AlievPanfilov.cpp

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///////////////////////////////////////////////////////////////////////////////
//
// File AlievPanfilov.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: Aliev-Panfilov phenomological cell model.
//
///////////////////////////////////////////////////////////////////////////////
 
#include <iostream>
#include <string>
 
#include <CardiacEPSolver/CellModels/AlievPanfilov.h>
#include <LibUtilities/BasicUtils/Vmath.hpp>
 
namespace Nektar
{
/**
 * Registers the class with the Factory.
 */
std::string CellModelAlievPanfilov::className =
    GetCellModelFactory().RegisterCreatorFunction(
        "AlievPanfilov", CellModelAlievPanfilov::create,
        "Phenomological model of canine cardiac electrophysiology.");
 
CellModelAlievPanfilov::CellModelAlievPanfilov(
    const LibUtilities::SessionReaderSharedPtr &pSession,
    const MultiRegions::ExpListSharedPtr &pField)
    : CellModel(pSession, pField)
{
    pSession->LoadParameter("k", m_k, 0.0);
    pSession->LoadParameter("a", m_a, 0.0);
    pSession->LoadParameter("mu1", m_mu1, 0.0);
    pSession->LoadParameter("mu2", m_mu2, 0.0);
    pSession->LoadParameter("eps", m_eps, 0.0);
 
    m_uu   = Array<OneD, NekDouble>(m_nq, 0.0);
    m_uuu  = Array<OneD, NekDouble>(m_nq, 0.0);
    m_tmp1 = Array<OneD, NekDouble>(m_nq, 0.0);
    m_tmp2 = Array<OneD, NekDouble>(m_nq, 0.0);
 
    m_nvar = 2;
    m_concentrations.push_back(1);
}
 
void CellModelAlievPanfilov::v_Update(
    const Array<OneD, const Array<OneD, NekDouble>> &inarray,
    Array<OneD, Array<OneD, NekDouble>> &outarray, const NekDouble time)
{
    // inarray[0] holds initial physical u values throughout
    // inarray[1] holds initial physical v values throughout
 
    // compute u^2: m_u = u*u
    Vmath::Vmul(m_nq, &inarray[0][0], 1, &inarray[0][0], 1, &m_uu[0], 1);
 
    // compute u^3: m_u = u*u*u
    Vmath::Vmul(m_nq, &inarray[0][0], 1, &m_uu[0], 1, &m_uuu[0], 1);
 
    // --------------------------------------
    // Compute reaction term f(u,v)
    // --------------------------------------
    //        if (m_spatialParameters->Exists("a"))
    //        {
    //          Vmath::Vmul(m_nq,
    //          &m_spatialParameters->GetData("a")->GetPhys()[0], 1,
    //                           &inarray[0][0], 1, &m_tmp1[0], 1);
    //
    //          Vmath::Vvtvm(m_nq,
    //          &m_spatialParameters->GetData("a")->GetPhys()[0], 1,
    //                           &m_uu[0], 1, &m_tmp1[0], 1, &m_tmp1[0], 1);
    //
    //          Vmath::Svtvm(m_nq, -1.0, &m_uu[0], 1, &m_tmp1[0], 1, &m_tmp1[0],
    //          1);
    //        }
    //        else
    //        {
    // Ru = au
    Vmath::Smul(m_nq, m_a, &inarray[0][0], 1, &m_tmp1[0], 1);
    // Ru = (-1-a)u*u + au
    Vmath::Svtvp(m_nq, (-1.0 - m_a), &m_uu[0], 1, &m_tmp1[0], 1, &m_tmp1[0], 1);
    //        }
    // Ru = u*u*u - (1+a)u*u + au
    Vmath::Vadd(m_nq, &m_uuu[0], 1, &m_tmp1[0], 1, &m_tmp1[0], 1);
    // Ru = k(u*u*u - (1+a)u*u + au)
    //        if (m_spatialParameters->Exists("k"))
    //        {
    //          Vmath::Vmul(m_nq,
    //          &m_spatialParameters->GetData("k")->GetPhys()[0], 1,
    //                          &m_tmp1[0], 1, &m_tmp1[0], 1);
    //        }
    //        else
    //        {
    Vmath::Smul(m_nq, m_k, &m_tmp1[0], 1, &m_tmp1[0], 1);
    //        }
 
    // Ru = k(u*u*u - (1+a)u*u + au) + I_stim
    Vmath::Vadd(m_nq, &outarray[0][0], 1, &m_tmp1[0], 1, &outarray[0][0], 1);
 
    // Ru = k(u*u*u - (1+a)u*u + au) + uv + I_stim
    Vmath::Vvtvp(m_nq, &inarray[0][0], 1, &inarray[1][0], 1, &m_tmp1[0], 1,
                 &outarray[0][0], 1);
    // Ru = -k(u*u*u - (1+a)u*u + au) - uv - I_stim
    Vmath::Neg(m_nq, &outarray[0][0], 1);
 
    // --------------------------------------
    // Compute reaction term g(u,v)
    // --------------------------------------
    // tmp2 = mu2 + u
    Vmath::Sadd(m_nq, m_mu2, &inarray[0][0], 1, &m_tmp2[0], 1);
 
    // tmp2 = v/(mu2 + u)
    Vmath::Vdiv(m_nq, &inarray[1][0], 1, &m_tmp2[0], 1, &m_tmp2[0], 1);
 
    // tmp2 = mu1*v/(mu2 + u)
    Vmath::Smul(m_nq, m_mu1, &m_tmp2[0], 1, &m_tmp2[0], 1);
 
    // tmp1 = Eps + mu1*v/(mu2+u)
    Vmath::Sadd(m_nq, m_eps, &m_tmp2[0], 1, &m_tmp2[0], 1);
 
    // tmp1 = (-a-1) + u
    //        if (m_spatialParameters->Exists("a"))
    //        {
    //          Vmath::Vsub(m_nq, &inarray[0][0], 1,
    //                          &m_spatialParameters->GetData("a")->GetPhys()[0],
    //                          1, &m_tmp1[0], 1);
    //
    //          Vmath::Sadd(m_nq, -1.0, &inarray[0][0], 1, &m_tmp1[0], 1);
    //        }
    //        else
    //        {
    Vmath::Sadd(m_nq, (-m_a - 1), &inarray[0][0], 1, &m_tmp1[0], 1);
    //        }
 
    // tmp1 = k(u-a-1)
    //        if (m_spatialParameters->Exists("k"))
    //        {
    //          Vmath::Vmul(m_nq,
    //          &m_spatialParameters->GetData("k")->GetPhys()[0], 1,
    //                          &m_tmp1[0], 1, &m_tmp1[0], 1);
    //        }
    //        else
    //        {
    Vmath::Smul(m_nq, m_k, &m_tmp1[0], 1, &m_tmp1[0], 1);
    //        }
 
    // tmp1 = ku(u-a-1) + v
    Vmath::Vvtvp(m_nq, &inarray[0][0], 1, &m_tmp1[0], 1, &inarray[1][0], 1,
                 &m_tmp1[0], 1);
 
    // tmp1 = -ku(u-a-1)-v
    Vmath::Neg(m_nq, &m_tmp1[0], 1);
 
    // outarray = [Eps + mu1*v/(mu2+u)] * [-ku(u-a-1)-v]
    Vmath::Vmul(m_nq, &m_tmp1[0], 1, &m_tmp2[0], 1, &outarray[1][0], 1);
}
 
/**
 *
 */
void CellModelAlievPanfilov::v_GenerateSummary(SummaryList &s)
{
    SolverUtils::AddSummaryItem(s, "Cell model", "Aliev-Panfilov");
    SolverUtils::AddSummaryItem(s, "k", m_k);
    SolverUtils::AddSummaryItem(s, "a", m_a);
    SolverUtils::AddSummaryItem(s, "eps", m_eps);
    SolverUtils::AddSummaryItem(s, "mu1", m_mu1);
    SolverUtils::AddSummaryItem(s, "mu2", m_mu2);
}
 
/**
 *
 */
void CellModelAlievPanfilov::v_SetInitialConditions()
{
    Vmath::Fill(m_nq, 0.0, m_cellSol[0], 1);
    Vmath::Fill(m_nq, 0.0, m_cellSol[1], 1);
}
} // namespace Nektar