Chaste  Release::3.4
AbstractCvodeCell.hpp
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35 
36 #ifdef CHASTE_CVODE
37 #ifndef _ABSTRACTCVODECELL_HPP_
38 #define _ABSTRACTCVODECELL_HPP_
39 
40 // Serialization headers
41 #include "ChasteSerialization.hpp"
42 #include "ClassIsAbstract.hpp"
43 #include <boost/serialization/base_object.hpp>
44 #include <boost/shared_ptr.hpp>
45 #include <boost/serialization/shared_ptr.hpp>
46 
47 // Chaste headers
48 #include "AbstractOdeSystemInformation.hpp"
49 #include "AbstractStimulusFunction.hpp"
50 #include "AbstractIvpOdeSolver.hpp"
51 #include "AbstractCvodeSystem.hpp"
52 #include "AbstractCardiacCellInterface.hpp"
54 
55 
79 {
80 private:
89  template<class Archive>
90  void serialize(Archive & archive, const unsigned int version)
91  {
92  // This calls serialize on the base classes.
93  archive & boost::serialization::base_object<AbstractCvodeSystem>(*this);
94  archive & boost::serialization::base_object<AbstractCardiacCellInterface>(*this);
95  archive & mMaxDt;
96  }
97 
98 protected:
100  double mMaxDt;
101 
102 public:
113  AbstractCvodeCell(boost::shared_ptr<AbstractIvpOdeSolver> pSolver,
114  unsigned numberOfStateVariables,
115  unsigned voltageIndex,
116  boost::shared_ptr<AbstractStimulusFunction> pIntracellularStimulus);
117 
121  virtual ~AbstractCvodeCell();
122 
127  double GetVoltage();
128 
133  void SetVoltage(double voltage);
134 
140  void SetMaxTimestep(double maxDt);
141 
151  void SetTimestep(double maxDt);
152 
156  double GetTimestep();
157 
168  virtual void SolveAndUpdateState(double tStart, double tEnd);
169 
183  OdeSolution Compute(double tStart, double tEnd, double tSamp=0.0);
184 
192  void ComputeExceptVoltage(double tStart, double tEnd);
193 
199  void SetVoltageDerivativeToZero(bool clamp=true);
200 
210  unsigned GetNumberOfStateVariables() const;
211 
221  unsigned GetNumberOfParameters() const;
222 
232  std::vector<double> GetStdVecStateVariables();
233 
243  const std::vector<std::string>& rGetStateVariableNames() const;
244 
254  void SetStateVariables(const std::vector<double>& rVariables);
255 
260  void SetStateVariables(const N_Vector& rVariables);
261 
272  void SetStateVariable(unsigned index, double newValue);
273 
284  void SetStateVariable(const std::string& rName, double newValue);
285 
297  double GetAnyVariable(const std::string& rName, double time=0.0);
298 
309  double GetParameter(const std::string& rParameterName);
310 
319  double GetParameter(unsigned parameterIndex);
320 
331  void SetParameter(const std::string& rParameterName, double value);
332 
333 };
334 
336 
337 #endif // _ABSTRACTCVODECELL_HPP_
338 #endif // CHASTE_CVODE
void SetStateVariable(unsigned index, double newValue)
void SetVoltage(double voltage)
friend class boost::serialization::access
void SetMaxTimestep(double maxDt)
void SetTimestep(double maxDt)
const std::vector< std::string > & rGetStateVariableNames() const
OdeSolution Compute(double tStart, double tEnd, double tSamp=0.0)
#define CLASS_IS_ABSTRACT(T)
void SetParameter(const std::string &rParameterName, double value)
unsigned GetNumberOfParameters() const
AbstractCvodeCell(boost::shared_ptr< AbstractIvpOdeSolver > pSolver, unsigned numberOfStateVariables, unsigned voltageIndex, boost::shared_ptr< AbstractStimulusFunction > pIntracellularStimulus)
void serialize(Archive &archive, const unsigned int version)
void SetStateVariables(const std::vector< double > &rVariables)
void SetVoltageDerivativeToZero(bool clamp=true)
double GetParameter(const std::string &rParameterName)
void ComputeExceptVoltage(double tStart, double tEnd)
std::vector< double > GetStdVecStateVariables()
unsigned GetNumberOfStateVariables() const
virtual void SolveAndUpdateState(double tStart, double tEnd)
double GetAnyVariable(const std::string &rName, double time=0.0)