doxygen/5.4.0/_luo_rudy91_8cpp_source.html

///////////////////////////////////////////////////////////////////////////////

//

// File: LuoRudy91.cpp

//

// For more information, please see: http://www.nektar.info

//

// The MIT License

//

// Copyright (c) 2006 Division of Applied Mathematics, Brown University (USA),

// Department of Aeronautics, Imperial College London (UK), and Scientific

// Computing and Imaging Institute, University of Utah (USA).

//

// Permission is hereby granted, free of charge, to any person obtaining a

// copy of this software and associated documentation files (the "Software"),

// to deal in the Software without restriction, including without limitation

// the rights to use, copy, modify, merge, publish, distribute, sublicense,

// and/or sell copies of the Software, and to permit persons to whom the

// Software is furnished to do so, subject to the following conditions:

//

// The above copyright notice and this permission notice shall be included

// in all copies or substantial portions of the Software.

//

// THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS

// OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,

// FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL

// THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER

// LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING

// FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER

// DEALINGS IN THE SOFTWARE.

//

// Description:

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///////////////////////////////////////////////////////////////////////////////


//! @file

//!

//! This source file was generated from CellML.

//!

//! Model: luo_rudy_1991

//!

//! Processed by pycml - CellML Tools in Python

//!     (translators: 12434, pycml: 12383, optimize: 12408)

//! on Thu Oct 20 12:52:22 2011

//!

//! <autogenerated>


#include <iostream>

#include <string>

//#inc lude <LibUtilities/BasicUtils/Vmath.hpp>

#include <CardiacEPSolver/CellModels/LuoRudy91.h>


namespace Nektar

{

std::string LuoRudy91::className =

    GetCellModelFactory().RegisterCreatorFunction(

        "LuoRudy91", LuoRudy91::create, "Luo Rudy 1991 model.");


/**

 *

 */

LuoRudy91::LuoRudy91(const LibUtilities::SessionReaderSharedPtr &pSession,

                     const MultiRegions::ExpListSharedPtr &pField)

    : CellModel(pSession, pField)

{

    m_nq = pField->GetNpoints();


    m_nvar = 8;

    m_gates.push_back(1);

    m_gates.push_back(2);

    m_gates.push_back(3);

    m_gates.push_back(4);

    m_gates.push_back(5);

    m_gates.push_back(6);

    m_concentrations.push_back(7);

}


void LuoRudy91::v_Update(

    const Array<OneD, const Array<OneD, NekDouble>> &inarray,

    Array<OneD, Array<OneD, NekDouble>> &outarray, const NekDouble time)

{

    boost::ignore_unused(time);


    for (size_t i = 0; i < m_nq; ++i)

    {

        // Inputs:

        // Time units: millisecond

        NekDouble var_chaste_interface__membrane__V = inarray[0][i];

        // Units: millivolt; Initial value: -84.3801107371

        NekDouble var_chaste_interface__fast_sodium_current_m_gate__m =

            inarray[1][i];

        // Units: dimensionless; Initial value: 0.00171338077730188

        NekDouble var_chaste_interface__fast_sodium_current_h_gate__h =

            inarray[2][i];

        // Units: dimensionless; Initial value: 0.982660523699656

        NekDouble var_chaste_interface__fast_sodium_current_j_gate__j =

            inarray[3][i];

        // Units: dimensionless; Initial value: 0.989108212766685

        NekDouble var_chaste_interface__slow_inward_current_d_gate__d =

            inarray[4][i];

        // Units: dimensionless; Initial value: 0.00302126301779861

        NekDouble var_chaste_interface__slow_inward_current_f_gate__f =

            inarray[5][i];

        // Units: dimensionless; Initial value: 0.999967936476325

        NekDouble

            var_chaste_interface__time_dependent_potassium_current_X_gate__X =

                inarray[6][i];

        // Units: dimensionless; Initial value: 0.0417603108167287

        NekDouble

            var_chaste_interface__intracellular_calcium_concentration__Cai =

                inarray[7][i];

        // Units: millimolar; Initial value: 0.00017948816388306


        // Mathematics

        NekDouble d_dt_chaste_interface__membrane__V;

        const NekDouble var_fast_sodium_current__j =

            var_chaste_interface__fast_sodium_current_j_gate__j; // dimensionless

        const NekDouble var_fast_sodium_current__h =

            var_chaste_interface__fast_sodium_current_h_gate__h; // dimensionless

        const NekDouble var_fast_sodium_current__m =

            var_chaste_interface__fast_sodium_current_m_gate__m; // dimensionless

        const NekDouble var_fast_sodium_current__V =

            var_chaste_interface__membrane__V; // millivolt

        const NekDouble var_slow_inward_current__d =

            var_chaste_interface__slow_inward_current_d_gate__d; // dimensionless

        const NekDouble var_slow_inward_current__f =

            var_chaste_interface__slow_inward_current_f_gate__f; // dimensionless

        const NekDouble var_slow_inward_current__V =

            var_chaste_interface__membrane__V; // millivolt

        const NekDouble var_slow_inward_current__Cai =

            var_chaste_interface__intracellular_calcium_concentration__Cai; // millimolar

        const NekDouble var_slow_inward_current__E_si =

            7.7 -

            (13.0287 * log(var_slow_inward_current__Cai / 1.0)); // millivolt

        const NekDouble var_slow_inward_current__i_si =

            0.09 * var_slow_inward_current__d * var_slow_inward_current__f *

            (var_slow_inward_current__V -

             var_slow_inward_current__E_si); // microA_per_cm2

        const NekDouble var_time_dependent_potassium_current__V =

            var_chaste_interface__membrane__V; // millivolt

        const NekDouble var_time_dependent_potassium_current__X =

            var_chaste_interface__time_dependent_potassium_current_X_gate__X; // dimensionless

#if 0

            const NekDouble var_fast_sodium_current_m_gate__m = var_fast_sodium_current__m; // dimensionless

#endif

        const NekDouble var_fast_sodium_current_m_gate__V =

            var_fast_sodium_current__V; // millivolt

        const NekDouble var_fast_sodium_current_m_gate__alpha_m =

            (0.32 * (var_fast_sodium_current_m_gate__V + 47.13)) /

            (1.0 - exp((-0.1) * (var_fast_sodium_current_m_gate__V +

                                 47.13))); // per_millisecond

        const NekDouble var_fast_sodium_current_m_gate__beta_m =

            0.08 *

            exp((-var_fast_sodium_current_m_gate__V) / 11.0); // per_millisecond

#if 0

            const NekDouble var_fast_sodium_current_m_gate__d_m_d_environment__time = (var_fast_sodium_current_m_gate__alpha_m * (1.0 - var_fast_sodium_current_m_gate__m)) - (var_fast_sodium_current_m_gate__beta_m * var_fast_sodium_current_m_gate__m); // per_millisecond

            const NekDouble var_fast_sodium_current__fast_sodium_current_m_gate__d_m_d_environment__time = var_fast_sodium_current_m_gate__d_m_d_environment__time; // per_millisecond

#endif

        const NekDouble var_fast_sodium_current_h_gate__V =

            var_fast_sodium_current__V; // millivolt

        const NekDouble var_fast_sodium_current_h_gate__beta_h =

            (var_fast_sodium_current_h_gate__V < (-40.0))

                ? ((3.56 * exp(0.079 * var_fast_sodium_current_h_gate__V)) +

                   (310000.0 * exp(0.35 * var_fast_sodium_current_h_gate__V)))

                : (1.0 / (0.13 * (1.0 + exp((var_fast_sodium_current_h_gate__V +

                                             10.66) /

                                            (-11.1))))); // per_millisecond

        const NekDouble var_fast_sodium_current_h_gate__alpha_h =

            (var_fast_sodium_current_h_gate__V < (-40.0))

                ? (0.135 *

                   exp((80.0 + var_fast_sodium_current_h_gate__V) / (-6.8)))

                : 0.0; // per_millisecond

#if 0

            const NekDouble var_fast_sodium_current_h_gate__h = var_fast_sodium_current__h; // dimensionless

            const NekDouble var_fast_sodium_current_h_gate__d_h_d_environment__time = (var_fast_sodium_current_h_gate__alpha_h * (1.0 - var_fast_sodium_current_h_gate__h)) - (var_fast_sodium_current_h_gate__beta_h * var_fast_sodium_current_h_gate__h); // per_millisecond

            const NekDouble var_fast_sodium_current__fast_sodium_current_h_gate__d_h_d_environment__time = var_fast_sodium_current_h_gate__d_h_d_environment__time; // per_millisecond

#endif

        const NekDouble var_fast_sodium_current_j_gate__V =

            var_fast_sodium_current__V; // millivolt

        const NekDouble var_fast_sodium_current_j_gate__alpha_j =

            (var_fast_sodium_current_j_gate__V < (-40.0))

                ? (((((-127140.0) *

                      exp(0.2444 * var_fast_sodium_current_j_gate__V)) -

                     (3.474e-05 *

                      exp((-0.04391) * var_fast_sodium_current_j_gate__V))) *

                    (var_fast_sodium_current_j_gate__V + 37.78)) /

                   (1.0 +

                    exp(0.311 * (var_fast_sodium_current_j_gate__V + 79.23))))

                : 0.0; // per_millisecond

        const NekDouble var_fast_sodium_current_j_gate__beta_j =

            (var_fast_sodium_current_j_gate__V < (-40.0))

                ? ((0.1212 *

                    exp((-0.01052) * var_fast_sodium_current_j_gate__V)) /

                   (1.0 + exp((-0.1378) *

                              (var_fast_sodium_current_j_gate__V + 40.14))))

                : ((0.3 *

                    exp((-2.535e-07) * var_fast_sodium_current_j_gate__V)) /

                   (1.0 + exp((-0.1) * (var_fast_sodium_current_j_gate__V +

                                        32.0)))); // per_millisecond

#if 0

            const NekDouble var_fast_sodium_current_j_gate__j = var_fast_sodium_current__j; // dimensionless

            const NekDouble var_fast_sodium_current_j_gate__d_j_d_environment__time = (var_fast_sodium_current_j_gate__alpha_j * (1.0 - var_fast_sodium_current_j_gate__j)) - (var_fast_sodium_current_j_gate__beta_j * var_fast_sodium_current_j_gate__j); // per_millisecond

            const NekDouble var_fast_sodium_current__fast_sodium_current_j_gate__d_j_d_environment__time = var_fast_sodium_current_j_gate__d_j_d_environment__time; // per_millisecond

#endif

        const NekDouble var_slow_inward_current_d_gate__V =

            var_slow_inward_current__V; // millivolt

        const NekDouble var_slow_inward_current_d_gate__alpha_d =

            (0.095 * exp((-0.01) * (var_slow_inward_current_d_gate__V - 5.0))) /

            (1.0 + exp((-0.072) * (var_slow_inward_current_d_gate__V -

                                   5.0))); // per_millisecond

#if 0

            const NekDouble var_slow_inward_current_d_gate__d = var_slow_inward_current__d; // dimensionless

#endif

        const NekDouble var_slow_inward_current_d_gate__beta_d =

            (0.07 *

             exp((-0.017) * (var_slow_inward_current_d_gate__V + 44.0))) /

            (1.0 + exp(0.05 * (var_slow_inward_current_d_gate__V +

                               44.0))); // per_millisecond

#if 0

            const NekDouble var_slow_inward_current_d_gate__d_d_d_environment__time = (var_slow_inward_current_d_gate__alpha_d * (1.0 - var_slow_inward_current_d_gate__d)) - (var_slow_inward_current_d_gate__beta_d * var_slow_inward_current_d_gate__d); // per_millisecond

            const NekDouble var_slow_inward_current__slow_inward_current_d_gate__d_d_d_environment__time = var_slow_inward_current_d_gate__d_d_d_environment__time; // per_millisecond

            const NekDouble var_slow_inward_current_f_gate__f = var_slow_inward_current__f; // dimensionless

#endif

        const NekDouble var_slow_inward_current_f_gate__V =

            var_slow_inward_current__V; // millivolt

        const NekDouble var_slow_inward_current_f_gate__alpha_f =

            (0.012 *

             exp((-0.008) * (var_slow_inward_current_f_gate__V + 28.0))) /

            (1.0 + exp(0.15 * (var_slow_inward_current_f_gate__V +

                               28.0))); // per_millisecond

        const NekDouble var_slow_inward_current_f_gate__beta_f =

            (0.0065 *

             exp((-0.02) * (var_slow_inward_current_f_gate__V + 30.0))) /

            (1.0 + exp((-0.2) * (var_slow_inward_current_f_gate__V +

                                 30.0))); // per_millisecond

#if 0

            const NekDouble var_slow_inward_current_f_gate__d_f_d_environment__time = (var_slow_inward_current_f_gate__alpha_f * (1.0 - var_slow_inward_current_f_gate__f)) - (var_slow_inward_current_f_gate__beta_f * var_slow_inward_current_f_gate__f); // per_millisecond

            const NekDouble var_slow_inward_current__slow_inward_current_f_gate__d_f_d_environment__time = var_slow_inward_current_f_gate__d_f_d_environment__time; // per_millisecond

            const NekDouble var_time_dependent_potassium_current_X_gate__X = var_time_dependent_potassium_current__X; // dimensionless

#endif

        const NekDouble var_time_dependent_potassium_current_X_gate__V =

            var_time_dependent_potassium_current__V; // millivolt

        const NekDouble var_time_dependent_potassium_current_X_gate__beta_X =

            (0.0013 *

             exp((-0.06) *

                 (var_time_dependent_potassium_current_X_gate__V + 20.0))) /

            (1.0 +

             exp((-0.04) * (var_time_dependent_potassium_current_X_gate__V +

                            20.0))); // per_millisecond

        const NekDouble var_time_dependent_potassium_current_X_gate__alpha_X =

            (0.0005 *

             exp(0.083 *

                 (var_time_dependent_potassium_current_X_gate__V + 50.0))) /

            (1.0 + exp(0.057 * (var_time_dependent_potassium_current_X_gate__V +

                                50.0))); // per_millisecond

#if 0

            const NekDouble var_time_dependent_potassium_current_X_gate__d_X_d_environment__time = (var_time_dependent_potassium_current_X_gate__alpha_X * (1.0 - var_time_dependent_potassium_current_X_gate__X)) - (var_time_dependent_potassium_current_X_gate__beta_X * var_time_dependent_potassium_current_X_gate__X); // per_millisecond

            const NekDouble var_time_dependent_potassium_current__time_dependent_potassium_current_X_gate__d_X_d_environment__time = var_time_dependent_potassium_current_X_gate__d_X_d_environment__time; // per_millisecond

#endif

        const NekDouble var_intracellular_calcium_concentration__Cai =

            var_chaste_interface__intracellular_calcium_concentration__Cai; // millimolar

        const NekDouble var_intracellular_calcium_concentration__i_si =

            var_slow_inward_current__i_si; // microA_per_cm2

        const NekDouble

            var_intracellular_calcium_concentration__d_Cai_d_environment__time =

                (((-0.0001) / 1.0) *

                 var_intracellular_calcium_concentration__i_si) +

                (0.07 *

                 (0.0001 -

                  var_intracellular_calcium_concentration__Cai)); // 'millimole

                                                                  // per litre

                                                                  // per

                                                                  // millisecond'

#if 0

            const NekDouble var_chaste_interface__fast_sodium_current_m_gate__d_m_d_environment__time = var_fast_sodium_current__fast_sodium_current_m_gate__d_m_d_environment__time; // per_millisecond

            const NekDouble var_chaste_interface__fast_sodium_current_h_gate__d_h_d_environment__time = var_fast_sodium_current__fast_sodium_current_h_gate__d_h_d_environment__time; // per_millisecond

            const NekDouble var_chaste_interface__fast_sodium_current_j_gate__d_j_d_environment__time = var_fast_sodium_current__fast_sodium_current_j_gate__d_j_d_environment__time; // per_millisecond

            const NekDouble var_chaste_interface__slow_inward_current_d_gate__d_d_d_environment__time = var_slow_inward_current__slow_inward_current_d_gate__d_d_d_environment__time; // per_millisecond

            const NekDouble var_chaste_interface__slow_inward_current_f_gate__d_f_d_environment__time = var_slow_inward_current__slow_inward_current_f_gate__d_f_d_environment__time; // per_millisecond

            const NekDouble var_chaste_interface__time_dependent_potassium_current_X_gate__d_X_d_environment__time = var_time_dependent_potassium_current__time_dependent_potassium_current_X_gate__d_X_d_environment__time; // per_millisecond

#endif

        const NekDouble

            var_chaste_interface__intracellular_calcium_concentration__d_Cai_d_environment__time =

                var_intracellular_calcium_concentration__d_Cai_d_environment__time; // ___units_16

#if 0

            const NekDouble d_dt_chaste_interface__fast_sodium_current_m_gate__m = var_chaste_interface__fast_sodium_current_m_gate__d_m_d_environment__time; // per_millisecond

            const NekDouble d_dt_chaste_interface__fast_sodium_current_h_gate__h = var_chaste_interface__fast_sodium_current_h_gate__d_h_d_environment__time; // per_millisecond

            const NekDouble d_dt_chaste_interface__fast_sodium_current_j_gate__j = var_chaste_interface__fast_sodium_current_j_gate__d_j_d_environment__time; // per_millisecond

            const NekDouble d_dt_chaste_interface__slow_inward_current_d_gate__d = var_chaste_interface__slow_inward_current_d_gate__d_d_d_environment__time; // per_millisecond

            const NekDouble d_dt_chaste_interface__slow_inward_current_f_gate__f = var_chaste_interface__slow_inward_current_f_gate__d_f_d_environment__time; // per_millisecond

            const NekDouble d_dt_chaste_interface__time_dependent_potassium_current_X_gate__X = var_chaste_interface__time_dependent_potassium_current_X_gate__d_X_d_environment__time; // per_millisecond

#endif

        const NekDouble

            d_dt_chaste_interface__intracellular_calcium_concentration__Cai =

                var_chaste_interface__intracellular_calcium_concentration__d_Cai_d_environment__time; // 'millimole per litre per millisecond'


        const NekDouble var_membrane__R = 8314.0;  // joule_per_kilomole_kelvin

        const NekDouble var_membrane__T = 310.0;   // kelvin

        const NekDouble var_membrane__F = 96484.6; // coulomb_per_mole

        const NekDouble var_membrane__C = 1.0;     // microF_per_cm2

        const NekDouble var_chaste_interface__membrane__I_stim = 0.0;

        const NekDouble var_membrane__I_stim =

            var_chaste_interface__membrane__I_stim;           // microA_per_cm2

        const NekDouble var_fast_sodium_current__g_Na = 23.0; // milliS_per_cm2

        const NekDouble var_fast_sodium_current__R =

            var_membrane__R; // joule_per_kilomole_kelvin

        const NekDouble var_fast_sodium_current__F =

            var_membrane__F; // coulomb_per_mole

        const NekDouble var_ionic_concentrations__Nao = 140.0; // millimolar

        const NekDouble var_fast_sodium_current__Nao =

            var_ionic_concentrations__Nao;                    // millimolar

        const NekDouble var_ionic_concentrations__Nai = 18.0; // millimolar

        const NekDouble var_fast_sodium_current__Nai =

            var_ionic_concentrations__Nai; // millimolar

        const NekDouble var_fast_sodium_current__T = var_membrane__T; // kelvin

        const NekDouble var_fast_sodium_current__E_Na =

            ((var_fast_sodium_current__R * var_fast_sodium_current__T) /

             var_fast_sodium_current__F) *

            log(var_fast_sodium_current__Nao /

                var_fast_sodium_current__Nai); // millivolt

        const NekDouble var_fast_sodium_current__i_Na =

            var_fast_sodium_current__g_Na *

            pow(var_fast_sodium_current__m, 3.0) * var_fast_sodium_current__h *

            var_fast_sodium_current__j *

            (var_fast_sodium_current__V -

             var_fast_sodium_current__E_Na); // microA_per_cm2

        const NekDouble var_membrane__i_Na =

            var_fast_sodium_current__i_Na; // microA_per_cm2

        const NekDouble var_membrane__i_si =

            var_slow_inward_current__i_si; // microA_per_cm2

        const NekDouble var_time_dependent_potassium_current_Xi_gate__V =

            var_time_dependent_potassium_current__V; // millivolt

        const NekDouble var_time_dependent_potassium_current_Xi_gate__Xi =

            (var_time_dependent_potassium_current_Xi_gate__V > (-100.0))

                ? ((2.837 *

                    (exp(0.04 *

                         (var_time_dependent_potassium_current_Xi_gate__V +

                          77.0)) -

                     1.0)) /

                   ((var_time_dependent_potassium_current_Xi_gate__V + 77.0) *

                    exp(0.04 *

                        (var_time_dependent_potassium_current_Xi_gate__V +

                         35.0))))

                : 1.0; // dimensionless

        const NekDouble var_time_dependent_potassium_current__Xi =

            var_time_dependent_potassium_current_Xi_gate__Xi; // dimensionless

        const NekDouble var_ionic_concentrations__Ko = 5.4;   // millimolar

        const NekDouble var_time_dependent_potassium_current__Ko =

            var_ionic_concentrations__Ko; // millimolar

        const NekDouble var_time_dependent_potassium_current__g_K =

            0.282 * sqrt(var_time_dependent_potassium_current__Ko /

                         5.4); // milliS_per_cm2

        const NekDouble var_time_dependent_potassium_current__PR_NaK =

            0.01833; // dimensionless

        const NekDouble var_time_dependent_potassium_current__F =

            var_membrane__F; // coulomb_per_mole

        const NekDouble var_time_dependent_potassium_current__Nao =

            var_ionic_concentrations__Nao;                    // millimolar

        const NekDouble var_ionic_concentrations__Ki = 145.0; // millimolar

        const NekDouble var_time_dependent_potassium_current__Ki =

            var_ionic_concentrations__Ki; // millimolar

        const NekDouble var_time_dependent_potassium_current__Nai =

            var_ionic_concentrations__Nai; // millimolar

        const NekDouble var_time_dependent_potassium_current__T =

            var_membrane__T; // kelvin

        const NekDouble var_time_dependent_potassium_current__R =

            var_membrane__R; // joule_per_kilomole_kelvin

        const NekDouble var_time_dependent_potassium_current__E_K =

            ((var_time_dependent_potassium_current__R *

              var_time_dependent_potassium_current__T) /

             var_time_dependent_potassium_current__F) *

            log((var_time_dependent_potassium_current__Ko +

                 (var_time_dependent_potassium_current__PR_NaK *

                  var_time_dependent_potassium_current__Nao)) /

                (var_time_dependent_potassium_current__Ki +

                 (var_time_dependent_potassium_current__PR_NaK *

                  var_time_dependent_potassium_current__Nai))); // millivolt

        const NekDouble var_time_dependent_potassium_current__i_K =

            var_time_dependent_potassium_current__g_K *

            var_time_dependent_potassium_current__X *

            var_time_dependent_potassium_current__Xi *

            (var_time_dependent_potassium_current__V -

             var_time_dependent_potassium_current__E_K); // microA_per_cm2

        const NekDouble var_membrane__i_K =

            var_time_dependent_potassium_current__i_K; // microA_per_cm2

        const NekDouble var_time_independent_potassium_current__V =

            var_chaste_interface__membrane__V; // millivolt

        const NekDouble var_time_independent_potassium_current_K1_gate__V =

            var_time_independent_potassium_current__V; // millivolt

        const NekDouble var_time_independent_potassium_current__Ki =

            var_ionic_concentrations__Ki; // millimolar

        const NekDouble var_time_independent_potassium_current__R =

            var_membrane__R; // joule_per_kilomole_kelvin

        const NekDouble var_time_independent_potassium_current__F =

            var_membrane__F; // coulomb_per_mole

        const NekDouble var_time_independent_potassium_current__Ko =

            var_ionic_concentrations__Ko; // millimolar

        const NekDouble var_time_independent_potassium_current__T =

            var_membrane__T; // kelvin

        const NekDouble var_time_independent_potassium_current__E_K1 =

            ((var_time_independent_potassium_current__R *

              var_time_independent_potassium_current__T) /

             var_time_independent_potassium_current__F) *

            log(var_time_independent_potassium_current__Ko /

                var_time_independent_potassium_current__Ki); // millivolt

        const NekDouble var_time_independent_potassium_current_K1_gate__E_K1 =

            var_time_independent_potassium_current__E_K1; // millivolt

        const NekDouble

            var_time_independent_potassium_current_K1_gate__beta_K1 =

                ((0.49124 *

                  exp(0.08032 *

                      ((var_time_independent_potassium_current_K1_gate__V +

                        5.476) -

                       var_time_independent_potassium_current_K1_gate__E_K1))) +

                 (1.0 *

                  exp(0.06175 *

                      (var_time_independent_potassium_current_K1_gate__V -

                       (var_time_independent_potassium_current_K1_gate__E_K1 +

                        594.31))))) /

                (1.0 +

                 exp((-0.5143) *

                     ((var_time_independent_potassium_current_K1_gate__V -

                       var_time_independent_potassium_current_K1_gate__E_K1) +

                      4.753))); // per_millisecond

        const NekDouble

            var_time_independent_potassium_current_K1_gate__alpha_K1 =

                1.02 /

                (1.0 +

                 exp(0.2385 *

                     ((var_time_independent_potassium_current_K1_gate__V -

                       var_time_independent_potassium_current_K1_gate__E_K1) -

                      59.215))); // per_millisecond

        const NekDouble

            var_time_independent_potassium_current_K1_gate__K1_infinity =

                var_time_independent_potassium_current_K1_gate__alpha_K1 /

                (var_time_independent_potassium_current_K1_gate__alpha_K1 +

                 var_time_independent_potassium_current_K1_gate__beta_K1); // dimensionless

        const NekDouble var_time_independent_potassium_current__K1_infinity =

            var_time_independent_potassium_current_K1_gate__K1_infinity; // dimensionless

        const NekDouble var_time_independent_potassium_current__g_K1 =

            0.6047 * sqrt(var_time_independent_potassium_current__Ko /

                          5.4); // milliS_per_cm2

        const NekDouble var_time_independent_potassium_current__i_K1 =

            var_time_independent_potassium_current__g_K1 *

            var_time_independent_potassium_current__K1_infinity *

            (var_time_independent_potassium_current__V -

             var_time_independent_potassium_current__E_K1); // microA_per_cm2

        const NekDouble var_membrane__i_K1 =

            var_time_independent_potassium_current__i_K1; // microA_per_cm2

        const NekDouble var_plateau_potassium_current__g_Kp =

            0.0183; // milliS_per_cm2

        const NekDouble var_plateau_potassium_current__V =

            var_chaste_interface__membrane__V; // millivolt

        const NekDouble var_plateau_potassium_current__Kp =

            1.0 / (1.0 + exp((7.488 - var_plateau_potassium_current__V) /

                             5.98)); // dimensionless

        const NekDouble var_plateau_potassium_current__E_K1 =

            var_time_independent_potassium_current__E_K1; // millivolt

        const NekDouble var_plateau_potassium_current__E_Kp =

            var_plateau_potassium_current__E_K1; // millivolt

        const NekDouble var_plateau_potassium_current__i_Kp =

            var_plateau_potassium_current__g_Kp *

            var_plateau_potassium_current__Kp *

            (var_plateau_potassium_current__V -

             var_plateau_potassium_current__E_Kp); // microA_per_cm2

        const NekDouble var_membrane__i_Kp =

            var_plateau_potassium_current__i_Kp;               // microA_per_cm2

        const NekDouble var_background_current__E_b = -59.87;  // millivolt

        const NekDouble var_background_current__g_b = 0.03921; // milliS_per_cm2

        const NekDouble var_background_current__V =

            var_chaste_interface__membrane__V; // millivolt

        const NekDouble var_background_current__i_b =

            var_background_current__g_b *

            (var_background_current__V -

             var_background_current__E_b); // microA_per_cm2

        const NekDouble var_membrane__i_b =

            var_background_current__i_b; // microA_per_cm2

        const NekDouble var_membrane__d_V_d_environment__time =

            ((-1.0) / var_membrane__C) *

            (var_membrane__I_stim + var_membrane__i_Na + var_membrane__i_si +

             var_membrane__i_K + var_membrane__i_K1 + var_membrane__i_Kp +

             var_membrane__i_b); // 'millivolt per millisecond'

        const NekDouble

            var_chaste_interface__membrane__d_V_d_environment__time =

                var_membrane__d_V_d_environment__time; // ___units_1

        d_dt_chaste_interface__membrane__V =

            var_chaste_interface__membrane__d_V_d_environment__time; // 'millivolt

                                                                     // per

                                                                     // millisecond'

        const NekDouble m_inf = var_fast_sodium_current_m_gate__alpha_m /

                                (var_fast_sodium_current_m_gate__alpha_m +

                                 var_fast_sodium_current_m_gate__beta_m);

        const NekDouble m_tau = 1.0 / (var_fast_sodium_current_m_gate__alpha_m +

                                       var_fast_sodium_current_m_gate__beta_m);

        const NekDouble h_inf = var_fast_sodium_current_h_gate__alpha_h /

                                (var_fast_sodium_current_h_gate__alpha_h +

                                 var_fast_sodium_current_h_gate__beta_h);

        const NekDouble h_tau = 1.0 / (var_fast_sodium_current_h_gate__alpha_h +

                                       var_fast_sodium_current_h_gate__beta_h);

        const NekDouble j_inf = var_fast_sodium_current_j_gate__alpha_j /

                                (var_fast_sodium_current_j_gate__alpha_j +

                                 var_fast_sodium_current_j_gate__beta_j);

        const NekDouble j_tau = 1.0 / (var_fast_sodium_current_j_gate__alpha_j +

                                       var_fast_sodium_current_j_gate__beta_j);

        const NekDouble d_inf = var_slow_inward_current_d_gate__alpha_d /

                                (var_slow_inward_current_d_gate__alpha_d +

                                 var_slow_inward_current_d_gate__beta_d);

        const NekDouble d_tau = 1.0 / (var_slow_inward_current_d_gate__alpha_d +

                                       var_slow_inward_current_d_gate__beta_d);

        const NekDouble f_inf = var_slow_inward_current_f_gate__alpha_f /

                                (var_slow_inward_current_f_gate__alpha_f +

                                 var_slow_inward_current_f_gate__beta_f);

        const NekDouble f_tau = 1.0 / (var_slow_inward_current_f_gate__alpha_f +

                                       var_slow_inward_current_f_gate__beta_f);

        const NekDouble X_inf =

            var_time_dependent_potassium_current_X_gate__alpha_X /

            (var_time_dependent_potassium_current_X_gate__alpha_X +

             var_time_dependent_potassium_current_X_gate__beta_X);

        const NekDouble X_tau =

            1.0 / (var_time_dependent_potassium_current_X_gate__alpha_X +

                   var_time_dependent_potassium_current_X_gate__beta_X);


        outarray[0][i]    = d_dt_chaste_interface__membrane__V;

        outarray[1][i]    = m_inf;

        m_gates_tau[0][i] = m_tau;

        outarray[2][i]    = h_inf;

        m_gates_tau[1][i] = h_tau;

        outarray[3][i]    = j_inf;

        m_gates_tau[2][i] = j_tau;

        outarray[4][i]    = d_inf;

        m_gates_tau[3][i] = d_tau;

        outarray[5][i]    = f_inf;

        m_gates_tau[4][i] = f_tau;

        outarray[6][i]    = X_inf;

        m_gates_tau[5][i] = X_tau;

        outarray[7][i] =

            d_dt_chaste_interface__intracellular_calcium_concentration__Cai;

    }

}


/**

 *

 */

void LuoRudy91::v_GenerateSummary(SummaryList &s)

{

    SolverUtils::AddSummaryItem(s, "Cell model", "Luo-Rudy 1991");

}


/**

 *

 */

void LuoRudy91::v_SetInitialConditions()

{

    Vmath::Fill(m_nq, -84.3801107371, m_cellSol[0], 1);

    Vmath::Fill(m_nq, 0.00171338077730188, m_cellSol[1], 1);

    Vmath::Fill(m_nq, 0.982660523699656, m_cellSol[2], 1);

    Vmath::Fill(m_nq, 0.989108212766685, m_cellSol[3], 1);

    Vmath::Fill(m_nq, 0.00017948816388306, m_cellSol[4], 1);

    Vmath::Fill(m_nq, 0.00302126301779861, m_cellSol[5], 1);

    Vmath::Fill(m_nq, 0.999967936476325, m_cellSol[6], 1);

    Vmath::Fill(m_nq, 0.0417603108167287, m_cellSol[7], 1);

}

} // namespace Nektar

LuoRudy91.h

Nektar::Array
Definition: SharedArray.hpp:53

Nektar::CellModel
Cell model base class.
Definition: CellModel.h:66

Nektar::CellModel::m_cellSol
Array< OneD, Array< OneD, NekDouble > > m_cellSol
Cell model solution variables.
Definition: CellModel.h:126

Nektar::CellModel::m_concentrations
std::vector< int > m_concentrations
Indices of cell model variables which are concentrations.
Definition: CellModel.h:139

Nektar::CellModel::m_gates
std::vector< int > m_gates
Indices of cell model variables which are gates.
Definition: CellModel.h:141

Nektar::CellModel::m_nq
size_t m_nq
Number of physical points.
Definition: CellModel.h:117

Nektar::CellModel::m_nvar
size_t m_nvar
Number of variables in cell model (inc. transmembrane voltage)
Definition: CellModel.h:119

Nektar::CellModel::m_gates_tau
Array< OneD, Array< OneD, NekDouble > > m_gates_tau
Storage for gate tau values.
Definition: CellModel.h:143

Nektar::LibUtilities::NekFactory::RegisterCreatorFunction
tKey RegisterCreatorFunction(tKey idKey, CreatorFunction classCreator, std::string pDesc="")
Register a class with the factory.
Definition: NekFactory.hpp:198

Nektar::LuoRudy91::create
static CellModelSharedPtr create(const LibUtilities::SessionReaderSharedPtr &pSession, const MultiRegions::ExpListSharedPtr &pField)
Creates an instance of this class.
Definition: LuoRudy91.h:46

Nektar::LuoRudy91::v_SetInitialConditions
virtual void v_SetInitialConditions() override
Set initial conditions for the cell model.
Definition: LuoRudy91.cpp:551

Nektar::LuoRudy91::v_Update
virtual void v_Update(const Array< OneD, const Array< OneD, NekDouble > > &inarray, Array< OneD, Array< OneD, NekDouble > > &outarray, const NekDouble time) override
Computes the reaction terms $f(u,v)$ and $g(u,v)$.
Definition: LuoRudy91.cpp:77

Nektar::LuoRudy91::LuoRudy91
LuoRudy91(const LibUtilities::SessionReaderSharedPtr &pSession, const MultiRegions::ExpListSharedPtr &pField)
Constructor.
Definition: LuoRudy91.cpp:61

Nektar::LuoRudy91::v_GenerateSummary
virtual void v_GenerateSummary(SummaryList &s) override
Prints a summary of the model parameters.
Definition: LuoRudy91.cpp:543

Nektar::LuoRudy91::className
static std::string className
Name of class.
Definition: LuoRudy91.h:54

Nektar::LibUtilities::SessionReaderSharedPtr
std::shared_ptr< SessionReader > SessionReaderSharedPtr
Definition: SessionReader.h:115

Nektar::MultiRegions::ExpListSharedPtr
std::shared_ptr< ExpList > ExpListSharedPtr
Shared pointer to an ExpList object.
Definition: LocTraceToTraceMap.h:56

Nektar::SolverUtils::SummaryList
std::vector< std::pair< std::string, std::string > > SummaryList
Definition: Misc.h:48

Nektar::SolverUtils::AddSummaryItem
void AddSummaryItem(SummaryList &l, const std::string &name, const std::string &value)
Adds a summary item to the summary info list.
Definition: Misc.cpp:49

Nektar
The above copyright notice and this permission notice shall be included.
Definition: CoupledSolver.h:2

Nektar::GetCellModelFactory
CellModelFactory & GetCellModelFactory()
Definition: CellModel.cpp:46

Nektar::NekDouble
double NekDouble
Definition: NektarUnivTypeDefs.hpp:43

Vmath::Fill
void Fill(int n, const T alpha, T *x, const int incx)
Fill a vector with a constant value.
Definition: Vmath.cpp:43

tinysimd::log
scalarT< T > log(scalarT< T > in)
Definition: scalar.hpp:303

tinysimd::sqrt
scalarT< T > sqrt(scalarT< T > in)
Definition: scalar.hpp:294

Nektar::OneD
Definition: NektarUnivTypeDefs.hpp:54