Bidomain.h

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///////////////////////////////////////////////////////////////////////////////
//
// File Bidomain.h
//
// For more information, please see: http://www.nektar.info
//
// The MIT License
//
// Copyright (c) 2006 Division of Applied Mathematics, Brown University (USA),
// Department of Aeronautics, Imperial College London (UK), and Scientific
// Computing and Imaging Institute, University of Utah (USA).
//
// Permission is hereby granted, free of charge, to any person obtaining a
// copy of this software and associated documentation files (the "Software"),
// to deal in the Software without restriction, including without limitation
// the rights to use, copy, modify, merge, publish, distribute, sublicense,
// and/or sell copies of the Software, and to permit persons to whom the
// Software is furnished to do so, subject to the following conditions:
//
// The above copyright notice and this permission notice shall be included
// in all copies or substantial portions of the Software.
//
// THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
// OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
// FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
// THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
// LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
// FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
// DEALINGS IN THE SOFTWARE.
//
// Description: Bidomain cardiac electrophysiology homogenised model.
//
///////////////////////////////////////////////////////////////////////////////

#ifndef NEKTAR_SOLVERS_ADRSOLVER_EQUATIONSYSTEMS_BIDOMAIN_H
#define NEKTAR_SOLVERS_ADRSOLVER_EQUATIONSYSTEMS_BIDOMAIN_H

#include <SolverUtils/UnsteadySystem.h>
#include <CardiacEPSolver/CellModels/CellModel.h>

using namespace Nektar::SolverUtils;

namespace Nektar
{


    /// A model for cardiac conduction.
    class Bidomain : public UnsteadySystem
    {
    public:
        friend class MemoryManager<Bidomain>;

        /// Creates an instance of this class
        static EquationSystemSharedPtr create(
            const LibUtilities::SessionReaderSharedPtr& pSession,
            const SpatialDomains::MeshGraphSharedPtr& pGraph)
        {
            EquationSystemSharedPtr p = MemoryManager<Bidomain>
                ::AllocateSharedPtr(pSession, pGraph);
            p->InitObject();
            return p;
        }

        /// Name of class
        static std::string className;

        /// Desctructor
        virtual ~Bidomain();

    protected:
        /// Constructor
        Bidomain(
            const LibUtilities::SessionReaderSharedPtr& pSession,
            const SpatialDomains::MeshGraphSharedPtr& pGraph);

        virtual void v_InitObject();

        /// Solve for the diffusion term.
        void DoImplicitSolve(
                const Array<OneD, const Array<OneD, NekDouble> >&inarray,
                      Array<OneD, Array<OneD, NekDouble> >&outarray,
                      NekDouble time,
                      NekDouble lambda);

        /// Computes the reaction terms \f$f(u,v)\f$ and \f$g(u,v)\f$.
        void DoOdeRhs(
                const Array<OneD, const  Array<OneD, NekDouble> >&inarray,
                      Array<OneD,        Array<OneD, NekDouble> >&outarray,
                const NekDouble time);

        /// Sets a custom initial condition.
        virtual void v_SetInitialConditions(NekDouble initialtime,
                                bool dumpInitialConditions,
                                const int domain);

        /// Prints a summary of the model parameters.
        virtual void v_GenerateSummary(SummaryList& s);

    private:
        /// Cell model.
        CellModelSharedPtr m_cell;

        NekDouble m_chi, m_capMembrane, m_sigmaix, m_sigmaiy, m_sigmaiz, m_sigmaex, m_sigmaey, m_sigmaez; 

        StdRegions::VarCoeffMap m_vardiffi;
        StdRegions::VarCoeffMap m_vardiffie;

    Array<OneD, Array<OneD, NekDouble> > tmp1;
    Array<OneD, Array<OneD, NekDouble> > tmp2;
    Array<OneD, Array<OneD, NekDouble> > tmp3;

        /// Stimulus current
        NekDouble m_stimDuration;
    };

}

#endif