CardiacElectroMechanicsVtkHandler.cpp

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#include "CardiacElectroMechanicsVtkHandler.hpp"
 
template<unsigned DIM, unsigned ELEC_PROB_DIM>
CardiacElectroMechanicsVtkHandler<DIM,ELEC_PROB_DIM>::CardiacElectroMechanicsVtkHandler(AbstractNonlinearElasticitySolver<DIM>& rMechanicsSolver,
    QuadraticMesh<DIM>& rQuadMesh,
    TetrahedralMesh<DIM,DIM>& rElectricsMesh,
    ReplicatableVector& rElectricsInitialCondition,
    const std::string& rOutputDir)
   : mrMechanicsSolver(rMechanicsSolver),
     mpVtkElastictyWriter(NULL),
     mpInterpolater(NULL)
{
 
#ifdef CHASTE_VTK // Requires "sudo aptitude install libvtk5-dev" or similar
    //create an internal copy of the quadratic mesh (we will modify node locations for oputput)
    mpVtkOutputMesh = new QuadraticMesh<DIM>();
    mpVtkOutputMesh->ConstructFromMesh(rQuadMesh);
    assert(mpVtkOutputMesh->GetNumNodes() == rQuadMesh.GetNumNodes());
 
    //cretae the writer, using the output mesh voltage and other quantities
    mpVtkWriter =  new VtkDeformedMeshWriter<DIM>(mpVtkOutputMesh, rOutputDir + "/vtk","deformed_mechanics_mesh_",true);         
    //set up voltage interpolating object
    mpInterpolater = new VoltageInterpolaterOntoMechanicsMesh<DIM>(rElectricsMesh,*mpVtkOutputMesh);
    mpVtkElastictyWriter = new VtkNonlinearElasticitySolutionWriter<DIM>(rMechanicsSolver);
 
    //allocate memory for the interpolated voltages (once on initialize)
    mInterpolatedVoltagesNodeWise.assign(mpVtkOutputMesh->GetNumNodes(),0.0);
    //allocate memory for displacements
    c_vector<double,DIM> no_displ;
    c_matrix<double,DIM,DIM> zero_strains;
    for (unsigned i=0u ; i < DIM; ++i)
    {
        no_displ(i) = 0.0;
        for (unsigned j=0u; j < DIM; ++j)
        {
            zero_strains(i,j) = 0.0;
        } 
    }
    mDisplacements.assign(mpVtkOutputMesh->GetNumNodes(),no_displ);
    mStrains.assign(mpVtkOutputMesh->GetNumElements(),zero_strains);
 
    //Create initial condition vector for the voltages (passed in)
    ReplicatableVector init_cond(rElectricsMesh.GetNumNodes());
    for (unsigned i = 0u; i < init_cond.GetSize(); ++i)
    {
        //the following line assumes interleaved solution for ELEC_PROB_DIM>1 (e.g, [Vm_0, phi_e_0, Vm1, phi_e_1...])
        init_cond[i] = rElectricsInitialCondition[ELEC_PROB_DIM*i];
    }
    mpInterpolater->InterpolateOnCoarseMesh(mInterpolatedVoltagesNodeWise,init_cond);
 
    mpVtkWriter->SetOutputBaseFileName("deformed_mechanics_mesh_" + std::to_string(0));
    mpVtkWriter->AddPointData("V", mInterpolatedVoltagesNodeWise);
    mpVtkWriter->AddPointData("displacements", mDisplacements);
    mpVtkWriter->AddTensorCellData("deformation_gradient_F", mStrains);
    assert(mInterpolatedVoltagesNodeWise.size()==rQuadMesh.GetNumNodes());
    mpVtkWriter->WriteDeformedFiles();
 
#endif //CHASTE_VTK
}
 
template<unsigned DIM, unsigned ELEC_PROB_DIM>
CardiacElectroMechanicsVtkHandler<DIM,ELEC_PROB_DIM>::~CardiacElectroMechanicsVtkHandler()
{
#ifdef CHASTE_VTK // Requires "sudo aptitude install libvtk5-dev" or similar
    delete mpVtkWriter;
    delete mpVtkOutputMesh;
#endif
    delete mpInterpolater;
    delete mpVtkElastictyWriter;
}
 
template<unsigned DIM, unsigned ELEC_PROB_DIM>
void CardiacElectroMechanicsVtkHandler<DIM,ELEC_PROB_DIM>::WriteSolution(unsigned counter, ReplicatableVector& rElectricsSolution)
{
#ifdef CHASTE_VTK // Requires "sudo aptitude install libvtk5-dev" or similar
    //Apply deformation solution to mechanics mesh (the one in the writer object, not the one used by the solver!)
    mpVtkWriter->ApplyDeformation(mrMechanicsSolver.rGetDeformedPosition());
    mpVtkWriter->SetOutputBaseFileName("deformed_mechanics_mesh_" + std::to_string(counter));
    mpVtkWriter->SetWriteMeshCells(false);
    
    //voltage
    mpInterpolater->InterpolateOnCoarseMesh(mInterpolatedVoltagesNodeWise,rElectricsSolution);//VTK output. Determine voltage on coarse nodes 
    mpVtkWriter->AddPointData("V", mInterpolatedVoltagesNodeWise);
    
    //displacement
    mpVtkElastictyWriter->CalculateDisplacements(mDisplacements);
    mpVtkWriter->AddPointData("displacements", mDisplacements);
 
    //Strains
    mpVtkElastictyWriter->SetWriteElementWiseStrains(DEFORMATION_GRADIENT_F);
    std::string name;
    mpVtkElastictyWriter->CalculateStrains(name, mStrains);
    mpVtkWriter->AddTensorCellData(name,mStrains);
 
    //write to file
    mpVtkWriter->WriteDeformedFiles();
#endif
}
 
 
// Explicit instantiation
template class CardiacElectroMechanicsVtkHandler<2,1>;
template class CardiacElectroMechanicsVtkHandler<3,1>;
template class CardiacElectroMechanicsVtkHandler<2,2>;
template class CardiacElectroMechanicsVtkHandler<3,2>;