Chaste  Release::3.4
AbstractCvodeCell.cpp
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35 
36 #ifdef CHASTE_CVODE
37 
38 #include <sstream>
39 #include <iostream>
40 #include <cmath>
41 
42 #include "AbstractCvodeCell.hpp"
43 #include "Exception.hpp"
44 #include "HeartConfig.hpp"
46 
47 
48 AbstractCvodeCell::AbstractCvodeCell(boost::shared_ptr<AbstractIvpOdeSolver> /* unused */,
49  unsigned numberOfStateVariables,
50  unsigned voltageIndex,
51  boost::shared_ptr<AbstractStimulusFunction> pIntracellularStimulus)
52  : AbstractCardiacCellInterface(boost::shared_ptr<AbstractIvpOdeSolver>(), voltageIndex, pIntracellularStimulus),
53  AbstractCvodeSystem(numberOfStateVariables),
54  mMaxDt(DOUBLE_UNSET)
55 {
56 }
57 
58 
60 {
61 }
62 
64 {
65  assert(mStateVariables);
67 }
68 
69 void AbstractCvodeCell::SetVoltage(double voltage)
70 {
71  assert(mStateVariables);
72  SetAnyVariable(mVoltageIndex, voltage);
73  SetFixedVoltage(voltage);
74 }
75 
76 
78 {
79  SetTimestep(maxDt); // Note: SetTimestep() sets the maximum timestep.
80 }
81 
83 {
84  mMaxDt = maxDt;
85 }
86 
88 {
89  return mMaxDt;
90 }
91 
92 
93 void AbstractCvodeCell::SolveAndUpdateState(double tStart, double tEnd)
94 {
95  if (mMaxDt == DOUBLE_UNSET)
96  {
97  SetTimestep(HeartConfig::Instance()->GetPrintingTimeStep());
98  }
99  Solve(tStart, tEnd, mMaxDt);
100 }
101 
102 OdeSolution AbstractCvodeCell::Compute(double tStart, double tEnd, double tSamp)
103 {
104  if (tSamp == 0.0)
105  {
107  }
108  if (mMaxDt == DOUBLE_UNSET)
109  {
110  SetTimestep(tSamp);
111  }
112  return Solve(tStart, tEnd, mMaxDt, tSamp);
113 }
114 
115 
116 void AbstractCvodeCell::ComputeExceptVoltage(double tStart, double tEnd)
117 {
118  double saved_voltage = GetVoltage();
119 
121  SolveAndUpdateState(tStart, tEnd);
123 
124  SetVoltage(saved_voltage); // In case of naughty models
125 
126 #ifndef NDEBUG
127  // Note that tests which rely on this throwing (e.g. such-and-such a variable is out of range)
128  // ought to be annotated with the NDEBUG macro
130 #endif // NDEBUG
131 }
132 
133 
135 {
136  if (clamp != mSetVoltageDerivativeToZero)
137  {
138  ResetSolver();
139  }
141 }
142 
144 {
146 }
147 
149 {
151 }
152 
154 {
155  std::vector<double> state_variables(GetNumberOfStateVariables());
157  return state_variables;
158 }
159 
160 const std::vector<std::string>& AbstractCvodeCell::rGetStateVariableNames() const
161 {
163 }
164 
165 void AbstractCvodeCell::SetStateVariables(const std::vector<double>& rVariables)
166 {
167  N_Vector vars = MakeNVector(rVariables);
169  DeleteVector(vars);
170 }
171 
173 {
175 }
176 
177 void AbstractCvodeCell::SetStateVariable(unsigned index, double newValue)
178 {
179  AbstractCvodeSystem::SetStateVariable(index, newValue);
180 }
181 
182 void AbstractCvodeCell::SetStateVariable(const std::string& rName, double newValue)
183 {
184  AbstractCvodeSystem::SetStateVariable(rName, newValue);
185 }
186 
187 double AbstractCvodeCell::GetAnyVariable(const std::string& rName, double time)
188 {
189  return AbstractCvodeSystem::GetAnyVariable(rName,time);
190 }
191 
192 double AbstractCvodeCell::GetParameter(const std::string& rParameterName)
193 {
194  return AbstractCvodeSystem::GetParameter(rParameterName);
195 }
196 
197 double AbstractCvodeCell::GetParameter(unsigned parameterIndex)
198 {
199  return AbstractCvodeSystem::GetParameter(parameterIndex);
200 }
201 
202 void AbstractCvodeCell::SetParameter(const std::string& rParameterName, double value)
203 {
204  AbstractCvodeSystem::SetParameter(rParameterName,value);
205 }
206 
207 #endif // CHASTE_CVODE
void SetStateVariable(unsigned index, double newValue)
void SetVoltage(double voltage)
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)
void SetParameter(const std::string &rParameterName, double value)
N_Vector MakeNVector(const std::vector< double > &rSrc)
unsigned GetNumberOfParameters() const
double GetPrintingTimeStep() const
AbstractCvodeCell(boost::shared_ptr< AbstractIvpOdeSolver > pSolver, unsigned numberOfStateVariables, unsigned voltageIndex, boost::shared_ptr< AbstractStimulusFunction > pIntracellularStimulus)
void SetStateVariables(const N_Vector &rStateVariables)
const std::vector< std::string > & rGetStateVariableNames() const
double GetParameter(unsigned index) const
const double DOUBLE_UNSET
Definition: Exception.hpp:56
void SetStateVariables(const std::vector< double > &rVariables)
void SetVoltageDerivativeToZero(bool clamp=true)
double GetParameter(const std::string &rParameterName)
void ComputeExceptVoltage(double tStart, double tEnd)
void SetAnyVariable(unsigned index, double value)
std::vector< double > GetStdVecStateVariables()
void SetParameter(const std::string &rName, double value)
virtual void SetVoltageDerivativeToZero(bool clamp=true)
unsigned GetNumberOfStateVariables() const
OdeSolution Solve(realtype tStart, realtype tEnd, realtype maxDt, realtype tSamp)
virtual void SolveAndUpdateState(double tStart, double tEnd)
void SetStateVariable(unsigned index, double newValue)
void CopyToStdVector(const VECTOR &rSrc, std::vector< double > &rDest)
static HeartConfig * Instance()
void DeleteVector(VECTOR &rVec)
double GetAnyVariable(unsigned index, double time=0.0, N_Vector *pDerivedQuantities=NULL)
double GetAnyVariable(const std::string &rName, double time=0.0)