ImplicitCardiacMechanicsAssembler.hpp

/*

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/>.

*/


#ifndef IMPLICITCARDIACMECHANICSASSEMBLER_HPP_
#define IMPLICITCARDIACMECHANICSASSEMBLER_HPP_

#include "NonlinearElasticityAssembler.hpp"
#include "QuadraticBasisFunction.hpp"
#include "LinearBasisFunction.hpp"
#include "NhsSystemWithImplicitSolver.hpp"
#include "NashHunterPoleZeroLaw.hpp"
#include "LogFile.hpp"
#include <cfloat>


template<unsigned DIM>
class ImplicitCardiacMechanicsAssembler : public NonlinearElasticityAssembler<DIM>
{
friend class TestImplicitCardiacMechanicsAssembler;

private:
    static const unsigned STENCIL_SIZE = NonlinearElasticityAssembler<DIM>::STENCIL_SIZE;
    static const unsigned NUM_NODES_PER_ELEMENT = NonlinearElasticityAssembler<DIM>::NUM_NODES_PER_ELEMENT;
    static const unsigned NUM_VERTICES_PER_ELEMENT = NonlinearElasticityAssembler<DIM>::NUM_VERTICES_PER_ELEMENT;
    std::vector<NhsSystemWithImplicitSolver> mCellMechSystems;

    std::vector<double> mLambdaLastTimeStep;

    std::vector<double> mLambda;

    double mCurrentTime;
    double mNextTime;
    double mOdeTimestep;

    bool mAllocatedMaterialLawMemory;

    unsigned mTotalQuadPoints;

public:
    ImplicitCardiacMechanicsAssembler(QuadraticMesh<DIM>* pQuadMesh,
                                      std::string outputDirectory,
                                      std::vector<unsigned>& rFixedNodes,
                                      AbstractIncompressibleMaterialLaw<DIM>* pMaterialLaw = NULL);

    ~ImplicitCardiacMechanicsAssembler();

    unsigned GetTotalNumQuadPoints();

    GaussianQuadratureRule<DIM>* GetQuadratureRule();

    void SetIntracellularCalciumConcentrations(std::vector<double>& caI);

    std::vector<double>& rGetLambda();

    void Solve(double time, double nextTime, double odeTimestep);


private:

    void AssembleOnElement(Element<DIM, DIM>& rElement,
                           c_matrix<double,STENCIL_SIZE,STENCIL_SIZE>& rAElem,
                           c_matrix<double,STENCIL_SIZE,STENCIL_SIZE>& rAElemPrecond,
                           c_vector<double,STENCIL_SIZE>& rBElem,
                           bool assembleResidual,
                           bool assembleJacobian);
};


//public:
//    std::vector<std::vector<unsigned> > mNodesContainedInElement;
//
//    void ComputeElementsContainingNodes(TetrahedralMesh<DIM,DIM>* pOtherMesh)
//    {
//        assert(DIM==2);
//
//        mNodesContainedInElement.resize(this->mpMesh->n_active_cells());
//
//        unsigned element_number = 0;
//        typename DoFHandler<DIM>::active_cell_iterator  element_iter = this->mDofHandler.begin_active();
//
//        while (element_iter!=this->mDofHandler.end())
//        {
//            double xmin = element_iter->vertex(0)(0);
//            double xmax = element_iter->vertex(1)(0);
//            double ymin = element_iter->vertex(0)(1);
//            double ymax = element_iter->vertex(3)(1);
//
//            assert(element_iter->vertex(2)(0)==xmax);
//            assert(element_iter->vertex(2)(1)==ymax);
//
//            for(unsigned i=0; i<pOtherMesh->GetNumNodes(); i++)
//            {
//                double x = pOtherMesh->GetNode(i)->rGetLocation()[0];
//                double y = pOtherMesh->GetNode(i)->rGetLocation()[1];
//                if((x>=xmin) && (x<=xmax) && (y>=ymin) && (y<=ymax))
//                {
//                    mNodesContainedInElement[element_number].push_back(i);
//                }
//            }
//
//            element_iter++;
//            element_number++;
//        }
//    }
//
//    void WriteLambda(std::string directory, std::string fileName)
//    {
//        OutputFileHandler handler(directory,false);
//        out_stream p_file = handler.OpenOutputFile(fileName);
//
//        std::vector<std::vector<double> > quad_point_posns
//           = FiniteElasticityTools<DIM>::GetQuadPointPositions(*(this->mpMesh), this->GetNumQuadPointsInEachDimension());
//
//
//        for(unsigned i=0; i<quad_point_posns.size(); i++)
//        {
//            (*p_file) << quad_point_posns[i][0] << " " << quad_point_posns[i][1] << " "
//                      << mCellMechSystems[i].GetLambda() << "\n";
//        }
//    }
//
//
//    void CalculateCinverseAtNodes(TetrahedralMesh<DIM,DIM>* pOtherMesh, std::vector<std::vector<double> >& rValuesAtNodes)
//    {
//        assert(DIM==2);
//        rValuesAtNodes.resize(pOtherMesh->GetNumNodes());
//
//        unsigned element_number = 0;
//
//        static QTrapez<DIM>   trapezoid_quadrature_formula; //trapeziod rule - values at NODES
//        const unsigned n_q_points = trapezoid_quadrature_formula.n_quadrature_points;
//
//        FEValues<DIM> fe_values(this->mFeSystem, trapezoid_quadrature_formula,
//                                UpdateFlags(update_values    |
//                                            update_gradients |
//                                            update_q_points  |     // needed for interpolating u and u' on the quad point
//                                            update_JxW_values));
//
//        std::vector< Vector<double> >                  local_solution_values(n_q_points);
//        std::vector< std::vector< Tensor<1,DIM> > >    local_solution_gradients(n_q_points);
//
//        for (unsigned q_point=0; q_point<n_q_points; q_point++)
//        {
//            local_solution_values[q_point].reinit(DIM+1);
//            local_solution_gradients[q_point].resize(DIM+1);
//        }
//
//
//        Tensor<2,DIM> identity;
//        for (unsigned i=0; i<DIM; i++)
//        {
//            for (unsigned j=0; j<DIM; j++)
//            {
//                identity[i][j] = i==j ? 1.0 : 0.0;
//            }
//        }
//
//        typename DoFHandler<DIM>::active_cell_iterator  element_iter = this->mDofHandler.begin_active();
//
//        while (element_iter!=this->mDofHandler.end())
//        {
//            double xmin = element_iter->vertex(0)(0);
//            double xmax = element_iter->vertex(1)(0);
//            double ymin = element_iter->vertex(0)(1);
//            double ymax = element_iter->vertex(3)(1);
//            assert(element_iter->vertex(2)(0)==xmax);
//            assert(element_iter->vertex(2)(1)==ymax);
//
//            fe_values.reinit(element_iter); // compute fe values for this element
//            fe_values.get_function_values(this->mCurrentSolution, local_solution_values);
//            fe_values.get_function_grads(this->mCurrentSolution, local_solution_gradients);
//
//            std::vector<Point<DIM> > quad_points =fe_values.get_quadrature_points();
//
//
//            AbstractIncompressibleMaterialLaw<DIM>* p_material_law = this->GetMaterialLawForElement(element_iter);
//
//            std::vector<Tensor<2,DIM> > inv_C_at_nodes(4);// 4=2^DIM
//
//            for (unsigned q_point=0; q_point<n_q_points; q_point++)
//            {
//                const std::vector< Tensor<1,DIM> >& grad_u_p = local_solution_gradients[q_point];
//                static Tensor<2,DIM> F;
//                static Tensor<2,DIM> C;
//
//                for (unsigned i=0; i<DIM; i++)
//                {
//                    for (unsigned j=0; j<DIM; j++)
//                    {
//                        F[i][j] = identity[i][j] + grad_u_p[i][j];
//                    }
//                }
//
//                C = transpose(F) * F;
//                inv_C_at_nodes[q_point] = invert(C);
//            }
//
//
//
//
//
//            for(unsigned j=0; j<mNodesContainedInElement[element_number].size(); j++)
//            {
//                unsigned node_num = mNodesContainedInElement[element_number][j];
//                double x = pOtherMesh->GetNode(node_num)->rGetLocation()[0];
//                double y = pOtherMesh->GetNode(node_num)->rGetLocation()[1];
//
//                assert((x>=xmin) && (x<=xmax) && (y>=ymin) && (y<=ymax));
//                double xi  = (x-xmin)/(xmax-xmin);
//                double eta = (y-ymin)/(ymax-ymin);
//                assert((0<=xi) && (x<=1) && (0<=eta) && (eta<=1));
//
//                rValuesAtNodes[node_num][0] = InterpolateCinverse(xi,eta,inv_C_at_nodes,0,0);
//                rValuesAtNodes[node_num][1] = InterpolateCinverse(xi,eta,inv_C_at_nodes,0,1);
//                rValuesAtNodes[node_num][2] = InterpolateCinverse(xi,eta,inv_C_at_nodes,1,1);
//            }
//
//
//            element_iter++;
//            element_number++;
//        }
//    }
//
//
//    double InterpolateCinverse(const double xi, const double eta,
//                               const std::vector<Tensor<2,DIM> >& inverseCAtNodes,
//                               unsigned i, unsigned j)
//    {
//        return    inverseCAtNodes[0][i][j] * (1-xi) * (1-eta)
//                + inverseCAtNodes[1][i][j] * (1-xi) *   eta
//                + inverseCAtNodes[2][i][j] *   xi   * (1-eta)
//                + inverseCAtNodes[3][i][j] *   xi   *   eta;
//    }


#endif /*IMPLICITCARDIACMECHANICSASSEMBLER_HPP_*/

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