ExtendedBidomainProblem.cpp

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#include "ExtendedBidomainProblem.hpp"
#include "ExtendedBidomainSolver.hpp"
#include "AbstractDynamicLinearPdeSolver.hpp"
#include "HeartConfig.hpp"
#include "Exception.hpp"
#include "DistributedVector.hpp"
#include "ReplicatableVector.hpp"



template<unsigned DIM>
ExtendedBidomainProblem<DIM>::ExtendedBidomainProblem(
            AbstractCardiacCellFactory<DIM>* pCellFactory, AbstractCardiacCellFactory<DIM>* pSecondCellFactory, bool hasBath)
    : AbstractCardiacProblem<DIM,DIM, 3>(pCellFactory),
      mpSecondCellFactory(pSecondCellFactory),
      mpExtendedBidomainTissue(NULL),
      mUserSpecifiedSecondCellConductivities(false),
      mUserHasSetBidomainValuesExplicitly(false),
      mpExtracellularStimulusFactory(NULL),
      mRowForAverageOfPhiZeroed(INT_MAX),
      mApplyAveragePhieZeroConstraintAfterSolving(false),
      mUserSuppliedExtracellularStimulus(false),
      mHasBath(hasBath)
{
    mFixedExtracellularPotentialNodes.resize(0);
}

template<unsigned DIM>
ExtendedBidomainProblem<DIM>::ExtendedBidomainProblem()
    : AbstractCardiacProblem<DIM,DIM, 3>(),
      mpSecondCellFactory(NULL),
      mpExtendedBidomainTissue(NULL),
      mUserSpecifiedSecondCellConductivities(false),
      mUserHasSetBidomainValuesExplicitly(false),
      mpExtracellularStimulusFactory(NULL),
      mRowForAverageOfPhiZeroed(INT_MAX),
      mApplyAveragePhieZeroConstraintAfterSolving(false),
      mUserSuppliedExtracellularStimulus(false)
{
    mFixedExtracellularPotentialNodes.resize(0);
}


template<unsigned DIM>
Vec ExtendedBidomainProblem<DIM>::CreateInitialCondition()
{

    DistributedVectorFactory* p_factory = this->mpMesh->GetDistributedVectorFactory();
    Vec initial_condition = p_factory->CreateVec(3);
    DistributedVector ic = p_factory->CreateDistributedVector(initial_condition);
    std::vector<DistributedVector::Stripe> stripe;
    stripe.reserve(3);

    stripe.push_back(DistributedVector::Stripe(ic, 0));
    stripe.push_back(DistributedVector::Stripe(ic, 1));
    stripe.push_back(DistributedVector::Stripe(ic, 2));

    for (DistributedVector::Iterator index = ic.Begin();
         index != ic.End();
         ++index)
    {
        stripe[0][index] = mpExtendedBidomainTissue->GetCardiacCell(index.Global)->GetVoltage();//phi_i of frrst cell = Vm first cell at the start
        stripe[1][index] = mpExtendedBidomainTissue->GetCardiacSecondCell(index.Global)->GetVoltage();//phi_i of second cell = Vm second cell at the start
        stripe[2][index] = 0.0;//
    }
    ic.Restore();

    return initial_condition;
}

template<unsigned DIM>
void ExtendedBidomainProblem<DIM>::ProcessExtracellularStimulus()
{
    if ( mpExtracellularStimulusFactory == NULL )//user has not passed in any extracellular stimulus in any form
    {
        mpExtracellularStimulusFactory = new AbstractStimulusFactory<DIM>();
        //create one (with default implementation to zero stimulus everywhere)
    }

    assert(mpExtracellularStimulusFactory);//should be created by now, either above or by the user...
    mpExtracellularStimulusFactory->SetMesh(this->mpMesh);//so, set the mesh into it.
    mpExtracellularStimulusFactory->SetCompatibleExtracellularStimulus();//make sure compatibility condition will be valid

    std::vector<AbstractChasteRegion<DIM>* > grounded_regions = mpExtracellularStimulusFactory->GetRegionsToBeGrounded();

    if ( (mUserSuppliedExtracellularStimulus) && grounded_regions.size() > 0 ) //we check for grunded nodes here
    {
        std::vector<unsigned> grounded_indices;
        for (unsigned global_node_index = 0; global_node_index < this->mpMesh->GetNumNodes(); global_node_index++)
        {
            if (this->mpMesh->GetDistributedVectorFactory()->IsGlobalIndexLocal(global_node_index))
            {
                for (unsigned region_index = 0; region_index <grounded_regions.size(); region_index++)
                {
                    if ( grounded_regions[region_index]->DoesContain( this->mpMesh->GetNode(global_node_index)->GetPoint() ) )
                    {
                        grounded_indices.push_back( this->mpMesh->GetNode(global_node_index)->GetIndex() );
                    }
                }
            }
        }
        PetscTools::Barrier();
        SetFixedExtracellularPotentialNodes(grounded_indices);
    }
}

template<unsigned DIM>
AbstractCardiacTissue<DIM> * ExtendedBidomainProblem<DIM>::CreateCardiacTissue()
{
    //set the mesh into the second cell factory as well.
    mpSecondCellFactory->SetMesh(this->mpMesh);

    //deal with extracellular stimulus, if any
    ProcessExtracellularStimulus();

    //Now create the tissue object
    mpExtendedBidomainTissue = new ExtendedBidomainTissue<DIM>(this->mpCellFactory, mpSecondCellFactory,mpExtracellularStimulusFactory);

    //Let the Tissue know if the user wants an extracellular stimulus (or if we had to create a default zero one).
    mpExtendedBidomainTissue->SetUserSuppliedExtracellularStimulus(mUserSuppliedExtracellularStimulus);

    //if the user remembered to set a different value for the sigma of the second cell...
    if (mUserSpecifiedSecondCellConductivities)
    {
        mpExtendedBidomainTissue->SetIntracellularConductivitiesSecondCell(mIntracellularConductivitiesSecondCell);
    }
    else //..otherwise it gets the same as the first cell (according to heartconfig...)
    {
        c_vector<double, DIM> intra_conductivities;
        HeartConfig::Instance()->GetIntracellularConductivities(intra_conductivities);
        mpExtendedBidomainTissue->SetIntracellularConductivitiesSecondCell(intra_conductivities);
    }

    //the conductivities for the first cell are created within the tissue constructor in the abstract class
    //here we create the ones for the second cell
    mpExtendedBidomainTissue->CreateIntracellularConductivityTensorSecondCell();

    if (mUserHasSetBidomainValuesExplicitly)
    {
        mpExtendedBidomainTissue->SetAmFirstCell(mAmFirstCell);
        mpExtendedBidomainTissue->SetAmSecondCell(mAmSecondCell);
        mpExtendedBidomainTissue->SetAmGap(mAmGap);
        mpExtendedBidomainTissue->SetGGap(mGGap);
        mpExtendedBidomainTissue->SetCmFirstCell(mCmFirstCell);
        mpExtendedBidomainTissue->SetCmSecondCell(mCmSecondCell);
    }
    else//we set all the Am and Cm to the values set by the heartconfig (only one value for all Am and one value for all Cms)
    {
        mpExtendedBidomainTissue->SetAmFirstCell(HeartConfig::Instance()->GetSurfaceAreaToVolumeRatio());
        mpExtendedBidomainTissue->SetAmSecondCell(HeartConfig::Instance()->GetSurfaceAreaToVolumeRatio());
        mpExtendedBidomainTissue->SetAmGap(HeartConfig::Instance()->GetSurfaceAreaToVolumeRatio());
        mpExtendedBidomainTissue->SetGGap(0.0);
        mpExtendedBidomainTissue->SetCmFirstCell(HeartConfig::Instance()->GetCapacitance());
        mpExtendedBidomainTissue->SetCmSecondCell(HeartConfig::Instance()->GetCapacitance());
    }

    mpExtendedBidomainTissue->SetGgapHeterogeneities(mGgapHeterogeneityRegions, mGgapHeterogenousValues);//set user input into the tissue class
    mpExtendedBidomainTissue->CreateGGapConductivities();//if vectors are empty, mGgap will be put everywhere by this method.

    return mpExtendedBidomainTissue;
}

template<unsigned DIM>
void ExtendedBidomainProblem<DIM>::SetExtendedBidomainParameters(double Am1, double Am2, double AmGap, double Cm1, double Cm2, double Ggap)
{
     mAmFirstCell = Am1;
     mAmSecondCell = Am2;
     mAmGap = AmGap;
     mCmFirstCell = Cm1;
     mCmSecondCell = Cm2;
     mGGap = Ggap;

     mUserHasSetBidomainValuesExplicitly = true;
}

template <unsigned DIM>
void ExtendedBidomainProblem<DIM>::SetGgapHeterogeneities ( std::vector<boost::shared_ptr<AbstractChasteRegion<DIM> > >& rGgapHeterogeneityRegions, std::vector<double>& rGgapValues)
{
    if (rGgapHeterogeneityRegions.size() != rGgapValues.size() )
    {
        EXCEPTION  ("Gap junction heterogeneity areas must be of the same number as the heterogeneity values");
    }
    mGgapHeterogeneityRegions = rGgapHeterogeneityRegions;
    mGgapHeterogenousValues =rGgapValues;
}

template <unsigned DIM>
void ExtendedBidomainProblem<DIM>::SetExtracellularStimulusFactory( AbstractStimulusFactory<DIM>* pFactory)
{
    mpExtracellularStimulusFactory = pFactory;
    mUserSuppliedExtracellularStimulus = true;
}

template<unsigned DIM>
AbstractDynamicLinearPdeSolver<DIM, DIM, 3>* ExtendedBidomainProblem<DIM>::CreateSolver()
{
    /*
     * NOTE: The this->mpBoundaryConditionsContainer.get() lines below convert a
     * boost::shared_ptr to a normal pointer, as this is what the assemblers are
     * expecting. We have to be a bit careful though as boost could decide to delete
     * them whenever it feels like as it won't count the assemblers as using them.
     *
     * As long as they are kept as member variables here for as long as they are
     * required in the assemblers it should all work OK.
     */

    mpSolver = new ExtendedBidomainSolver<DIM,DIM>( mHasBath,
                                                    this->mpMesh,
                                                    mpExtendedBidomainTissue,
                                                    this->mpBoundaryConditionsContainer.get());

    try
    {
        mpSolver->SetFixedExtracellularPotentialNodes(mFixedExtracellularPotentialNodes);
        mpSolver->SetRowForAverageOfPhiZeroed(mRowForAverageOfPhiZeroed);
    }
    catch (const Exception& e)
    {
        delete mpSolver;
        throw e;
    }

    return mpSolver;
}

template<unsigned DIM>
ExtendedBidomainProblem<DIM>::~ExtendedBidomainProblem()
{
    if (!mUserSuppliedExtracellularStimulus)
    {
        delete mpExtracellularStimulusFactory;
    }
}

template<unsigned DIM>
void ExtendedBidomainProblem<DIM>::SetIntracellularConductivitiesForSecondCell(c_vector<double, DIM> conductivities)
{
    for (unsigned i = 0; i < DIM; i++)
    {
        mIntracellularConductivitiesSecondCell[i] = conductivities[i];
    }
    mUserSpecifiedSecondCellConductivities = true;
}

template<unsigned DIM>
void ExtendedBidomainProblem<DIM>::SetFixedExtracellularPotentialNodes(std::vector<unsigned> nodes)
{
    assert(mFixedExtracellularPotentialNodes.size() == 0); 
    mFixedExtracellularPotentialNodes.resize(nodes.size());
    for (unsigned i=0; i<nodes.size(); i++)
    {
        // the assembler checks that the nodes[i] is less than
        // the number of nodes in the mesh so this is not done here
        mFixedExtracellularPotentialNodes[i] = nodes[i];
    }
}

template<unsigned DIM>
void ExtendedBidomainProblem<DIM>::SetNodeForAverageOfPhiZeroed(unsigned node)
{
    if (node==0)
    {
        mRowForAverageOfPhiZeroed = 2;
    }
    else
    {
        //Phie is every three lines, starting from zero...
        mRowForAverageOfPhiZeroed = 3*node  - 1;
    }
}

template<unsigned DIM>
ExtendedBidomainTissue<DIM>* ExtendedBidomainProblem<DIM>::GetExtendedBidomainTissue()
{
    assert(mpExtendedBidomainTissue!=NULL);
    return mpExtendedBidomainTissue;
}

template<unsigned DIM>
void ExtendedBidomainProblem<DIM>::WriteInfo(double time)
{
    if (PetscTools::AmMaster())
    {
        std::cout << "Solved to time " << time << "\n" << std::flush;
    }

    double V_max_first_cell, V_min_first_cell, V_max_second_cell, V_min_second_cell, phi_e_min, phi_e_max;

    VecStrideMax( this->mSolution, 0, PETSC_NULL, &V_max_first_cell );
    VecStrideMin( this->mSolution, 0, PETSC_NULL, &V_min_first_cell );

    VecStrideMax( this->mSolution, 1, PETSC_NULL, &V_max_second_cell );
    VecStrideMin( this->mSolution, 1, PETSC_NULL, &V_min_second_cell );

    VecStrideMax( this->mSolution, 2, PETSC_NULL, &phi_e_max );
    VecStrideMin( this->mSolution, 2, PETSC_NULL, &phi_e_min );

    if (PetscTools::AmMaster())
    {
        std::cout << " V first cell = "  << "[" <<V_min_first_cell << ",   " << V_max_first_cell << "]" << ";\n"
                  << " V second cell = " << "[" <<V_min_second_cell << ", " << V_max_second_cell << "]" << ";\n"
                  << " Phi_e = "         << "[" <<phi_e_min << ", "         << phi_e_max << "]" << ";\n"
                  << std::flush;
    }
}

template<unsigned DIM>
void ExtendedBidomainProblem<DIM>::DefineWriterColumns(bool extending)
{
    if (!extending)
    {
        if ( this->mNodesToOutput.empty() )
        {
            //Set writer to output all nodes
            this->mpWriter->DefineFixedDimension( this->mpMesh->GetNumNodes() );
        }
//        else
//        {
//            //Output only the nodes indicted
//            this->mpWriter->DefineFixedDimension( this->mNodesToOutput, this->mpMesh->GetNumNodes() );
//        }
        //mNodeColumnId = mpWriter->DefineVariable("Node", "dimensionless");
        mVoltageColumnId_Vm1 = this->mpWriter->DefineVariable("V","mV");
        mVoltageColumnId_Vm2 = this->mpWriter->DefineVariable("V_2","mV");
        mVoltageColumnId_Phie = this->mpWriter->DefineVariable("Phi_e","mV");
        mVariablesIDs.push_back(mVoltageColumnId_Vm1);
        mVariablesIDs.push_back(mVoltageColumnId_Vm2);
        mVariablesIDs.push_back(mVoltageColumnId_Phie);

        // Only used to get an estimate of the # of timesteps below (copied from Abstract class)
        TimeStepper stepper(AbstractCardiacProblem<DIM,DIM,3>::mCurrentTime,
                            HeartConfig::Instance()->GetSimulationDuration(),
                            HeartConfig::Instance()->GetPrintingTimeStep());
        this->mpWriter->DefineUnlimitedDimension("Time", "msecs", stepper.EstimateTimeSteps()+1); // +1 for start and end
    }
    else
    {
        mVoltageColumnId_Vm1 = this->mpWriter->GetVariableByName("V");
        mVoltageColumnId_Vm2 = this->mpWriter->GetVariableByName("V_2");
        mVoltageColumnId_Phie = this->mpWriter->GetVariableByName("Phi_e");
    }
    //define any extra variable. NOTE: it must be in the first cell (not the second)
    AbstractCardiacProblem<DIM,DIM,3>::DefineExtraVariablesWriterColumns(extending);

}

template<unsigned DIM>
void ExtendedBidomainProblem<DIM>::WriteOneStep(double time, Vec voltageVec)
{
    this->mpWriter->PutUnlimitedVariable(time);

   // Create a striped vector
    Vec ordered_voltages =  this->mpMesh->GetDistributedVectorFactory()->CreateVec(3);
    DistributedVector wrapped_ordered_solution = this->mpMesh->GetDistributedVectorFactory()->CreateDistributedVector(ordered_voltages);
    DistributedVector wrapped_solution = this->mpMesh->GetDistributedVectorFactory()->CreateDistributedVector(voltageVec);

    DistributedVector::Stripe V_first_cell_stripe(wrapped_solution,0);
    DistributedVector::Stripe V_second_cell_stripe(wrapped_solution,1);
    DistributedVector::Stripe phi_e_stripe(wrapped_solution,2);

    DistributedVector::Stripe wrapped_ordered_solution_first_stripe(wrapped_ordered_solution,0);
    DistributedVector::Stripe wrapped_ordered_solution_second_stripe(wrapped_ordered_solution,1);
    DistributedVector::Stripe wrapped_ordered_solution_third_stripe(wrapped_ordered_solution,2);

    for (DistributedVector::Iterator index = wrapped_solution.Begin();
         index != wrapped_solution.End();
         ++index)
    {
        wrapped_ordered_solution_first_stripe[index] = V_first_cell_stripe[index];
        wrapped_ordered_solution_second_stripe[index] = V_second_cell_stripe[index];
        wrapped_ordered_solution_third_stripe[index] = phi_e_stripe[index];
    }
    wrapped_solution.Restore();
    wrapped_ordered_solution.Restore();

    this->mpWriter->PutStripedVector(mVariablesIDs, ordered_voltages);
    PetscTools::Destroy(ordered_voltages);
    //write any extra variable. Note that this method in the parent class will
    //take the extra variable only from the first cell.
    AbstractCardiacProblem<DIM,DIM,3>::WriteExtraVariablesOneStep();
}

template<unsigned DIM>
void ExtendedBidomainProblem<DIM>::PreSolveChecks()
{
    AbstractCardiacProblem<DIM,DIM, 3>::PreSolveChecks();
    if (mFixedExtracellularPotentialNodes.empty())
    {
        // We're not pinning any nodes.
        if (mRowForAverageOfPhiZeroed==INT_MAX)
        {
            // We're not using the constrain Average phi_e to 0 method, hence use a null space
            // Check that the KSP solver isn't going to do anything stupid:
            // phi_e is not bounded, so it'd be wrong to use a relative tolerance
            if (HeartConfig::Instance()->GetUseRelativeTolerance())
            {
                EXCEPTION("Bidomain external voltage is not bounded in this simulation - use KSP *absolute* tolerance");
            }
        }
    }
}

template<unsigned DIM>
bool ExtendedBidomainProblem<DIM>::GetHasBath()
{
    return mHasBath;
}


template<unsigned DIM>
void ExtendedBidomainProblem<DIM>::SetHasBath(bool hasBath)
{
    mHasBath = hasBath;
}

// Explicit instantiation

template class ExtendedBidomainProblem<1>;
template class ExtendedBidomainProblem<2>;
template class ExtendedBidomainProblem<3>;

// Serialization for Boost >= 1.36
#include "SerializationExportWrapperForCpp.hpp"
EXPORT_TEMPLATE_CLASS_SAME_DIMS(ExtendedBidomainProblem)