BidomainDg0Assembler.cpp

/*

Copyright (C) University of Oxford, 2005-2009

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 "BidomainDg0Assembler.hpp"
#include <boost/numeric/ublas/vector_proxy.hpp>

#include "Exception.hpp"
#include "DistributedVector.hpp"
#include "ConstBoundaryCondition.hpp"

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void BidomainDg0Assembler<ELEMENT_DIM,SPACE_DIM>::ResetInterpolatedQuantities( void )
{
    mIionic=0;
    mIIntracellularStimulus=0;
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void BidomainDg0Assembler<ELEMENT_DIM,SPACE_DIM>::InitialiseForSolve(Vec initialSolution)
{
    if (this->mpLinearSystem != NULL)
    {
        return;
    }
    BaseClassType::InitialiseForSolve(initialSolution);
    if (HeartConfig::Instance()->GetUseAbsoluteTolerance())
    {
        this->mpLinearSystem->SetAbsoluteTolerance(mpConfig->GetAbsoluteTolerance());
    }
    else
    {
        this->mpLinearSystem->SetRelativeTolerance(mpConfig->GetRelativeTolerance());
    }
    this->mpLinearSystem->SetKspType(HeartConfig::Instance()->GetKSPSolver());
    this->mpLinearSystem->SetPcType(HeartConfig::Instance()->GetKSPPreconditioner());
}


template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void BidomainDg0Assembler<ELEMENT_DIM,SPACE_DIM>::IncrementInterpolatedQuantities(double phi_i, const Node<SPACE_DIM>* pNode)
{
    unsigned node_global_index = pNode->GetIndex();

    mIionic                 += phi_i * mpBidomainPde->rGetIionicCacheReplicated()[ node_global_index ];
    mIIntracellularStimulus += phi_i * mpBidomainPde->rGetIntracellularStimulusCacheReplicated()[ node_global_index ];
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
c_matrix<double,2*(ELEMENT_DIM+1),2*(ELEMENT_DIM+1)>
    BidomainDg0Assembler<ELEMENT_DIM,SPACE_DIM>::ComputeMatrixTerm(
            c_vector<double, ELEMENT_DIM+1> &rPhi,
            c_matrix<double, ELEMENT_DIM, ELEMENT_DIM+1> &rGradPhi,
            ChastePoint<SPACE_DIM> &rX,
            c_vector<double,2> &u,
            c_matrix<double, 2, SPACE_DIM> &rGradU /* not used */,
            Element<ELEMENT_DIM,SPACE_DIM>* pElement)
{
    // get bidomain parameters
    double Am = mpConfig->GetSurfaceAreaToVolumeRatio();
    double Cm = mpConfig->GetCapacitance();

    const c_matrix<double, SPACE_DIM, SPACE_DIM>& sigma_i = mpBidomainPde->rGetIntracellularConductivityTensor(pElement->GetIndex());
    const c_matrix<double, SPACE_DIM, SPACE_DIM>& sigma_e = mpBidomainPde->rGetExtracellularConductivityTensor(pElement->GetIndex());


    c_matrix<double, ELEMENT_DIM, ELEMENT_DIM+1> temp = prod(sigma_i, rGradPhi);
    c_matrix<double, ELEMENT_DIM+1, ELEMENT_DIM+1> grad_phi_sigma_i_grad_phi =
        prod(trans(rGradPhi), temp);

    c_matrix<double, ELEMENT_DIM+1, ELEMENT_DIM+1> basis_outer_prod =
        outer_prod(rPhi, rPhi);

    c_matrix<double, ELEMENT_DIM, ELEMENT_DIM+1> temp2 = prod(sigma_e, rGradPhi);
    c_matrix<double, ELEMENT_DIM+1, ELEMENT_DIM+1> grad_phi_sigma_e_grad_phi =
        prod(trans(rGradPhi), temp2);


    c_matrix<double,2*(ELEMENT_DIM+1),2*(ELEMENT_DIM+1)> ret;

    // even rows, even columns
    matrix_slice<c_matrix<double, 2*ELEMENT_DIM+2, 2*ELEMENT_DIM+2> >
    slice00(ret, slice (0, 2, ELEMENT_DIM+1), slice (0, 2, ELEMENT_DIM+1));
    slice00 = (Am*Cm/this->mDt)*basis_outer_prod + grad_phi_sigma_i_grad_phi;

    // odd rows, even columns
    matrix_slice<c_matrix<double, 2*ELEMENT_DIM+2, 2*ELEMENT_DIM+2> >
    slice10(ret, slice (1, 2, ELEMENT_DIM+1), slice (0, 2, ELEMENT_DIM+1));
    slice10 = grad_phi_sigma_i_grad_phi;

    // even rows, odd columns
    matrix_slice<c_matrix<double, 2*ELEMENT_DIM+2, 2*ELEMENT_DIM+2> >
    slice01(ret, slice (0, 2, ELEMENT_DIM+1), slice (1, 2, ELEMENT_DIM+1));
    slice01 = grad_phi_sigma_i_grad_phi;

    // odd rows, odd columns
    matrix_slice<c_matrix<double, 2*ELEMENT_DIM+2, 2*ELEMENT_DIM+2> >
    slice11(ret, slice (1, 2, ELEMENT_DIM+1), slice (1, 2, ELEMENT_DIM+1));
    slice11 = grad_phi_sigma_i_grad_phi + grad_phi_sigma_e_grad_phi;

    return ret;
}


template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
c_vector<double,2*(ELEMENT_DIM+1)>
    BidomainDg0Assembler<ELEMENT_DIM,SPACE_DIM>::ComputeVectorTerm(
            c_vector<double, ELEMENT_DIM+1> &rPhi,
            c_matrix<double, ELEMENT_DIM, ELEMENT_DIM+1> &rGradPhi,
            ChastePoint<SPACE_DIM> &rX,
            c_vector<double,2> &u,
            c_matrix<double, 2, SPACE_DIM> &rGradU /* not used */,
            Element<ELEMENT_DIM,SPACE_DIM>* pElement)
{
    // get bidomain parameters
    double Am = mpConfig->GetSurfaceAreaToVolumeRatio();
    double Cm = mpConfig->GetCapacitance();

    c_vector<double,2*(ELEMENT_DIM+1)> ret;

    vector_slice<c_vector<double, 2*(ELEMENT_DIM+1)> > slice_V  (ret, slice (0, 2, ELEMENT_DIM+1));
    vector_slice<c_vector<double, 2*(ELEMENT_DIM+1)> > slice_Phi(ret, slice (1, 2, ELEMENT_DIM+1));

    // u(0) = voltage
    noalias(slice_V)   = (Am*Cm*u(0)/this->mDt - Am*mIionic - mIIntracellularStimulus) * rPhi;
    noalias(slice_Phi) = zero_vector<double>(ELEMENT_DIM+1);

    return ret;
}



#define COVERAGE_IGNORE
// never called, since no non-zero neumann conditions
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
c_vector<double, 2*ELEMENT_DIM> BidomainDg0Assembler<ELEMENT_DIM,SPACE_DIM>::ComputeVectorSurfaceTerm(
    const BoundaryElement<ELEMENT_DIM-1,SPACE_DIM> &rSurfaceElement,
    c_vector<double,ELEMENT_DIM> &rPhi,
    ChastePoint<SPACE_DIM> &rX)
{
    // D_times_gradu_dot_n = [D grad(u)].n, D=diffusion matrix
    double D_times_grad_v_dot_n     = this->mpBoundaryConditions->GetNeumannBCValue(&rSurfaceElement, rX, 0);
    double D_times_grad_phi_e_dot_n = this->mpBoundaryConditions->GetNeumannBCValue(&rSurfaceElement, rX, 1);

    c_vector<double, 2*ELEMENT_DIM> ret;
    for (unsigned i=0; i<ELEMENT_DIM; i++)
    {
        ret(2*i)   = rPhi(i)*D_times_grad_v_dot_n;
        ret(2*i+1) = rPhi(i)*D_times_grad_phi_e_dot_n;
    }

    return ret;
}
#undef COVERAGE_IGNORE


template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void BidomainDg0Assembler<ELEMENT_DIM,SPACE_DIM>::PrepareForAssembleSystem(Vec currentSolution, double time)
{
    mpBidomainPde->SolveCellSystems(currentSolution, time, time+this->mDt);
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void BidomainDg0Assembler<ELEMENT_DIM,SPACE_DIM>::FinaliseAssembleSystem(Vec currentSolution, double currentTime)
{
    if (mFixedExtracellularPotentialNodes.empty())
    {
        // We're not pinning any nodes.
        if (mRowForAverageOfPhiZeroed==INT_MAX)
        {
            // We're not using the 'Average phi_e = 0' method, hence use a null space
            if (!mNullSpaceCreated)
            {
                // No null space set up, so create one and pass it to the linear system
                Vec nullbasis[1];
                nullbasis[0]=DistributedVector::CreateVec(2);
                DistributedVector dist_null_basis(nullbasis[0]);
                DistributedVector::Stripe null_basis_stripe_0(dist_null_basis,0);
                DistributedVector::Stripe null_basis_stripe_1(dist_null_basis,1);
                for (DistributedVector::Iterator index = DistributedVector::Begin();
                     index != DistributedVector::End();
                     ++index)
                {
                    null_basis_stripe_0[index] = 0;
                    null_basis_stripe_1[index] = 1;
                }
                dist_null_basis.Restore();

                this->mpLinearSystem->SetNullBasis(nullbasis, 1);

                VecDestroy(nullbasis[0]);
                mNullSpaceCreated = true;

                //Make a mask to use if we need to shift the external voltage
                VecDuplicate(currentSolution, &mExternalVoltageMask);
                DistributedVector mask(mExternalVoltageMask);
                DistributedVector::Stripe v_m(mask,0);
                DistributedVector::Stripe phi_e(mask,1);
                for (DistributedVector::Iterator index = DistributedVector::Begin();
                     index != DistributedVector::End();
                     ++index)
                {
                    v_m[index] = 0.0;
                    phi_e[index] = 1.0;
                }
                mask.Restore();
            }
            //Try to fudge the solution vector with respect to the external voltage
            //Find the largest absolute value
            double min, max;

#if (PETSC_VERSION_MINOR == 2) //Old API
            PetscInt position;
            VecMax(currentSolution, &position, &max);
            VecMin(currentSolution, &position, &min);
#else
            VecMax(currentSolution, PETSC_NULL, &max);
            VecMin(currentSolution, PETSC_NULL, &min);
#endif
            if ( -min > max )
            {
                //Largest value is negative
                max=min;
            }
            //Standard transmembrane potentials are within +-100 mV
            if (fabs(max) > 500)
            {
#define COVERAGE_IGNORE
                // std::cout<<"warning: shifting phi_e by "<<-max<<"\n";
                //Use mask currentSolution=currentSolution - max*mExternalVoltageMask
#if (PETSC_VERSION_MINOR == 2) //Old API
                max *= -1;
                VecAXPY(&max, mExternalVoltageMask, currentSolution);
#else
                VecAXPY(currentSolution, -max, mExternalVoltageMask);
#endif
#undef COVERAGE_IGNORE
            }
        }
        else
        {
            // mRowForAverageOfPhiZeroed!=INT_MAX, i.e. we're using the 'Average phi_e = 0; method
            // Set average phi_e to zero
            unsigned matrix_size = this->mpLinearSystem->GetSize();
            if (!this->mMatrixIsAssembled)
            {

                // Set the mRowForAverageOfPhiZeroed-th matrix row to 0 1 0 1 ...
                this->mpLinearSystem->ZeroMatrixRow(mRowForAverageOfPhiZeroed);
                for (unsigned col_index=0; col_index<matrix_size; col_index++)
                {
                    if (col_index%2 == 1)
                    {
                        this->mpLinearSystem->SetMatrixElement(mRowForAverageOfPhiZeroed, col_index, 1);
                    }
                }
                this->mpLinearSystem->AssembleFinalLhsMatrix();

            }
            // Set the mRowForAverageOfPhiZeroed-th rhs vector row to 0
            this->mpLinearSystem->SetRhsVectorElement(mRowForAverageOfPhiZeroed, 0);

            this->mpLinearSystem->AssembleRhsVector();
        }
    }
}


template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
BidomainDg0Assembler<ELEMENT_DIM,SPACE_DIM>::BidomainDg0Assembler(
            AbstractMesh<ELEMENT_DIM,SPACE_DIM>* pMesh,
            BidomainPde<SPACE_DIM>* pPde,
            BoundaryConditionsContainer<ELEMENT_DIM, SPACE_DIM, 2>* pBcc,
            unsigned numQuadPoints)
    : AbstractAssembler<ELEMENT_DIM,SPACE_DIM,2>(),
      BaseClassType(numQuadPoints),
      AbstractDynamicAssemblerMixin<ELEMENT_DIM,SPACE_DIM,2>()
{
    assert(pPde != NULL);
    assert(pMesh != NULL);
    assert(pBcc != NULL);

    mpBidomainPde = pPde;
    this->SetMesh(pMesh);

    this->mpBoundaryConditions = pBcc;

    mNullSpaceCreated = false;

    this->SetMatrixIsConstant();

    mRowForAverageOfPhiZeroed = INT_MAX; //this->mpLinearSystem->GetSize() - 1;
    
    mpConfig = HeartConfig::Instance();
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
BidomainDg0Assembler<ELEMENT_DIM,SPACE_DIM>::~BidomainDg0Assembler()
{
    if (mNullSpaceCreated)
    {
        VecDestroy(mExternalVoltageMask);
    }
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void BidomainDg0Assembler<ELEMENT_DIM,SPACE_DIM>::SetFixedExtracellularPotentialNodes(
            std::vector<unsigned> fixedExtracellularPotentialNodes)
{
    for (unsigned i=0; i<fixedExtracellularPotentialNodes.size(); i++)
    {
        if (fixedExtracellularPotentialNodes[i] >= this->mpMesh->GetNumNodes() )
        {
            EXCEPTION("Fixed node number must be less than total number nodes");
        }
    }

    mFixedExtracellularPotentialNodes = fixedExtracellularPotentialNodes;

    for (unsigned i=0; i<mFixedExtracellularPotentialNodes.size(); i++)
    {
        ConstBoundaryCondition<SPACE_DIM>* p_boundary_condition
         = new ConstBoundaryCondition<SPACE_DIM>(0.0);

        Node<SPACE_DIM>* p_node = this->mpMesh->GetNode(mFixedExtracellularPotentialNodes[i]);

        this->mpBoundaryConditions->AddDirichletBoundaryCondition(p_node, p_boundary_condition, 1);
    }
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void BidomainDg0Assembler<ELEMENT_DIM,SPACE_DIM>::SetRowForAverageOfPhiZeroed(unsigned row)
{
    // Row should be odd in C++-like indexing
    if (row % 2 == 0)
    {
        EXCEPTION("Row for applying the constraint 'Average of phi_e = zero' should be odd in C++ like indexing");
    }

    mRowForAverageOfPhiZeroed = row;
}

// Explicit instantiation

template class BidomainDg0Assembler<1,1>;
template class BidomainDg0Assembler<2,2>;
template class BidomainDg0Assembler<3,3>;

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