Chaste  Release::2018.1
AbstractCardiacCell.cpp
1 /*
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3 Copyright (c) 2005-2018, University of Oxford.
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34 */
35 #include "AbstractCardiacCell.hpp"
36 
37 #include <cassert>
38 #include <iostream>
39 
40 #include "HeartConfig.hpp"
41 #include "Exception.hpp"
42 
43 AbstractCardiacCell::AbstractCardiacCell(boost::shared_ptr<AbstractIvpOdeSolver> pOdeSolver,
44  unsigned numberOfStateVariables,
45  unsigned voltageIndex,
46  boost::shared_ptr<AbstractStimulusFunction> pIntracellularStimulus)
47  : AbstractCardiacCellInterface(pOdeSolver, voltageIndex, pIntracellularStimulus),
48  AbstractOdeSystem(numberOfStateVariables),
49  mDt(HeartConfig::Instance()->GetOdeTimeStep())
50 {
51  // The second clause is to allow for FakeBathCell.
52  assert(voltageIndex < mNumberOfStateVariables || mNumberOfStateVariables == 0);
53 }
54 
56 {
57 }
58 
60 {
62  mParameters.resize(rGetParameterNames().size());
63 }
64 
66 {
67  mDt = dt;
68 }
69 
70 void AbstractCardiacCell::SolveAndUpdateState(double tStart, double tEnd)
71 {
72  mpOdeSolver->SolveAndUpdateStateVariable(this, tStart, tEnd, mDt);
73 }
74 
75 OdeSolution AbstractCardiacCell::Compute(double tStart, double tEnd, double tSamp)
76 {
77  if (tSamp < mDt)
78  {
79  tSamp = mDt;
80  }
81  return mpOdeSolver->Solve(this, rGetStateVariables(), tStart, tEnd, mDt, tSamp);
82 }
83 
84 void AbstractCardiacCell::ComputeExceptVoltage(double tStart, double tEnd)
85 {
86  double saved_voltage = GetVoltage();
87 
89  mpOdeSolver->SolveAndUpdateStateVariable(this, tStart, tEnd, mDt);
91 
92  SetVoltage(saved_voltage); // In case of naughty models
93 
94 #ifndef NDEBUG
95  // Note that tests which rely on this throwing (e.g. such-and-such a variable is out of range)
96  // ought to be annotated with the NDEBUG macro
98 #endif // NDEBUG
99 }
100 
102 {
103  SetAnyVariable(mVoltageIndex, voltage);
104  SetFixedVoltage(voltage);
105 }
106 
108 {
110 }
111 
113 {
115 }
116 
118 {
120 }
121 
123 {
125 }
126 
127 const std::vector<std::string>& AbstractCardiacCell::rGetStateVariableNames() const
128 {
130 }
131 
132 void AbstractCardiacCell::SetStateVariables(const std::vector<double>& rVariables)
133 {
135 }
136 
137 void AbstractCardiacCell::SetStateVariable(unsigned index, double newValue)
138 {
139  AbstractOdeSystem::SetStateVariable(index, newValue);
140 }
141 
142 void AbstractCardiacCell::SetStateVariable(const std::string& rName, double newValue)
143 {
144  AbstractOdeSystem::SetStateVariable(rName, newValue);
145 }
146 
147 double AbstractCardiacCell::GetAnyVariable(const std::string& rName, double time)
148 {
149  return AbstractOdeSystem::GetAnyVariable(rName, time);
150 }
151 
152 double AbstractCardiacCell::GetParameter(const std::string& rParameterName)
153 {
154  return AbstractOdeSystem::GetParameter(rParameterName);
155 }
156 
157 double AbstractCardiacCell::GetParameter(unsigned parameterIndex)
158 {
159  return AbstractOdeSystem::GetParameter(parameterIndex);
160 }
161 
162 void AbstractCardiacCell::SetParameter(const std::string& rParameterName, double value)
163 {
164  AbstractOdeSystem::SetParameter(rParameterName,value);
165 }
166 
167 #include "LuoRudy1991.hpp"
168 #include "LuoRudy1991BackwardEuler.hpp"
170 {
171  if (dynamic_cast<CellLuoRudy1991FromCellML*>(this) || dynamic_cast<CellLuoRudy1991FromCellMLBackwardEuler*>(this))
172  {
173  // If you do reach this, then you can try un-commenting the below, but you would be better re-generating your archive with a new version of Chaste.
175 // // The LR91 model saved in previous Chaste versions had a different ordering of state variables...
176 // // Old is h, j, m, CaI, V, d, f, x
177 // // New is V, m, h, j, d, f, X, [Ca]
178 // assert(GetNumberOfStateVariables() == 8);
179 // unsigned var_index_map[8] = {2, 3, 1, 7, 0, 4, 5, 6};
180 // std::vector<double> old_state(this->mStateVariables);
181 // for (unsigned i=0; i<8; i++)
182 // {
183 // this->mStateVariables[var_index_map[i]] = old_state[i];
184 // }
185 // // It also didn't used to have parameters...
186 // this->mParameters.resize(this->rGetParameterNames().size());
187 // assert(this->mParameters.size() == 3u);
188 // this->mParameters[0] = 0.09;
189 // this->mParameters[1] = 23.0;
190 // this->mParameters[2] = 0.282;
191  }
192 }
193 
194 
195 /*
196  * METHODS NEEDED BY FAST CARDIAC CELLS
197  */
198 void AbstractCardiacCell::SetState(CellModelState state)
199 {
200  EXCEPTION("Non fast-slow cell model being used in a fast-slow problem.");
201 }
202 
203 void AbstractCardiacCell::SetSlowValues(const std::vector<double> &rSlowValues)
204 {
205  EXCEPTION("Non fast-slow cell model being used in a fast-slow problem.");
206 }
207 
208 void AbstractCardiacCell::GetSlowValues(std::vector<double>& rSlowValues)
209 {
210  EXCEPTION("Non fast-slow cell model being used in a fast-slow problem.");
211 }
212 
214 {
215  EXCEPTION("Non fast-slow cell model being used in a fast-slow problem.");
216 }
217 
219 {
220  EXCEPTION("Non fast-slow cell model being used in a fast-slow problem.");
221 }
222 
223 void AbstractCardiacCell::AdjustOutOfRangeSlowValues(std::vector<double>& rSlowValues)
224 {
225  EXCEPTION("Non fast-slow cell model being used in a fast-slow problem.");
226 }
virtual void SetSlowValues(const std::vector< double > &rSlowValues)
virtual unsigned GetNumSlowValues()
AbstractCardiacCell(boost::shared_ptr< AbstractIvpOdeSolver > pOdeSolver, unsigned numberOfStateVariables, unsigned voltageIndex, boost::shared_ptr< AbstractStimulusFunction > pIntracellularStimulus)
#define EXCEPTION(message)
Definition: Exception.hpp:143
double GetParameter(const std::string &rParameterName)
std::vector< double > GetStdVecStateVariables()
const std::vector< std::string > & rGetStateVariableNames() const
void SetStateVariables(const std::vector< double > &rStateVariables)
const std::vector< std::string > & rGetStateVariableNames() const
#define NEVER_REACHED
Definition: Exception.hpp:206
double GetAnyVariable(const std::string &rName, double time=0.0)
virtual void SetState(CellModelState state)
virtual OdeSolution Compute(double tStart, double tEnd, double tSamp=0.0)
void SetAnyVariable(unsigned index, double value)
void SetParameter(const std::string &rName, double value)
void SetStateVariables(const std::vector< double > &rVariables)
virtual void SolveAndUpdateState(double tStart, double tEnd)
void SetParameter(const std::string &rParameterName, double value)
unsigned GetNumberOfParameters() const
void SetStateVariable(unsigned index, double newValue)
void SetTimestep(double dt)
virtual void GetSlowValues(std::vector< double > &rSlowValues)
virtual void SetVoltageDerivativeToZero(bool clamp=true)
boost::shared_ptr< AbstractIvpOdeSolver > mpOdeSolver
void SetStateVariable(unsigned index, double newValue)
void SetVoltage(double voltage)
virtual void AdjustOutOfRangeSlowValues(std::vector< double > &rSlowValues)
unsigned GetNumberOfStateVariables() const
virtual void ComputeExceptVoltage(double tStart, double tEnd)
const std::vector< std::string > & rGetParameterNames() const
double GetAnyVariable(unsigned index, double time=0.0, std::vector< double > *pDerivedQuantities=NULL)