Chaste  Release::3.4
CvodeAdaptor.hpp
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35 
36 #ifdef CHASTE_CVODE
37 #ifndef _CVODEADAPTOR_HPP_
38 #define _CVODEADAPTOR_HPP_
39 
40 #include <vector>
41 
42 #include "ChasteSerialization.hpp"
43 #include <boost/serialization/base_object.hpp>
44 
45 #include "AbstractIvpOdeSolver.hpp"
46 #include "OdeSolution.hpp"
47 
48 // CVODE headers
49 #include <cvode/cvode.h>
50 #include <nvector/nvector_serial.h>
51 
52 
59 void CvodeErrorHandler(int errorCode, const char *module, const char *function,
60  char *message, void* pData);
61 // Note: declared here since it's also used by AbstractCvodeCell.
62 
63 
68 typedef struct CvodeData_ {
70  std::vector<realtype>* pY;
73 } CvodeData;
74 
93 {
94 private:
103  template<class Archive>
104  void serialize(Archive & archive, const unsigned int version)
105  {
106  archive & boost::serialization::base_object<AbstractIvpOdeSolver>(*this);
107  archive & mRelTol;
108  archive & mAbsTol;
109  archive & mLastInternalStepSize;
110  archive & mMaxSteps;
111  archive & mCheckForRoots;
112  // All other member variables given values on each call.
113  }
114 
116  void* mpCvodeMem;
117 
120 
122  double mRelTol;
123 
125  double mAbsTol;
126 
129 
134  long int mMaxSteps;
135 
138 
141 
144 
147 
150 
156  void RecordStoppingPoint(double stopTime, N_Vector yEnd);
157 
158 protected:
159 
168  void SetupCvode(AbstractOdeSystem* pOdeSystem,
169  std::vector<double>& rInitialY,
170  double startTime, double maxStep);
171 
175  void FreeCvodeMemory();
176 
186  void CvodeError(int flag, const char * msg);
187 
188 public:
189 
197  CvodeAdaptor(double relTol=1e-4, double absTol=1e-6);
198 
203  ~CvodeAdaptor();
204 
212  void SetTolerances(double relTol=1e-4, double absTol=1e-6);
213 
217  double GetRelativeTolerance();
218 
222  double GetAbsoluteTolerance();
223 
227  double GetLastStepSize();
228 
236  void SetForceReset(bool autoReset);
237 
245  void SetMinimalReset(bool minimalReset);
246 
257  void ResetSolver();
258 
271  OdeSolution Solve(AbstractOdeSystem* pOdeSystem,
272  std::vector<double>& rYValues,
273  double startTime,
274  double endTime,
275  double maxStep,
276  double timeSampling);
277 
288  void Solve(AbstractOdeSystem* pOdeSystem,
289  std::vector<double>& rYValues,
290  double startTime,
291  double endTime,
292  double maxStep);
293 
299  void CheckForStoppingEvents();
300 
307  void SetMaxSteps(long int numSteps);
308 
313  long int GetMaxSteps();
314 
315 };
316 
319 
320 #endif // _CVODEADAPTOR_HPP_
321 #endif // CHASTE_CVODE
AbstractOdeSystem * pSystem
void SetupCvode(AbstractOdeSystem *pOdeSystem, std::vector< double > &rInitialY, double startTime, double maxStep)
CvodeAdaptor(double relTol=1e-4, double absTol=1e-6)
void ResetSolver()
void CheckForStoppingEvents()
N_Vector mLastSolutionState
void FreeCvodeMemory()
long int GetMaxSteps()
double mLastInternalStepSize
double GetAbsoluteTolerance()
void CvodeError(int flag, const char *msg)
void SetMinimalReset(bool minimalReset)
bool mForceMinimalReset
std::vector< realtype > * pY
void SetTolerances(double relTol=1e-4, double absTol=1e-6)
friend class boost::serialization::access
#define CHASTE_CLASS_EXPORT(T)
void RecordStoppingPoint(double stopTime, N_Vector yEnd)
void SetForceReset(bool autoReset)
double mLastSolutionTime
void serialize(Archive &archive, const unsigned int version)
CvodeData mData
long int mMaxSteps
void SetMaxSteps(long int numSteps)
double GetLastStepSize()
double GetRelativeTolerance()
OdeSolution Solve(AbstractOdeSystem *pOdeSystem, std::vector< double > &rYValues, double startTime, double endTime, double maxStep, double timeSampling)