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// ______ ______ _ _ _____ ______ |
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// | ____| ____| | (_)/ ____| | ____| |
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// | |__ | |__ | | _| (___ ___| |__ |
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// | __| | __| | | | |\___ \ / __| __| |
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// | | | |____| |____| |____) | (__| |____ |
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// |_| |______|______|_|_____/ \___|______| |
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// Finite Elements for Life Sciences and Engineering |
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// |
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// License: LGL2.1 License |
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// FELiScE default license: LICENSE in root folder |
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// |
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// Main authors: A. Collin |
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// |
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#ifndef _BIDOMAINMODEL_HPP |
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#define _BIDOMAINMODEL_HPP |
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// System includes |
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// External includes |
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#include "Core/NoThirdPartyWarning/Petsc/vec.hpp" |
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// Project includes |
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#include "Model/model.hpp" |
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#include "Solver/linearProblemBidomain.hpp" |
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#include "Solver/schafSolver.hpp" |
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#include "Solver/schafRevisedSolver.hpp" |
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#include "Solver/FhNSolver.hpp" |
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#include "Solver/courtemancheSolver.hpp" |
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#include "Solver/MVSolver.hpp" |
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#include "Solver/PaciSolver.hpp" |
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#include "Solver/BCLSolver.hpp" |
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#include "Solver/bdf.hpp" |
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#include "Solver/cardiacFunction.hpp" |
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#include "PETScInterface/romPETSC.hpp" |
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namespace felisce { |
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class BidomainModel: |
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public Model { |
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public: |
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///Construtor. |
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BidomainModel(); |
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///Destructor. |
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~BidomainModel() override; |
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void initializeDerivedModel() override; |
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virtual void userDefinedIonicModel() {} |
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void initializeDerivedLinearProblem() override; |
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void preAssemblingMatrixRHS(std::size_t iProblem=0) override; |
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void postAssemblingMatrixRHS(std::size_t iProblem=0) override; |
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void updateTime(const FlagMatrixRHS flagMatrixRHS=FlagMatrixRHS::matrix_and_rhs) override; |
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void writeSolution(); |
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void userDefinedInitialConditions(std::size_t iProblem=0) override; |
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/// Manage time iteration. |
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void forward() override; |
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void forwardROM(); |
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/// Initialize the SchafSolver and evaluate heterogeneous parameters of SchafSolver. |
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void initializeSchafParameter(); |
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/// Initialize the MinimalVentricular and evaluate heterogeneous parameters of SchafSolver. |
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void initializeMVParameter(); |
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/// Initialize the BCL and evaluate heterogeneous parameters of SchafSolver. |
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void initializeBCLParameter(); |
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/// Initialize the FithughNagumo and evaluate heterogeneous parameters of SchafSolver. |
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void initializeFhNParameter(); |
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/// Initialize the CourtemancheSolver and evaluate heterogeneous parameters of CourtemancheSolver. |
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void initializeCourtParameter(); |
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// void initializeMVParameter(); |
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virtual void finalizeRHSDP(int iProblem=0); |
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virtual void initializeAppCurrent(); |
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virtual void initializeAppCurrentExt(); |
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void evalIapp(); |
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void evalIappExt(); |
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MVSolver* getMVSolver();//For assimilation method----> get and std::set values |
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std::vector<LinearProblemBidomain*> vecLPB() { |
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return m_linearProblemBidomain; |
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} |
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#ifdef FELISCE_WITH_CVGRAPH |
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void forwardLight(); |
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void startIterationCVG() override; |
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felInt m_kount; |
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#endif |
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protected: |
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RomPETSC* m_rom; |
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int m_verbose; |
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bool m_buildIonic; |
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bool m_buildCourt; |
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///EDO solvers. |
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IonicSolver* m_ionic; |
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SchafSolver* m_schaf; |
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FhNSolver* m_fhn; |
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CourtemancheSolver* m_court; |
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MVSolver* m_mv; |
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PaciSolver* m_paci; |
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BCLSolver* m_bcl; |
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///EDP time scheme. |
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Bdf m_bdfEdp; |
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///Initialization vectors. |
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std::vector<PetscVector> m_W_0; |
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//For courtemanche model: |
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//Gate conditions |
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// INa |
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PetscVector m_m; |
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PetscVector m_h; |
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PetscVector m_j; |
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// ITo |
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PetscVector m_ao; |
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PetscVector m_io; |
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// IKur |
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PetscVector m_ua; |
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PetscVector m_ui; |
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// IKr |
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PetscVector m_xr; |
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// IKs |
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PetscVector m_xs; |
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// ICaL |
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PetscVector m_d; |
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PetscVector m_f; |
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PetscVector m_fca; |
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// Irel |
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PetscVector m_urel; |
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PetscVector m_vrel; |
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PetscVector m_wrel; |
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// Ion concentrations |
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PetscVector m_nai; |
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PetscVector m_nao; |
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PetscVector m_cao; |
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PetscVector m_ki; |
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PetscVector m_ko; |
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PetscVector m_cai; |
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//Currents |
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PetscVector m_naiont; |
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PetscVector m_kiont; |
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PetscVector m_caiont; |
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PetscVector m_ileak; |
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PetscVector m_iup; |
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PetscVector m_itr; |
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PetscVector m_irel; |
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// Ca: |
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PetscVector m_cmdn; /* Calmodulin Buffered Ca Concentration (mM) */ |
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PetscVector m_trpn; /* Troponin Buffered Ca Concentration (mM) */ |
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PetscVector m_nsr; /* NSR Ca Concentration (mM) */ |
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PetscVector m_jsr; /* JSR Ca Concentration (mM) */ |
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PetscVector m_csqn; /* Calsequestrin Buffered Ca Concentration (mM) */ |
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AppCurrent* m_iApp; |
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std::vector <double> m_iAppValue; |
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AppCurrent* m_iAppExt; |
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std::vector <double> m_iAppValueExt; |
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/// Matrix of the luenberger filter |
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PetscMatrix m_luenbFlter; |
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std::vector<LinearProblemBidomain*> m_linearProblemBidomain; |
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///Data for schaf solver from EDP solution. |
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PetscVector m_extrapolate; |
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private: |
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/// Case of the observation |
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EnsightCase * m_observations; |
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/// Vector to store Observations |
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PetscVector m_Observ; |
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bool m_extrapolateIsCreated; |
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// Restart vectors |
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PetscVector m_bdf_sol_n; |
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PetscVector m_bdf_sol_n_1; |
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PetscVector m_bdf_sol_n_2; |
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std::vector<PetscVector> m_ionic_sol_n; |
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std::vector<PetscVector> m_ionic_sol_n_1; |
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std::vector<PetscVector> m_ionic_sol_n_2; |
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std::vector<PetscVector> m_courtVarInit; |
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}; |
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} |
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#endif |
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