polyMesh.C

/*---------------------------------------------------------------------------*\
  =========                 |
  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
   \\    /   O peration     |
    \\  /    A nd           | Copyright (C) 1991-2009 OpenCFD Ltd.
     \\/     M anipulation  |
-------------------------------------------------------------------------------
License
    This file is part of OpenFOAM.

    OpenFOAM is free software; you can redistribute it and/or modify it
    under the terms of the GNU General Public License as published by the
    Free Software Foundation; either version 2 of the License, or (at your
    option) any later version.

    OpenFOAM is distributed in the hope that it will be useful, but WITHOUT
    ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
    FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License
    for more details.

    You should have received a copy of the GNU General Public License
    along with OpenFOAM; if not, write to the Free Software Foundation,
    Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA

\*---------------------------------------------------------------------------*/

#include "polyMesh.H"
#include "Time.H"
#include "cellIOList.H"
#include "SubList.H"
#include "wedgePolyPatch.H"
#include "emptyPolyPatch.H"
#include "globalMeshData.H"
#include "processorPolyPatch.H"
#include "OSspecific.H"
#include "demandDrivenData.H"

#include "pointMesh.H"

// * * * * * * * * * * * * * * Static Data Members * * * * * * * * * * * * * //

defineTypeNameAndDebug(Foam::polyMesh, 0);


Foam::word Foam::polyMesh::defaultRegion = "region0";
Foam::word Foam::polyMesh::meshSubDir = "polyMesh";


// * * * * * * * * * * * * * Private Member Functions  * * * * * * * * * * * //

void Foam::polyMesh::calcDirections() const
{
    for (direction cmpt=0; cmpt<vector::nComponents; cmpt++)
    {
        solutionD_[cmpt] = 1;
    }

    // Knock out empty and wedge directions. Note:they will be present on all
    // domains.

    label nEmptyPatches = 0;
    label nWedgePatches = 0;

    vector emptyDirVec = vector::zero;
    vector wedgeDirVec = vector::zero;

    forAll(boundaryMesh(), patchi)
    {
        if (boundaryMesh()[patchi].size())
        {
            if (isA<emptyPolyPatch>(boundaryMesh()[patchi]))
            {
                nEmptyPatches++;
                emptyDirVec += sum(cmptMag(boundaryMesh()[patchi].faceAreas()));
            }
            else if (isA<wedgePolyPatch>(boundaryMesh()[patchi]))
            {
                const wedgePolyPatch& wpp = refCast<const wedgePolyPatch>
                (
                    boundaryMesh()[patchi]
                );

                nWedgePatches++;
                wedgeDirVec += cmptMag(wpp.centreNormal());
            }
        }
    }

    if (nEmptyPatches)
    {
        reduce(emptyDirVec, sumOp<vector>());

        emptyDirVec /= mag(emptyDirVec);

        for (direction cmpt=0; cmpt<vector::nComponents; cmpt++)
        {
            if (emptyDirVec[cmpt] > 1e-6)
            {
                solutionD_[cmpt] = -1;
            }
            else
            {
                solutionD_[cmpt] = 1;
            }
        }
    }


    // Knock out wedge directions

    geometricD_ = solutionD_;

    if (nWedgePatches)
    {
        reduce(wedgeDirVec, sumOp<vector>());

        wedgeDirVec /= mag(wedgeDirVec);

        for (direction cmpt=0; cmpt<vector::nComponents; cmpt++)
        {
            if (wedgeDirVec[cmpt] > 1e-6)
            {
                geometricD_[cmpt] = -1;
            }
            else
            {
                geometricD_[cmpt] = 1;
            }
        }
    }
}


// * * * * * * * * * * * * * * * * Constructors  * * * * * * * * * * * * * * //

Foam::polyMesh::polyMesh(const IOobject& io)
:
    objectRegistry(io),
    primitiveMesh(),
    points_
    (
        IOobject
        (
            "points",
            time().findInstance(meshDir(), "points"),
            meshSubDir,
            *this,
            IOobject::MUST_READ,
            IOobject::NO_WRITE
        )
    ),
    faces_
    (
        IOobject
        (
            "faces",
            time().findInstance(meshDir(), "faces"),
            meshSubDir,
            *this,
            IOobject::MUST_READ,
            IOobject::NO_WRITE
        )
    ),
    owner_
    (
        IOobject
        (
            "owner",
            time().findInstance(meshDir(), "faces"),
            meshSubDir,
            *this,
            IOobject::READ_IF_PRESENT,
            IOobject::NO_WRITE
        )
    ),
    neighbour_
    (
        IOobject
        (
            "neighbour",
            time().findInstance(meshDir(), "faces"),
            meshSubDir,
            *this,
            IOobject::READ_IF_PRESENT,
            IOobject::NO_WRITE
        )
    ),
    clearedPrimitives_(false),
    boundary_
    (
        IOobject
        (
            "boundary",
            time().findInstance(meshDir(), "boundary"),
            meshSubDir,
            *this,
            IOobject::MUST_READ,
            IOobject::NO_WRITE
        ),
        *this
    ),
    bounds_(points_),
    geometricD_(Vector<label>::zero),
    solutionD_(Vector<label>::zero),
    pointZones_
    (
        IOobject
        (
            "pointZones",
            time().findInstance
            (
                meshDir(),
                "pointZones",
                IOobject::READ_IF_PRESENT
            ),
            meshSubDir,
            *this,
            IOobject::READ_IF_PRESENT,
            IOobject::NO_WRITE
        ),
        *this
    ),
    faceZones_
    (
        IOobject
        (
            "faceZones",
            time().findInstance
            (
                meshDir(),
                "faceZones",
                IOobject::READ_IF_PRESENT
            ),
            meshSubDir,
            *this,
            IOobject::READ_IF_PRESENT,
            IOobject::NO_WRITE
        ),
        *this
    ),
    cellZones_
    (
        IOobject
        (
            "cellZones",
            time().findInstance
            (
                meshDir(),
                "cellZones",
                IOobject::READ_IF_PRESENT
            ),
            meshSubDir,
            *this,
            IOobject::READ_IF_PRESENT,
            IOobject::NO_WRITE
        ),
        *this
    ),
    globalMeshDataPtr_(NULL),
    moving_(false),
    changing_(false),
    curMotionTimeIndex_(time().timeIndex()),
    oldPointsPtr_(NULL)
{
    if (exists(owner_.objectPath()))
    {
        initMesh();
    }
    else
    {
        cellIOList cLst
        (
            IOobject
            (
                "cells",
                time().findInstance(meshDir(), "cells"),
                meshSubDir,
                *this,
                IOobject::MUST_READ,
                IOobject::NO_WRITE
            )
        );

        // Set the primitive mesh
        initMesh(cLst);

        owner_.write();
        neighbour_.write();
    }

    // Calculate topology for the patches (processor-processor comms etc.)
    boundary_.updateMesh();

    // Calculate the geometry for the patches (transformation tensors etc.)
    boundary_.calcGeometry();

    // Warn if global empty mesh (constructs globalData!)
    if (globalData().nTotalPoints() == 0)
    {
        WarningIn("polyMesh(const IOobject&)")
            << "no points in mesh" << endl;
    }
    if (globalData().nTotalCells() == 0)
    {
        WarningIn("polyMesh(const IOobject&)")
            << "no cells in mesh" << endl;
    }
}


Foam::polyMesh::polyMesh
(
    const IOobject& io,
    const Xfer<pointField>& points,
    const Xfer<faceList>& faces,
    const Xfer<labelList>& owner,
    const Xfer<labelList>& neighbour,
    const bool syncPar
)
:
    objectRegistry(io),
    primitiveMesh(),
    points_
    (
        IOobject
        (
            "points",
            instance(),
            meshSubDir,
            *this,
            IOobject::NO_READ,
            IOobject::AUTO_WRITE
        ),
        points
    ),
    faces_
    (
        IOobject
        (
            "faces",
            instance(),
            meshSubDir,
            *this,
            IOobject::NO_READ,
            IOobject::AUTO_WRITE
        ),
        faces
    ),
    owner_
    (
        IOobject
        (
            "owner",
            instance(),
            meshSubDir,
            *this,
            IOobject::NO_READ,
            IOobject::AUTO_WRITE
        ),
        owner
    ),
    neighbour_
    (
        IOobject
        (
            "neighbour",
            instance(),
            meshSubDir,
            *this,
            IOobject::NO_READ,
            IOobject::AUTO_WRITE
        ),
        neighbour
    ),
    clearedPrimitives_(false),
    boundary_
    (
        IOobject
        (
            "boundary",
            instance(),
            meshSubDir,
            *this,
            IOobject::NO_READ,
            IOobject::AUTO_WRITE
        ),
        *this,
        0
    ),
    bounds_(points_, syncPar),
    geometricD_(Vector<label>::zero),
    solutionD_(Vector<label>::zero),
    pointZones_
    (
        IOobject
        (
            "pointZones",
            instance(),
            meshSubDir,
            *this,
            IOobject::NO_READ,
            IOobject::NO_WRITE
        ),
        *this,
        0
    ),
    faceZones_
    (
        IOobject
        (
            "faceZones",
            instance(),
            meshSubDir,
            *this,
            IOobject::NO_READ,
            IOobject::NO_WRITE
        ),
        *this,
        0
    ),
    cellZones_
    (
        IOobject
        (
            "cellZones",
            instance(),
            meshSubDir,
            *this,
            IOobject::NO_READ,
            IOobject::NO_WRITE
        ),
        *this,
        0
    ),
    globalMeshDataPtr_(NULL),
    moving_(false),
    changing_(false),
    curMotionTimeIndex_(time().timeIndex()),
    oldPointsPtr_(NULL)
{
    // Check if the faces and cells are valid
    forAll (faces_, faceI)
    {
        const face& curFace = faces_[faceI];

        if (min(curFace) < 0 || max(curFace) > points_.size())
        {
            FatalErrorIn
            (
                "polyMesh::polyMesh\n"
                "(\n"
                "    const IOobject& io,\n"
                "    const pointField& points,\n"
                "    const faceList& faces,\n"
                "    const cellList& cells\n"
                ")\n"
            )   << "Face " << faceI << "contains vertex labels out of range: "
                << curFace << " Max point index = " << points_.size()
                << abort(FatalError);
        }
    }

    // Set the primitive mesh
    initMesh();
}


Foam::polyMesh::polyMesh
(
    const IOobject& io,
    const Xfer<pointField>& points,
    const Xfer<faceList>& faces,
    const Xfer<cellList>& cells,
    const bool syncPar
)
:
    objectRegistry(io),
    primitiveMesh(),
    points_
    (
        IOobject
        (
            "points",
            instance(),
            meshSubDir,
            *this,
            IOobject::NO_READ,
            IOobject::AUTO_WRITE
        ),
        points
    ),
    faces_
    (
        IOobject
        (
            "faces",
            instance(),
            meshSubDir,
            *this,
            IOobject::NO_READ,
            IOobject::AUTO_WRITE
        ),
        faces
    ),
    owner_
    (
        IOobject
        (
            "owner",
            instance(),
            meshSubDir,
            *this,
            IOobject::NO_READ,
            IOobject::AUTO_WRITE
        ),
        0
    ),
    neighbour_
    (
        IOobject
        (
            "neighbour",
            instance(),
            meshSubDir,
            *this,
            IOobject::NO_READ,
            IOobject::AUTO_WRITE
        ),
        0
    ),
    clearedPrimitives_(false),
    boundary_
    (
        IOobject
        (
            "boundary",
            instance(),
            meshSubDir,
            *this,
            IOobject::NO_READ,
            IOobject::AUTO_WRITE
        ),
        *this,
        0
    ),
    bounds_(points_, syncPar),
    geometricD_(Vector<label>::zero),
    solutionD_(Vector<label>::zero),
    pointZones_
    (
        IOobject
        (
            "pointZones",
            instance(),
            meshSubDir,
            *this,
            IOobject::NO_READ,
            IOobject::NO_WRITE
        ),
        *this,
        0
    ),
    faceZones_
    (
        IOobject
        (
            "faceZones",
            instance(),
            meshSubDir,
            *this,
            IOobject::NO_READ,
            IOobject::NO_WRITE
        ),
        *this,
        0
    ),
    cellZones_
    (
        IOobject
        (
            "cellZones",
            instance(),
            meshSubDir,
            *this,
            IOobject::NO_READ,
            IOobject::NO_WRITE
        ),
        *this,
        0
    ),
    globalMeshDataPtr_(NULL),
    moving_(false),
    changing_(false),
    curMotionTimeIndex_(time().timeIndex()),
    oldPointsPtr_(NULL)
{
    // Check if faces are valid
    forAll (faces_, faceI)
    {
        const face& curFace = faces_[faceI];

        if (min(curFace) < 0 || max(curFace) > points_.size())
        {
            FatalErrorIn
            (
                "polyMesh::polyMesh\n"
                "(\n"
                "    const IOobject&,\n"
                "    const Xfer<pointField>&,\n"
                "    const Xfer<faceList>&,\n"
                "    const Xfer<cellList>&\n"
                ")\n"
            )   << "Face " << faceI << "contains vertex labels out of range: "
                << curFace << " Max point index = " << points_.size()
                << abort(FatalError);
        }
    }

    // transfer in cell list
    cellList cLst(cells);

    // Check if cells are valid
    forAll (cLst, cellI)
    {
        const cell& curCell = cLst[cellI];

        if (min(curCell) < 0 || max(curCell) > faces_.size())
        {
            FatalErrorIn
            (
                "polyMesh::polyMesh\n"
                "(\n"
                "    const IOobject&,\n"
                "    const Xfer<pointField>&,\n"
                "    const Xfer<faceList>&,\n"
                "    const Xfer<cellList>&\n"
                ")\n"
            )   << "Cell " << cellI << "contains face labels out of range: "
                << curCell << " Max face index = " << faces_.size()
                << abort(FatalError);
        }
    }

    // Set the primitive mesh
    initMesh(cLst);
}


void Foam::polyMesh::resetPrimitives
(
    const Xfer<pointField>& points,
    const Xfer<faceList>& faces,
    const Xfer<labelList>& owner,
    const Xfer<labelList>& neighbour,
    const labelList& patchSizes,
    const labelList& patchStarts,
    const bool validBoundary
)
{
    // Clear addressing. Keep geometric props for mapping.
    clearAddressing();

    // Take over new primitive data.
    // Optimized to avoid overwriting data at all
    if (&points)
    {
        points_.transfer(points());
        bounds_ = boundBox(points_, validBoundary);
    }

    if (&faces)
    {
        faces_.transfer(faces());
    }

    if (&owner)
    {
        owner_.transfer(owner());
    }

    if (&neighbour)
    {
        neighbour_.transfer(neighbour());
    }


    // Reset patch sizes and starts
    forAll(boundary_, patchI)
    {
        boundary_[patchI] = polyPatch
        (
            boundary_[patchI].name(),
            patchSizes[patchI],
            patchStarts[patchI],
            patchI,
            boundary_
        );
    }


    // Flags the mesh files as being changed
    setInstance(time().timeName());

    // Check if the faces and cells are valid
    forAll (faces_, faceI)
    {
        const face& curFace = faces_[faceI];

        if (min(curFace) < 0 || max(curFace) > points_.size())
        {
            FatalErrorIn
            (
                "polyMesh::polyMesh::resetPrimitives\n"
                "(\n"
                "    const Xfer<pointField>&,\n"
                "    const Xfer<faceList>&,\n"
                "    const Xfer<labelList>& owner,\n"
                "    const Xfer<labelList>& neighbour,\n"
                "    const labelList& patchSizes,\n"
                "    const labelList& patchStarts\n"
                ")\n"
            )   << "Face " << faceI << " contains vertex labels out of range: "
                << curFace << " Max point index = " << points_.size()
                << abort(FatalError);
        }
    }


    // Set the primitive mesh from the owner_, neighbour_.
    // Works out from patch end where the active faces stop.
    initMesh();


    if (validBoundary)
    {
        // Note that we assume that all the patches stay the same and are
        // correct etc. so we can already use the patches to do
        // processor-processor comms.

        // Calculate topology for the patches (processor-processor comms etc.)
        boundary_.updateMesh();

        // Calculate the geometry for the patches (transformation tensors etc.)
        boundary_.calcGeometry();

        // Warn if global empty mesh (constructs globalData!)
        if (globalData().nTotalPoints() == 0 || globalData().nTotalCells() == 0)
        {
            FatalErrorIn
            (
                "polyMesh::polyMesh::resetPrimitives\n"
                "(\n"
                "    const Xfer<pointField>&,\n"
                "    const Xfer<faceList>&,\n"
                "    const Xfer<labelList>& owner,\n"
                "    const Xfer<labelList>& neighbour,\n"
                "    const labelList& patchSizes,\n"
                "    const labelList& patchStarts\n"
                ")\n"
            )
                << "no points or no cells in mesh" << endl;
        }
    }
}


// * * * * * * * * * * * * * * * * Destructor  * * * * * * * * * * * * * * * //

Foam::polyMesh::~polyMesh()
{
    clearOut();
    resetMotion();
}


// * * * * * * * * * * * * * * * Member Functions  * * * * * * * * * * * * * //

const Foam::fileName& Foam::polyMesh::dbDir() const
{
    if (objectRegistry::dbDir() == defaultRegion)
    {
        return parent().dbDir();
    }
    else
    {
        return objectRegistry::dbDir();
    }
}


Foam::fileName Foam::polyMesh::meshDir() const
{
    return dbDir()/meshSubDir;
}


const Foam::fileName& Foam::polyMesh::pointsInstance() const
{
    return points_.instance();
}


const Foam::fileName& Foam::polyMesh::facesInstance() const
{
    return faces_.instance();
}


const Foam::Vector<Foam::label>& Foam::polyMesh::geometricD() const
{
    if (geometricD_.x() == 0)
    {
        calcDirections();
    }

    return geometricD_;
}


Foam::label Foam::polyMesh::nGeometricD() const
{
    return cmptSum(geometricD() + Vector<label>::one)/2;
}


const Foam::Vector<Foam::label>& Foam::polyMesh::solutionD() const
{
    if (solutionD_.x() == 0)
    {
        calcDirections();
    }

    return solutionD_;
}


Foam::label Foam::polyMesh::nSolutionD() const
{
    return cmptSum(solutionD() + Vector<label>::one)/2;
}


// Add boundary patches. Constructor helper
void Foam::polyMesh::addPatches
(
    const List<polyPatch*>& p,
    const bool validBoundary
)
{
    if (boundaryMesh().size())
    {
        FatalErrorIn
        (
            "void polyMesh::addPatches(const List<polyPatch*>&, const bool)"
        )   << "boundary already exists"
            << abort(FatalError);
    }

    // Reset valid directions
    geometricD_ = Vector<label>::zero;
    solutionD_ = Vector<label>::zero;

    boundary_.setSize(p.size());

    // Copy the patch pointers
    forAll (p, pI)
    {
        boundary_.set(pI, p[pI]);
    }

    // parallelData depends on the processorPatch ordering so force
    // recalculation. Problem: should really be done in removeBoundary but
    // there is some info in parallelData which might be interesting inbetween
    // removeBoundary and addPatches.
    deleteDemandDrivenData(globalMeshDataPtr_);

    if (validBoundary)
    {
        // Calculate topology for the patches (processor-processor comms etc.)
        boundary_.updateMesh();

        // Calculate the geometry for the patches (transformation tensors etc.)
        boundary_.calcGeometry();

        boundary_.checkDefinition();
    }
}


// Add mesh zones. Constructor helper
void Foam::polyMesh::addZones
(
    const List<pointZone*>& pz,
    const List<faceZone*>& fz,
    const List<cellZone*>& cz
)
{
    if (pointZones().size() || faceZones().size() || cellZones().size())
    {
        FatalErrorIn
        (
            "void addZones\n"
            "(\n"
            "    const List<pointZone*>&,\n"
            "    const List<faceZone*>&,\n"
            "    const List<cellZone*>&\n"
            ")"
        )   << "point, face or cell zone already exists"
            << abort(FatalError);
    }

    // Point zones
    if (pz.size())
    {
        pointZones_.setSize(pz.size());

        // Copy the zone pointers
        forAll (pz, pI)
        {
            pointZones_.set(pI, pz[pI]);
        }

        pointZones_.writeOpt() = IOobject::AUTO_WRITE;
    }

    // Face zones
    if (fz.size())
    {
        faceZones_.setSize(fz.size());

        // Copy the zone pointers
        forAll (fz, fI)
        {
            faceZones_.set(fI, fz[fI]);
        }

        faceZones_.writeOpt() = IOobject::AUTO_WRITE;
    }

    // Cell zones
    if (cz.size())
    {
        cellZones_.setSize(cz.size());

        // Copy the zone pointers
        forAll (cz, cI)
        {
            cellZones_.set(cI, cz[cI]);
        }

        cellZones_.writeOpt() = IOobject::AUTO_WRITE;
    }
}


const Foam::pointField& Foam::polyMesh::points() const
{
    if (clearedPrimitives_)
    {
        FatalErrorIn("const pointField& polyMesh::points() const")
            << "points deallocated"
            << abort(FatalError);
    }

    return points_;
}


const Foam::faceList& Foam::polyMesh::faces() const
{
    if (clearedPrimitives_)
    {
        FatalErrorIn("const faceList& polyMesh::faces() const")
            << "faces deallocated"
            << abort(FatalError);
    }

    return faces_;
}


const Foam::labelList& Foam::polyMesh::faceOwner() const
{
    return owner_;
}


const Foam::labelList& Foam::polyMesh::faceNeighbour() const
{
    return neighbour_;
}


// Return old mesh motion points
const Foam::pointField& Foam::polyMesh::oldPoints() const
{
    if (!oldPointsPtr_)
    {
        if (debug)
        {