Chaste Commit::baa90ac2819b962188b7562f2326be23c47859a7
AbstractRushLarsenCardiacCell.cpp
1/*
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34*/
35
36#include "AbstractRushLarsenCardiacCell.hpp"
37
38#include <cassert>
39#include <cmath>
40
41#include "Exception.hpp"
42#include "OdeSolution.hpp"
43#include "TimeStepper.hpp"
44
46 unsigned voltageIndex,
47 boost::shared_ptr<AbstractStimulusFunction> pIntracellularStimulus)
48 : AbstractCardiacCell(boost::shared_ptr<AbstractIvpOdeSolver>(),
49 numberOfStateVariables,
50 voltageIndex,
51 pIntracellularStimulus)
52{}
53
56
57OdeSolution AbstractRushLarsenCardiacCell::Compute(double tStart, double tEnd, double tSamp)
58{
59 // In this method, we iterate over timesteps, doing the following for each:
60 // - update V using a forward Euler step
61 // - do as in ComputeExceptVoltage(t) to update the remaining state variables
62 // using Rush Larsen method or forward Euler as appropriate
63
64 // Check length of time interval
65 if (tSamp < mDt)
66 {
67 tSamp = mDt;
68 }
69 const unsigned n_steps = (unsigned) floor((tEnd - tStart)/tSamp + 0.5);
70 assert(fabs(tStart+n_steps*tSamp - tEnd) < 1e-12);
71 const unsigned n_small_steps = (unsigned) floor(tSamp/mDt+0.5);
72 assert(fabs(mDt*n_small_steps - tSamp) < 1e-12);
73
74 // Initialise solution store
75 OdeSolution solutions;
76 solutions.SetNumberOfTimeSteps(n_steps);
77 solutions.rGetSolutions().push_back(rGetStateVariables());
78 solutions.rGetTimes().push_back(tStart);
80
81 std::vector<double> dy(mNumberOfStateVariables, 0);
82 std::vector<double> alpha(mNumberOfStateVariables, 0);
83 std::vector<double> beta(mNumberOfStateVariables, 0);
84
85 // Loop over time
86 for (unsigned i=0; i<n_steps; i++)
87 {
88 double curr_time = tStart;
89 for (unsigned j=0; j<n_small_steps; j++)
90 {
91 curr_time = tStart + i*tSamp + j*mDt;
92 EvaluateEquations(curr_time, dy, alpha, beta);
94 ComputeOneStepExceptVoltage(dy, alpha, beta);
96 }
97
98 // Update solutions
99 solutions.rGetSolutions().push_back(rGetStateVariables());
100 solutions.rGetTimes().push_back(curr_time+mDt);
101 }
102
103 return solutions;
104}
105
107{
109 TimeStepper stepper(tStart, tEnd, mDt);
110
111 std::vector<double> dy(mNumberOfStateVariables, 0);
112 std::vector<double> alpha(mNumberOfStateVariables, 0);
113 std::vector<double> beta(mNumberOfStateVariables, 0);
114
115 while (!stepper.IsTimeAtEnd())
116 {
117 EvaluateEquations(stepper.GetTime(), dy, alpha, beta);
118 ComputeOneStepExceptVoltage(dy, alpha, beta);
119
120#ifndef NDEBUG
121 // Check gating variables are still in range
123#endif // NDEBUG
124
125 stepper.AdvanceOneTimeStep();
126 }
128}
129
131{
132 TimeStepper stepper(tStart, tEnd, mDt);
133
134 std::vector<double> dy(mNumberOfStateVariables, 0);
135 std::vector<double> alpha(mNumberOfStateVariables, 0);
136 std::vector<double> beta(mNumberOfStateVariables, 0);
137
138 while (!stepper.IsTimeAtEnd())
139 {
140 EvaluateEquations(stepper.GetTime(), dy, alpha, beta);
142 ComputeOneStepExceptVoltage(dy, alpha, beta);
144
145 stepper.AdvanceOneTimeStep();
146 }
147}
148
150{
151 unsigned v_index = GetVoltageIndex();
152 rGetStateVariables()[v_index] += mDt*rDY[v_index];
153}
virtual void ComputeOneStepExceptVoltage(const std::vector< double > &rDY, const std::vector< double > &rAlphaOrTau, const std::vector< double > &rBetaOrInf)=0
OdeSolution Compute(double tStart, double tEnd, double tSamp=0.0)
AbstractRushLarsenCardiacCell(unsigned numberOfStateVariables, unsigned voltageIndex, boost::shared_ptr< AbstractStimulusFunction > pIntracellularStimulus)
void SolveAndUpdateState(double tStart, double tEnd)
virtual void EvaluateEquations(double time, std::vector< double > &rDY, std::vector< double > &rAlphaOrTau, std::vector< double > &rBetaOrInf)=0
void UpdateTransmembranePotential(const std::vector< double > &rDY)
void ComputeExceptVoltage(double tStart, double tEnd)
boost::shared_ptr< AbstractOdeSystemInformation > mpSystemInfo
void SetNumberOfTimeSteps(unsigned numTimeSteps)
std::vector< std::vector< double > > & rGetSolutions()
std::vector< double > & rGetTimes()
void SetOdeSystemInformation(boost::shared_ptr< const AbstractOdeSystemInformation > pOdeSystemInfo)
bool IsTimeAtEnd() const
double GetTime() const
void AdvanceOneTimeStep()