FasterCard/IonicModel.cpp at main · cesare-corrado/FasterCard · GitHub

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#include<stdio.h>
#include<cstdlib>
#include<math.h>
#include "IonicModel.hpp"

#ifndef NEWTON_TOLL
#define NEWTON_TOLL 1E-4
#endif
#ifndef NEWTON_MAXIT
#define NEWTON_MAXIT 100
#endif

//Default constructor
IonicModel::IonicModel()
:_nlSolver(1),
_Variables(0),
_VariablesN(0),
_VariablesInit(0),
_Parameters(0),
_VariablesOut(0),
_VariablesOutNames(0),
_Cm(1.0),
_vmin(-80.0),
_vmax(20.0),
_IEiko(1.0),
_Idiff(NULL),
_Iapp(NULL),
_diffCurr(false),
_Vm(NULL),
_Vmn(NULL),
_tstim(0.4),
_arest(1.0),
_APD(0.0),
_RP(0.0),
_DI(1.e32),
_tdep(0.0),
_trep(0.0),
_dep(false),
_rep(false),
nb_of_ionic_variables(0),
nb_of_ionic_parameters(0),
_nsubiter(0),
_dt(0.0),
_dtGlobal(0.0),
_tau_cell_react(0.0),
_isExcitable(true)
{
    clearData();
}


//Destructor
IonicModel::~IonicModel()
{
    clearData();
}


void IonicModel::reset()
{
    initVar();
    setExcitable();
}


// Set time step and number of subiterations
void IonicModel::set_dt(const double & theDtGlobal, const int & nsubit)
{
    _dtGlobal=theDtGlobal;
    _nsubiter=nsubit;
    _dt = _dtGlobal/static_cast<double>(_nsubiter);
}


//Set the ionic parameters
void IonicModel::set_ionic_parameters(const std::vector<double> & vectorParam)
{
    nb_of_ionic_parameters=static_cast<unsigned>(vectorParam.size());
    _Parameters=vectorParam;
}


//Protected functions
//Convert Vm between dimensionless (0,1) and dimensional (vmin,vmax) forms
double IonicModel::convertVm(const double & vmValue, bool toAdim)
{
  double result=0.0;
  double _dV=(_vmax-_vmin);
  if(toAdim)
  {
    result=(vmValue-_vmin)/_dV;
  }
  else
  {
    result=_dV*vmValue+_vmin;
  }
  return(result);
}


void IonicModel::initVar()
{
    _VariablesN=_VariablesInit;
    _Variables=_VariablesInit;
    if(_Vmn!=NULL)
    {
        (*_Vmn)=convertVm(_VariablesN[0],false);
    }
    if(_Vm!=NULL)
    {
        (*_Vm)=convertVm(_Variables[0],false);
    }

}


// Private functions
// Clear the variable vectors
void IonicModel::clearData()
{
        _Variables.clear();
        _VariablesN.clear();
        _VariablesInit.clear();
        _Parameters.clear();
        _VariablesOut.clear();
        _VariablesOutNames.clear();
        nb_of_ionic_variables=0;
        nb_of_ionic_parameters=0;
        _Idiff=NULL;
        _Iapp=NULL;
        _diffCurr=false;
        _Vm=NULL;
        _Vmn=NULL;
}


//Set the initial state
void IonicModel::set_InitialState(const std::vector<double> & u0)
{
    nb_of_ionic_variables=static_cast<unsigned>(u0.size());
    _VariablesInit=u0;
    _VariablesN=u0;
    _Variables=u0;
    if(_Vmn!=NULL)
    {
        (*_Vmn)=convertVm(_VariablesN[0],false);
    }
    if(_Vm!=NULL)
    {
        (*_Vm)=convertVm(_Variables[0],false);
    }
}