Chaste Commit::baa90ac2819b962188b7562f2326be23c47859a7
AbstractGeneralizedRushLarsenCardiacCell.cpp
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35
36/*
37Megan E. Marsh, Raymond J. Spiteri
38Numerical Simulation Laboratory
39University of Saskatchewan
40December 2011
41Partial support provided by research grants from the National
42Science and Engineering Research Council (NSERC) of Canada
43and the MITACS/Mprime Canadian Network of Centres of Excellence.
44*/
45
46#include "AbstractGeneralizedRushLarsenCardiacCell.hpp"
47#include <cassert>
48#include <cmath>
49#include "Exception.hpp"
50#include "OdeSolution.hpp"
51#include "TimeStepper.hpp"
52
54 unsigned voltageIndex,
55 boost::shared_ptr<AbstractStimulusFunction> pIntracellularStimulus)
56 : AbstractCardiacCell(boost::shared_ptr<AbstractIvpOdeSolver>(),
57 numberOfStateVariables,
58 voltageIndex,
59 pIntracellularStimulus),
60 mHasAnalyticJacobian(false)
61{
62 mPartialF.resize(numberOfStateVariables);
63 mEvalF.resize(numberOfStateVariables);
64 mYInit.resize(numberOfStateVariables);
65}
66
69
70OdeSolution AbstractGeneralizedRushLarsenCardiacCell::Compute(double tStart, double tEnd, double tSamp)
71{
72 // Check length of time interval
73 if (tSamp < mDt)
74 {
75 tSamp = mDt;
76 }
77 const unsigned n_steps = (unsigned) floor((tEnd - tStart)/tSamp + 0.5);
78 assert(fabs(tStart+n_steps*tSamp - tEnd) < 1e-12);
79 const unsigned n_small_steps = (unsigned) floor(tSamp/mDt+0.5);
80 assert(fabs(mDt*n_small_steps - tSamp) < 1e-12);
81
82 // Initialise solution store
83 OdeSolution solutions;
84 solutions.SetNumberOfTimeSteps(n_steps);
85 solutions.rGetSolutions().push_back(rGetStateVariables());
86 solutions.rGetTimes().push_back(tStart);
88
89 // Loop over time
90 double v_old, v_new;
91 double& r_V = rGetStateVariables()[GetVoltageIndex()];
92 for (unsigned i=0; i<n_steps; i++)
93 {
94 double curr_time = tStart;
95 for (unsigned j=0; j<n_small_steps; j++)
96 {
97 curr_time = tStart + i*tSamp + j*mDt;
98 v_old = r_V;
100 v_new = r_V;
101 r_V = v_old;
103 r_V = v_new;
105 }
106
107 // Update solutions
108 solutions.rGetSolutions().push_back(rGetStateVariables());
109 solutions.rGetTimes().push_back(curr_time+mDt);
110 }
111
112 return solutions;
113}
114
116{
118 TimeStepper stepper(tStart, tEnd, mDt);
119
120 while (!stepper.IsTimeAtEnd())
121 {
123
124#ifndef NDEBUG
125 // Check gating variables are still in range
127#endif // NDEBUG
128
129 stepper.AdvanceOneTimeStep();
130 }
132}
133
135{
136 TimeStepper stepper(tStart, tEnd, mDt);
137
138 double v_old, v_new;
139 double& r_V = rGetStateVariables()[GetVoltageIndex()];
140 while (!stepper.IsTimeAtEnd())
141 {
142 v_old = r_V;
144 v_new = r_V;
145 r_V = v_old;
147 r_V = v_new;
149
150 stepper.AdvanceOneTimeStep();
151 }
152}
153
158
160{
161 if (!useNumericalJacobian)
162 {
163 EXCEPTION("Using analytic Jacobian terms for generalised Rush-Larsen is not yet supported.");
164 }
165// if (!useNumericalJacobian && !mHasAnalyticJacobian)
166// {
167// EXCEPTION("Analytic Jacobian requested, but this ODE system doesn't have one. You can check this with HasAnalyticJacobian().");
168// }
169 mUseAnalyticJacobian = !useNumericalJacobian;
170}
#define EXCEPTION(message)
virtual void SetVoltageDerivativeToZero(bool clamp=true)
virtual void UpdateTransmembranePotential(double time)=0
OdeSolution Compute(double tStart, double tEnd, double tSamp=0.0)
virtual void ComputeOneStepExceptVoltage(double time)=0
AbstractGeneralizedRushLarsenCardiacCell(unsigned numberOfStateVariables, unsigned voltageIndex, boost::shared_ptr< AbstractStimulusFunction > pIntracellularStimulus)
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()