HeartSolver.hpp 18.6 KB
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//
//  HeartSolver.cpp
//  LifeV
//
//  Created by Thomas Kummer on 03.05.16.
//  Copyright © 2016 Thomas Kummer. All rights reserved.
//

#ifndef _HEARTDATA_H_
#define _HEARTDATA_H_


#include <stdio.h>
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#include <lifev/em/solver/EMSolver.hpp>
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#include <lifev/em/solver/circulation/Circulation.hpp>
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#include <lifev/em/solver/HeartData.hpp>
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namespace LifeV
{

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#define PI 3.14159265359
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template <class EmSolver>
class HeartSolver {
   
public:
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    typedef RegionMesh<LinearTetra>                         mesh_Type;
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    typedef boost::shared_ptr<mesh_Type>                    meshPtr_Typ;
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    typedef ExporterHDF5<mesh_Type>                         exporter_Type;
    typedef boost::shared_ptr<exporter_Type>                exporterPtr_Type;
    
    
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    HeartSolver(EmSolver& emSolver,  Circulation& circulationSolver) :
        M_emSolver          (emSolver),
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        M_circulationSolver (circulationSolver),
        M_heartData         (HeartData())
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    {}
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    virtual ~HeartSolver() {}
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    EmSolver& emSolver()
    {
        return M_emSolver;
    }
    
    Circulation& circulation()
    {
        return M_heartData;
    }
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    const HeartData& data() const
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    {
        return M_heartData;
    }
    
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    void setup(const GetPot& datafile)
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    {
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        M_heartData.setup(datafile);
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    }
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    template <class lambda>
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    void preload(const lambda& modifyFeBC, const std::vector<Real>& bcValues)
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    {
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        M_emSolver.structuralOperatorPtr() -> data() -> dataTime() -> setTime(0.0);
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        auto preloadPressure = [] (std::vector<double> p, const int& step, const int& steps)
        {
            for (auto& i : p) {i *= double(step) / double(steps);}
            return p;
        };
        
        LifeChrono chronoSave;
        chronoSave.start();
        
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        M_emSolver.saveSolution (-1.0);
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        if ( 0 == M_emSolver.comm()->MyPID() )
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        {
            std::cout << "\n*****************************************************************";
            std::cout << "\nData stored in " << chronoSave.diff() << " s";
            std::cout << "\n*****************************************************************\n";
        }
        
        LifeChrono chronoPreload;
        chronoPreload.start();
        
        for (int i (1); i <= data().preloadSteps(); i++)
        {
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            if ( 0 == M_emSolver.comm()->MyPID() )
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            {
                std::cout << "\n*****************************************************************";
                std::cout << "\nPreload step: " << i << " / " << data().preloadSteps();
                std::cout << "\n*****************************************************************\n";
            }
            
            // Update pressure b.c.
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            modifyFeBC(preloadPressure(bcValues, i, data().preloadSteps() ));
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            // Solve mechanics
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            M_emSolver.bcInterfacePtr() -> updatePhysicalSolverVariables();
            M_emSolver.solveMechanics();
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            // Safe preload steps
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            if ( data().safePreload() ) M_emSolver.saveSolution (i-1);
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        }
        
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        if ( 0 == M_emSolver.comm()->MyPID() )
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        {
            std::cout << "\n*****************************************************************";
            std::cout << "\nPreload done in: " << chronoPreload.diff();
            std::cout << "\n*****************************************************************\n";
        }

    }
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    void restart(std::string& restartInput, const GetPot& command_line, Real& t)
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    {
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        const std::string restartDir = ""; //command_line.follow (problemFolder.c_str(), 2, "-rd", "--restartDir");
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        Real dtExport = 10.;
        
        // Set time variable
        const unsigned int restartInputStr = std::stoi(restartInput);
        const unsigned int nIter = (restartInputStr - 1) * dtExport / data().dt_mechanics();
        t = nIter * data().dt_mechanics();
        
        // Set time exporter time index
        M_emSolver.setTimeIndex(restartInputStr + 1);
        //solver.importHdf5();
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        // Load restart solutions from output files
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        std::string polynomialDegree = data().elementOrder();
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        ElectrophysiologyUtility::importVectorField ( M_emSolver.structuralOperatorPtr() -> displacementPtr(), "MechanicalSolution" , "displacement", M_emSolver.localMeshPtr(), restartDir, polynomialDegree, restartInput );
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        ElectrophysiologyUtility::importScalarField (M_emSolver.activationModelPtr() -> fiberActivationPtr(), "ActivationSolution" , "Activation", M_emSolver.localMeshPtr(), restartDir, polynomialDegree, restartInput );
        //ElectrophysiologyUtility::importScalarField (solver.activationTimePtr(), "ActivationTimeSolution" , "Activation Time", solver.localMeshPtr(), restartDir, polynomialDegree, restartInput );
        
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        for ( unsigned int i = 0; i < M_emSolver.electroSolverPtr()->globalSolution().size() ; ++i )
        {
            ElectrophysiologyUtility::importScalarField (M_emSolver.electroSolverPtr()->globalSolution().at(i), "ElectroSolution" , ("Variable" + std::to_string(i)), M_emSolver.localMeshPtr(), restartDir, polynomialDegree, restartInput );
        }
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        if ( 0 == M_emSolver.comm()->MyPID() )
        {
            std::cout << "\nLoad from restart: " << restartInput << ",  nIterCirculation = " << nIter << ",  time = " << t << std::endl;
        }
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        M_circulationSolver.restartFromFile ( restartDir + "solution.dat" , nIter );
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    }
    
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    void createPatch (EMSolver<RegionMesh<LinearTetra>, EMMonodomainSolver<RegionMesh<LinearTetra> > >& solver, const Vector3D& center, const Real& radius, const int& currentFlag, const int& newFlag)
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    {
        for (auto& mesh : solver.mesh())
        {
            for (int j(0); j < mesh->numBoundaryFacets(); j++)
            {
                auto& face = mesh->boundaryFacet(j);
                auto faceFlag = face.markerID();
                
                if (faceFlag == currentFlag || faceFlag == 470 || faceFlag == 471)
                {
                    int numPointsInsidePatch (0);
                    
                    for (int k(0); k < 3; ++k)
                    {
                        auto coord = face.point(k).coordinates();
                        bool pointInPatch = (coord - center).norm() < radius;
                        
                        if (pointInPatch)
                        {
                            ++numPointsInsidePatch;
                        }
                    }
                    
                    if (numPointsInsidePatch > 2)
                    {
                        face.setMarkerID(newFlag);
                    }
                    
                }
            }
        }
    }
    
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    boost::shared_ptr<VectorEpetra> directionalVectorField (const boost::shared_ptr<FESpace<RegionMesh<LinearTetra>, MapEpetra >> dFeSpace, Vector3D& direction, const Real& disp)
    {
        boost::shared_ptr<VectorEpetra> vectorField (new VectorEpetra( dFeSpace->map(), Repeated ));
        auto nCompLocalDof = vectorField->epetraVector().MyLength() / 3;
        
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        direction.normalize();
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        direction *= disp;
        
        for (int j (0); j < nCompLocalDof; ++j)
        {
            UInt iGID = vectorField->blockMap().GID (j);
            UInt jGID = vectorField->blockMap().GID (j + nCompLocalDof);
            UInt kGID = vectorField->blockMap().GID (j + 2 * nCompLocalDof);
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            (*vectorField)[iGID] = direction[0];
            (*vectorField)[jGID] = direction[1];
            (*vectorField)[kGID] = direction[2];
        }
        
        return vectorField;
    }
    
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    static Real Iapp (const Real& t, const Real&  X, const Real& Y, const Real& Z, const ID& /*i*/)
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    {
        bool coords ( Y < -7. );
        //bool coords ( Y > 4. ); //( Y > 1.5 && Y < 3 );
        bool time ( fmod(t, 800.) < 4 && fmod(t, 800.) > 2);
        return ( coords && time ? 30 : 0 );
    }
    
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    Real sinSquared (const Real& time, const Real& Tmax, const Real& tmax, const Real& tduration) const
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    {
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        Real timeInPeriod = fmod(time-tmax+0.5*tduration, 800.);
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        bool inPeriod ( timeInPeriod < tduration && timeInPeriod > 0);
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        Real sinusSquared = std::pow( std::sin(timeInPeriod * PI / tduration) , 2 ) * Tmax;
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        return ( inPeriod ? sinusSquared : 0 );
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    }
    
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    template<class bcVectorType>
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    void extrapolate4thOrderAdamBashforth(bcVectorType& bcValues, bcVectorType& bcValuesPre, const Real& dpMax)
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    {
        VectorSmall<4> ABcoef;
        ABcoef (0) = 55/24; ABcoef (1) = -59/24; ABcoef (2) = 37/24; ABcoef (3) = -3/8;
        
        for ( unsigned int i = ABcoef.size() - 1; i > 0; --i )
        {
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            m_ABdplv(i) = m_ABdplv(i-1);
            m_ABdprv(i) = m_ABdprv(i-1);
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        }
        
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        m_ABdplv(0) = bcValues[0] - bcValuesPre[0];
        m_ABdprv(0) = bcValues[1] - bcValuesPre[1];
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        bcValuesPre = bcValues;
        
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        bcValues[0] += std::min( std::max( ABcoef.dot( m_ABdplv ) , - dpMax ) , dpMax );
        bcValues[1] += std::min( std::max( ABcoef.dot( m_ABdprv ) , - dpMax ) , dpMax );
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    }
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    void setupExporter(std::string problemFolder = "./", std::string outputFileName = "humanHeartSolution")
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    {
        m_exporter.reset (new exporter_Type());
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        setupExporter<mesh_Type>(*m_exporter, M_emSolver.localMeshPtr(), M_emSolver.comm(), outputFileName, problemFolder);
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        m_exporter->addVariable (    ExporterData<RegionMesh<LinearTetra> >::VectorField,
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                                     "Displacement",
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                                     M_emSolver.structuralOperatorPtr()->dispFESpacePtr(),
                                     M_emSolver.structuralOperatorPtr()->displacementPtr(),
                                     UInt (0) );
        
        m_exporter->addVariable (    ExporterData<RegionMesh<LinearTetra> >::ScalarField,
                                     "Von Mises Stress",
                                     M_emSolver.electroSolverPtr()->feSpacePtr(),
                                     M_emSolver.tensionEstimator().vonMisesStressPtr(),
                                     UInt (0) );
        
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        m_exporter->addVariable (    ExporterData<RegionMesh<LinearTetra> >::ScalarField,
                                     "Principal Stress",
                                     M_emSolver.electroSolverPtr()->feSpacePtr(),
                                     M_emSolver.tensionEstimator().principal stresses(),
                                     UInt (0) );
        
        
        // export stresses
        // export global eigenvalue vector
        
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        m_exporter->addVariable (    ExporterData<RegionMesh<LinearTetra> >::VectorField,
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                                     "Fibers",
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                                     M_emSolver.structuralOperatorPtr()->dispFESpacePtr(),
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                                     M_emSolver.structuralOperatorPtr()->fPtr(),
                                     // M_emSolver.structuralOperatorPtr()->EMMaterial()->fiberVectorPtr(),
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                                     UInt (0) );
        
        m_exporter->addVariable (    ExporterData<RegionMesh<LinearTetra> >::VectorField,
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                                     "Sheets",
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                                     M_emSolver.structuralOperatorPtr()->dispFESpacePtr(),
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                                     M_emSolver.structuralOperatorPtr()->sPtr(),
                                     //M_emSolver.structuralOperatorPtr()->EMMaterial()->sheetVectorPtr(),
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                                     UInt (0) );
        
        m_exporter->addVariable (    ExporterData<RegionMesh<LinearTetra> >::ScalarField,
                                     "Activation",
                                     M_emSolver.electroSolverPtr()->feSpacePtr(),
                                     M_emSolver.activationModelPtr()->fiberActivationPtr(),
                                     UInt (0) );
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        m_exporter -> addVariable ( ExporterData<RegionMesh<LinearTetra> >::ScalarField,
                                    "Activation Time",
                                    M_emSolver.electroSolverPtr() -> feSpacePtr(),
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                                    M_emSolver.activationTimePtr(),
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                                    UInt (0) );
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        for (int i = 0; i < M_emSolver.electroSolverPtr()->ionicModelPtr()->Size(); ++i)
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        {
            std::string variableName = "Ionic Variable " + boost::lexical_cast<std::string> (i);
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            m_exporter->addVariable (ExporterData<mesh_Type>::ScalarField,
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                                     variableName,
                                     M_emSolver.electroSolverPtr()->feSpacePtr(),
                                     M_emSolver.electroSolverPtr()->globalSolution().at(i),
                                     UInt (0) );
        }

        
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    }

    
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    template<class Mesh>
    void setupExporter (ExporterHDF5<Mesh>& exporter,
                        boost::shared_ptr<Mesh> localMeshPtr,
                        boost::shared_ptr<Epetra_Comm> commPtr,
                        std::string fileName,
                        std::string folder)
    {
        exporter.setMeshProcId (localMeshPtr, commPtr->MyPID() );
        exporter.setPrefix (fileName);
        exporter.exportPID (localMeshPtr, commPtr);
        exporter.setPostDir (folder);
    }
    
    
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    void postProcess(const Real& time)
    {
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        // Compute Von Mises stress
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        M_emSolver.tensionEstimator().setDisplacement ( M_emSolver.structuralOperatorPtr()->displacement() );
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        M_emSolver.tensionEstimator().analyzeTensionsRecoveryVonMisesStress();

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        // Compute deformed fiber direction
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        M_emSolver.computeDeformedFiberDirection (M_emSolver.structuralOperatorPtr()->f(), *M_emSolver.structuralOperatorPtr()->EMMaterial()->fiberVectorPtr(), *M_emSolver.structuralOperatorPtr()->displacementPtr(), M_emSolver.structuralOperatorPtr()->dispFESpacePtr());
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        // Compute deformed sheet direction
        M_emSolver.computeDeformedFiberDirection (M_emSolver.structuralOperatorPtr()->s(), *M_emSolver.structuralOperatorPtr()->EMMaterial()->sheetVectorPtr(), *M_emSolver.structuralOperatorPtr()->displacementPtr(), M_emSolver.structuralOperatorPtr()->dispFESpacePtr());
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        // Write on hdf5 output file
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        m_exporter->postProcess(time);
    }
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    exporterPtr_Type exporter()
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    {
        return m_exporter;
    }
    
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    Real
    externalPower ( const VectorEpetra& dispCurrent,
                   const VectorEpetra& dispPrevious,
                   const boost::shared_ptr<ETFESpace< RegionMesh<LinearTetra>, MapEpetra, 3, 3 > > dispETFESpace,
                   Real pressure,
                   Real dt,
                   const unsigned int bdFlag) const
    {
        VectorEpetra traction ( dispCurrent.map() );
        VectorEpetra velocity ( (dispCurrent - dispPrevious) / dt );
        
        MatrixSmall<3,3> Id;
        Id(0,0) = 1.; Id(0,1) = 0., Id(0,2) = 0.;
        Id(1,0) = 0.; Id(1,1) = 1., Id(1,2) = 0.;
        Id(2,0) = 0.; Id(2,1) = 0., Id(2,2) = 1.;
        
        {
            using namespace ExpressionAssembly;
            
            auto I = value(Id);
            auto Grad_u = grad( dispETFESpace, dispCurrent, 0);
            auto F =  Grad_u + I;
            auto FmT = minusT(F);
            auto J = det(F);
            auto p = value(pressure);
            
            QuadratureBoundary myBDQR (buildTetraBDQR (quadRuleTria7pt) );
            
            integrate ( boundary ( dispETFESpace->mesh(), bdFlag),
                       myBDQR,
                       dispETFESpace,
                       p * J * dot( FmT * Nface,  phi_i)
                       //p * J * dot( FmT * Nface,  phi_i)
                       //value(-1.0) * J * dot (vE1, FmT * Nface) * phi_i) >> intergral
                       ) >> traction;
            
            traction.globalAssemble();
        }
        
        return traction.dot(velocity);
    }

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protected:
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    EmSolver& M_emSolver;
    Circulation& M_circulationSolver;
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    HeartData M_heartData;
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    exporterPtr_Type m_exporter;
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    VectorSmall<2> M_pressure;
    VectorSmall<2> M_volume;

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    VectorSmall<4> m_ABdplv, m_ABdprv;
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    std::string pipeToString ( const char* command )
    {
        FILE* file = popen( command, "r" ) ;
        std::ostringstream stm ;
        char line[6] ;
        fgets( line, 6, file );
        stm << line;
        pclose(file) ;
        return stm.str() ;
    };
    
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    Real patchDispFunNormal (const Real& t, const Real&  X, const Real& Y, const Real& Z, const ID& i)
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    {
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        return (-0.000 - 0.00005*t);// sinSquared(t, 0.1, 50, 100)); // -0.001;// (t * 1e-5);
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    }
    
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    Real patchFunction (const Real& t, const Real&  X, const Real& Y, const Real& Z, const ID& /*i*/)
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    {
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        Real disp = std::pow( std::sin(fmod(t, 800.) * 3.14159265359/300) , 2 )*15;
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        return disp;
    }
    
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    Real potentialMultiplyerFcn (const Real& t, const Real&  X, const Real& Y, const Real& Z, const ID& /*i*/)
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    {
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        bool time ( fmod(t, 800.) < 4 && fmod(t, 800.) > 2);
        return 1.4 * time; // ( Y < 2.5 && Y > 0.5 ? 1.0 : 0.0 );
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    }
    
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    Real patchDispFun1 (const Real& t, const Real&  X, const Real& Y, const Real& Z, const ID& i)
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    {
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        switch (i)
        {
            case 0:
                return (t);
                break;
            case 1:
                return 0;
                break;
            case 2:
                return (t);
                break;
            default:
                ERROR_MSG ("This entry is not allowed");
                return 0.;
                break;
        }
    }
    
    Real patchDispFun2 (const Real& t, const Real&  X, const Real& Y, const Real& Z, const ID& i)
    {
        switch (i)
        {
            case 0:
                return (-t);
                break;
            case 1:
                return 0;
                break;
            case 2:
                return (-t);
                break;
            default:
                ERROR_MSG ("This entry is not allowed");
                return 0.;
                break;
        }
    }
    
    Real normalDirection ( const Real& /*t*/, const Real& x , const Real& y, const Real& z, const ID& i)
    {
        Real nnorm = std::sqrt(x * x + y * y + z * z);
        switch (i)
        {
            case 0:
                return 1/std::sqrt(2);
                break;
            case 1:
                return 0;
                break;
            case 2:
                return 1/std::sqrt(2);
                break;
            default:
                ERROR_MSG ("This entry is not allowed");
                return 0.;
                break;
        }
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    }
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};

}

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#endif