Chaste  Release::2018.1
AbstractOdeSystem.hpp
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35 
36 #ifndef _ABSTRACTODESYSTEM_HPP_
37 #define _ABSTRACTODESYSTEM_HPP_
38 
39 #include <vector>
40 #include <string>
41 #include <algorithm>
42 
43 
44 #include "ChasteSerialization.hpp"
46 #include <boost/serialization/split_member.hpp>
47 #include <boost/serialization/vector.hpp>
48 #include "ClassIsAbstract.hpp"
49 
50 #include "AbstractParameterisedSystem.hpp"
51 #include "Exception.hpp"
52 
87 class AbstractOdeSystem : public AbstractParameterisedSystem<std::vector<double> >
88 {
89  friend class TestAbstractOdeSystem;
90 
91 private:
92 
93 
94  friend class boost::serialization::access;
101  template<class Archive>
102  void save(Archive & archive, const unsigned int version) const
103  {
104  // Despite the fact that 3 of these variables actually live in our base class,
105  // we still archive them here to maintain backwards compatibility.
106  // Since the N_Vector version of mStateVariables and mParameters needs converting
107  // to a standard vector before archiving, this doesn't hurt too much.
108  archive & mNumberOfStateVariables;
109  archive & mUseAnalyticJacobian;
110  archive & mStateVariables;
111  archive & mParameters;
112 
113  if (version > 0)
114  {
115  archive & rGetParameterNames();
116  }
117 
118  // This is always set up by subclass constructors, and is essentially
119  // 'static' data, so shouldn't go in the archive.
120  //archive &mpSystemInfo;
121  }
128  template<class Archive>
129  void load(Archive & archive, const unsigned int version)
130  {
131  archive & mNumberOfStateVariables;
132  archive & mUseAnalyticJacobian;
133  archive & mStateVariables;
134  std::vector<double> parameters;
135  archive & parameters;
136 
137  if (version > 0)
138  {
139  std::vector<std::string> param_names;
140  archive & param_names;
141 
142  CheckParametersOnLoad(parameters,param_names);
143  }
144  else
145  {
146  mParameters = parameters;
147  }
148  }
149  BOOST_SERIALIZATION_SPLIT_MEMBER()
150 
151 protected:
152 
155 
156 public:
157 
163  AbstractOdeSystem(unsigned numberOfStateVariables);
164 
168  virtual ~AbstractOdeSystem();
169 
177  virtual void EvaluateYDerivatives(double time, const std::vector<double>& rY,
178  std::vector<double>& rDY)=0;
179 
192  virtual bool CalculateStoppingEvent(double time, const std::vector<double>& rY);
193 
205  virtual double CalculateRootFunction(double time, const std::vector<double>& rY);
206 
212  bool GetUseAnalyticJacobian();
213 
219  const std::vector<double>& rGetConstStateVariables() const;
220 };
221 
222 CLASS_IS_ABSTRACT(AbstractOdeSystem)
223 BOOST_CLASS_VERSION(AbstractOdeSystem, 1u)
224 
225 #endif //_ABSTRACTODESYSTEM_HPP_
void save(Archive &archive, const unsigned int version) const
#define CLASS_IS_ABSTRACT(T)
virtual void EvaluateYDerivatives(double time, const std::vector< double > &rY, std::vector< double > &rDY)=0
const std::vector< double > & rGetConstStateVariables() const
virtual double CalculateRootFunction(double time, const std::vector< double > &rY)
void load(Archive &archive, const unsigned int version)
gcov doesn't like this file...
void CheckParametersOnLoad(const std::vector< double > &rParameters, const std::vector< std::string > &rParameterNames)
const std::vector< std::string > & rGetParameterNames() const
virtual bool CalculateStoppingEvent(double time, const std::vector< double > &rY)