CardiacProblem.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/problem/timed/HeatProblem.hpp"
#include "ode/ionicModels/AllIonicModels.hpp"
 
class CardiacProblem : public HeatProblem
{
  public:
 
    struct UnknownsName
    {
      static constexpr const char* vm = "Transmembrane voltage (mV)";
      static constexpr const char* ue = "Extracellular potential (mV)";
    };
 
  public:
 
    explicit CardiacProblem(Geometry* g, InputParameters* params = nullptr);
 
    ~CardiacProblem() override;
 
    // ---------------------------------------------------------------------------
    // Common problem definition: homogeneous neumann boundary conditions (ie, do nothing)
    // Initial transmembrane voltage from ionic models
 
    virtual CepsVector<Unknown*>
    getTMVUnknowns() const = 0;
 
    virtual CepsVector<Unknown*>
    getCardiacUnknowns() const = 0;
 
    void
    getInitialCondition(DHVecPtr v) const override;
 
    CepsVector<AbstractIonicModel*>
    getIonicModels() const;
 
    ScalarField<DegreeOfFreedom>*
    getAm() const;
 
    ScalarField<DegreeOfFreedom>*
    getCm() const;
 
    TensorField<GeomCell>*
    getSigmaI() const;
 
    TensorField<GeomCell>*
    getSigmaE() const;
 
    const CepsSet<CepsAttribute>&
    getTissueAttributes() const;
 
    void
    initializeEquation() override;
 
    void
    initializeCm();
 
    void
    initializeAm();
 
    void
    initializeIonicModels();
 
    // This is an overload with no argument, in case there is only a single conductivity 
    // same mesh cells
    virtual void
    initializeConductivities();
 
    // Suffix must be provided and non empty if different conducitivity fields must be defined on the 
    // same mesh cells
    virtual void
    initializeConductivities(
      CepsString sigmaIOpts, 
      CepsString sigmaEOpts,
      TensorField<GeomCell>*& sigmaI, 
      TensorField<GeomCell>*& sigmaE,
      CepsString fiberOptions,
      CepsString suffix=""
    );
 
    virtual void
    initializeStimulations();
 
    void
    defineBoundaryConditions() override;
 
    void
    defineSourceTerms() override;
 
  protected:
 
    void
    setupWithParameters(InputParameters* params) override;
 
    void
    createFibersAndConductivities(
      CepsString              fiberOptions,
      TensorField<GeomCell>*& sigmaI, 
      TensorField<GeomCell>*& sigmaE,
      CepsString              suffix=""
    );
 
    class FiberAligner : public TensorSAFunc
    {
 
      public:
 
        FiberAligner(
          VectorSAFunc* fL, 
          VectorSAFunc* fT, 
          VectorSAFunc* fN, 
          TensorSAFunc* sT = nullptr,
          VectorSAFunc* sV = nullptr
        ); 
 
        CepsMathTensor
        eval(CepsStandardArgs args) override;
 
        CepsEnum
        getFlags() const override;
 
      private:
 
        VectorSAFunc* m_fL; 
        VectorSAFunc* m_fT; 
        VectorSAFunc* m_fN; 
        TensorSAFunc* m_sT; 
        VectorSAFunc* m_sV; 
 
    }; 
 
 
  protected:
 
    // ------------------------
    // Input parameters
 
    CepsString m_CmOptions;       
    CepsString m_AmOptions;       
    CepsString m_ionOptions;      
    CepsString m_fibersOptions;   
    CepsString m_sigmaIOptions;   
    CepsString m_sigmaEOptions;   
    CepsString m_volFracOptions;  
    CepsString m_volFracItpFileI; 
    CepsString m_volFracItpFileE; 
    CepsString m_stimOptions;     
    CepsString m_bcStimOptions;   
    
    // ------------------------
    // Tissue properties
 
    CepsSet<CepsAttribute> m_tissueAttributes; 
 
    ScalarField<DegreeOfFreedom>* m_Cm; 
    ScalarField<DegreeOfFreedom>* m_Am; 
 
    CepsVector<AbstractIonicModel*> m_ionicModels; 
 
    TensorField<GeomCell>* m_sigmaI;  
    TensorField<GeomCell>* m_sigmaE;  
    ScalarField<GeomCell>* m_volFrac; 
 
};