Chaste  Release::3.4
AbstractCardiacCellInterface.cpp
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35 
36 #include "HeartConfig.hpp" // First for Boost 1.33/PETSc 2.2
37 #include "AbstractCardiacCellInterface.hpp"
38 #include "Exception.hpp"
39 
40 #include "Citations.hpp"
41 static PetscBool CardiacCellChasteCite = PETSC_FALSE;
42 const char CardiacCellChasteCitation[] = "@article{cooper2015cce,\n"
43 " title = {{Cellular cardiac electrophysiology modelling with Chaste and CellML}},\n"
44 " author = {Cooper, Jonathan and Spiteri, Raymond and Mirams, Gary R},\n"
45 " year = {2015},\n"
46 " journal = {Frontiers in Physiology},\n"
47 " pages = {511},\n"
48 " url = {http://journal.frontiersin.org/Journal/10.3389/fphys.2014.00511},\n"
49 " volume = {5},\n"
50 " doi = {10.3389/fphys.2014.00511},\n"
51 "}\n";
52 
54  boost::shared_ptr<AbstractIvpOdeSolver> pOdeSolver,
55  unsigned voltageIndex,
56  boost::shared_ptr<AbstractStimulusFunction> pIntracellularStimulus)
57  : mVoltageIndex(voltageIndex),
58  mpOdeSolver(pOdeSolver),
59  mpIntracellularStimulus(pIntracellularStimulus),
60  mSetVoltageDerivativeToZero(false),
61  mIsUsedInTissue(false),
62  mHasDefaultStimulusFromCellML(false),
63  mFixedVoltage(DOUBLE_UNSET)
64 {
65  // Record a reference for the calculations performed using this class,
66  // can be extracted with the '-citations' flag as an argument to any executable.
67  Citations::Register(CardiacCellChasteCitation, &CardiacCellChasteCite);
68 }
69 
70 
72 {
73 }
74 
75 
77 {
78  return mVoltageIndex;
79 }
80 
81 
82 void AbstractCardiacCellInterface::SetStimulusFunction(boost::shared_ptr<AbstractStimulusFunction> pStimulus)
83 {
85 }
86 
87 
89 {
90  return GetIntracellularStimulus(time);
91 }
92 
93 
94 void AbstractCardiacCellInterface::SetIntracellularStimulusFunction(boost::shared_ptr<AbstractStimulusFunction> pStimulus)
95 {
96  mpIntracellularStimulus = pStimulus;
97 }
98 
99 
101 {
102  return mpIntracellularStimulus->GetStimulus(time);
103 }
104 
105 
107 {
108  double stim;
109  if (mIsUsedInTissue)
110  {
111  // Convert from uA/cm^3 to uA/cm^2 by dividing by Am
113  }
114  else
115  {
116  stim = GetIntracellularStimulus(time);
117  }
118  return stim;
119 }
120 
122 {
123  mIsUsedInTissue = tissue;
124 }
125 
126 boost::shared_ptr<RegularStimulus> AbstractCardiacCellInterface::UseCellMLDefaultStimulus()
127 {
129  EXCEPTION("This class has no default stimulus from CellML metadata.");
130  return boost::shared_ptr<RegularStimulus>();
131 }
132 
134 {
136 }
137 
138 boost::shared_ptr<AbstractStimulusFunction> AbstractCardiacCellInterface::GetStimulusFunction()
139 {
141 }
142 
143 // Methods needed by boost serialization.
144 const boost::shared_ptr<AbstractStimulusFunction> AbstractCardiacCellInterface::GetStimulusFunction() const
145 {
147 }
148 
149 const boost::shared_ptr<AbstractIvpOdeSolver> AbstractCardiacCellInterface::GetSolver() const
150 {
151  return mpOdeSolver;
152 }
153 
154 void AbstractCardiacCellInterface::SetSolver(boost::shared_ptr<AbstractIvpOdeSolver> pSolver)
155 {
156  mpOdeSolver = pSolver;
157 }
158 
160 {
162  if (clamp)
163  {
165  }
166 }
167 
169 {
170  mFixedVoltage = voltage;
171 }
172 
174 {
175  EXCEPTION("AbstractCardiacCellInterface::GetIntracellularCalciumConcentration() called. "
176  "Either model has no [Ca_i] or method has not been implemented yet");
177 }
178 
179 
AbstractCardiacCellInterface(boost::shared_ptr< AbstractIvpOdeSolver > pOdeSolver, unsigned voltageIndex, boost::shared_ptr< AbstractStimulusFunction > pIntracellularStimulus)
boost::shared_ptr< AbstractStimulusFunction > mpIntracellularStimulus
const boost::shared_ptr< AbstractIvpOdeSolver > GetSolver() const
virtual double GetVoltage()=0
#define EXCEPTION(message)
Definition: Exception.hpp:143
void SetStimulusFunction(boost::shared_ptr< AbstractStimulusFunction > pStimulus)
void SetIntracellularStimulusFunction(boost::shared_ptr< AbstractStimulusFunction > pStimulus)
const double DOUBLE_UNSET
Definition: Exception.hpp:56
virtual boost::shared_ptr< RegularStimulus > UseCellMLDefaultStimulus()
static void Register(const char *pCitation, PetscBool *pSet)
Definition: Citations.cpp:43
virtual void SetVoltageDerivativeToZero(bool clamp=true)
boost::shared_ptr< AbstractStimulusFunction > GetStimulusFunction()
boost::shared_ptr< AbstractIvpOdeSolver > mpOdeSolver
double GetSurfaceAreaToVolumeRatio() const
void SetSolver(boost::shared_ptr< AbstractIvpOdeSolver > pSolver)
static HeartConfig * Instance()