Chaste Commit::baa90ac2819b962188b7562f2326be23c47859a7
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#include <DeltaNotchInteriorOdeSystem.hpp>
Public Member Functions | |
DeltaNotchInteriorOdeSystem (std::vector< double > stateVariables=std::vector< double >()) | |
~DeltaNotchInteriorOdeSystem () | |
void | EvaluateYDerivatives (double time, const std::vector< double > &rY, std::vector< double > &rDY) |
Public Member Functions inherited from AbstractOdeSystem | |
AbstractOdeSystem (unsigned numberOfStateVariables) | |
virtual | ~AbstractOdeSystem () |
virtual bool | CalculateStoppingEvent (double time, const std::vector< double > &rY) |
virtual double | CalculateRootFunction (double time, const std::vector< double > &rY) |
bool | GetUseAnalyticJacobian () |
const std::vector< double > & | rGetConstStateVariables () const |
Public Member Functions inherited from AbstractParameterisedSystem< std::vector< double > > | |
AbstractParameterisedSystem (unsigned numberOfStateVariables) | |
std::vector< double > & | rGetStateVariables () |
std::vector< double > | GetStateVariables () |
void | SetStateVariables (const std::vector< double > &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 std::vector< double > &rInitialConditions) |
void | SetDefaultInitialCondition (unsigned index, double initialCondition) |
std::vector< double > | 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, std::vector< double > *pDerivedQuantities=NULL) |
double | GetAnyVariable (const std::string &rName, double time=0.0, std::vector< double > *pDerivedQuantities=NULL) |
void | SetAnyVariable (unsigned index, double value) |
void | SetAnyVariable (const std::string &rName, double value) |
virtual std::vector< double > | ComputeDerivedQuantities (double time, const std::vector< double > &rState) |
std::vector< double > | ComputeDerivedQuantitiesFromCurrentState (double time) |
Public Member Functions inherited from AbstractUntemplatedParameterisedSystem | |
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 |
Private Member Functions | |
template<class Archive > | |
void | serialize (Archive &archive, const unsigned int version) |
Friends | |
class | boost::serialization::access |
Additional Inherited Members | |
Protected Member Functions inherited from AbstractParameterisedSystem< std::vector< double > > | |
std::string | DumpState (const std::string &rMessage) |
std::string | DumpState (const std::string &rMessage, std::vector< double > Y) |
std::string | DumpState (const std::string &rMessage, std::vector< double > Y, double time) |
void | CheckParametersOnLoad (const std::vector< double > &rParameters, const std::vector< std::string > &rParameterNames) |
Protected Attributes inherited from AbstractOdeSystem | |
bool | mUseAnalyticJacobian |
Protected Attributes inherited from AbstractParameterisedSystem< std::vector< double > > | |
std::vector< double > | mStateVariables |
std::vector< double > | mParameters |
Protected Attributes inherited from AbstractUntemplatedParameterisedSystem | |
unsigned | mNumberOfStateVariables |
boost::shared_ptr< AbstractOdeSystemInformation > | mpSystemInfo |
Represents the Delta-Notch ODE system described by Collier et al, "Pattern formation by lateral inhibition with feedback: a mathematical model of delta-notch intercellular signalling" (Journal of Theoretical Biology 183:429-446, 1996). Here, however, we include edge based model: instead of using mean neighbouring delta we simply use neighbours edge data
Definition at line 55 of file DeltaNotchInteriorOdeSystem.hpp.
DeltaNotchInteriorOdeSystem::DeltaNotchInteriorOdeSystem | ( | std::vector< double > | stateVariables = std::vector<double>() | ) |
Default constructor.
stateVariables | optional initial conditions for state variables (only used in archiving) |
The state variables are as follows:
0 - Notch concentration for this cell 1 - Delta concentration for this cell
We store the last state variable so that it can be written to file at each time step alongside the others, and visualized.
Definition at line 39 of file DeltaNotchInteriorOdeSystem.cpp.
References AbstractParameterisedSystem< std::vector< double > >::mParameters, AbstractUntemplatedParameterisedSystem::mpSystemInfo, AbstractParameterisedSystem< std::vector< double > >::SetDefaultInitialCondition(), and AbstractParameterisedSystem< std::vector< double > >::SetStateVariables().
DeltaNotchInteriorOdeSystem::~DeltaNotchInteriorOdeSystem | ( | ) |
Destructor.
Definition at line 66 of file DeltaNotchInteriorOdeSystem.cpp.
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virtual |
Compute the RHS of the Collier et al. system of ODEs except that here we use values of Delta in neighbouring edges and Notch in edges of this cell Returns a vector representing the RHS of the ODEs at each time step, y' = [y1' ... yn']. An ODE solver will call this function repeatedly to solve for y = [y1 ... yn].
time | used to evaluate the RHS. |
rY | value of the solution vector used to evaluate the RHS. |
rDY | filled in with the resulting derivatives. |
Implements AbstractOdeSystem.
Definition at line 70 of file DeltaNotchInteriorOdeSystem.cpp.
References AbstractParameterisedSystem< std::vector< double > >::mParameters.
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inlineprivate |
Serialize the object and its member variables.
archive | the archive |
version | the current version of this class |
Definition at line 67 of file DeltaNotchInteriorOdeSystem.hpp.
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friend |
Definition at line 59 of file DeltaNotchInteriorOdeSystem.hpp.