Chaste  Release::2018.1
AbstractCardiacCellInterface.hpp
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35 
36 #ifndef ABSTRACTCARDIACCELLINTERFACE_HPP_
37 #define ABSTRACTCARDIACCELLINTERFACE_HPP_
38 
39 #include <boost/shared_ptr.hpp>
40 
41 #include "ChasteSerialization.hpp"
43 #include "ClassIsAbstract.hpp"
44 
45 #include "AbstractIvpOdeSolver.hpp"
46 #include "RegularStimulus.hpp"
47 #include "OdeSolution.hpp"
48 #include "AbstractLookupTableCollection.hpp"
49 
59 {
60 public:
73  AbstractCardiacCellInterface(boost::shared_ptr<AbstractIvpOdeSolver> pOdeSolver,
74  unsigned voltageIndex,
75  boost::shared_ptr<AbstractStimulusFunction> pIntracellularStimulus);
76 
79 
85  virtual void SetTimestep(double dt)=0;
86 
94  virtual unsigned GetNumberOfStateVariables() const=0;
95 
101  virtual unsigned GetNumberOfParameters() const=0;
102 
112  virtual std::vector<double> GetStdVecStateVariables()=0;
113 
121  virtual const std::vector<std::string>& rGetStateVariableNames() const=0;
122 
123 
131  virtual void SetStateVariables(const std::vector<double>& rVariables)=0;
132 
141  virtual void SetStateVariable(unsigned index, double newValue)=0;
142 
152  virtual void SetStateVariable(const std::string& rName, double newValue)=0;
153 
163  virtual double GetAnyVariable(const std::string& rName, double time)=0;
164 
173  virtual double GetParameter(const std::string& rParameterName)=0;
174 
183  virtual double GetParameter(unsigned parameterIndex)=0;
184 
193  virtual void SetParameter(const std::string& rParameterName, double value)=0;
194 
203  virtual void SolveAndUpdateState(double tStart, double tEnd)=0;
204 
215  virtual OdeSolution Compute(double tStart, double tEnd, double tSamp=0.0)=0;
216 
225  virtual void ComputeExceptVoltage(double tStart, double tEnd)=0;
226 
256  virtual double GetIIonic(const std::vector<double>* pStateVariables=NULL)=0;
257 
262  virtual void SetVoltage(double voltage)=0;
263 
267  virtual double GetVoltage()=0;
268 
275  unsigned GetVoltageIndex();
276 
282  void SetStimulusFunction(boost::shared_ptr<AbstractStimulusFunction> pStimulus);
283 
289  double GetStimulus(double time);
290 
297  void SetIntracellularStimulusFunction(boost::shared_ptr<AbstractStimulusFunction> pStimulus);
298 
306  double GetIntracellularStimulus(double time);
307 
314  double GetIntracellularAreaStimulus(double time);
315 
324  void SetUsedInTissueSimulation(bool tissue=true);
325 
333  virtual boost::shared_ptr<RegularStimulus> UseCellMLDefaultStimulus();
334 
339 
347  {
348  return NULL;
349  }
350 
354  boost::shared_ptr<AbstractStimulusFunction> GetStimulusFunction();
355 
362  const boost::shared_ptr<AbstractStimulusFunction> GetStimulusFunction() const;
363 
370  const boost::shared_ptr<AbstractIvpOdeSolver> GetSolver() const;
371 
379  void SetSolver(boost::shared_ptr<AbstractIvpOdeSolver> pSolver);
380 
385  virtual void SetVoltageDerivativeToZero(bool clamp=true);
386 
394  void SetFixedVoltage(double voltage);
395 
403  virtual void SetStretch(double stretch)
404  {
405  }
406 
415  virtual double GetIntracellularCalciumConcentration();
416 
417 protected:
424  unsigned mVoltageIndex;
425 
427  boost::shared_ptr<AbstractIvpOdeSolver> mpOdeSolver;
428 
430  boost::shared_ptr<AbstractStimulusFunction> mpIntracellularStimulus;
431 
438 
441 
444 
447 
448 private:
457  template<class Archive>
458  void serialize(Archive & archive, const unsigned int version)
459  {
460  // For version 0 these were archived by AbstractCardiacCell, now
461  // we have AbstractCvodeCells too, so doing it here.
462  if (version > 0)
463  {
464  archive & mSetVoltageDerivativeToZero;
465  archive & mIsUsedInTissue;
467  // archive & mFixedVoltage; - this doesn't need archiving as it is reset every PDE time step if used.
468  }
469  // archive & mVoltageIndex; - always set by constructor - called by concrete class
470  // archive & mpOdeSolver; - always set by constructor - called by concrete class
471  // archive & mpIntracellularStimulus; - always set by constructor - called by concrete class
472  }
473 };
474 
476 BOOST_CLASS_VERSION(AbstractCardiacCellInterface, 1)
477 
478 #endif /*ABSTRACTCARDIACCELLINTERFACE_HPP_*/
AbstractCardiacCellInterface(boost::shared_ptr< AbstractIvpOdeSolver > pOdeSolver, unsigned voltageIndex, boost::shared_ptr< AbstractStimulusFunction > pIntracellularStimulus)
virtual void SetStretch(double stretch)
virtual double GetAnyVariable(const std::string &rName, double time)=0
boost::shared_ptr< AbstractStimulusFunction > mpIntracellularStimulus
virtual unsigned GetNumberOfParameters() const =0
virtual void SetParameter(const std::string &rParameterName, double value)=0
const boost::shared_ptr< AbstractIvpOdeSolver > GetSolver() const
#define CLASS_IS_ABSTRACT(T)
virtual double GetVoltage()=0
void SetStimulusFunction(boost::shared_ptr< AbstractStimulusFunction > pStimulus)
void SetIntracellularStimulusFunction(boost::shared_ptr< AbstractStimulusFunction > pStimulus)
virtual const std::vector< std::string > & rGetStateVariableNames() const =0
virtual std::vector< double > GetStdVecStateVariables()=0
virtual void SetStateVariables(const std::vector< double > &rVariables)=0
virtual unsigned GetNumberOfStateVariables() const =0
virtual double GetParameter(const std::string &rParameterName)=0
virtual void SetTimestep(double dt)=0
virtual AbstractLookupTableCollection * GetLookupTableCollection()
virtual OdeSolution Compute(double tStart, double tEnd, double tSamp=0.0)=0
virtual double GetIIonic(const std::vector< double > *pStateVariables=NULL)=0
virtual boost::shared_ptr< RegularStimulus > UseCellMLDefaultStimulus()
virtual void ComputeExceptVoltage(double tStart, double tEnd)=0
virtual void SolveAndUpdateState(double tStart, double tEnd)=0
void serialize(Archive &archive, const unsigned int version)
virtual void SetVoltage(double voltage)=0
virtual void SetVoltageDerivativeToZero(bool clamp=true)
boost::shared_ptr< AbstractStimulusFunction > GetStimulusFunction()
gcov doesn't like this file...
friend class boost::serialization::access
boost::shared_ptr< AbstractIvpOdeSolver > mpOdeSolver
virtual void SetStateVariable(unsigned index, double newValue)=0
void SetSolver(boost::shared_ptr< AbstractIvpOdeSolver > pSolver)