updating molecularDynamics functionality with Graham's latest changes

applications/utilities/preProcessing/molConfig/Make/files

+latticeStructures = latticeStructures
+velocityDistributions = velocityDistributions
+
+createMolecules.C
+molConfig.C
+genMolConfig.C
+
+EXE = $(FOAM_APPBIN)/molConfig

applications/utilities/preProcessing/molConfig/correctVelocities.H

+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;

applications/utilities/preProcessing/molConfig/createMolecules.C

+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  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;
+}
+
+
+// ************************************************************************* //

applications/utilities/preProcessing/molConfig/createPositions.H

+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);
+}

applications/utilities/preProcessing/molConfig/createVelocities.H

+vector velocity;
+
+vector momentumSum = vector::zero;
+
+if (velocityDistribution == "uniform")
+{
+#    include "uniform.H"
+}
+
+if (velocityDistribution == "maxwellian")
+{
+#    include "maxwellian.H"
+}

applications/utilities/preProcessing/molConfig/genMolConfig.C

+/*---------------------------------------------------------------------------*\
+ =========                   |
+ \\      /   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;
+}
+
+
+// ************************************************************************* //

applications/utilities/preProcessing/molConfig/latticeStructures/BCC.H

+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")