MutableMesh.hpp

/*

Copyright (c) 2005-2012, University of Oxford.
All rights reserved.

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This file is part of Chaste.

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modification, are permitted provided that the following conditions are met:
 * Redistributions of source code must retain the above copyright notice,
   this list of conditions and the following disclaimer.
 * Redistributions in binary form must reproduce the above copyright notice,
   this list of conditions and the following disclaimer in the documentation
   and/or other materials provided with the distribution.
 * Neither the name of the University of Oxford nor the names of its
   contributors may be used to endorse or promote products derived from this
   software without specific prior written permission.

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE
LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
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HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

*/

#ifndef MUTABLEMESH_HPP_
#define MUTABLEMESH_HPP_

#include "ChasteSerialization.hpp"
#include <boost/serialization/base_object.hpp>

#include "TetrahedralMesh.hpp"
#include "NodeMap.hpp"

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
class MutableMesh : public TetrahedralMesh<ELEMENT_DIM, SPACE_DIM>
{
    friend class boost::serialization::access;

    template<class Archive>
    void serialize(Archive & archive, const unsigned int version)
    {
        archive & boost::serialization::base_object<TetrahedralMesh<ELEMENT_DIM, SPACE_DIM> >(*this);

        // Do a remesh after archiving has finished to get right number of boundary nodes etc.
        // (strictly only relevant for load - but doesn't take long in the scheme of things.)
        // NOTE - Subclasses must archive their member variables BEFORE calling this method.
        NodeMap map(this->GetNumNodes());
        this->ReMesh(map);
        assert(map.IsIdentityMap()); // Otherwise the mesh will get VERY confused.
    }

protected:

    std::vector<unsigned> mDeletedElementIndices;

    std::vector<unsigned> mDeletedBoundaryElementIndices;

    std::vector<unsigned> mDeletedNodeIndices;

    bool mAddedNodes;

private:

#define COVERAGE_IGNORE

    bool CheckIsVoronoi(Element<ELEMENT_DIM, SPACE_DIM>* pElement, double maxPenetration);
#undef COVERAGE_IGNORE

public:

    MutableMesh();

    MutableMesh(std::vector<Node<SPACE_DIM> *> nodes);

    virtual ~MutableMesh();

    void Clear();

    unsigned GetNumNodes() const;

    unsigned GetNumElements() const;

    unsigned GetNumBoundaryElements() const;


    void RescaleMeshFromBoundaryNode(ChastePoint<1> updatedPoint, unsigned boundaryNodeIndex);

    virtual unsigned AddNode(Node<SPACE_DIM>* pNewNode);

    virtual void SetNode(unsigned index, ChastePoint<SPACE_DIM> point, bool concreteMove=true);

    void MoveMergeNode(unsigned index, unsigned targetIndex, bool concreteMove=true);

#define COVERAGE_IGNORE

    virtual void DeleteNode(unsigned index);
#undef COVERAGE_IGNORE

#define COVERAGE_IGNORE

    void DeleteNodePriorToReMesh(unsigned index);
#undef COVERAGE_IGNORE

    unsigned RefineElement(Element<ELEMENT_DIM,SPACE_DIM>* pElement, ChastePoint<SPACE_DIM> point);

    void DeleteBoundaryNodeAt(unsigned index);

#define COVERAGE_IGNORE

    void ReIndex(NodeMap& map);
#undef COVERAGE_IGNORE

#define COVERAGE_IGNORE

    virtual void ReMesh(NodeMap& map);
#undef COVERAGE_IGNORE


#define COVERAGE_IGNORE

    void ReMesh();
#undef COVERAGE_IGNORE

#define COVERAGE_IGNORE

    bool CheckIsVoronoi(double maxPenetration=0.0);
#undef COVERAGE_IGNORE
};

#include "SerializationExportWrapper.hpp"
EXPORT_TEMPLATE_CLASS_ALL_DIMS(MutableMesh)

#endif /*MUTABLEMESH_HPP_*/