+    }
+
+    Info << tab << molsRemoved << " molecules removed" << endl;
+}
+
+
+// ************************************************************************* //
diff --git a/src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudRemoveHighEnergyOverlapsRealCells.H b/src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudRemoveHighEnergyOverlapsRealCells.H
new file mode 100755
index 0000000000..fe6d792842
--- /dev/null
+++ b/src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudRemoveHighEnergyOverlapsRealCells.H
@@ -0,0 +1,55 @@
+{ 
+    vector rIJ;
+
+    scalar rIJMag;
+
+    scalar rIJMagSq;
+
+    label idI;
+
+    label idJ;
+
+    mol = this->begin();
+
+    molecule* molI = &mol();
+
+    molecule* molJ = &mol();
+
+    DynamicList<molecule*> molsToDelete;
+
+    forAll(directInteractionList_, dIL)
+    {
+        forAll(cellOccupancy_[dIL],cellIMols)
+        {
+            molI = cellOccupancy_[dIL][cellIMols];
+
+            forAll(directInteractionList_[dIL], interactingCells)
+            {
+                List< molecule* > cellJ =
+                    cellOccupancy_[directInteractionList_[dIL][interactingCells]];
+
+                forAll(cellJ, cellJMols)
+                {
+                    molJ = cellJ[cellJMols];
+
+#                   include "moleculeCloudRemoveHighEnergyOverlapsRealCellsCalculationStep.H"
+                }
+            }
+
+            forAll(cellOccupancy_[dIL],cellIOtherMols)
+            {
+                molJ = cellOccupancy_[dIL][cellIOtherMols];
+
+                if (molJ > molI)
+                {
+#                   include "moleculeCloudRemoveHighEnergyOverlapsRealCellsCalculationStep.H"
+                }
+            }
+        }
+    }
+
+    forAll (molsToDelete, mTD)
+    {
+        deleteParticle(*(molsToDelete[mTD]));
+    }
+}
diff --git a/src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudRemoveHighEnergyOverlapsRealCellsCalculationStep.H b/src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudRemoveHighEnergyOverlapsRealCellsCalculationStep.H
new file mode 100755
index 0000000000..04f9ffd8ba
--- /dev/null
+++ b/src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudRemoveHighEnergyOverlapsRealCellsCalculationStep.H
@@ -0,0 +1,79 @@
+idI = molI->id();
+
+idJ = molJ->id();
+
+rIJ = molI->position() - molJ->position();
+
+rIJMagSq = magSqr(rIJ);
+
+if (pairPotentials_.rCutSqr(idI, idJ, rIJMagSq))
+{
+    rIJMag = mag(rIJ);
+
+    bool remove = false;
+
+    // Guard against pairPotentials_.energy being evaluated
+    // if rIJMag < SMALL. A floating point exception will
+    // happen otherwise.
+
+    if (rIJMag < SMALL)
+    {
+        WarningIn("moleculeCloud::removeHighEnergyOverlaps()")
+            << "Real molecule pair "
+            << " idI = " << idI
+            << " at position " << molI->position()
+            << " idJ = " << idJ
+            << " at position " << molJ->position()
+            << " are closer than " << SMALL
+            << ": mag separation = " << rIJMag
+            << ". These may have been placed on top of each"
+            << " other by a rounding error in molConfig in parallel"
+            << " or a block filled with molecules twice."
+            << " Removing one of the molecules."
+            << endl;
+
+        remove = true;
+    }
+    
+    // Guard against pairPotentials_.energy being evaluated
+    // if rIJMag < rMin. A tabulation lookup error will occur otherwise.
+
+    if (rIJMag < pairPotentials_.rMin(idI, idJ))
+    {
+        remove = true;
+    }
+
+    if (!remove)
+    {
+        if
+        (
+            pairPotentials_.energy(idI, idJ, rIJMag) > potentialEnergyLimit_
+        )
+        {
+           
+            remove = true;
+        }
+    }
+
+    if (remove)
+    {
+        if
+        (
+            idI == idJ
+         || findIndex(removalOrder_, idJ) < findIndex(removalOrder_, idI)
+        )
+        {
+            if (findIndex(molsToDelete, molJ) == -1)
+            {
+                molsToDelete.append(molJ);
+            }
+        }
+        else
+        {
+            if (findIndex(molsToDelete, molI) == -1)
+            {
+                molsToDelete.append(molI);
+            }
+        }
+    }
+}
diff --git a/src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudRemoveHighEnergyOverlapsReferredCells.H b/src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudRemoveHighEnergyOverlapsReferredCells.H
new file mode 100755
index 0000000000..c0914b1a11
--- /dev/null
+++ b/src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudRemoveHighEnergyOverlapsReferredCells.H
@@ -0,0 +1,152 @@
+{
+    vector rKL;
+
+    scalar rKLMag;
+
+    scalar rKLMagSq;
+
+    label idK;
+
+    label idL;
+
+    molecule* molK = &mol();
+
+    DynamicList<molecule*> molsToDelete;
+
+    forAll(referredInteractionList_, rIL)
+    {
+        referredCell& refCell = referredInteractionList_[rIL];
+
+        forAll(refCell, refMols)
+        {
+            referredMolecule* molL = &(refCell[refMols]);
+
+            List <label> realCells = refCell.realCellsForInteraction();
+
+            forAll(realCells, rC)
+            {
+                label cellK = realCells[rC];
+
+                List<molecule*> cellKMols = cellOccupancy_[cellK];
+
+                forAll(cellKMols, cKM)
+                {
+                    molK = cellKMols[cKM];
+
+                    idK = molK->id();
+
+                    idL = molL->id();
+
+                    rKL = molK->position() - molL->position();
+
+                    rKLMagSq = magSqr(rKL);
+
+                    if (pairPotentials_.rCutSqr(idK, idL, rKLMagSq))
+                    {
+                        rKLMag = mag(rKL);
+
+                        bool remove = false;
+
+                        // Guard against pairPotentials_.energy being evaluated
+                        // if rKLMag < SMALL. A floating point exception will
+                        // happen otherwise.
+
+                        if (rKLMag < SMALL)
+                        {
+                            WarningIn
+                            (
+                                "moleculeCloud::removeHighEnergyOverlaps()"
+                            )
+                                << "Real-referred molecule pair "
+                                << " idK = " << idK << " (real)"
+                                << " at position " << molK->position()
+                                << " idL = " << idL << " (referred)"
+                                << " at position " << molL->position()
+                                << " are closer than " << SMALL
+                                << ": mag separation = " << rKLMag
+                                << ". These may have been placed on top of each"
+                                << " other by a rounding error in molConfig in"
+                                << " parallel, a block filled with molecules"
+                                << " twice, or a lattice ending very close"
+                                << " to the edge of the mesh."
+                                << " Removing one of the molecules."
+                                << endl;
+
+                                remove = true;
+                        }
+
+                        // Guard against pairPotentials_.energy being evaluated
+                        // if rIJMag < rMin. A tubulation lookup error will occur otherwise.
+
+                        if (rKLMag < pairPotentials_.rMin(idK, idL))
+                        {
+                            remove = true;
+                        }
+
+                        if (!remove)
+                        {
+                            if
+                            (
+                                pairPotentials_.energy(idK, idL, rKLMag)
+                              > potentialEnergyLimit_
+                            )
+                            {
+                                remove = true;
+                            }
+                        }
+
+                        if (remove)
+                        {
+                            if
+                            (
+                                findIndex(removalOrder_, idK)
+                              < findIndex(removalOrder_, idL)
+                            )
+                            {
+                                if (findIndex(molsToDelete, molK) == -1)
+                                {
+                                    molsToDelete.append(molK);
+                                }
+                            }
+
+                            else if
+                            (
+                                findIndex(removalOrder_, idK)
+                             == findIndex(removalOrder_, idL)
+                            )
+                            {
+                                if
+                                (
+                                    Pstream::myProcNo() == refCell.sourceProc()
+                                 && cellK <= refCell.sourceCell()
+                                )
+                                {
+                                    if (findIndex(molsToDelete, molK) == -1)
+                                    {
+                                        molsToDelete.append(molK);
+                                    }
+                                }
+
+                                else if
+                                (
+                                    Pstream::myProcNo() < refCell.sourceProc()
+                                )
+                                {
+                                    if (findIndex(molsToDelete, molK) == -1)
+                                    {
+                                        molsToDelete.append(molK);
+                                    }
+                                }
+                            }
+                        }
+                    }
+                }
+            }
+        }
+    }
+
+    forAll (molsToDelete, mTD)
+    {
+        deleteParticle(*(molsToDelete[mTD]));
+    }
+}
diff --git a/src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudTestEdgeEdgeDistance.C b/src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudTestEdgeEdgeDistance.C
new file mode 100755
index 0000000000..1e8fd26630
--- /dev/null
+++ b/src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudTestEdgeEdgeDistance.C
@@ -0,0 +1,86 @@
+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+   \\    /   O peration     |
+    \\  /    A nd           | Copyright (C) 1991-2005 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 "moleculeCloud.H"
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+bool Foam::moleculeCloud::testEdgeEdgeDistance
+(
+    const edge& eI,
+    const edge& eJ
+) const
+{
+    const vector& eJs(mesh_.points()[eJ.start()]);
+    const vector& eJe(mesh_.points()[eJ.end()]);
+
+    return testEdgeEdgeDistance(eI, eJs, eJe);
+}
+
+bool Foam::moleculeCloud::testEdgeEdgeDistance
+(
+    const edge& eI,
+    const vector& eJs,
+    const vector& eJe
+) const
+{
+    vector a(eI.vec(mesh_.points()));
+    vector b(eJe - eJs);
+
+    const vector& eIs(mesh_.points()[eI.start()]);
+
+    vector c(eJs - eIs);
+
+    vector crossab = a ^ b;
+    scalar magCrossSqr = magSqr(crossab);
+
+    if (magCrossSqr > VSMALL)
+    {
+        // If the edges are parallel then a point-face
+        // search will pick them up
+
+        scalar s = ((c ^ b) & crossab)/magCrossSqr;
+        scalar t = ((c ^ a) & crossab)/magCrossSqr;
+
+        // Check for end points outside of range 0..1
+        // If the closest point is outside this range
+        // a point-face search will have found it.
+
+        return
+        (
+            s >= 0
+         && s <= 1
+         && t >= 0
+         && t <= 1
+         && magSqr(eIs + a*s - eJs - b*t) <= pairPotentials_.rCutMaxSqr()
+        );
+    }
+
+    return false;
+}
+
+
+// ************************************************************************* //
diff --git a/src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudTestPointFaceDistance.C b/src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudTestPointFaceDistance.C
new file mode 100755
index 0000000000..03a30873a7
--- /dev/null
+++ b/src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudTestPointFaceDistance.C
@@ -0,0 +1,235 @@
+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+   \\    /   O peration     |
+    \\  /    A nd           | Copyright (C) 1991-2005 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 "moleculeCloud.H"
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+bool Foam::moleculeCloud::testPointFaceDistance
+(
+    const label p,
+    const label faceNo
+) const
+{
+    const vector& pointPosition(mesh_.points()[p]);
+
+    return testPointFaceDistance(pointPosition, faceNo);
+}
+
+bool Foam::moleculeCloud::testPointFaceDistance
+(
+    const label p,
+    const referredCell& refCell
+) const
+{
+    const vector& pointPosition(mesh_.points()[p]);
+
+    forAll (refCell.faces(), rCF)
+    {
+        if
+        (
+            testPointFaceDistance
+            (
+                pointPosition,
+                refCell.faces()[rCF],
+                refCell.vertexPositions(),
+                refCell.faceCentres()[rCF],
+                refCell.faceAreas()[rCF]
+            )
+        )
+        {
+            return true;
+        }
+    }
+
+    return false;
+}
+
+bool Foam::moleculeCloud::testPointFaceDistance
+(
+    const vectorList& pointsToTest,
+    const label faceNo
+) const
+{
+    forAll(pointsToTest, pTT)
+    {
+        const vector& p(pointsToTest[pTT]);
+
+        // if any point in the list is in range of the face
+        // then the rest do not need to be tested and
+        // true can be returned
+
+        if (testPointFaceDistance(p, faceNo))
+        {
+            return true;
+        }
+    }
+
+    return false;
+}
+
+bool Foam::moleculeCloud::testPointFaceDistance
+(
+    const vector& p,
+    const label faceNo
+) const
+{
+    const face& faceToTest(mesh_.faces()[faceNo]);
+
+    const vector& faceC(mesh_.faceCentres()[faceNo]);
+
+    const vector& faceA(mesh_.faceAreas()[faceNo]);
+
+    const vectorList& points(mesh_.points());
+
+    return testPointFaceDistance
+    (
+        p,
+        faceToTest,
+        points,
+        faceC,
+        faceA
+    );
+}
+
+bool Foam::moleculeCloud::testPointFaceDistance
+(
+    const vector& p,
+    const labelList& faceToTest,
+    const vectorList& points,
+    const vector& faceC,
+    const vector& faceA
+) const
+{
+    vector faceN(faceA/mag(faceA));
+
+    scalar perpDist((p - faceC) & faceN);
+
+    if (mag(perpDist) > pairPotentials_.rCutMax())
+    {
+        return false;
+    }
+
+    vector pointOnPlane = (p - faceN * perpDist);
+
+    if (magSqr(faceC - pointOnPlane) < pairPotentials_.rCutMaxSqr()*1e-8)
+    {
+        // If pointOnPlane is very close to the face centre
+        // then defining the local axes will be inaccurate
+        // and it is very likely that pointOnPlane will be
+        // inside the face, so return true if the points
+        // are in range to be safe
+
+        return (magSqr(pointOnPlane - p) <= pairPotentials_.rCutMaxSqr());
+    }
+
+    vector xAxis = (faceC - pointOnPlane)/mag(faceC - pointOnPlane);
+
+    vector yAxis =
+        ((faceC - pointOnPlane) ^ faceN)
+       /mag((faceC - pointOnPlane) ^ faceN);
+
+    List<vector2D> local2DVertices(faceToTest.size());
+
+    forAll(faceToTest, fTT)
+    {
+        const vector& V(points[faceToTest[fTT]]);
+
+        if (magSqr(V-p) <= pairPotentials_.rCutMaxSqr())
+        {
+            return true;
+        }
+
+        local2DVertices[fTT] = vector2D
+        (
+            ((V - pointOnPlane) & xAxis),
+            ((V - pointOnPlane) & yAxis)
+        );
+    }
+
+    scalar localFaceCx((faceC - pointOnPlane) & xAxis);
+
+    scalar la_valid = -1;
+
+    forAll(local2DVertices, fV)
+    {
+        const vector2D& va(local2DVertices[fV]);
+
+        const vector2D& vb
+        (
+            local2DVertices[(fV + 1) % local2DVertices.size()]
+        );
+
+        if (mag(vb.y()-va.y()) > SMALL)
+        {
+            scalar la =
+                (
+                    va.x() - va.y()*((vb.x() - va.x())/(vb.y() - va.y()))
+                )
+               /localFaceCx;
+
+            scalar lv = -va.y()/(vb.y() - va.y());
+
+
+            if (la >= 0 && la <= 1 && lv >= 0 && lv <= 1)
+            {
+                la_valid = la;
+
+                break;
+            }
+        }
+    }
+
+    if (la_valid < 0)
+    {
+        // perpendicular point inside face, nearest point is pointOnPlane;
+        return (magSqr(pointOnPlane-p) <= pairPotentials_.rCutMaxSqr());
+    }
+    else
+    {
+        // perpendicular point outside face, nearest point is
+        // on edge that generated la_valid;
+        return
+        (
+            magSqr(pointOnPlane + la_valid*(faceC - pointOnPlane) - p)
+         <= pairPotentials_.rCutMaxSqr()
+        );
+    }
+
+    // if the algorithm hasn't returned anything by now then something has
+    // gone wrong.
+
+    FatalErrorIn("moleculeCloudTestPointAndFaceDistance.C") << nl
+        << "point " << p << " to face " << faceToTest
+        << " comparison did not find a nearest point"
+        << " to be inside or outside face."
+        << abort(FatalError);
+
+    return false;
+}
+
+
+// ************************************************************************* //
diff --git a/src/lagrangian/molecularDynamics/molecule/reducedUnits/reducedUnits.C b/src/lagrangian/molecularDynamics/molecule/reducedUnits/reducedUnits.C
new file mode 100644
index 0000000000..3536893f8e
--- /dev/null
+++ b/src/lagrangian/molecularDynamics/molecule/reducedUnits/reducedUnits.C
@@ -0,0 +1,165 @@
+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  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 "reducedUnits.H"
+
+// * * * * * * * * * * * * * * Static Data Members * * * * * * * * * * * * * //
+
+const  Foam::scalar Foam::reducedUnits::kb = 1.3806504e-23;
+
+
+// * * * * * * * * * * * * * Private Member Functions  * * * * * * * * * * * //
+
+void Foam::reducedUnits::calcRefValues()
+{
+    if
+    (
+        refTime_ < VSMALL
+     || refLength_ < VSMALL
+     || refMass_ < VSMALL
+    )
+    {
+        FatalErrorIn("Foam::reducedUnits::calcRefValues() ")
+            << "One of more referencence values too small for floating point "
+            << "calculation: "
+            << "refTime_ = " << refTime_
+            << ", refLength = " << refTemp_
+            << ", refMass = " << refMass_
+            << nl << abort(FatalError);
+    }
+
+    refEnergy_ = refLength_*refLength_*refMass_/(refTime_*refTime_);
+
+    refTemp_ = refEnergy_ / kb;
+
+    refForce_ = refEnergy_/refLength_;
+
+    refVelocity_ = Foam::sqrt(refEnergy_/refMass_);
+
+    refVolume_ = Foam::pow(refLength_,3.0);
+
+    refPressure_ = refEnergy_/refVolume_;
+
+    refMassDensity_ = refMass_/refVolume_;
+
+    refNumberDensity_ = 1.0/refVolume_;
+}
+
+
+// * * * * * * * * * * * * * * * * Constructors  * * * * * * * * * * * * * * //
+
+Foam::reducedUnits::reducedUnits()
+:
+    refLength_(1e-9),
+    refTime_(1e-12),
+    refMass_(1.660538782e-27)
+{
+    calcRefValues();
+}
+
+
+Foam::reducedUnits::reducedUnits
+(
+    scalar refLength,
+    scalar refTime,
+    scalar refMass
+)
+:
+    refLength_(refLength),
+    refTime_(refTime),
+    refMass_(refMass)
+{
+    calcRefValues();
+}
+
+
+Foam::reducedUnits::reducedUnits(const IOdictionary& reducedUnitsDict)
+:
+    refLength_(),
+    refTime_(),
+    refMass_()
+{
+    setRefValues(reducedUnitsDict);
+}
+
+
+// * * * * * * * * * * * * * * * * Destructor  * * * * * * * * * * * * * * * //
+
+Foam::reducedUnits::~reducedUnits()
+{}
+
+
+// * * * * * * * * * * * * * * * Member Functions  * * * * * * * * * * * * * //
+
+void Foam::reducedUnits::setRefValues
+(
+    scalar refLength,
+    scalar refTime,
+    scalar refMass
+)
+{
+    refLength_ = refLength;
+
+    refTime_ = refTime;
+
+    refMass_ = refMass;
+
+    calcRefValues();
+}
+
+
+void Foam::reducedUnits::setRefValues
+(
+    const IOdictionary& reducedUnitsDict
+)
+{
+    refLength_ = readScalar(reducedUnitsDict.lookup("refLength"));
+
+    refTime_ = readScalar(reducedUnitsDict.lookup("refTime"));
+
+    refMass_  = readScalar(reducedUnitsDict.lookup("refMass"));
+
+    calcRefValues();
+}
+
+
+// * * * * * * * * * * * * * * * Member Operators  * * * * * * * * * * * * * //
+
+void Foam::reducedUnits::operator=(const reducedUnits& rhs)
+{
+    // Check for assignment to self
+    if (this == &rhs)
+    {
+        FatalErrorIn
+        (
+            "Foam::reducedUnits::operator=(const Foam::reducedUnits&)"
+        )   << "Attempted assignment to self"
+            << abort(FatalError);
+    }
+}
+
+
+// ************************************************************************* //
diff --git a/src/lagrangian/molecularDynamics/molecule/reducedUnits/reducedUnits.H b/src/lagrangian/molecularDynamics/molecule/reducedUnits/reducedUnits.H
new file mode 100644
index 0000000000..6a1379ecac
--- /dev/null
+++ b/src/lagrangian/molecularDynamics/molecule/reducedUnits/reducedUnits.H
@@ -0,0 +1,184 @@
+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  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::reducedUnits
+
+Description
+
+SourceFiles
+    reducedUnitsI.H
+    reducedUnits.C
+    reducedUnitsIO.C
+
+\*---------------------------------------------------------------------------*/
+
+#ifndef reducedUnits_H
+#define reducedUnits_H
+
+#include "scalar.H"
+#include "IOdictionary.H"
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+namespace Foam
+{
+
+/*---------------------------------------------------------------------------*\
+                           Class reducedUnits Declaration
+\*---------------------------------------------------------------------------*/
+
+class reducedUnits
+{
+    // Private data
+
+        // Reduced units
+
+            // Fundamental values
+
+                scalar refLength_;
+
+                scalar refTime_;
+
+                scalar refMass_;
+
+            // Derived values
+
+                scalar refEnergy_;
+
+                scalar refTemp_;
+
+                scalar refForce_;
+
+                scalar refVelocity_;
+
+                scalar refVolume_;
+
+                scalar refPressure_;
+
+               scalar refMassDensity_;
+
+                scalar refNumberDensity_;
+
+
+    // Private Member Functions
+
+        void calcRefValues();
+
+        //- Disallow default bitwise copy construct
+        reducedUnits(const reducedUnits&);
+
+        //- Disallow default bitwise assignment
+        void operator=(const reducedUnits&);
+
+
+public:
+
+    // Static data members
+
+        //- Static data someStaticData
+        static const scalar kb;
+
+
+    // Constructors
+
+        //- Construct with no argument, uses default values:
+        // length  = 1nm
+        // mass = 1.660538782e−27kg (unified atomic mass unit)
+        // temperature = 1K (therefore, energy = 1*kb)
+        reducedUnits();
+
+        //- Construct from components
+        reducedUnits
+        (
+            scalar refLength,
+            scalar refTime,
+            scalar refMass
+        );
+
+        //- Construct from dictionary
+        reducedUnits(const IOdictionary& reducedUnitsDict);
+
+
+    // Destructor
+
+        ~reducedUnits();
+
+
+    // Member Functions
+
+        void setRefValues
+        (
+            scalar refLength,
+            scalar refTime,
+            scalar refMass
+        );
+
+        void setRefValues(const IOdictionary& reducedUnitsDict);
+
+
+        // Access
+
+            inline scalar refLength() const;
+
+            inline scalar refTime() const;
+
+            inline scalar refMass() const;
+
+            inline scalar refTemp() const;
+
+            inline scalar refEnergy() const;
+
+            inline scalar refForce() const;
+
+            inline scalar refVelocity() const;
+
+            inline scalar refVolume() const;
+
+            inline scalar refPressure() const;
+
+            inline scalar refMassDensity() const;
+
+            inline scalar refNumberDensity() const;
+
+
+    // IOstream Operators
+
+        friend Ostream& operator<<(Ostream&, const reducedUnits&);
+};
+
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+} // End namespace Foam
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+#include "reducedUnitsI.H"
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+#endif
+
+// ************************************************************************* //
diff --git a/src/lagrangian/molecularDynamics/molecule/reducedUnits/reducedUnitsI.H b/src/lagrangian/molecularDynamics/molecule/reducedUnits/reducedUnitsI.H
new file mode 100644
index 0000000000..8098885d68
--- /dev/null
+++ b/src/lagrangian/molecularDynamics/molecule/reducedUnits/reducedUnitsI.H
@@ -0,0 +1,95 @@
+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  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
+
+\*---------------------------------------------------------------------------*/
+
+// * * * * * * * * * * * * * * * Member Functions  * * * * * * * * * * * * * //
+
+inline Foam::scalar Foam::reducedUnits::refLength() const
+{
+    return refLength_;
+}
+
+
+inline Foam::scalar Foam::reducedUnits::refTime() const
+{
+    return refTime_;
+}
+
+
+inline Foam::scalar Foam::reducedUnits::refMass() const
+{
+    return refMass_;
+}
+
+
+inline Foam::scalar Foam::reducedUnits::refTemp() const
+{
+    return refTemp_;
+}
+
+
+inline Foam::scalar Foam::reducedUnits::refEnergy() const
+{
+    return refEnergy_;
+}
+
+
+inline Foam::scalar Foam::reducedUnits::refForce() const
+{
+    return refForce_;
+}
+
+
+inline Foam::scalar Foam::reducedUnits::refVelocity() const
+{
+    return refVelocity_;
+}
+
+
+inline Foam::scalar Foam::reducedUnits::refVolume() const
+{
+    return refVolume_;
+}
+
+
+inline Foam::scalar Foam::reducedUnits::refPressure() const
+{
+    return refPressure_;
+}
+
+
+inline Foam::scalar Foam::reducedUnits::refMassDensity() const
+{
+    return refMassDensity_;
+}
+
+
+inline Foam::scalar Foam::reducedUnits::refNumberDensity() const
+{
+    return refNumberDensity_;
+}
+
+
+// ************************************************************************* //
diff --git a/src/lagrangian/molecularDynamics/molecule/reducedUnits/reducedUnitsIO.C b/src/lagrangian/molecularDynamics/molecule/reducedUnits/reducedUnitsIO.C
new file mode 100644
index 0000000000..88d110a5be
--- /dev/null
+++ b/src/lagrangian/molecularDynamics/molecule/reducedUnits/reducedUnitsIO.C
@@ -0,0 +1,61 @@
+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  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 "reducedUnits.H"
+#include "IOstreams.H"
+
+// * * * * * * * * * * * * * * * IOstream Operators  * * * * * * * * * * * * //
+
+Foam::Ostream& Foam::operator<<(Ostream& os, const reducedUnits& rU)
+{
+    os  << nl << "Defined: " << nl
+        << tab << "refLength = " << rU.refLength() << " m" << nl
+        << tab << "refTime = " << rU.refTime() << " s" << nl
+        << tab << "refMass = " << rU.refMass() << " kg" << nl
+        << tab << "Boltzmann constant, kb = " << reducedUnits::kb << " J/K"
+        << nl << "Calculated: " << nl
+        << tab << "refEnergy = " << rU.refEnergy() << " J" << nl
+        << tab << "refTemp = " << rU.refTemp() << " K" << nl
+        << tab << "refForce = " << rU.refForce() << " N" << nl
+        << tab << "refVelocity = " << rU.refVelocity() << " m/s" << nl
+        << tab << "refVolume = " << rU.refVolume() << " m^3" << nl
+        << tab << "refPressure = " << rU.refPressure() << " N/m^2" << nl
+        << tab << "refMassDensity = " << rU.refMassDensity() << " kg/m^3" << nl
+        << tab << "refNumberDensity = " << rU.refNumberDensity() << " m^-3"
+        << endl;
+
+    // Check state of Ostream
+    os.check
+    (
+        "Foam::Ostream& Foam::operator<<(Foam::Ostream&, "
+        "const Foam::reducedUnits&)"
+    );
+
+    return os;
+}
+
+
+// ************************************************************************* //
diff --git a/src/lagrangian/molecularDynamics/molecule/referralLists/receivingReferralList.C b/src/lagrangian/molecularDynamics/molecule/referralLists/receivingReferralList.C
new file mode 100755
index 0000000000..e35c660b74
--- /dev/null
+++ b/src/lagrangian/molecularDynamics/molecule/referralLists/receivingReferralList.C
@@ -0,0 +1,181 @@
+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+   \\    /   O peration     |
+    \\  /    A nd           | Copyright (C) 1991-2005 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 "receivingReferralList.H"
+
+namespace Foam
+{
+
+// * * * * * * * * * * * * * * * * Constructors  * * * * * * * * * * * * * * //
+
+receivingReferralList::receivingReferralList()
+:
+    labelListList(),
+    sourceProc_(-1)
+{}
+
+
+receivingReferralList::receivingReferralList
+(
+    const label sourceProc,
+    const labelListList& refCellsToSendTo
+)
+:
+    labelListList(refCellsToSendTo),
+    sourceProc_(sourceProc)
+{}
+
+
+receivingReferralList::receivingReferralList
+(
+    const receivingReferralList& rL
+)
+:
+    labelListList(rL),
+    sourceProc_(rL.sourceProc())
+{}
+
+
+// * * * * * * * * * * * * * * * * Destructor  * * * * * * * * * * * * * * * //
+
+receivingReferralList::~receivingReferralList()
+{}
+
+
+// * * * * * * * * * * * * * * * Member Operators  * * * * * * * * * * * * * //
+
+void receivingReferralList::operator=(const receivingReferralList& rhs)
+{
+    // Check for assignment to self
+    if (this == &rhs)
+    {
+        FatalErrorIn
+        (
+            "Foam::receivingReferralList::operator="
+            "(const Foam::receivingReferralList&)"
+        )
+            << "Attempted assignment to self"
+            << abort(FatalError);
+    }
+
+    labelListList::operator=(rhs);
+
+    sourceProc_ = rhs.sourceProc();
+}
+
+
+// * * * * * * * * * * * * * * * Friend Operators  * * * * * * * * * * * * * //
+
+bool operator==
+(
+    const receivingReferralList& a,
+    const receivingReferralList& b
+)
+{
+    // Trivial reject: lists are different size
+    if (a.size() != b.size())
+    {
+        return false;
+    }
+
+    // Or if source processors are not the same.
+    if (a.sourceProc() != b.sourceProc())
+    {
+        return false;
+    }
+
+    List<bool> fnd(a.size(), false);
+
+    forAll (b, bI)
+    {
+        labelList curLList = b[bI];
+
+        bool found = false;
+
+        forAll (a, aI)
+        {
+            if (a[aI] == curLList)
+            {
+                found = true;
+                fnd[aI] = true;
+                break;
+            }
+        }
+
+        if (!found)
+        {
+            return false;
+        }
+    }
+
+    // check if all LLists on a were marked
+    bool result = true;
+
+    forAll (fnd, aI)
+    {
+        result = (result && fnd[aI]);
+    }
+
+    return result;
+}
+
+
+Istream& operator>>(Istream& is, receivingReferralList& rRL)
+{
+    is >> rRL.sourceProc_ >> static_cast<labelListList&>(rRL);
+
+    is.check
+    (
+        "Istream& operator<<(Istream& f, const receivingReferralList& rRL"
+    );
+
+    return is;
+}
+
+
+Ostream& operator<<
+(
+    Ostream& os,
+    const receivingReferralList& rRL
+)
+{
+    os << rRL.sourceProc() << token::SPACE
+        << static_cast< const labelListList& >(rRL);
+
+    os.check
+    (
+        "Ostream& operator<<(Ostream& f, const receivingReferralList& rRL"
+    );
+
+    return os;
+}
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+} // End namespace Foam
+
+
+// ************************************************************************* //
diff --git a/src/lagrangian/molecularDynamics/molecule/referralLists/receivingReferralList.H b/src/lagrangian/molecularDynamics/molecule/referralLists/receivingReferralList.H
new file mode 100755
index 0000000000..e64a0836f8
--- /dev/null
+++ b/src/lagrangian/molecularDynamics/molecule/referralLists/receivingReferralList.H
@@ -0,0 +1,138 @@
+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+   \\    /   O peration     |
+    \\  /    A nd           | Copyright (C) 1991-2005 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::receivingReferralList
+
+Description
+
+SourceFiles
+    receivingReferralListI.H
+    receivingReferralList.C
+    receivingReferralListIO.C
+
+\*---------------------------------------------------------------------------*/
+
+#ifndef receivingReferralList_H
+#define receivingReferralList_H
+
+#include "labelList.H"
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+namespace Foam
+{
+
+/*---------------------------------------------------------------------------*\
+                    Class receivingReferralList Declaration
+\*---------------------------------------------------------------------------*/
+
+class receivingReferralList
+:
+    public labelListList
+{
+    // Private data
+
+        label sourceProc_;
+
+
+public:
+
+    // Constructors
+
+        //- Construct null
+        receivingReferralList();
+
+        //- Construct from components
+        receivingReferralList
+        (
+            const label sourceProc,
+            const labelListList& refCellsToSendTo
+        );
+
+        //- Construct as copy
+        receivingReferralList(const receivingReferralList&);
+
+
+    // Destructor
+
+        ~receivingReferralList();
+
+
+    // Member Functions
+
+        // Access
+
+            inline label sourceProc() const;
+
+
+    // Member Operators
+
+        void operator=(const receivingReferralList&);
+
+
+    // Friend Operators
+
+        friend bool operator==
+        (
+            const receivingReferralList& a,
+            const receivingReferralList& b
+        );
+
+        inline friend bool operator!=
+        (
+            const receivingReferralList& a,
+            const receivingReferralList& b
+        );
+
+
+    // IOstream Operators
+
+        friend Istream& operator>>
+        (
+            Istream&,
+            receivingReferralList&
+        );
+
+        friend Ostream& operator<<
+        (
+            Ostream&,
+            const receivingReferralList&
+        );
+};
+
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+} // End namespace Foam
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+#include "receivingReferralListI.H"
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+#endif
+
+// ************************************************************************* //
diff --git a/src/lagrangian/molecularDynamics/molecule/referralLists/receivingReferralListI.H b/src/lagrangian/molecularDynamics/molecule/referralLists/receivingReferralListI.H
new file mode 100755
index 0000000000..d91e01fe08
--- /dev/null
+++ b/src/lagrangian/molecularDynamics/molecule/referralLists/receivingReferralListI.H
@@ -0,0 +1,56 @@
+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+   \\    /   O peration     |
+    \\  /    A nd           | Copyright (C) 1991-2005 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
+{
+
+// * * * * * * * * * * * * * * * Member Functions  * * * * * * * * * * * * * //
+
+inline label receivingReferralList::sourceProc() const
+{
+    return sourceProc_;
+}
+
+
+// * * * * * * * * * * * * * * * Friend Operators  * * * * * * * * * * * * * //
+
+inline bool operator!=
+(
+    const receivingReferralList& a,
+    const receivingReferralList& b
+)
+{
+    return (!(a == b));
+}
+
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+} // End namespace Foam
+
+// ************************************************************************* //
diff --git a/src/lagrangian/molecularDynamics/molecule/referralLists/sendingReferralList.C b/src/lagrangian/molecularDynamics/molecule/referralLists/sendingReferralList.C
new file mode 100755
index 0000000000..9065102193
--- /dev/null
+++ b/src/lagrangian/molecularDynamics/molecule/referralLists/sendingReferralList.C
@@ -0,0 +1,178 @@
+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+   \\    /   O peration     |
+    \\  /    A nd           | Copyright (C) 1991-2005 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 "sendingReferralList.H"
+
+namespace Foam
+{
+
+// * * * * * * * * * * * * * * * * Constructors  * * * * * * * * * * * * * * //
+
+sendingReferralList::sendingReferralList()
+:
+    labelList(),
+    destinationProc_(-1)
+{}
+
+
+sendingReferralList::sendingReferralList
+(
+    const label destinationProc,
+    const labelList& cellsToSend
+)
+:
+    labelList(cellsToSend),
+    destinationProc_(destinationProc)
+{}
+
+
+sendingReferralList::sendingReferralList
+(
+    const sendingReferralList& rL
+)
+:
+    labelList(rL),
+    destinationProc_(rL.destinationProc())
+{}
+
+
+// * * * * * * * * * * * * * * * * Destructor  * * * * * * * * * * * * * * * //
+
+sendingReferralList::~sendingReferralList()
+{}
+
+
+// * * * * * * * * * * * * * * * Member Operators  * * * * * * * * * * * * * //
+
+void sendingReferralList::operator=(const sendingReferralList& rhs)
+{
+    // Check for assignment to self
+    if (this == &rhs)
+    {
+        FatalErrorIn
+        (
+            "Foam::distribution::operator=(const Foam::distribution&)"
+        )
+            << "Attempted assignment to self"
+            << abort(FatalError);
+    }
+
+    labelList::operator=(rhs);
+
+    destinationProc_ = rhs.destinationProc();
+}
+
+
+// * * * * * * * * * * * * * * * Friend Operators  * * * * * * * * * * * * * //
+
+bool operator==
+(
+    const sendingReferralList& a,
+    const sendingReferralList& b
+)
+{
+    // Trivial reject: lists are different size
+    if (a.size() != b.size())
+    {
+        return false;
+    }
+
+    // Or if source processors are not the same.
+    if (a.destinationProc() != b.destinationProc())
+    {
+        return false;
+    }
+
+    List<bool> fnd(a.size(), false);
+
+    forAll (b, bI)
+    {
+        label curLabel = b[bI];
+
+        bool found = false;
+
+        forAll (a, aI)
+        {
+            if (a[aI] == curLabel)
+            {
+                found = true;
+                fnd[aI] = true;
+                break;
+            }
+        }
+
+        if (!found)
+        {
+            return false;
+        }
+    }
+
+    // check if all labels on a were marked
+    bool result = true;
+
+    forAll (fnd, aI)
+    {
+        result = (result && fnd[aI]);
+    }
+
+    return result;
+}
+
+
+Istream& operator>>
+(
+    Istream& is,
+    sendingReferralList& sRL
+)
+{
+    is >> sRL.destinationProc_ >> static_cast<labelList&>(sRL);
+
+    is.check("Istream& operator<<(Istream& f, const sendingReferralList& sRL");
+
+    return is;
+}
+
+
+Ostream& operator<<
+(
+    Ostream& os,
+    const sendingReferralList& rL
+)
+{
+    os << rL.destinationProc() << token::SPACE
+        << static_cast< const labelList& >(rL);
+
+    os.check("Ostream& operator<<(Ostream& f, const sendingReferralList& rL");
+
+    return os;
+}
+
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+} // End namespace Foam
+
+// ************************************************************************* //
diff --git a/src/lagrangian/molecularDynamics/molecule/referralLists/sendingReferralList.H b/src/lagrangian/molecularDynamics/molecule/referralLists/sendingReferralList.H
new file mode 100755
index 0000000000..0d729e35be
--- /dev/null
+++ b/src/lagrangian/molecularDynamics/molecule/referralLists/sendingReferralList.H
@@ -0,0 +1,138 @@
+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+   \\    /   O peration     |
+    \\  /    A nd           | Copyright (C) 1991-2005 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::sendingReferralList
+
+Description
+
+SourceFiles
+    sendingReferralListI.H
+    sendingReferralList.C
+    sendingReferralListIO.C
+
+\*---------------------------------------------------------------------------*/
+
+#ifndef sendingReferralList_H
+#define sendingReferralList_H
+
+#include "labelList.H"
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+namespace Foam
+{
+
+/*---------------------------------------------------------------------------*\
+                      Class sendingReferralList Declaration
+\*---------------------------------------------------------------------------*/
+
+class sendingReferralList
+:
+    public labelList
+{
+    // Private data
+
+        label destinationProc_;
+
+
+public:
+
+    // Constructors
+
+        //- Construct null
+        sendingReferralList();
+
+        //- Construct from components
+        sendingReferralList
+        (
+            const label destinationProc,
+            const labelList& cellsToSend
+        );
+
+        //- Construct as copy
+        sendingReferralList(const sendingReferralList&);
+
+
+    // Destructor
+
+        ~sendingReferralList();
+
+
+    // Member Functions
+
+        // Access
+
+            inline label destinationProc() const;
+
+
+    // Member Operators
+
+        void operator=(const sendingReferralList&);
+
+
+    // Friend Operators
+
+        friend bool operator==
+        (
+            const sendingReferralList& a,
+            const sendingReferralList& b
+        );
+
+        inline friend bool operator!=
+        (
+            const sendingReferralList& a,
+            const sendingReferralList& b
+        );
+
+
+    // IOstream Operators
+
+        friend Istream& operator>>
+        (
+            Istream&,
+            sendingReferralList&
+        );
+
+        friend Ostream& operator<<
+        (
+            Ostream&,
+            const sendingReferralList&
+        );
+};
+
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+} // End namespace Foam
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+#include "sendingReferralListI.H"
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+#endif
+
+// ************************************************************************* //
diff --git a/src/lagrangian/molecularDynamics/molecule/referralLists/sendingReferralListI.H b/src/lagrangian/molecularDynamics/molecule/referralLists/sendingReferralListI.H
new file mode 100755
index 0000000000..d571962f5d
--- /dev/null
+++ b/src/lagrangian/molecularDynamics/molecule/referralLists/sendingReferralListI.H
@@ -0,0 +1,56 @@
+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+   \\    /   O peration     |
+    \\  /    A nd           | Copyright (C) 1991-2005 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
+{
+
+// * * * * * * * * * * * * * * * Member Functions  * * * * * * * * * * * * * //
+
+inline label sendingReferralList::destinationProc() const
+{
+    return destinationProc_;
+}
+
+
+// * * * * * * * * * * * * * * * Friend Operators  * * * * * * * * * * * * * //
+
+inline bool operator!=
+(
+    const sendingReferralList& a,
+    const sendingReferralList& b
+)
+{
+    return (!(a == b));
+}
+
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+} // End namespace Foam
+
+// ************************************************************************* //
diff --git a/src/lagrangian/molecularDynamics/molecule/referredCell/referredCell.C b/src/lagrangian/molecularDynamics/molecule/referredCell/referredCell.C
new file mode 100755
index 0000000000..c60ae69bf4
--- /dev/null
+++ b/src/lagrangian/molecularDynamics/molecule/referredCell/referredCell.C
@@ -0,0 +1,441 @@
+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+   \\    /   O peration     |
+    \\  /    A nd           | Copyright (C) 1991-2005 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 "referredCell.H"
+#include "moleculeCloud.H"
+
+namespace Foam
+{
+
+// * * * * * * * * * * * * * Private Member Functions  * * * * * * * * * * * //
+
+void referredCell::setConstructionData
+(
+    const polyMesh& mesh,
+    const label sourceCell
+)
+{
+    // * * * * * * * * * * * Points * * * * * * * * * * *
+
+    const labelList& points = mesh.cellPoints()[sourceCell];
+
+    vectorList sourceCellVertices(points.size());
+
+    forAll(sourceCellVertices, sCV)
+    {
+        sourceCellVertices[sCV] = mesh.points()[points[sCV]];
+    }
+
+    vertexPositions_ = referPositions(sourceCellVertices);
+
+    // * * * * * * * * * * * Edges * * * * * * * * * * *
+
+    const labelList& edges = mesh.cellEdges()[sourceCell];
+
+    edgeList sourceCellEdges(edges.size());
+
+    forAll(sourceCellEdges, sCE)
+    {
+        sourceCellEdges[sCE] = mesh.edges()[edges[sCE]];
+    }
+
+    locallyMapEdgeList(points, sourceCellEdges);
+
+    // * * * * * * * * * * * Faces * * * * * * * * * * *
+
+    labelList faces(mesh.cells()[sourceCell]);
+
+    vectorList sourceCellFaceCentres(faces.size());
+
+    vectorList sourceCellFaceAreas(faces.size());
+
+    labelListList sourceCellFaces(faces.size());
+
+    forAll(faces, f)
+    {
+        sourceCellFaces[f] = mesh.faces()[faces[f]];
+
+        sourceCellFaceCentres[f] = mesh.faceCentres()[faces[f]];
+
+        sourceCellFaceAreas[f] = mesh.faceAreas()[faces[f]];
+    }
+
+    locallyMapFaceList(points, sourceCellFaces);
+
+    faceCentres_ = referPositions(sourceCellFaceCentres);
+
+    faceAreas_ = rotateVectors(sourceCellFaceAreas);
+}
+
+
+void referredCell::locallyMapEdgeList
+(
+    const labelList& points,
+    const edgeList& sourceCellEdges
+)
+{
+    edges_.setSize(sourceCellEdges.size());
+
+    forAll(sourceCellEdges, sCE)
+    {
+        const edge& e(sourceCellEdges[sCE]);
+
+        edges_[sCE].start() = findIndex(points, e.start());
+
+        edges_[sCE].end() = findIndex(points, e.end());
+
+        if
+        (
+            edges_[sCE].start() == -1
+         || edges_[sCE].end() == -1
+        )
+        {
+            FatalErrorIn("Foam::referredCell::locallyMapEdgeList")
+                << "edgeList and points labelList for "
+                << "referred cell do not match: "
+                << nl << "points: " << points
+                << nl << "egdes: " << sourceCellEdges
+                << abort(FatalError);
+        }
+    }
+}
+
+
+void referredCell::locallyMapFaceList
+(
+    const labelList& points,
+    const labelListList& sourceCellFaces
+)
+{
+    faces_.setSize(sourceCellFaces.size());
+
+    forAll(sourceCellFaces, sCF)
+    {
+        const labelList& sourceCellFace(sourceCellFaces[sCF]);
+
+        labelList& localFace(faces_[sCF]);
+
+        localFace.setSize(sourceCellFace.size());
+
+        forAll(sourceCellFace, p)
+        {
+            localFace[p] = findIndex(points, sourceCellFace[p]);
+
+            if (localFace[p] == -1)
+            {
+                FatalErrorIn("Foam::referredCell::locallyMapEdgeList")
+                    << "edgeList and points labelList for "
+                    << "referred cell do not match: "
+                    << nl << "points: " << points
+                    << nl << "faces: " << sourceCellFaces
+                    << abort(FatalError);
+            }
+        }
+    }
+}
+
+
+vector referredCell::referPosition(const vector& positionToRefer)
+{
+    return offset_ + (rotation_ & positionToRefer);
+}
+
+
+vectorList referredCell::referPositions(const vectorList& positionsToRefer)
+{
+    return offset_ + (rotation_ & positionsToRefer);
+}
+
+
+vector referredCell::rotateVector(const vector& vectorToRotate)
+{
+    return rotation_ & vectorToRotate;
+}
+
+
+vectorList referredCell::rotateVectors(const vectorList& vectorsToRotate)
+{
+    return rotation_ & vectorsToRotate;
+}
+
+
+// * * * * * * * * * * * * * * * * Constructors  * * * * * * * * * * * * * * //
+
+referredCell::referredCell()
+:
+    DynamicList<referredMolecule>(),
+    sourceProc_(-1),
+    sourceCell_(-1),
+    vertexPositions_(),
+    offset_(vector::zero),
+    rotation_(I)
+{}
+
+
+referredCell::referredCell
+(
+    const polyMesh& mesh,
+    const label sourceProc,
+    const label sourceCell,
+    const vector& offset,
+    const tensor& rotation
+)
+:
+    DynamicList<referredMolecule>(),
+    sourceProc_(sourceProc),
+    sourceCell_(sourceCell),
+    offset_(offset),
+    rotation_(rotation)
+{
+    setConstructionData(mesh, sourceCell);
+}
+
+
+referredCell::referredCell
+(
+    const label sourceProc,
+    const label sourceCell,
+    const vectorList& vertexPositions,
+    const edgeList& localEdges,
+    const labelListList& localFaces,
+    const vectorList& faceCentres,
+    const vectorList& faceAreas,
+    const vector& offset,
+    const tensor& rotation
+)
+:
+    DynamicList<referredMolecule>(),
+    sourceProc_(sourceProc),
+    sourceCell_(sourceCell),
+    edges_(localEdges),
+    faces_(localFaces),
+    offset_(offset),
+    rotation_(rotation)
+{
+    // Supplied vertexPositions, faceCentres and faceAreas are of the
+    // "original" cell, and need to be transformed to the referred
+    // locations on construction
+
+    vertexPositions_ = referPositions(vertexPositions);
+
+    faceCentres_ = referPositions(faceCentres);
+
+    faceAreas_ = rotateVectors(faceAreas);
+}
+
+
+referredCell::referredCell
+(
+    const polyMesh& mesh,
+    const label sourceProc,
+    const label sourceCell,
+    const vector& cS,
+    const vector& cD,
+    const vector& nS,
+    const vector& nD
+)
+:
+    DynamicList<referredMolecule>(),
+    sourceProc_(sourceProc),
+    sourceCell_(sourceCell)
+{
+    // It is assumed that the vectors originating from the faces being referred
+    // here are correct periodic faces - i.e. they have the same area etc.
+
+    vector nA = -nS/mag(nS);
+    vector nB = nD/mag(nD);
+
+    rotation_ = rotationTensor(nA, nB);
+
+    offset_ = cD - (rotation_ & cS);
+
+    // Allow sourceCell = -1 to create a dummy referredCell
+    // to obtain the transformation
+
+    if(sourceCell >= 0)
+    {
+        setConstructionData(mesh, sourceCell);
+    }
+}
+
+
+// * * * * * * * * * * * * * * * * Destructor  * * * * * * * * * * * * * * * //
+
+referredCell::~referredCell()
+{}
+
+
+// * * * * * * * * * * * * * * * Member Functions  * * * * * * * * * * * * * //
+
+referredCell referredCell::reRefer
+(
+    const vector& cS,
+    const vector& cD,
+    const vector& nS,
+    const vector& nD
+)
+{
+    vector nA = -nS/mag(nS);
+    vector nB = nD/mag(nD);
+
+    tensor newRotation = rotationTensor(nA, nB);
+
+    vector newOffset = cD - (newRotation & cS);
+
+    tensor reReferredRotation = newRotation & rotation_;
+
+    vector reReferredOffset = newOffset + (newRotation & offset_);
+
+    return referredCell
+    (
+        sourceProc_,
+        sourceCell_,
+        rotation_.T() & (vertexPositions_ - offset_),
+        edges_,
+        faces_,
+        rotation_.T() & (faceCentres_ - offset_),
+        rotation_.T() & (faceAreas_),
+        reReferredOffset,
+        reReferredRotation
+    );
+}
+
+
+vector referredCell::referPosition(const vector& positionToRefer) const
+{
+    return offset_ + (rotation_ & positionToRefer);
+}
+
+
+vectorList referredCell::referPositions
+(
+    const vectorList& positionsToRefer
+) const
+{
+    return offset_ + (rotation_ & positionsToRefer);
+}
+
+
+vector referredCell::rotateVector(const vector& vectorToRotate) const
+{
+    return rotation_ & vectorToRotate;
+}
+
+
+vectorList referredCell::rotateVectors(const vectorList& vectorsToRotate) const
+{
+    return rotation_ & vectorsToRotate;
+}
+
+
+void referredCell::referInMols(const List<referredMolecule>& incomingMols)
+{
+    clear();
+
+    forAll(incomingMols, iM)
+    {
+        append
+        (
+            referredMolecule
+            (
+                incomingMols[iM].id(),
+                referPosition
+                (
+                    incomingMols[iM].position()
+                )
+            )
+        );
+    }
+}
+
+
+bool referredCell::duplicate(const referredCell& refCellDupl) const
+{
+    return
+    (
+        sourceProc_ == refCellDupl.sourceProc()
+        && sourceCell_ == refCellDupl.sourceCell()
+        && mag(offset_ - refCellDupl.offset()) < moleculeCloud::transTol
+    );
+}
+
+
+bool referredCell::duplicate(const label procNo,const label nCells) const
+{
+    return
+    (
+        sourceProc_ == procNo
+        && sourceCell_ < nCells
+        && mag(offset_) < moleculeCloud::transTol
+    );
+}
+
+
+// * * * * * * * * * * * * * * * Friend Functions  * * * * * * * * * * * * * //
+
+Istream& operator>>(Istream& is, referredCell& rC)
+{
+
+    is >> rC.sourceProc_
+        >> rC.sourceCell_
+        >> rC.vertexPositions_
+        >> rC.edges_
+        >> rC.faces_
+        >> rC.faceCentres_
+        >> rC.faceAreas_
+        >> rC.offset_
+        >> rC.rotation_;
+
+    is.check("Istream& operator<<(Istream& f, const referredCell& rC");
+
+    return is;
+}
+
+
+Ostream& operator<<(Ostream& os, const referredCell& rC)
+{
+
+    os << rC.sourceProc()
+        << token::SPACE << rC.sourceCell()
+        << token::SPACE << rC.vertexPositions()
+        << token::SPACE << rC.edges()
+        << token::SPACE << rC.faces()
+        << token::SPACE << rC.faceCentres()
+        << token::SPACE << rC.faceAreas()
+        << token::SPACE << rC.offset()
+        << token::SPACE << rC.rotation();
+
+    os.check("Ostream& operator<<(Ostream& f, const referredCell& rC");
+
+    return os;
+}
+
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+}  // End namespace Foam
+
+// ************************************************************************* //
diff --git a/src/lagrangian/molecularDynamics/molecule/referredCell/referredCell.H b/src/lagrangian/molecularDynamics/molecule/referredCell/referredCell.H
new file mode 100755
index 0000000000..27aaf730fc
--- /dev/null
+++ b/src/lagrangian/molecularDynamics/molecule/referredCell/referredCell.H
@@ -0,0 +1,277 @@
+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+   \\    /   O peration     |
+    \\  /    A nd           | Copyright (C) 1991-2005 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::referredCell
+
+Description
+
+SourceFiles
+    referredCellI.H
+    referredCell.C
+
+\*---------------------------------------------------------------------------*/
+
+#ifndef referredCell_H
+#define referredCell_H
+
+#include "vector.H"
+#include "vectorList.H"
+#include "tensor.H"
+#include "transform.H"
+#include "DynamicList.H"
+#include "labelList.H"
+#include "edgeList.H"
+#include "polyMesh.H"
+
+#include "referredMolecule.H"
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+namespace Foam
+{
+
+/*---------------------------------------------------------------------------*\
+                           Class referredCell Declaration
+\*---------------------------------------------------------------------------*/
+
+class referredCell
+:
+    public DynamicList<referredMolecule>
+{
+    // Private data
+
+        label sourceProc_;
+
+        label sourceCell_;
+
+        //- Referred vertex positions
+        vectorList vertexPositions_;
+
+        edgeList edges_;
+
+        labelListList faces_;
+
+        vectorList faceCentres_;
+
+        vectorList faceAreas_;
+
+        labelList realCellsForInteraction_;
+
+        vector offset_;
+
+        tensor rotation_;
+
+
+    // Private Member Functions
+
+        void setConstructionData
+        (
+            const polyMesh& mesh,
+            const label sourceCell
+        );
+
+        void locallyMapEdgeList
+        (
+            const labelList& points,
+            const edgeList& sourceCellEdges
+        );
+
+        void locallyMapFaceList
+        (
+            const labelList& points,
+            const labelListList& sourceCellFaces
+        );
+
+        vector referPosition(const vector& positionToRefer);
+
+        vectorList referPositions(const vectorList& positionsToRefer);
+
+        vector rotateVector(const vector& vectorToRotate);
+
+        vectorList rotateVectors(const vectorList& vectorsToRotate);
+
+
+public:
+
+    // Constructors
+
+        //- Construct null
+
+        referredCell();
+
+        //- Construct from components with external edge information
+        referredCell
+        (
+            const polyMesh& mesh,
+            const label sourceProc,
+            const label sourceCell,
+            const vector& offset,
+            const tensor& rotation
+        );
+
+        //- Construct from components with existing local edge information
+        referredCell
+        (
+            const label sourceProc,
+            const label sourceCell,
+            const vectorList& vertexPositions,
+            const edgeList& localEdges,
+            const labelListList& localFaces,
+            const vectorList& faceCentres,
+            const vectorList& faceAreas,
+            const vector& offset,
+            const tensor& rotation
+        );
+
+        //- Construct from pair of face centers (c) and plain
+        //  face normals (n) (no need to make unit vectors or
+        //  reverse one direction)
+        //  Order of vectors important (S = source, D = Destination).
+        //  External edge information.
+
+        referredCell
+        (
+            const polyMesh& mesh,
+            const label sourceProc,
+            const label sourceCell,
+            const vector& cS,
+            const vector& cD,
+            const vector& nS,
+            const vector& nD
+        );
+
+
+    // Destructor
+
+        virtual ~referredCell();
+
+
+    // Member Functions
+
+        //- Take this referredCell object that has already had it's transform
+        //  calculated and refer it on again, retaining same source info.
+        referredCell reRefer
+        (
+            const vector& cS,
+            const vector& cD,
+            const vector& nS,
+            const vector& nD
+        );
+
+        //- Use internal transformatation values to transform the given
+        //  postion to its new location.
+        vector referPosition(const vector& positionToRefer) const;
+
+        //- Use internal transformatation values to transform the given
+        //  list of postions to their new locations.
+        vectorList referPositions(const vectorList& positionsToRefer) const;
+
+        //- Use internal transformatation values to rotate the given vector
+        vector rotateVector(const vector& vectorToRotate) const;
+
+        //- Use internal transformatation values to rotate the given
+        // list of vectors
+        vectorList rotateVectors(const vectorList& vectorsToRotate) const;
+
+        //- referInMols clears, the stored list of referred mols and takes
+        //  in a list of referred mols coming from a source processor,
+        //  transformingtheir positions
+        void referInMols(const List<referredMolecule>& incomingMols);
+
+        //- duplicate() function to test whether a referred or real cell
+        //  supplied by arguement is a duplicate of this referredCell.
+        //  Can be used bi-directionally - i.e. can be called on an existing
+        //  referred cell with a proposed referredCell as argument,
+        //  or vice versa.  Can only be called by a proposed referredCell with
+        //  a real cell index as arguement to test to see if the proposed
+        //  referredCell is a duplicate.
+        //  A duplicate cell is defined as one which has the same source
+        //  processor, source cell, and an equal offset. Real cells have zero
+        //  offset by definition.
+        bool duplicate(const referredCell& refCellDupl) const;
+
+        bool duplicate(const label procNo, const label nCells) const;
+
+
+        // Access
+
+            inline label sourceProc() const;
+
+            inline label sourceCell() const;
+
+            inline const vector& offset() const;
+
+            inline const tensor& rotation() const;
+
+            inline const vectorList& vertexPositions() const;
+
+            inline const edgeList& edges() const;
+
+            inline const labelListList& faces() const;
+
+            inline const vectorList& faceCentres() const;
+
+            inline const vectorList& faceAreas() const;
+
+            inline labelList& realCells();
+
+            inline const labelList& realCellsForInteraction() const;
+
+
+    // Friend Operators
+
+        inline friend bool operator==
+        (
+            const referredCell& a,
+            const referredCell& b
+        );
+
+        inline friend bool operator!=
+        (
+            const referredCell& a,
+            const referredCell& b
+        );
+
+
+    // IOstream Operators
+
+        friend Istream& operator>>(Istream&, referredCell&);
+        friend Ostream& operator<<(Ostream&, const referredCell&);
+};
+
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+} // End namespace Foam
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+#include "referredCellI.H"
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+#endif
+
+// ************************************************************************* //
diff --git a/src/lagrangian/molecularDynamics/molecule/referredCell/referredCellI.H b/src/lagrangian/molecularDynamics/molecule/referredCell/referredCellI.H
new file mode 100755
index 0000000000..4135f7ff6e
--- /dev/null
+++ b/src/lagrangian/molecularDynamics/molecule/referredCell/referredCellI.H
@@ -0,0 +1,127 @@
+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+   \\    /   O peration     |
+    \\  /    A nd           | Copyright (C) 1991-2005 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
+{
+
+// * * * * * * * * * * * * * * * Member Functions  * * * * * * * * * * * * * //
+
+inline label referredCell::sourceProc() const
+{
+    return sourceProc_;
+}
+
+
+inline label referredCell::sourceCell() const
+{
+    return sourceCell_;
+}
+
+
+inline const vector& referredCell::offset() const
+{
+    return offset_;
+}
+
+
+inline const tensor& referredCell::rotation() const
+{
+    return rotation_;
+}
+
+
+inline const vectorList& referredCell::vertexPositions() const
+{
+    return vertexPositions_;
+}
+
+
+inline const edgeList& referredCell::edges() const
+{
+    return edges_;
+}
+
+
+inline const labelListList& referredCell::faces() const
+{
+    return faces_;
+}
+
+
+inline const vectorList& referredCell::faceCentres() const
+{
+    return faceCentres_;
+}
+
+
+inline const vectorList& referredCell::faceAreas() const
+{
+    return faceAreas_;
+}
+
+
+inline labelList& referredCell::realCells()
+{
+    return realCellsForInteraction_;
+}
+
+
+inline const labelList& referredCell::realCellsForInteraction() const
+{
+    return realCellsForInteraction_;
+}
+
+
+// * * * * * * * * * * * * * * * Friend Operators  * * * * * * * * * * * * * //
+
+inline bool operator==
+(
+    const referredCell& a,
+    const referredCell& b
+)
+{
+    return const_cast<referredCell&>(a).duplicate
+    (
+        const_cast<const referredCell&>(b)
+    );
+}
+
+
+inline bool operator!=
+(
+    const referredCell& a,
+    const referredCell& b
+)
+{
+    return !(a == b);
+}
+
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+} // End namespace Foam
+
+// ************************************************************************* //
diff --git a/src/lagrangian/molecularDynamics/molecule/referredCellList/referredCellList.C b/src/lagrangian/molecularDynamics/molecule/referredCellList/referredCellList.C
new file mode 100755
index 0000000000..cd69a1d9d4
--- /dev/null
+++ b/src/lagrangian/molecularDynamics/molecule/referredCellList/referredCellList.C
@@ -0,0 +1,327 @@
+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+   \\    /   O peration     |
+    \\  /    A nd           | Copyright (C) 1991-2005 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 "referredCellList.H"
+#include "moleculeCloud.H"
+
+namespace Foam
+{
+
+// * * * * * * * * * * * * * * * * Constructors  * * * * * * * * * * * * * * //
+
+referredCellList::referredCellList(moleculeCloud& molCloud)
+:
+    List<referredCell >(),
+    molCloud_(molCloud)
+{}
+
+
+referredCellList::referredCellList
+(
+    moleculeCloud& molCloud,
+    const List<referredCell>& referredCells,
+    const List<label>& realCells
+)
+:
+    List< referredCell >(referredCells),
+    molCloud_(molCloud)
+{}
+
+
+// * * * * * * * * * * * * * * * * Destructor  * * * * * * * * * * * * * * * //
+
+referredCellList::~referredCellList()
+{}
+
+
+// * * * * * * * * * * * * * * * Member Functions  * * * * * * * * * * * * * //
+
+void referredCellList::setRealCellsInRange()
+{
+    Info<< nl << "Finding real cells in range of referred cells" << endl;
+
+    forAll(*this, rC)
+    {
+        const polyMesh& mesh(molCloud_.mesh());
+
+        referredCell& refCell = (*this)[rC];
+
+        DynamicList<label> realCellsFoundInRange;
+
+        const vectorList& refCellPoints = refCell.vertexPositions();
+
+        forAll(molCloud_.realFacesWithinRCutMaxOfAnyReferringPatch(), rCF)
+        {
+            const label f
+            (
+                molCloud_.realFacesWithinRCutMaxOfAnyReferringPatch()[rCF]
+            );
+
+            if (molCloud_.testPointFaceDistance(refCellPoints,f))
+            {
+                const label cellO(mesh.faceOwner()[f]);
+
+                if (findIndex(realCellsFoundInRange, cellO) == -1)
+                {
+                    realCellsFoundInRange.append(cellO);
+                }
+
+                if (mesh.isInternalFace(f))
+                {
+                    // boundary faces will not have neighbour information
+
+                    const label cellN(mesh.faceNeighbour()[f]);
+
+                    if (findIndex(realCellsFoundInRange, cellN) == -1)
+                    {
+                        realCellsFoundInRange.append(cellN);
+                    }
+                }
+            }
+        }
+
+        forAll(molCloud_.realPointsWithinRCutMaxOfAnyReferringPatch(), rCP)
+        {
+            const label p
+            (
+                molCloud_.realPointsWithinRCutMaxOfAnyReferringPatch()[rCP]
+            );
+
+            if (molCloud_.testPointFaceDistance(p,refCell))
+            {
+                const labelList& pCells(mesh.pointCells()[p]);
+
+                forAll(pCells, pC)
+                {
+                    const label cellI(pCells[pC]);
+
+                    if (findIndex(realCellsFoundInRange, cellI) == -1)
+                    {
+                        realCellsFoundInRange.append(cellI);
+                    }
+                }
+            }
+        }
+
+
+        const edgeList& refCellEdges = refCell.edges();
+
+        forAll(molCloud_.realEdgesWithinRCutMaxOfAnyReferringPatch(), rCE)
+        {
+            const label edgeIIndex
+            (
+                molCloud_.realEdgesWithinRCutMaxOfAnyReferringPatch()[rCE]
+            );
+
+            const edge& eI(mesh.edges()[edgeIIndex]);
+
+            forAll(refCellEdges, rCE)
+            {
+                const edge& eJ(refCellEdges[rCE]);
+
+                if
+                (
+                    molCloud_.testEdgeEdgeDistance
+                    (
+                        eI,
+                        refCellPoints[eJ.start()],
+                        refCellPoints[eJ.end()]
+                    )
+                )
+                {
+                    const labelList& eICells(mesh.edgeCells()[edgeIIndex]);
+
+                    forAll(eICells, eIC)
+                    {
+                        const label cellI(eICells[eIC]);
+
+                        if (findIndex(realCellsFoundInRange, cellI) == -1)
+                        {
+                            realCellsFoundInRange.append(cellI);
+                        }
+                    }
+                }
+            }
+        }
+
+//         scalar rCutMaxSqr = molCloud_.rCutMax()*molCloud_.rCutMax();
+//
+//         forAll (molCloud_.mesh().points(), pointIIndex)
+//         {
+//             const point& ptI
+//             (
+//                 molCloud_.mesh().points()[pointIIndex]
+//             );
+//
+//             forAll(refCellPoints, rCP)
+//             {
+//                 if (magSqr(ptI - refCellPoints[rCP]) <= rCutMaxSqr)
+//                 {
+//                     const labelList& ptICells
+//                     (
+//                         molCloud_.mesh().pointCells()[pointIIndex]
+//                     );
+//
+//                     forAll(ptICells, pIC)
+//                     {
+//                         const label cellI(ptICells[pIC]);
+//
+//                         if(findIndex(realCellsFoundInRange, cellI) == -1)
+//                         {
+//                             realCellsFoundInRange.append(cellI);
+//                         }
+//                     }
+//                 }
+//             }
+//         }
+
+        refCell.realCells() = realCellsFoundInRange.shrink();
+    }
+}
+
+
+void referredCellList::referMolecules()
+{
+    // Create referred molecules for sending using cell occupancy and
+    // cellSendingReferralLists
+
+    const List<DynamicList<molecule*> >& cellOccupancy
+    (
+        molCloud_.cellOccupancy()
+    );
+
+    forAll(molCloud_.cellSendingReferralLists(), cSRL)
+    {
+        const sendingReferralList& sRL
+        (
+            molCloud_.cellSendingReferralLists()[cSRL]
+        );
+
+        List<DynamicList<referredMolecule> > molsToReferOut(sRL.size());
+
+        forAll(sRL, sRLI)
+        {
+            List<molecule*> realMols = cellOccupancy[sRL[sRLI]];
+
+            forAll (realMols, rM)
+            {
+                molecule* mol = realMols[rM];
+
+                molsToReferOut[sRLI].append
+                (
+                    referredMolecule
+                    (
+                        mol->id(),
+                        mol->position()
+                    )
+                );
+            }
+
+            molsToReferOut[sRLI].shrink();
+        }
+
+        // Send lists of referred molecules to other processors
+
+        if (sRL.destinationProc() != Pstream::myProcNo())
+        {
+            if (Pstream::parRun())
+            {
+                OPstream toInteractingProc
+                (
+                    Pstream::blocking,
+                    sRL.destinationProc()
+                );
+
+                toInteractingProc << molsToReferOut;
+            }
+        }
+        else
+        {
+            // Refer molecules directly for referred cells on the same
+            // processor.
+
+            const receivingReferralList& rRL
+            (
+                molCloud_.cellReceivingReferralLists()[cSRL]
+            );
+
+            forAll(rRL, rRLI)
+            {
+                forAll(rRL[rRLI], rC)
+                {
+                    referredCell& refCellToRefMolsTo = (*this)[rRL[rRLI][rC]];
+
+                    refCellToRefMolsTo.referInMols(molsToReferOut[rRLI]);
+                }
+            }
+        }
+    }
+
+    // Receive referred molecule lists to and distribute to referredCells
+    // according tocellReceivingReferralLists, referredCells deal with the
+    // transformations themselves
+
+    forAll(molCloud_.cellReceivingReferralLists(), cRRL)
+    {
+        const receivingReferralList& rRL
+        (
+            molCloud_.cellReceivingReferralLists()[cRRL]
+        );
+
+        List<List<referredMolecule> > molsToReferIn(rRL.size());
+
+        if (rRL.sourceProc() != Pstream::myProcNo())
+        {
+            if (Pstream::parRun())
+            {
+                IPstream fromInteractingProc
+                (
+                    Pstream::blocking,
+                    rRL.sourceProc()
+                );
+
+                fromInteractingProc >> molsToReferIn;
+            }
+
+            forAll(rRL, rRLI)
+            {
+                forAll(rRL[rRLI], rC)
+                {
+                    referredCell& refCellToRefMolsTo = (*this)[rRL[rRLI][rC]];
+
+                    refCellToRefMolsTo.referInMols(molsToReferIn[rRLI]);
+                }
+            }
+        }
+    }
+}
+
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+} // End namespace Foam
+
+// ************************************************************************* //
diff --git a/src/lagrangian/molecularDynamics/molecule/referredCellList/referredCellList.H b/src/lagrangian/molecularDynamics/molecule/referredCellList/referredCellList.H
new file mode 100755
index 0000000000..c025de52eb
--- /dev/null
+++ b/src/lagrangian/molecularDynamics/molecule/referredCellList/referredCellList.H
@@ -0,0 +1,103 @@
+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+   \\    /   O peration     |
+    \\  /    A nd           | Copyright (C) 1991-2005 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::referredCellList
+
+Description
+
+SourceFiles
+    referredCellListI.H
+    referredCellList.C
+
+\*---------------------------------------------------------------------------*/
+
+#ifndef referredCellList_H
+#define referredCellList_H
+
+#include "referredCell.H"
+#include "molecule.H"
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+namespace Foam
+{
+
+/*---------------------------------------------------------------------------*\
+                        Class referredCellList Declaration
+\*---------------------------------------------------------------------------*/
+
+class referredCellList
+:
+    public List< referredCell >
+{
+    // Private data
+
+        moleculeCloud& molCloud_;
+
+
+public:
+
+    // Constructors
+
+        //- Construct from moleculeCloud
+        referredCellList(moleculeCloud& molCloud);
+
+        //- Construct from components
+        referredCellList
+        (
+            moleculeCloud& molCloud,
+            const List<referredCell>& referredCells,
+            const List<label>& realCells
+        );
+
+
+    // Destructor
+
+        ~referredCellList();
+
+
+    // Member Functions
+
+        void setRealCellsInRange();
+
+        void referMolecules();
+
+        inline const moleculeCloud& molCloud();
+};
+
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+} // End namespace Foam
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+#include "referredCellListI.H"
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+#endif
+
+// ************************************************************************* //
diff --git a/src/lagrangian/molecularDynamics/molecule/referredCellList/referredCellListI.H b/src/lagrangian/molecularDynamics/molecule/referredCellList/referredCellListI.H
new file mode 100755
index 0000000000..34767d88b6
--- /dev/null
+++ b/src/lagrangian/molecularDynamics/molecule/referredCellList/referredCellListI.H
@@ -0,0 +1,42 @@
+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+   \\    /   O peration     |
+    \\  /    A nd           | Copyright (C) 1991-2005 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
+{
+
+// * * * * * * * * * * * * * * * Member Operators  * * * * * * * * * * * * * //
+
+inline const Foam::moleculeCloud& Foam::referredCellList::molCloud()
+{
+    return molCloud_;
+}
+
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+} // End namespace Foam
+
+// ************************************************************************* //
diff --git a/src/lagrangian/molecularDynamics/molecule/referredMolecule/referredMolecule.C b/src/lagrangian/molecularDynamics/molecule/referredMolecule/referredMolecule.C
new file mode 100755
index 0000000000..2453ca2f58
--- /dev/null
+++ b/src/lagrangian/molecularDynamics/molecule/referredMolecule/referredMolecule.C
@@ -0,0 +1,89 @@
+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+   \\    /   O peration     |
+    \\  /    A nd           | Copyright (C) 1991-2005 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 "referredMolecule.H"
+
+namespace Foam
+{
+
+// * * * * * * * * * * * * * * * * Constructors  * * * * * * * * * * * * * * //
+
+referredMolecule::referredMolecule()
+{}
+
+
+referredMolecule::referredMolecule
+(
+    const label id,
+    const vector& position
+)
+:
+    id_(id),
+    position_(position)
+{}
+
+
+// * * * * * * * * * * * * * * * * Destructor  * * * * * * * * * * * * * * * //
+
+referredMolecule::~referredMolecule()
+{}
+
+
+// * * * * * * * * * * * * * * * Friend Operators  * * * * * * * * * * * * * //
+
+Istream& operator>>
+(
+    Istream& is,
+    referredMolecule& rM
+)
+{
+    is >> rM.id_ >> rM.position_;
+
+    is.check("Istream& operator<<(Istream& f, const referredMolecule& sRL");
+
+    return is;
+}
+
+
+Ostream& operator<<
+(
+    Ostream& os,
+    const referredMolecule& rM
+)
+{
+    os << rM.id() << token::SPACE << rM.position();
+
+    os.check("Ostream& operator<<(Ostream& f, const referredMolecule& rM");
+
+    return os;
+}
+
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+} // End namespace Foam
+
+// ************************************************************************* //
diff --git a/src/lagrangian/molecularDynamics/molecule/referredMolecule/referredMolecule.H b/src/lagrangian/molecularDynamics/molecule/referredMolecule/referredMolecule.H
new file mode 100755
index 0000000000..fcac7925a9
--- /dev/null
+++ b/src/lagrangian/molecularDynamics/molecule/referredMolecule/referredMolecule.H
@@ -0,0 +1,129 @@
+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+   \\    /   O peration     |
+    \\  /    A nd           | Copyright (C) 1991-2005 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::referredMolecule
+
+Description
+
+SourceFiles
+    referredMoleculeI.H
+    referredMolecule.C
+
+\*---------------------------------------------------------------------------*/
+
+#ifndef referredMolecule_H
+#define referredMolecule_H
+
+#include "vector.H"
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+namespace Foam
+{
+/*---------------------------------------------------------------------------*\
+                           Class referredMolecule Declaration
+\*---------------------------------------------------------------------------*/
+
+class referredMolecule
+{
+    // Private data
+
+        label id_;
+
+        vector position_;
+
+
+public:
+
+    // Constructors
+
+        //- Construct null
+        referredMolecule();
+
+        //- Construct from components
+        referredMolecule
+        (
+            const label id,
+            const vector& position
+        );
+
+
+    // Destructor
+
+        virtual ~referredMolecule();
+
+
+    // Member Functions
+
+        // Access
+
+            inline label id() const;
+
+            inline const vector& position() const;
+
+
+    // Friend Operators
+
+        inline friend bool operator==
+        (
+            const referredMolecule& a,
+            const referredMolecule& b
+        );
+
+        inline friend bool operator!=
+        (
+            const referredMolecule& a,
+            const referredMolecule& b
+        );
+
+    // IOstream Operators
+
+        friend Istream& operator>>
+        (
+            Istream&,
+            referredMolecule&
+        );
+
+        friend Ostream& operator<<
+        (
+            Ostream&,
+            const referredMolecule&
+        );
+};
+
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+} // End namespace Foam
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+#include "referredMoleculeI.H"
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+#endif
+
+// ************************************************************************* //
diff --git a/src/lagrangian/molecularDynamics/molecule/referredMolecule/referredMoleculeI.H b/src/lagrangian/molecularDynamics/molecule/referredMolecule/referredMoleculeI.H
new file mode 100755
index 0000000000..b51b56035d
--- /dev/null
+++ b/src/lagrangian/molecularDynamics/molecule/referredMolecule/referredMoleculeI.H
@@ -0,0 +1,75 @@
+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+   \\    /   O peration     |
+    \\  /    A nd           | Copyright (C) 1991-2005 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
+{
+
+// * * * * * * * * * * * * * * * Member Functions  * * * * * * * * * * * * * //
+
+inline label referredMolecule::id() const
+{
+    return id_;
+}
+
+
+inline const vector& referredMolecule::position() const
+{
+    return position_;
+}
+
+
+// * * * * * * * * * * * * * * * Friend Operators  * * * * * * * * * * * * * //
+
+inline bool operator==
+(
+    const referredMolecule& a,
+    const referredMolecule& b
+)
+{
+    return
+    (
+        a.id() == b.id()
+     && a.position() == b.position()
+    );
+}
+
+
+inline bool operator!=
+(
+    const referredMolecule& a,
+    const referredMolecule& b
+)
+{
+    return !(a == b);
+}
+
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+} // End namespace Foam
+
+
+// ************************************************************************* //
diff --git a/src/lagrangian/molecularDynamics/molecule/tetherPotential/tetherPotential.C b/src/lagrangian/molecularDynamics/molecule/tetherPotential/tetherPotential.C
new file mode 100755
index 0000000000..46c097b36d
--- /dev/null
+++ b/src/lagrangian/molecularDynamics/molecule/tetherPotential/tetherPotential.C
@@ -0,0 +1,94 @@
+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+   \\    /   O peration     |
+    \\  /    A nd           | Copyright (C) 1991-2005 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 "tetherPotential.H"
+
+namespace Foam
+{
+
+// * * * * * * * * * * * * * * * * Constructors  * * * * * * * * * * * * * * //
+
+tetherPotential::tetherPotential()
+{}
+
+
+tetherPotential::tetherPotential
+(
+    const word& tetherPotentialName,
+    const word& tetherPotentialType,
+    const scalar springConstant
+)
+:
+    tetherPotentialName_(tetherPotentialName),
+    tetherPotentialType_(tetherPotentialType),
+    springConstant_(springConstant)
+{}
+
+
+// * * * * * * * * * * * * * * * * Destructor  * * * * * * * * * * * * * * * //
+
+tetherPotential::~tetherPotential()
+{}
+
+
+// * * * * * * * * * * * * * * * Member Functions  * * * * * * * * * * * * * //
+
+void tetherPotential::write(Ostream& os) const
+{
+    os << tetherPotentialName_
+       << nl << tetherPotentialType_
+       << nl << springConstant_
+       << endl;
+}
+
+
+scalar tetherPotential::force(const scalar rITMag) const
+{
+    return -springConstant_ * rITMag;
+}
+
+
+scalar tetherPotential::energy(const scalar rITMag) const
+{
+    return 0.5*springConstant_*rITMag*rITMag;
+}
+
+
+// * * * * * * * * * * * * * * * Friend Functions  * * * * * * * * * * * * * //
+
+Ostream& operator<<(Ostream& os, const tetherPotential& pot)
+{
+    pot.write(os);
+    os.check("Ostream& operator<<(Ostream& f, const tetherPotential& pot");
+    return os;
+}
+
+
+// * * * * * * * * * * * * * * * Friend Operators  * * * * * * * * * * * * * //
+
+} // End namespace Foam
+
+// ************************************************************************* //
diff --git a/src/lagrangian/molecularDynamics/molecule/tetherPotential/tetherPotential.H b/src/lagrangian/molecularDynamics/molecule/tetherPotential/tetherPotential.H
new file mode 100755
index 0000000000..afa9a35e69
--- /dev/null
+++ b/src/lagrangian/molecularDynamics/molecule/tetherPotential/tetherPotential.H
@@ -0,0 +1,125 @@
+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+   \\    /   O peration     |
+    \\  /    A nd           | Copyright (C) 1991-2005 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::tetherPotential
+
+Description
+
+SourceFiles
+    tetherPotentialI.H
+    tetherPotential.C
+
+\*---------------------------------------------------------------------------*/
+
+#ifndef tetherPotential_H
+#define tetherPotential_H
+
+#include "vector.H"
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+namespace Foam
+{
+
+/*---------------------------------------------------------------------------*\
+                       Class tetherPotential Declaration
+\*---------------------------------------------------------------------------*/
+
+class tetherPotential
+{
+    // Private data
+
+        // At the moment this is hard coded to be a "harmonicSpring"
+        // potential.  In future use templated classes virtual functions,
+        // function pointers and all kinds of good stuff to make this a
+        // generic tether force,
+
+        word tetherPotentialName_;
+
+        word tetherPotentialType_;
+
+        scalar springConstant_;
+
+
+public:
+
+    // Constructors
+
+        //- Construct null
+        tetherPotential();
+
+        //- Construct from components
+        tetherPotential
+        (
+            const word& tetherPotentialName,
+            const word& tetherPotentialType,
+            const scalar springConstant_
+        );
+
+
+    // Destructor
+
+        virtual ~tetherPotential();
+
+
+    // Member Functions
+
+        // Access
+
+            inline const word& tetherPotentialName() const;
+
+            inline const word& tetherPotentialType() const;
+
+            inline scalar springConstant() const;
+
+            scalar force(const scalar rITMag) const;
+
+            scalar energy(const scalar rITMag) const;
+
+
+        // Write
+
+            virtual void write(Ostream&) const;
+
+
+    // IOstream Operators
+
+        friend Ostream& operator<<(Ostream&, const tetherPotential&);
+};
+
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+} // End namespace Foam
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+#include "tetherPotentialI.H"
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+#endif
+
+// ************************************************************************* //
diff --git a/src/lagrangian/molecularDynamics/molecule/tetherPotential/tetherPotentialI.H b/src/lagrangian/molecularDynamics/molecule/tetherPotential/tetherPotentialI.H
new file mode 100755
index 0000000000..d9ca0dae1a
--- /dev/null
+++ b/src/lagrangian/molecularDynamics/molecule/tetherPotential/tetherPotentialI.H
@@ -0,0 +1,56 @@
+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+   \\    /   O peration     |
+    \\  /    A nd           | Copyright (C) 1991-2005 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
+{
+
+// * * * * * * * * * * * * * * * Member Functions  * * * * * * * * * * * * * //
+
+inline const word& tetherPotential::tetherPotentialName() const
+{
+    return tetherPotentialName_;
+}
+
+
+inline const word& tetherPotential::tetherPotentialType() const
+{
+    return tetherPotentialType_;
+}
+
+
+inline scalar tetherPotential::springConstant() const
+{
+    return springConstant_;
+}
+
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+} // End namespace Foam
+
+// ************************************************************************* //
diff --git a/src/lagrangian/molecularDynamics/molecule/tetherPotential/tetherPotentialList.C b/src/lagrangian/molecularDynamics/molecule/tetherPotential/tetherPotentialList.C
new file mode 100755
index 0000000000..ac32daf60f
--- /dev/null
+++ b/src/lagrangian/molecularDynamics/molecule/tetherPotential/tetherPotentialList.C
@@ -0,0 +1,146 @@
+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+   \\    /   O peration     |
+    \\  /    A nd           | Copyright (C) 1991-2005 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 "tetherPotentialList.H"
+
+namespace Foam
+{
+
+// * * * * * * * * * * * * * Private Member Functions  * * * * * * * * * * * //
+
+label tetherPotentialList::tetherPotentialIndex(const label a)
+{
+    label index(findIndex(tetherIds_,a));
+
+    if (index == -1)
+    {
+        FatalErrorIn
+        (
+            "Foam::tetherPotentialList::tetherPotentialIndex(const label a)"
+        )
+            << "Attempting to access a tetherPotential with an unknown id"
+            << abort(FatalError);
+
+        return 0;
+    }
+    else
+    {
+        return index;
+    }
+}
+
+
+// * * * * * * * * * * * * * * * * Constructors  * * * * * * * * * * * * * * //
+
+Foam::tetherPotentialList::tetherPotentialList()
+:
+    List<tetherPotential> ()
+{}
+
+
+Foam::tetherPotentialList::tetherPotentialList
+(
+    const List<label> tetherIds
+)
+:
+    List<tetherPotential> (tetherIds.size()),
+    tetherIds_(tetherIds_)
+{}
+
+
+// * * * * * * * * * * * * * * * * Destructor  * * * * * * * * * * * * * * * //
+
+tetherPotentialList::~tetherPotentialList()
+{}
+
+
+// * * * * * * * * * * * * * * * Member Functions  * * * * * * * * * * * * * //
+
+void tetherPotentialList::setSizeAndTetherIds (const List<label>& tetherIds)
+{
+    tetherIds_ = tetherIds;
+    setSize(tetherIds.size());
+}
+
+
+void tetherPotentialList::addPotential
+(
+    const label a,
+    const tetherPotential& pot
+)
+{
+        (*this)[tetherPotentialIndex (a)] = pot;
+}
+
+
+tetherPotential& tetherPotentialList::tetherPotentialFunction (const label a)
+{
+    return (*this)[tetherPotentialIndex (a)];
+}
+
+
+scalar tetherPotentialList::force (const label a, const scalar rITMag)
+{
+    scalar f = (*this)[tetherPotentialIndex (a)].force(rITMag);
+
+    return f;
+}
+
+
+scalar tetherPotentialList::energy (const label a, const scalar rITMag)
+{
+    scalar e = (*this)[tetherPotentialIndex (a)].energy(rITMag);
+
+    return e;
+}
+
+
+// * * * * * * * * * * * * * * * Member Operators  * * * * * * * * * * * * * //
+
+void tetherPotentialList::operator=(const tetherPotentialList& rhs)
+{
+    // Check for assignment to self
+    if (this == &rhs)
+    {
+        FatalErrorIn
+        (
+            "Foam::tetherPotentialList::operator="
+            "(const Foam::tetherPotentialList&)"
+        )   << "Attempted assignment to self"
+            << abort(FatalError);
+    }
+
+    List<tetherPotential>::operator=(rhs);
+
+    tetherIds_ = rhs.tetherIds();
+}
+
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+} // End namespace Foam
+
+// ************************************************************************* //
diff --git a/src/lagrangian/molecularDynamics/molecule/tetherPotential/tetherPotentialList.H b/src/lagrangian/molecularDynamics/molecule/tetherPotential/tetherPotentialList.H
new file mode 100755
index 0000000000..ebd24e57f0
--- /dev/null
+++ b/src/lagrangian/molecularDynamics/molecule/tetherPotential/tetherPotentialList.H
@@ -0,0 +1,125 @@
+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+   \\    /   O peration     |
+    \\  /    A nd           | Copyright (C) 1991-2005 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::tetherPotentialList
+
+Description
+
+SourceFiles
+    tetherPotentialListI.H
+    tetherPotentialList.C
+
+\*---------------------------------------------------------------------------*/
+
+#ifndef tetherPotentialList_H
+#define tetherPotentialList_H
+
+#include "ListOps.H"
+#include "tetherPotential.H"
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+namespace Foam
+{
+
+/*---------------------------------------------------------------------------*\
+                      Class tetherPotentialList Declaration
+\*---------------------------------------------------------------------------*/
+
+class tetherPotentialList
+:
+    public List<tetherPotential>
+{
+    // Private data
+
+        List<label> tetherIds_;
+
+
+    // Private Member Functions
+
+        label tetherPotentialIndex(const label a);
+
+        //- Disallow default bitwise copy construct
+        tetherPotentialList(const tetherPotentialList&);
+
+
+public:
+
+    // Constructors
+
+        //- Construct null
+        tetherPotentialList();
+
+        //- Construct from list of tetherIDs
+        tetherPotentialList(const List<label> tetherIds);
+
+
+    // Destructor
+
+        ~tetherPotentialList();
+
+
+    // Member Functions
+
+        // Access
+
+            inline const List<label>& tetherIds() const;
+
+            inline label nTetherPotentials() const;
+
+            void setSizeAndTetherIds (const List<label>&);
+
+            void addPotential
+            (
+                const label a,
+                const tetherPotential& pot
+            );
+
+            tetherPotential& tetherPotentialFunction (const label a);
+
+            scalar force (const label a, const scalar rITMag);
+
+            scalar energy (const label a, const scalar rITMag);
+
+
+    // Member Operators
+
+        void operator=(const tetherPotentialList&);
+};
+
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+} // End namespace Foam
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+#include "tetherPotentialListI.H"
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+#endif
+
+// ************************************************************************* //
diff --git a/src/lagrangian/molecularDynamics/molecule/tetherPotential/tetherPotentialListI.H b/src/lagrangian/molecularDynamics/molecule/tetherPotential/tetherPotentialListI.H
new file mode 100755
index 0000000000..4f89783918
--- /dev/null
+++ b/src/lagrangian/molecularDynamics/molecule/tetherPotential/tetherPotentialListI.H
@@ -0,0 +1,50 @@
+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+   \\    /   O peration     |
+    \\  /    A nd           | Copyright (C) 1991-2005 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
+{
+
+// * * * * * * * * * * * * * * * Member Functions  * * * * * * * * * * * * * //
+
+inline const List<label>& tetherPotentialList::tetherIds() const
+{
+    return tetherIds_;
+}
+
+
+inline label tetherPotentialList::nTetherPotentials() const
+{
+    return tetherIds_.size();
+}
+
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+} // End namespace Foam
+
+// ************************************************************************* //
diff --git a/src/lagrangian/molecularDynamics/potential/Make/files b/src/lagrangian/molecularDynamics/potential/Make/files
new file mode 100644
index 0000000000..43cf0bb737
--- /dev/null
+++ b/src/lagrangian/molecularDynamics/potential/Make/files
@@ -0,0 +1,35 @@
+pairPotential = pairPotential
+
+$(pairPotential)/pairPotentialList/pairPotentialList.C
+
+$(pairPotential)/basic/pairPotential.C
+$(pairPotential)/basic/pairPotentialIO.C
+$(pairPotential)/basic/newPairPotential.C
+
+$(pairPotential)/derived/lennardJones/lennardJones.C
+$(pairPotential)/derived/maitlandSmith/maitlandSmith.C
+$(pairPotential)/derived/azizChen/azizChen.C
+
+energyScalingFunction = energyScalingFunction
+
+$(energyScalingFunction)/basic/energyScalingFunction.C
+$(energyScalingFunction)/basic/newEnergyScalingFunction.C
+
+$(energyScalingFunction)/derived/shifted/shifted.C
+$(energyScalingFunction)/derived/shiftedForce/shiftedForce.C
+$(energyScalingFunction)/derived/noScaling/noScaling.C
+$(energyScalingFunction)/derived/sigmoid/sigmoid.C
+$(energyScalingFunction)/derived/doubleSigmoid/doubleSigmoid.C
+
+tetherPotential = tetherPotential
+
+$(tetherPotential)/tetherPotentialList/tetherPotentialList.C
+
+$(tetherPotential)/basic/tetherPotential.C
+$(tetherPotential)/basic/newTetherPotential.C
+
+$(tetherPotential)/derived/harmonicSpring/harmonicSpring.C
+$(tetherPotential)/derived/restrainedHarmonicSpring/restrainedHarmonicSpring.C
+
+LIB = $(FOAM_LIBBIN)/libpotential
+
diff --git a/src/lagrangian/molecularDynamics/potential/Make/options b/src/lagrangian/molecularDynamics/potential/Make/options
new file mode 100644
index 0000000000..a412632ebb
--- /dev/null
+++ b/src/lagrangian/molecularDynamics/potential/Make/options
@@ -0,0 +1,6 @@
+EXE_INC = \
+    -I.. \
+    -I$(LIB_SRC)/finiteVolume/lnInclude
+
+LIB_LIBS = \
+    -lfiniteVolume
diff --git a/src/lagrangian/molecularDynamics/potential/energyScalingFunction/basic/energyScalingFunction.C b/src/lagrangian/molecularDynamics/potential/energyScalingFunction/basic/energyScalingFunction.C
new file mode 100644
index 0000000000..1ebd4b4005
--- /dev/null
+++ b/src/lagrangian/molecularDynamics/potential/energyScalingFunction/basic/energyScalingFunction.C
@@ -0,0 +1,76 @@
+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  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
+    energyScalingFunction
+
+\*---------------------------------------------------------------------------*/
+
+#include "energyScalingFunction.H"
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+namespace Foam
+{
+
+// * * * * * * * * * * * * * * Static Data Members * * * * * * * * * * * * * //
+
+defineTypeNameAndDebug(energyScalingFunction, 0);
+defineRunTimeSelectionTable(energyScalingFunction, dictionary);
+
+// * * * * * * * * * * * * * Private Member Functions  * * * * * * * * * * * //
+
+// * * * * * * * * * * * * * * * * Constructors  * * * * * * * * * * * * * * //
+
+Foam::energyScalingFunction::energyScalingFunction
+(
+    const word& name,
+    const dictionary& energyScalingFunctionProperties,
+    const pairPotential& pairPot
+)
+:
+    name_(name),
+    energyScalingFunctionProperties_(energyScalingFunctionProperties),
+    pairPot_(pairPot)
+{}
+
+
+// * * * * * * * * * * * * * * Member Functions  * * * * * * * * * * * * * * //
+
+
+bool Foam::energyScalingFunction::read
+(
+    const dictionary& energyScalingFunctionProperties
+)
+{
+    energyScalingFunctionProperties_ = energyScalingFunctionProperties;
+
+    return true;
+}
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+} // End namespace Foam
+
+// ************************************************************************* //
diff --git a/src/lagrangian/molecularDynamics/potential/energyScalingFunction/basic/energyScalingFunction.H b/src/lagrangian/molecularDynamics/potential/energyScalingFunction/basic/energyScalingFunction.H
new file mode 100644
index 0000000000..e2f38b2a83
--- /dev/null
+++ b/src/lagrangian/molecularDynamics/potential/energyScalingFunction/basic/energyScalingFunction.H
@@ -0,0 +1,149 @@
+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  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
+    energyScalingFunction
+
+Description
+
+SourceFiles
+    energyScalingFunction.C
+    newEnergyScalingFunction.C
+
+\*---------------------------------------------------------------------------*/
+
+#ifndef energyScalingFunction_H
+#define energyScalingFunction_H
+
+#include "IOdictionary.H"
+#include "typeInfo.H"
+#include "runTimeSelectionTables.H"
+#include "autoPtr.H"
+#include "pairPotential.H"
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+namespace Foam
+{
+
+/*---------------------------------------------------------------------------*\
+                Class energyScalingFunction Declaration
+\*---------------------------------------------------------------------------*/
+
+class energyScalingFunction
+{
+
+protected:
+
+    // Protected data
+
+        word name_;
+        
+        dictionary energyScalingFunctionProperties_;
+
+        const pairPotential& pairPot_;
+
+    // Private Member Functions
+
+        //- Disallow copy construct
+        energyScalingFunction(const energyScalingFunction&);
+
+        //- Disallow default bitwise assignment
+        void operator=(const energyScalingFunction&);
+
+public:
+
+    //- Runtime type information
+    TypeName("energyScalingFunction");
+
+
+    // Declare run-time constructor selection table
+
+        declareRunTimeSelectionTable
+        (
+            autoPtr,
+            energyScalingFunction,
+            dictionary,
+            (
+                const word& name,
+                const dictionary& energyScalingFunctionProperties,
+                const pairPotential& pairPot
+            ),
+            (name, energyScalingFunctionProperties, pairPot)
+        );
+
+
+    // Selectors
+
+        //- Return a reference to the selected viscosity model
+        static autoPtr<energyScalingFunction> New
+        (
+            const word& name,
+            const dictionary& energyScalingFunctionProperties,
+            const pairPotential& pairPot
+        );
+
+
+    // Constructors
+
+        //- Construct from components
+        energyScalingFunction
+        (
+            const word& name,
+            const dictionary& energyScalingFunctionProperties,
+            const pairPotential& pairPot
+        );
+
+
+    // Destructor
+
+        virtual ~energyScalingFunction()
+        {}
+
+
+    // Member Functions
+
+        virtual void scaleEnergy(scalar& e, const scalar r) const = 0;
+
+        const dictionary& energyScalingFunctionProperties() const
+        {
+            return energyScalingFunctionProperties_;
+        }
+
+        //- Read energyScalingFunction dictionary
+        virtual bool read(const dictionary& energyScalingFunctionProperties) = 0;
+};
+
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+} // End namespace Foam
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+#endif
+
+// ************************************************************************* //
diff --git a/src/lagrangian/molecularDynamics/potential/energyScalingFunction/basic/newEnergyScalingFunction.C b/src/lagrangian/molecularDynamics/potential/energyScalingFunction/basic/newEnergyScalingFunction.C
new file mode 100644
index 0000000000..bb8153a383
--- /dev/null
+++ b/src/lagrangian/molecularDynamics/potential/energyScalingFunction/basic/newEnergyScalingFunction.C
@@ -0,0 +1,79 @@
+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  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
+    energyScalingFunction
+
+\*---------------------------------------------------------------------------*/
+
+#include "energyScalingFunction.H"
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+namespace Foam
+{
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+autoPtr<energyScalingFunction> energyScalingFunction::New
+(
+    const word& name,
+    const dictionary& energyScalingFunctionProperties,
+    const pairPotential& pairPot
+)
+{
+    word energyScalingFunctionTypeName
+    (
+        energyScalingFunctionProperties.lookup("energyScalingFunction")
+    );
+
+    Info<< "Selecting energy scaling function "
+        << energyScalingFunctionTypeName << " for "
+        << name << " potential energy." << endl;
+
+    dictionaryConstructorTable::iterator cstrIter =
+        dictionaryConstructorTablePtr_->find(energyScalingFunctionTypeName);
+
+    if (cstrIter == dictionaryConstructorTablePtr_->end())
+    {
+        FatalErrorIn
+        (
+            "energyScalingFunction::New()"
+        )   << "Unknown energyScalingFunction type "
+            << energyScalingFunctionTypeName << endl << endl
+            << "Valid  energyScalingFunctions are : " << endl
+            << dictionaryConstructorTablePtr_->toc()
+            << exit(FatalError);
+    }
+
+    return autoPtr<energyScalingFunction>
+        (cstrIter()(name, energyScalingFunctionProperties, pairPot));
+}
+
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+} // End namespace Foam
+
+// ************************************************************************* //
diff --git a/src/lagrangian/molecularDynamics/potential/energyScalingFunction/derived/doubleSigmoid/doubleSigmoid.C b/src/lagrangian/molecularDynamics/potential/energyScalingFunction/derived/doubleSigmoid/doubleSigmoid.C
new file mode 100644
index 0000000000..63fabd6ad9
--- /dev/null
+++ b/src/lagrangian/molecularDynamics/potential/energyScalingFunction/derived/doubleSigmoid/doubleSigmoid.C
@@ -0,0 +1,104 @@
+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  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 "doubleSigmoid.H"
+#include "addToRunTimeSelectionTable.H"
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+namespace Foam
+{
+namespace energyScalingFunctions
+{
+
+// * * * * * * * * * * * * * * Static Data Members * * * * * * * * * * * * * //
+
+defineTypeNameAndDebug(doubleSigmoid, 0);
+
+addToRunTimeSelectionTable
+(
+    energyScalingFunction,
+    doubleSigmoid,
+    dictionary
+);
+
+// * * * * * * * * * * * * Private Member Functions  * * * * * * * * * * * * //
+
+scalar doubleSigmoid::sigmoidScale
+    (
+        const scalar r,
+        const scalar shift,
+        const scalar scale
+    ) const
+{
+    return 1.0 / (1.0 + exp( scale * (r - shift)));
+}
+
+// * * * * * * * * * * * * * * * * Constructors  * * * * * * * * * * * * * * //
+
+doubleSigmoid::doubleSigmoid
+(
+    const word& name,
+    const dictionary& energyScalingFunctionProperties,
+    const pairPotential& pairPot
+)
+:
+    energyScalingFunction(name, energyScalingFunctionProperties, pairPot),
+    doubleSigmoidCoeffs_(energyScalingFunctionProperties.subDict(typeName + "Coeffs")),
+    shift1_(readScalar(doubleSigmoidCoeffs_.lookup("shift1"))),
+    scale1_(readScalar(doubleSigmoidCoeffs_.lookup("scale1"))),
+    shift2_(readScalar(doubleSigmoidCoeffs_.lookup("shift2"))),
+    scale2_(readScalar(doubleSigmoidCoeffs_.lookup("scale2")))
+{}
+
+// * * * * * * * * * * * * * * Member Functions  * * * * * * * * * * * * * * //
+
+void doubleSigmoid::scaleEnergy(scalar& e, const scalar r) const
+{
+    e *= sigmoidScale(r, shift1_, scale1_) * sigmoidScale(r, shift2_, scale2_);
+}
+
+bool doubleSigmoid::read(const dictionary& energyScalingFunctionProperties)
+{
+    energyScalingFunction::read(energyScalingFunctionProperties);
+
+    doubleSigmoidCoeffs_ = energyScalingFunctionProperties.subDict(typeName + "Coeffs");
+
+    doubleSigmoidCoeffs_.lookup("shift1") >> shift1_;
+    doubleSigmoidCoeffs_.lookup("scale1") >> scale1_;
+    doubleSigmoidCoeffs_.lookup("shift2") >> shift2_;
+    doubleSigmoidCoeffs_.lookup("scale2") >> scale2_;
+    
+    return true;
+}
+
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+} // End namespace energyScalingFunctions
+} // End namespace Foam
+
+// ************************************************************************* //
diff --git a/src/lagrangian/molecularDynamics/potential/energyScalingFunction/derived/doubleSigmoid/doubleSigmoid.H b/src/lagrangian/molecularDynamics/potential/energyScalingFunction/derived/doubleSigmoid/doubleSigmoid.H
new file mode 100644
index 0000000000..38dba03a92
--- /dev/null
+++ b/src/lagrangian/molecularDynamics/potential/energyScalingFunction/derived/doubleSigmoid/doubleSigmoid.H
@@ -0,0 +1,114 @@
+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  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
+    doubleSigmoid
+
+Description
+     
+
+SourceFiles
+    doubleSigmoid.C
+
+\*---------------------------------------------------------------------------*/
+
+#ifndef doubleSigmoid_H
+#define doubleSigmoid_H
+
+#include "energyScalingFunction.H"
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+namespace Foam
+{
+namespace energyScalingFunctions
+{
+
+/*---------------------------------------------------------------------------*\
+                           Class doubleSigmoid Declaration
+\*---------------------------------------------------------------------------*/
+
+class doubleSigmoid
+:
+    public energyScalingFunction
+{
+    // Private data
+        
+        dictionary doubleSigmoidCoeffs_;
+
+        scalar shift1_;
+        scalar scale1_;
+        scalar shift2_;
+        scalar scale2_;
+        
+    // Private Member Functions
+
+        scalar sigmoidScale
+        (
+            const scalar r,
+            const scalar shift,
+            const scalar scale
+        ) const;
+
+public:
+
+    //- Runtime type information
+    TypeName("doubleSigmoid");
+
+
+    // Constructors
+
+        //- Construct from components
+        doubleSigmoid
+        (
+            const word& name,
+            const dictionary& energyScalingFunctionProperties,
+            const pairPotential& pairPot
+        );
+
+
+    // Destructor
+
+        ~doubleSigmoid()
+        {}
+
+    // Member Functions
+
+        void scaleEnergy(scalar& e, const scalar r) const;
+
+        //- Read transportProperties dictionary
+        bool read(const dictionary& energyScalingFunctionProperties);
+};
+
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+} // End namespace energyScalingFunctions
+} // End namespace Foam
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+#endif
+
+// ************************************************************************* //
diff --git a/src/lagrangian/molecularDynamics/potential/energyScalingFunction/derived/noScaling/noScaling.C b/src/lagrangian/molecularDynamics/potential/energyScalingFunction/derived/noScaling/noScaling.C
new file mode 100644
index 0000000000..08daf130cb
--- /dev/null
+++ b/src/lagrangian/molecularDynamics/potential/energyScalingFunction/derived/noScaling/noScaling.C
@@ -0,0 +1,81 @@
+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  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 "noScaling.H"
+#include "addToRunTimeSelectionTable.H"
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+namespace Foam
+{
+namespace energyScalingFunctions
+{
+
+// * * * * * * * * * * * * * * Static Data Members * * * * * * * * * * * * * //
+
+defineTypeNameAndDebug(noScaling, 0);
+
+addToRunTimeSelectionTable
+(
+    energyScalingFunction,
+    noScaling,
+    dictionary
+);
+
+// * * * * * * * * * * * * Private Member Functions  * * * * * * * * * * * * //
+
+
+// * * * * * * * * * * * * * * * * Constructors  * * * * * * * * * * * * * * //
+
+noScaling::noScaling
+(
+    const word& name,
+    const dictionary& energyScalingFunctionProperties,
+    const pairPotential& pairPot
+)
+:
+    energyScalingFunction(name, energyScalingFunctionProperties, pairPot)
+{}
+
+// * * * * * * * * * * * * * * Member Functions  * * * * * * * * * * * * * * //
+
+void noScaling::scaleEnergy(scalar& e, const scalar r) const
+{}
+
+bool noScaling::read(const dictionary& energyScalingFunctionProperties)
+{
+    energyScalingFunction::read(energyScalingFunctionProperties);
+    
+    return true;
+}
+
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+} // End namespace energyScalingFunctions
+} // End namespace Foam
+
+// ************************************************************************* //
diff --git a/src/lagrangian/molecularDynamics/potential/energyScalingFunction/derived/noScaling/noScaling.H b/src/lagrangian/molecularDynamics/potential/energyScalingFunction/derived/noScaling/noScaling.H
new file mode 100644
index 0000000000..01ee2c2f90
--- /dev/null
+++ b/src/lagrangian/molecularDynamics/potential/energyScalingFunction/derived/noScaling/noScaling.H
@@ -0,0 +1,98 @@
+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  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
+    noScaling
+
+Description
+     
+
+SourceFiles
+    noScaling.C
+
+\*---------------------------------------------------------------------------*/
+
+#ifndef noScaling_H
+#define noScaling_H
+
+#include "energyScalingFunction.H"
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+namespace Foam
+{
+namespace energyScalingFunctions
+{
+
+/*---------------------------------------------------------------------------*\
+                           Class noScaling Declaration
+\*---------------------------------------------------------------------------*/
+
+class noScaling
+:
+    public energyScalingFunction
+{
+    // Private data
+
+public:
+
+    //- Runtime type information
+    TypeName("noScaling");
+
+
+    // Constructors
+
+        //- Construct from components
+        noScaling
+        (
+            const word& name,
+            const dictionary& energyScalingFunctionProperties,
+            const pairPotential& pairPot
+        );
+
+
+    // Destructor
+
+        ~noScaling()
+        {}
+
+    // Member Functions
+
+        void scaleEnergy(scalar& e, const scalar r) const;
+
+        //- Read transportProperties dictionary
+        bool read(const dictionary& energyScalingFunctionProperties);
+};
+
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+} // End namespace energyScalingFunctions
+} // End namespace Foam
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+#endif
+
+// ************************************************************************* //
diff --git a/src/lagrangian/molecularDynamics/potential/energyScalingFunction/derived/shifted/shifted.C b/src/lagrangian/molecularDynamics/potential/energyScalingFunction/derived/shifted/shifted.C
new file mode 100644
index 0000000000..28882fb118
--- /dev/null
+++ b/src/lagrangian/molecularDynamics/potential/energyScalingFunction/derived/shifted/shifted.C
@@ -0,0 +1,84 @@
+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  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 "shifted.H"
+#include "addToRunTimeSelectionTable.H"
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+namespace Foam
+{
+namespace energyScalingFunctions
+{
+
+// * * * * * * * * * * * * * * Static Data Members * * * * * * * * * * * * * //
+
+defineTypeNameAndDebug(shifted, 0);
+
+addToRunTimeSelectionTable
+(
+    energyScalingFunction,
+    shifted,
+    dictionary
+);
+
+// * * * * * * * * * * * * Private Member Functions  * * * * * * * * * * * * //
+
+
+// * * * * * * * * * * * * * * * * Constructors  * * * * * * * * * * * * * * //
+
+shifted::shifted
+(
+    const word& name,
+    const dictionary& energyScalingFunctionProperties,
+    const pairPotential& pairPot
+)
+:
+    energyScalingFunction(name, energyScalingFunctionProperties, pairPot),
+    e_at_rCut_(pairPot.unscaledEnergy(pairPot.rCut()))
+{}
+
+// * * * * * * * * * * * * * * Member Functions  * * * * * * * * * * * * * * //
+
+void shifted::scaleEnergy(scalar& e, const scalar r) const
+{
+    e -= e_at_rCut_;
+}
+
+bool shifted::read(const dictionary& energyScalingFunctionProperties)
+{
+    energyScalingFunction::read(energyScalingFunctionProperties);
+    
+    return true;
+}
+
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+} // End namespace energyScalingFunctions
+} // End namespace Foam
+
+// ************************************************************************* //
diff --git a/src/lagrangian/molecularDynamics/potential/energyScalingFunction/derived/shifted/shifted.H b/src/lagrangian/molecularDynamics/potential/energyScalingFunction/derived/shifted/shifted.H
new file mode 100644
index 0000000000..4d7d77f22e
--- /dev/null
+++ b/src/lagrangian/molecularDynamics/potential/energyScalingFunction/derived/shifted/shifted.H
@@ -0,0 +1,100 @@
+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  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
+    shifted
+
+Description
+     
+
+SourceFiles
+    shifted.C
+
+\*---------------------------------------------------------------------------*/
+
+#ifndef shifted_H
+#define shifted_H
+
+#include "energyScalingFunction.H"
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+namespace Foam
+{
+namespace energyScalingFunctions
+{
+
+/*---------------------------------------------------------------------------*\
+                           Class shifted Declaration
+\*---------------------------------------------------------------------------*/
+
+class shifted
+:
+    public energyScalingFunction
+{
+    // Private data
+        
+        scalar e_at_rCut_;
+
+public:
+
+    //- Runtime type information
+    TypeName("shifted");
+
+
+    // Constructors
+
+        //- Construct from components
+        shifted
+        (
+            const word& name,
+            const dictionary& energyScalingFunctionProperties,
+            const pairPotential& pairPot
+        );
+
+
+    // Destructor
+
+        ~shifted()
+        {}
+
+    // Member Functions
+
+        void scaleEnergy(scalar& e, const scalar r) const;
+
+        //- Read transportProperties dictionary
+        bool read(const dictionary& energyScalingFunctionProperties);
+};
+
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+} // End namespace energyScalingFunctions
+} // End namespace Foam
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+#endif
+
+// ************************************************************************* //
diff --git a/src/lagrangian/molecularDynamics/potential/energyScalingFunction/derived/shiftedForce/shiftedForce.C b/src/lagrangian/molecularDynamics/potential/energyScalingFunction/derived/shiftedForce/shiftedForce.C
new file mode 100644
index 0000000000..c619c3fc06
--- /dev/null
+++ b/src/lagrangian/molecularDynamics/potential/energyScalingFunction/derived/shiftedForce/shiftedForce.C
@@ -0,0 +1,86 @@
+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  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 "shiftedForce.H"
+#include "addToRunTimeSelectionTable.H"
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+namespace Foam
+{
+namespace energyScalingFunctions
+{
+
+// * * * * * * * * * * * * * * Static Data Members * * * * * * * * * * * * * //
+
+defineTypeNameAndDebug(shiftedForce, 0);
+
+addToRunTimeSelectionTable
+(
+    energyScalingFunction,
+    shiftedForce,
+    dictionary
+);
+
+// * * * * * * * * * * * * Private Member Functions  * * * * * * * * * * * * //
+
+
+// * * * * * * * * * * * * * * * * Constructors  * * * * * * * * * * * * * * //
+
+shiftedForce::shiftedForce
+(
+    const word& name,
+    const dictionary& energyScalingFunctionProperties,
+    const pairPotential& pairPot
+)
+:
+    energyScalingFunction(name, energyScalingFunctionProperties, pairPot),
+    rCut_(pairPot.rCut()),
+    e_at_rCut_(pairPot.unscaledEnergy(rCut_)),
+    de_dr_at_rCut_(pairPot.energyDerivative(rCut_, false))
+{}
+
+// * * * * * * * * * * * * * * Member Functions  * * * * * * * * * * * * * * //
+
+void shiftedForce::scaleEnergy(scalar& e, const scalar r) const
+{
+    e -= ( e_at_rCut_ + de_dr_at_rCut_ * (r - rCut_) );
+}
+
+bool shiftedForce::read(const dictionary& energyScalingFunctionProperties)
+{
+    energyScalingFunction::read(energyScalingFunctionProperties);
+    
+    return true;
+}
+
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+} // End namespace energyScalingFunctions
+} // End namespace Foam
+
+// ************************************************************************* //
diff --git a/src/lagrangian/molecularDynamics/potential/energyScalingFunction/derived/shiftedForce/shiftedForce.H b/src/lagrangian/molecularDynamics/potential/energyScalingFunction/derived/shiftedForce/shiftedForce.H
new file mode 100644
index 0000000000..5900b2a869
--- /dev/null
+++ b/src/lagrangian/molecularDynamics/potential/energyScalingFunction/derived/shiftedForce/shiftedForce.H
@@ -0,0 +1,106 @@
+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  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
+    shiftedForce
+
+Description
+     
+
+SourceFiles
+    shiftedForce.C
+
+\*---------------------------------------------------------------------------*/
+
+#ifndef shiftedForce_H
+#define shiftedForce_H
+
+#include "energyScalingFunction.H"
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+namespace Foam
+{
+namespace energyScalingFunctions
+{
+
+/*---------------------------------------------------------------------------*\
+                           Class shiftedForce Declaration
+\*---------------------------------------------------------------------------*/
+
+class shiftedForce
+:
+    public energyScalingFunction
+{
+    // Private data
+        
+        scalar rCut_;
+
+        scalar e_at_rCut_;
+
+        scalar de_dr_at_rCut_;
+
+    // Private Member Functions
+
+public:
+
+    //- Runtime type information
+    TypeName("shiftedForce");
+
+
+    // Constructors
+
+        //- Construct from components
+        shiftedForce
+        (
+            const word& name,
+            const dictionary& energyScalingFunctionProperties,
+            const pairPotential& pairPot
+        );
+
+
+    // Destructor
+
+        ~shiftedForce()
+        {}
+
+    // Member Functions
+        
+        void scaleEnergy(scalar& e, const scalar r) const;
+
+        //- Read transportProperties dictionary
+        bool read(const dictionary& energyScalingFunctionProperties);
+};
+
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+} // End namespace energyScalingFunctions
+} // End namespace Foam
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+#endif
+
+// ************************************************************************* //
diff --git a/src/lagrangian/molecularDynamics/potential/energyScalingFunction/derived/sigmoid/sigmoid.C b/src/lagrangian/molecularDynamics/potential/energyScalingFunction/derived/sigmoid/sigmoid.C
new file mode 100644
index 0000000000..5523cff338
--- /dev/null
+++ b/src/lagrangian/molecularDynamics/potential/energyScalingFunction/derived/sigmoid/sigmoid.C
@@ -0,0 +1,100 @@
+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  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 "sigmoid.H"
+#include "addToRunTimeSelectionTable.H"
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+namespace Foam
+{
+namespace energyScalingFunctions
+{
+
+// * * * * * * * * * * * * * * Static Data Members * * * * * * * * * * * * * //
+
+defineTypeNameAndDebug(sigmoid, 0);
+
+addToRunTimeSelectionTable
+(
+    energyScalingFunction,
+    sigmoid,
+    dictionary
+);
+
+// * * * * * * * * * * * * Private Member Functions  * * * * * * * * * * * * //
+
+scalar sigmoid::sigmoidScale
+    (
+        const scalar r,
+        const scalar shift,
+        const scalar scale
+    ) const
+{
+    return 1.0 / (1.0 + exp( scale * (r - shift)));
+}
+
+// * * * * * * * * * * * * * * * * Constructors  * * * * * * * * * * * * * * //
+
+sigmoid::sigmoid
+(
+    const word& name,
+    const dictionary& energyScalingFunctionProperties,
+    const pairPotential& pairPot
+)
+:
+    energyScalingFunction(name, energyScalingFunctionProperties, pairPot),
+    sigmoidCoeffs_(energyScalingFunctionProperties.subDict(typeName + "Coeffs")),
+    shift_(readScalar(sigmoidCoeffs_.lookup("shift"))),
+    scale_(readScalar(sigmoidCoeffs_.lookup("scale")))
+{}
+
+// * * * * * * * * * * * * * * Member Functions  * * * * * * * * * * * * * * //
+
+void sigmoid::scaleEnergy(scalar& e, const scalar r) const
+{
+    e *= sigmoidScale(r, shift_, scale_);
+}
+
+bool sigmoid::read(const dictionary& energyScalingFunctionProperties)
+{
+    energyScalingFunction::read(energyScalingFunctionProperties);
+
+    sigmoidCoeffs_ = energyScalingFunctionProperties.subDict(typeName + "Coeffs");
+
+    sigmoidCoeffs_.lookup("shift") >> shift_;
+    sigmoidCoeffs_.lookup("scale") >> shift_;
+    
+    return true;
+}
+
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+} // End namespace energyScalingFunctions
+} // End namespace Foam
+
+// ************************************************************************* //
diff --git a/src/lagrangian/molecularDynamics/potential/energyScalingFunction/derived/sigmoid/sigmoid.H b/src/lagrangian/molecularDynamics/potential/energyScalingFunction/derived/sigmoid/sigmoid.H
new file mode 100644
index 0000000000..0ceb56b0df
--- /dev/null
+++ b/src/lagrangian/molecularDynamics/potential/energyScalingFunction/derived/sigmoid/sigmoid.H
@@ -0,0 +1,112 @@
+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  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
+    sigmoid
+
+Description
+     
+
+SourceFiles
+    sigmoid.C
+
+\*---------------------------------------------------------------------------*/
+
+#ifndef sigmoid_H
+#define sigmoid_H
+
+#include "energyScalingFunction.H"
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+namespace Foam
+{
+namespace energyScalingFunctions
+{
+
+/*---------------------------------------------------------------------------*\
+                           Class sigmoid Declaration
+\*---------------------------------------------------------------------------*/
+
+class sigmoid
+:
+    public energyScalingFunction
+{
+    // Private data
+        
+        dictionary sigmoidCoeffs_;
+
+        scalar shift_;
+        scalar scale_;
+        
+    // Private Member Functions
+
+        scalar sigmoidScale
+        (
+            const scalar r,
+            const scalar shift,
+            const scalar scale
+        ) const;
+
+public:
+
+    //- Runtime type information
+    TypeName("sigmoid");
+
+
+    // Constructors
+
+        //- Construct from components
+        sigmoid
+        (
+            const word& name,
+            const dictionary& energyScalingFunctionProperties,
+            const pairPotential& pairPot
+        );
+
+
+    // Destructor
+
+        ~sigmoid()
+        {}
+
+    // Member Functions
+
+        void scaleEnergy(scalar& e, const scalar r) const;
+
+        //- Read transportProperties dictionary
+        bool read(const dictionary& energyScalingFunctionProperties);
+};
+
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+} // End namespace energyScalingFunctions
+} // End namespace Foam
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+#endif
+
+// ************************************************************************* //
diff --git a/src/lagrangian/molecularDynamics/potential/pairPotential/basic/newPairPotential.C b/src/lagrangian/molecularDynamics/potential/pairPotential/basic/newPairPotential.C
new file mode 100644
index 0000000000..f10b0aa84d
--- /dev/null
+++ b/src/lagrangian/molecularDynamics/potential/pairPotential/basic/newPairPotential.C
@@ -0,0 +1,75 @@
+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  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
+    pairPotential
+
+\*---------------------------------------------------------------------------*/
+
+#include "pairPotential.H"
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+namespace Foam
+{
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+autoPtr<pairPotential> pairPotential::New
+(
+    const word& name,
+    const dictionary& pairPotentialProperties
+)
+{
+    word pairPotentialTypeName(pairPotentialProperties.lookup("pairPotential"));
+
+    Info<< nl << "Selecting intermolecular pair potential "
+        << pairPotentialTypeName << " for "
+        << name << " interaction." << endl;
+
+    dictionaryConstructorTable::iterator cstrIter =
+        dictionaryConstructorTablePtr_->find(pairPotentialTypeName);
+
+    if (cstrIter == dictionaryConstructorTablePtr_->end())
+    {
+        FatalErrorIn
+        (
+            "pairPotential::New()"
+        )   << "Unknown pairPotential type "
+            << pairPotentialTypeName << endl << endl
+            << "Valid  pairPotentials are : " << endl
+            << dictionaryConstructorTablePtr_->toc()
+            << exit(FatalError);
+    }
+
+    return autoPtr<pairPotential>
+        (cstrIter()(name, pairPotentialProperties));
+}
+
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+} // End namespace Foam
+
+// ************************************************************************* //
diff --git a/src/lagrangian/molecularDynamics/potential/pairPotential/basic/pairPotential.C b/src/lagrangian/molecularDynamics/potential/pairPotential/basic/pairPotential.C
new file mode 100644
index 0000000000..86e6ae386f
--- /dev/null
+++ b/src/lagrangian/molecularDynamics/potential/pairPotential/basic/pairPotential.C
@@ -0,0 +1,238 @@
+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  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
+    pairPotential
+
+\*---------------------------------------------------------------------------*/
+
+#include "pairPotential.H"
+#include "energyScalingFunction.H"
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+namespace Foam
+{
+
+// * * * * * * * * * * * * * * Static Data Members * * * * * * * * * * * * * //
+
+defineTypeNameAndDebug(pairPotential, 0);
+defineRunTimeSelectionTable(pairPotential, dictionary);
+
+// * * * * * * * * * * * * * Private Member Functions  * * * * * * * * * * * //
+
+
+void Foam::pairPotential::scaleEnergy(scalar& e, const scalar r) const
+{
+    if (!esfPtr_)
+    {
+        esfPtr_ = energyScalingFunction::New
+        (
+            name_, pairPotentialProperties_, *this
+        ).ptr();
+    }
+    
+    esfPtr_->scaleEnergy(e, r);
+}
+
+
+// * * * * * * * * * * * * * * * * Constructors  * * * * * * * * * * * * * * //
+
+Foam::pairPotential::pairPotential
+(
+    const word& name,
+    const dictionary& pairPotentialProperties
+)
+:
+    name_(name),
+    pairPotentialProperties_(pairPotentialProperties),
+    rCut_(readScalar(pairPotentialProperties_.lookup("rCut"))),
+    rCutSqr_(rCut_*rCut_),
+    rMin_(readScalar(pairPotentialProperties_.lookup("rMin"))),
+    dr_(readScalar(pairPotentialProperties_.lookup("dr"))),
+    forceLookup_(0),
+    energyLookup_(0),
+    esfPtr_(NULL),
+    writeTables_(Switch(pairPotentialProperties_.lookup("writeTables")))
+{}
+
+// * * * * * * * * * * * * * * Member Functions  * * * * * * * * * * * * * * //
+
+void Foam::pairPotential::setLookupTables()
+{
+    label N = label((rCut_ - rMin_)/dr_) + 1;
+
+    forceLookup_.setSize(N);
+
+    energyLookup_.setSize(N);
+
+    forAll(forceLookup_, k)
+    {
+        energyLookup_[k] = scaledEnergy(k*dr_ + rMin_);
+
+        forceLookup_[k] = -energyDerivative( (k * dr_ + rMin_), true);
+    }
+}
+
+
+Foam::scalar Foam::pairPotential::forceLookup(const scalar r) const
+{
+    scalar k_rIJ = (r - rMin_)/dr_;
+
+    label k(k_rIJ);
+
+    if (k < 0)
+    {
+        FatalErrorIn("pairPotential.C") << nl
+        << "r less than rMin" << nl
+        << abort(FatalError);
+    }
+
+    scalar f =
+        (k_rIJ - k)*forceLookup_[k+1]
+      + (k + 1 - k_rIJ)*forceLookup_[k];
+
+    return f;
+}
+
+
+Foam::List< Foam::Pair< Foam::scalar > >
+Foam::pairPotential::forceTable() const
+{
+    List< Pair<scalar> > forceTab(forceLookup_.size());
+
+    forAll(forceLookup_,k)
+    {
+        forceTab[k].first() = rMin_ + k*dr_;
+
+        forceTab[k].second() = forceLookup_[k];
+    }
+
+    return forceTab;
+}
+
+
+Foam::scalar Foam::pairPotential::energyLookup(const scalar r) const
+{
+    scalar k_rIJ = (r - rMin_)/dr_;
+
+    label k(k_rIJ);
+
+    if (k < 0)
+    {
+        FatalErrorIn("pairPotential.C") << nl
+        << "r less than rMin" << nl
+        << abort(FatalError);
+    }
+
+    scalar e =
+        (k_rIJ - k)*energyLookup_[k+1]
+      + (k + 1 - k_rIJ)*energyLookup_[k];
+
+    return e;
+}
+
+
+Foam::List< Foam::Pair< Foam::scalar > >
+    Foam::pairPotential::energyTable() const
+{
+    List< Pair<scalar> > energyTab(energyLookup_.size());
+
+    forAll(energyLookup_,k)
+    {
+        energyTab[k].first() = rMin_ + k*dr_;
+
+        energyTab[k].second() = energyLookup_[k];
+    }
+
+    return energyTab;
+}
+
+
+Foam::scalar Foam::pairPotential::scaledEnergy(const scalar r) const
+{
+    scalar e = unscaledEnergy(r);
+    
+    scaleEnergy(e, r);
+
+    return e;
+}
+
+
+Foam::scalar Foam::pairPotential::energyDerivative
+(
+    const scalar r,
+    const bool scaledEnergyDerivative
+) const
+{
+    // Local quadratic fit to energy: E = a0 + a1*r + a2*r^2
+    // Differentiate to give f = -dE/dr = -a1 - 2*a2*r
+
+    scalar ra = r - dr_;
+    scalar rf = r;
+    scalar rb = r + dr_;
+    
+    scalar Ea, Ef, Eb;
+
+    if (scaledEnergyDerivative)
+    {
+        Ea = scaledEnergy(ra);
+        Ef = scaledEnergy(rf);
+        Eb = scaledEnergy(rb);
+    }
+    else
+    {
+        Ea = unscaledEnergy(ra);
+        Ef = unscaledEnergy(rf);
+        Eb = unscaledEnergy(rb);
+    }
+    
+    scalar denominator = (ra - rf)*(ra - rb)*(rf - rb);
+    
+    scalar a1 =
+    (
+        rb*rb*(Ea - Ef) + ra*ra*(Ef - Eb) + rf*rf*(Eb - Ea)
+    ) / denominator;
+
+    scalar a2 = 
+    (
+        rb*(Ef - Ea) + rf*(Ea - Eb) + ra*(Eb - Ef)
+    ) / denominator;
+
+    return a1 + 2.0 * a2 * r;
+}
+
+
+bool Foam::pairPotential::read(const dictionary& pairPotentialProperties)
+{
+    pairPotentialProperties_ = pairPotentialProperties;
+
+    return true;
+}
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+} // End namespace Foam
+
+// ************************************************************************* //
diff --git a/src/lagrangian/molecularDynamics/potential/pairPotential/basic/pairPotential.H b/src/lagrangian/molecularDynamics/potential/pairPotential/basic/pairPotential.H
new file mode 100644
index 0000000000..a303750ba5
--- /dev/null
+++ b/src/lagrangian/molecularDynamics/potential/pairPotential/basic/pairPotential.H
@@ -0,0 +1,195 @@
+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  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
+    pairPotential
+
+Description
+
+SourceFiles
+    pairPotential.C
+    newPairPotential.C
+
+\*---------------------------------------------------------------------------*/
+
+#ifndef pairPotential_H
+#define pairPotential_H
+
+#include "IOdictionary.H"
+#include "typeInfo.H"
+#include "runTimeSelectionTables.H"
+#include "autoPtr.H"
+#include "List.H"
+#include "Pair.H"
+#include "Switch.H"
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+namespace Foam
+{
+
+// Forward declaration of classes
+class energyScalingFunction;
+
+/*---------------------------------------------------------------------------*\
+                Class pairPotential Declaration
+\*---------------------------------------------------------------------------*/
+
+class pairPotential
+{
+
+protected:
+
+    // Protected data
+
+        word name_;
+        dictionary pairPotentialProperties_;
+
+        scalar rCut_;
+        scalar rCutSqr_;
+
+        scalar rMin_;
+        scalar dr_;
+
+        List<scalar> forceLookup_;
+        List<scalar> energyLookup_;
+
+        mutable energyScalingFunction* esfPtr_;
+
+        bool writeTables_;
+
+    // Private Member Functions
+
+        void scaleEnergy(scalar& e, const scalar r) const;
+        
+        //- Disallow copy construct
+        pairPotential(const pairPotential&);
+
+        //- Disallow default bitwise assignment
+        void operator=(const pairPotential&);
+
+public:
+
+    //- Runtime type information
+    TypeName("pairPotential");
+
+
+    // Declare run-time constructor selection table
+
+        declareRunTimeSelectionTable
+        (
+            autoPtr,
+            pairPotential,
+            dictionary,
+            (
+                const word& name,
+                const dictionary& pairPotentialProperties
+            ),
+            (name, pairPotentialProperties)
+        );
+
+
+    // Selectors
+
+        //- Return a reference to the selected viscosity model
+        static autoPtr<pairPotential> New
+        (
+            const word& name,
+            const dictionary& pairPotentialProperties
+        );
+
+
+    // Constructors
+
+        //- Construct from components
+        pairPotential
+        (
+            const word& name,
+            const dictionary& pairPotentialProperties
+        );
+
+
+    // Destructor
+
+        virtual ~pairPotential()
+        {}
+
+
+    // Member Functions
+
+        void setLookupTables();
+
+        inline scalar rMin() const;
+
+        inline scalar dr() const;
+
+        inline scalar rCut() const;
+
+        inline scalar rCutSqr() const;
+
+        scalar energyLookup (const scalar r) const;
+
+        scalar forceLookup (const scalar r) const;
+
+        List< Pair <scalar> > energyTable() const;
+
+        List< Pair <scalar> > forceTable() const;
+
+        inline bool writeTables() const;
+
+        virtual scalar unscaledEnergy (const scalar r) const = 0;
+
+        scalar scaledEnergy(const scalar r) const;
+
+        scalar energyDerivative
+        (
+            const scalar r,
+            const bool scaledEnergyDerivative = true
+        ) const;
+
+        const dictionary& pairPotentialProperties() const
+        {
+            return pairPotentialProperties_;
+        }
+
+        bool writeEnergyAndForceTables(Ostream& os) const;
+
+        //- Read pairPotential dictionary
+        virtual bool read(const dictionary& pairPotentialProperties) = 0;
+};
+
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+} // End namespace Foam
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+#include "pairPotentialI.H"
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+#endif
+
+// ************************************************************************* //
diff --git a/src/lagrangian/molecularDynamics/potential/pairPotential/basic/pairPotentialI.H b/src/lagrangian/molecularDynamics/potential/pairPotential/basic/pairPotentialI.H
new file mode 100755
index 0000000000..67dbbfd253
--- /dev/null
+++ b/src/lagrangian/molecularDynamics/potential/pairPotential/basic/pairPotentialI.H
@@ -0,0 +1,58 @@
+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+   \\    /   O peration     |
+    \\  /    A nd           | Copyright (C) 1991-2005 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
+
+\*---------------------------------------------------------------------------*/
+
+// * * * * * * * * * * * * * * * Member Functions  * * * * * * * * * * * * * //
+
+inline Foam::scalar Foam::pairPotential::rMin() const
+{
+    return rMin_;
+}
+
+
+inline Foam::scalar Foam::pairPotential::dr() const
+{
+    return dr_;
+}
+
+
+inline Foam::scalar Foam::pairPotential::rCut() const
+{
+    return rCut_;
+}
+
+
+inline Foam::scalar Foam::pairPotential::rCutSqr() const
+{
+    return rCutSqr_;
+}
+
+
+inline bool Foam::pairPotential::writeTables() const
+{
+    return writeTables_;
+}
+
+// ************************************************************************* //
diff --git a/src/lagrangian/molecularDynamics/potential/pairPotential/basic/pairPotentialIO.C b/src/lagrangian/molecularDynamics/potential/pairPotential/basic/pairPotentialIO.C
new file mode 100644
index 0000000000..79ab55e737
--- /dev/null
+++ b/src/lagrangian/molecularDynamics/potential/pairPotential/basic/pairPotentialIO.C
@@ -0,0 +1,53 @@
+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  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 "pairPotential.H"
+#include "IOstreams.H"
+
+bool Foam::pairPotential::writeEnergyAndForceTables(Ostream& os) const
+{
+    Info<< "Writing energy and force tables to file for potential "
+        << name_ << endl;
+
+    List< Pair <scalar> > eTab(energyTable());
+
+    List< Pair <scalar> > fTab(forceTable());
+
+    forAll(eTab, e)
+    {
+        os<< eTab[e].first()
+          << token::SPACE
+          << eTab[e].second()
+          << token::SPACE
+          << fTab[e].second()
+          << nl;
+    }
+
+    return os.good();
+}
+
+
+// ************************************************************************* //
diff --git a/src/lagrangian/molecularDynamics/potential/pairPotential/derived/azizChen/azizChen.C b/src/lagrangian/molecularDynamics/potential/pairPotential/derived/azizChen/azizChen.C
new file mode 100644
index 0000000000..b9cbbb1e54
--- /dev/null
+++ b/src/lagrangian/molecularDynamics/potential/pairPotential/derived/azizChen/azizChen.C
@@ -0,0 +1,125 @@
+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  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 "azizChen.H"
+#include "addToRunTimeSelectionTable.H"
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+namespace Foam
+{
+namespace pairPotentials
+{
+
+// * * * * * * * * * * * * * * Static Data Members * * * * * * * * * * * * * //
+
+defineTypeNameAndDebug(azizChen, 0);
+
+addToRunTimeSelectionTable
+(
+    pairPotential,
+    azizChen,
+    dictionary
+);
+
+// * * * * * * * * * * * * Private Member Functions  * * * * * * * * * * * * //
+
+
+// * * * * * * * * * * * * * * * * Constructors  * * * * * * * * * * * * * * //
+
+azizChen::azizChen
+(
+    const word& name,
+    const dictionary& azizChen
+)
+:
+    pairPotential(name, azizChen),
+    azizChenCoeffs_(azizChen.subDict(typeName + "Coeffs")),
+    epsilon_(readScalar(azizChenCoeffs_.lookup("epsilon"))),
+    rm_(readScalar(azizChenCoeffs_.lookup("rm"))),
+    A_(readScalar(azizChenCoeffs_.lookup("A"))),
+    alpha_(readScalar(azizChenCoeffs_.lookup("alpha"))),
+    C6_(readScalar(azizChenCoeffs_.lookup("C6"))),
+    C8_(readScalar(azizChenCoeffs_.lookup("C8"))),
+    C10_(readScalar(azizChenCoeffs_.lookup("C10"))),
+    D_(readScalar(azizChenCoeffs_.lookup("D"))),
+    gamma_(readScalar(azizChenCoeffs_.lookup("gamma")))
+{
+    setLookupTables();
+}
+
+// * * * * * * * * * * * * * * Member Functions  * * * * * * * * * * * * * * //
+
+scalar azizChen::unscaledEnergy(const scalar r) const
+{
+    scalar x = r/rm_;
+
+    scalar F = 1.0;
+
+    if (x < D_)
+    {
+        F = exp(-pow(((D_ / x) - 1.0),2));
+    }
+
+    return epsilon_ *
+    (
+        A_ * Foam::pow(x, gamma_) * exp(-alpha_ * x)
+      - (
+            (C6_/ Foam::pow(x, 6))
+          + (C8_/ Foam::pow(x, 8))
+          + (C10_/ Foam::pow(x, 10))
+        )
+      * F
+    );
+}
+
+
+bool azizChen::read(const dictionary& azizChen)
+{
+    pairPotential::read(azizChen);
+
+    azizChenCoeffs_ = azizChen.subDict(typeName + "Coeffs");
+
+    azizChenCoeffs_.lookup("epsilon") >> epsilon_;
+    azizChenCoeffs_.lookup("rm") >> rm_;
+    azizChenCoeffs_.lookup("A") >> A_;
+    azizChenCoeffs_.lookup("alpha") >> alpha_;
+    azizChenCoeffs_.lookup("C6") >> C6_;
+    azizChenCoeffs_.lookup("C8") >> C8_;
+    azizChenCoeffs_.lookup("C10") >> C10_;
+    azizChenCoeffs_.lookup("D") >> D_;
+    azizChenCoeffs_.lookup("gamma") >> gamma_;
+    
+    return true;
+}
+
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+} // End namespace pairPotentials
+} // End namespace Foam
+
+// ************************************************************************* //
diff --git a/src/lagrangian/molecularDynamics/potential/pairPotential/derived/azizChen/azizChen.H b/src/lagrangian/molecularDynamics/potential/pairPotential/derived/azizChen/azizChen.H
new file mode 100644
index 0000000000..d0513b277f
--- /dev/null
+++ b/src/lagrangian/molecularDynamics/potential/pairPotential/derived/azizChen/azizChen.H
@@ -0,0 +1,126 @@
+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  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
+    azizChen
+
+Description
+
+    From:
+
+    @article{MA_Aziz_Chen,
+    author = {R. A. Aziz and H. H. Chen},
+    collaboration = {},
+    title = {An accurate intermolecular potential for argon},
+    publisher = {AIP},
+    year = {1977},
+    journal = {The Journal of Chemical Physics},
+    volume = {67},
+    number = {12},
+    pages = {5719-5726},
+    url = {http://link.aip.org/link/?JCP/67/5719/1},
+    doi = {10.1063/1.434827}
+    }
+
+SourceFiles
+    azizChen.C
+
+\*---------------------------------------------------------------------------*/
+
+#ifndef azizChen_H
+#define azizChen_H
+
+#include "pairPotential.H"
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+namespace Foam
+{
+
+namespace pairPotentials
+{
+
+/*---------------------------------------------------------------------------*\
+                           Class azizChen Declaration
+\*---------------------------------------------------------------------------*/
+
+class azizChen
+:
+    public pairPotential
+{
+    // Private data
+
+        dictionary azizChenCoeffs_;
+
+        scalar epsilon_;
+        scalar rm_;
+        scalar A_;
+        scalar alpha_;
+        scalar C6_;
+        scalar C8_;
+        scalar C10_;
+        scalar D_;
+        scalar gamma_;
+
+public:
+
+    //- Runtime type information
+    TypeName("azizChen");
+
+
+    // Constructors
+
+        //- Construct from components
+        azizChen
+        (
+            const word& name,
+            const dictionary& pairPotentialProperties
+        );
+
+
+    // Destructor
+
+        ~azizChen()
+        {}
+
+
+    // Member Functions
+
+        scalar unscaledEnergy(const scalar r) const;
+
+        //- Read transportProperties dictionary
+        bool read(const dictionary& pairPotentialProperties);
+};
+
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+} // End namespace pairPotentials
+} // End namespace Foam
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+#endif
+
+// ************************************************************************* //
diff --git a/src/lagrangian/molecularDynamics/potential/pairPotential/derived/lennardJones/lennardJones.C b/src/lagrangian/molecularDynamics/potential/pairPotential/derived/lennardJones/lennardJones.C
new file mode 100644
index 0000000000..58968a6d29
--- /dev/null
+++ b/src/lagrangian/molecularDynamics/potential/pairPotential/derived/lennardJones/lennardJones.C
@@ -0,0 +1,99 @@
+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  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 "lennardJones.H"
+#include "addToRunTimeSelectionTable.H"
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+namespace Foam
+{
+namespace pairPotentials
+{
+
+// * * * * * * * * * * * * * * Static Data Members * * * * * * * * * * * * * //
+
+defineTypeNameAndDebug(lennardJones, 0);
+
+addToRunTimeSelectionTable
+(
+    pairPotential,
+    lennardJones,
+    dictionary
+);
+
+// * * * * * * * * * * * * Private Member Functions  * * * * * * * * * * * * //
+
+
+// * * * * * * * * * * * * * * * * Constructors  * * * * * * * * * * * * * * //
+
+lennardJones::lennardJones
+(
+    const word& name,
+    const dictionary& pairPotentialProperties
+)
+:
+    pairPotential(name, pairPotentialProperties),
+    lennardJonesCoeffs_(pairPotentialProperties.subDict(typeName + "Coeffs")),
+    sigma_(readScalar(lennardJonesCoeffs_.lookup("sigma"))),
+    epsilon_(readScalar(lennardJonesCoeffs_.lookup("epsilon")))
+{
+    setLookupTables();
+}
+
+// * * * * * * * * * * * * * * Member Functions  * * * * * * * * * * * * * * //
+
+scalar lennardJones::unscaledEnergy(const scalar r) const
+{
+    // (rIJ/sigma)^-2
+    scalar ir2 = (sigma_/r)*(sigma_/r);
+
+    // (rIJ/sigma)^-6
+    scalar ir6 = ir2*ir2*ir2;
+
+    return 4.0 * epsilon_ * (ir6 * (ir6 - 1.0));
+}
+
+
+bool lennardJones::read(const dictionary& pairPotentialProperties)
+{
+    pairPotential::read(pairPotentialProperties);
+
+    lennardJonesCoeffs_ = pairPotentialProperties.subDict(typeName + "Coeffs");
+
+    lennardJonesCoeffs_.lookup("sigma") >> sigma_;
+    lennardJonesCoeffs_.lookup("epsilon") >> epsilon_;
+    
+    return true;
+}
+
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+} // End namespace pairPotentials
+} // End namespace Foam
+
+// ************************************************************************* //
diff --git a/src/lagrangian/molecularDynamics/potential/pairPotential/derived/lennardJones/lennardJones.H b/src/lagrangian/molecularDynamics/potential/pairPotential/derived/lennardJones/lennardJones.H
new file mode 100644
index 0000000000..f879549ef8
--- /dev/null
+++ b/src/lagrangian/molecularDynamics/potential/pairPotential/derived/lennardJones/lennardJones.H
@@ -0,0 +1,103 @@
+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  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
+    lennardJones
+
+Description
+     
+
+SourceFiles
+    lennardJones.C
+
+\*---------------------------------------------------------------------------*/
+
+#ifndef lennardJones_H
+#define lennardJones_H
+
+#include "pairPotential.H"
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+namespace Foam
+{
+namespace pairPotentials
+{
+
+/*---------------------------------------------------------------------------*\
+                           Class lennardJones Declaration
+\*---------------------------------------------------------------------------*/
+
+class lennardJones
+:
+    public pairPotential
+{
+    // Private data
+
+        dictionary lennardJonesCoeffs_;
+
+        scalar sigma_;
+        scalar epsilon_;
+
+public:
+
+    //- Runtime type information
+    TypeName("lennardJones");
+
+
+    // Constructors
+
+        //- Construct from components
+        lennardJones
+        (
+            const word& name,
+            const dictionary& pairPotentialProperties
+        );
+
+
+    // Destructor
+
+        ~lennardJones()
+        {}
+
+
+    // Member Functions
+
+        scalar unscaledEnergy(const scalar r) const;
+
+        //- Read transportProperties dictionary
+        bool read(const dictionary& pairPotentialProperties);
+};
+
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+} // End namespace pairPotentials
+} // End namespace Foam
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+#endif
+
+// ************************************************************************* //
diff --git a/src/lagrangian/molecularDynamics/potential/pairPotential/derived/maitlandSmith/maitlandSmith.C b/src/lagrangian/molecularDynamics/potential/pairPotential/derived/maitlandSmith/maitlandSmith.C
new file mode 100644
index 0000000000..4915f2a1fd
--- /dev/null
+++ b/src/lagrangian/molecularDynamics/potential/pairPotential/derived/maitlandSmith/maitlandSmith.C
@@ -0,0 +1,103 @@
+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  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 "maitlandSmith.H"
+#include "addToRunTimeSelectionTable.H"
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+namespace Foam
+{
+namespace pairPotentials
+{
+
+// * * * * * * * * * * * * * * Static Data Members * * * * * * * * * * * * * //
+
+defineTypeNameAndDebug(maitlandSmith, 0);
+
+addToRunTimeSelectionTable
+(
+    pairPotential,
+    maitlandSmith,
+    dictionary
+);
+
+// * * * * * * * * * * * * Private Member Functions  * * * * * * * * * * * * //
+
+
+// * * * * * * * * * * * * * * * * Constructors  * * * * * * * * * * * * * * //
+
+maitlandSmith::maitlandSmith
+(
+    const word& name,
+    const dictionary& maitlandSmith
+)
+:
+    pairPotential(name, maitlandSmith),
+    maitlandSmithCoeffs_(maitlandSmith.subDict(typeName + "Coeffs")),
+    m_(readScalar(maitlandSmithCoeffs_.lookup("m"))),
+    gamma_(readScalar(maitlandSmithCoeffs_.lookup("gamma"))),
+    rm_(readScalar(maitlandSmithCoeffs_.lookup("rm"))),
+    epsilon_(readScalar(maitlandSmithCoeffs_.lookup("epsilon")))
+{
+    setLookupTables();
+}
+
+// * * * * * * * * * * * * * * Member Functions  * * * * * * * * * * * * * * //
+
+scalar maitlandSmith::unscaledEnergy(const scalar r) const
+{
+    scalar nr = (m_ + gamma_*(r/rm_ - 1.0));
+
+    return epsilon_
+       *(
+            (6.0 / (nr - 6.0))*Foam::pow(r/rm_, -nr)
+          - (nr / (nr - 6.0))*Foam::pow(r/rm_, -6)
+        );
+}
+
+
+bool maitlandSmith::read(const dictionary& maitlandSmith)
+{
+    pairPotential::read(maitlandSmith);
+
+    maitlandSmithCoeffs_ = maitlandSmith.subDict(typeName + "Coeffs");
+
+    maitlandSmithCoeffs_.lookup("m") >> m_;
+    maitlandSmithCoeffs_.lookup("gamma") >> gamma_;
+    maitlandSmithCoeffs_.lookup("rm") >> rm_;
+    maitlandSmithCoeffs_.lookup("epsilon") >> epsilon_;
+    
+    return true;
+}
+
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+} // End namespace pairPotentials
+} // End namespace Foam
+
+// ************************************************************************* //
diff --git a/src/lagrangian/molecularDynamics/potential/pairPotential/derived/maitlandSmith/maitlandSmith.H b/src/lagrangian/molecularDynamics/potential/pairPotential/derived/maitlandSmith/maitlandSmith.H
new file mode 100644
index 0000000000..64747a369a
--- /dev/null
+++ b/src/lagrangian/molecularDynamics/potential/pairPotential/derived/maitlandSmith/maitlandSmith.H
@@ -0,0 +1,127 @@
+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  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
+    maitlandSmith
+
+Description
+
+    From:
+
+    @ARTICLE{MA_Maitland_Smith,
+    author = {{Maitland}, G.~C. and {Smith}, E.~B.},
+    title = {A simplified representation of intermolecular potential energy},
+    journal = {Chemical Physics Letters},
+    year = 1973,
+    month = oct,
+    volume = 22,
+    pages = {443-446},
+    adsurl = {http://adsabs.harvard.edu/abs/1973CPL....22..443M},
+    adsnote = {Provided by the SAO/NASA Astrophysics Data System}
+    }
+
+    Parameters for other monoatomics from:
+    @BOOK{MD_Maitland_Rigby_Smith_Wakeham,
+    AUTHOR =       {Geoffrey C. Maitland and Maurice Rigby and E. Brian Smith and William A. Wakeham},
+    TITLE =        {Intermolecular Forces: Their Origin and Determination},
+    PUBLISHER =    {Oxford University Press},
+    YEAR =         {1981}
+    }
+
+SourceFiles
+    maitlandSmith.C
+
+\*---------------------------------------------------------------------------*/
+
+#ifndef maitlandSmith_H
+#define maitlandSmith_H
+
+#include "pairPotential.H"
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+namespace Foam
+{
+
+namespace pairPotentials
+{
+
+/*---------------------------------------------------------------------------*\
+                           Class maitlandSmith Declaration
+\*---------------------------------------------------------------------------*/
+
+class maitlandSmith
+:
+    public pairPotential
+{
+    // Private data
+
+        dictionary maitlandSmithCoeffs_;
+
+        scalar m_;
+        scalar gamma_;
+        scalar rm_;
+        scalar epsilon_;
+
+public:
+
+    //- Runtime type information
+    TypeName("maitlandSmith");
+
+
+    // Constructors
+
+        //- Construct from components
+        maitlandSmith
+        (
+            const word& name,
+            const dictionary& pairPotentialProperties
+        );
+
+
+    // Destructor
+
+        ~maitlandSmith()
+        {}
+
+
+    // Member Functions
+
+        scalar unscaledEnergy(const scalar r) const;
+
+        //- Read transportProperties dictionary
+        bool read(const dictionary& pairPotentialProperties);
+};
+
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+} // End namespace pairPotentials
+} // End namespace Foam
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+#endif
+
+// ************************************************************************* //
diff --git a/src/lagrangian/molecularDynamics/potential/pairPotential/pairPotentialList/pairPotentialList.C b/src/lagrangian/molecularDynamics/potential/pairPotential/pairPotentialList/pairPotentialList.C
new file mode 100755
index 0000000000..44207d13ba
--- /dev/null
+++ b/src/lagrangian/molecularDynamics/potential/pairPotential/pairPotentialList/pairPotentialList.C
@@ -0,0 +1,284 @@
+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+   \\    /   O peration     |
+    \\  /    A nd           | Copyright (C) 1991-2005 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 "pairPotentialList.H"
+#include "OFstream.H"
+#include "Time.H"
+
+// * * * * * * * * * * * * * Private Member Functions  * * * * * * * * * * * //
+
+void Foam::pairPotentialList::readPairPotentialDict
+(
+    const dictionary& pairPotentialDict,
+    const polyMesh& mesh
+)
+{
+    Info<< nl << "Building pair potentials." << endl;   
+
+    rCutMax_ = 0.0;
+
+    for (label a = 0; a < nIds(); ++a)
+    {
+        word idA = idList_[a];
+    
+        for (label b = a; b < nIds(); ++b)
+        {
+            word idB = idList_[b];
+
+            word pairPotentialName;
+
+            if (a==b)
+            {
+                if(pairPotentialDict.found(idA+"-"+idB))
+                {
+                    pairPotentialName = idA+"-"+idB;
+                }
+                else
+                {
+                    FatalErrorIn("pairPotentialList::buildPotentials") << nl
+                            << "Pair pairPotential specification subDict "
+                            << idA+"-"+idB << " not found"
+                            << abort(FatalError);
+                }
+            }
+            else
+            {
+                if(pairPotentialDict.found(idA+"-"+idB))
+                {
+                    pairPotentialName = idA+"-"+idB;
+                }
+    
+                else if(pairPotentialDict.found(idB+"-"+idA))
+                {
+                    pairPotentialName = idB+"-"+idA;
+                }
+    
+                else
+                {
+                    FatalErrorIn("pairPotentialList::buildPotentials") << nl
+                            << "Pair pairPotential specification subDict "
+                            << idA+"-"+idB << " or " << idB+"-"+idA << " not found"
+                            << abort(FatalError);
+                }
+    
+                if
+                (
+                    pairPotentialDict.found(idA+"-"+idB)
+                 && pairPotentialDict.found(idB+"-"+idA)
+                )
+                {
+                    FatalErrorIn("pairPotentialList::buildPotentials") << nl
+                            << "Pair pairPotential specification subDict "
+                            << idA+"-"+idB << " and "
+                            << idB+"-"+idA << " found - multiple definition"
+                            << abort(FatalError);
+                }
+            }
+
+            (*this).set
+            (
+                pairPotentialIndex(a,b),
+                pairPotential::New
+                (
+                    pairPotentialName,
+                    pairPotentialDict.subDict(pairPotentialName)
+                )
+            );
+
+            if ((*this)[pairPotentialIndex(a,b)].rCut() > rCutMax_)
+            {
+                rCutMax_ = (*this)[pairPotentialIndex(a,b)].rCut();
+            }
+
+//             Info<< pairPotentialName << ": "
+//                 << (*this)[pairPotentialIndex(a,b)].pairPotentialProperties()
+//                 << endl;
+
+            if ((*this)[pairPotentialIndex(a,b)].writeTables())
+            {
+                OFstream ppTabFile(mesh.time().path()/pairPotentialName);
+            
+                if 
+                (
+                    !(*this)[pairPotentialIndex(a,b)].writeEnergyAndForceTables
+                    (
+                        ppTabFile
+                    )
+                )
+                {
+                    FatalErrorIn("pairPotentialList::readPairPotentialDict")
+                        << "Failed writing to "
+                        << ppTabFile.name()
+                        << abort(FatalError);
+                }
+            }
+        }
+    }
+
+    rCutMaxSqr_ = rCutMax_ * rCutMax_;
+
+    Info << nl << "rCutMax = " << rCutMax_ << endl;
+}
+
+// * * * * * * * * * * * * * * * * Constructors  * * * * * * * * * * * * * * //
+
+Foam::pairPotentialList::pairPotentialList()
+:
+    PtrList<pairPotential>(),
+    idList_()
+{}
+
+Foam::pairPotentialList::pairPotentialList
+(
+    const dictionary& idListDict,
+    const dictionary& pairPotentialDict,
+    const polyMesh& mesh
+)
+:
+    PtrList<pairPotential>(),
+    idList_()
+{
+    buildPotentials(idListDict, pairPotentialDict, mesh);
+}
+
+// * * * * * * * * * * * * * * * * Destructor  * * * * * * * * * * * * * * * //
+
+Foam::pairPotentialList::~pairPotentialList()
+{}
+
+// * * * * * * * * * * * * * * * Member Functions  * * * * * * * * * * * * * //
+
+void Foam::pairPotentialList::buildPotentials
+(
+    const dictionary& idListDict,
+    const dictionary& pairPotentialDict,
+    const polyMesh& mesh
+)
+{
+    idList_ = List<word>(idListDict.lookup("idList"));
+
+    setSize(((idList_.size() * (idList_.size() + 1))/2));
+
+    readPairPotentialDict(pairPotentialDict, mesh);
+}
+
+
+const Foam::pairPotential& Foam::pairPotentialList::pairPotentialFunction
+(
+    const label a,
+    const label b
+) const
+{
+    return (*this)[pairPotentialIndex (a,b)];
+}
+
+
+bool Foam::pairPotentialList::rCutSqr
+(
+    const label a,
+    const label b,
+    const scalar rIJMagSqr
+) const
+{
+    if(rIJMagSqr <= rCutSqr (a,b))
+    {
+        return true;
+    }
+    else
+    {
+        return false;
+    }
+}
+
+
+Foam::scalar Foam::pairPotentialList::rMin
+(
+    const label a,
+    const label b
+) const
+{
+    return (*this)[pairPotentialIndex (a,b)].rMin();
+}
+
+
+Foam::scalar Foam::pairPotentialList::dr
+(
+    const label a,
+    const label b
+) const
+{
+    return (*this)[pairPotentialIndex (a,b)].dr();
+}
+
+
+Foam::scalar Foam::pairPotentialList::rCutSqr
+(
+    const label a,
+    const label b
+) const
+{
+    return (*this)[pairPotentialIndex (a,b)].rCutSqr();
+}
+
+
+Foam::scalar Foam::pairPotentialList::rCut
+(
+    const label a,
+    const label b
+) const
+{
+    return (*this)[pairPotentialIndex (a,b)].rCut();
+}
+
+
+Foam::scalar Foam::pairPotentialList::force
+(
+    const label a,
+    const label b,
+    const scalar rIJMag
+) const
+{
+    scalar f = (*this)[pairPotentialIndex (a,b)].forceLookup(rIJMag);
+
+    return f;
+}
+
+
+Foam::scalar Foam::pairPotentialList::energy
+(
+    const label a,
+    const label b,
+    const scalar rIJMag
+) const
+{
+    scalar e = (*this)[pairPotentialIndex (a,b)].energyLookup(rIJMag);
+
+    return e;
+}
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+// ************************************************************************* //
diff --git a/src/lagrangian/molecularDynamics/potential/pairPotential/pairPotentialList/pairPotentialList.H b/src/lagrangian/molecularDynamics/potential/pairPotential/pairPotentialList/pairPotentialList.H
new file mode 100755
index 0000000000..92526cf479
--- /dev/null
+++ b/src/lagrangian/molecularDynamics/potential/pairPotential/pairPotentialList/pairPotentialList.H
@@ -0,0 +1,172 @@
+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+   \\    /   O peration     |
+    \\  /    A nd           | Copyright (C) 1991-2005 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::pairPotentialList
+
+Description
+
+SourceFiles
+    pairPotentialListI.H
+    pairPotentialList.C
+
+\*---------------------------------------------------------------------------*/
+
+#ifndef pairPotentialList_H
+#define pairPotentialList_H
+
+#include "PtrList.H"
+#include "word.H"
+#include "pairPotential.H"
+#include "polyMesh.H"
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+namespace Foam
+{
+
+/*---------------------------------------------------------------------------*\
+                           Class pairPotentialList Declaration
+\*---------------------------------------------------------------------------*/
+
+class pairPotentialList
+:
+    public PtrList<pairPotential>
+{
+    // Private data
+
+        List<word> idList_;
+        
+        scalar rCutMax_;
+
+        scalar rCutMaxSqr_;
+
+    // Private Member Functions
+
+        inline label pairPotentialIndex
+        (
+            const label a,
+            const label b
+        ) const;
+
+        void readPairPotentialDict
+        (
+            const dictionary& pairPotentialDict,
+            const polyMesh& mesh
+        );
+
+        //- Disallow default bitwise assignment
+        void operator=(const pairPotentialList&);
+
+        //- Disallow default bitwise copy construct
+        pairPotentialList(const pairPotentialList&);
+
+public:
+
+    // Constructors
+
+        pairPotentialList();
+
+        //- Construct from idList and potental dictionaries
+        pairPotentialList
+        (
+            const dictionary& idListDict,
+            const dictionary& pairPotentialDict,
+            const polyMesh& mesh
+        );
+
+    // Destructor
+
+        ~pairPotentialList();
+
+    // Member Functions
+        
+        void buildPotentials
+        (
+            const dictionary& idListDict,
+            const dictionary& pairPotentialDict,
+            const polyMesh& mesh
+        );
+
+        // Access
+
+            inline const List<word>& idList() const;
+
+            inline label nIds() const;
+
+            inline scalar rCutMax() const;
+
+            inline scalar rCutMaxSqr() const;
+
+            const pairPotential& pairPotentialFunction
+            (
+                const label a,
+                const label b
+            ) const;
+
+            // Return true if rIJ is within rCut for this pair.
+            bool rCutSqr
+            (
+                const label a,
+                const label b,
+                const scalar rIJMagSqr
+            ) const;
+
+            scalar rMin (const label a, const label b) const;
+
+            scalar dr (const label a, const label b) const;
+
+            scalar rCutSqr (const label a, const label b) const;
+
+            scalar rCut (const label a, const label b) const;
+
+            scalar force
+            (
+                const label a,
+                const label b,
+                const scalar rIJMag
+            ) const;
+
+            scalar energy
+            (
+                const label a,
+                const label b,
+                const scalar rIJMag
+            ) const;
+};
+
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+} // End namespace Foam
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+#include "pairPotentialListI.H"
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+#endif
+
+// ************************************************************************* //
diff --git a/src/lagrangian/molecularDynamics/potential/pairPotential/pairPotentialList/pairPotentialListI.H b/src/lagrangian/molecularDynamics/potential/pairPotential/pairPotentialList/pairPotentialListI.H
new file mode 100755
index 0000000000..ed02ca3b7c
--- /dev/null
+++ b/src/lagrangian/molecularDynamics/potential/pairPotential/pairPotentialList/pairPotentialListI.H
@@ -0,0 +1,84 @@
+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+   \\    /   O peration     |
+    \\  /    A nd           | Copyright (C) 1991-2005 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
+
+\*---------------------------------------------------------------------------*/
+
+// * * * * * * * * * * * * * Private Member Functions  * * * * * * * * * * * //
+
+inline Foam::label Foam::pairPotentialList::pairPotentialIndex
+(
+    const label a,
+    const label b
+) const
+{
+    label index;
+
+    if (a < b)
+    {
+        index = a*(2 * nIds() - a - 1) / 2 + b;
+    }
+
+    else
+    {
+        index = b*(2 * nIds() - b - 1) / 2 + a;
+    }
+
+    if (index > size() - 1)
+    {
+        FatalErrorIn("Foam::pairPotentialList::pairPotentialIndex ")
+            << "Attempting to access a pairPotential with too high an index."
+            << nl << "a = " << a << ", b = " << b << ", index = " << index
+            << nl << "max index = " << size() - 1
+            << nl << abort(FatalError);
+    }
+
+    return index;
+}
+
+// * * * * * * * * * * * * * * * Member Functions  * * * * * * * * * * * * * //
+
+inline Foam::label Foam::pairPotentialList::nIds() const
+{
+    return idList_.size();
+}
+
+
+inline const Foam::List<Foam::word>& Foam::pairPotentialList::idList() const
+{
+    return idList_;
+}
+
+
+inline Foam::scalar Foam::pairPotentialList::rCutMax() const
+{
+    return rCutMax_;
+}
+
+
+inline Foam::scalar Foam::pairPotentialList::rCutMaxSqr() const
+{
+    return rCutMaxSqr_;
+}
+
+// ************************************************************************* //
diff --git a/src/lagrangian/molecularDynamics/potential/tetherPotential/basic/newTetherPotential.C b/src/lagrangian/molecularDynamics/potential/tetherPotential/basic/newTetherPotential.C
new file mode 100644
index 0000000000..d9aaf566fc
--- /dev/null
+++ b/src/lagrangian/molecularDynamics/potential/tetherPotential/basic/newTetherPotential.C
@@ -0,0 +1,75 @@
+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  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
+    tetherPotential
+
+\*---------------------------------------------------------------------------*/
+
+#include "tetherPotential.H"
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+namespace Foam
+{
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+autoPtr<tetherPotential> tetherPotential::New
+(
+    const word& name,
+    const dictionary& tetherPotentialProperties
+)
+{
+    word tetherPotentialTypeName(tetherPotentialProperties.lookup("tetherPotential"));
+
+    Info<< nl << "Selecting tether potential "
+        << tetherPotentialTypeName << " for "
+        << name << endl;
+
+    dictionaryConstructorTable::iterator cstrIter =
+        dictionaryConstructorTablePtr_->find(tetherPotentialTypeName);
+
+    if (cstrIter == dictionaryConstructorTablePtr_->end())
+    {
+        FatalErrorIn
+        (
+            "tetherPotential::New()"
+        )   << "Unknown tetherPotential type "
+            << tetherPotentialTypeName << endl << endl
+            << "Valid  tetherPotentials are : " << endl
+            << dictionaryConstructorTablePtr_->toc()
+            << exit(FatalError);
+    }
+
+    return autoPtr<tetherPotential>
+        (cstrIter()(name, tetherPotentialProperties));
+}
+
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+} // End namespace Foam
+
+// ************************************************************************* //
diff --git a/src/lagrangian/molecularDynamics/potential/tetherPotential/basic/tetherPotential.C b/src/lagrangian/molecularDynamics/potential/tetherPotential/basic/tetherPotential.C
new file mode 100644
index 0000000000..de06d6607c
--- /dev/null
+++ b/src/lagrangian/molecularDynamics/potential/tetherPotential/basic/tetherPotential.C
@@ -0,0 +1,71 @@
+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  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
+    tetherPotential
+
+\*---------------------------------------------------------------------------*/
+
+#include "tetherPotential.H"
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+namespace Foam
+{
+
+// * * * * * * * * * * * * * * Static Data Members * * * * * * * * * * * * * //
+
+defineTypeNameAndDebug(tetherPotential, 0);
+defineRunTimeSelectionTable(tetherPotential, dictionary);
+
+// * * * * * * * * * * * * * Private Member Functions  * * * * * * * * * * * //
+
+
+// * * * * * * * * * * * * * * * * Constructors  * * * * * * * * * * * * * * //
+
+Foam::tetherPotential::tetherPotential
+(
+    const word& name,
+    const dictionary& tetherPotentialProperties
+)
+:
+    name_(name),
+    tetherPotentialProperties_(tetherPotentialProperties)
+{}
+
+// * * * * * * * * * * * * * * Member Functions  * * * * * * * * * * * * * * //
+
+
+bool Foam::tetherPotential::read(const dictionary& tetherPotentialProperties)
+{
+    tetherPotentialProperties_ = tetherPotentialProperties;
+
+    return true;
+}
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+} // End namespace Foam
+
+// ************************************************************************* //
diff --git a/src/lagrangian/molecularDynamics/potential/tetherPotential/basic/tetherPotential.H b/src/lagrangian/molecularDynamics/potential/tetherPotential/basic/tetherPotential.H
new file mode 100644
index 0000000000..4fb5bb8e73
--- /dev/null
+++ b/src/lagrangian/molecularDynamics/potential/tetherPotential/basic/tetherPotential.H
@@ -0,0 +1,143 @@
+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  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
+    tetherPotential
+
+Description
+
+SourceFiles
+    tetherPotential.C
+    newTetherPotential.C
+
+\*---------------------------------------------------------------------------*/
+
+#ifndef tetherPotential_H
+#define tetherPotential_H
+
+#include "IOdictionary.H"
+#include "typeInfo.H"
+#include "runTimeSelectionTables.H"
+#include "autoPtr.H"
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+namespace Foam
+{
+
+/*---------------------------------------------------------------------------*\
+                Class tetherPotential Declaration
+\*---------------------------------------------------------------------------*/
+
+class tetherPotential
+{
+
+protected:
+
+    // Protected data
+
+        word name_;
+        dictionary tetherPotentialProperties_;
+
+
+    // Private Member Functions
+        
+        //- Disallow copy construct
+        tetherPotential(const tetherPotential&);
+
+        //- Disallow default bitwise assignment
+        void operator=(const tetherPotential&);
+
+public:
+
+    //- Runtime type information
+    TypeName("tetherPotential");
+
+
+    // Declare run-time constructor selection table
+
+        declareRunTimeSelectionTable
+        (
+            autoPtr,
+            tetherPotential,
+            dictionary,
+            (
+                const word& name,
+                const dictionary& tetherPotentialProperties
+            ),
+            (name, tetherPotentialProperties)
+        );
+
+
+    // Selectors
+
+        //- Return a reference to the selected viscosity model
+        static autoPtr<tetherPotential> New
+        (
+            const word& name,
+            const dictionary& tetherPotentialProperties
+        );
+
+
+    // Constructors
+
+        //- Construct from components
+        tetherPotential
+        (
+            const word& name,
+            const dictionary& tetherPotentialProperties
+        );
+
+
+    // Destructor
+
+        virtual ~tetherPotential()
+        {}
+
+
+    // Member Functions
+
+        virtual scalar energy (const scalar r) const = 0;
+
+        virtual scalar force (const scalar r) const = 0;
+
+        const dictionary& tetherPotentialProperties() const
+        {
+            return tetherPotentialProperties_;
+        }
+
+        //- Read tetherPotential dictionary
+        virtual bool read(const dictionary& tetherPotentialProperties) = 0;
+};
+
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+} // End namespace Foam
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+#endif
+
+// ************************************************************************* //
diff --git a/src/lagrangian/molecularDynamics/potential/tetherPotential/derived/harmonicSpring/harmonicSpring.C b/src/lagrangian/molecularDynamics/potential/tetherPotential/derived/harmonicSpring/harmonicSpring.C
new file mode 100644
index 0000000000..4e5248f96c
--- /dev/null
+++ b/src/lagrangian/molecularDynamics/potential/tetherPotential/derived/harmonicSpring/harmonicSpring.C
@@ -0,0 +1,93 @@
+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  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 "harmonicSpring.H"
+#include "addToRunTimeSelectionTable.H"
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+namespace Foam
+{
+namespace tetherPotentials
+{
+
+// * * * * * * * * * * * * * * Static Data Members * * * * * * * * * * * * * //
+
+defineTypeNameAndDebug(harmonicSpring, 0);
+
+addToRunTimeSelectionTable
+(
+    tetherPotential,
+    harmonicSpring,
+    dictionary
+);
+
+// * * * * * * * * * * * * Private Member Functions  * * * * * * * * * * * * //
+
+
+// * * * * * * * * * * * * * * * * Constructors  * * * * * * * * * * * * * * //
+
+harmonicSpring::harmonicSpring
+(
+    const word& name,
+    const dictionary& tetherPotentialProperties
+)
+:
+    tetherPotential(name, tetherPotentialProperties),
+    harmonicSpringCoeffs_(tetherPotentialProperties.subDict(typeName + "Coeffs")),
+    springConstant_(readScalar(harmonicSpringCoeffs_.lookup("springConstant")))
+{}
+
+// * * * * * * * * * * * * * * Member Functions  * * * * * * * * * * * * * * //
+
+scalar harmonicSpring::energy(const scalar r) const
+{
+    return 0.5 * springConstant_ * r * r;
+}
+
+scalar harmonicSpring::force(const scalar r) const
+{
+    return -springConstant_ * r;
+}
+
+bool harmonicSpring::read(const dictionary& tetherPotentialProperties)
+{
+    tetherPotential::read(tetherPotentialProperties);
+
+    harmonicSpringCoeffs_ = tetherPotentialProperties.subDict(typeName + "Coeffs");
+
+    harmonicSpringCoeffs_.lookup("springConstant") >> springConstant_;
+    
+    return true;
+}
+
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+} // End namespace tetherPotentials
+} // End namespace Foam
+
+// ************************************************************************* //
diff --git a/src/lagrangian/molecularDynamics/potential/tetherPotential/derived/harmonicSpring/harmonicSpring.H b/src/lagrangian/molecularDynamics/potential/tetherPotential/derived/harmonicSpring/harmonicSpring.H
new file mode 100644
index 0000000000..92f9908c0a
--- /dev/null
+++ b/src/lagrangian/molecularDynamics/potential/tetherPotential/derived/harmonicSpring/harmonicSpring.H
@@ -0,0 +1,104 @@
+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  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
+    harmonicSpring
+
+Description
+     
+
+SourceFiles
+    harmonicSpring.C
+
+\*---------------------------------------------------------------------------*/
+
+#ifndef harmonicSpring_H
+#define harmonicSpring_H
+
+#include "tetherPotential.H"
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+namespace Foam
+{
+namespace tetherPotentials
+{
+
+/*---------------------------------------------------------------------------*\
+                           Class harmonicSpring Declaration
+\*---------------------------------------------------------------------------*/
+
+class harmonicSpring
+:
+    public tetherPotential
+{
+    // Private data
+
+        dictionary harmonicSpringCoeffs_;
+
+        scalar springConstant_;
+
+public:
+
+    //- Runtime type information
+    TypeName("harmonicSpring");
+
+
+    // Constructors
+
+        //- Construct from components
+        harmonicSpring
+        (
+            const word& name,
+            const dictionary& tetherPotentialProperties
+        );
+
+
+    // Destructor
+
+        ~harmonicSpring()
+        {}
+
+
+    // Member Functions
+
+        scalar energy(const scalar r) const;
+
+        scalar force(const scalar r) const;
+
+        //- Read transportProperties dictionary
+        bool read(const dictionary& tetherPotentialProperties);
+};
+
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+} // End namespace tetherPotentials
+} // End namespace Foam
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+#endif
+
+// ************************************************************************* //
diff --git a/src/lagrangian/molecularDynamics/potential/tetherPotential/derived/restrainedHarmonicSpring/restrainedHarmonicSpring.C b/src/lagrangian/molecularDynamics/potential/tetherPotential/derived/restrainedHarmonicSpring/restrainedHarmonicSpring.C
new file mode 100644
index 0000000000..7baa584b30
--- /dev/null
+++ b/src/lagrangian/molecularDynamics/potential/tetherPotential/derived/restrainedHarmonicSpring/restrainedHarmonicSpring.C
@@ -0,0 +1,121 @@
+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  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 "restrainedHarmonicSpring.H"
+#include "addToRunTimeSelectionTable.H"
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+namespace Foam
+{
+namespace tetherPotentials
+{
+
+// * * * * * * * * * * * * * * Static Data Members * * * * * * * * * * * * * //
+
+defineTypeNameAndDebug(restrainedHarmonicSpring, 0);
+
+addToRunTimeSelectionTable
+(
+    tetherPotential,
+    restrainedHarmonicSpring,
+    dictionary
+);
+
+// * * * * * * * * * * * * Private Member Functions  * * * * * * * * * * * * //
+
+
+// * * * * * * * * * * * * * * * * Constructors  * * * * * * * * * * * * * * //
+
+restrainedHarmonicSpring::restrainedHarmonicSpring
+(
+    const word& name,
+    const dictionary& tetherPotentialProperties
+)
+:
+    tetherPotential(name, tetherPotentialProperties),
+    restrainedHarmonicSpringCoeffs_
+    (
+        tetherPotentialProperties.subDict(typeName + "Coeffs")
+    ),
+    springConstant_
+    (
+        readScalar(restrainedHarmonicSpringCoeffs_.lookup("springConstant"))
+    ),
+    rR_
+    (
+        readScalar(restrainedHarmonicSpringCoeffs_.lookup("rR"))
+    )
+{}
+
+// * * * * * * * * * * * * * * Member Functions  * * * * * * * * * * * * * * //
+
+scalar restrainedHarmonicSpring::energy(const scalar r) const
+{
+    if (r < rR_)
+    {
+        return 0.5 * springConstant_ * r * r;
+    }
+    else
+    {
+        return 0.5 * springConstant_ * rR_ * rR_
+            + springConstant_ * rR_ * (r - rR_);
+    }
+}
+
+scalar restrainedHarmonicSpring::force(const scalar r) const
+{
+    if (r < rR_)
+    {
+        return -springConstant_ * r;
+    }
+    else
+    {
+        return -springConstant_ * rR_;
+    }
+    
+}
+
+bool restrainedHarmonicSpring::read(const dictionary& tetherPotentialProperties)
+{
+    tetherPotential::read(tetherPotentialProperties);
+
+    restrainedHarmonicSpringCoeffs_ =
+        tetherPotentialProperties.subDict(typeName + "Coeffs");
+
+    restrainedHarmonicSpringCoeffs_.lookup("springConstant") >> springConstant_;
+    restrainedHarmonicSpringCoeffs_.lookup("rR") >> rR_;
+    
+    return true;
+}
+
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+} // End namespace tetherPotentials
+} // End namespace Foam
+
+// ************************************************************************* //
diff --git a/src/lagrangian/molecularDynamics/potential/tetherPotential/derived/restrainedHarmonicSpring/restrainedHarmonicSpring.H b/src/lagrangian/molecularDynamics/potential/tetherPotential/derived/restrainedHarmonicSpring/restrainedHarmonicSpring.H
new file mode 100644
index 0000000000..021fdd1f6c
--- /dev/null
+++ b/src/lagrangian/molecularDynamics/potential/tetherPotential/derived/restrainedHarmonicSpring/restrainedHarmonicSpring.H
@@ -0,0 +1,106 @@
+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  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
+    restrainedHarmonicSpring
+
+Description
+     
+
+SourceFiles
+    restrainedHarmonicSpring.C
+
+\*---------------------------------------------------------------------------*/
+
+#ifndef restrainedHarmonicSpring_H
+#define restrainedHarmonicSpring_H
+
+#include "tetherPotential.H"
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+namespace Foam
+{
+namespace tetherPotentials
+{
+
+/*---------------------------------------------------------------------------*\
+                           Class restrainedHarmonicSpring Declaration
+\*---------------------------------------------------------------------------*/
+
+class restrainedHarmonicSpring
+:
+    public tetherPotential
+{
+    // Private data
+
+        dictionary restrainedHarmonicSpringCoeffs_;
+
+        scalar springConstant_;
+
+        scalar rR_;
+
+public:
+
+    //- Runtime type information
+    TypeName("restrainedHarmonicSpring");
+
+
+    // Constructors
+
+        //- Construct from components
+        restrainedHarmonicSpring
+        (
+            const word& name,
+            const dictionary& tetherPotentialProperties
+        );
+
+
+    // Destructor
+
+        ~restrainedHarmonicSpring()
+        {}
+
+
+    // Member Functions
+
+        scalar energy(const scalar r) const;
+
+        scalar force(const scalar r) const;
+
+        //- Read transportProperties dictionary
+        bool read(const dictionary& tetherPotentialProperties);
+};
+
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+} // End namespace tetherPotentials
+} // End namespace Foam
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+#endif
+
+// ************************************************************************* //
diff --git a/src/lagrangian/molecularDynamics/potential/tetherPotential/tetherPotentialList/tetherPotentialList.C b/src/lagrangian/molecularDynamics/potential/tetherPotential/tetherPotentialList/tetherPotentialList.C
new file mode 100755
index 0000000000..8bb11b72cd
--- /dev/null
+++ b/src/lagrangian/molecularDynamics/potential/tetherPotential/tetherPotentialList/tetherPotentialList.C
@@ -0,0 +1,166 @@
+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+   \\    /   O peration     |
+    \\  /    A nd           | Copyright (C) 1991-2005 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 "tetherPotentialList.H"
+
+// * * * * * * * * * * * * * Private Member Functions  * * * * * * * * * * * //
+
+void Foam::tetherPotentialList::readTetherPotentialDict
+(
+    const dictionary& tetherPotentialDict,  
+    const List<word>& idList,
+    const List<label>& tetherIds
+)
+{
+    if (!tetherIds.size())
+    {
+        Info<< nl << "No tethered molecules found." << endl;
+
+        idMap_.setSize(0);
+    }
+    else
+    {
+        Info<< nl << "Building tether potentials." << endl;
+
+        idMap_ = List<label>(idList.size(), -1);
+
+        label tetherMapIndex = 0;
+
+        forAll(tetherIds, t)
+        {
+            const label tetherId = tetherIds[t];
+
+            word tetherPotentialName = idList[tetherId];
+
+            if (!tetherPotentialDict.found(tetherPotentialName))
+            {
+                FatalErrorIn("tetherPotentialList::readTetherPotentialDict")
+                        << nl << "tether potential specification subDict "
+                        << tetherPotentialName << " not found"
+                        << abort(FatalError);
+            }
+
+            (*this).set
+            (
+                tetherMapIndex,
+                tetherPotential::New
+                (
+                    tetherPotentialName,
+                    tetherPotentialDict.subDict(tetherPotentialName)
+                )
+            );
+
+            idMap_[tetherId] = tetherMapIndex;
+
+            tetherMapIndex++;
+
+//             Info<< tetherPotentialName << ": "
+//                 << (*this)[tetherPotentialIndex(tetherId)].tetherPotentialProperties()
+//                 << endl;
+
+        }
+    }
+}
+
+// * * * * * * * * * * * * * * * * Constructors  * * * * * * * * * * * * * * //
+
+Foam::tetherPotentialList::tetherPotentialList()
+:
+    PtrList<tetherPotential>(),
+    idMap_()
+{}
+
+
+Foam::tetherPotentialList::tetherPotentialList
+(
+    const dictionary& idListDict,
+    const dictionary& tetherPotentialDict,
+    const List<label>& tetherIds
+)
+:
+    PtrList<tetherPotential>(),
+    idMap_()
+{
+    buildPotentials(idListDict, tetherPotentialDict, tetherIds);
+}
+
+// * * * * * * * * * * * * * * * * Destructor  * * * * * * * * * * * * * * * //
+
+Foam::tetherPotentialList::~tetherPotentialList()
+{}
+
+// * * * * * * * * * * * * * * * Member Functions  * * * * * * * * * * * * * //
+
+void Foam::tetherPotentialList::buildPotentials
+(
+    const dictionary& idListDict,
+    const dictionary& tetherPotentialDict,
+    const List<label>& tetherIds
+)
+{
+    setSize(tetherIds.size());
+
+    const List<word>& idList = List<word>(idListDict.lookup("idList"));
+
+    readTetherPotentialDict(tetherPotentialDict, idList, tetherIds);
+}
+
+
+const Foam::tetherPotential& Foam::tetherPotentialList::tetherPotentialFunction
+(
+    const label a
+) const
+{
+    return (*this)[tetherPotentialIndex (a)];
+}
+
+
+Foam::scalar Foam::tetherPotentialList::force
+(
+    const label a,
+    const scalar rITMag
+) const
+{
+    scalar f = (*this)[tetherPotentialIndex (a)].force(rITMag);
+
+    return f;
+}
+
+
+Foam::scalar Foam::tetherPotentialList::energy
+(
+    const label a,
+    const scalar rITMag
+) const
+{
+    scalar e = (*this)[tetherPotentialIndex (a)].energy(rITMag);
+
+    return e;
+}
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+// ************************************************************************* //
diff --git a/src/lagrangian/molecularDynamics/potential/tetherPotential/tetherPotentialList/tetherPotentialList.H b/src/lagrangian/molecularDynamics/potential/tetherPotential/tetherPotentialList/tetherPotentialList.H
new file mode 100755
index 0000000000..515a9d0710
--- /dev/null
+++ b/src/lagrangian/molecularDynamics/potential/tetherPotential/tetherPotentialList/tetherPotentialList.H
@@ -0,0 +1,141 @@
+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+   \\    /   O peration     |
+    \\  /    A nd           | Copyright (C) 1991-2005 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::tetherPotentialList
+
+Description
+
+SourceFiles
+    tetherPotentialList.C
+
+\*---------------------------------------------------------------------------*/
+
+#ifndef tetherPotentialList_H
+#define tetherPotentialList_H
+
+#include "PtrList.H"
+#include "word.H"
+#include "tetherPotential.H"
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+namespace Foam
+{
+
+/*---------------------------------------------------------------------------*\
+                           Class tetherPotentialList Declaration
+\*---------------------------------------------------------------------------*/
+
+class tetherPotentialList
+:
+    public PtrList<tetherPotential>
+{
+    // Private data
+
+        List<label> idMap_;
+
+    // Private Member Functions
+
+        inline label tetherPotentialIndex
+        (
+            const label a
+        ) const;
+
+        void readTetherPotentialDict
+        (
+            const dictionary& tetherPotentialDict,
+            const List<word>& idList,
+            const List<label>& tetherIds
+        );
+
+        //- Disallow default bitwise assignment
+        void operator=(const tetherPotentialList&);
+
+        //- Disallow default bitwise copy construct
+        tetherPotentialList(const tetherPotentialList&);
+
+public:
+
+    // Constructors
+
+        tetherPotentialList();
+
+        //- Construct from idList and potental dictionaries
+        tetherPotentialList
+        (
+            const dictionary& idListDict,
+            const dictionary& tetherPotentialDict,
+            const List<label>& tetherIds
+        );
+
+    // Destructor
+
+        ~tetherPotentialList();
+
+    // Member Functions
+        
+        void buildPotentials
+        (
+            const dictionary& idListDict,
+            const dictionary& tetherPotentialDict,
+            const List<label>& tetherIds
+        );
+
+        // Access
+
+            inline const List<word>& idMap() const;
+
+            const tetherPotential& tetherPotentialFunction
+            (
+                const label a
+            ) const;
+
+            scalar force
+            (
+                const label a,
+                const scalar rIJMag
+            ) const;
+
+            scalar energy
+            (
+                const label a,
+                const scalar rIJMag
+            ) const;
+};
+
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+} // End namespace Foam
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+#include "tetherPotentialListI.H"
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+#endif
+
+// ************************************************************************* //
diff --git a/src/lagrangian/molecularDynamics/potential/tetherPotential/tetherPotentialList/tetherPotentialListI.H b/src/lagrangian/molecularDynamics/potential/tetherPotential/tetherPotentialList/tetherPotentialListI.H
new file mode 100755
index 0000000000..fb75f16db7
--- /dev/null
+++ b/src/lagrangian/molecularDynamics/potential/tetherPotential/tetherPotentialList/tetherPotentialListI.H
@@ -0,0 +1,53 @@
+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+   \\    /   O peration     |
+    \\  /    A nd           | Copyright (C) 1991-2005 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
+
+\*---------------------------------------------------------------------------*/
+
+// * * * * * * * * * * * * * Private Member Functions  * * * * * * * * * * * //
+
+inline Foam::label Foam::tetherPotentialList::tetherPotentialIndex
+(
+    const label a
+) const
+{
+    label index = idMap_[a];
+
+    if (index == -1 || a >= idMap_.size())
+    {
+        FatalErrorIn
+        (
+            "Foam::tetherPotentialList::tetherPotentialIndex(const label a)"
+        )
+            << "Attempting to access an undefined tetherPotential."
+            << abort(FatalError);
+
+        return -1;
+    }
+    else
+    {
+        return index;
+    }
+}
+
+// ************************************************************************* //

From 217f01e02668db9e2b8fa44ba9f0652d3685d8a1 Mon Sep 17 00:00:00 2001
From: graham <graham.macpherson@strath.ac.uk>
Date: Tue, 17 Jun 2008 16:08:28 +0100
Subject: [PATCH 3/5] Updated gnemdFoam, mdEquilibrationFoam and molConfig
 applications to use new separate potential and molecule libraries.  Updated
 potentialDict description in mdEquilibrationFoam/periodicCube test case to
 new format.

---
 .../molecularDynamics/gnemdFoam/Make/options  |  6 ++--
 .../mdEquilibrationFoam/Make/options          |  6 ++--
 .../preProcessing/molConfig/Make/options      |  6 ++--
 tutorials/mdEquilibrationFoam/Allclean        | 13 ++++++++
 tutorials/mdEquilibrationFoam/Allrun          | 19 +++++++++++
 .../mdEquilibrationFoam/periodicCube/Allrun   | 10 ------
 .../periodicCube/system/mdSolution            |  2 --
 .../periodicCube/system/potentialDict         | 32 +++++++++++++------
 8 files changed, 67 insertions(+), 27 deletions(-)
 create mode 100755 tutorials/mdEquilibrationFoam/Allclean
 create mode 100755 tutorials/mdEquilibrationFoam/Allrun
 delete mode 100755 tutorials/mdEquilibrationFoam/periodicCube/Allrun

diff --git a/applications/solvers/molecularDynamics/gnemdFoam/Make/options b/applications/solvers/molecularDynamics/gnemdFoam/Make/options
index 80f9773456..89431d0625 100755
--- a/applications/solvers/molecularDynamics/gnemdFoam/Make/options
+++ b/applications/solvers/molecularDynamics/gnemdFoam/Make/options
@@ -1,5 +1,6 @@
 EXE_INC = \
-    -I$(LIB_SRC)/lagrangian/molecule/lnInclude \
+    -I$(LIB_SRC)/lagrangian/molecularDynamics/molecule/lnInclude \
+    -I$(LIB_SRC)/lagrangian/molecularDynamics/potential/lnInclude \
     -I$(LIB_SRC)/finiteVolume/lnInclude \
     -I$(LIB_SRC)/lagrangian/basic/lnInclude \
     -I$(LIB_SRC)/meshTools/lnInclude
@@ -8,4 +9,5 @@ EXE_LIBS = \
     -lmeshTools \
     -lfiniteVolume \
     -llagrangian \
-    -lmolecule
+    -lmolecule \
+    -lpotential
diff --git a/applications/solvers/molecularDynamics/mdEquilibrationFoam/Make/options b/applications/solvers/molecularDynamics/mdEquilibrationFoam/Make/options
index 80f9773456..89431d0625 100755
--- a/applications/solvers/molecularDynamics/mdEquilibrationFoam/Make/options
+++ b/applications/solvers/molecularDynamics/mdEquilibrationFoam/Make/options
@@ -1,5 +1,6 @@
 EXE_INC = \
-    -I$(LIB_SRC)/lagrangian/molecule/lnInclude \
+    -I$(LIB_SRC)/lagrangian/molecularDynamics/molecule/lnInclude \
+    -I$(LIB_SRC)/lagrangian/molecularDynamics/potential/lnInclude \
     -I$(LIB_SRC)/finiteVolume/lnInclude \
     -I$(LIB_SRC)/lagrangian/basic/lnInclude \
     -I$(LIB_SRC)/meshTools/lnInclude
@@ -8,4 +9,5 @@ EXE_LIBS = \
     -lmeshTools \
     -lfiniteVolume \
     -llagrangian \
-    -lmolecule
+    -lmolecule \
+    -lpotential
diff --git a/applications/utilities/preProcessing/molConfig/Make/options b/applications/utilities/preProcessing/molConfig/Make/options
index 196a4d66dd..aab9a2ca4f 100755
--- a/applications/utilities/preProcessing/molConfig/Make/options
+++ b/applications/utilities/preProcessing/molConfig/Make/options
@@ -3,7 +3,8 @@ EXE_INC = \
     -I$(velocityDistributions) \
     -I$(LIB_SRC)/meshTools/lnInclude \
     -I$(LIB_SRC)/dynamicMesh/lnInclude \
-    -I$(LIB_SRC)/lagrangian/molecule/lnInclude \
+    -I$(LIB_SRC)/lagrangian/molecularDynamics/molecule/lnInclude \
+    -I$(LIB_SRC)/lagrangian/molecularDynamics/potential/lnInclude \
     -I$(LIB_SRC)/lagrangian/basic/lnInclude \
     -I$(LIB_SRC)/finiteVolume/lnInclude
 
@@ -12,4 +13,5 @@ EXE_LIBS = \
     -ldynamicMesh \
     -lfiniteVolume \
     -llagrangian \
-    -lmolecule
+    -lmolecule \
+    -lpotential
diff --git a/tutorials/mdEquilibrationFoam/Allclean b/tutorials/mdEquilibrationFoam/Allclean
new file mode 100755
index 0000000000..3d688adfb3
--- /dev/null
+++ b/tutorials/mdEquilibrationFoam/Allclean
@@ -0,0 +1,13 @@
+#!/bin/sh
+
+currDir=`pwd`
+application=`basename $currDir`
+cases="periodicCube"
+
+tutorialPath=`dirname $0`/..
+. $tutorialPath/CleanFunctions
+
+for case in $cases
+do
+    cleanCase $case
+done
diff --git a/tutorials/mdEquilibrationFoam/Allrun b/tutorials/mdEquilibrationFoam/Allrun
new file mode 100755
index 0000000000..eefbf1aded
--- /dev/null
+++ b/tutorials/mdEquilibrationFoam/Allrun
@@ -0,0 +1,19 @@
+#!/bin/sh
+
+currDir=`pwd`
+application=`basename $currDir`
+cases="periodicCube"
+
+tutorialPath=`dirname $0`/..
+. $tutorialPath/RunFunctions
+. $tutorialPath/CleanFunctions
+
+
+for case in $cases
+do
+    runApplication blockMesh $case
+
+    runApplication molConfig $case
+
+    runApplication $application $case
+done
diff --git a/tutorials/mdEquilibrationFoam/periodicCube/Allrun b/tutorials/mdEquilibrationFoam/periodicCube/Allrun
deleted file mode 100755
index 2121179f1c..0000000000
--- a/tutorials/mdEquilibrationFoam/periodicCube/Allrun
+++ /dev/null
@@ -1,10 +0,0 @@
-#!/bin/sh
-# Source tutorial run functions
-. $WM_PROJECT_DIR/bin/tools/RunFunctions
-
-# Get application name from directory
-application=`basename $PWD`
-
-runApplication blockMesh
-runApplication molConfig
-runApplication $application
diff --git a/tutorials/mdEquilibrationFoam/periodicCube/system/mdSolution b/tutorials/mdEquilibrationFoam/periodicCube/system/mdSolution
index 681963175d..c72bb260fa 100644
--- a/tutorials/mdEquilibrationFoam/periodicCube/system/mdSolution
+++ b/tutorials/mdEquilibrationFoam/periodicCube/system/mdSolution
@@ -26,6 +26,4 @@ integrationMethod               verletLeapfrog;
 
 potentialEnergyLimit            5.256e-20;
 
-guardRadius                     0;
-
 // ************************************************************************* //
\ No newline at end of file
diff --git a/tutorials/mdEquilibrationFoam/periodicCube/system/potentialDict b/tutorials/mdEquilibrationFoam/periodicCube/system/potentialDict
index 78fa1c7746..f4d27d298b 100644
--- a/tutorials/mdEquilibrationFoam/periodicCube/system/potentialDict
+++ b/tutorials/mdEquilibrationFoam/periodicCube/system/potentialDict
@@ -22,7 +22,7 @@ FoamFile
 
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
 
-// Subdictionaries specifying types of intermoleular potential.
+// Subdictionaries specifying types of intermolecular potential.
 // Sub-sub dictionaries specify the potentials themselves.
 
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
@@ -52,14 +52,24 @@ pair
 {
     Ar-Ar
     {
-        potentialType   maitlandSmithTabulated;
-        m               13.0;
-        gamma           7.5;
-        rm              0.3756e-9;
-        epsilon         1.990108438e-21;
-        rCut            1.0e-9;
+        pairPotential   azizChen;
+        rCut            1.2e-9;
         rMin            0.15e-9;
         dr              2e-14;
+        azizChenCoeffs
+        {
+            epsilon     1.97742255e-21;
+            rm          3.759e-10;
+            A           0.9502720e7;
+            alpha       16.345655;
+            C6          1.0914254;
+            C8          0.6002595;
+            C10         0.3700113;
+            D           1.4;
+            gamma       2.0;
+        }
+        energyScalingFunction   noScaling;
+        writeTables     yes;
     }
 }
 
@@ -70,8 +80,12 @@ tether
 {
     Ar
     {
-        potentialType   harmonicSpring;
-        springConstant  0.0277;
+        tetherPotential restrainedHarmonicSpring;
+        restrainedHarmonicSpringCoeffs
+        {
+            springConstant  0.0277;
+            rR              1.2e-9;
+        }
     }
 }
 

From 29d1571274bf1ac9202426d90a7def796952b479 Mon Sep 17 00:00:00 2001
From: graham <graham.macpherson@strath.ac.uk>
Date: Tue, 17 Jun 2008 16:59:46 +0100
Subject: [PATCH 4/5] Updated src/lagrangian/Allwmake

---
 src/lagrangian/Allwmake | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/src/lagrangian/Allwmake b/src/lagrangian/Allwmake
index 567f7a10de..088a4a3b5d 100755
--- a/src/lagrangian/Allwmake
+++ b/src/lagrangian/Allwmake
@@ -5,4 +5,7 @@ wmake libso basic
 wmake libso solidParticle
 wmake libso intermediate
 wmake libso dieselSpray
-wmake libso molecule
+wmake libso molecularDynamics/potential
+wmake libso molecularDynamics/molecule
+
+ 

From ff8991246b0fd3f58ebb4cf5ff8c2081eef9286f Mon Sep 17 00:00:00 2001
From: graham <graham.macpherson@strath.ac.uk>
Date: Tue, 17 Jun 2008 18:01:27 +0100
Subject: [PATCH 5/5] Updated etc/settings.sh for gcc 4.3.1

---
 etc/settings.csh | 2 +-
 etc/settings.sh  | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/etc/settings.csh b/etc/settings.csh
index 1e4d509e8a..7219d4be24 100644
--- a/etc/settings.csh
+++ b/etc/settings.csh
@@ -89,7 +89,7 @@ switch ("$WM_COMPILER_INST")
 case OpenFOAM:
     switch ("$WM_COMPILER")
     case Gcc43:
-        setenv WM_COMPILER_DIR $WM_THIRD_PARTY_DIR/gcc-4.3.0/platforms/$WM_ARCH$WM_COMPILER_ARCH
+        setenv WM_COMPILER_DIR $WM_THIRD_PARTY_DIR/gcc-4.3.1/platforms/$WM_ARCH$WM_COMPILER_ARCH
     breaksw
     case Gcc:
         setenv WM_COMPILER_DIR $WM_THIRD_PARTY_DIR/gcc-4.2.2/platforms/$WM_ARCH$WM_COMPILER_ARCH
diff --git a/etc/settings.sh b/etc/settings.sh
index 7631ac900e..cf63d1584d 100644
--- a/etc/settings.sh
+++ b/etc/settings.sh
@@ -105,7 +105,7 @@ case "$WM_COMPILER_INST" in
 OpenFOAM)
     case "$WM_COMPILER" in
     Gcc43)
-        export WM_COMPILER_DIR=$WM_THIRD_PARTY_DIR/gcc-4.3.0/platforms/$WM_ARCH$WM_COMPILER_ARCH
+        export WM_COMPILER_DIR=$WM_THIRD_PARTY_DIR/gcc-4.3.1/platforms/$WM_ARCH$WM_COMPILER_ARCH
         ;;
     Gcc)
         export WM_COMPILER_DIR=$WM_THIRD_PARTY_DIR/gcc-4.2.2/platforms/$WM_ARCH$WM_COMPILER_ARCH