#include <SingleTraceOutputModifier.hpp>

Inheritance diagram for SingleTraceOutputModifier:

Collaboration diagram for SingleTraceOutputModifier:

Public Member Functions
	SingleTraceOutputModifier (const std::string &rFilename, unsigned globalIndex, double flushTime=0.0)

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)

	SingleTraceOutputModifier ()

Private Attributes
unsigned	mGlobalIndex

unsigned	mLocalIndex

out_stream	mFileStream

Friends
class	TestMonodomainProblem

class	boost::serialization::access

class	TestOutputModifiers

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

Protected Attributes inherited from AbstractOutputModifier
std::string	mFilename

double	mFlushTime

Detailed Description

Provide the trace for a transmembrane potential at a single mode of the mesh. File updated during the simulation.

WARNING: If you checkpoint this class then the file output will not be saved in the checkpoint. The state of the output file will be unchanged (up to the most recent file flush) but may be overwritten by a restarted simulation. You will need to manually move the output file before restarting the simulation and then merge the two files together at a later point.

Definition at line 54 of file SingleTraceOutputModifier.hpp.

Constructor & Destructor Documentation

◆ SingleTraceOutputModifier() [1/2]

SingleTraceOutputModifier::SingleTraceOutputModifier ( )

inlineprivate

Private constructor that resets process-specific data, for archiving

Definition at line 87 of file SingleTraceOutputModifier.hpp.

◆ SingleTraceOutputModifier() [2/2]

SingleTraceOutputModifier::SingleTraceOutputModifier	(	const std::string &	rFilename,
		unsigned	globalIndex,
		double	flushTime = `0.0`
	)

inline

Constructor

Parameters

globalIndex	The global index of the node which is to be output. This is the index in the original mesh. If you are running in parallel your index in the original mesh will be automatically converted to the runtime index using the node permutation in the mesh. That is, is you ask for node 5 in the original mesh then you will automatically get unsigned new_index_for_5 = mesh.rGetNodePermutation()[5]; mesh Definition triangle.cpp:740 which is the runtime index of the same node in space.
rFilename	The file which is eventually produced by this modifier
flushTime	The simulation time between manual file flushes (if required)

Definition at line 109 of file SingleTraceOutputModifier.hpp.

Member Function Documentation

◆ FinaliseAtEnd()

void SingleTraceOutputModifier::FinaliseAtEnd ( )

virtual

Finalise the modifier (close the file)

Implements AbstractOutputModifier.

Definition at line 63 of file SingleTraceOutputModifier.cpp.

References mFileStream, and mLocalIndex.

◆ InitialiseAtStart()

void SingleTraceOutputModifier::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 41 of file SingleTraceOutputModifier.cpp.

References DistributedVectorFactory::GetLow(), HeartConfig::Instance(), DistributedVectorFactory::IsGlobalIndexLocal(), AbstractOutputModifier::mFilename, mFileStream, mGlobalIndex, mLocalIndex, and OutputFileHandler::OpenOutputFile().

◆ ProcessSolutionAtTimeStep()

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

virtual

Process a solution time-step (dump a small line to file)

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

Implements AbstractOutputModifier.

Definition at line 73 of file SingleTraceOutputModifier.cpp.

References mFileStream, AbstractOutputModifier::mFlushTime, and mLocalIndex.

◆ serialize()

template<class Archive >

void SingleTraceOutputModifier::serialize	(	Archive &	archive,
		const unsigned int	version
	)

inlineprivate

Archive the output modifier, never used directly - boost uses this.

Parameters

archive	the archive
version	the current version of this class

Definition at line 78 of file SingleTraceOutputModifier.hpp.

References mGlobalIndex.

Friends And Related Symbol Documentation

◆ boost::serialization::access

friend class boost::serialization::access

friend

Needed for serialization.

Definition at line 60 of file SingleTraceOutputModifier.hpp.

◆ TestMonodomainProblem

friend class TestMonodomainProblem

friend

For testing

Definition at line 58 of file SingleTraceOutputModifier.hpp.

◆ TestOutputModifiers

friend class TestOutputModifiers

friend

Definition at line 69 of file SingleTraceOutputModifier.hpp.

Member Data Documentation

◆ mFileStream

out_stream SingleTraceOutputModifier::mFileStream

private

Output file stream (remains open during solve).

Definition at line 67 of file SingleTraceOutputModifier.hpp.

Referenced by FinaliseAtEnd(), InitialiseAtStart(), and ProcessSolutionAtTimeStep().

◆ mGlobalIndex

unsigned SingleTraceOutputModifier::mGlobalIndex

private

The global index of the node for which the trace is to be made. This is the index *in memory at solve time*. If you are running in parallel and you want a specific index/location in your mesh then you will need to look in the mesh permutation.

Definition at line 65 of file SingleTraceOutputModifier.hpp.

Referenced by InitialiseAtStart(), and serialize().