CRN98.hpp

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/*~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   This file is part of CEPS.
 
   CEPS is free software: you can redistribute it and/or modify
   it under the terms of the GNU General Public License as published by
   the Free Software Foundation, either version 3 of the License, or
   (at your option) any later version.
 
   CEPS 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 General Public License for more details.
 
   You should have received a copy of the GNU General Public License
   along with CEPS (see file LICENSE at root of project).
   If not, see <https://www.gnu.org/licenses/>.
 
 
   Copyright 2019-2024 Inria, Universite de Bordeaux
 
   Authors, in alphabetical order:
 
     Pierre-Elliott BECUE, Florian CARO, Yves COUDIERE(*), Andjela DAVIDOVIC, 
     Charlie DOUANLA-LONTSI, Marc FUENTES, Mehdi JUHOOR, Michael LEGUEBE(*), 
     Pauline MIGERDITICHAN, Valentin PANNETIER(*), Nejib ZEMZEMI.
     * : currently active authors
 
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~*/
#pragma once
 
#include "ode/ionicModels/AbstractIonicModel.hpp"
#include "pde/problem/AbstractPdeProblem.hpp"
 
class CRN98 : public AbstractIonicModel
{
 
  public :
 
    CRN98(
      Unknown*                      u, 
      const CepsSet<CepsAttribute>& attrs={},
      InputParameters*              params=nullptr
    );
 
    virtual ~CRN98() = default;
 
    void 
    getInitialCondition(CepsReal* v, CepsReal* y) const final;
 
    void 
    computeRates(
      CepsReal         t,
      CepsReal*        y, 
      CepsReal*        v, 
      CepsReal*        dtyL, 
      CepsReal*        dtyNL,
      CepsReal*        dtv, 
      DegreeOfFreedom* dof
    ) const final;
 
    CepsReal
    convertCurrentFromCepsUnit(const CepsReal& i) const override;
 
    CepsReal
    convertCmFromCepsUnit(const CepsReal& cm) const override;
 
    CepsReal
    convertCmToCepsUnit(const CepsReal& cm) const override;
 
 
  protected: 
 
    void
    setupWithParameters(InputParameters* p, FunctionDictionary* dico);
 
 
  protected :
 
    CepsReal m_cellSurface; 
 
    // aliases for constants
    static constexpr const CepsInt _R        = 0;  
    static constexpr const CepsInt _T        = 1;  
    static constexpr const CepsInt _F        = 2;  
    static constexpr const CepsInt _vcell    = 3;  
    static constexpr const CepsInt _vi       = 4;  
    static constexpr const CepsInt _vup      = 5;  
    static constexpr const CepsInt _vrel     = 6;  
    static constexpr const CepsInt _ko       = 7;  
    static constexpr const CepsInt _nao      = 8;  
    static constexpr const CepsInt _cao      = 9;  
    static constexpr const CepsInt _gna      = 10; 
    static constexpr const CepsInt _gk1      = 11; 
    static constexpr const CepsInt _gto      = 12; 
    static constexpr const CepsInt _gkr      = 13; 
    static constexpr const CepsInt _gks      = 14; 
    static constexpr const CepsInt _gcal     = 15; 
    static constexpr const CepsInt _gbca     = 16; 
    static constexpr const CepsInt _gbna     = 17; 
    static constexpr const CepsInt _inakmax  = 18; 
    static constexpr const CepsInt _inacamax = 19; 
    static constexpr const CepsInt _icapmax  = 20; 
    static constexpr const CepsInt _iupmax   = 21; 
    static constexpr const CepsInt _kq10     = 22; 
    static constexpr const CepsInt _sigma    = 23; 
    static constexpr const CepsInt _kmnai    = 24; 
    static constexpr const CepsInt _kmko     = 25; 
    static constexpr const CepsInt _kmna     = 26; 
    static constexpr const CepsInt _kmca     = 27; 
    static constexpr const CepsInt _ksat     = 28; 
    static constexpr const CepsInt _krel     = 29; 
    static constexpr const CepsInt _kup      = 30; 
    static constexpr const CepsInt _caupmax  = 31; 
    static constexpr const CepsInt _cmdnmax  = 32; 
    static constexpr const CepsInt _trpnmax  = 33; 
    static constexpr const CepsInt _csqnmax  = 34; 
    static constexpr const CepsInt _kmcmdn   = 35; 
    static constexpr const CepsInt _kmtrpn   = 36; 
    static constexpr const CepsInt _kmcsqn   = 37; 
    static constexpr const CepsInt _taufca   = 38; 
    static constexpr const CepsInt _tautr    = 39; 
    static constexpr const CepsInt _gbk      = 40; 
    static constexpr const CepsInt _gamma    = 41; 
    static constexpr const CepsInt _tauu     = 42; 
 
    // State var indices, same order as cellml
    static constexpr const CepsInt _nai   = 0;  
    static constexpr const CepsInt _m     = 1;  
    static constexpr const CepsInt _h     = 2;  
    static constexpr const CepsInt _j     = 3;  
    static constexpr const CepsInt _ki    = 4;  
    static constexpr const CepsInt _oa    = 5;  
    static constexpr const CepsInt _oi    = 6;  
    static constexpr const CepsInt _ua    = 7;  
    static constexpr const CepsInt _ui    = 8;  
    static constexpr const CepsInt _xr    = 9;  
    static constexpr const CepsInt _xs    = 10; 
    static constexpr const CepsInt _cai   = 11; 
    static constexpr const CepsInt _d     = 12; 
    static constexpr const CepsInt _f     = 13; 
    static constexpr const CepsInt _fca   = 14; 
    static constexpr const CepsInt _carel = 15; 
    static constexpr const CepsInt _u     = 16; 
    static constexpr const CepsInt _v     = 17; 
    static constexpr const CepsInt _w     = 18; 
    static constexpr const CepsInt _caup  = 19; 
 
};