#include <ActivationOutputModifier.hpp>

Inheritance diagram for ActivationOutputModifier:

Collaboration diagram for ActivationOutputModifier:

Public Member Functions
	ActivationOutputModifier (const std::string &rFilename, double threshold)

virtual void	InitialiseAtStart (DistributedVectorFactory *pVectorFactory, const std::vector< unsigned > &rNodePermutation)

virtual void	FinaliseAtEnd ()

virtual void	ProcessSolutionAtTimeStep (double time, Vec solution, unsigned problemDim)

Public Member Functions inherited from AbstractOutputModifier
	AbstractOutputModifier (const std::string &rFilename, double flushTime=0.0)

virtual	~AbstractOutputModifier ()

Private Member Functions
template<class Archive >
void	serialize (Archive &archive, const unsigned int version)

	ActivationOutputModifier ()

Private Attributes
double	mThreshold

unsigned	mLocalSize

std::vector< double >	mFirstActivitationTimes

std::vector< double >	mFirstRecoveryTimes

std::vector< double >	mSecondActivitationTimes

std::vector< double >	mSecondRecoveryTimes

Friends
class	TestOutputModifiers

class	boost::serialization::access

Additional Inherited Members
Protected Member Functions inherited from AbstractOutputModifier
	AbstractOutputModifier ()

Protected Attributes inherited from AbstractOutputModifier
std::string	mFilename

double	mFlushTime

Detailed Description

Specialised class for on-the-fly calculation of activation and recovery times. This is hard-coded for the first 2 rounds of activation/recovery.

Times are relative to simulation start and are listed in node order and in 4 columns comma separated (.CSV)

node_0_activation, node_0_recovery, node_0_later_activation, node_0_later_recovery node_1_activation, node_1_recovery, node_1_later_activation, node_1_later_recovery ...

Any missing data (node was not activated a second time or did not recover) is marked with -1.

WARNING: If you checkpoint this class then the partial results will not be stored. This is because the sizes of the activation time vectors will be dependent on the number of processes involved in the parallel code. To fix this: archive as PETSc vectors? Then check ProcessSolutionAtTimeStep logic...

Definition at line 61 of file ActivationOutputModifier.hpp.

Constructor & Destructor Documentation

◆ ActivationOutputModifier() [1/2]

ActivationOutputModifier::ActivationOutputModifier ( )

inlineprivate

Private constructor that does nothing, for archiving

Definition at line 92 of file ActivationOutputModifier.hpp.

◆ ActivationOutputModifier() [2/2]

ActivationOutputModifier::ActivationOutputModifier	(	const std::string &	rFilename,
		double	threshold
	)

inline

Constructor

Parameters

rFilename	The file which is eventually produced by this modifier
threshold	The transmembrane voltage threshold (in mV) at which activation is deemed to have been trigged. This is also used for calculating relaxation time (this is not so sophisticated as an APD90 calculation).

Definition at line 104 of file ActivationOutputModifier.hpp.

Member Function Documentation

◆ FinaliseAtEnd()

void ActivationOutputModifier::FinaliseAtEnd ( )

virtual

Finalise the modifier (write all results to the file)

Implements AbstractOutputModifier.

Definition at line 49 of file ActivationOutputModifier.cpp.

References PetscTools::AmMaster(), PetscTools::BeginRoundRobin(), PetscTools::EndRoundRobin(), PetscTools::GetMyRank(), HeartConfig::Instance(), AbstractOutputModifier::mFilename, mFirstActivitationTimes, mFirstRecoveryTimes, mLocalSize, mSecondActivitationTimes, mSecondRecoveryTimes, and OutputFileHandler::OpenOutputFile().

◆ InitialiseAtStart()

void ActivationOutputModifier::InitialiseAtStart	(	DistributedVectorFactory *	pVectorFactory,
		const std::vector< unsigned > &	rNodePermutation
	)

virtual

Initialise the modifier (open a file or make some memory) when the solve loop is starting

Note the problem passes parameters in a non-templated fashion in order to keep the interface as lightweight as possible. That is, it might have been slicker to pass in the mesh but that would require multiple templates.

Parameters

pVectorFactory	The vector factory which is associated with the calling problem's mesh
rNodePermutation	The permutation associated with the calling problem's mesh (when running with parallel partitioning)

Implements AbstractOutputModifier.

Definition at line 40 of file ActivationOutputModifier.cpp.

References DistributedVectorFactory::GetLocalOwnership(), mFirstActivitationTimes, mFirstRecoveryTimes, mLocalSize, mSecondActivitationTimes, and mSecondRecoveryTimes.

◆ ProcessSolutionAtTimeStep()

void ActivationOutputModifier::ProcessSolutionAtTimeStep	(	double	time,
		Vec	solution,
		unsigned	problemDim
	)

virtual

Process a solution time-step (memorise all new activations)

Parameters

time	The current simulation time
solution	A working copy of the solution at the current time-step. This is the PETSc vector which is distributed across the processes.
problemDim	The calling problem dimension. Used here to avoid probing the size of the solution vector