MutableMesh.hpp

/*

Copyright (C) University of Oxford, 2005-2010

University of Oxford means the Chancellor, Masters and Scholars of the
University of Oxford, having an administrative office at Wellington
Square, Oxford OX1 2JD, UK.

This file is part of Chaste.

Chaste is free software: you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License as published
by the Free Software Foundation, either version 2.1 of the License, or
(at your option) any later version.

Chaste 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 Lesser General Public
License for more details. The offer of Chaste under the terms of the
License is subject to the License being interpreted in accordance with
English Law and subject to any action against the University of Oxford
being under the jurisdiction of the English Courts.

You should have received a copy of the GNU Lesser General Public License
along with Chaste. If not, see <http://www.gnu.org/licenses/>.

*/

#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 tissue 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

    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_*/