ExtendedBidomainSolver.cpp

/*

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/>.

*/


#include "ExtendedBidomainSolver.hpp"
#include "ExtendedBidomainMassMatrixAssembler.hpp"
#include "ExtendedBidomainAssembler.hpp"

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void ExtendedBidomainSolver<ELEMENT_DIM,SPACE_DIM>::InitialiseForSolve(Vec initialSolution)
{
    if (this->mpLinearSystem != NULL)
    {
        return;
    }
    AbstractExtendedBidomainSolver<ELEMENT_DIM,SPACE_DIM>::InitialiseForSolve(initialSolution);

    // initialise matrix-based RHS vector and matrix, and use the linear
    // system rhs as a template
    Vec& r_template = this->mpLinearSystem->rGetRhsVector();
    VecDuplicate(r_template, &mVecForConstructingRhs);
    PetscInt ownership_range_lo;
    PetscInt ownership_range_hi;
    VecGetOwnershipRange(r_template, &ownership_range_lo, &ownership_range_hi);
    PetscInt local_size = ownership_range_hi - ownership_range_lo;
    PetscTools::SetupMat(mMassMatrix, 3*this->mpMesh->GetNumNodes(), 3*this->mpMesh->GetNumNodes(),
                         3*this->mpMesh->CalculateMaximumNodeConnectivityPerProcess(),
                         local_size, local_size);
}


template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void ExtendedBidomainSolver<ELEMENT_DIM,SPACE_DIM>::SetupLinearSystem(
        Vec currentSolution,
        bool computeMatrix)
{
    assert(this->mpLinearSystem->rGetLhsMatrix() != NULL);
    assert(this->mpLinearSystem->rGetRhsVector() != NULL);
    assert(currentSolution != NULL);


    // set up LHS matrix (and mass matrix)
    if(computeMatrix)
    {
        mpExtendedBidomainAssembler->SetMatrixToAssemble(this->mpLinearSystem->rGetLhsMatrix());
        mpExtendedBidomainAssembler->AssembleMatrix();

        // the ExtendedBidomainMassMatrixAssembler deals with the mass matrix
        // for both bath and nonbath problems
        assert(SPACE_DIM==ELEMENT_DIM);
        ExtendedBidomainMassMatrixAssembler<SPACE_DIM> mass_matrix_assembler(this->mpMesh);
        mass_matrix_assembler.SetMatrixToAssemble(mMassMatrix);
        mass_matrix_assembler.Assemble();

        this->mpLinearSystem->SwitchWriteModeLhsMatrix();
        PetscMatTools::Finalise(mMassMatrix);
    }


    HeartEventHandler::BeginEvent(HeartEventHandler::ASSEMBLE_RHS);

    // Set up z in b=Mz
    DistributedVectorFactory* p_factory = this->mpMesh->GetDistributedVectorFactory();

    // get bidomain parameters
    double Am1 = this->mpExtendedBidomainTissue->GetAmFirstCell();
    double Am2 = this->mpExtendedBidomainTissue->GetAmSecondCell();
    double AmGap = this->mpExtendedBidomainTissue->GetAmGap();
    double Cm1 = this->mpExtendedBidomainTissue->GetCmFirstCell();
    double Cm2 = this->mpExtendedBidomainTissue->GetCmSecondCell();

    // dist stripe for the current Voltage
    DistributedVector distributed_current_solution = p_factory->CreateDistributedVector(currentSolution);
    DistributedVector::Stripe distributed_current_solution_v_first_cell(distributed_current_solution, 0);
    DistributedVector::Stripe distributed_current_solution_v_second_cell(distributed_current_solution, 1);
    DistributedVector::Stripe distributed_current_solution_phi_e(distributed_current_solution, 2);

    // dist stripe for z
    DistributedVector dist_vec_matrix_based = p_factory->CreateDistributedVector(mVecForConstructingRhs);
    DistributedVector::Stripe dist_vec_matrix_based_v_first_cell(dist_vec_matrix_based, 0);
    DistributedVector::Stripe dist_vec_matrix_based_v_second_cell(dist_vec_matrix_based, 1);
    DistributedVector::Stripe dist_vec_matrix_based_phi_e(dist_vec_matrix_based, 2);

    for (DistributedVector::Iterator index = dist_vec_matrix_based.Begin();
         index!= dist_vec_matrix_based.End();
         ++index)
    {
        double V_first_cell = distributed_current_solution_v_first_cell[index];
        double V_second_Cell = distributed_current_solution_v_second_cell[index];
        double Phi_e = distributed_current_solution_phi_e[index];

        double i_ionic_first_cell = this->mpExtendedBidomainTissue->rGetIionicCacheReplicated()[index.Global];
        double i_ionic_second_cell = this->mpExtendedBidomainTissue->rGetIionicCacheReplicatedSecondCell()[index.Global];
        double intracellular_stimulus_first_cell = this->mpExtendedBidomainTissue->rGetIntracellularStimulusCacheReplicated()[index.Global];
        double intracellular_stimulus_second_cell = this->mpExtendedBidomainTissue->rGetIntracellularStimulusCacheReplicatedSecondCell()[index.Global];
        double extracellular_stimulus =  this->mpExtendedBidomainTissue->rGetExtracellularStimulusCacheReplicated()[index.Global];
        double g_gap = this->mpExtendedBidomainTissue->rGetGgapCacheReplicated()[index.Global];
        double delta_t = PdeSimulationTime::GetPdeTimeStep();
        dist_vec_matrix_based_v_first_cell[index] = Am1*Cm1*V_first_cell/delta_t - Am1*Cm1*Phi_e/delta_t - Am1*i_ionic_first_cell + AmGap*g_gap*(V_second_Cell - V_first_cell) -  intracellular_stimulus_first_cell;
        dist_vec_matrix_based_v_second_cell[index] = Am2*Cm2*V_second_Cell/delta_t- Am2*Cm2*Phi_e/delta_t - Am2*i_ionic_second_cell + AmGap*g_gap*(V_first_cell - V_second_Cell) - intracellular_stimulus_second_cell;

        if (this->mpExtendedBidomainTissue->HasTheUserSuppliedExtracellularStimulus() )
        {
            assert((fabs(intracellular_stimulus_first_cell) < 1e-12)
            && (fabs(intracellular_stimulus_second_cell) < 1e-12));

            dist_vec_matrix_based_phi_e[index] = -extracellular_stimulus;
        }
        else
        {
            dist_vec_matrix_based_phi_e[index] = 0.0;
        }
    }


    dist_vec_matrix_based.Restore();

    // b = Mz

    MatMult(mMassMatrix, mVecForConstructingRhs, this->mpLinearSystem->rGetRhsVector());

    // assembling RHS is not finished yet, as Neumann bcs are added below, but
    // the event will be begun again inside mpExtendedBidomainAssembler->AssembleVector();
    HeartEventHandler::EndEvent(HeartEventHandler::ASSEMBLE_RHS);

    // apply Neumann boundary conditions
    mpExtendedBidomainNeumannSurfaceTermAssembler->ResetBoundaryConditionsContainer(this->mpBoundaryConditions); // as the BCC can change
    mpExtendedBidomainNeumannSurfaceTermAssembler->SetVectorToAssemble(this->mpLinearSystem->rGetRhsVector(), false/*don't zero vector!*/);
    mpExtendedBidomainNeumannSurfaceTermAssembler->AssembleVector();

    this->mpLinearSystem->FinaliseRhsVector();

    this->mpBoundaryConditions->ApplyDirichletToLinearProblem(*(this->mpLinearSystem), computeMatrix);

    if(computeMatrix)
    {
        this->mpLinearSystem->FinaliseLhsMatrix();
    }
    this->mpLinearSystem->FinaliseRhsVector();
}


template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
ExtendedBidomainSolver<ELEMENT_DIM,SPACE_DIM>::ExtendedBidomainSolver(
        bool bathSimulation,
        AbstractTetrahedralMesh<ELEMENT_DIM,SPACE_DIM>* pMesh,
        ExtendedBidomainTissue<SPACE_DIM>* pTissue,
        BoundaryConditionsContainer<ELEMENT_DIM,SPACE_DIM,3>* pBoundaryConditions,
        unsigned numQuadPoints)
    : AbstractExtendedBidomainSolver<ELEMENT_DIM,SPACE_DIM>(bathSimulation,pMesh,pTissue,pBoundaryConditions)
{
    // Tell Tissue there's no need to replicate ionic caches
    pTissue->SetCacheReplication(false);
    mVecForConstructingRhs = NULL;

    // create assembler
    if(this->mBathSimulation)
    {
        //this->mpExtendedExtendedBidomainAssembler = new ExtendedExtendedBidomainWithBathAssembler<ELEMENT_DIM,SPACE_DIM>(this->mpMesh,this->mpExtendedExtendedBidomainTissue,this->mDt,this->mNumQuadPoints);
        EXCEPTION("Bath simulations are not yet supported for extended bidomain problems");
    }
    else
    {
        mpExtendedBidomainAssembler = new ExtendedBidomainAssembler<ELEMENT_DIM,SPACE_DIM>(this->mpMesh,this->mpExtendedBidomainTissue,this->mNumQuadPoints);
    }

    mpExtendedBidomainNeumannSurfaceTermAssembler = new ExtendedBidomainNeumannSurfaceTermAssembler<ELEMENT_DIM,SPACE_DIM>(pMesh,pBoundaryConditions);

}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
ExtendedBidomainSolver<ELEMENT_DIM,SPACE_DIM>::~ExtendedBidomainSolver()
{
    delete mpExtendedBidomainAssembler;
    delete mpExtendedBidomainNeumannSurfaceTermAssembler;

    if(mVecForConstructingRhs)
    {
        VecDestroy(mVecForConstructingRhs);
        MatDestroy(mMassMatrix);
    }
}

// explicit instantiation

template class ExtendedBidomainSolver<1,1>;
template class ExtendedBidomainSolver<2,2>;
template class ExtendedBidomainSolver<3,3>;