IonicSolver.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 "pde/common/AbstractDiscretization.hpp"
#include "pde/common/functions/Field.hpp"
#include "ode/solver/AbstractOdeSolver.hpp"
#include "ode/ionicModels/AbstractIonicModel.hpp"
 
class IonicSolver
{
 
 
  public:
 
    using EvolFunction = ceps::Function<void(CepsReal,CepsReal*,CepsReal*,CepsUInt)>;
 
  public:
 
    IonicSolver(
      CepsString              opts, 
      AbstractIonicModel*     m, 
      AbstractDiscretization* discr
    );
  
    ~IonicSolver ();
  
    // Interface with pde ==========================================================================
 
    void
    setActionPotential(DHVecPtr vPde);
 
    void
    takeOneStep(CepsReal t, CepsReal dt, DHVecPtr vPde);
  
    void
    takeOneSubStep(CepsReal t, CepsReal dt, DHVecPtr vPde);
  
    void 
    addDtv(DHVecPtr dtv, CepsReal t=0) const;
 
    void 
    fillPdeVm(DHVecPtr vPde) const;
 
    CepsReal
    getVm(CepsBool convert) const;
 
    CepsReal*
    getStates() const;
 
    CepsReal*
    getDtv() const;
 
    CepsUInt
    getNbMultiSteps() const;
 
  protected:
 
    void 
    computeIndexMapping();
 
    void
    createSolvers(CepsString opts);
 
    void
    initializeSolver();
 
    void
    computeModelRates(CepsReal t, CepsReal* y);
 
    void
    computeRatesLin(CepsReal t, CepsReal* w, CepsReal* dtw, CepsUInt n);
 
    void
    computeRatesNonLin(CepsReal t, CepsReal* w, CepsReal* dtw, CepsUInt n);
 
 
  protected :
 
    AbstractIonicModel* m_model; 
    EvolFunction*       m_fLin;  
    EvolFunction*       m_fNLin; 
 
    // Spatial discretization is needed to determine on which rows the ionic current will be added
    AbstractDiscretization* m_sDiscr; 
 
    AbstractOdeSolver *m_solver;  
 
    // Data
    CepsReal* m_y;       
    CepsReal* m_dtyLin;  
    CepsReal* m_dtyNLin; 
    CepsReal* m_v;       
    CepsReal* m_dtv; 
 
    CepsBool m_tauOk; 
 
    // Ptr on ptr because we perform rotations between several arrays in multistep methods
    DHVecPtr* m_vPde; 
 
    CepsVector<CepsIndex> m_localToGlobal; 
 
    CepsUInt m_size; 
 
};