From 12e0fc01c0c233c33b59fc69d558bf797d2d6ab1 Mon Sep 17 00:00:00 2001
From: andy <a.heather@opencfd.co.uk>
Date: Mon, 23 Jun 2008 17:42:05 +0100
Subject: [PATCH] removed molecular dynamics functionality (being updated)

---
 .../preProcessing/molConfig/Make/files        |   8 -
 .../molConfig/correctVelocities.H             |  21 --
 .../preProcessing/molConfig/createMolecules.C | 253 ------------------
 .../preProcessing/molConfig/createPositions.H |  26 --
 .../molConfig/createVelocities.H              |  13 -
 .../preProcessing/molConfig/genMolConfig.C    | 129 ---------
 .../molConfig/latticeStructures/BCC.H         | 179 -------------
 .../molConfig/latticeStructures/FCC.H         | 217 ---------------
 .../molConfig/latticeStructures/SC.H          | 127 ---------
 .../preProcessing/molConfig/molConfig.C       |  50 ----
 .../preProcessing/molConfig/molConfig.H       | 147 ----------
 .../preProcessing/molConfig/molConfigI.H      |  98 -------
 .../preProcessing/molConfig/origin.H          |  49 ----
 .../preProcessing/molConfig/readZoneSubDict.H |  93 -------
 .../preProcessing/molConfig/startingPoint.H   |  97 -------
 .../velocityDistributions/maxwellian.H        |  26 --
 .../molConfig/velocityDistributions/uniform.H |  27 --
 .../constant/polyMesh/blockMeshDict           |  73 -----
 .../periodicCube/system/fvSchemes             |  67 -----
 .../periodicCube/system/fvSolution            |  40 ---
 .../periodicCube/system/mdEquilibrationDict   |  27 --
 .../periodicCube/system/molConfigDict         |  43 ---
 22 files changed, 1810 deletions(-)
 delete mode 100755 applications/utilities/preProcessing/molConfig/Make/files
 delete mode 100644 applications/utilities/preProcessing/molConfig/correctVelocities.H
 delete mode 100644 applications/utilities/preProcessing/molConfig/createMolecules.C
 delete mode 100644 applications/utilities/preProcessing/molConfig/createPositions.H
 delete mode 100644 applications/utilities/preProcessing/molConfig/createVelocities.H
 delete mode 100644 applications/utilities/preProcessing/molConfig/genMolConfig.C
 delete mode 100644 applications/utilities/preProcessing/molConfig/latticeStructures/BCC.H
 delete mode 100644 applications/utilities/preProcessing/molConfig/latticeStructures/FCC.H
 delete mode 100644 applications/utilities/preProcessing/molConfig/latticeStructures/SC.H
 delete mode 100644 applications/utilities/preProcessing/molConfig/molConfig.C
 delete mode 100644 applications/utilities/preProcessing/molConfig/molConfig.H
 delete mode 100644 applications/utilities/preProcessing/molConfig/molConfigI.H
 delete mode 100644 applications/utilities/preProcessing/molConfig/origin.H
 delete mode 100644 applications/utilities/preProcessing/molConfig/readZoneSubDict.H
 delete mode 100644 applications/utilities/preProcessing/molConfig/startingPoint.H
 delete mode 100644 applications/utilities/preProcessing/molConfig/velocityDistributions/maxwellian.H
 delete mode 100644 applications/utilities/preProcessing/molConfig/velocityDistributions/uniform.H
 delete mode 100644 tutorials/mdEquilibrationFoam/periodicCube/constant/polyMesh/blockMeshDict
 delete mode 100644 tutorials/mdEquilibrationFoam/periodicCube/system/fvSchemes
 delete mode 100644 tutorials/mdEquilibrationFoam/periodicCube/system/fvSolution
 delete mode 100644 tutorials/mdEquilibrationFoam/periodicCube/system/mdEquilibrationDict
 delete mode 100644 tutorials/mdEquilibrationFoam/periodicCube/system/molConfigDict

diff --git a/applications/utilities/preProcessing/molConfig/Make/files b/applications/utilities/preProcessing/molConfig/Make/files
deleted file mode 100755
index 6501e68426..0000000000
--- a/applications/utilities/preProcessing/molConfig/Make/files
+++ /dev/null
@@ -1,8 +0,0 @@
-latticeStructures = latticeStructures
-velocityDistributions = velocityDistributions
-
-createMolecules.C
-molConfig.C
-genMolConfig.C
-
-EXE = $(FOAM_APPBIN)/molConfig
diff --git a/applications/utilities/preProcessing/molConfig/correctVelocities.H b/applications/utilities/preProcessing/molConfig/correctVelocities.H
deleted file mode 100644
index 0c69f15c7c..0000000000
--- a/applications/utilities/preProcessing/molConfig/correctVelocities.H
+++ /dev/null
@@ -1,21 +0,0 @@
-for (molN = totalMols; molN < totalMols + totalZoneMols; molN++)
-{
-
-    // Remove bulk momentum introduced by random numbers and add
-    // desired bulk velocity
-
-    // For systems with molecules of significantly differing masses, this may
-    // need to be an iterative process or employ a better algorithm for
-    // removing an appropriate share of the excess momentum from each molecule.
-
-    initialVelocities(molN) += bulkVelocity - momentumSum/totalZoneMols/mass;
-}
-
-// momentumSum = vector::zero;
-//
-// for (molN = totalMols; molN < totalMols + totalZoneMols; molN++)
-// {
-//     momentumSum += mass*initialVelocities(molN);
-// }
-//
-// Info << "Check momentum adjustment: " << momentumSum << endl;
diff --git a/applications/utilities/preProcessing/molConfig/createMolecules.C b/applications/utilities/preProcessing/molConfig/createMolecules.C
deleted file mode 100644
index 20318f06d6..0000000000
--- a/applications/utilities/preProcessing/molConfig/createMolecules.C
+++ /dev/null
@@ -1,253 +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 "molConfig.H"
-
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-void Foam::molConfig::createMolecules()
-{
-    Info<< nl << "Creating molecules from zone specifications\n" << endl;
-
-    DynamicList<vector> initialPositions(0);
-
-    DynamicList<label> initialIds(0);
-
-    DynamicList<scalar> initialMasses(0);
-
-    DynamicList<label> initialCelli(0);
-
-    DynamicList<vector> initialVelocities(0);
-
-    DynamicList<vector> initialAccelerations(0);
-
-    DynamicList<label> initialTethered(0);
-
-    DynamicList<vector> initialTetherPositions(0);
-
-    label totalMols = 0;
-
-    label idAssign;
-
-    Random rand(clock::getTime());
-
-// * * * * * * * * Building the IdList * * * * * * * * * //
-
-//Notes: - each processor will have an identical idList_.
-//       - The order of id's inside the idList_ depends on the order
-//         of subDicts inside the molConigDict.
-
-    Info<< "Building the idList: " ;
-
-    forAll(molConfigDescription_.toc(), cZs)
-    {
-        word subDictName (molConfigDescription_.toc()[cZs]);
-
-        word iD (molConfigDescription_.subDict(subDictName).lookup("id"));
-
-        if (findIndex(idList_,iD) == -1)
-        {
-            idList_.append(iD);
-        }
-    }
-
-    forAll(idList_, i)
-    {
-        Info << " " << idList_[i];
-    }
-
-    Info << nl << endl;
-
-// * * * * * * * * Filling the Mesh * * * * * * * * * //
-
-    const cellZoneMesh& cellZoneI = mesh_.cellZones();
-
-    if (cellZoneI.size())
-    {
-        Info<< "Filling the zones with molecules." << nl << endl;
-    }
-    else
-    {
-        FatalErrorIn("void createMolecules()\n")
-            << "No cellZones found in mesh description."
-            << abort(FatalError);
-    }
-
-    forAll (cellZoneI, cZ)
-    {
-        if (cellZoneI[cZ].size())
-        {
-            if (!molConfigDescription_.found(cellZoneI[cZ].name()))
-            {
-                Info << "Zone specification subDictionary: "
-                    << cellZoneI[cZ].name() << " not found." << endl;
-            }
-            else
-            {
-                label n = 0;
-
-                label totalZoneMols = 0;
-
-                label molsPlacedThisIteration;
-
-#               include "readZoneSubDict.H"
-
-                idAssign = findIndex(idList_,id);
-
-#               include "startingPoint.H"
-
-                // Continue trying to place molecules as long as at
-                // least one molecule is placed in each iteration.
-                // The "|| totalZoneMols == 0" condition means that the
-                // algorithm will continue if the origin is outside the
-                // zone - it will cause an infinite loop if no molecules
-                // are ever placed by the algorithm.
-
-                if (latticeStructure != "empty")
-                {
-
-                    while
-                    (
-                        molsPlacedThisIteration != 0
-                     || totalZoneMols == 0
-                    )
-                    {
-                        molsPlacedThisIteration = 0;
-
-                        bool partOfLayerInBounds = false;
-
-#                       include "createPositions.H"
-
-                        if
-                        (
-                            totalZoneMols == 0
-                         && !partOfLayerInBounds
-                        )
-                        {
-                            WarningIn("molConfig::createMolecules()")
-                                << "A whole layer of unit cells was placed "
-                                << "outside the bounds of the mesh, but no "
-                                << "molecules have been placed in zone '"
-                                << cellZoneI[cZ].name()
-                                << "'.  This is likely to be because the zone "
-                                << "has few cells ("
-                                << cellZoneI[cZ].size()
-                                << " in this case) and no lattice position "
-                                << "fell inside them.  "
-                                << "Aborting filling this zone."
-                                << endl;
-
-                            break;
-                        }
-
-                        totalZoneMols += molsPlacedThisIteration;
-
-                        n++;
-                    }
-
-                    label molN;
-
-                    for
-                    (
-                        molN = totalMols;
-                        molN < totalMols + totalZoneMols;
-                        molN++
-                    )
-                    {
-                        initialIds.append(idAssign);
-
-                        initialMasses.append(mass);
-
-                        initialAccelerations.append(vector::zero);
-
-                        if (tethered)
-                        {
-                            initialTethered.append(1);
-
-                            initialTetherPositions.append
-                            (
-                                initialPositions[molN]
-                            );
-                        }
-
-                        else
-                        {
-                            initialTethered.append(0);
-
-                            initialTetherPositions.append(vector::zero);
-                        }
-                    }
-
-#                   include "createVelocities.H"
-
-#                   include "correctVelocities.H"
-
-                }
-
-                totalMols += totalZoneMols;
-            }
-        }
-    }
-
-    idList_.shrink();
-
-    positions_ = initialPositions;
-
-    positions_.setSize(initialPositions.size());
-
-    id_ = initialIds;
-
-    id_.setSize(initialIds.size());
-
-    mass_ = initialMasses;
-
-    mass_.setSize(initialMasses.size());
-
-    cells_ = initialCelli;
-
-    cells_.setSize(initialCelli.size());
-
-    U_ = initialVelocities;
-
-    U_.setSize(initialVelocities.size());
-
-    A_ = initialAccelerations;
-
-    A_.setSize(initialAccelerations.size());
-
-    tethered_ = initialTethered;
-
-    tethered_.setSize(initialTethered.size());
-
-    tetherPositions_ = initialTetherPositions;
-
-    tetherPositions_.setSize(initialTetherPositions.size());
-
-    nMol_ = totalMols;
-}
-
-
-// ************************************************************************* //
diff --git a/applications/utilities/preProcessing/molConfig/createPositions.H b/applications/utilities/preProcessing/molConfig/createPositions.H
deleted file mode 100644
index b26486338c..0000000000
--- a/applications/utilities/preProcessing/molConfig/createPositions.H
+++ /dev/null
@@ -1,26 +0,0 @@
-vector latticePosition;
-
-vector globalPosition;
-
-if (latticeStructure == "SC")
-{
-#   include "SC.H"
-}
-
-else if (latticeStructure == "FCC")
-{
-#   include "FCC.H"
-}
-
-else if (latticeStructure == "BCC")
-{
-#   include "BCC.H"
-}
-
-else
-{
-    FatalErrorIn("createPositions.H\n")
-        << "latticeStructure " << latticeStructure
-        << " not supported."
-        << abort(FatalError);
-}
diff --git a/applications/utilities/preProcessing/molConfig/createVelocities.H b/applications/utilities/preProcessing/molConfig/createVelocities.H
deleted file mode 100644
index d014ffd146..0000000000
--- a/applications/utilities/preProcessing/molConfig/createVelocities.H
+++ /dev/null
@@ -1,13 +0,0 @@
-vector velocity;
-
-vector momentumSum = vector::zero;
-
-if (velocityDistribution == "uniform")
-{
-#    include "uniform.H"
-}
-
-if (velocityDistribution == "maxwellian")
-{
-#    include "maxwellian.H"
-}
diff --git a/applications/utilities/preProcessing/molConfig/genMolConfig.C b/applications/utilities/preProcessing/molConfig/genMolConfig.C
deleted file mode 100644
index 91bc5c8d24..0000000000
--- a/applications/utilities/preProcessing/molConfig/genMolConfig.C
+++ /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
-
-\*---------------------------------------------------------------------------*/
-
-#include "molConfig.H"
-#include "fvCFD.H"
-
-using namespace Foam;
-
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-// Main program:
-
-int main(int argc, char *argv[])
-{
-#   include "setRootCase.H"
-#   include "createTime.H"
-#   include "createMesh.H"
-
-    Info<< nl << "Reading molecular configuration description dictionary"
-        << endl;
-
-    IOobject molConfigDescriptionIOobject
-    (
-        "molConfigDict",
-        runTime.system(),
-        runTime,
-        IOobject::MUST_READ,
-        IOobject::NO_WRITE,
-        false
-    );
-
-    if (!molConfigDescriptionIOobject.headerOk())
-    {
-        FatalErrorIn(args.executable())
-            << "Cannot find molConfig description file " << nl
-            << args.caseName()/runTime.system()/"molConfig"/"molConfigDict"
-            << nl << exit(FatalError);
-    }
-
-    IOdictionary molConfigDescription(molConfigDescriptionIOobject);
-
-
-    // Create molCloud, registering object with mesh
-
-    Info<< nl << "Creating molecular configuration" << endl;
-
-    molConfig molecules(molConfigDescription, mesh);
-
-    label totalMolecules = molecules.nMol();
-
-    if (Pstream::parRun())
-    {
-        reduce(totalMolecules, sumOp<label>());
-    }
-
-    Info<< nl << "Total number of molecules added: " << totalMolecules
-        << nl << endl;
-
-    moleculeCloud molCloud
-    (
-        mesh,
-        molecules.nMol(),
-        molecules.id(),
-        molecules.mass(),
-        molecules.positions(),
-        molecules.cells(),
-        molecules.U(),
-        molecules.A(),
-        molecules.tethered(),
-        molecules.tetherPositions()
-    );
-
-    IOdictionary idListDict
-    (
-        IOobject
-        (
-            "idList",
-            mesh.time().constant(),
-            mesh,
-            IOobject::NO_READ,
-            IOobject::AUTO_WRITE
-        )
-    );
-
-    idListDict.add("idList", molecules.molIdList());
-
-    IOstream::defaultPrecision(12);
-
-    Info << nl << "Writing molecular configuration" << endl;
-
-    if (!mesh.write())
-    {
-        FatalErrorIn(args.executable())
-            << "Failed writing moleculeCloud."
-            << nl << exit(FatalError);
-    }
-
-    Info<< nl << "ClockTime = " << runTime.elapsedClockTime() << " s"
-        << nl << endl;
-
-    Info << nl << "End\n" << endl;
-
-    return 0;
-}
-
-
-// ************************************************************************* //
diff --git a/applications/utilities/preProcessing/molConfig/latticeStructures/BCC.H b/applications/utilities/preProcessing/molConfig/latticeStructures/BCC.H
deleted file mode 100644
index cd3cbdf100..0000000000
--- a/applications/utilities/preProcessing/molConfig/latticeStructures/BCC.H
+++ /dev/null
@@ -1,179 +0,0 @@
-labelVector iN(0,0,0);
-
-vector gap = (vector::one)*pow((numberDensity/2.0),-(1.0/3.0));
-
-#include "origin.H"
-
-// Info<< "gap = " << gap << endl;
-
-// Special treatment is required for the first position, i.e. iteration zero.
-
-if (n == 0)
-{
-    latticePosition.x() = (iN.x()*gap.x());
-
-    latticePosition.y() = (iN.y()*gap.y());
-
-    latticePosition.z() = (iN.z()*gap.z());
-
-    // Placing 2 molecules in each unit cell, using the algorithm from
-    // D. Rapaport, The Art of Molecular Dynamics Simulation, 2nd Ed, p68
-
-    for (label iU = 0; iU < 2; iU++)
-    {
-        vector unitCellLatticePosition = latticePosition;
-
-        if (iU == 1)
-        {
-            unitCellLatticePosition += 0.5 * gap;
-        }
-
-        if (originSpecifies == "corner")
-        {
-            unitCellLatticePosition -= 0.25*gap;
-        }
-
-//         Info << nl << n << ", " << unitCellLatticePosition;
-
-        globalPosition =
-            origin + transform(latticeToGlobal,unitCellLatticePosition);
-
-        partOfLayerInBounds = mesh_.bounds().contains(globalPosition);
-
-        if
-        (
-             findIndex(mesh_.cellZones()[cZ], mesh_.findCell(globalPosition))
-           != -1
-        )
-        {
-            molsPlacedThisIteration++;
-
-            initialPositions.append(globalPosition);
-
-            initialCelli.append(mesh_.findCell(globalPosition));
-        }
-    }
-}
-else
-{
-    // Place top and bottom caps.
-
-    for (iN.z() = -n; iN.z() <= n; iN.z() += 2*n)
-    {
-        for (iN.y() = -n; iN.y() <= n; iN.y()++)
-        {
-            for (iN.x() = -n; iN.x() <= n; iN.x()++)
-            {
-                latticePosition.x() = (iN.x() * gap.x());
-
-                latticePosition.y() = (iN.y() * gap.y());
-
-                latticePosition.z() = (iN.z() * gap.z());
-
-                for (label iU = 0; iU < 2; iU++)
-                {
-                    vector unitCellLatticePosition = latticePosition;
-
-                    if (iU == 1)
-                    {
-                        unitCellLatticePosition += 0.5*gap;
-                    }
-
-                    if(originSpecifies == "corner")
-                    {
-                        unitCellLatticePosition -= 0.25*gap;
-                    }
-
-//                     Info << nl << iN << ", " << unitCellLatticePosition;
-
-                    globalPosition =
-                        origin
-                      + transform(latticeToGlobal,unitCellLatticePosition);
-
-                    partOfLayerInBounds =
-                        mesh_.bounds().contains(globalPosition);
-
-                    if
-                    (
-                        findIndex
-                        (
-                             mesh_.cellZones()[cZ],
-                             mesh_.findCell(globalPosition)
-                        )
-                     != -1)
-                    {
-                        molsPlacedThisIteration++;
-
-                        initialPositions.append(globalPosition);
-
-                        initialCelli.append(mesh_.findCell(globalPosition));
-                    }
-                }
-            }
-        }
-    }
-
-//     Placing sides
-
-    for (iN.z() = -(n-1); iN.z() <= (n-1); iN.z()++)
-    {
-        for (label iR = 0; iR <= 2*n -1; iR++)
-        {
-            latticePosition.x() = (n*gap.x());
-
-            latticePosition.y() = ((-n + (iR + 1))*gap.y());
-
-            latticePosition.z() = (iN.z() * gap.z());
-
-            for (label iK = 0; iK < 4; iK++)
-            {
-                for (label iU = 0; iU < 2; iU++)
-                {
-                    vector unitCellLatticePosition = latticePosition;
-
-                    if (iU == 1)
-                    {
-                        unitCellLatticePosition += 0.5 * gap;
-                    }
-
-                    if (originSpecifies == "corner")
-                    {
-                        unitCellLatticePosition -= 0.25*gap;
-                    }
-
-                    globalPosition =
-                        origin
-                      + transform(latticeToGlobal,unitCellLatticePosition);
-
-                    partOfLayerInBounds =
-                        mesh_.bounds().contains(globalPosition);
-
-                    if
-                    (
-                        findIndex
-                         (
-                             mesh_.cellZones()[cZ],
-                             mesh_.findCell(globalPosition)
-                         )
-                      != -1
-                    )
-                    {
-                        molsPlacedThisIteration++;
-
-                        initialPositions.append(globalPosition);
-
-                        initialCelli.append(mesh_.findCell(globalPosition));
-                    }
-                }
-
-                latticePosition =
-                    vector
-                    (
-                      - latticePosition.y(),
-                        latticePosition.x(),
-                        latticePosition.z()
-                    );
-            }
-        }
-    }
-}
diff --git a/applications/utilities/preProcessing/molConfig/latticeStructures/FCC.H b/applications/utilities/preProcessing/molConfig/latticeStructures/FCC.H
deleted file mode 100644
index 313ebf96cb..0000000000
--- a/applications/utilities/preProcessing/molConfig/latticeStructures/FCC.H
+++ /dev/null
@@ -1,217 +0,0 @@
-labelVector iN(0,0,0);
-
-vector gap = (vector::one)*pow((numberDensity/4.0),-(1.0/3.0));
-
-#include "origin.H"
-
-// Info<< "gap = " << gap << endl;
-
-// Special treatment is required for the first position, i.e. iteration zero.
-
-if (n == 0)
-{
-    latticePosition.x() = (iN.x() * gap.x());
-
-    latticePosition.y() = (iN.y() * gap.y());
-
-    latticePosition.z() = (iN.z() * gap.z());
-
-    // Placing 4 molecules in each unit cell, using the algorithm from
-    // D. Rapaport, The Art of Molecular Dynamics Simulation, 2nd Ed, p68
-
-    for (label iU = 0; iU < 4; iU++)
-    {
-        vector unitCellLatticePosition = latticePosition;
-
-        if (iU != 3)
-        {
-            if (iU != 0)
-            {
-                unitCellLatticePosition.x() += 0.5 * gap.x();
-            }
-
-            if (iU != 1)
-            {
-                unitCellLatticePosition.y() += 0.5 * gap.y();
-            }
-
-            if (iU != 2)
-            {
-                unitCellLatticePosition.z() += 0.5 * gap.z();
-            }
-        }
-
-        if (originSpecifies == "corner")
-        {
-            unitCellLatticePosition -= 0.25*gap;
-        }
-
-//         Info << nl << n << ", " << unitCellLatticePosition;
-
-        globalPosition =
-            origin + transform(latticeToGlobal,unitCellLatticePosition);
-
-        partOfLayerInBounds = mesh_.bounds().contains(globalPosition);
-
-        if
-        (
-            findIndex(mesh_.cellZones()[cZ], mesh_.findCell(globalPosition))
-          != -1
-        )
-        {
-            molsPlacedThisIteration++;
-
-            initialPositions.append(globalPosition);
-
-            initialCelli.append(mesh_.findCell(globalPosition));
-        }
-    }
-}
-else
-{
-    // Place top and bottom caps.
-
-    for (iN.z() = -n; iN.z() <= n; iN.z() += 2*n)
-    {
-        for (iN.y() = -n; iN.y() <= n; iN.y()++)
-        {
-            for (iN.x() = -n; iN.x() <= n; iN.x()++)
-            {
-                latticePosition.x() = (iN.x() * gap.x());
-
-                latticePosition.y() = (iN.y() * gap.y());
-
-                latticePosition.z() = (iN.z() * gap.z());
-
-                for (label iU = 0; iU < 4; iU++)
-                {
-                    vector unitCellLatticePosition = latticePosition;
-
-                    if (iU != 3)
-                    {
-                        if (iU != 0)
-                        {
-                            unitCellLatticePosition.x() += 0.5 * gap.x();
-                        }
-
-                        if (iU != 1)
-                        {
-                            unitCellLatticePosition.y() += 0.5 * gap.y();
-                        }
-
-                        if (iU != 2)
-                        {
-                            unitCellLatticePosition.z() += 0.5 * gap.z();
-                        }
-                    }
-
-                    if (originSpecifies == "corner")
-                    {
-                        unitCellLatticePosition -= 0.25*gap;
-                    }
-
-                    globalPosition =
-                        origin
-                      + transform(latticeToGlobal,unitCellLatticePosition);
-
-                    partOfLayerInBounds =
-                        mesh_.bounds().contains(globalPosition);
-
-                    if
-                    (
-                        findIndex
-                        (
-                            mesh_.cellZones()[cZ],
-                            mesh_.findCell(globalPosition)
-                        )
-                     != -1
-                    )
-                    {
-                        molsPlacedThisIteration++;
-
-                        initialPositions.append(globalPosition);
-
-                        initialCelli.append(mesh_.findCell(globalPosition));
-                    }
-                }
-            }
-        }
-    }
-
-//     Placing sides
-
-    for (iN.z() = -(n-1); iN.z() <= (n-1); iN.z()++)
-    {
-        for (label iR = 0; iR <= 2*n -1; iR++)
-        {
-            latticePosition.x() = (n * gap.x());
-
-            latticePosition.y() = ((-n + (iR + 1)) * gap.y());
-
-            latticePosition.z() = (iN.z() * gap.z());
-
-            for (label iK = 0; iK < 4; iK++)
-            {
-                for (label iU = 0; iU < 4; iU++)
-                {
-                    vector unitCellLatticePosition = latticePosition;
-
-                    if (iU != 3)
-                    {
-                        if (iU != 0)
-                        {
-                            unitCellLatticePosition.x() += 0.5 * gap.x();
-                        }
-
-                        if (iU != 1)
-                        {
-                            unitCellLatticePosition.y() += 0.5 * gap.y();
-                        }
-
-                        if (iU != 2)
-                        {
-                            unitCellLatticePosition.z() += 0.5 * gap.z();
-                        }
-                    }
-
-                    if (originSpecifies == "corner")
-                    {
-                        unitCellLatticePosition -= 0.25*gap;
-                    }
-
-                    globalPosition =
-                        origin
-                      + transform(latticeToGlobal,unitCellLatticePosition);
-
-                    partOfLayerInBounds =
-                        mesh_.bounds().contains(globalPosition);
-
-                    if
-                    (
-                        findIndex
-                        (
-                            mesh_.cellZones()[cZ],
-                            mesh_.findCell(globalPosition)
-                        )
-                     != -1
-                    )
-                    {
-                        molsPlacedThisIteration++;
-
-                        initialPositions.append(globalPosition);
-
-                        initialCelli.append(mesh_.findCell(globalPosition));
-                    }
-                }
-
-                latticePosition =
-                    vector
-                    (
-                      - latticePosition.y(),
-                        latticePosition.x(),
-                        latticePosition.z()
-                    );
-            }
-        }
-    }
-}
diff --git a/applications/utilities/preProcessing/molConfig/latticeStructures/SC.H b/applications/utilities/preProcessing/molConfig/latticeStructures/SC.H
deleted file mode 100644
index dd0ff7c00f..0000000000
--- a/applications/utilities/preProcessing/molConfig/latticeStructures/SC.H
+++ /dev/null
@@ -1,127 +0,0 @@
-labelVector iN(0,0,0);
-
-vector gap = (vector::one)*pow(numberDensity, -(1.0/3.0));
-
-#include "origin.H"
-
-// Info<< "gap = " << gap << endl;
-
-// Special treatment is required for the first position, i.e. iteration zero.
-
-if (n == 0)
-{
-    latticePosition = vector::zero;
-
-    if (originSpecifies == "corner")
-    {
-        latticePosition += 0.5*gap;
-    }
-
-    globalPosition = origin + transform(latticeToGlobal,latticePosition);
-
-    partOfLayerInBounds = mesh_.bounds().contains(globalPosition);
-
-    if (findIndex(mesh_.cellZones()[cZ], mesh_.findCell(globalPosition)) != -1)
-    {
-        molsPlacedThisIteration++;
-
-        initialPositions.append(globalPosition);
-
-        initialCelli.append(mesh_.findCell(globalPosition));
-    }
-}
-else
-{
-    for (iN.z() = -n; iN.z() <= n; iN.z() += 2*n)
-    {
-        for (iN.y() = -n; iN.y() <= n; iN.y()++)
-        {
-            for (iN.x() = -n; iN.x() <= n; iN.x()++)
-            {
-                latticePosition.x() = (iN.x() * gap.x());
-
-                latticePosition.y() = (iN.y() * gap.y());
-
-                latticePosition.z() = (iN.z() * gap.z());
-
-                if (originSpecifies == "corner")
-                {
-                    latticePosition += 0.5*gap;
-                }
-
-                globalPosition =
-                    origin + transform(latticeToGlobal,latticePosition);
-
-                partOfLayerInBounds = mesh_.bounds().contains(globalPosition);
-
-                if
-                (
-                    findIndex
-                    (
-                        mesh_.cellZones()[cZ],
-                        mesh_.findCell(globalPosition)
-                    )
-                 != -1
-                )
-                {
-                    molsPlacedThisIteration++;
-
-                    initialPositions.append(globalPosition);
-
-                    initialCelli.append(mesh_.findCell(globalPosition));
-                }
-            }
-        }
-    }
-
-    tensor quarterRotate(EulerCoordinateRotation(-90, 0, 0, true).R());
-
-    iN.x() = n;
-    for (iN.z() = -(n-1); iN.z() <= (n-1); iN.z()++)
-    {
-        for (iN.y() = -(n-1); iN.y() <= n; iN.y()++)
-        {
-            latticePosition.x() = (iN.x()*gap.x());
-
-            latticePosition.y() = (iN.y()*gap.y());
-
-            latticePosition.z() = (iN.z()*gap.z());
-
-            for (label iR = 0; iR < 4; iR++)
-            {
-                vector offsetCorrectedLatticePosition = latticePosition;
-
-                if (originSpecifies == "corner")
-                {
-                    offsetCorrectedLatticePosition += 0.5*gap;
-                }
-
-                globalPosition =
-                    origin
-                  + transform(latticeToGlobal,offsetCorrectedLatticePosition);
-
-                partOfLayerInBounds = mesh_.bounds().contains(globalPosition);
-
-                if
-                (
-                    findIndex
-                    (
-                        mesh_.cellZones()[cZ],
-                        mesh_.findCell(globalPosition)
-                    )
-                 != -1
-                )
-                {
-                    molsPlacedThisIteration++;
-
-                    initialPositions.append(globalPosition);
-
-                    initialCelli.append(mesh_.findCell(globalPosition));
-                }
-
-                latticePosition = transform(quarterRotate,latticePosition);
-            }
-        }
-    }
-}
-
diff --git a/applications/utilities/preProcessing/molConfig/molConfig.C b/applications/utilities/preProcessing/molConfig/molConfig.C
deleted file mode 100644
index e837346b97..0000000000
--- a/applications/utilities/preProcessing/molConfig/molConfig.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 "molConfig.H"
-
-// * * * * * * * * * * * * * * * * Constructor * * * * * * * * * * * * * * * //
-
-Foam::molConfig::molConfig
-(
-    IOdictionary& molConfigDescription,
-    const polyMesh& mesh
-)
-:
-    molConfigDescription_(molConfigDescription),
-    mesh_(mesh)
-{
-    createMolecules();
-}
-
-
-// * * * * * * * * * * * * * * * * Destructor  * * * * * * * * * * * * * * * //
-
-Foam::molConfig::~molConfig()
-{}
-
-
-// ************************************************************************* //
diff --git a/applications/utilities/preProcessing/molConfig/molConfig.H b/applications/utilities/preProcessing/molConfig/molConfig.H
deleted file mode 100644
index a9d549da12..0000000000
--- a/applications/utilities/preProcessing/molConfig/molConfig.H
+++ /dev/null
@@ -1,147 +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::molConfig
-
-Description
-
-SourceFiles
-    molConfigI.H
-    molConfig.C
-    molConfigIO.C
-
-\*---------------------------------------------------------------------------*/
-
-#ifndef molConfig_H
-#define molConfig_H
-
-#include "labelVector.H"
-#include "scalar.H"
-#include "vector.H"
-#include "labelField.H"
-#include "scalarField.H"
-#include "vectorField.H"
-#include "IOField.H"
-#include "EulerCoordinateRotation.H"
-#include "Random.H"
-
-#include "Time.H"
-#include "IOdictionary.H"
-#include "IOstreams.H"
-#include "moleculeCloud.H"
-
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-namespace Foam
-{
-
-/*---------------------------------------------------------------------------*\
-                           Class molConfig Declaration
-\*---------------------------------------------------------------------------*/
-
-class molConfig
-{
-    // Private data
-
-        const IOdictionary& molConfigDescription_;
-
-        const polyMesh& mesh_;
-
-        DynamicList<word> idList_;
-
-        labelField id_;
-
-        scalarField mass_;
-
-        vectorField positions_;
-
-        labelField cells_;
-
-        vectorField U_;
-
-        vectorField A_;
-
-        labelField tethered_;
-
-        vectorField tetherPositions_;
-
-        label nMol_;
-
-
-public:
-
-    // Constructors
-
-        //- Construct from IOdictionary and mesh
-        molConfig(IOdictionary&, const polyMesh&);
-
-
-    // Destructor
-
-        ~molConfig();
-
-
-    // Member Functions
-
-        void createMolecules();
-
-
-        // Access
-
-            inline const List<word>& molIdList() const;
-
-            inline const labelField& id() const;
-
-            inline const scalarField& mass() const;
-
-            inline const vectorField& positions() const;
-
-            inline const labelField& cells() const;
-
-            inline const vectorField& U() const;
-
-            inline const vectorField& A() const;
-
-            inline const labelField& tethered() const;
-
-            inline const vectorField& tetherPositions() const;
-
-            inline label nMol() const;
-};
-
-
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-} // End namespace Foam
-
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-#include "molConfigI.H"
-
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-#endif
-
-// ************************************************************************* //
diff --git a/applications/utilities/preProcessing/molConfig/molConfigI.H b/applications/utilities/preProcessing/molConfig/molConfigI.H
deleted file mode 100644
index b85a656c03..0000000000
--- a/applications/utilities/preProcessing/molConfig/molConfigI.H
+++ /dev/null
@@ -1,98 +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<word>& molConfig::molIdList() const
-{
-    return idList_;
-}
-
-
-inline const labelField& molConfig::id() const
-{
-    return id_;
-}
-
-
-inline const scalarField& molConfig::mass() const
-{
-    return mass_;
-}
-
-
-inline const vectorField& molConfig::positions() const
-{
-    return positions_;
-}
-
-
-inline const labelField& molConfig::cells() const
-{
-    return cells_;
-}
-
-
-inline const vectorField& molConfig::U() const
-{
-    return U_;
-}
-
-
-inline const vectorField& molConfig::A() const
-{
-    return A_;
-}
-
-
-inline const labelField& molConfig::tethered() const
-{
-    return tethered_;
-}
-
-
-inline const vectorField& molConfig::tetherPositions() const
-{
-    return tetherPositions_;
-}
-
-
-inline label molConfig::nMol() const
-{
-    return nMol_;
-}
-
-
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-} // End namespace Foam
-
-// ************************************************************************* //
diff --git a/applications/utilities/preProcessing/molConfig/origin.H b/applications/utilities/preProcessing/molConfig/origin.H
deleted file mode 100644
index 24bc994d34..0000000000
--- a/applications/utilities/preProcessing/molConfig/origin.H
+++ /dev/null
@@ -1,49 +0,0 @@
-// Please refer to notes
-
-// 1. Determine the unit cell dimensions: xU, yU and zU
-
-const scalar xU = gap.x();
-const scalar yU = gap.y();
-const scalar zU = gap.z();
-
-// 2. Determine the anchorPoint co-ordinates: xA, yA  and zA
-
-const scalar xA = anchorPoint.x();
-const scalar yA = anchorPoint.y();
-const scalar zA = anchorPoint.z();
-
-// 3. Determine the vector rAB from global co-ordinate system:
-
-const vector rAB((xMid - xA), (yMid - yA), (zMid - zA));
-
-// 4. Transform vector rAS into lattice co-ordinate system:
-
-const vector rASTransf = transform(latticeToGlobal.T(), rAB);
-
-// Info << "The vector rAS = " << rAS << endl;
-// Info << "The vector rAStransf = " << rAStransf << endl;
-
-// 5. Calculate the integer values: ni, nj and nk
-scalar nIscalar = rASTransf.x()/xU;
-scalar nJscalar = rASTransf.y()/yU;
-scalar nKscalar = rASTransf.z()/zU;
-
-// Info << "The nI, nJ, nK values before are: " << nIscalar <<" "<< nJscalar <<" "<< nKscalar << endl;
-
-label nI = label(nIscalar + 0.5*sign(nIscalar));
-label nJ = label(nJscalar + 0.5*sign(nJscalar));
-label nK = label(nKscalar + 0.5*sign(nKscalar));
-
-// Info << "The nI, nJ, nK values after are: " << nI <<" "<< nJ <<" "<< nK << endl;
-
-// 6. Calculate the corrected starting point, rAC (in the lattice co-ordinate system):
-const vector rAC((nI*xU), (nJ*yU), (nK*zU));
-
-// 7. Transform the corrected starting point in the global co-ordinate system, rC:
-const vector rC = anchorPoint + transform(latticeToGlobal, rAC);
-
-
-const vector& origin = rC;
-
-// Pout << "The Corrected Starting Point: " << origin << endl;
-
diff --git a/applications/utilities/preProcessing/molConfig/readZoneSubDict.H b/applications/utilities/preProcessing/molConfig/readZoneSubDict.H
deleted file mode 100644
index 72705c761e..0000000000
--- a/applications/utilities/preProcessing/molConfig/readZoneSubDict.H
+++ /dev/null
@@ -1,93 +0,0 @@
-
-// Info << "Zone description subDict " << cZ <<": "  << cellZoneI[cZ].name() << endl;
-
-const dictionary& subDictI =
-    molConfigDescription_.subDict(cellZoneI[cZ].name());
-
-const scalar temperature(readScalar(subDictI.lookup("temperature")));
-
-const word velocityDistribution(subDictI.lookup("velocityDistribution"));
-
-const vector bulkVelocity(subDictI.lookup("bulkVelocity"));
-
-const word id(subDictI.lookup("id"));
-
-const scalar mass(readScalar(subDictI.lookup("mass")));
-
-scalar numberDensity_read(0.0);
-
-if (subDictI.found("numberDensity"))
-{
-    numberDensity_read = readScalar(subDictI.lookup("numberDensity"));
-}
-else if (subDictI.found("massDensity"))
-{
-    numberDensity_read = readScalar(subDictI.lookup("massDensity"))/mass;
-}
-else
-{
-    FatalErrorIn("readZoneSubDict.H\n")
-        << "massDensity or numberDensity not specified " << nl
-        << abort(FatalError);
-}
-
-const scalar numberDensity(numberDensity_read);
-
-const word latticeStructure(subDictI.lookup("latticeStructure"));
-
-const vector anchorPoint(subDictI.lookup("anchor"));
-
-const word originSpecifies(subDictI.lookup("anchorSpecifies"));
-
-if
-(
-    originSpecifies != "corner"
- && originSpecifies != "molecule"
-)
-{
-    FatalErrorIn("readZoneSubDict.H\n")
-        << "anchorSpecifies must be either 'corner' or 'molecule', found "
-        << originSpecifies << nl
-        << abort(FatalError);
-}
-
-bool tethered = false;
-
-if (subDictI.found("tethered"))
-{
-    tethered = Switch(subDictI.lookup("tethered"));
-}
-
-const vector orientationAngles(subDictI.lookup("orientationAngles"));
-
-scalar phi(orientationAngles.x()*mathematicalConstant::pi/180.0);
-scalar theta(orientationAngles.y()*mathematicalConstant::pi/180.0);
-scalar psi(orientationAngles.z()*mathematicalConstant::pi/180.0);
-
-const tensor latticeToGlobal
-(
-    cos(psi)*cos(phi) - cos(theta)*sin(phi)*sin(psi),
-    cos(psi)*sin(phi) + cos(theta)*cos(phi)*sin(psi),
-    sin(psi)*sin(theta),
-  - sin(psi)*cos(phi) - cos(theta)*sin(phi)*cos(psi),
-  - sin(psi)*sin(phi) + cos(theta)*cos(phi)*cos(psi),
-    cos(psi)*sin(theta),
-    sin(theta)*sin(phi),
-  - sin(theta)*cos(phi),
-    cos(theta)
-);
-
-// Info << "\tcells: " << cellZoneI[cZ].size() << endl;
-// Info << "\tnumberDensity: " << numberDensity << endl;
-// Info << "\ttemperature: " << temperature << endl;
-// Info << "\tvelocityDistribution: " << velocityDistribution << endl;
-// Info << "\tbulkVelocity: " << bulkVelocity << endl;
-// Info << "\tid: " << id << endl;
-// Info << "\tmass: " << mass << endl;
-// Info << "\tlatticeStructure: " << latticeStructure << endl;
-// Info << "\tanchor: " << anchorPoint << endl;
-// Info << "\toriginSpecifies: " << originSpecifies << endl;
-// Info << "\ttethered: " << tethered << endl;
-// Info << "\torientationAngles: " << orientationAngles << endl;
-// Info << "\tlatticeToGlobal: " << latticeToGlobal << endl;
-
diff --git a/applications/utilities/preProcessing/molConfig/startingPoint.H b/applications/utilities/preProcessing/molConfig/startingPoint.H
deleted file mode 100644
index 6ae01c83f1..0000000000
--- a/applications/utilities/preProcessing/molConfig/startingPoint.H
+++ /dev/null
@@ -1,97 +0,0 @@
-scalar xMax = 0;
-
-scalar yMax = 0;
-
-scalar zMax = 0;
-
-scalar xMin = 0;
-
-scalar yMin = 0;
-
-scalar zMin = 0;
-
-label xMaxPtLabel = 0;
-
-label yMaxPtLabel = 0;
-
-label zMaxPtLabel = 0;
-
-label xMinPtLabel = 0;
-
-label yMinPtLabel = 0;
-
-label zMinPtLabel = 0;
-
-forAll (cellZoneI[cZ], nC)
-{
-    const labelList& cellPointsJ = mesh_.cellPoints()[cellZoneI[cZ][nC]];
-
-    forAll(cellPointsJ, nP)
-    {
-        const point& ptI = mesh_.points()[cellPointsJ[nP]];
-
-        const label& ptILabel = cellPointsJ[nP];
-
-        if (ptI.x() > xMax || nC == 0)
-        {
-            xMax = ptI.x();
-            xMaxPtLabel = ptILabel;
-        }
-        if (ptI.y() > yMax || nC == 0)
-        {
-            yMax = ptI.y();
-            yMaxPtLabel = ptILabel;
-        }
-        if (ptI.z() > zMax || nC == 0)
-        {
-            zMax = ptI.z();
-            zMaxPtLabel = ptILabel;
-        }
-        if (ptI.x() < xMin || nC == 0)
-        {
-            xMin = ptI.x();
-            xMinPtLabel = ptILabel;
-        }
-        if (ptI.y() < yMin || nC == 0)
-        {
-            yMin = ptI.y();
-            yMinPtLabel = ptILabel;
-        }
-        if (ptI.z() < zMin || nC == 0)
-        {
-            zMin = ptI.z();
-            zMinPtLabel = ptILabel;
-        }
-    }
-}
-
-// Info << "Xmax: label = " << xMaxPtLabel2 << "; vector = " <<mesh_.points()[xMaxPtLabel2]
-//      <<"; x-component = " << mesh_.points()[xMaxPtLabel2].x() << endl;
-// Info << "Ymax: label = " << yMaxPtLabel2 << "; vector = " <<mesh_.points()[yMaxPtLabel2]
-//      <<"; y-component = " << mesh_.points()[yMaxPtLabel2].y() << endl;
-// Info << "Zmax: label = " << zMaxPtLabel2 << "; vector = " <<mesh_.points()[zMaxPtLabel2]
-//      <<"; z-component = " << mesh_.points()[zMaxPtLabel2].z() << endl;
-//
-// Info << "Xmin: label = " << xMinPtLabel << "; vector = " <<mesh_.points()[xMinPtLabel]
-//      <<"; x-component = " << mesh_.points()[xMinPtLabel].x() << endl;
-// Info << "Ymin: label = " << yMinPtLabel << "; vector = " <<mesh_.points()[yMinPtLabel]
-//      <<"; y-component = " << mesh_.points()[yMinPtLabel].y() << endl;
-// Info << "Zmin: label = " << zMinPtLabel << "; vector = " <<mesh_.points()[zMinPtLabel]
-//      <<"; z-component = " << mesh_.points()[zMinPtLabel].z() << endl;
-
-scalar xMid =
-    (mesh_.points()[xMaxPtLabel].x()
-  + mesh_.points()[xMinPtLabel].x()) / 2;
-
-scalar yMid =
-    (mesh_.points()[yMaxPtLabel].y()
-  + mesh_.points()[yMinPtLabel].y()) / 2;
-
-scalar zMid =
-    (mesh_.points()[zMaxPtLabel].z()
-  + mesh_.points()[zMinPtLabel].z()) / 2;
-
-vector rS(xMid, yMid, zMid);
-
-// Info << "\t The Estimated Starting Point: " << rS << endl;
-
diff --git a/applications/utilities/preProcessing/molConfig/velocityDistributions/maxwellian.H b/applications/utilities/preProcessing/molConfig/velocityDistributions/maxwellian.H
deleted file mode 100644
index 01c3ff8716..0000000000
--- a/applications/utilities/preProcessing/molConfig/velocityDistributions/maxwellian.H
+++ /dev/null
@@ -1,26 +0,0 @@
-scalar velCmptMag = sqrt(moleculeCloud::kb*temperature/mass);
-
-for (molN = totalMols; molN < totalMols + totalZoneMols; molN++)
-{
-    // Assign velocity: random direction, magnitude determined by desired
-    // maxwellian distribution at temperature
-
-    // Temperature gradients could be created by specifying a gradient in the
-    // zone subDict, or by reading a field from a mesh.
-
-    // The velocities are treated on a zone-by-zone basis for the purposes of
-    // removal of bulk momentum - hence nMols becomes totalZoneMols
-
-    velocity = vector
-    (
-        velCmptMag*rand.GaussNormal(),
-        velCmptMag*rand.GaussNormal(),
-        velCmptMag*rand.GaussNormal()
-    );
-
-    momentumSum += mass*velocity;
-
-    initialVelocities.append(velocity);
-}
-
-
diff --git a/applications/utilities/preProcessing/molConfig/velocityDistributions/uniform.H b/applications/utilities/preProcessing/molConfig/velocityDistributions/uniform.H
deleted file mode 100644
index 9c178af262..0000000000
--- a/applications/utilities/preProcessing/molConfig/velocityDistributions/uniform.H
+++ /dev/null
@@ -1,27 +0,0 @@
-scalar initVelMag =
-    sqrt
-    (
-        3.0*(1.0 - 1.0 / totalZoneMols)
-       *moleculeCloud::kb*temperature
-       /mass
-    );
-
-for (molN = totalMols; molN < totalMols + totalZoneMols; molN++)
-{
-    // Assign velocity: random direction, magnitude determined by desired
-    // temperature
-
-    // Temperature gradients could be created by specifying a gradient in the
-    // zone subDict, or by reading a field from a mesh.
-
-    // The velocities are treated on a zone-by-zone basis for the purposes of
-    // removal of bulk momentum - hence nMols becomes totalZoneMols
-
-    velocity = (2.0*rand.vector01() - vector::one);
-
-    velocity *= initVelMag/mag(velocity);
-
-    momentumSum += mass*velocity;
-
-    initialVelocities.append(velocity);
-}
diff --git a/tutorials/mdEquilibrationFoam/periodicCube/constant/polyMesh/blockMeshDict b/tutorials/mdEquilibrationFoam/periodicCube/constant/polyMesh/blockMeshDict
deleted file mode 100644
index 23a2ee9874..0000000000
--- a/tutorials/mdEquilibrationFoam/periodicCube/constant/polyMesh/blockMeshDict
+++ /dev/null
@@ -1,73 +0,0 @@
-/*---------------------------------------------------------------------------*\
-| =========                 |                                                 |
-| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
-|  \\    /   O peration     | Version:  1.3                                   |
-|   \\  /    A nd           | Web:      http://www.openfoam.org               |
-|    \\/     M anipulation  |                                                 |
-\*---------------------------------------------------------------------------*/
-
-FoamFile
-{
-    version         2.0;
-    format          ascii;
-
-    root            "";
-    case            "";
-    instance        "";
-    local           "";
-
-    class           dictionary;
-    object          blockMeshDict;
-}
-
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-convertToMeters 2.462491658e-9;
-
-vertices
-(
-    (-1 -1 -1)
-    (1 -1 -1)
-    (1 1 -1)
-    (-1 1 -1)
-    (-1 -1 1)
-    (1 -1 1)
-    (1 1 1)
-    (-1 1 1)
-);
-
-blocks
-(
-    hex (0 1 2 3 4 5 6 7) liquid (12 12 12) simpleGrading (1 1 1)
-);
-
-patches
-(
-    cyclic
-    periodicX
-    (
-        (1 2 6 5)
-        (0 4 7 3)
-    )
-
-    cyclic
-    periodicY
-    (
-        (2 3 7 6)
-        (0 1 5 4)
-    )
-
-    cyclic
-    periodicZ
-    (
-        (0 3 2 1)
-        (4 5 6 7)
-    )
-)
-
-mergePatchPairs
-(
-);
-
-
-// ************************************************************************* //
diff --git a/tutorials/mdEquilibrationFoam/periodicCube/system/fvSchemes b/tutorials/mdEquilibrationFoam/periodicCube/system/fvSchemes
deleted file mode 100644
index 8504e0fd45..0000000000
--- a/tutorials/mdEquilibrationFoam/periodicCube/system/fvSchemes
+++ /dev/null
@@ -1,67 +0,0 @@
-/*---------------------------------------------------------------------------*\
-| =========                 |                                                 |
-| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
-|  \\    /   O peration     | Version:  1.3                                   |
-|   \\  /    A nd           | Web:      http://www.openfoam.org               |
-|    \\/     M anipulation  |                                                 |
-\*---------------------------------------------------------------------------*/
-
-FoamFile
-{
-    version         2.0;
-    format          ascii;
-
-    root            "";
-    case            "";
-    instance        "";
-    local           "";
-
-    class           dictionary;
-    object          fvSchemes;
-}
-
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-ddtSchemes
-{
-    default         Euler;
-}
-
-gradSchemes
-{
-    default         Gauss linear;
-    grad(p)         Gauss linear;
-}
-
-divSchemes
-{
-    default         none;
-    div(phi,U)      Gauss linear;
-}
-
-laplacianSchemes
-{
-    default         none;
-    laplacian(nu,U) Gauss linear corrected;
-    laplacian(1|A(U),p) Gauss linear corrected;
-}
-
-interpolationSchemes
-{
-    default         linear;
-    interpolate(HbyA) linear;
-}
-
-snGradSchemes
-{
-    default         corrected;
-}
-
-fluxRequired
-{
-    default         no;
-    p;
-}
-
-
-// ************************************************************************* //
diff --git a/tutorials/mdEquilibrationFoam/periodicCube/system/fvSolution b/tutorials/mdEquilibrationFoam/periodicCube/system/fvSolution
deleted file mode 100644
index c85c7b791b..0000000000
--- a/tutorials/mdEquilibrationFoam/periodicCube/system/fvSolution
+++ /dev/null
@@ -1,40 +0,0 @@
-/*---------------------------------------------------------------------------*\
-| =========                 |                                                 |
-| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
-|  \\    /   O peration     | Version:  1.3                                   |
-|   \\  /    A nd           | Web:      http://www.openfoam.org               |
-|    \\/     M anipulation  |                                                 |
-\*---------------------------------------------------------------------------*/
-
-FoamFile
-{
-    version         2.0;
-    format          ascii;
-
-    root            "";
-    case            "";
-    instance        "";
-    local           "";
-
-    class           dictionary;
-    object          fvSolution;
-}
-
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-solvers
-{
-    p               ICCG 1e-06 0;
-    U               BICCG 1e-05 0;
-}
-
-PISO
-{
-    nCorrectors     2;
-    nNonOrthogonalCorrectors 0;
-    pRefCell        0;
-    pRefValue       0;
-}
-
-
-// ************************************************************************* //
diff --git a/tutorials/mdEquilibrationFoam/periodicCube/system/mdEquilibrationDict b/tutorials/mdEquilibrationFoam/periodicCube/system/mdEquilibrationDict
deleted file mode 100644
index e2323961f5..0000000000
--- a/tutorials/mdEquilibrationFoam/periodicCube/system/mdEquilibrationDict
+++ /dev/null
@@ -1,27 +0,0 @@
-/*---------------------------------------------------------------------------*\
-| =========                 |                                                 |
-| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
-|  \\    /   O peration     | Version:  1.4.1                                  |
-|   \\  /    A nd           | Web:      http://www.openfoam.org               |
-|    \\/     M anipulation  |                                                 |
-\*---------------------------------------------------------------------------*/
-
-FoamFile
-{
-    version         2.0;
-    format          ascii;
-
-    root            "";
-    case            "";
-    instance        "";
-    local           "";
-
-    class           dictionary;
-    object          mdEquilibrationDict;
-}
-
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-equilibrationTargetTemperature  300.0;
-
-// ************************************************************************* //
\ No newline at end of file
diff --git a/tutorials/mdEquilibrationFoam/periodicCube/system/molConfigDict b/tutorials/mdEquilibrationFoam/periodicCube/system/molConfigDict
deleted file mode 100644
index b01cd00edb..0000000000
--- a/tutorials/mdEquilibrationFoam/periodicCube/system/molConfigDict
+++ /dev/null
@@ -1,43 +0,0 @@
-/*---------------------------------------------------------------------------*\
-| =========                 |                                                 |
-| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
-|  \\    /   O peration     | Version:  1.3                                   |
-|   \\  /    A nd           | Web:      http://www.openfoam.org               |
-|    \\/     M anipulation  |                                                 |
-\*---------------------------------------------------------------------------*/
-
-FoamFile
-{
-    version         2.0;
-    format          ascii;
-
-    root            "";
-    case            "";
-    instance        "";
-    local           "";
-
-    class           dictionary;
-    object          molConfigDict;
-}
-
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-// Euler angles, expressed in degrees as phi, theta, psi,
-// see http://mathworld.wolfram.com/EulerAngles.html
-
-liquid
-{
-    massDensity             1220.0;
-    temperature             300.0;
-    velocityDistribution    maxwellian;
-    bulkVelocity            (0.0 0.0 0.0);
-    id                      Ar;
-    mass                    6.63352033e-26;
-    latticeStructure        SC;
-    anchor                  (0.0 0.0 0.0);
-    anchorSpecifies         molecule;
-    tethered                no;
-    orientationAngles       (0 0 0);
-}
-
-// ************************************************************************* //