FitzhughNagumo.cpp

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///////////////////////////////////////////////////////////////////////////////
//
// File: FitzhughNagumo.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
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// DEALINGS IN THE SOFTWARE.
//
// Description: FitzhughNagumo phenomological cell model.
//
///////////////////////////////////////////////////////////////////////////////
 
#include <iostream>
#include <string>
 
#include <CardiacEPSolver/CellModels/FitzhughNagumo.h>
#include <LibUtilities/BasicUtils/Vmath.hpp>
 
namespace Nektar
{
/**
 * Registers the class with the Factory.
 */
std::string CellModelFitzHughNagumo::className =
    GetCellModelFactory().RegisterCreatorFunction(
        "FitzHughNagumo", CellModelFitzHughNagumo::create,
        "Phenomological model of squid nerve cell.");
 
CellModelFitzHughNagumo::CellModelFitzHughNagumo(
    const LibUtilities::SessionReaderSharedPtr &pSession,
    const MultiRegions::ExpListSharedPtr &pField)
    : CellModel(pSession, pField)
{
    pSession->LoadParameter("beta", m_beta, 0.0);
    pSession->LoadParameter("epsilon", m_epsilon, 1.0);
 
    m_uuu = Array<OneD, NekDouble>(m_nq, 0.0);
 
    m_nvar = 2;
    m_concentrations.push_back(1);
}
 
void CellModelFitzHughNagumo::v_Update(
    const Array<OneD, const Array<OneD, NekDouble>> &inarray,
    Array<OneD, Array<OneD, NekDouble>> &outarray, const NekDouble time)
{
    boost::ignore_unused(time);
 
    NekDouble m_gamma = 0.5;
 
    // compute u^2: m_u = u*u
    Vmath::Vmul(m_nq, &inarray[0][0], 1, &inarray[0][0], 1, &m_uuu[0], 1);
 
    // compute u^3: m_u = u*u*u
    Vmath::Vmul(m_nq, &inarray[0][0], 1, &m_uuu[0], 1, &m_uuu[0], 1);
 
    // For u: (1/m_epsilon)*( u*-u*u*u/3 - v )
    // physfield = u - (1.0/3.0)*u*u*u
    Vmath::Svtvp(m_nq, (-1.0 / 3.0), &m_uuu[0], 1, &inarray[0][0], 1,
                 &outarray[0][0], 1);
 
    Vmath::Vsub(m_nq, &inarray[1][0], 1, &outarray[0][0], 1, &outarray[0][0],
                1);
    Vmath::Smul(m_nq, -1.0 / m_epsilon, &outarray[0][0], 1, &outarray[0][0], 1);
 
    // For v: m_epsilon*( u + m_beta - m_gamma*v )
    Vmath::Svtvp(m_nq, -1.0 * m_gamma, &inarray[1][0], 1, &inarray[0][0], 1,
                 &outarray[1][0], 1);
    Vmath::Sadd(m_nq, m_beta, &outarray[1][0], 1, &outarray[1][0], 1);
    Vmath::Smul(m_nq, m_epsilon, &outarray[1][0], 1, &outarray[1][0], 1);
}
 
/**
 *
 */
void CellModelFitzHughNagumo::v_GenerateSummary(SummaryList &s)
{
    SolverUtils::AddSummaryItem(s, "Cell model", "FitzHugh-Nagumo");
    SolverUtils::AddSummaryItem(s, "Cell model beta", m_beta);
}
 
/**
 *
 */
void CellModelFitzHughNagumo::v_SetInitialConditions()
{
    Vmath::Fill(m_nq, 0.0, m_cellSol[0], 1);
    Vmath::Fill(m_nq, 0.0, m_cellSol[1], 1);
}
 
} // namespace Nektar