CellModel.h

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///////////////////////////////////////////////////////////////////////////////
//
// File CellModel.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: Cell model base class.
//
///////////////////////////////////////////////////////////////////////////////
 
#ifndef NEKTAR_SOLVERS_ADRSOLVER_CELLMODELS_CELLMODEL
#define NEKTAR_SOLVERS_ADRSOLVER_CELLMODELS_CELLMODEL
 
#include <LibUtilities/BasicUtils/NekFactory.hpp>
#include <LibUtilities/BasicUtils/SessionReader.h>
#include <LibUtilities/BasicUtils/SharedArray.hpp>
//#include <SpatialDomains/SpatialData.h>
#include <MultiRegions/ExpList.h>
#include <StdRegions/StdNodalTriExp.h>
#include <StdRegions/StdNodalTetExp.h>
#include <SolverUtils/Core/Misc.h>
 
namespace Nektar
{
    // Forward declaration
    class CellModel;
 
    typedef std::vector<std::pair<std::string, std::string> > SummaryList;
 
    /// A shared pointer to an EquationSystem object
    typedef std::shared_ptr<CellModel> CellModelSharedPtr;
    /// Datatype of the NekFactory used to instantiate classes derived from
    /// the EquationSystem class.
    typedef LibUtilities::NekFactory< std::string, CellModel,
                const LibUtilities::SessionReaderSharedPtr&,
                const MultiRegions::ExpListSharedPtr&> CellModelFactory;
    CellModelFactory& GetCellModelFactory();
 
    /// Cell model base class.
    class CellModel
    {
    public:
        CellModel(const LibUtilities::SessionReaderSharedPtr& pSession,
                const MultiRegions::ExpListSharedPtr& pField);
 
        virtual ~CellModel() {}
 
        /// Initialise the cell model storage and set initial conditions
        void Initialise();
 
        /// Time integrate the cell model by one PDE timestep
        void TimeIntegrate(
                const Array<OneD, const Array<OneD, NekDouble> > &inarray,
                      Array<OneD,       Array<OneD, NekDouble> > &outarray,
                const NekDouble time);
 
        /// Compute the derivatives of cell model variables
        void Update(
                const Array<OneD, const  Array<OneD, NekDouble> >&inarray,
                      Array<OneD,        Array<OneD, NekDouble> >&outarray,
                const NekDouble time)
        {
            v_Update(inarray, outarray, time);
        }
 
        /// Print a summary of the cell model
        void GenerateSummary(SummaryList& s)
        {
            v_GenerateSummary(s);
        }
 
        unsigned int GetNumCellVariables()
        {
            return m_nvar;
        }
 
        std::string GetCellVarName(unsigned int idx)
        {
            return v_GetCellVarName(idx);
        }
 
        Array<OneD, NekDouble> GetCellSolutionCoeffs(unsigned int idx);
 
        Array<OneD, NekDouble> GetCellSolution(unsigned int idx);
 
    protected:
        /// Session
        LibUtilities::SessionReaderSharedPtr m_session;
        /// Transmembrane potential field from PDE system
        MultiRegions::ExpListSharedPtr m_field;
        /// Number of physical points.
        int m_nq;
        /// Number of variables in cell model (inc. transmembrane voltage)
        int m_nvar;
        /// Timestep for pde model
        NekDouble m_lastTime;
        /// Number of substeps to take
        int m_substeps;
 
        /// Cell model solution variables
        Array<OneD, Array<OneD, NekDouble> > m_cellSol;
        /// Cell model integration workspace
        Array<OneD, Array<OneD, NekDouble> > m_wsp;
 
        /// Flag indicating whether nodal projection in use
        bool m_useNodal;
        /// StdNodalTri for cell model calculations
        StdRegions::StdNodalTriExpSharedPtr m_nodalTri;
        StdRegions::StdNodalTetExpSharedPtr m_nodalTet;
        /// Temporary array for nodal projection
        Array<OneD, Array<OneD, NekDouble> > m_nodalTmp;
 
        /// Indices of cell model variables which are concentrations
        std::vector<int> m_concentrations;
        /// Indices of cell model variables which are gates
        std::vector<int> m_gates;
        /// Storage for gate tau values
        Array<OneD, Array<OneD, NekDouble> > m_gates_tau;
 
        virtual void v_Update(
                const Array<OneD, const  Array<OneD, NekDouble> >&inarray,
                      Array<OneD,        Array<OneD, NekDouble> >&outarray,
                const NekDouble time) = 0;
 
        virtual void v_GenerateSummary(SummaryList& s) = 0;
 
        virtual std::string v_GetCellVarName(unsigned int idx)
        {
            return "Var" + boost::lexical_cast<std::string>(idx);
        }
 
        virtual void v_SetInitialConditions() = 0;
 
        void LoadCellModel();
    };
 
}
 
#endif /* CELLMODEL_H_ */