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Chaste Commit::333233612e3dcc941d260418acd7b5ccdc30390e
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#include <AbstractCvodeSystem.hpp>
Public Member Functions | |
AbstractCvodeSystem (unsigned numberOfStateVariables) | |
virtual | ~AbstractCvodeSystem () |
virtual void | EvaluateYDerivatives (realtype time, const N_Vector y, N_Vector ydot)=0 |
virtual void | EvaluateAnalyticJacobian (realtype time, N_Vector y, N_Vector ydot, CHASTE_CVODE_DENSE_MATRIX jacobian, N_Vector tmp1, N_Vector tmp2, N_Vector tmp3) |
void | SetForceReset (bool autoReset) |
void | SetMinimalReset (bool minimalReset) |
bool | GetMinimalReset () |
Get whether we want to run with minimal reset or not (no reinitialisation of the solver if variables change) | |
bool | GetForceReset () |
Get whether we will force a solver reset on every call to Solve() | |
void | ResetSolver () |
OdeSolution | Solve (realtype tStart, realtype tEnd, realtype maxDt, realtype tSamp) |
void | Solve (realtype tStart, realtype tEnd, realtype maxDt) |
void | SetMaxSteps (long int numSteps) |
long int | GetMaxSteps () |
void | SetTolerances (double relTol=1e-5, double absTol=1e-7) |
double | GetRelativeTolerance () |
double | GetAbsoluteTolerance () |
double | GetLastStepSize () |
bool | GetUseAnalyticJacobian () const |
bool | HasAnalyticJacobian () const |
void | ForceUseOfNumericalJacobian (bool useNumericalJacobian=true) |
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AbstractParameterisedSystem (unsigned numberOfStateVariables) | |
N_Vector & | rGetStateVariables () |
N_Vector | GetStateVariables () |
void | SetStateVariables (const N_Vector &rStateVariables) |
double | GetStateVariable (unsigned index) const |
double | GetStateVariable (const std::string &rName) const |
void | SetStateVariable (unsigned index, double newValue) |
void | SetStateVariable (const std::string &rName, double newValue) |
virtual void | VerifyStateVariables () |
void | SetDefaultInitialConditions (const N_Vector &rInitialConditions) |
void | SetDefaultInitialCondition (unsigned index, double initialCondition) |
N_Vector | GetInitialConditions () const |
void | ResetToInitialConditions () |
double | GetParameter (unsigned index) const |
double | GetParameter (const std::string &rName) const |
void | SetParameter (const std::string &rName, double value) |
void | SetParameter (unsigned index, double value) |
double | GetAnyVariable (unsigned index, double time=0.0, N_Vector *pDerivedQuantities=NULL) |
double | GetAnyVariable (const std::string &rName, double time=0.0, N_Vector *pDerivedQuantities=NULL) |
void | SetAnyVariable (unsigned index, double value) |
void | SetAnyVariable (const std::string &rName, double value) |
virtual N_Vector | ComputeDerivedQuantities (double time, const N_Vector &rState) |
N_Vector | ComputeDerivedQuantitiesFromCurrentState (double time) |
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AbstractUntemplatedParameterisedSystem (unsigned numberOfStateVariables) | |
virtual | ~AbstractUntemplatedParameterisedSystem () |
boost::shared_ptr< const AbstractOdeSystemInformation > | GetSystemInformation () const |
std::string | GetSystemName () const |
unsigned | GetNumberOfAttributes () const |
bool | HasAttribute (const std::string &rName) const |
double | GetAttribute (const std::string &rName) const |
unsigned | GetNumberOfStateVariables () const |
const std::vector< std::string > & | rGetStateVariableNames () const |
const std::vector< std::string > & | rGetStateVariableUnits () const |
unsigned | GetStateVariableIndex (const std::string &rName) const |
bool | HasStateVariable (const std::string &rName) const |
std::string | GetStateVariableUnits (unsigned index) const |
unsigned | GetNumberOfParameters () const |
const std::vector< std::string > & | rGetParameterNames () const |
const std::vector< std::string > & | rGetParameterUnits () const |
unsigned | GetParameterIndex (const std::string &rName) const |
bool | HasParameter (const std::string &rName) const |
std::string | GetParameterUnits (unsigned index) const |
unsigned | GetNumberOfDerivedQuantities () const |
const std::vector< std::string > & | rGetDerivedQuantityNames () const |
const std::vector< std::string > & | rGetDerivedQuantityUnits () const |
unsigned | GetDerivedQuantityIndex (const std::string &rName) const |
bool | HasDerivedQuantity (const std::string &rName) const |
std::string | GetDerivedQuantityUnits (unsigned index) const |
unsigned | GetAnyVariableIndex (const std::string &rName) const |
bool | HasAnyVariable (const std::string &rName) const |
std::string | GetAnyVariableUnits (unsigned index) const |
std::string | GetAnyVariableUnits (const std::string &rName) const |
Protected Member Functions | |
void | Init () |
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std::string | DumpState (const std::string &rMessage) |
std::string | DumpState (const std::string &rMessage, N_Vector Y) |
std::string | DumpState (const std::string &rMessage, N_Vector Y, double time) |
void | CheckParametersOnLoad (const std::vector< double > &rParameters, const std::vector< std::string > &rParameterNames) |
Protected Attributes | |
bool | mHasAnalyticJacobian |
bool | mUseAnalyticJacobian |
double | mRelTol |
double | mAbsTol |
void * | mpCvodeMem |
long int | mMaxSteps |
double | mLastInternalStepSize |
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N_Vector | mStateVariables |
N_Vector | mParameters |
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unsigned | mNumberOfStateVariables |
boost::shared_ptr< AbstractOdeSystemInformation > | mpSystemInfo |
Private Member Functions | |
template<class Archive > | |
void | save (Archive &archive, const unsigned int version) const |
template<class Archive > | |
void | load (Archive &archive, const unsigned int version) |
void | SetupCvode (N_Vector initialConditions, realtype tStart, realtype maxDt) |
void | RecordStoppingPoint (double stopTime) |
void | FreeCvodeMemory () |
void | CvodeError (int flag, const char *msg, const double &rTime, const double &rStartTime, const double &rEndTime) |
Private Attributes | |
N_Vector | mLastSolutionState |
double | mLastSolutionTime |
bool | mForceReset |
bool | mForceMinimalReset |
Friends | |
class | TestAbstractCvodeSystem |
class | boost::serialization::access |
Abstract OdeSystem class for Cvode systems (N_Vector instead of std::vector)
Sets up variables and functions for a general CVODE system, and uses an inbuilt CVODE solver.
N.B. The CvodeAdaptor solver is not used by AbstractCvodeSystems, it is only used to translate when the ODE system uses the normal std::vector<double> state variables. For Chaste developers - this means there is some duplication of code between this class and CvodeAdaptor as both set up and use CVODE to solve systems. If you change one you should probably change both!
ODE systems are specified primarily by the EvaluateYDerivatives() method, which calculates the right-hand side of the system.
You can also specify an EvaluateAnalyticJacobian() method which will allow CVODE to evaluate the Jacobian matrix precisely instead of using multiple calls to EvaluateYDerivatives() to make an approximation to it. This generally provides extra accuracy and better convergence, and so gives a speed up for a given tolerance. Cardiac action potential model Jacobians are calculated automatically by chaste_codegen.
Instances can store their state internally in the mStateVariables vector in our base class AbstractParameterisedSystem (see also GetNumberOfStateVariables(), SetStateVariables() and rGetStateVariables()), although this is not essential - the vector may be empty, in which case AbstractIvpOdeSolver::SolveAndUpdateStateVariable may not be used to solve the system.
CVODE systems may also have a vector of parameters, which can be accessed through the GetParameter() and SetParameter() methods of our base class.
Information about what the parameters and state variables represent is provided by a subclass of AbstractOdeSystemInformation. Various wrapper methods (e.g. rGetStateVariableNames()) are provided in our base class to access this information.
Also, subclasses may define a condition at which ODE solvers should stop prematurely. For this class CVODE solvers are being used, so CalculateRootFunction() should be used to detect the stopping time.
Note that the default tolerances for the solver are set by SetTolerances(), these can make quite a difference to the time it takes to solve the ODE system.
Repeated calls to Solve will no longer set up and delete CVODE memory, unless the following method is called:
SetForceReset(true) - reset each time Solve() is called
default - reset if state variables change, or we ask to solve from a different time than the last solve call finished.
SetMinimalReset(true) - ignore changes in state vars and just reset if the time is inconsistent.
Definition at line 141 of file AbstractCvodeSystem.hpp.
AbstractCvodeSystem::AbstractCvodeSystem | ( | unsigned | numberOfStateVariables | ) |
Constructor.
numberOfStateVariables | the number of state variables in the ODE system |
Definition at line 158 of file AbstractCvodeSystem.cpp.
References SetTolerances().
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Virtual destructor since we have virtual methods.
Definition at line 199 of file AbstractCvodeSystem.cpp.
References DeleteVector(), FreeCvodeMemory(), mLastSolutionState, AbstractParameterisedSystem< N_Vector >::mParameters, and AbstractParameterisedSystem< N_Vector >::mStateVariables.
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Report an error from CVODE.
flag | CVODE error code |
msg | Our description of the error |
rTime | The time that the solver got to |
rStartTime | The time that the solver started at. |
rEndTime | The time that the solver was supposed to solve up to. |
Definition at line 566 of file AbstractCvodeSystem.cpp.
References EXCEPTION, FreeCvodeMemory(), MakeStdVec(), mpCvodeMem, AbstractParameterisedSystem< N_Vector >::mStateVariables, and AbstractUntemplatedParameterisedSystem::rGetStateVariableNames().
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This method is called by AbstractCvodeSystemJacAdaptor method in the .cpp file.
It provides an interface between the methods different versions of CVODE are expecting and the Jacobians provided by Chaste CVODE systems.
time | the current time (used by ODE systems like y' = f(t,y) only I guess) |
y | the current state variables y for y' = f(t,y) |
ydot | the current set of derivatives y' = f(t,y) |
jacobian | a pointer to a jacobian, populated by this method. |
tmp1 | working memory of the correct size provided by CVODE for temporary calculations |
tmp2 | working memory of the correct size provided by CVODE for temporary calculations |
tmp3 | working memory of the correct size provided by CVODE for temporary calculations |
Definition at line 356 of file AbstractCvodeSystem.hpp.
References EXCEPTION.
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Method to evaluate the derivatives of the system.
time | the current time |
y | the current values of the state variables |
ydot | storage for the derivatives of the system; will be filled in on return |
void AbstractCvodeSystem::ForceUseOfNumericalJacobian | ( | bool | useNumericalJacobian = true | ) |
Force the use of a numerical Jacobian, even if an analytic form is provided. This is needed for a handful of troublesome models.
useNumericalJacobian | Whether to use a numerical instead of the analytic Jacobian. |
Definition at line 621 of file AbstractCvodeSystem.cpp.
References EXCEPTION, FreeCvodeMemory(), mHasAnalyticJacobian, and mUseAnalyticJacobian.
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Free CVODE memory when finished with.
Definition at line 541 of file AbstractCvodeSystem.cpp.
References mpCvodeMem.
Referenced by ~AbstractCvodeSystem(), CvodeError(), and ForceUseOfNumericalJacobian().
double AbstractCvodeSystem::GetAbsoluteTolerance | ( | ) |
Definition at line 352 of file AbstractCvodeSystem.cpp.
References mAbsTol.
bool AbstractCvodeSystem::GetForceReset | ( | ) |
Get whether we will force a solver reset on every call to Solve()
Definition at line 376 of file AbstractCvodeSystem.cpp.
References mForceReset.
double AbstractCvodeSystem::GetLastStepSize | ( | ) |
Definition at line 357 of file AbstractCvodeSystem.cpp.
References mLastInternalStepSize.
long int AbstractCvodeSystem::GetMaxSteps | ( | ) |
Definition at line 335 of file AbstractCvodeSystem.cpp.
References mMaxSteps.
bool AbstractCvodeSystem::GetMinimalReset | ( | ) |
Get whether we want to run with minimal reset or not (no reinitialisation of the solver if variables change)
Definition at line 371 of file AbstractCvodeSystem.cpp.
References mForceMinimalReset.
double AbstractCvodeSystem::GetRelativeTolerance | ( | ) |
Definition at line 347 of file AbstractCvodeSystem.cpp.
References mRelTol.
bool AbstractCvodeSystem::GetUseAnalyticJacobian | ( | ) | const |
Definition at line 616 of file AbstractCvodeSystem.cpp.
References mUseAnalyticJacobian.
bool AbstractCvodeSystem::HasAnalyticJacobian | ( | ) | const |
Definition at line 611 of file AbstractCvodeSystem.cpp.
References mHasAnalyticJacobian.
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Must be called by concrete subclass constructors to initialise the state variables, after setting mpSystemInfo.
Definition at line 183 of file AbstractCvodeSystem.cpp.
References DeleteVector(), AbstractParameterisedSystem< N_Vector >::GetInitialConditions(), AbstractParameterisedSystem< N_Vector >::mParameters, AbstractParameterisedSystem< N_Vector >::mStateVariables, and AbstractUntemplatedParameterisedSystem::rGetParameterNames().
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Archive the member variables.
archive | the archive |
version | the current version of this class |
Definition at line 196 of file AbstractCvodeSystem.hpp.
References AbstractParameterisedSystem< N_Vector >::CheckParametersOnLoad(), CopyFromStdVector(), mAbsTol, mForceMinimalReset, mForceReset, mHasAnalyticJacobian, mLastInternalStepSize, mLastSolutionTime, mMaxSteps, AbstractUntemplatedParameterisedSystem::mNumberOfStateVariables, mRelTol, AbstractParameterisedSystem< N_Vector >::mStateVariables, and mUseAnalyticJacobian.
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Record where the last solve got to so we know whether to re-initialise.
stopTime | the finishing time |
Definition at line 520 of file AbstractCvodeSystem.cpp.
References CreateVectorIfEmpty(), AbstractUntemplatedParameterisedSystem::GetNumberOfStateVariables(), GetVectorComponent(), mForceReset, mLastSolutionState, mLastSolutionTime, AbstractParameterisedSystem< N_Vector >::mStateVariables, and SetVectorComponent().
void AbstractCvodeSystem::ResetSolver | ( | ) |
Successive calls to Solve will attempt to intelligently determine whether to re-initialise the internal CVODE solver, or whether we are simply extending the previous solution forward in time. This mechanism compares the state vector to its previous value, and the start time to the end of the last solve, which captures most cases where re-initialisation is required. However, changes to the RHS function can also require this, and cannot be automatically detected. In such cases users must call this function to force re-initialisation.
Definition at line 390 of file AbstractCvodeSystem.cpp.
References DeleteVector(), and mLastSolutionState.
Referenced by SetForceReset(), SetTolerances(), and AbstractCvodeCell::SetVoltageDerivativeToZero().
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Archive the member variables.
archive | the archive |
version | the current version of this class |
Definition at line 154 of file AbstractCvodeSystem.hpp.
References mAbsTol, MakeStdVec(), mForceMinimalReset, mForceReset, mHasAnalyticJacobian, mLastInternalStepSize, mLastSolutionTime, mMaxSteps, AbstractUntemplatedParameterisedSystem::mNumberOfStateVariables, AbstractParameterisedSystem< N_Vector >::mParameters, mRelTol, AbstractParameterisedSystem< N_Vector >::mStateVariables, mUseAnalyticJacobian, and AbstractUntemplatedParameterisedSystem::rGetParameterNames().
void AbstractCvodeSystem::SetForceReset | ( | bool | autoReset | ) |
Set whether to automatically re-initialise CVODE on every call to Solve, or whether to attempt to guess when re-initialisation is needed. For example it will re-initialise if the time changes, or any state variables change. You can safely change parameters between solve calls with or without resets.
See also ResetSolver and SetMinimalReset
autoReset | whether to reset on every Solve |
Definition at line 362 of file AbstractCvodeSystem.cpp.
References mForceReset, and ResetSolver().
Referenced by SetMinimalReset().
void AbstractCvodeSystem::SetMaxSteps | ( | long int | numSteps | ) |
Change the maximum number of steps to be taken by the solver in its attempt to reach the next output time. Default is 500 (set by CVODE).
numSteps | new maximum |
Definition at line 330 of file AbstractCvodeSystem.cpp.
References mMaxSteps.
void AbstractCvodeSystem::SetMinimalReset | ( | bool | minimalReset | ) |
Set whether to reduce the checking done when guessing when re-initialisation is needed, so it ignores changes in the state variables. If called with true argument, will call SetForceReset(false). You can safely change parameters between solve calls with or without resets.
minimalReset | whether to avoid checking for changes in state variables |
Definition at line 381 of file AbstractCvodeSystem.cpp.
References mForceMinimalReset, and SetForceReset().
Set relative and absolute tolerances; both scalars. If no parameters are given, tolerances will be reset to default values.
relTol | the relative tolerance for the solver (defaults to 1e-5) |
absTol | the absolute tolerance for the solver (defaults to 1e-7) |
Definition at line 340 of file AbstractCvodeSystem.cpp.
References mAbsTol, mRelTol, and ResetSolver().
Referenced by AbstractCvodeSystem().
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Set up the CVODE data structures needed to solve the given system from a given point.
initialConditions | initial conditions |
tStart | start time of simulation |
maxDt | maximum time step to take |
Definition at line 395 of file AbstractCvodeSystem.cpp.
References EXCEPTION, AbstractUntemplatedParameterisedSystem::GetNumberOfStateVariables(), GetVectorComponent(), mAbsTol, mForceMinimalReset, mForceReset, mLastSolutionState, mLastSolutionTime, mMaxSteps, mpCvodeMem, mRelTol, AbstractParameterisedSystem< N_Vector >::mStateVariables, mUseAnalyticJacobian, and CompareDoubles::WithinAnyTolerance().
void AbstractCvodeSystem::Solve | ( | realtype | tStart, |
realtype | tEnd, | ||
realtype | maxDt | ||
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Simulate the cell, updating its internal state variables.
Uses the current values of the state variables at initial conditions. If the state variables have not been set (either by a prior solve, or a call to SetStateVariables) the initial conditions (given by GetInitialConditions) will be used.
tStart | start time of simulation |
tEnd | end time of simulation |
maxDt | maximum time step to be taken by the adaptive solver (set this appropriately to avoid missing a stimulus) |
Definition at line 276 of file AbstractCvodeSystem.cpp.
References CvodeError(), mLastInternalStepSize, mpCvodeMem, AbstractParameterisedSystem< N_Vector >::mStateVariables, RecordStoppingPoint(), SetupCvode(), UNUSED_OPT, and AbstractParameterisedSystem< N_Vector >::VerifyStateVariables().
OdeSolution AbstractCvodeSystem::Solve | ( | realtype | tStart, |
realtype | tEnd, | ||
realtype | maxDt, | ||
realtype | tSamp | ||
) |
Simulate the cell, returning a sampling of the state variables.
Uses the current values of the state variables at initial conditions. If the state variables have not been set (either by a prior solve, or a call to SetStateVariables) the initial conditions (given by GetInitialConditions) will be used.
The final values of the state variables will also be stored in this object.
tStart | start time of simulation |
tEnd | end time of simulation |
maxDt | maximum time step to be taken by the adaptive solver (set this appropriately to avoid missing a stimulus) |
tSamp | sampling interval at which to store results |
Definition at line 214 of file AbstractCvodeSystem.cpp.
References TimeStepper::AdvanceOneTimeStep(), CvodeError(), TimeStepper::EstimateTimeSteps(), TimeStepper::GetNextTime(), TimeStepper::GetTime(), TimeStepper::GetTotalTimeStepsTaken(), TimeStepper::IsTimeAtEnd(), MakeStdVec(), mLastInternalStepSize, mpCvodeMem, AbstractUntemplatedParameterisedSystem::mpSystemInfo, AbstractParameterisedSystem< N_Vector >::mStateVariables, RecordStoppingPoint(), OdeSolution::rGetSolutions(), OdeSolution::rGetTimes(), OdeSolution::SetNumberOfTimeSteps(), OdeSolution::SetOdeSystemInformation(), SetupCvode(), UNUSED_OPT, and AbstractParameterisedSystem< N_Vector >::VerifyStateVariables().
Referenced by AbstractCvodeCell::Compute(), and AbstractCvodeCell::SolveAndUpdateState().
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Definition at line 146 of file AbstractCvodeSystem.hpp.
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Definition at line 144 of file AbstractCvodeSystem.hpp.
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Absolute tolerance for solver.
Definition at line 296 of file AbstractCvodeSystem.hpp.
Referenced by GetAbsoluteTolerance(), load(), save(), SetTolerances(), and SetupCvode().
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Whether to ignore changes in the state variables when deciding whether to reset.
Definition at line 276 of file AbstractCvodeSystem.hpp.
Referenced by GetMinimalReset(), load(), save(), SetMinimalReset(), and SetupCvode().
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Whether to automatically reset CVODE on each Solve call.
Definition at line 273 of file AbstractCvodeSystem.hpp.
Referenced by GetForceReset(), load(), RecordStoppingPoint(), save(), SetForceReset(), and SetupCvode().
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Whether we have an analytic Jacobian.
Definition at line 287 of file AbstractCvodeSystem.hpp.
Referenced by ForceUseOfNumericalJacobian(), HasAnalyticJacobian(), load(), and save().
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The size of the previous timestep.
Definition at line 308 of file AbstractCvodeSystem.hpp.
Referenced by GetLastStepSize(), load(), save(), Solve(), and Solve().
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Remember where the last solve got to so we know whether to re-initialise.
Definition at line 267 of file AbstractCvodeSystem.hpp.
Referenced by ~AbstractCvodeSystem(), RecordStoppingPoint(), ResetSolver(), and SetupCvode().
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Remember where the last solve got to so we know whether to re-initialise.
Definition at line 270 of file AbstractCvodeSystem.hpp.
Referenced by load(), RecordStoppingPoint(), save(), and SetupCvode().
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The maximum number of steps to be taken by the solver in its attempt to reach the next output time.
Definition at line 305 of file AbstractCvodeSystem.hpp.
Referenced by GetMaxSteps(), load(), save(), SetMaxSteps(), and SetupCvode().
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CVODE's internal data.
Definition at line 299 of file AbstractCvodeSystem.hpp.
Referenced by CvodeError(), FreeCvodeMemory(), SetupCvode(), Solve(), and Solve().
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Relative tolerance for solver.
Definition at line 293 of file AbstractCvodeSystem.hpp.
Referenced by GetRelativeTolerance(), load(), save(), SetTolerances(), and SetupCvode().
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Whether to use an analytic Jacobian.
Definition at line 290 of file AbstractCvodeSystem.hpp.
Referenced by ForceUseOfNumericalJacobian(), GetUseAnalyticJacobian(), load(), save(), and SetupCvode().