MutableVertexMesh.hpp

/*

Copyright (C) University of Oxford, 2005-2011

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 MUTABLEVERTEXMESH_HPP_
#define MUTABLEVERTEXMESH_HPP_

// Forward declaration prevents circular include chain
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
class VertexMeshWriter;

#include <iostream>
#include <map>
#include <algorithm>

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

#include "VertexMesh.hpp"

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
class MutableVertexMesh : public VertexMesh<ELEMENT_DIM, SPACE_DIM>
{
    friend class TestMutableVertexMesh;
    friend class TestMutableVertexMeshReMesh;

protected:

    double mCellRearrangementThreshold;

    double mCellRearrangementRatio;

    double mT2Threshold;

    bool mCheckForInternalIntersections;

    std::vector<unsigned> mDeletedNodeIndices;

    std::vector<unsigned> mDeletedElementIndices;

    std::vector< c_vector<double, SPACE_DIM> > mLocationsOfT1Swaps;

    std::vector< c_vector<double, SPACE_DIM> > mLocationsOfT3Swaps;

    unsigned DivideElement(VertexElement<ELEMENT_DIM,SPACE_DIM>* pElement,
                           unsigned nodeAIndex,
                           unsigned nodeBIndex,
                           bool placeOriginalElementBelow=false);

    bool CheckForT1Swaps(VertexElementMap& rElementMap);

    bool CheckForT2Swaps(VertexElementMap& rElementMap);

    bool CheckForIntersections();

    void IdentifySwapType(Node<SPACE_DIM>* pNodeA, Node<SPACE_DIM>* pNodeB, VertexElementMap& rElementMap);

    void PerformNodeMerge(Node<SPACE_DIM>* pNodeA, Node<SPACE_DIM>* pNodeB);

    void PerformT1Swap(Node<SPACE_DIM>* pNodeA, Node<SPACE_DIM>* pNodeB, std::set<unsigned>& rElementsContainingNodes);

    void PerformIntersectionSwap(Node<SPACE_DIM>* pNode, unsigned elementIndex);

    void PerformT2Swap(VertexElement<ELEMENT_DIM,SPACE_DIM>& rElement);

    void PerformT3Swap(Node<SPACE_DIM>* pNode, unsigned elementIndex);

    void PerformVoidRemoval(Node<SPACE_DIM>* pNodeA, Node<SPACE_DIM>* pNodeB, Node<SPACE_DIM>* pNodeC);

    friend class boost::serialization::access;

    template<class Archive>
    void serialize(Archive & archive, const unsigned int version)
    {
        // NOTE - Subclasses must archive their member variables BEFORE calling this method.
        archive & mCellRearrangementThreshold;
        archive & mCellRearrangementRatio;
        archive & mT2Threshold;
        archive & mCheckForInternalIntersections;
        archive & mDeletedNodeIndices;
        archive & mDeletedElementIndices;
//        archive & mLocationsOfT1Swaps;
//        archive & mLocationsOfT3Swaps;

        archive & boost::serialization::base_object<VertexMesh<ELEMENT_DIM, SPACE_DIM> >(*this);
    }

public:

    MutableVertexMesh(std::vector<Node<SPACE_DIM>*> nodes,
                      std::vector<VertexElement<ELEMENT_DIM, SPACE_DIM>*> vertexElements,
                      double cellRearrangementThreshold=0.01,
                      double t2Threshold=0.001,
                      double cellRearrangementRatio=1.5);

    MutableVertexMesh();

    virtual ~MutableVertexMesh();

    void SetCellRearrangementThreshold(double cellRearrangementThreshold);

    void SetT2Threshold(double t2Threshold);

    void SetCellRearrangementRatio(double cellRearrangementRatio);

    virtual void SetNode(unsigned nodeIndex, ChastePoint<SPACE_DIM> point);

    void SetCheckForInternalIntersections(bool checkForInternalIntersections);

    double GetCellRearrangementThreshold() const;

    double GetT2Threshold() const;

    double GetCellRearrangementRatio() const;

    unsigned GetNumNodes() const;

    unsigned GetNumElements() const;

    bool GetCheckForInternalIntersections() const;

    std::vector< c_vector<double, SPACE_DIM> > GetLocationsOfT1Swaps();

    std::vector< c_vector<double, SPACE_DIM> > GetLocationsOfT3Swaps();

    void ClearLocationsOfT1Swaps();

    void ClearLocationsOfT3Swaps();


    unsigned AddNode(Node<SPACE_DIM>* pNewNode);

    void DeleteElementPriorToReMesh(unsigned index);

    void DeleteNodePriorToReMesh(unsigned index);

    unsigned DivideElementAlongShortAxis(VertexElement<ELEMENT_DIM,SPACE_DIM>* pElement,
                                         bool placeOriginalElementBelow=false);

    unsigned DivideElementAlongGivenAxis(VertexElement<ELEMENT_DIM,SPACE_DIM>* pElement,
                                         c_vector<double, SPACE_DIM> axisOfDivision,
                                         bool placeOriginalElementBelow=false);

    unsigned AddElement(VertexElement<ELEMENT_DIM, SPACE_DIM>* pNewElement);

    void Clear();

    void DivideEdge(Node<SPACE_DIM>* pNodeA, Node<SPACE_DIM>* pNodeB);

    void RemoveDeletedNodesAndElements(VertexElementMap& rElementMap);

    void RemoveDeletedNodes();

    void ReMesh(VertexElementMap& rElementMap);

    void ReMesh();
};

#include "SerializationExportWrapper.hpp"
EXPORT_TEMPLATE_CLASS_ALL_DIMS(MutableVertexMesh);

#endif /*MUTABLEVERTEXMESH_HPP_*/