PeriodicNodesOnlyMesh.hpp

/*

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*/

#ifndef PERIODICNODESONLYMESH_HPP_
#define PERIODICNODESONLYMESH_HPP_

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

#include "NodesOnlyMesh.hpp"

template<unsigned SPACE_DIM>
class PeriodicNodesOnlyMesh: public NodesOnlyMesh<SPACE_DIM>
{
private:
    c_vector<double,SPACE_DIM> mWidth;

    /*
     * Whether a dimension is periodic
     */
    c_vector<bool,SPACE_DIM> mIsDimPeriodic;

    friend class TestPeriodicNodesOnlyMesh;

    friend class boost::serialization::access;
    template<class Archive>
    void serialize(Archive & archive, const unsigned int version)
    {
        archive & boost::serialization::base_object<NodesOnlyMesh<SPACE_DIM> >(*this);
        archive & mWidth;
        archive & mIsDimPeriodic;
    }

public:

    PeriodicNodesOnlyMesh(c_vector<double,SPACE_DIM> width);

    virtual void SetUpBoxCollection(double cutOffLength, c_vector<double, 2*SPACE_DIM> domainSize, int numLocalRows = PETSC_DECIDE,  c_vector<bool,SPACE_DIM> isDimPeriodic = zero_vector<bool>(SPACE_DIM));

    c_vector<double, SPACE_DIM> GetVectorFromAtoB(const c_vector<double, SPACE_DIM>& rLocation1, const c_vector<double, SPACE_DIM>& rLocation2);

    double GetWidth(const unsigned& rDimension) const;

    /*
     * Method to get the width of the periodic dimensions
     * @return The value of the mWidth vector
    */
    c_vector<double,SPACE_DIM> GetPeriodicWidths() const;

    /*
     * Overridden SetNode() method.
     *
     * If the location should be set outside a cylindrical boundary
     * move it back onto the cylinder.
     *
     * @param nodeIndex is the index of the node to be moved
     * @param point is the new target location of the node
     * @param concreteMove is set to false if we want to skip the signed area tests in the parent Class Note this should always be false here
     */

    void SetNode(unsigned nodeIndex, ChastePoint<SPACE_DIM> point, bool concreteMove = false);

    unsigned AddNode(Node<SPACE_DIM>* pNewNode);

    void RefreshMesh();
};

namespace boost
{
namespace serialization
{
template<class Archive, unsigned SPACE_DIM>
inline void save_construct_data(
    Archive & ar, const PeriodicNodesOnlyMesh<SPACE_DIM> * t, const unsigned int file_version)
{
    // Save data required to construct instance
    const c_vector<double,SPACE_DIM> width = t->GetPeriodicWidths();
    for ( unsigned i=0; i < SPACE_DIM; i++ )
    {
        ar << width(i);
    }
}

template<class Archive, unsigned SPACE_DIM>
inline void load_construct_data(
    Archive & ar, PeriodicNodesOnlyMesh<SPACE_DIM> * t, const unsigned int file_version)
{
    // Retrieve data from archive required to construct new instance of the mesh
    c_vector<double,SPACE_DIM> width;
    for (unsigned i=0; i<SPACE_DIM; i++)
    {
        double current_width;
        ar & current_width;
        width(i) = current_width;
    }

    // Invoke inplace constructor to initialise instance
    ::new(t)PeriodicNodesOnlyMesh<SPACE_DIM>(width);
}
}
} // namespace ...

#include "SerializationExportWrapper.hpp"
EXPORT_TEMPLATE_CLASS_SAME_DIMS(PeriodicNodesOnlyMesh)

#endif /*PERIODICNODESONLYMESH_HPP_*/