AbstractIonicModel.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 "linearAlgebra/DistributedHaloVector.hpp"
#include "pde/common/Unknown.hpp"
#include "pde/common/DegreeOfFreedom.hpp"
#include "pde/common/functions/SourceTerm.hpp"
 
class IonicSolver;
 
class AbstractIonicModel : public ceps::HoldsAttributes
{
 
  public:
 
    virtual ~AbstractIonicModel();
 
    // Model properties ============================================================================
 
    CepsString 
    getName() const;
 
    Unknown* 
    getUnknown() const;
 
    ScalarField<DegreeOfFreedom>*
    getCm() const;
 
    void
    setCm(ScalarField<DegreeOfFreedom>*);
 
    CepsReal
    getPaperCm(CepsBool cepsUnit) const;
 
    CepsReal
    getPaperStim() const;
 
    void
    addStimulation(ScalarSourceTerm* stim);
 
    CepsReal
    getStimulation(DegreeOfFreedom* x, CepsReal t) const;
 
    virtual CepsUInt 
    getNbStateVariables() const;
 
    CepsString
    getStateVariableName(CepsUInt i) const;
 
    virtual void 
    getInitialCondition(CepsReal* v, CepsReal* y) const = 0;
 
    virtual void 
    computeRates(
      CepsReal         t,
      CepsReal*        y, 
      CepsReal*        v, 
      CepsReal*        dtyL, 
      CepsReal*        dtyNL,
      CepsReal*        dtv, 
      DegreeOfFreedom* dof
    ) const = 0;
 
    // Unit conversion methods =====================================================================
 
    virtual CepsReal
    convertVoltageFromCepsUnit(const CepsReal& v) const;
 
    virtual CepsReal
    convertVoltageToCepsUnit(const CepsReal& v) const;
 
    virtual CepsReal
    convertDtvToCepsUnit(const CepsReal& dtv) const;
 
    virtual CepsReal
    convertCurrentFromCepsUnit(const CepsReal& i) const;
 
    virtual CepsReal
    convertCmFromCepsUnit(const CepsReal& cm) const;
 
    virtual CepsReal
    convertCmToCepsUnit(const CepsReal& cm) const;
 
    // Solver linking ==============================================================================
 
    void
    setLinkedSolver(IonicSolver* solver);
 
    IonicSolver*
    getLinkedSolver() const;
 
 
  protected:
 
    AbstractIonicModel(
      Unknown*                      u, 
      const CepsSet<CepsAttribute>& attrs={}
    );
 
    CepsReal
    getCmInternal(CepsReal t, DegreeOfFreedom* dof) const;
 
    CepsReal
    sigmoid(CepsReal x, CepsReal c, CepsReal k) const;
  
    CepsReal
    gaussian(CepsReal x, CepsReal c, CepsReal s) const;
 
    CepsReal
    uOverExpm1u(CepsReal u) const;
 
  protected:
 
    Unknown*                      m_unknown;       
    CepsReal*                     m_constants;     
    CepsReal*                     m_dconstants;    
    ScalarField<DegreeOfFreedom>* m_cm;            
    CepsReal                      m_paperCm;       
    CepsReal                      m_paperStim;     
    CepsVector<ScalarSourceTerm*> m_stims;         
    CepsUInt                      m_nStateVars;    
    CepsVector<CepsString>        m_stateVarNames; 
    CepsString                    m_name;          
    IonicSolver*                  m_solver;        
};