SimpleBathProblemSetup.hpp

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/*

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 SIMPLEBATHPROBLEMSETUP_HPP_
#define SIMPLEBATHPROBLEMSETUP_HPP_

#include "AbstractCardiacCellFactory.hpp"
#include "SimpleStimulus.hpp"
#include "LuoRudy1991.hpp"
#include "HeartRegionCodes.hpp"

template<unsigned DIM, class CELLTYPE=CellLuoRudy1991FromCellML>
class BathCellFactory : public AbstractCardiacCellFactory<DIM>
{
private:
    boost::shared_ptr<SimpleStimulus> mpStimulus;
    c_vector<double,DIM> mStimulatedPoint;

public:
    BathCellFactory(double stimulusMagnitude, c_vector<double,DIM> stimulatedPoint)
        : AbstractCardiacCellFactory<DIM>(),
          mpStimulus(new SimpleStimulus(stimulusMagnitude, 0.5)),
          mStimulatedPoint(stimulatedPoint)
    {
    }

    AbstractCardiacCell* CreateCardiacCellForTissueNode(unsigned node)
    {
        // paranoia - check this is really a tissue node
        assert(HeartRegionCode::IsRegionTissue( this->GetMesh()->GetNode(node)->GetRegion() ));

        // stimulate centre node normally..
        bool is_centre;

        if (DIM==1)
        {
            is_centre = (fabs(this->GetMesh()->GetNode(node)->GetPoint()[0]-mStimulatedPoint(0)) < 1e-6);
        }
        else if (DIM==2)
        {
            is_centre = (    (fabs(this->GetMesh()->GetNode(node)->GetPoint()[0]-mStimulatedPoint(0)) < 1e-6)
                          && (fabs(this->GetMesh()->GetNode(node)->GetPoint()[1]-mStimulatedPoint(1)) < 1e-6) );
        }
        else
        {
            is_centre = (    (fabs(this->GetMesh()->GetNode(node)->GetPoint()[0]-mStimulatedPoint(0)) < 1e-6)
                          && (fabs(this->GetMesh()->GetNode(node)->GetPoint()[1]-mStimulatedPoint(1)) < 1e-6)
                          && (fabs(this->GetMesh()->GetNode(node)->GetPoint()[2]-mStimulatedPoint(2)) < 1e-6) );
        }

        if (is_centre)
        {
            return new CELLTYPE(this->mpSolver, mpStimulus);
        }
        else
        {
            return new CELLTYPE(this->mpSolver, this->mpZeroStimulus);
        }
    }
};

template<class MeshType>
void SetCircularTissueIn2dMesh(MeshType* pMesh,
                               double centreX, double centreY, double radius)
{
    for (typename MeshType::ElementIterator it = pMesh->GetElementIteratorBegin();
         it != pMesh->GetElementIteratorEnd();
         ++it)
    {
        double x = it->CalculateCentroid()[0];
        double y = it->CalculateCentroid()[1];
        if ( (x-centreX)*(x-centreX) + (y-centreY)*(y-centreY) > radius*radius )
        {
            it->SetRegion(HeartRegionCode::GetValidBathId());
        }
    }
    pMesh->SetMeshHasChangedSinceLoading();
}

template<class MeshType>
MeshType* Load2dMeshAndSetCircularTissue(const std::string& rMeshPath,
                                         double centreX, double centreY, double radius)
{
    TrianglesMeshReader<2,2> reader(rMeshPath);
    MeshType* p_mesh = new MeshType;
    p_mesh->ConstructFromMeshReader(reader);

    SetCircularTissueIn2dMesh(p_mesh, centreX, centreY, radius);

    return p_mesh;
}

template<>
DistributedTetrahedralMesh<2,2>* Load2dMeshAndSetCircularTissue(const std::string& rMeshPath,
                                                                double centreX, double centreY, double radius)
{
    TrianglesMeshReader<2,2> reader(rMeshPath);
    // Force dumb partitioning so migration tests pass!
    DistributedTetrahedralMesh<2,2>* p_mesh = new DistributedTetrahedralMesh<2,2>(DistributedTetrahedralMeshPartitionType::DUMB);
    p_mesh->ConstructFromMeshReader(reader);

    SetCircularTissueIn2dMesh(p_mesh, centreX, centreY, radius);

    return p_mesh;
}

#endif /*SIMPLEBATHPROBLEMSETUP_HPP_*/