Chaste Commit::baa90ac2819b962188b7562f2326be23c47859a7
CvodeAdaptor.hpp
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34*/
35
36#ifdef CHASTE_CVODE
37#ifndef _CVODEADAPTOR_HPP_
38#define _CVODEADAPTOR_HPP_
39
40#include <vector>
41
42#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#if CHASTE_SUNDIALS_VERSION >= 30000
53#include <sunlinsol/sunlinsol_dense.h> /* access to dense SUNLinearSolver */
54#include <sunmatrix/sunmatrix_dense.h> /* access to dense SUNMatrix */
55#endif
56
63void CvodeErrorHandler(int errorCode, const char* module, const char* function,
64 char* message, void* pData);
65// Note: declared here since it's also used by AbstractCvodeCell.
66
71typedef struct CvodeData_
72{
74 std::vector<realtype>* pY;
77} CvodeData;
78
106{
107private:
116 template <class Archive>
117 void serialize(Archive& archive, const unsigned int version)
118 {
119 archive& boost::serialization::base_object<AbstractIvpOdeSolver>(*this);
120 archive& mRelTol;
121 archive& mAbsTol;
122 archive& mLastInternalStepSize;
123 archive& mMaxSteps;
124 archive& mCheckForRoots;
125 // All other member variables given values on each call.
126 }
127
130
133
135 double mRelTol;
136
138 double mAbsTol;
139
142
147 long int mMaxSteps;
148
151
154
157
160
163
164#if CHASTE_SUNDIALS_VERSION >= 30000
166 SUNMatrix mpSundialsDenseMatrix;
168 SUNLinearSolver mpSundialsLinearSolver;
169#endif
170
176 void RecordStoppingPoint(double stopTime, N_Vector yEnd);
177
178protected:
187 void SetupCvode(AbstractOdeSystem* pOdeSystem,
188 std::vector<double>& rInitialY,
189 double startTime, double maxStep);
190
194 void FreeCvodeMemory();
195
205 void CvodeError(int flag, const char* msg);
206
207public:
215 CvodeAdaptor(double relTol = 1e-4, double absTol = 1e-6);
216
222
230 void SetTolerances(double relTol = 1e-4, double absTol = 1e-6);
231
235 double GetRelativeTolerance();
236
240 double GetAbsoluteTolerance();
241
245 double GetLastStepSize();
246
254 void SetForceReset(bool autoReset);
255
263 void SetMinimalReset(bool minimalReset);
264
275 void ResetSolver();
276
290 std::vector<double>& rYValues,
291 double startTime,
292 double endTime,
293 double maxStep,
294 double timeSampling);
295
306 void Solve(AbstractOdeSystem* pOdeSystem,
307 std::vector<double>& rYValues,
308 double startTime,
309 double endTime,
310 double maxStep);
311
318
325 void SetMaxSteps(long int numSteps);
326
331 long int GetMaxSteps();
332};
333
336
337#endif // _CVODEADAPTOR_HPP_
338#endif // CHASTE_CVODE
gcov doesn't like this file...
#define CHASTE_CLASS_EXPORT(T)
double GetAbsoluteTolerance()
long int GetMaxSteps()
void CvodeError(int flag, const char *msg)
long int mMaxSteps
void SetMinimalReset(bool minimalReset)
void serialize(Archive &archive, const unsigned int version)
N_Vector mLastSolutionState
void SetMaxSteps(long int numSteps)
void FreeCvodeMemory()
void SetForceReset(bool autoReset)
void CheckForStoppingEvents()
CvodeData mData
OdeSolution Solve(AbstractOdeSystem *pOdeSystem, std::vector< double > &rYValues, double startTime, double endTime, double maxStep, double timeSampling)
double GetLastStepSize()
double mLastInternalStepSize
friend class boost::serialization::access
void RecordStoppingPoint(double stopTime, N_Vector yEnd)
void SetupCvode(AbstractOdeSystem *pOdeSystem, std::vector< double > &rInitialY, double startTime, double maxStep)
double mLastSolutionTime
double GetRelativeTolerance()
void SetTolerances(double relTol=1e-4, double absTol=1e-6)
AbstractOdeSystem * pSystem
std::vector< realtype > * pY