BidomainRoth.h

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///////////////////////////////////////////////////////////////////////////////
//
// File BidomainRoth.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).
//
// License for the specific language governing rights and limitations under
// 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:
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// The above copyright notice and this permission notice shall be included
// in all copies or substantial portions of the Software.
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// THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
// OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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//
// Description: Bidomain cardiac electrophysiology model - Roth formulation.
//
///////////////////////////////////////////////////////////////////////////////

#ifndef NEKTAR_SOLVERS_ADRSOLVER_EQUATIONSYSTEMS_BIDOMAINROTH_H
#define NEKTAR_SOLVERS_ADRSOLVER_EQUATIONSYSTEMS_BIDOMAINROTH_H

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

namespace Nektar
{


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

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

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

    /// Desctructor
    virtual ~BidomainRoth();

protected:
    /// Constructor
    BidomainRoth(
            const LibUtilities::SessionReaderSharedPtr& pSession);

    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;

    std::vector<StimulusSharedPtr> m_stimulus;

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

    NekDouble m_chi;
    NekDouble m_capMembrane;

    /// Stimulus current
    NekDouble m_stimDuration;

    void LoadStimuli();
};

}

#endif