Chaste  Release::2018.1
AbstractGeneralizedRushLarsenCardiacCell.hpp
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35 
36 #ifndef ABSTRACTGENERALIZEDRUSHLARSENCARDIACCELL_HPP_
37 #define ABSTRACTGENERALIZEDRUSHLARSENCARDIACCELL_HPP_
38 
39 #include "ChasteSerialization.hpp"
40 #include <boost/serialization/base_object.hpp>
41 #include "ClassIsAbstract.hpp"
42 #include "AbstractCardiacCell.hpp"
43 #include "PetscTools.hpp"
44 
45 /*
46 Megan E. Marsh, Raymond J. Spiteri
47 Numerical Simulation Laboratory
48 University of Saskatchewan
49 December 2011
50 Partial support provided by research grants from the National
51 Science and Engineering Research Council (NSERC) of Canada
52 and the MITACS/Mprime Canadian Network of Centres of Excellence.
53 */
54 
60 {
61 private:
70  template<class Archive>
71  void serialize(Archive & archive, const unsigned int version)
72  {
73  // This calls serialize on the base class.
74  archive & boost::serialization::base_object<AbstractCardiacCell>(*this);
75  }
76 
77 public:
92  unsigned numberOfStateVariables,
93  unsigned voltageIndex,
94  boost::shared_ptr<AbstractStimulusFunction> pIntracellularStimulus);
95 
98 
110  OdeSolution Compute(double tStart, double tEnd, double tSamp=0.0);
111 
122  void ComputeExceptVoltage(double tStart, double tEnd);
123 
131  void SolveAndUpdateState(double tStart, double tEnd);
132 
133 
137  bool HasAnalyticJacobian() const;
138 
145  void ForceUseOfNumericalJacobian(bool useNumericalJacobian = true);
146 
147 
148 private:
149 // LCOV_EXCL_START
157  void EvaluateYDerivatives(double time, const std::vector<double>& rY, std::vector<double>& rDY)
158  {
160  }
161 // LCOV_EXCL_STOP
162 
163 protected:
169  virtual void ComputeOneStepExceptVoltage(double time)=0;
170 
176  virtual void UpdateTransmembranePotential(double time)=0;
177 
179  std::vector<double> mPartialF;
180 
182  std::vector<double> mEvalF;
183 
185  std::vector<double> mYInit;
186 
189 };
190 
192 
193 #endif // ABSTRACTGENERALIZEDRUSHLARSENCARDIACCELL_HPP_
void serialize(Archive &archive, const unsigned int version)
void EvaluateYDerivatives(double time, const std::vector< double > &rY, std::vector< double > &rDY)
#define CLASS_IS_ABSTRACT(T)
#define NEVER_REACHED
Definition: Exception.hpp:206
AbstractGeneralizedRushLarsenCardiacCell(unsigned numberOfStateVariables, unsigned voltageIndex, boost::shared_ptr< AbstractStimulusFunction > pIntracellularStimulus)
virtual void UpdateTransmembranePotential(double time)=0
OdeSolution Compute(double tStart, double tEnd, double tSamp=0.0)
virtual void ComputeOneStepExceptVoltage(double time)=0