mirror of
https://develop.openfoam.com/Development/openfoam.git
synced 2025-11-28 03:28:01 +00:00
ENH: molecularDynamics now using new InteractionLists.
This commit is contained in:
graham
@ -39,6 +39,20 @@ int main(int argc, char *argv[])
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# include "createTime.H"
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# include "createMesh.H"
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Info<< "\nReading field U\n" << endl;
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volVectorField U
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(
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IOobject
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(
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"U",
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runTime.timeName(),
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mesh,
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IOobject::MUST_READ,
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IOobject::AUTO_WRITE
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),
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mesh
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);
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potential pot(mesh);
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moleculeCloud molecules(mesh, pot);
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@ -39,6 +39,20 @@ int main(int argc, char *argv[])
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# include "createTime.H"
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# include "createMesh.H"
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Info<< "\nReading field U\n" << endl;
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volVectorField U
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(
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IOobject
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(
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"U",
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runTime.timeName(),
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mesh,
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IOobject::MUST_READ,
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IOobject::AUTO_WRITE
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),
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mesh
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);
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potential pot(mesh);
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moleculeCloud molecules(mesh, pot);
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@ -1,24 +1,9 @@
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interactionLists = interactionLists
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referredMolecule = $(interactionLists)/referredMolecule
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referredCellList = $(interactionLists)/referredCellList
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referredCell = $(interactionLists)/referredCell
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directInteractionList = $(interactionLists)/directInteractionList
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reducedUnits/reducedUnits.C
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reducedUnits/reducedUnitsIO.C
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$(referredCellList)/referredCellList.C
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$(referredCell)/referredCell.C
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$(referredMolecule)/referredMolecule.C
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$(directInteractionList)/directInteractionList.C
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$(interactionLists)/interactionLists.C
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molecule/molecule.C
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molecule/moleculeIO.C
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reducedUnits = reducedUnits
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$(reducedUnits)/reducedUnits.C
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$(reducedUnits)/reducedUnitsIO.C
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molecule = molecule
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$(molecule)/molecule.C
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$(molecule)/moleculeIO.C
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moleculeCloud = moleculeCloud
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$(moleculeCloud)/moleculeCloud.C
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moleculeCloud/moleculeCloud.C
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LIB = $(FOAM_LIBBIN)/libmolecule
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@ -1,11 +1,13 @@
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EXE_INC = \
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-I$(LIB_SRC)/finiteVolume/lnInclude \
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-I$(LIB_SRC)/meshTools/lnInclude \
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-I$(LIB_SRC)/lagrangian/basic/lnInclude \
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-I$(LIB_SRC)/lagrangian/molecularDynamics/potential/lnInclude \
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-I$(LIB_SRC)/lagrangian/molecularDynamics/molecularMeasurements/lnInclude
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EXE_LIBS = \
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-lfiniteVolume \
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-lmeshTools \
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-llagrangian \
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-lpotential \
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-lmolecularMeasurements
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@ -1,346 +0,0 @@
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/*---------------------------------------------------------------------------*\
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========= |
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||||
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
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\\ / O peration |
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||||
\\ / A nd | Copyright (C) 2008-2010 OpenCFD Ltd.
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||||
\\/ M anipulation |
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||||
-------------------------------------------------------------------------------
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||||
License
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||||
This file is part of OpenFOAM.
|
||||
|
||||
OpenFOAM is free software: you can redistribute it and/or modify it
|
||||
under the terms of the GNU General Public License as published by
|
||||
the Free Software Foundation, either version 3 of the License, or
|
||||
(at your option) any later version.
|
||||
|
||||
OpenFOAM is distributed in the hope that it will be useful, but WITHOUT
|
||||
ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
|
||||
FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License
|
||||
for more details.
|
||||
|
||||
You should have received a copy of the GNU General Public License
|
||||
along with OpenFOAM. If not, see <http://www.gnu.org/licenses/>.
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||||
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\*---------------------------------------------------------------------------*/
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#include "directInteractionList.H"
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#include "interactionLists.H"
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// * * * * * * * * * * * * * Private Member Functions * * * * * * * * * * * //
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void Foam::directInteractionList::buildDirectInteractionList
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(
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bool pointPointListBuild
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)
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{
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Info<< nl << "Building list of direct interaction neighbours" << endl;
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const polyMesh& mesh(il_.mesh());
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List<DynamicList<label> > directInteractionList(mesh.nCells());
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if (pointPointListBuild)
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{
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Info<< tab << "Point-Point direct interaction list build." << endl;
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label pointJIndex;
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forAll(mesh.points(), pointIIndex)
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{
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for
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(
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pointJIndex = pointIIndex;
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pointJIndex != mesh.points().size();
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++pointJIndex
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)
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{
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if (il_.testPointPointDistance(pointIIndex, pointJIndex))
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{
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const labelList& ptICells
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(
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mesh.pointCells()[pointIIndex]
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);
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const labelList& ptJCells
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(
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mesh.pointCells()[pointJIndex]
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);
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forAll(ptICells, pIC)
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{
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const label cellI(ptICells[pIC]);
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forAll(ptJCells, pJC)
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{
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const label cellJ(ptJCells[pJC]);
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if (cellJ > cellI)
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{
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if
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(
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findIndex
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(
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directInteractionList[cellI],
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cellJ
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)
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== -1
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)
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{
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directInteractionList[cellI].append(cellJ);
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}
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}
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if (cellI > cellJ)
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{
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if
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(
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findIndex
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(
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directInteractionList[cellJ],
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cellI
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)
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==
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-1
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)
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{
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directInteractionList[cellJ].append(cellI);
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}
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}
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}
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}
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}
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}
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}
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}
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else
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{
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Info<< tab << "Point-Face, Edge-Edge direct interaction list build."
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<< endl;
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forAll(mesh.points(), p)
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{
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forAll(mesh.faces(), f)
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{
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if (il_.testPointFaceDistance(p, f))
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{
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const labelList& pCells(mesh.pointCells()[p]);
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const label cellO(mesh.faceOwner()[f]);
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forAll(pCells, pC)
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{
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const label cellI(pCells[pC]);
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// cells are not added to their own DIL
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if (cellO > cellI)
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{
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if
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(
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findIndex
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(
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directInteractionList[cellI],
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cellO
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)
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==
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-1
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)
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{
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directInteractionList[cellI].append(cellO);
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}
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}
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if (cellI > cellO)
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{
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if
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(
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findIndex
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(
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directInteractionList[cellO],
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cellI
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)
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==
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-1
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)
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{
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directInteractionList[cellO].append(cellI);
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}
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}
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if (mesh.isInternalFace(f))
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{
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// boundary faces will not have neighbour
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// information
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const label cellN(mesh.faceNeighbour()[f]);
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if (cellN > cellI)
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{
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if
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(
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findIndex
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(
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directInteractionList[cellI],
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cellN
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)
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==
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-1
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)
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{
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directInteractionList[cellI].append(cellN);
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}
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}
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if (cellI > cellN)
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{
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if
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(
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findIndex
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(
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directInteractionList[cellN],
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cellI
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)
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==
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-1
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)
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{
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directInteractionList[cellN].append(cellI);
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}
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}
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}
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}
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}
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}
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}
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label edgeJIndex;
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forAll(mesh.edges(), edgeIIndex)
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{
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const edge& eI(mesh.edges()[edgeIIndex]);
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for
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(
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edgeJIndex = edgeIIndex + 1;
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edgeJIndex != mesh.edges().size();
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++edgeJIndex
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)
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{
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const edge& eJ(mesh.edges()[edgeJIndex]);
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if (il_.testEdgeEdgeDistance(eI, eJ))
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{
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const labelList& eICells(mesh.edgeCells()[edgeIIndex]);
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const labelList& eJCells(mesh.edgeCells()[edgeJIndex]);
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forAll(eICells, eIC)
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{
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const label cellI(eICells[eIC]);
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forAll(eJCells, eJC)
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{
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const label cellJ(eJCells[eJC]);
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|
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if (cellJ > cellI)
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{
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if
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(
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findIndex
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(
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directInteractionList[cellI],
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cellJ
|
||||
)
|
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==
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-1
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)
|
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{
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directInteractionList[cellI].append(cellJ);
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}
|
||||
}
|
||||
|
||||
if (cellI > cellJ)
|
||||
{
|
||||
if
|
||||
(
|
||||
findIndex
|
||||
(
|
||||
directInteractionList[cellJ],
|
||||
cellI
|
||||
)
|
||||
==
|
||||
-1
|
||||
)
|
||||
{
|
||||
directInteractionList[cellJ].append(cellI);
|
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}
|
||||
}
|
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}
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}
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}
|
||||
}
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||||
}
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||||
}
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forAll(directInteractionList, transDIL)
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{
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(*this)[transDIL].transfer
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||||
(
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directInteractionList[transDIL].shrink()
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||||
);
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||||
}
|
||||
|
||||
// sorting DILs
|
||||
|
||||
forAll((*this), dIL)
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||||
{
|
||||
sort((*this)[dIL]);
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
// * * * * * * * * * * * * * * * * Constructors * * * * * * * * * * * * * * //
|
||||
|
||||
Foam::directInteractionList::directInteractionList
|
||||
(
|
||||
const interactionLists& il,
|
||||
bool pointPointListBuild
|
||||
)
|
||||
:
|
||||
labelListList(il.mesh().nCells()),
|
||||
il_(il)
|
||||
{
|
||||
if ((*this).size() > 1)
|
||||
{
|
||||
buildDirectInteractionList(pointPointListBuild);
|
||||
}
|
||||
else if ((*this).size() == 1)
|
||||
{
|
||||
Info<< nl
|
||||
<< "Single cell mesh, no direct interaction lists required."
|
||||
<< endl;
|
||||
|
||||
(*this)[0].setSize(0);
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
Foam::directInteractionList::directInteractionList
|
||||
(
|
||||
const interactionLists& il
|
||||
)
|
||||
:
|
||||
labelListList(il.mesh().nCells()),
|
||||
il_(il)
|
||||
{
|
||||
Info<< "Read directInteractionList from disk not implemented" << endl;
|
||||
}
|
||||
|
||||
|
||||
// * * * * * * * * * * * * * * * * Destructor * * * * * * * * * * * * * * * //
|
||||
|
||||
Foam::directInteractionList::~directInteractionList()
|
||||
{}
|
||||
|
||||
|
||||
// ************************************************************************* //
|
||||
@ -1,124 +0,0 @@
|
||||
/*---------------------------------------------------------------------------*\
|
||||
========= |
|
||||
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
|
||||
\\ / O peration |
|
||||
\\ / A nd | Copyright (C) 2008-2010 OpenCFD Ltd.
|
||||
\\/ M anipulation |
|
||||
-------------------------------------------------------------------------------
|
||||
License
|
||||
This file is part of OpenFOAM.
|
||||
|
||||
OpenFOAM is free software: you can redistribute it and/or modify it
|
||||
under the terms of the GNU General Public License as published by
|
||||
the Free Software Foundation, either version 3 of the License, or
|
||||
(at your option) any later version.
|
||||
|
||||
OpenFOAM is distributed in the hope that it will be useful, but WITHOUT
|
||||
ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
|
||||
FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License
|
||||
for more details.
|
||||
|
||||
You should have received a copy of the GNU General Public License
|
||||
along with OpenFOAM. If not, see <http://www.gnu.org/licenses/>.
|
||||
|
||||
Class
|
||||
Foam::directInteractionList
|
||||
|
||||
Description
|
||||
|
||||
SourceFiles
|
||||
directInteractionListI.H
|
||||
directInteractionList.C
|
||||
|
||||
\*---------------------------------------------------------------------------*/
|
||||
|
||||
#ifndef directInteractionList_H
|
||||
#define directInteractionList_H
|
||||
|
||||
#include "polyMesh.H"
|
||||
#include "List.H"
|
||||
|
||||
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
|
||||
|
||||
namespace Foam
|
||||
{
|
||||
|
||||
// Forward declaration of classes
|
||||
class interactionLists;
|
||||
|
||||
/*---------------------------------------------------------------------------*\
|
||||
Class directInteractionList Declaration
|
||||
\*---------------------------------------------------------------------------*/
|
||||
|
||||
class directInteractionList
|
||||
:
|
||||
public labelListList
|
||||
{
|
||||
// Private data
|
||||
|
||||
const interactionLists& il_;
|
||||
|
||||
|
||||
// Private Member Functions
|
||||
|
||||
void buildDirectInteractionList
|
||||
(
|
||||
bool pointPointListBuild
|
||||
);
|
||||
|
||||
//- Disallow default bitwise copy construct
|
||||
directInteractionList(const directInteractionList&);
|
||||
|
||||
//- Disallow default bitwise assignment
|
||||
void operator=(const directInteractionList&);
|
||||
|
||||
|
||||
public:
|
||||
|
||||
// Constructors
|
||||
|
||||
//- Construct lists by searching the mesh
|
||||
directInteractionList
|
||||
(
|
||||
const interactionLists& il,
|
||||
bool pointPointListBuild
|
||||
);
|
||||
|
||||
//- Construct from file
|
||||
directInteractionList
|
||||
(
|
||||
const interactionLists& il
|
||||
);
|
||||
|
||||
|
||||
//- Destructor
|
||||
~directInteractionList();
|
||||
|
||||
|
||||
// Member Functions
|
||||
|
||||
// Access
|
||||
|
||||
inline const interactionLists& il() const;
|
||||
|
||||
|
||||
// IOstream Operators
|
||||
|
||||
friend Istream& operator>>(Istream&, directInteractionList&);
|
||||
friend Ostream& operator<<(Ostream&, const directInteractionList&);
|
||||
};
|
||||
|
||||
|
||||
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
|
||||
|
||||
} // End namespace Foam
|
||||
|
||||
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
|
||||
|
||||
#include "directInteractionListI.H"
|
||||
|
||||
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
|
||||
|
||||
#endif
|
||||
|
||||
// ************************************************************************* //
|
||||
@ -1,34 +0,0 @@
|
||||
/*---------------------------------------------------------------------------*\
|
||||
========= |
|
||||
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
|
||||
\\ / O peration |
|
||||
\\ / A nd | Copyright (C) 2008-2010 OpenCFD Ltd.
|
||||
\\/ M anipulation |
|
||||
-------------------------------------------------------------------------------
|
||||
License
|
||||
This file is part of OpenFOAM.
|
||||
|
||||
OpenFOAM is free software: you can redistribute it and/or modify it
|
||||
under the terms of the GNU General Public License as published by
|
||||
the Free Software Foundation, either version 3 of the License, or
|
||||
(at your option) any later version.
|
||||
|
||||
OpenFOAM is distributed in the hope that it will be useful, but WITHOUT
|
||||
ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
|
||||
FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License
|
||||
for more details.
|
||||
|
||||
You should have received a copy of the GNU General Public License
|
||||
along with OpenFOAM. If not, see <http://www.gnu.org/licenses/>.
|
||||
|
||||
\*---------------------------------------------------------------------------*/
|
||||
|
||||
// * * * * * * * * * * * * * * * Member Functions * * * * * * * * * * * * * //
|
||||
|
||||
inline const Foam::interactionLists& Foam::directInteractionList::il() const
|
||||
{
|
||||
return il_;
|
||||
}
|
||||
|
||||
|
||||
// ************************************************************************* //
|
||||
@ -1,691 +0,0 @@
|
||||
/*---------------------------------------------------------------------------*\
|
||||
========= |
|
||||
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
|
||||
\\ / O peration |
|
||||
\\ / A nd | Copyright (C) 2008-2010 OpenCFD Ltd.
|
||||
\\/ M anipulation |
|
||||
-------------------------------------------------------------------------------
|
||||
License
|
||||
This file is part of OpenFOAM.
|
||||
|
||||
OpenFOAM is free software: you can redistribute it and/or modify it
|
||||
under the terms of the GNU General Public License as published by
|
||||
the Free Software Foundation, either version 3 of the License, or
|
||||
(at your option) any later version.
|
||||
|
||||
OpenFOAM is distributed in the hope that it will be useful, but WITHOUT
|
||||
ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
|
||||
FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License
|
||||
for more details.
|
||||
|
||||
You should have received a copy of the GNU General Public License
|
||||
along with OpenFOAM. If not, see <http://www.gnu.org/licenses/>.
|
||||
|
||||
\*---------------------------------------------------------------------------*/
|
||||
|
||||
#include "interactionLists.H"
|
||||
|
||||
// * * * * * * * * * * * * * * Static Data Members * * * * * * * * * * * * * //
|
||||
|
||||
Foam::scalar Foam::interactionLists::transTol = 1e-12;
|
||||
|
||||
|
||||
// * * * * * * * * * * * * * Private Member Functions * * * * * * * * * * * //
|
||||
|
||||
void Foam::interactionLists::buildCellReferralLists()
|
||||
{
|
||||
Info<< nl << "Determining molecule referring schedule" << endl;
|
||||
|
||||
const referredCellList& refIntL(ril());
|
||||
|
||||
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]
|
||||
);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
// * * * * * * * * * * * * * * * * Constructors * * * * * * * * * * * * * * //
|
||||
|
||||
|
||||
Foam::interactionLists::interactionLists
|
||||
(
|
||||
const polyMesh& mesh,
|
||||
scalar rCutMaxSqr,
|
||||
bool pointPointListBuild
|
||||
)
|
||||
:
|
||||
mesh_(mesh),
|
||||
rCutMaxSqr_(rCutMaxSqr),
|
||||
dil_(*this, pointPointListBuild),
|
||||
ril_(*this, pointPointListBuild),
|
||||
cellSendingReferralLists_(),
|
||||
cellReceivingReferralLists_()
|
||||
{
|
||||
buildCellReferralLists();
|
||||
}
|
||||
|
||||
|
||||
Foam::interactionLists::interactionLists(const polyMesh& mesh)
|
||||
:
|
||||
mesh_(mesh),
|
||||
dil_(*this),
|
||||
ril_(*this)
|
||||
{}
|
||||
|
||||
|
||||
// * * * * * * * * * * * * * * * * Destructor * * * * * * * * * * * * * * * //
|
||||
|
||||
Foam::interactionLists::~interactionLists()
|
||||
{}
|
||||
|
||||
|
||||
// * * * * * * * * * * * * * * * Member Functions * * * * * * * * * * * * * //
|
||||
|
||||
bool Foam::interactionLists::testPointPointDistance
|
||||
(
|
||||
const label ptI,
|
||||
const label ptJ
|
||||
) const
|
||||
{
|
||||
return (magSqr(mesh_.points()[ptI] - mesh_.points()[ptJ]) <= rCutMaxSqr_);
|
||||
}
|
||||
|
||||
|
||||
bool Foam::interactionLists::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::interactionLists::testPointFaceDistance
|
||||
(
|
||||
const label p,
|
||||
const label faceNo
|
||||
) const
|
||||
{
|
||||
const vector& pointPosition(mesh_.points()[p]);
|
||||
|
||||
return testPointFaceDistance(pointPosition, faceNo);
|
||||
}
|
||||
|
||||
|
||||
bool Foam::interactionLists::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::interactionLists::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::interactionLists::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::interactionLists::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 (magSqr(perpDist) > rCutMaxSqr_)
|
||||
{
|
||||
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
|
||||
(
|
||||
"interactionLists::testPointFaceDistance"
|
||||
"("
|
||||
"const vector&, "
|
||||
"const labelList&, "
|
||||
"const vectorList&, "
|
||||
"const vector&, "
|
||||
"const vector&"
|
||||
") const"
|
||||
) << "point " << p << " to face " << faceToTest
|
||||
<< " comparison did not find a nearest point"
|
||||
<< " to be inside or outside face."
|
||||
<< abort(FatalError);
|
||||
|
||||
return false;
|
||||
}
|
||||
|
||||
|
||||
bool Foam::interactionLists::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;
|
||||
}
|
||||
|
||||
|
||||
const Foam::labelList Foam::interactionLists::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);
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
return realCellsFoundInRange.shrink();
|
||||
}
|
||||
|
||||
|
||||
const Foam::labelList Foam::interactionLists::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();
|
||||
}
|
||||
|
||||
|
||||
// ************************************************************************* //
|
||||
@ -1,214 +0,0 @@
|
||||
/*---------------------------------------------------------------------------*\
|
||||
========= |
|
||||
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
|
||||
\\ / O peration |
|
||||
\\ / A nd | Copyright (C) 2008-2010 OpenCFD Ltd.
|
||||
\\/ M anipulation |
|
||||
-------------------------------------------------------------------------------
|
||||
License
|
||||
This file is part of OpenFOAM.
|
||||
|
||||
OpenFOAM is free software: you can redistribute it and/or modify it
|
||||
under the terms of the GNU General Public License as published by
|
||||
the Free Software Foundation, either version 3 of the License, or
|
||||
(at your option) any later version.
|
||||
|
||||
OpenFOAM is distributed in the hope that it will be useful, but WITHOUT
|
||||
ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
|
||||
FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License
|
||||
for more details.
|
||||
|
||||
You should have received a copy of the GNU General Public License
|
||||
along with OpenFOAM. If not, see <http://www.gnu.org/licenses/>.
|
||||
|
||||
Class
|
||||
Foam::interactionLists
|
||||
|
||||
Description
|
||||
|
||||
SourceFiles
|
||||
interactionListsI.H
|
||||
interactionLists.C
|
||||
interactionListsIO.C
|
||||
|
||||
\*---------------------------------------------------------------------------*/
|
||||
|
||||
#ifndef interactionLists_H
|
||||
#define interactionLists_H
|
||||
|
||||
#include "polyMesh.H"
|
||||
#include "vector2D.H"
|
||||
#include "directInteractionList.H"
|
||||
#include "referredCell.H"
|
||||
#include "referredCellList.H"
|
||||
#include "sendingReferralList.H"
|
||||
#include "receivingReferralList.H"
|
||||
|
||||
|
||||
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
|
||||
|
||||
namespace Foam
|
||||
{
|
||||
|
||||
/*---------------------------------------------------------------------------*\
|
||||
Class interactionLists Declaration
|
||||
\*---------------------------------------------------------------------------*/
|
||||
|
||||
class interactionLists
|
||||
{
|
||||
// Private data
|
||||
|
||||
const polyMesh& mesh_;
|
||||
|
||||
scalar rCutMaxSqr_;
|
||||
|
||||
directInteractionList dil_;
|
||||
|
||||
referredCellList ril_;
|
||||
|
||||
List<sendingReferralList> cellSendingReferralLists_;
|
||||
|
||||
List<receivingReferralList> cellReceivingReferralLists_;
|
||||
|
||||
|
||||
// Private Member Functions
|
||||
|
||||
//- Build referralLists which define how to send information
|
||||
// to referredCells to source cells
|
||||
void buildCellReferralLists();
|
||||
|
||||
//- Disallow default bitwise copy construct
|
||||
interactionLists(const interactionLists&);
|
||||
|
||||
//- Disallow default bitwise assignment
|
||||
void operator=(const interactionLists&);
|
||||
|
||||
|
||||
public:
|
||||
|
||||
// Static data members
|
||||
|
||||
//- Tolerance for checking that faces on a patch segment
|
||||
static scalar transTol;
|
||||
|
||||
|
||||
// Constructors
|
||||
|
||||
//- Construct and create all information from the mesh
|
||||
interactionLists
|
||||
(
|
||||
const polyMesh& mesh,
|
||||
scalar rCutMaxSqr,
|
||||
bool pointPointListBuild = false
|
||||
);
|
||||
|
||||
//- Construct from file
|
||||
interactionLists(const polyMesh& mesh);
|
||||
|
||||
|
||||
//- Destructor
|
||||
~interactionLists();
|
||||
|
||||
|
||||
// Member Functions
|
||||
|
||||
bool testPointPointDistance
|
||||
(
|
||||
const label ptI,
|
||||
const label ptJ
|
||||
) const;
|
||||
|
||||
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;
|
||||
|
||||
|
||||
// Access
|
||||
|
||||
inline const polyMesh& mesh() const;
|
||||
|
||||
inline const directInteractionList& dil() const;
|
||||
|
||||
inline const referredCellList& ril() const;
|
||||
inline referredCellList& ril();
|
||||
|
||||
inline const List<sendingReferralList>&
|
||||
cellSendingReferralLists() const;
|
||||
|
||||
inline const List<receivingReferralList>&
|
||||
cellReceivingReferralLists() const;
|
||||
|
||||
inline label nInteractingProcs() const;
|
||||
};
|
||||
|
||||
|
||||
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
|
||||
|
||||
} // End namespace Foam
|
||||
|
||||
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
|
||||
|
||||
#include "interactionListsI.H"
|
||||
|
||||
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
|
||||
|
||||
#endif
|
||||
|
||||
// ************************************************************************* //
|
||||
@ -1,77 +0,0 @@
|
||||
/*---------------------------------------------------------------------------*\
|
||||
========= |
|
||||
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
|
||||
\\ / O peration |
|
||||
\\ / A nd | Copyright (C) 2008-2010 OpenCFD Ltd.
|
||||
\\/ M anipulation |
|
||||
-------------------------------------------------------------------------------
|
||||
License
|
||||
This file is part of OpenFOAM.
|
||||
|
||||
OpenFOAM is free software: you can redistribute it and/or modify it
|
||||
under the terms of the GNU General Public License as published by
|
||||
the Free Software Foundation, either version 3 of the License, or
|
||||
(at your option) any later version.
|
||||
|
||||
OpenFOAM is distributed in the hope that it will be useful, but WITHOUT
|
||||
ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
|
||||
FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License
|
||||
for more details.
|
||||
|
||||
You should have received a copy of the GNU General Public License
|
||||
along with OpenFOAM. If not, see <http://www.gnu.org/licenses/>.
|
||||
|
||||
\*---------------------------------------------------------------------------*/
|
||||
|
||||
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
|
||||
|
||||
// * * * * * * * * * * * * * * * Member Functions * * * * * * * * * * * * * //
|
||||
|
||||
const Foam::polyMesh& Foam::interactionLists::mesh() const
|
||||
{
|
||||
return mesh_;
|
||||
}
|
||||
|
||||
|
||||
const Foam::directInteractionList& Foam::interactionLists::dil() const
|
||||
{
|
||||
return dil_;
|
||||
}
|
||||
|
||||
|
||||
inline const Foam::referredCellList& Foam::interactionLists::ril() const
|
||||
{
|
||||
return ril_;
|
||||
}
|
||||
|
||||
|
||||
inline Foam::referredCellList& Foam::interactionLists::ril()
|
||||
{
|
||||
return ril_;
|
||||
}
|
||||
|
||||
|
||||
inline const Foam::List<Foam::sendingReferralList>&
|
||||
Foam::interactionLists::cellSendingReferralLists() const
|
||||
{
|
||||
return cellSendingReferralLists_;
|
||||
}
|
||||
|
||||
|
||||
inline const Foam::List<Foam::receivingReferralList>&
|
||||
Foam::interactionLists::cellReceivingReferralLists() const
|
||||
{
|
||||
return cellReceivingReferralLists_;
|
||||
}
|
||||
|
||||
|
||||
inline Foam::label Foam::interactionLists::nInteractingProcs() const
|
||||
{
|
||||
return cellReceivingReferralLists_.size();
|
||||
}
|
||||
|
||||
|
||||
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
|
||||
|
||||
|
||||
// ************************************************************************* //
|
||||
@ -1,448 +0,0 @@
|
||||
/*---------------------------------------------------------------------------*\
|
||||
========= |
|
||||
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
|
||||
\\ / O peration |
|
||||
\\ / A nd | Copyright (C) 2008-2010 OpenCFD Ltd.
|
||||
\\/ M anipulation |
|
||||
-------------------------------------------------------------------------------
|
||||
License
|
||||
This file is part of OpenFOAM.
|
||||
|
||||
OpenFOAM is free software: you can redistribute it and/or modify it
|
||||
under the terms of the GNU General Public License as published by
|
||||
the Free Software Foundation, either version 3 of the License, or
|
||||
(at your option) any later version.
|
||||
|
||||
OpenFOAM is distributed in the hope that it will be useful, but WITHOUT
|
||||
ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
|
||||
FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License
|
||||
for more details.
|
||||
|
||||
You should have received a copy of the GNU General Public License
|
||||
along with OpenFOAM. If not, see <http://www.gnu.org/licenses/>.
|
||||
|
||||
\*----------------------------------------------------------------------------*/
|
||||
|
||||
#include "referredCell.H"
|
||||
#include "interactionLists.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::referPosition
|
||||
(
|
||||
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()
|
||||
),
|
||||
referPosition
|
||||
(
|
||||
incomingMols[iM].sitePositions()
|
||||
)
|
||||
)
|
||||
);
|
||||
}
|
||||
|
||||
shrink();
|
||||
}
|
||||
|
||||
|
||||
bool referredCell::duplicate(const referredCell& refCellDupl) const
|
||||
{
|
||||
return
|
||||
(
|
||||
sourceProc_ == refCellDupl.sourceProc()
|
||||
&& sourceCell_ == refCellDupl.sourceCell()
|
||||
&& mag(offset_ - refCellDupl.offset()) < interactionLists::transTol
|
||||
);
|
||||
}
|
||||
|
||||
|
||||
bool referredCell::duplicate(const label procNo,const label nCells) const
|
||||
{
|
||||
return
|
||||
(
|
||||
sourceProc_ == procNo
|
||||
&& sourceCell_ < nCells
|
||||
&& mag(offset_) < interactionLists::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
|
||||
|
||||
// ************************************************************************* //
|
||||
@ -1,275 +0,0 @@
|
||||
/*---------------------------------------------------------------------------*\
|
||||
========= |
|
||||
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
|
||||
\\ / O peration |
|
||||
\\ / A nd | Copyright (C) 2008-2010 OpenCFD Ltd.
|
||||
\\/ M anipulation |
|
||||
-------------------------------------------------------------------------------
|
||||
License
|
||||
This file is part of OpenFOAM.
|
||||
|
||||
OpenFOAM is free software: you can redistribute it and/or modify it
|
||||
under the terms of the GNU General Public License as published by
|
||||
the Free Software Foundation, either version 3 of the License, or
|
||||
(at your option) any later version.
|
||||
|
||||
OpenFOAM is distributed in the hope that it will be useful, but WITHOUT
|
||||
ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
|
||||
FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License
|
||||
for more details.
|
||||
|
||||
You should have received a copy of the GNU General Public License
|
||||
along with OpenFOAM. If not, see <http://www.gnu.org/licenses/>.
|
||||
|
||||
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 its 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 referPosition(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
|
||||
|
||||
// ************************************************************************* //
|
||||
@ -1,126 +0,0 @@
|
||||
/*---------------------------------------------------------------------------*\
|
||||
========= |
|
||||
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
|
||||
\\ / O peration |
|
||||
\\ / A nd | Copyright (C) 2008-2010 OpenCFD Ltd.
|
||||
\\/ M anipulation |
|
||||
-------------------------------------------------------------------------------
|
||||
License
|
||||
This file is part of OpenFOAM.
|
||||
|
||||
OpenFOAM is free software: you can redistribute it and/or modify it
|
||||
under the terms of the GNU General Public License as published by
|
||||
the Free Software Foundation, either version 3 of the License, or
|
||||
(at your option) any later version.
|
||||
|
||||
OpenFOAM is distributed in the hope that it will be useful, but WITHOUT
|
||||
ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
|
||||
FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License
|
||||
for more details.
|
||||
|
||||
You should have received a copy of the GNU General Public License
|
||||
along with OpenFOAM. If not, see <http://www.gnu.org/licenses/>.
|
||||
|
||||
\*---------------------------------------------------------------------------*/
|
||||
|
||||
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
|
||||
|
||||
// ************************************************************************* //
|
||||
File diff suppressed because it is too large
Load Diff
@ -1,109 +0,0 @@
|
||||
/*---------------------------------------------------------------------------*\
|
||||
========= |
|
||||
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
|
||||
\\ / O peration |
|
||||
\\ / A nd | Copyright (C) 2008-2010 OpenCFD Ltd.
|
||||
\\/ M anipulation |
|
||||
-------------------------------------------------------------------------------
|
||||
License
|
||||
This file is part of OpenFOAM.
|
||||
|
||||
OpenFOAM is free software: you can redistribute it and/or modify it
|
||||
under the terms of the GNU General Public License as published by
|
||||
the Free Software Foundation, either version 3 of the License, or
|
||||
(at your option) any later version.
|
||||
|
||||
OpenFOAM is distributed in the hope that it will be useful, but WITHOUT
|
||||
ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
|
||||
FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License
|
||||
for more details.
|
||||
|
||||
You should have received a copy of the GNU General Public License
|
||||
along with OpenFOAM. If not, see <http://www.gnu.org/licenses/>.
|
||||
|
||||
Class
|
||||
Foam::referredCellList
|
||||
|
||||
Description
|
||||
|
||||
SourceFiles
|
||||
referredCellListI.H
|
||||
referredCellList.C
|
||||
|
||||
\*---------------------------------------------------------------------------*/
|
||||
|
||||
#ifndef referredCellList_H
|
||||
#define referredCellList_H
|
||||
|
||||
#include "referredCell.H"
|
||||
#include "molecule.H"
|
||||
|
||||
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
|
||||
|
||||
namespace Foam
|
||||
{
|
||||
|
||||
// Forward declaration of classes
|
||||
class interactionLists;
|
||||
|
||||
/*---------------------------------------------------------------------------*\
|
||||
Class referredCellList Declaration
|
||||
\*---------------------------------------------------------------------------*/
|
||||
|
||||
class referredCellList
|
||||
:
|
||||
public List<referredCell>
|
||||
{
|
||||
// Private data
|
||||
|
||||
const interactionLists& il_;
|
||||
|
||||
|
||||
// Private Member Functions
|
||||
|
||||
void buildReferredCellList
|
||||
(
|
||||
bool pointPointListBuild
|
||||
);
|
||||
|
||||
|
||||
public:
|
||||
|
||||
// Constructors
|
||||
|
||||
//- Construct lists by searching the mesh
|
||||
referredCellList
|
||||
(
|
||||
interactionLists& il,
|
||||
bool pointPointListBuild
|
||||
);
|
||||
|
||||
//- Construct from file
|
||||
referredCellList (interactionLists& il);
|
||||
|
||||
|
||||
//- Destructor
|
||||
~referredCellList();
|
||||
|
||||
|
||||
// Member Functions
|
||||
|
||||
void referMolecules(const List<DynamicList<molecule*> >& cellOccupancy);
|
||||
|
||||
inline const interactionLists& il() const;
|
||||
};
|
||||
|
||||
|
||||
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
|
||||
|
||||
} // End namespace Foam
|
||||
|
||||
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
|
||||
|
||||
#include "referredCellListI.H"
|
||||
|
||||
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
|
||||
|
||||
#endif
|
||||
|
||||
// ************************************************************************* //
|
||||
@ -1,34 +0,0 @@
|
||||
/*---------------------------------------------------------------------------*\
|
||||
========= |
|
||||
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
|
||||
\\ / O peration |
|
||||
\\ / A nd | Copyright (C) 2008-2010 OpenCFD Ltd.
|
||||
\\/ M anipulation |
|
||||
-------------------------------------------------------------------------------
|
||||
License
|
||||
This file is part of OpenFOAM.
|
||||
|
||||
OpenFOAM is free software: you can redistribute it and/or modify it
|
||||
under the terms of the GNU General Public License as published by
|
||||
the Free Software Foundation, either version 3 of the License, or
|
||||
(at your option) any later version.
|
||||
|
||||
OpenFOAM is distributed in the hope that it will be useful, but WITHOUT
|
||||
ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
|
||||
FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License
|
||||
for more details.
|
||||
|
||||
You should have received a copy of the GNU General Public License
|
||||
along with OpenFOAM. If not, see <http://www.gnu.org/licenses/>.
|
||||
|
||||
\*---------------------------------------------------------------------------*/
|
||||
|
||||
// * * * * * * * * * * * * * * * Member Operators * * * * * * * * * * * * * //
|
||||
|
||||
inline const Foam::interactionLists& Foam::referredCellList::il() const
|
||||
{
|
||||
return il_;
|
||||
}
|
||||
|
||||
|
||||
// ************************************************************************* //
|
||||
@ -1,85 +0,0 @@
|
||||
/*---------------------------------------------------------------------------*\
|
||||
========= |
|
||||
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
|
||||
\\ / O peration |
|
||||
\\ / A nd | Copyright (C) 2008-2010 OpenCFD Ltd.
|
||||
\\/ M anipulation |
|
||||
-------------------------------------------------------------------------------
|
||||
License
|
||||
This file is part of OpenFOAM.
|
||||
|
||||
OpenFOAM is free software: you can redistribute it and/or modify it
|
||||
under the terms of the GNU General Public License as published by
|
||||
the Free Software Foundation, either version 3 of the License, or
|
||||
(at your option) any later version.
|
||||
|
||||
OpenFOAM is distributed in the hope that it will be useful, but WITHOUT
|
||||
ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
|
||||
FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License
|
||||
for more details.
|
||||
|
||||
You should have received a copy of the GNU General Public License
|
||||
along with OpenFOAM. If not, see <http://www.gnu.org/licenses/>.
|
||||
|
||||
\*----------------------------------------------------------------------------*/
|
||||
|
||||
#include "referredMolecule.H"
|
||||
|
||||
// * * * * * * * * * * * * * * * * Constructors * * * * * * * * * * * * * * //
|
||||
|
||||
Foam::referredMolecule::referredMolecule()
|
||||
{}
|
||||
|
||||
|
||||
Foam::referredMolecule::referredMolecule
|
||||
(
|
||||
const label id,
|
||||
const vector& position,
|
||||
const List<vector>& sitePositions
|
||||
)
|
||||
:
|
||||
id_(id),
|
||||
position_(position),
|
||||
sitePositions_(sitePositions)
|
||||
{}
|
||||
|
||||
|
||||
// * * * * * * * * * * * * * * * * Destructor * * * * * * * * * * * * * * * //
|
||||
|
||||
Foam::referredMolecule::~referredMolecule()
|
||||
{}
|
||||
|
||||
|
||||
// * * * * * * * * * * * * * * * Friend Operators * * * * * * * * * * * * * //
|
||||
|
||||
Foam::Istream& Foam::operator>>
|
||||
(
|
||||
Istream& is,
|
||||
referredMolecule& rM
|
||||
)
|
||||
{
|
||||
is >> rM.id_ >> rM.position_ >> rM.sitePositions_;
|
||||
|
||||
is.check("Istream& operator<<(Istream& f, const referredMolecule& sRL");
|
||||
|
||||
return is;
|
||||
}
|
||||
|
||||
|
||||
Foam::Ostream& Foam::operator<<
|
||||
(
|
||||
Ostream& os,
|
||||
const referredMolecule& rM
|
||||
)
|
||||
{
|
||||
os << rM.id()
|
||||
<< token::SPACE << rM.position()
|
||||
<< token::SPACE << rM.sitePositions();
|
||||
|
||||
os.check("Ostream& operator<<(Ostream& f, const referredMolecule& rM");
|
||||
|
||||
return os;
|
||||
}
|
||||
|
||||
|
||||
// ************************************************************************* //
|
||||
@ -1,135 +0,0 @@
|
||||
/*---------------------------------------------------------------------------*\
|
||||
========= |
|
||||
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
|
||||
\\ / O peration |
|
||||
\\ / A nd | Copyright (C) 2008-2010 OpenCFD Ltd.
|
||||
\\/ M anipulation |
|
||||
-------------------------------------------------------------------------------
|
||||
License
|
||||
This file is part of OpenFOAM.
|
||||
|
||||
OpenFOAM is free software: you can redistribute it and/or modify it
|
||||
under the terms of the GNU General Public License as published by
|
||||
the Free Software Foundation, either version 3 of the License, or
|
||||
(at your option) any later version.
|
||||
|
||||
OpenFOAM is distributed in the hope that it will be useful, but WITHOUT
|
||||
ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
|
||||
FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License
|
||||
for more details.
|
||||
|
||||
You should have received a copy of the GNU General Public License
|
||||
along with OpenFOAM. If not, see <http://www.gnu.org/licenses/>.
|
||||
|
||||
Class
|
||||
Foam::referredMolecule
|
||||
|
||||
Description
|
||||
|
||||
SourceFiles
|
||||
referredMoleculeI.H
|
||||
referredMolecule.C
|
||||
|
||||
\*---------------------------------------------------------------------------*/
|
||||
|
||||
#ifndef referredMolecule_H
|
||||
#define referredMolecule_H
|
||||
|
||||
#include "vector.H"
|
||||
#include "List.H"
|
||||
|
||||
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
|
||||
|
||||
namespace Foam
|
||||
{
|
||||
|
||||
/*---------------------------------------------------------------------------*\
|
||||
Class referredMolecule Declaration
|
||||
\*---------------------------------------------------------------------------*/
|
||||
|
||||
class referredMolecule
|
||||
{
|
||||
// Private data
|
||||
|
||||
label id_;
|
||||
|
||||
vector position_;
|
||||
|
||||
List<vector> sitePositions_;
|
||||
|
||||
|
||||
public:
|
||||
|
||||
// Constructors
|
||||
|
||||
//- Construct null
|
||||
referredMolecule();
|
||||
|
||||
//- Construct from components
|
||||
referredMolecule
|
||||
(
|
||||
const label id,
|
||||
const vector& position,
|
||||
const List<vector>& sitePositions
|
||||
);
|
||||
|
||||
|
||||
//- Destructor
|
||||
virtual ~referredMolecule();
|
||||
|
||||
|
||||
// Member Functions
|
||||
|
||||
// Access
|
||||
|
||||
inline label id() const;
|
||||
|
||||
inline const vector& position() const;
|
||||
|
||||
inline const List<vector>& sitePositions() 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
|
||||
|
||||
// ************************************************************************* //
|
||||
@ -1,74 +0,0 @@
|
||||
/*---------------------------------------------------------------------------*\
|
||||
========= |
|
||||
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
|
||||
\\ / O peration |
|
||||
\\ / A nd | Copyright (C) 2008-2010 OpenCFD Ltd.
|
||||
\\/ M anipulation |
|
||||
-------------------------------------------------------------------------------
|
||||
License
|
||||
This file is part of OpenFOAM.
|
||||
|
||||
OpenFOAM is free software: you can redistribute it and/or modify it
|
||||
under the terms of the GNU General Public License as published by
|
||||
the Free Software Foundation, either version 3 of the License, or
|
||||
(at your option) any later version.
|
||||
|
||||
OpenFOAM is distributed in the hope that it will be useful, but WITHOUT
|
||||
ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
|
||||
FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License
|
||||
for more details.
|
||||
|
||||
You should have received a copy of the GNU General Public License
|
||||
along with OpenFOAM. If not, see <http://www.gnu.org/licenses/>.
|
||||
|
||||
\*---------------------------------------------------------------------------*/
|
||||
|
||||
|
||||
// * * * * * * * * * * * * * * * Member Functions * * * * * * * * * * * * * //
|
||||
|
||||
inline Foam::label Foam::referredMolecule::id() const
|
||||
{
|
||||
return id_;
|
||||
}
|
||||
|
||||
|
||||
inline const Foam::vector& Foam::referredMolecule::position() const
|
||||
{
|
||||
return position_;
|
||||
}
|
||||
|
||||
|
||||
inline const Foam::List<Foam::vector>&
|
||||
Foam::referredMolecule::sitePositions() const
|
||||
{
|
||||
return sitePositions_;
|
||||
}
|
||||
|
||||
|
||||
// * * * * * * * * * * * * * * * Friend Operators * * * * * * * * * * * * * //
|
||||
|
||||
inline bool Foam::operator==
|
||||
(
|
||||
const Foam::referredMolecule& a,
|
||||
const Foam::referredMolecule& b
|
||||
)
|
||||
{
|
||||
return
|
||||
(
|
||||
a.id() == b.id()
|
||||
&& a.position() == b.position()
|
||||
);
|
||||
}
|
||||
|
||||
|
||||
inline bool Foam::operator!=
|
||||
(
|
||||
const Foam::referredMolecule& a,
|
||||
const Foam::referredMolecule& b
|
||||
)
|
||||
{
|
||||
return !(a == b);
|
||||
}
|
||||
|
||||
|
||||
// ************************************************************************* //
|
||||
@ -209,8 +209,20 @@ bool Foam::molecule::move(molecule::trackData& td)
|
||||
|
||||
void Foam::molecule::transformProperties(const tensor& T)
|
||||
{
|
||||
Particle<molecule>::transformProperties(T);
|
||||
|
||||
Q_ = T & Q_;
|
||||
|
||||
v_ = transform(T, v_);
|
||||
|
||||
a_ = transform(T, a_);
|
||||
|
||||
pi_ = Q_.T() & transform(T, Q_ & pi_);
|
||||
|
||||
tau_ = Q_.T() & transform(T, Q_ & tau_);
|
||||
|
||||
rf_ = transform(T, rf_);
|
||||
|
||||
sitePositions_ = position_ + (T & (sitePositions_ - position_));
|
||||
|
||||
siteForces_ = T & siteForces_;
|
||||
@ -219,10 +231,14 @@ void Foam::molecule::transformProperties(const tensor& T)
|
||||
|
||||
void Foam::molecule::transformProperties(const vector& separation)
|
||||
{
|
||||
Particle<molecule>::transformProperties(separation);
|
||||
|
||||
if (special_ == SPECIAL_TETHERED)
|
||||
{
|
||||
specialPosition_ += separation;
|
||||
}
|
||||
|
||||
sitePositions_ = sitePositions_ + separation;
|
||||
}
|
||||
|
||||
|
||||
|
||||
@ -182,13 +182,6 @@ private:
|
||||
|
||||
// Private data
|
||||
|
||||
//- Be careful with the ordering of data.
|
||||
// It has an impact on binary transfer:
|
||||
// -# Put the largest data members 1st
|
||||
// -# Pair up labels,
|
||||
// -# Don't go scalar-label, scalar-label, because in 64bit mode,
|
||||
// the labels will be padded by 4bytes.
|
||||
|
||||
tensor Q_;
|
||||
|
||||
vector v_;
|
||||
|
||||
@ -242,11 +242,17 @@ void Foam::molecule::writeFields(const Cloud<molecule>& mC)
|
||||
orientation2.write();
|
||||
orientation3.write();
|
||||
|
||||
const moleculeCloud& m = dynamic_cast<const moleculeCloud&>(mC);
|
||||
m.writeXYZ
|
||||
(
|
||||
m.mesh().time().timePath() + "/lagrangian" + "/moleculeCloud.xmol"
|
||||
);
|
||||
Info<< "writeFields " << mC.name() << endl;
|
||||
|
||||
if (isA<moleculeCloud>(mC))
|
||||
{
|
||||
const moleculeCloud& m = dynamic_cast<const moleculeCloud&>(mC);
|
||||
|
||||
m.writeXYZ
|
||||
(
|
||||
m.mesh().time().timePath()/cloud::prefix/"moleculeCloud.xmol"
|
||||
);
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
|
||||
@ -123,23 +123,23 @@ void Foam::moleculeCloud::buildCellOccupancy()
|
||||
{
|
||||
cellOccupancy_[cO].shrink();
|
||||
}
|
||||
|
||||
il_.ril().referMolecules(cellOccupancy());
|
||||
}
|
||||
|
||||
|
||||
void Foam::moleculeCloud::calculatePairForce()
|
||||
{
|
||||
iterator mol(this->begin());
|
||||
PstreamBuffers pBufs(Pstream::nonBlocking);
|
||||
|
||||
// Start sending referred data
|
||||
il_.sendReferredData(cellOccupancy(), pBufs);
|
||||
|
||||
molecule* molI = NULL;
|
||||
molecule* molJ = NULL;
|
||||
|
||||
{
|
||||
// Real-Real interactions
|
||||
|
||||
molecule* molI = &mol();
|
||||
|
||||
molecule* molJ = &mol();
|
||||
|
||||
const directInteractionList& dil(il_.dil());
|
||||
const labelListList& dil = il_.dil();
|
||||
|
||||
forAll(dil, d)
|
||||
{
|
||||
@ -149,54 +149,62 @@ void Foam::moleculeCloud::calculatePairForce()
|
||||
|
||||
forAll(dil[d], interactingCells)
|
||||
{
|
||||
List< molecule* > cellJ =
|
||||
cellOccupancy_[dil[d][interactingCells]];
|
||||
List<molecule*> cellJ =
|
||||
cellOccupancy_[dil[d][interactingCells]];
|
||||
|
||||
forAll(cellJ, cellJMols)
|
||||
{
|
||||
molJ = cellJ[cellJMols];
|
||||
|
||||
evaluatePair(molI, molJ);
|
||||
evaluatePair(*molI, *molJ);
|
||||
}
|
||||
}
|
||||
|
||||
forAll(cellOccupancy_[d],cellIOtherMols)
|
||||
forAll(cellOccupancy_[d], cellIOtherMols)
|
||||
{
|
||||
molJ = cellOccupancy_[d][cellIOtherMols];
|
||||
|
||||
if (molJ > molI)
|
||||
{
|
||||
evaluatePair(molI, molJ);
|
||||
evaluatePair(*molI, *molJ);
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
// Receive referred data
|
||||
il_.receiveReferredData(pBufs);
|
||||
|
||||
{
|
||||
// Real-Referred interactions
|
||||
|
||||
molecule* molK = &mol();
|
||||
const labelListList& ril = il_.ril();
|
||||
|
||||
referredCellList& ril(il_.ril());
|
||||
List<IDLList<molecule> >& referredMols = il_.referredParticles();
|
||||
|
||||
forAll(ril, r)
|
||||
{
|
||||
const List<label>& realCells = ril[r].realCellsForInteraction();
|
||||
const List<label>& realCells = ril[r];
|
||||
|
||||
forAll(ril[r], refMols)
|
||||
IDLList<molecule>& refMols = referredMols[r];
|
||||
|
||||
forAllIter
|
||||
(
|
||||
IDLList<molecule>,
|
||||
refMols,
|
||||
refMol
|
||||
)
|
||||
{
|
||||
referredMolecule* molL(&(ril[r][refMols]));
|
||||
|
||||
forAll(realCells, rC)
|
||||
{
|
||||
List<molecule*> cellK = cellOccupancy_[realCells[rC]];
|
||||
List<molecule*> cellI = cellOccupancy_[realCells[rC]];
|
||||
|
||||
forAll(cellK, cellKMols)
|
||||
forAll(cellI, cellIMols)
|
||||
{
|
||||
molK = cellK[cellKMols];
|
||||
molI = cellI[cellIMols];
|
||||
|
||||
evaluatePair(molK, molL);
|
||||
evaluatePair(*molI, refMol());
|
||||
}
|
||||
}
|
||||
}
|
||||
@ -259,18 +267,14 @@ void Foam::moleculeCloud::removeHighEnergyOverlaps()
|
||||
buildCellOccupancy();
|
||||
|
||||
// Real-Real interaction
|
||||
iterator mol(this->begin());
|
||||
|
||||
molecule* molI = NULL;
|
||||
molecule* molJ = NULL;
|
||||
|
||||
{
|
||||
mol = this->begin();
|
||||
|
||||
molecule* molI = &mol();
|
||||
|
||||
molecule* molJ = &mol();
|
||||
|
||||
DynamicList<molecule*> molsToDelete;
|
||||
|
||||
const directInteractionList& dil(il_.dil());
|
||||
const labelListList& dil(il_.dil());
|
||||
|
||||
forAll(dil, d)
|
||||
{
|
||||
@ -280,14 +284,14 @@ void Foam::moleculeCloud::removeHighEnergyOverlaps()
|
||||
|
||||
forAll(dil[d], interactingCells)
|
||||
{
|
||||
List< molecule* > cellJ =
|
||||
cellOccupancy_[dil[d][interactingCells]];
|
||||
List<molecule*> cellJ =
|
||||
cellOccupancy_[dil[d][interactingCells]];
|
||||
|
||||
forAll(cellJ, cellJMols)
|
||||
{
|
||||
molJ = cellJ[cellJMols];
|
||||
|
||||
if (evaluatePotentialLimit(molI, molJ))
|
||||
if (evaluatePotentialLimit(*molI, *molJ))
|
||||
{
|
||||
label idI = molI->id();
|
||||
|
||||
@ -297,7 +301,7 @@ void Foam::moleculeCloud::removeHighEnergyOverlaps()
|
||||
(
|
||||
idI == idJ
|
||||
|| findIndex(pot_.removalOrder(), idJ)
|
||||
< findIndex(pot_.removalOrder(), idI)
|
||||
< findIndex(pot_.removalOrder(), idI)
|
||||
)
|
||||
{
|
||||
if (findIndex(molsToDelete, molJ) == -1)
|
||||
@ -314,13 +318,13 @@ void Foam::moleculeCloud::removeHighEnergyOverlaps()
|
||||
}
|
||||
}
|
||||
|
||||
forAll(cellOccupancy_[d],cellIOtherMols)
|
||||
forAll(cellOccupancy_[d], cellIOtherMols)
|
||||
{
|
||||
molJ = cellOccupancy_[d][cellIOtherMols];
|
||||
|
||||
if (molJ > molI)
|
||||
{
|
||||
if (evaluatePotentialLimit(molI, molJ))
|
||||
if (evaluatePotentialLimit(*molI, *molJ))
|
||||
{
|
||||
label idI = molI->id();
|
||||
|
||||
@ -330,7 +334,7 @@ void Foam::moleculeCloud::removeHighEnergyOverlaps()
|
||||
(
|
||||
idI == idJ
|
||||
|| findIndex(pot_.removalOrder(), idJ)
|
||||
< findIndex(pot_.removalOrder(), idI)
|
||||
< findIndex(pot_.removalOrder(), idI)
|
||||
)
|
||||
{
|
||||
if (findIndex(molsToDelete, molJ) == -1)
|
||||
@ -355,79 +359,81 @@ void Foam::moleculeCloud::removeHighEnergyOverlaps()
|
||||
|
||||
buildCellOccupancy();
|
||||
|
||||
PstreamBuffers pBufs(Pstream::nonBlocking);
|
||||
|
||||
// Start sending referred data
|
||||
il_.sendReferredData(cellOccupancy(), pBufs);
|
||||
|
||||
// Receive referred data
|
||||
il_.receiveReferredData(pBufs);
|
||||
|
||||
// Real-Referred interaction
|
||||
|
||||
{
|
||||
molecule* molK = &mol();
|
||||
|
||||
DynamicList<molecule*> molsToDelete;
|
||||
|
||||
referredCellList& ril(il_.ril());
|
||||
const labelListList& ril(il_.ril());
|
||||
|
||||
List<IDLList<molecule> >& referredMols = il_.referredParticles();
|
||||
|
||||
forAll(ril, r)
|
||||
{
|
||||
referredCell& refCell = ril[r];
|
||||
IDLList<molecule>& refMols = referredMols[r];
|
||||
|
||||
forAll(refCell, refMols)
|
||||
forAllIter
|
||||
(
|
||||
IDLList<molecule>,
|
||||
refMols,
|
||||
refMol
|
||||
)
|
||||
{
|
||||
referredMolecule* molL = &(refCell[refMols]);
|
||||
molJ = &refMol();
|
||||
|
||||
List <label> realCells = refCell.realCellsForInteraction();
|
||||
const List<label>& realCells = ril[r];
|
||||
|
||||
forAll(realCells, rC)
|
||||
{
|
||||
label cellK = realCells[rC];
|
||||
label cellI = realCells[rC];
|
||||
|
||||
List<molecule*> cellKMols = cellOccupancy_[cellK];
|
||||
List<molecule*> cellIMols = cellOccupancy_[cellI];
|
||||
|
||||
forAll(cellKMols, cKM)
|
||||
forAll(cellIMols, cIM)
|
||||
{
|
||||
molK = cellKMols[cKM];
|
||||
molI = cellIMols[cIM];
|
||||
|
||||
if (evaluatePotentialLimit(molK, molL))
|
||||
if (evaluatePotentialLimit(*molI, *molJ))
|
||||
{
|
||||
label idK = molK->id();
|
||||
label idI = molI->id();
|
||||
|
||||
label idL = molL->id();
|
||||
label idJ = molJ->id();
|
||||
|
||||
if
|
||||
(
|
||||
findIndex(pot_.removalOrder(), idK)
|
||||
< findIndex(pot_.removalOrder(), idL)
|
||||
findIndex(pot_.removalOrder(), idI)
|
||||
< findIndex(pot_.removalOrder(), idJ)
|
||||
)
|
||||
{
|
||||
if (findIndex(molsToDelete, molK) == -1)
|
||||
if (findIndex(molsToDelete, molI) == -1)
|
||||
{
|
||||
molsToDelete.append(molK);
|
||||
molsToDelete.append(molI);
|
||||
}
|
||||
}
|
||||
|
||||
else if
|
||||
(
|
||||
findIndex(pot_.removalOrder(), idK)
|
||||
== findIndex(pot_.removalOrder(), idL)
|
||||
findIndex(pot_.removalOrder(), idI)
|
||||
== findIndex(pot_.removalOrder(), idJ)
|
||||
)
|
||||
{
|
||||
if
|
||||
(
|
||||
Pstream::myProcNo() == refCell.sourceProc()
|
||||
&& cellK <= refCell.sourceCell()
|
||||
)
|
||||
{
|
||||
if (findIndex(molsToDelete, molK) == -1)
|
||||
{
|
||||
molsToDelete.append(molK);
|
||||
}
|
||||
}
|
||||
// Remove one of the molecules
|
||||
// arbitrarily, assuring that a
|
||||
// consistent decision is made for
|
||||
// both real-referred pairs.
|
||||
|
||||
else if
|
||||
(
|
||||
Pstream::myProcNo() < refCell.sourceProc()
|
||||
)
|
||||
if (molI->origId() > molJ->origId())
|
||||
{
|
||||
if (findIndex(molsToDelete, molK) == -1)
|
||||
if (findIndex(molsToDelete, molI) == -1)
|
||||
{
|
||||
molsToDelete.append(molK);
|
||||
molsToDelete.append(molI);
|
||||
}
|
||||
}
|
||||
}
|
||||
@ -445,6 +451,12 @@ void Foam::moleculeCloud::removeHighEnergyOverlaps()
|
||||
|
||||
buildCellOccupancy();
|
||||
|
||||
// Start sending referred data
|
||||
il_.sendReferredData(cellOccupancy(), pBufs);
|
||||
|
||||
// Receive referred data
|
||||
il_.receiveReferredData(pBufs);
|
||||
|
||||
label molsRemoved = initialSize - this->size();
|
||||
|
||||
if (Pstream::parRun())
|
||||
@ -713,19 +725,22 @@ void Foam::moleculeCloud::initialiseMolecules
|
||||
label id = findIndex(pot_.idList(), latticeIds[p]);
|
||||
|
||||
const vector& latticePosition =
|
||||
vector
|
||||
(
|
||||
unitCellLatticePosition.x(),
|
||||
unitCellLatticePosition.y(),
|
||||
unitCellLatticePosition.z()
|
||||
)
|
||||
+ latticePositions[p];
|
||||
vector
|
||||
(
|
||||
unitCellLatticePosition.x(),
|
||||
unitCellLatticePosition.y(),
|
||||
unitCellLatticePosition.z()
|
||||
)
|
||||
+ latticePositions[p];
|
||||
|
||||
point globalPosition =
|
||||
anchor + (R & (latticeCellShape & latticePosition));
|
||||
anchor
|
||||
+ (R & (latticeCellShape & latticePosition));
|
||||
|
||||
partOfLayerInBounds =
|
||||
mesh_.bounds().contains(globalPosition);
|
||||
partOfLayerInBounds = mesh_.bounds().contains
|
||||
(
|
||||
globalPosition
|
||||
);
|
||||
|
||||
label cell = mesh_.findCell(globalPosition);
|
||||
|
||||
@ -779,20 +794,29 @@ void Foam::moleculeCloud::initialiseMolecules
|
||||
);
|
||||
|
||||
const vector& latticePosition =
|
||||
vector
|
||||
(
|
||||
unitCellLatticePosition.x(),
|
||||
unitCellLatticePosition.y(),
|
||||
unitCellLatticePosition.z()
|
||||
)
|
||||
+ latticePositions[p];
|
||||
vector
|
||||
(
|
||||
unitCellLatticePosition.x(),
|
||||
unitCellLatticePosition.y(),
|
||||
unitCellLatticePosition.z()
|
||||
)
|
||||
+ latticePositions[p];
|
||||
|
||||
point globalPosition = anchor
|
||||
+ (R
|
||||
&(latticeCellShape & latticePosition));
|
||||
point globalPosition =
|
||||
anchor
|
||||
+ (
|
||||
R
|
||||
& (
|
||||
latticeCellShape
|
||||
& latticePosition
|
||||
)
|
||||
);
|
||||
|
||||
partOfLayerInBounds =
|
||||
mesh_.bounds().contains(globalPosition);
|
||||
mesh_.bounds().contains
|
||||
(
|
||||
globalPosition
|
||||
);
|
||||
|
||||
label cell = mesh_.findCell
|
||||
(
|
||||
@ -840,20 +864,29 @@ void Foam::moleculeCloud::initialiseMolecules
|
||||
);
|
||||
|
||||
const vector& latticePosition =
|
||||
vector
|
||||
(
|
||||
unitCellLatticePosition.x(),
|
||||
unitCellLatticePosition.y(),
|
||||
unitCellLatticePosition.z()
|
||||
)
|
||||
+ latticePositions[p];
|
||||
vector
|
||||
(
|
||||
unitCellLatticePosition.x(),
|
||||
unitCellLatticePosition.y(),
|
||||
unitCellLatticePosition.z()
|
||||
)
|
||||
+ latticePositions[p];
|
||||
|
||||
point globalPosition = anchor
|
||||
+ (R
|
||||
&(latticeCellShape & latticePosition));
|
||||
point globalPosition =
|
||||
anchor
|
||||
+ (
|
||||
R
|
||||
& (
|
||||
latticeCellShape
|
||||
& latticePosition
|
||||
)
|
||||
);
|
||||
|
||||
partOfLayerInBounds =
|
||||
mesh_.bounds().contains(globalPosition);
|
||||
mesh_.bounds().contains
|
||||
(
|
||||
globalPosition
|
||||
);
|
||||
|
||||
label cell = mesh_.findCell
|
||||
(
|
||||
@ -875,12 +908,12 @@ void Foam::moleculeCloud::initialiseMolecules
|
||||
}
|
||||
|
||||
unitCellLatticePosition =
|
||||
labelVector
|
||||
(
|
||||
- unitCellLatticePosition.y(),
|
||||
unitCellLatticePosition.x(),
|
||||
unitCellLatticePosition.z()
|
||||
);
|
||||
labelVector
|
||||
(
|
||||
- unitCellLatticePosition.y(),
|
||||
unitCellLatticePosition.x(),
|
||||
unitCellLatticePosition.z()
|
||||
);
|
||||
}
|
||||
}
|
||||
}
|
||||
@ -913,7 +946,7 @@ void Foam::moleculeCloud::initialiseMolecules
|
||||
}
|
||||
|
||||
molsPlacedThisIteration =
|
||||
this->size() - sizeBeforeIteration;
|
||||
this->size() - sizeBeforeIteration;
|
||||
|
||||
totalZoneMols += molsPlacedThisIteration;
|
||||
|
||||
@ -1041,7 +1074,7 @@ Foam::moleculeCloud::moleculeCloud
|
||||
mesh_(mesh),
|
||||
pot_(pot),
|
||||
cellOccupancy_(mesh_.nCells()),
|
||||
il_(mesh_, pot_.pairPotentials().rCutMaxSqr(), false),
|
||||
il_(mesh_, pot_.pairPotentials().rCutMax(), true),
|
||||
constPropList_(),
|
||||
rndGen_(clock::getTime())
|
||||
{
|
||||
@ -1071,7 +1104,7 @@ Foam::moleculeCloud::moleculeCloud
|
||||
Cloud<molecule>(mesh, "moleculeCloud", false),
|
||||
mesh_(mesh),
|
||||
pot_(pot),
|
||||
il_(mesh_),
|
||||
il_(mesh_, 0.0, false),
|
||||
constPropList_(),
|
||||
rndGen_(clock::getTime())
|
||||
{
|
||||
@ -1137,7 +1170,7 @@ void Foam::moleculeCloud::applyConstraintsAndThermostats
|
||||
)
|
||||
{
|
||||
scalar temperatureCorrectionFactor =
|
||||
sqrt(targetTemperature/measuredTemperature);
|
||||
sqrt(targetTemperature/max(VSMALL, measuredTemperature));
|
||||
|
||||
Info<< "----------------------------------------" << nl
|
||||
<< "Temperature equilibration" << nl
|
||||
|
||||
@ -40,7 +40,7 @@ SourceFiles
|
||||
#include "molecule.H"
|
||||
#include "IOdictionary.H"
|
||||
#include "potential.H"
|
||||
#include "interactionLists.H"
|
||||
#include "InteractionLists.H"
|
||||
#include "labelVector.H"
|
||||
#include "Random.H"
|
||||
#include "fileName.H"
|
||||
@ -69,7 +69,7 @@ private:
|
||||
|
||||
List<DynamicList<molecule*> > cellOccupancy_;
|
||||
|
||||
interactionLists il_;
|
||||
InteractionLists<molecule> il_;
|
||||
|
||||
List<molecule::constantProperties> constPropList_;
|
||||
|
||||
@ -89,26 +89,14 @@ private:
|
||||
|
||||
inline void evaluatePair
|
||||
(
|
||||
molecule* molI,
|
||||
molecule* molJ
|
||||
);
|
||||
|
||||
inline void evaluatePair
|
||||
(
|
||||
molecule* molReal,
|
||||
referredMolecule* molRef
|
||||
molecule& molI,
|
||||
molecule& molJ
|
||||
);
|
||||
|
||||
inline bool evaluatePotentialLimit
|
||||
(
|
||||
molecule* molI,
|
||||
molecule* molJ
|
||||
) const;
|
||||
|
||||
inline bool evaluatePotentialLimit
|
||||
(
|
||||
molecule* molReal,
|
||||
referredMolecule* molRef
|
||||
molecule& molI,
|
||||
molecule& molJ
|
||||
) const;
|
||||
|
||||
void calculateTetherForce();
|
||||
@ -197,7 +185,7 @@ public:
|
||||
|
||||
inline const List<DynamicList<molecule*> >& cellOccupancy() const;
|
||||
|
||||
inline const interactionLists& il() const;
|
||||
inline const InteractionLists<molecule>& il() const;
|
||||
|
||||
inline const List<molecule::constantProperties> constProps() const;
|
||||
|
||||
|
||||
@ -31,17 +31,17 @@ using namespace Foam::constant;
|
||||
|
||||
inline void Foam::moleculeCloud::evaluatePair
|
||||
(
|
||||
molecule* molI,
|
||||
molecule* molJ
|
||||
molecule& molI,
|
||||
molecule& molJ
|
||||
)
|
||||
{
|
||||
const pairPotentialList& pairPot = pot_.pairPotentials();
|
||||
|
||||
const pairPotential& electrostatic = pairPot.electrostatic();
|
||||
|
||||
label idI = molI->id();
|
||||
label idI = molI.id();
|
||||
|
||||
label idJ = molJ->id();
|
||||
label idJ = molJ.id();
|
||||
|
||||
const molecule::constantProperties& constPropI(constProps(idI));
|
||||
|
||||
@ -70,7 +70,7 @@ inline void Foam::moleculeCloud::evaluatePair
|
||||
if (pairPotentialSitesI[sI] && pairPotentialSitesJ[sJ])
|
||||
{
|
||||
vector rsIsJ =
|
||||
molI->sitePositions()[sI] - molJ->sitePositions()[sJ];
|
||||
molI.sitePositions()[sI] - molJ.sitePositions()[sJ];
|
||||
|
||||
scalar rsIsJMagSq = magSqr(rsIsJ);
|
||||
|
||||
@ -82,38 +82,34 @@ inline void Foam::moleculeCloud::evaluatePair
|
||||
(rsIsJ/rsIsJMag)
|
||||
*pairPot.force(idsI, idsJ, rsIsJMag);
|
||||
|
||||
molI->siteForces()[sI] += fsIsJ;
|
||||
molI.siteForces()[sI] += fsIsJ;
|
||||
|
||||
molJ->siteForces()[sJ] += -fsIsJ;
|
||||
molJ.siteForces()[sJ] += -fsIsJ;
|
||||
|
||||
scalar potentialEnergy
|
||||
(
|
||||
pairPot.energy(idsI, idsJ, rsIsJMag)
|
||||
);
|
||||
|
||||
molI->potentialEnergy() += 0.5*potentialEnergy;
|
||||
molI.potentialEnergy() += 0.5*potentialEnergy;
|
||||
|
||||
molJ->potentialEnergy() += 0.5*potentialEnergy;
|
||||
molJ.potentialEnergy() += 0.5*potentialEnergy;
|
||||
|
||||
vector rIJ = molI->position() - molJ->position();
|
||||
vector rIJ = molI.position() - molJ.position();
|
||||
|
||||
tensor virialContribution =
|
||||
(rsIsJ*fsIsJ)*(rsIsJ & rIJ)/rsIsJMagSq;
|
||||
|
||||
molI->rf() += virialContribution;
|
||||
molI.rf() += virialContribution;
|
||||
|
||||
molJ->rf() += virialContribution;
|
||||
|
||||
// molI->rf() += rsIsJ * fsIsJ;
|
||||
|
||||
// molJ->rf() += rsIsJ * fsIsJ;
|
||||
molJ.rf() += virialContribution;
|
||||
}
|
||||
}
|
||||
|
||||
if (electrostaticSitesI[sI] && electrostaticSitesJ[sJ])
|
||||
{
|
||||
vector rsIsJ =
|
||||
molI->sitePositions()[sI] - molJ->sitePositions()[sJ];
|
||||
molI.sitePositions()[sI] - molJ.sitePositions()[sJ];
|
||||
|
||||
scalar rsIsJMagSq = magSqr(rsIsJ);
|
||||
|
||||
@ -129,149 +125,26 @@ inline void Foam::moleculeCloud::evaluatePair
|
||||
(rsIsJ/rsIsJMag)
|
||||
*chargeI*chargeJ*electrostatic.force(rsIsJMag);
|
||||
|
||||
molI->siteForces()[sI] += fsIsJ;
|
||||
molI.siteForces()[sI] += fsIsJ;
|
||||
|
||||
molJ->siteForces()[sJ] += -fsIsJ;
|
||||
molJ.siteForces()[sJ] += -fsIsJ;
|
||||
|
||||
scalar potentialEnergy =
|
||||
chargeI*chargeJ
|
||||
*electrostatic.energy(rsIsJMag);
|
||||
|
||||
molI->potentialEnergy() += 0.5*potentialEnergy;
|
||||
molI.potentialEnergy() += 0.5*potentialEnergy;
|
||||
|
||||
molJ->potentialEnergy() += 0.5*potentialEnergy;
|
||||
molJ.potentialEnergy() += 0.5*potentialEnergy;
|
||||
|
||||
vector rIJ = molI->position() - molJ->position();
|
||||
vector rIJ = molI.position() - molJ.position();
|
||||
|
||||
tensor virialContribution =
|
||||
(rsIsJ*fsIsJ)*(rsIsJ & rIJ)/rsIsJMagSq;
|
||||
|
||||
molI->rf() += virialContribution;
|
||||
molI.rf() += virialContribution;
|
||||
|
||||
molJ->rf() += virialContribution;
|
||||
|
||||
// molI->rf() += rsIsJ * fsIsJ;
|
||||
|
||||
// molJ->rf() += rsIsJ * fsIsJ;
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
inline void Foam::moleculeCloud::evaluatePair
|
||||
(
|
||||
molecule* molReal,
|
||||
referredMolecule* molRef
|
||||
)
|
||||
{
|
||||
const pairPotentialList& pairPot = pot_.pairPotentials();
|
||||
|
||||
const pairPotential& electrostatic = pairPot.electrostatic();
|
||||
|
||||
label idReal = molReal->id();
|
||||
|
||||
label idRef = molRef->id();
|
||||
|
||||
const molecule::constantProperties& constPropReal(constProps(idReal));
|
||||
|
||||
const molecule::constantProperties& constPropRef(constProps(idRef));
|
||||
|
||||
List<label> siteIdsReal = constPropReal.siteIds();
|
||||
|
||||
List<label> siteIdsRef = constPropRef.siteIds();
|
||||
|
||||
List<bool> pairPotentialSitesReal = constPropReal.pairPotentialSites();
|
||||
|
||||
List<bool> electrostaticSitesReal = constPropReal.electrostaticSites();
|
||||
|
||||
List<bool> pairPotentialSitesRef = constPropRef.pairPotentialSites();
|
||||
|
||||
List<bool> electrostaticSitesRef = constPropRef.electrostaticSites();
|
||||
|
||||
forAll(siteIdsReal, sReal)
|
||||
{
|
||||
label idsReal(siteIdsReal[sReal]);
|
||||
|
||||
forAll(siteIdsRef, sRef)
|
||||
{
|
||||
label idsRef(siteIdsRef[sRef]);
|
||||
|
||||
if (pairPotentialSitesReal[sReal] && pairPotentialSitesRef[sRef])
|
||||
{
|
||||
vector rsRealsRef =
|
||||
molReal->sitePositions()[sReal]
|
||||
- molRef->sitePositions()[sRef];
|
||||
|
||||
scalar rsRealsRefMagSq = magSqr(rsRealsRef);
|
||||
|
||||
if (pairPot.rCutSqr(idsReal, idsRef, rsRealsRefMagSq))
|
||||
{
|
||||
scalar rsRealsRefMag = mag(rsRealsRef);
|
||||
|
||||
vector fsRealsRef =
|
||||
(rsRealsRef/rsRealsRefMag)
|
||||
*pairPot.force(idsReal, idsRef, rsRealsRefMag);
|
||||
|
||||
molReal->siteForces()[sReal] += fsRealsRef;
|
||||
|
||||
scalar potentialEnergy
|
||||
(
|
||||
pairPot.energy(idsReal, idsRef, rsRealsRefMag)
|
||||
);
|
||||
|
||||
molReal->potentialEnergy() += 0.5*potentialEnergy;
|
||||
|
||||
vector rRealRef = molReal->position() - molRef->position();
|
||||
|
||||
molReal->rf() +=
|
||||
(rsRealsRef*fsRealsRef)
|
||||
*(rsRealsRef & rRealRef)
|
||||
/rsRealsRefMagSq;
|
||||
|
||||
// molReal->rf() += rsRealsRef * fsRealsRef;
|
||||
|
||||
}
|
||||
}
|
||||
|
||||
if (electrostaticSitesReal[sReal] && electrostaticSitesRef[sRef])
|
||||
{
|
||||
vector rsRealsRef =
|
||||
molReal->sitePositions()[sReal]
|
||||
- molRef->sitePositions()[sRef];
|
||||
|
||||
scalar rsRealsRefMagSq = magSqr(rsRealsRef);
|
||||
|
||||
if (rsRealsRefMagSq <= electrostatic.rCutSqr())
|
||||
{
|
||||
scalar rsRealsRefMag = mag(rsRealsRef);
|
||||
|
||||
scalar chargeReal = constPropReal.siteCharges()[sReal];
|
||||
|
||||
scalar chargeRef = constPropRef.siteCharges()[sRef];
|
||||
|
||||
vector fsRealsRef =
|
||||
(rsRealsRef/rsRealsRefMag)
|
||||
*chargeReal*chargeRef
|
||||
*electrostatic.force(rsRealsRefMag);
|
||||
|
||||
molReal->siteForces()[sReal] += fsRealsRef;
|
||||
|
||||
scalar potentialEnergy =
|
||||
chargeReal*chargeRef
|
||||
*electrostatic.energy(rsRealsRefMag);
|
||||
|
||||
molReal->potentialEnergy() += 0.5*potentialEnergy;
|
||||
|
||||
vector rRealRef = molReal->position() - molRef->position();
|
||||
|
||||
molReal->rf() +=
|
||||
(rsRealsRef*fsRealsRef)
|
||||
*(rsRealsRef & rRealRef)
|
||||
/rsRealsRefMagSq;
|
||||
|
||||
// molReal->rf() += rsRealsRef * fsRealsRef;
|
||||
molJ.rf() += virialContribution;
|
||||
}
|
||||
}
|
||||
}
|
||||
@ -281,17 +154,17 @@ inline void Foam::moleculeCloud::evaluatePair
|
||||
|
||||
inline bool Foam::moleculeCloud::evaluatePotentialLimit
|
||||
(
|
||||
molecule* molI,
|
||||
molecule* molJ
|
||||
molecule& molI,
|
||||
molecule& molJ
|
||||
) const
|
||||
{
|
||||
const pairPotentialList& pairPot = pot_.pairPotentials();
|
||||
|
||||
const pairPotential& electrostatic = pairPot.electrostatic();
|
||||
|
||||
label idI = molI->id();
|
||||
label idI = molI.id();
|
||||
|
||||
label idJ = molJ->id();
|
||||
label idJ = molJ.id();
|
||||
|
||||
const molecule::constantProperties& constPropI(constProps(idI));
|
||||
|
||||
@ -320,7 +193,7 @@ inline bool Foam::moleculeCloud::evaluatePotentialLimit
|
||||
if (pairPotentialSitesI[sI] && pairPotentialSitesJ[sJ])
|
||||
{
|
||||
vector rsIsJ =
|
||||
molI->sitePositions()[sI] - molJ->sitePositions()[sJ];
|
||||
molI.sitePositions()[sI] - molJ.sitePositions()[sJ];
|
||||
|
||||
scalar rsIsJMagSq = magSqr(rsIsJ);
|
||||
|
||||
@ -369,7 +242,7 @@ inline bool Foam::moleculeCloud::evaluatePotentialLimit
|
||||
if (electrostaticSitesI[sI] && electrostaticSitesJ[sJ])
|
||||
{
|
||||
vector rsIsJ =
|
||||
molI->sitePositions()[sI] - molJ->sitePositions()[sJ];
|
||||
molI.sitePositions()[sI] - molJ.sitePositions()[sJ];
|
||||
|
||||
scalar rsIsJMagSq = magSqr(rsIsJ);
|
||||
|
||||
@ -422,157 +295,6 @@ inline bool Foam::moleculeCloud::evaluatePotentialLimit
|
||||
}
|
||||
|
||||
|
||||
inline bool Foam::moleculeCloud::evaluatePotentialLimit
|
||||
(
|
||||
molecule* molReal,
|
||||
referredMolecule* molRef
|
||||
) const
|
||||
{
|
||||
const pairPotentialList& pairPot = pot_.pairPotentials();
|
||||
|
||||
const pairPotential& electrostatic = pairPot.electrostatic();
|
||||
|
||||
label idReal = molReal->id();
|
||||
|
||||
label idRef = molRef->id();
|
||||
|
||||
const molecule::constantProperties& constPropReal(constProps(idReal));
|
||||
|
||||
const molecule::constantProperties& constPropRef(constProps(idRef));
|
||||
|
||||
List<label> siteIdsReal = constPropReal.siteIds();
|
||||
|
||||
List<label> siteIdsRef = constPropRef.siteIds();
|
||||
|
||||
List<bool> pairPotentialSitesReal = constPropReal.pairPotentialSites();
|
||||
|
||||
List<bool> electrostaticSitesReal = constPropReal.electrostaticSites();
|
||||
|
||||
List<bool> pairPotentialSitesRef = constPropRef.pairPotentialSites();
|
||||
|
||||
List<bool> electrostaticSitesRef = constPropRef.electrostaticSites();
|
||||
|
||||
forAll(siteIdsReal, sReal)
|
||||
{
|
||||
label idsReal(siteIdsReal[sReal]);
|
||||
|
||||
forAll(siteIdsRef, sRef)
|
||||
{
|
||||
label idsRef(siteIdsRef[sRef]);
|
||||
|
||||
if (pairPotentialSitesReal[sReal] && pairPotentialSitesRef[sRef])
|
||||
{
|
||||
vector rsRealsRef =
|
||||
molReal->sitePositions()[sReal]
|
||||
- molRef->sitePositions()[sRef];
|
||||
|
||||
scalar rsRealsRefMagSq = magSqr(rsRealsRef);
|
||||
|
||||
if (pairPot.rCutSqr(idsReal, idsRef, rsRealsRefMagSq))
|
||||
{
|
||||
scalar rsRealsRefMag = mag(rsRealsRef);
|
||||
|
||||
// Guard against pairPot.energy being evaluated
|
||||
// if rRealRefMag < SMALL. A floating point exception will
|
||||
// happen otherwise.
|
||||
|
||||
if (rsRealsRefMag < SMALL)
|
||||
{
|
||||
WarningIn("moleculeCloud::removeHighEnergyOverlaps()")
|
||||
<< "Molecule site pair closer than "
|
||||
<< SMALL
|
||||
<< ": mag separation = " << rsRealsRefMag
|
||||
<< ". These may have been placed on top of each"
|
||||
<< " other by a rounding error in mdInitialise in"
|
||||
<< " parallel or a block filled with molecules"
|
||||
<< " twice. Removing one of the molecules."
|
||||
<< endl;
|
||||
|
||||
return true;
|
||||
}
|
||||
|
||||
// Guard against pairPot.energy being evaluated if
|
||||
// rRealRefMag < rMin. A tabulation lookup error will occur
|
||||
// otherwise.
|
||||
|
||||
if (rsRealsRefMag < pairPot.rMin(idsReal, idsRef))
|
||||
{
|
||||
return true;
|
||||
}
|
||||
|
||||
if
|
||||
(
|
||||
mag(pairPot.energy(idsReal, idsRef, rsRealsRefMag))
|
||||
> pot_.potentialEnergyLimit()
|
||||
)
|
||||
{
|
||||
return true;
|
||||
};
|
||||
}
|
||||
}
|
||||
|
||||
if (electrostaticSitesReal[sReal] && electrostaticSitesRef[sRef])
|
||||
{
|
||||
vector rsRealsRef =
|
||||
molReal->sitePositions()[sReal]
|
||||
- molRef->sitePositions()[sRef];
|
||||
|
||||
scalar rsRealsRefMagSq = magSqr(rsRealsRef);
|
||||
|
||||
if (pairPot.rCutMaxSqr(rsRealsRefMagSq))
|
||||
{
|
||||
scalar rsRealsRefMag = mag(rsRealsRef);
|
||||
|
||||
// Guard against pairPot.energy being evaluated
|
||||
// if rRealRefMag < SMALL. A floating point exception will
|
||||
// happen otherwise.
|
||||
|
||||
if (rsRealsRefMag < SMALL)
|
||||
{
|
||||
WarningIn("moleculeCloud::removeHighEnergyOverlaps()")
|
||||
<< "Molecule site pair closer than "
|
||||
<< SMALL
|
||||
<< ": mag separation = " << rsRealsRefMag
|
||||
<< ". These may have been placed on top of each"
|
||||
<< " other by a rounding error in mdInitialise in"
|
||||
<< " parallel or a block filled with molecules"
|
||||
<< " twice. Removing one of the molecules."
|
||||
<< endl;
|
||||
|
||||
return true;
|
||||
}
|
||||
|
||||
if (rsRealsRefMag < electrostatic.rMin())
|
||||
{
|
||||
return true;
|
||||
}
|
||||
|
||||
scalar chargeReal = constPropReal.siteCharges()[sReal];
|
||||
|
||||
scalar chargeRef = constPropRef.siteCharges()[sRef];
|
||||
|
||||
if
|
||||
(
|
||||
mag
|
||||
(
|
||||
chargeReal
|
||||
*chargeRef
|
||||
*electrostatic.energy(rsRealsRefMag)
|
||||
)
|
||||
> pot_.potentialEnergyLimit()
|
||||
)
|
||||
{
|
||||
return true;
|
||||
};
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
return false;
|
||||
}
|
||||
|
||||
|
||||
inline Foam::vector Foam::moleculeCloud::equipartitionLinearVelocity
|
||||
(
|
||||
scalar temperature,
|
||||
@ -638,7 +360,7 @@ inline const Foam::List<Foam::DynamicList<Foam::molecule*> >&
|
||||
}
|
||||
|
||||
|
||||
inline const Foam::interactionLists&
|
||||
inline const Foam::InteractionLists<Foam::molecule>&
|
||||
Foam::moleculeCloud::il() const
|
||||
{
|
||||
return il_;
|
||||
|
||||
@ -0,0 +1,37 @@
|
||||
/*--------------------------------*- C++ -*----------------------------------*\
|
||||
| ========= | |
|
||||
| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
|
||||
| \\ / O peration | Version: 1.6 |
|
||||
| \\ / A nd | Web: http://www.OpenFOAM.org |
|
||||
| \\/ M anipulation | |
|
||||
\*---------------------------------------------------------------------------*/
|
||||
FoamFile
|
||||
{
|
||||
version 2.0;
|
||||
format ascii;
|
||||
class volVectorField;
|
||||
object U;
|
||||
}
|
||||
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
|
||||
|
||||
dimensions [0 1 -1 0 0 0 0];
|
||||
|
||||
internalField uniform (0 0 0);
|
||||
|
||||
boundaryField
|
||||
{
|
||||
periodicX
|
||||
{
|
||||
type cyclic;
|
||||
}
|
||||
periodicY
|
||||
{
|
||||
type cyclic;
|
||||
}
|
||||
periodicZ
|
||||
{
|
||||
type cyclic;
|
||||
}
|
||||
}
|
||||
|
||||
// ************************************************************************* //
|
||||
@ -0,0 +1,37 @@
|
||||
/*--------------------------------*- C++ -*----------------------------------*\
|
||||
| ========= | |
|
||||
| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
|
||||
| \\ / O peration | Version: 1.6 |
|
||||
| \\ / A nd | Web: http://www.OpenFOAM.org |
|
||||
| \\/ M anipulation | |
|
||||
\*---------------------------------------------------------------------------*/
|
||||
FoamFile
|
||||
{
|
||||
version 2.0;
|
||||
format ascii;
|
||||
class volVectorField;
|
||||
object U;
|
||||
}
|
||||
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
|
||||
|
||||
dimensions [0 1 -1 0 0 0 0];
|
||||
|
||||
internalField uniform (0 0 0);
|
||||
|
||||
boundaryField
|
||||
{
|
||||
periodicX
|
||||
{
|
||||
type cyclic;
|
||||
}
|
||||
periodicY
|
||||
{
|
||||
type cyclic;
|
||||
}
|
||||
periodicZ
|
||||
{
|
||||
type cyclic;
|
||||
}
|
||||
}
|
||||
|
||||
// ************************************************************************* //
|
||||
@ -0,0 +1,55 @@
|
||||
/*--------------------------------*- C++ -*----------------------------------*\
|
||||
| ========= | |
|
||||
| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
|
||||
| \\ / O peration | Version: 1.6 |
|
||||
| \\ / A nd | Web: http://www.OpenFOAM.org |
|
||||
| \\/ M anipulation | |
|
||||
\*---------------------------------------------------------------------------*/
|
||||
FoamFile
|
||||
{
|
||||
version 2.0;
|
||||
format ascii;
|
||||
class volVectorField;
|
||||
object U;
|
||||
}
|
||||
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
|
||||
|
||||
dimensions [0 1 -1 0 0 0 0];
|
||||
|
||||
internalField uniform (0 0 0);
|
||||
|
||||
boundaryField
|
||||
{
|
||||
sectionAEnd
|
||||
{
|
||||
type fixedValue;
|
||||
value uniform (0 0 0);
|
||||
}
|
||||
sectionCEnd
|
||||
{
|
||||
type fixedValue;
|
||||
value uniform (0 0 0);
|
||||
}
|
||||
front
|
||||
{
|
||||
type fixedValue;
|
||||
value uniform (0 0 0);
|
||||
}
|
||||
back
|
||||
{
|
||||
type fixedValue;
|
||||
value uniform (0 0 0);
|
||||
}
|
||||
top
|
||||
{
|
||||
type fixedValue;
|
||||
value uniform (0 0 0);
|
||||
}
|
||||
bottom
|
||||
{
|
||||
type fixedValue;
|
||||
value uniform (0 0 0);
|
||||
}
|
||||
}
|
||||
|
||||
// ************************************************************************* //
|
||||
Reference in New Issue
Block a user