Chaste Commit::1fd4e48e3990e67db148bc1bc4cf6991a0049d0c
SteadyStateRunner.cpp
1/*
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34*/
35
36#include "SteadyStateRunner.hpp"
37#include "ZeroStimulus.hpp"
38
39#ifdef CHASTE_CVODE
40
42{
43 // Get necessary things from stimulus current
44 boost::shared_ptr<RegularStimulus> p_reg_stim = boost::static_pointer_cast<RegularStimulus>(mpModel->GetStimulusFunction());
45 boost::shared_ptr<ZeroStimulus> p_zero_stim(new ZeroStimulus);
46 const double pacing_cycle_length = p_reg_stim->GetPeriod(); // ms
47 double stimulus_duration = p_reg_stim->GetDuration(); // ms
48 double stimulus_start_time = p_reg_stim->GetStartTime(); // ms
49 double stimulus_end_time = stimulus_start_time + stimulus_duration;
50 double maximum_time_step = pacing_cycle_length; // ms
51
52 bool force_reset_setting = mpModel->GetForceReset();
53 bool minimal_reset_setting = mpModel->GetMinimalReset();
54
55 mpModel->SetMaxSteps(1e5); // Per pace (or part of pace with stimulus start/stop).
56 mpModel->SetForceReset(true); // Best way to deal with discontinuities in the RHS according to CVODE
57
58 // Set up vectors to monitor progress
59 std::vector<double> old_state_vars;
60 std::vector<double> new_state_vars;
61 CopyToStdVector(mpModel->rGetStateVariables(), old_state_vars);
62
63 const unsigned num_paces_to_analyse = (mTwoPaceScan) ? 2u : 1u;
64 for (unsigned i = 0; i < mMaxNumPaces; i = i + num_paces_to_analyse)
65 {
66 // Look at two paces in the hope of detecting alternans and still saying we're steady-ish.
67 for (unsigned j = 0; j < num_paces_to_analyse; j++)
68 {
69 // Pre-stimulus (can skip if stimulus is applied at t=0)
70 if (stimulus_start_time > 0)
71 {
72 mpModel->SetMinimalReset(true); // We are just carrying on from last stop (not on stimulus) so don't need a solver reset.
73 mpModel->SetStimulusFunction(p_zero_stim);
74 mpModel->Solve((pacing_cycle_length) * (double)(i + j), (pacing_cycle_length) * (double)(i + j) + stimulus_start_time, maximum_time_step);
75 mpModel->SetForceReset(true); // Reset every solve call after this (next two) to deal with discontinuities in stimulus.
76 }
77
78 mpModel->SetStimulusFunction(p_reg_stim); // RegularStimulus applies at stimulus_start_time<=t<=stimulus_end_time (includes bounds).
79 mpModel->Solve((pacing_cycle_length) * (double)(i + j) + stimulus_start_time, (pacing_cycle_length) * (double)(i + j) + stimulus_end_time, maximum_time_step);
80
81 // Post-stimulus
82 mpModel->SetStimulusFunction(p_zero_stim); // added this because the RegularStimulus behaviour is to apply the stimulus at t=stimulus_end_time, which might confuse matters.
83 mpModel->Solve((pacing_cycle_length) * (double)(i + j) + stimulus_end_time, (pacing_cycle_length) * (double)(i + j + 1), maximum_time_step);
84 }
85
86 this->mNumEvaluations += num_paces_to_analyse;
87 CopyToStdVector(mpModel->rGetStateVariables(), new_state_vars);
88
89 // Calculate the change in the norm of the state variables
90 double temp = 0;
91 for (unsigned j = 0; j < old_state_vars.size(); j++)
92 {
93 temp += fabs(new_state_vars[j] - old_state_vars[j]);
94 }
95
96 if (temp < 1e-6)
97 {
98 break; // say we are converged enough to steady state to stop here.
99 }
100
101 old_state_vars = new_state_vars;
102 }
103
104 // Reset stimulus to normal
105 mpModel->SetStimulusFunction(p_reg_stim);
106 mpModel->SetForceReset(force_reset_setting);
107 mpModel->SetMinimalReset(minimal_reset_setting);
108}
109
110#endif // CHASTE_CVODE
void CopyToStdVector(const VECTOR &rSrc, std::vector< double > &rDest)
boost::shared_ptr< AbstractCvodeCell > mpModel
virtual void RunToSteadyStateImplementation()