AP95.cpp

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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
 
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~*/
#include "ode/ionicModels/AP95.hpp"
 
AP95::AP95(
  Unknown*                      u, 
  const CepsSet<CepsAttribute>& attrs,
  InputParameters*              params
):
  AbstractIonicModel(u,attrs)
{
 
  m_name          = "Aliev-Panfilov 2003";
  m_nStateVars    = 1;
  m_stateVarNames = {"h [adim]"};
 
  // ================================================================================
  // Default parameters
 
  m_vMin        = -90; 
  m_vMax        =  50;
  m_cellSurface =  1.;
  
  m_constants = new CepsReal[5];  
  m_constants[_k    ] = 8.0;
  m_constants[_a    ] = 0.15;
  m_constants[_mu1  ] = 0.2;
  m_constants[_mu2  ] = 0.3;
  m_constants[_eps0 ] = 2E-3;
 
  m_paperCm   = 1.;
  m_paperStim = 0.2;
 
  // ================================================================================
  // Parameters from text inputs, if any
  if (ceps::isValidPtr(params))
    setupWithParameters(params,nullptr);
  
}
 
void 
AP95::getInitialCondition(CepsReal* v, CepsReal* y) const
{
  *v = 0.0;
  y[_h] = 0.0;
}
 
void
AP95::computeRates(
  CepsReal         t,
  CepsReal*        y, 
  CepsReal*        vm, 
  CepsReal*        dtyLin, 
  CepsReal*        dtyNLin, 
  CepsReal*        dtv, 
  DegreeOfFreedom* dof
) const
{ 
 
  CepsReal* c = m_constants;
  CepsReal  v = *vm;
  CepsReal  h = y[_h];
 
  CepsReal eps = c[_eps0] + c[_mu1] * h / (c[_mu2] + v);
 
  dtyLin [_h] = 0;
  dtyNLin[_h] = eps * (-h - c[_k] * v * (v - c[_a] - 1));
 
  CepsReal cm    = getCmInternal(t,dof);
  CepsReal iStim = getStimulation(dof,t);
 
  *dtv  = -c[_k] * v * (v - c[_a]) * (v - 1) - h * v + iStim;
  *dtv /= cm;
}
 
CepsReal
AP95::convertVoltageToCepsUnit(const CepsReal& v) const
{
  return m_vMin + v*(m_vMax-m_vMin);
}
 
CepsReal
AP95::convertVoltageFromCepsUnit(const CepsReal& v) const
{
  return (v-m_vMin)/(m_vMax-m_vMin);
}
 
CepsReal
AP95::convertCurrentFromCepsUnit(const CepsReal& i) const
{
  return i/(m_vMax-m_vMin);
}
 
CepsReal
AP95::convertDtvToCepsUnit(const CepsReal& dtv) const
{
  return dtv*(m_vMax-m_vMin);
}
 
CepsReal
AP95::convertCmFromCepsUnit(const CepsReal& cm) const
{
  return cm;
}
 
CepsReal
AP95::convertCmToCepsUnit(const CepsReal& cm) const
{
  return cm;
}
 
void
AP95::setupWithParameters(InputParameters* params, FunctionDictionary* dico)
{
 
  m_constants[_k    ] = params->getReal("AP95 k     ",m_constants[_k    ]); 
  m_constants[_a    ] = params->getReal("AP95 a     ",m_constants[_a    ]); 
  m_constants[_mu1  ] = params->getReal("AP95 mu1   ",m_constants[_mu1  ]); 
  m_constants[_mu2  ] = params->getReal("AP95 mu2   ",m_constants[_mu2  ]); 
  m_constants[_eps0 ] = params->getReal("AP95 eps0  ",m_constants[_eps0 ]); 
 
  m_vMin        = params->getReal("AP95 vMin",m_vMin);
  m_vMax        = params->getReal("AP95 vMax",m_vMax);
  m_cellSurface = params->getReal("AP95 cell surface",m_cellSurface);
 
  return;
}