diff --git a/applications/utilities/preProcessing/molConfig/Make/files b/applications/utilities/preProcessing/molConfig/Make/files
deleted file mode 100755
index 6501e68426960c755a310e7a12b7b53548ddeb98..0000000000000000000000000000000000000000
--- a/applications/utilities/preProcessing/molConfig/Make/files
+++ /dev/null
@@ -1,8 +0,0 @@
-latticeStructures = latticeStructures
-velocityDistributions = velocityDistributions
-
-createMolecules.C
-molConfig.C
-genMolConfig.C
-
-EXE = $(FOAM_APPBIN)/molConfig
diff --git a/applications/utilities/preProcessing/molConfig/Make/options b/applications/utilities/preProcessing/molConfig/Make/options
deleted file mode 100755
index 196a4d66ddba259f0d7547f781a9c925db63b0eb..0000000000000000000000000000000000000000
--- a/applications/utilities/preProcessing/molConfig/Make/options
+++ /dev/null
@@ -1,15 +0,0 @@
-EXE_INC = \
- -I$(latticeStructures) \
- -I$(velocityDistributions) \
- -I$(LIB_SRC)/meshTools/lnInclude \
- -I$(LIB_SRC)/dynamicMesh/lnInclude \
- -I$(LIB_SRC)/lagrangian/molecule/lnInclude \
- -I$(LIB_SRC)/lagrangian/basic/lnInclude \
- -I$(LIB_SRC)/finiteVolume/lnInclude
-
-EXE_LIBS = \
- -lmeshTools \
- -ldynamicMesh \
- -lfiniteVolume \
- -llagrangian \
- -lmolecule
diff --git a/applications/utilities/preProcessing/molConfig/correctVelocities.H b/applications/utilities/preProcessing/molConfig/correctVelocities.H
deleted file mode 100644
index 0c69f15c7cda7cff0fa4387196c1dbea09c096e1..0000000000000000000000000000000000000000
--- 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 20318f06d666c6979d2f875b2f82381baa892097..0000000000000000000000000000000000000000
--- 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 b26486338caf7228188244aac4e989fb9380cb0d..0000000000000000000000000000000000000000
--- 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 d014ffd146044db0be9307b511e793ee490f0464..0000000000000000000000000000000000000000
--- 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 91bc5c8d246b6553d2e007f1547d79ce88d877ce..0000000000000000000000000000000000000000
--- 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 cd3cbdf100ba1c7fcafecca68e2c730ebfc2b97c..0000000000000000000000000000000000000000
--- 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 313ebf96cb89bf2b1111b45fe1de462133fb5197..0000000000000000000000000000000000000000
--- 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 dd0ff7c00f67453884b5693ed32003566f90b1b0..0000000000000000000000000000000000000000
--- 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 e837346b9796761bd887d51fe20a95442a1a9882..0000000000000000000000000000000000000000
--- 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 a9d549da12cbaadb570dd633afec17e1e1f4c7cb..0000000000000000000000000000000000000000
--- 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 b85a656c03a5abb0c56ca0ac0e9cf487ea08edbc..0000000000000000000000000000000000000000
--- 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 24bc994d34fe8eaee58b7c77a71613d1bf8bc004..0000000000000000000000000000000000000000
--- 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 72705c761e2650f4ec4f7faa72078235e1f288df..0000000000000000000000000000000000000000
--- 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 6ae01c83f11039a01d4307816c08951f1ad33d1c..0000000000000000000000000000000000000000
--- 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 01c3ff87168fc1a4057b4512472f58afec0bb5e0..0000000000000000000000000000000000000000
--- 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 9c178af262aabb88a239f9711b1c334cdd39e4e1..0000000000000000000000000000000000000000
--- 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/src/lagrangian/molecule/Make/files b/src/lagrangian/molecule/Make/files
deleted file mode 100755
index d8063d097437f7ca2dfa6b8e20a74cafa47723c9..0000000000000000000000000000000000000000
--- 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 = $(FOAM_LIBBIN)/libmolecule
-
diff --git a/src/lagrangian/molecule/Make/options b/src/lagrangian/molecule/Make/options
deleted file mode 100755
index a0fb316eecd4a5e63b9f261787d2ecf29ff957b9..0000000000000000000000000000000000000000
--- a/src/lagrangian/molecule/Make/options
+++ /dev/null
@@ -1,8 +0,0 @@
-EXE_INC = \
- -I$(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 c8a5ca0f307f5a5b5cb5a2d43a4bed5cd00aea6d..0000000000000000000000000000000000000000
--- 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 27bd52771ccf64271138184a77a7ec06f980d8d3..0000000000000000000000000000000000000000
--- 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 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 cb3bcc617e478bdbd46037cbdbf8afba4bf00a9d..0000000000000000000000000000000000000000
--- 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 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 5c6cf11da3eb3e98d04c0355e2d91ad5a0830fa4..0000000000000000000000000000000000000000
--- 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 ca63e1856cd4ce6ab5a848e33bb03cbf8e6f298d..0000000000000000000000000000000000000000
--- 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 fcd023e36374f10fa089269afab0407cfd5466b3..0000000000000000000000000000000000000000
--- 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 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/molecule/correlationFunction/correlationFunctionI.H b/src/lagrangian/molecule/correlationFunction/correlationFunctionI.H
deleted file mode 100644
index 6858f647a64478873d3b3a5d35c97033db3bd0ca..0000000000000000000000000000000000000000
--- 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 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/molecule/correlationFunction/correlationFunctionIO.C b/src/lagrangian/molecule/correlationFunction/correlationFunctionIO.C
deleted file mode 100644
index 0a080158aea2dc95a9b47570c1153acdf7e077f3..0000000000000000000000000000000000000000
--- 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 717929e5e42e6ad99634e8d790f43fa3d7aa70cd..0000000000000000000000000000000000000000
--- 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 c2de1055c16f1607c17aad261772828126cf6381..0000000000000000000000000000000000000000
--- 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 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 754ea8a0031755e47975d979d2406979bd90e699..0000000000000000000000000000000000000000
--- a/src/lagrangian/molecule/distribution/distributionI.H
+++ /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
-
-\*---------------------------------------------------------------------------*/
-
-// * * * * * * * * * * * * * * * Member Functions * * * * * * * * * * * * * //
-
-inline Foam::scalar Foam::distribution::binWidth() const
-{
- return binWidth_;
-}
-
-
-// ************************************************************************* //
diff --git a/src/lagrangian/molecule/distribution/distributionIO.C b/src/lagrangian/molecule/distribution/distributionIO.C
deleted file mode 100755
index 57f6e774bb1743a9b1522921de87420bd14af456..0000000000000000000000000000000000000000
--- 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 db0c24bc95e00bc77c0de6f358e5434ecffbf0fa..0000000000000000000000000000000000000000
--- 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 a7c4c326bb3c4dc17aa510f095bc44054bce25ab..0000000000000000000000000000000000000000
--- 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 af5c938da43cf3308ea2caf8ded6466cc27d09ad..0000000000000000000000000000000000000000
--- 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 15e0dab7e34c468856704e799a537d1889169ee7..0000000000000000000000000000000000000000
--- 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 3bec4493dcccb186c2c02206281ea6919cc5155e..0000000000000000000000000000000000000000
--- 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 f5742fd2c8fd89afdb9428abb5b90ff3e6523967..0000000000000000000000000000000000000000
--- 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 bbd6c6daf7bc378e10c1cec250febb9184dc9769..0000000000000000000000000000000000000000
--- 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 5c018694bd04e9554017011a0e87bded4cc5486e..0000000000000000000000000000000000000000
--- 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 043e63c5431e75e8c2cb620eae5831bce9fd0de2..0000000000000000000000000000000000000000
--- 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 e5fdbbd8a46b4947abf691e179ca205c3ab6f03a..0000000000000000000000000000000000000000
--- 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 0563700cb73d1008a4ce10857143e907abb3b29e..0000000000000000000000000000000000000000
--- 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 258cfac314a22658aeee8490f31b55ce46a4d400..0000000000000000000000000000000000000000
--- 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 c640809cda8fb1d5a5d60ec41f2e638340058840..0000000000000000000000000000000000000000
--- 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 0a46a0ca2cd67192e57bde7c8398cb04cdbe204a..0000000000000000000000000000000000000000
--- 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 a3e2099589e6c775fb3d889888b2930e049a367b..0000000000000000000000000000000000000000
--- 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 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;
-
-
- //- 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 bfbda044b14f3d43b864ab3c9eea0ce71ab2c855..0000000000000000000000000000000000000000
--- a/src/lagrangian/molecule/molecule/moleculeI.H
+++ /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
-
-\*---------------------------------------------------------------------------*/
-
-// * * * * * * * * * * * * * * * * Constructors * * * * * * * * * * * * * * //
-
-inline Foam::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 Foam::molecule::trackData::trackData
-(
- moleculeCloud& molCloud,
- label part
-)
-:
- Particle<molecule>::trackData(refCast<Cloud<molecule> >(molCloud)),
- molCloud_(molCloud),
- part_(part)
-{}
-
-
-// * * * * * * * * * * * * * * * Member Functions * * * * * * * * * * * * * //
-
-inline Foam::label Foam::molecule::id() const
-{
- return id_;
-}
-
-
-inline Foam::scalar Foam::molecule::mass() const
-{
- return mass_;
-}
-
-
-inline const Foam::vector& Foam::molecule::U() const
-{
- return U_;
-}
-
-
-inline Foam::vector& Foam::molecule::U()
-{
- return U_;
-}
-
-
-inline const Foam::vector& Foam::molecule::A() const
-{
- return A_;
-}
-
-
-inline Foam::vector& Foam::molecule::A()
-{
- return A_;
-}
-
-
-inline Foam::scalar Foam::molecule::potentialEnergy() const
-{
- return potentialEnergy_;
-}
-
-
-inline Foam::scalar& Foam::molecule::potentialEnergy()
-{
- return potentialEnergy_;
-}
-
-
-inline const Foam::tensor& Foam::molecule::rf() const
-{
- return rf_;
-}
-
-
-inline Foam::tensor& Foam::molecule::rf()
-{
- return rf_;
-}
-
-
-inline Foam::label Foam::molecule::tethered() const
-{
- return tethered_;
-}
-
-
-inline const Foam::vector& Foam::molecule::tetherPosition() const
-{
- return tetherPosition_;
-}
-
-
-inline Foam::moleculeCloud& Foam::molecule::trackData::molCloud()
-{
- return molCloud_;
-}
-
-
-inline Foam::label Foam::molecule::trackData::part() const
-{
- return part_;
-}
-
-
-// ************************************************************************* //
diff --git a/src/lagrangian/molecule/molecule/moleculeIO.C b/src/lagrangian/molecule/molecule/moleculeIO.C
deleted file mode 100755
index f87b80cd46a56f2de62b1b720141b4c4a30e847f..0000000000000000000000000000000000000000
--- 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 cf0ebebc7c98d4f70348551f1daf6afa06d9656e..0000000000000000000000000000000000000000
--- 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 37d8cf22bb1270c08da53ae2e2cd5fcaeea2577a..0000000000000000000000000000000000000000
--- 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 scalar rCutMax() const;
-
- inline 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 d44b247d7bf73b039d57aeec612311440ea0d83f..0000000000000000000000000000000000000000
--- 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 a8d9cc8db5678dffa1bc86605a0d67613a773bfe..0000000000000000000000000000000000000000
--- 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 f02be61f7efc30adfca2faee72eea507cd81c983..0000000000000000000000000000000000000000
--- 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 ea1521800f82b6c20b49f6f2f39f24d4efa4bab3..0000000000000000000000000000000000000000
--- 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 16c58efea3af289a1d8b518ece6b14225cdf8683..0000000000000000000000000000000000000000
--- 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 c5f2d887bf59e62a6ce2fcc887a4ef7a89493f2f..0000000000000000000000000000000000000000
--- 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 5e1de7206281e1b13805615048a1d11559c4ed7e..0000000000000000000000000000000000000000
--- 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 ea6320ecb5c459b4f266a39e442f3f7d3a0ec4c2..0000000000000000000000000000000000000000
--- 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 54aa9b1a426b5517caeaf153b26e644129745ddc..0000000000000000000000000000000000000000
--- 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 14b65c5a3c5a13fa5b1f1e527b27a4b85c2b0aac..0000000000000000000000000000000000000000
--- 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 c3b3f1e7cc431e61c36ff3381e29ff12fbda1a10..0000000000000000000000000000000000000000
--- 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 49e1e2d781b2462e80d44c6133be77acd9c5cdf9..0000000000000000000000000000000000000000
--- 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 c2fab2d10ef8cc14e55bff6cea7beeff9325ff4f..0000000000000000000000000000000000000000
--- 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 32b39a4089d8208884f24b5ed50edfd2b362da2c..0000000000000000000000000000000000000000
--- 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 330fa031dec088ad7fa8f6d729da932455cdb592..0000000000000000000000000000000000000000
--- 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 scalar moleculeCloud::rCutMax() const
-{
- return rCutMax_;
-}
-
-
-inline 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 dc2177d10b924017989d0f7266965093e96731a6..0000000000000000000000000000000000000000
--- 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 8ddc55ed45dcbfe4e545976f849d44bf0d81dcd0..0000000000000000000000000000000000000000
--- 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 f6d090bfb8c382da5d1b2d75da03e3bda06e1c53..0000000000000000000000000000000000000000
--- 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 07c6b30ff04bf4cac42342ad3e882a5c66499c15..0000000000000000000000000000000000000000
--- 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 b1bdb2045cce399db459b4b3eab29ede64bebacb..0000000000000000000000000000000000000000
--- 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 03100cfd3b1d2580f004f5c8add9ac72c531fb82..0000000000000000000000000000000000000000
--- 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 f2e553a85350aadd8f8b655f2879478637aba298..0000000000000000000000000000000000000000
--- 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 ac4385574fa69fa65a1f2116fff5debe6bbd1a76..0000000000000000000000000000000000000000
--- 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 fe6d792842bac5c1abc2510dc27b194c0855da92..0000000000000000000000000000000000000000
--- 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 bc36a600958e02e58c2b33d4b4e828d71063ffa5..0000000000000000000000000000000000000000
--- 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 5b6b76135f2066dd765012858fe1ef12c4a21236..0000000000000000000000000000000000000000
--- 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 285447974cf216b8ee508747e96918e9deb6200d..0000000000000000000000000000000000000000
--- 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 e01be864769728a17f9727db4a3fd4c194439e21..0000000000000000000000000000000000000000
--- 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 f7c96414e4282553fe26bfe9dfd39318035ddcde..0000000000000000000000000000000000000000
--- 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 42b507586acfec5ebaa500d2374e6a3b8387ba34..0000000000000000000000000000000000000000
--- 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 scalar m() const;
-
- inline scalar gamma() const ;
-
- inline scalar rm() const;
-
- inline scalar epsilon() const;
-
- inline scalar rCut() const;
-
- inline scalar rCutSqr() const;
-
- inline scalar rMin() const;
-
- inline 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 3a3efa223aa8a269bf58ffaa18e9e6c194fc9f46..0000000000000000000000000000000000000000
--- 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 Foam::scalar Foam::pairPotential::m() const
-{
- return m_;
-}
-
-
-inline Foam::scalar Foam::pairPotential::gamma() const
-{
- return gamma_;
-}
-
-
-inline Foam::scalar Foam::pairPotential::rm() const
-{
- return rm_;
-}
-
-
-inline Foam::scalar Foam::pairPotential::epsilon() const
-{
- return epsilon_;
-}
-
-
-inline Foam::scalar Foam::pairPotential::rCut() const
-{
- return rCut_;
-}
-
-
-inline Foam::scalar Foam::pairPotential::rCutSqr() const
-{
- return rCutSqr_;
-}
-
-
-inline Foam::scalar Foam::pairPotential::rMin() const
-{
- return rMin_;
-}
-
-
-inline 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 b38687dfc00d963e2e9ed1392a196e20934bb03e..0000000000000000000000000000000000000000
--- 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;
- }
-}
-
-
-scalar pairPotentialList::rCutSqr
-(
- const label a,
- const label b
-) const
-{
- return (*this)[pairPotentialIndex (a,b)].rCutSqr();
-}
-
-
-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 910ab5ab38667a2c2a152d677aaaf30f5ca847c7..0000000000000000000000000000000000000000
--- 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;
-
- 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/molecule/potentials/pairPotential/basic/pairPotentialListI.H b/src/lagrangian/molecule/potentials/pairPotential/basic/pairPotentialListI.H
deleted file mode 100755
index d58fa545df485ccc2984f7aa03fa586155a02372..0000000000000000000000000000000000000000
--- 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 1eab1aa40a1fb753f089f7257de7f4f3387bcac5..0000000000000000000000000000000000000000
--- 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 57dea3ab725b00c805cf34f9518dad9b57d83516..0000000000000000000000000000000000000000
--- 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 4e3a1a2f27c63584a5e6e0cdd8e512a4660b94d0..0000000000000000000000000000000000000000
--- 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 46c097b36d5abf8473bd8676ea24abb7787dd970..0000000000000000000000000000000000000000
--- 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 afa9a35e69d1ba4974a1688bdfc9c17036248765..0000000000000000000000000000000000000000
--- 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 d9ca0dae1a60582760f914e8ae621621a2b19d16..0000000000000000000000000000000000000000
--- 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 ac32daf60fa662f827d64e189f56469e721a8c49..0000000000000000000000000000000000000000
--- 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 ebd24e57f00f6a916cfc8d8b33dd3caa31989e41..0000000000000000000000000000000000000000
--- 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 4f897839183ae2779d93e98a5a4f1e493145952a..0000000000000000000000000000000000000000
--- 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 3536893f8e96efd64f9fbaeb0be484dfcd79bff7..0000000000000000000000000000000000000000
--- 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 7adc1051fd414ac75a66e64c79bacada4a5ba045..0000000000000000000000000000000000000000
--- 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 8098885d68663306aaaabc2d21672258e06e68c4..0000000000000000000000000000000000000000
--- 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 88d110a5be2e1e4e9d32dfd93fc2dfc812f35fe6..0000000000000000000000000000000000000000
--- 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 e35c660b741d1661f4b07cddaec55c07a5629683..0000000000000000000000000000000000000000
--- 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 e64a0836f802dd8ee4049b8c9970863f6c00d8c3..0000000000000000000000000000000000000000
--- 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 d91e01fe080cec457a3ac1aea27180ecda9adff1..0000000000000000000000000000000000000000
--- 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 90651021932a9ce6c68f940a9393af78ee33e1fa..0000000000000000000000000000000000000000
--- 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 0d729e35bed30f11b0b9da2e60dc3a5307669ab7..0000000000000000000000000000000000000000
--- 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 d571962f5ddf7af3eeb176638db62707e5c44b2d..0000000000000000000000000000000000000000
--- 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 c60ae69bf41ef6b76db13f9dd1001409639818e5..0000000000000000000000000000000000000000
--- 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 27aaf730fc6b978757f53aebebad403be161b0c9..0000000000000000000000000000000000000000
--- 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 4135f7ff6e952da5f993bbef8590b456911ba663..0000000000000000000000000000000000000000
--- 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 cd69a1d9d4ddeb968e3c53137ae198ad5daa33f4..0000000000000000000000000000000000000000
--- 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 c025de52eb158617b3281f7ad5d1f8a7a742f038..0000000000000000000000000000000000000000
--- 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 34767d88b6f24406a876f8af37a5b7abfa20ddce..0000000000000000000000000000000000000000
--- 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 2453ca2f58f5a388ef875a7fa54550c36dc7630d..0000000000000000000000000000000000000000
--- 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 fcac7925a9100e773f97cf773868c832ec393994..0000000000000000000000000000000000000000
--- 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 b51b56035dc9b85a0352cb70c72cf45de734901d..0000000000000000000000000000000000000000
--- 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
-
-
-// ************************************************************************* //
diff --git a/tutorials/mdEquilibrationFoam/periodicCube/Allrun b/tutorials/mdEquilibrationFoam/periodicCube/Allrun
deleted file mode 100755
index 1960716ea2235f8507db8493beeeb85c24684aa6..0000000000000000000000000000000000000000
--- 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="mdEquilibrationFoam"
-
-runApplication blockMesh
-runApplication molConfig
-runApplication $application
diff --git a/tutorials/mdEquilibrationFoam/periodicCube/constant/polyMesh/blockMeshDict b/tutorials/mdEquilibrationFoam/periodicCube/constant/polyMesh/blockMeshDict
deleted file mode 100644
index 23a2ee9874ef09ad03276bbe470cc179802a227c..0000000000000000000000000000000000000000
--- 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/controlDict b/tutorials/mdEquilibrationFoam/periodicCube/system/controlDict
deleted file mode 100644
index c3205b3ad1467e74f631cddba96f1537124cf22b..0000000000000000000000000000000000000000
--- a/tutorials/mdEquilibrationFoam/periodicCube/system/controlDict
+++ /dev/null
@@ -1,55 +0,0 @@
-/*---------------------------------------------------------------------------*\
-| ========= | |
-| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
-| \\ / O peration | Version: 1.4 |
-| \\ / A nd | Web: http://www.openfoam.org |
-| \\/ M anipulation | |
-\*---------------------------------------------------------------------------*/
-
-FoamFile
-{
- version 2.0;
- format ascii;
-
- root "";
- case "";
- instance "";
- local "";
-
- class dictionary;
- object controlDict;
-}
-
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-startFrom startTime;
-
-startTime 0;
-
-stopAt endTime;
-
-endTime 4e-10;
-
-deltaT 1e-14;
-
-writeControl runTime;
-
-writeInterval 5e-11;
-
-purgeWrite 0;
-
-writeFormat ascii;
-
-writePrecision 12;
-
-writeCompression uncompressed;
-
-timeFormat general;
-
-timePrecision 6;
-
-runTimeModifiable yes;
-
-adjustTimeStep no;
-
-// ************************************************************************* //
diff --git a/tutorials/mdEquilibrationFoam/periodicCube/system/decomposeParDict b/tutorials/mdEquilibrationFoam/periodicCube/system/decomposeParDict
deleted file mode 100644
index 1678f7f1b22a8fa0690862420bcb8668cb274c98..0000000000000000000000000000000000000000
--- a/tutorials/mdEquilibrationFoam/periodicCube/system/decomposeParDict
+++ /dev/null
@@ -1,70 +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 decomposeParDict;
-}
-
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-
-numberOfSubdomains 2;
-
-method simple;
-
-simpleCoeffs
-{
- n (2 1 1);
- delta 0.001;
-}
-
-hierarchicalCoeffs
-{
- n (1 1 1);
- delta 0.001;
- order xyz;
-}
-
-metisCoeffs
-{
- processorWeights
- (
- 1
- 1
- 1
- 4
- 1
- 5
- 1
- 2
- );
-}
-
-manualCoeffs
-{
- dataFile "";
-}
-
-distributed no;
-
-roots
-(
-);
-
-
-// ************************************************************************* //
diff --git a/tutorials/mdEquilibrationFoam/periodicCube/system/fvSchemes b/tutorials/mdEquilibrationFoam/periodicCube/system/fvSchemes
deleted file mode 100644
index 8504e0fd45187a8698a014b6428e758d6b408424..0000000000000000000000000000000000000000
--- 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 c85c7b791bf5766697f1b4c93699a69792329295..0000000000000000000000000000000000000000
--- 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 e2323961f5d07742db511acae8b961f49c4fa0ae..0000000000000000000000000000000000000000
--- 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/mdSolution b/tutorials/mdEquilibrationFoam/periodicCube/system/mdSolution
deleted file mode 100644
index 681963175de629fcb9ebab3a3a3ebd0b5893e716..0000000000000000000000000000000000000000
--- a/tutorials/mdEquilibrationFoam/periodicCube/system/mdSolution
+++ /dev/null
@@ -1,31 +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 mdSolution;
-}
-
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-integrationMethod verletLeapfrog;
-
-potentialEnergyLimit 5.256e-20;
-
-guardRadius 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 b01cd00edbb678fe9d1979de1442d6c23d1f0e6b..0000000000000000000000000000000000000000
--- 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);
-}
-
-// ************************************************************************* //
diff --git a/tutorials/mdEquilibrationFoam/periodicCube/system/potentialDict b/tutorials/mdEquilibrationFoam/periodicCube/system/potentialDict
deleted file mode 100644
index 78fa1c77465f435999e8df2b11c6388c64fa3b6b..0000000000000000000000000000000000000000
--- a/tutorials/mdEquilibrationFoam/periodicCube/system/potentialDict
+++ /dev/null
@@ -1,89 +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 potentials;
-}
-
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-// Subdictionaries specifying types of intermoleular potential.
-// Sub-sub dictionaries specify the potentials themselves.
-
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-// Removal order
-
-// This is the order in which to remove overlapping pairs if more than one
-// type of molecule is present. The most valuable molecule type is at the
-// right hand end, the molecule that will be removed 1st is 1st on the list.
-// Not all types need to be present, a molecule that is not present is
-// automatically less valuable than any on the list. For molecules of the
-// same type there is no control over which is removed.
-
-removalOrder 1 (Ar);
-
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-// Pair potentials
-
-// If there are r different type of molecules, and a pair force is required
-// between all combinations, then there are C = r(r+1)/2 combinations,
-// i.e. for r = {1,2,3,4}, C = {1,3,6,10} (sum of triangular numbers).
-
-// Pair potentials are specified by the combinaition of their ids,
-// for MOLA and MOLB, "MOLA-MOLB" OR "MOLB-MOLA" is acceptable
-// (strictly OR, both or neither will thrown an error)
-
-pair
-{
- Ar-Ar
- {
- potentialType maitlandSmithTabulated;
- m 13.0;
- gamma 7.5;
- rm 0.3756e-9;
- epsilon 1.990108438e-21;
- rCut 1.0e-9;
- rMin 0.15e-9;
- dr 2e-14;
- }
-}
-
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-// Tethering Potentials
-
-tether
-{
- Ar
- {
- potentialType harmonicSpring;
- springConstant 0.0277;
- }
-}
-
-// ************************************************************************* //
-
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-// External Forces
-
-// Bulk external forces (namely gravity) will be specified as forces rather
-// than potentials to allow their direction to be controlled.
-
-external
-{
- gravity (0 0 0);
-}