#include <CmguiDeformedSolutionsWriter.hpp>

Inheritance diagram for CmguiDeformedSolutionsWriter< DIM >:

Collaboration diagram for CmguiDeformedSolutionsWriter< DIM >:

Public Member Functions
	CmguiDeformedSolutionsWriter (std::string outputDirectory, std::string baseName, AbstractTetrahedralMesh< DIM, DIM > &rQuadraticMesh, CmguiMeshWriteType writeType)

void	WriteInitialMesh (std::string fileName="")

void	WriteDeformationPositions (std::vector< c_vector< double, DIM > > &rDeformedPositions, unsigned counter)

void	WriteCmguiScript (std::string fieldBaseName="", std::string undeformedBaseName="")

void	ConvertOutput (std::string inputDirectory, std::string inputFileBaseName, unsigned finalCounter)

Public Member Functions inherited from CmguiMeshWriter< DIM, DIM >
	CmguiMeshWriter (const std::string &rDirectory, const std::string &rBaseName, bool cleanDirectory=true)

void	WriteFiles ()

void	SetAdditionalFieldNames (std::vector< std::string > &rFieldNames)

void	SetRegionNames (std::vector< std::string > &rRegionNames)

virtual	~CmguiMeshWriter ()

Public Member Functions inherited from AbstractTetrahedralMeshWriter< ELEMENT_DIM, SPACE_DIM >
	AbstractTetrahedralMeshWriter (const std::string &rDirectory, const std::string &rBaseName, const bool clearOutputDir=true)

virtual	~AbstractTetrahedralMeshWriter ()

virtual void	WriteFilesUsingMesh (AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > &rMesh, bool keepOriginalElementIndexing=true)

void	WriteFilesUsingMeshReaderAndMesh (AbstractMeshReader< ELEMENT_DIM, SPACE_DIM > &rMeshReader, AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > &rMesh)

std::vector< double >	GetNextNode ()

ElementData	GetNextElement ()

ElementData	GetNextBoundaryElement ()

ElementData	GetNextCableElement ()

Public Member Functions inherited from AbstractMeshWriter< ELEMENT_DIM, SPACE_DIM >
	AbstractMeshWriter (const std::string &rDirectory, const std::string &rBaseName, const bool clearOutputDir=true)

virtual	~AbstractMeshWriter ()

std::string	GetOutputDirectory ()

unsigned	GetNumElements ()

unsigned	GetNumBoundaryFaces ()

unsigned	GetNumCableElements ()

void	WriteFilesUsingMeshReader (AbstractMeshReader< ELEMENT_DIM, SPACE_DIM > &rMeshReader)

Private Member Functions
unsigned	GetNumNodes ()

Private Attributes
AbstractTetrahedralMesh< DIM, DIM > *	mpQuadraticMesh

unsigned	mFinalCounter

unsigned	mNumNodesToUse

Additional Inherited Members
Protected Member Functions inherited from CmguiMeshWriter< DIM, DIM >
std::ios_base::openmode	GetOpenMode (bool append)

out_stream	OpenNodeFile (bool append=false)

std::vector< boost::shared_ptr< std::ofstream > >	OpenElementFiles (bool append=false)

void	WriteNodeFileHeader (out_stream &rpNodeFile)

void	WriteElementsFileHeader (std::vector< boost::shared_ptr< std::ofstream > > &rElemFiles)

void	CreateFilesWithHeaders ()

void	AppendLocalDataToFiles ()

void	WriteFilesFooter ()

Protected Attributes inherited from CmguiMeshWriter< DIM, DIM >
std::vector< std::string >	mAdditionalFieldNames

std::vector< std::string >	mRegionNames

std::string	mGroupName

std::string	mElementFileHeader

std::string	mCoordinatesFileHeader

std::string	mAdditionalFieldHeader

unsigned	mNumNodesPerElement

std::vector< unsigned >	mReordering

Protected Attributes inherited from AbstractTetrahedralMeshWriter< ELEMENT_DIM, SPACE_DIM >
unsigned	mNodesPerElement

unsigned	mNodesPerBoundaryElement

AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > *	mpMesh

DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > *	mpDistributedMesh

MixedDimensionMesh< ELEMENT_DIM, SPACE_DIM > *	mpMixedMesh

MeshWriterIterators< ELEMENT_DIM, SPACE_DIM > *	mpIters

bool	mIndexFromZero

bool	mWriteMetaFile

unsigned	mNodeCounterForParallelMesh

unsigned	mElementCounterForParallelMesh

unsigned	mBoundaryElementCounterForParallelMesh

unsigned	mCableElementCounterForParallelMesh

bool	mFilesAreBinary

Protected Attributes inherited from AbstractMeshWriter< ELEMENT_DIM, SPACE_DIM >
OutputFileHandler *	mpOutputFileHandler

std::string	mBaseName

AbstractMeshReader< ELEMENT_DIM, SPACE_DIM > *	mpMeshReader

unsigned	mNumNodes

unsigned	mNumElements

unsigned	mNumBoundaryElements

unsigned	mNumCableElements

Detailed Description

template<unsigned DIM>
class CmguiDeformedSolutionsWriter< DIM >

CmguiDeformedSolutionsWriter

A class for writing a mesh, and solutions from a solid mechanics (ie deformed meshes) problem, in Cmgui output format.

Inherits from CmguiMeshWriter

Definition at line 65 of file CmguiDeformedSolutionsWriter.hpp.

Constructor & Destructor Documentation

◆ CmguiDeformedSolutionsWriter()

template<unsigned DIM>

CmguiDeformedSolutionsWriter< DIM >::CmguiDeformedSolutionsWriter	(	std::string	outputDirectory,
		std::string	baseName,
		AbstractTetrahedralMesh< DIM, DIM > &	rQuadraticMesh,
		CmguiMeshWriteType	writeType
	)

Constructor

Parameters

outputDirectory	The output directory for the Cmgui files
baseName	The base name for the Cmgui output files - the files written will be [basename_0.exnode, [basename]_0.exelem; [basename]_1.exnode, [basename]_2.exnode, ..
rQuadraticMesh	The quadratic mesh used in the mechanics simulation
writeType	Should be equal to either WRITE_LINEAR_MESH or WRITE_QUADRATIC_MESH, depending on whether linear visualisation of the quadratic mesh (just vertices output) or full quadratic visualisation is required.

Definition at line 40 of file CmguiDeformedSolutionsWriter.cpp.

References EXCEPTION, AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetNumNodes(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetNumVertices(), CmguiMeshWriter< DIM, DIM >::mAdditionalFieldHeader, CmguiMeshWriter< DIM, DIM >::mCoordinatesFileHeader, CmguiMeshWriter< DIM, DIM >::mElementFileHeader, CmguiMeshWriter< DIM, DIM >::mNumNodesPerElement, CmguiDeformedSolutionsWriter< DIM >::mNumNodesToUse, CmguiDeformedSolutionsWriter< DIM >::mpQuadraticMesh, CmguiMeshWriter< DIM, DIM >::mReordering, and NEVER_REACHED.

Member Function Documentation

◆ ConvertOutput()

template<unsigned DIM>

void CmguiDeformedSolutionsWriter< DIM >::ConvertOutput	(	std::string	inputDirectory,
		std::string	inputFileBaseName,
		unsigned	finalCounter
	)

For a simulation that has already been run, convert the chaste output to cmgui format.

Parameters

inputDirectory	The directory the chaste output is in
inputFileBaseName	The base name for the chaste output
finalCounter	The final counter, ie the value N for the final file [basename]_N.nodes. The first file is assumed to be [basename]_0.nodes. The files [basename]_0.nodes up to [basename]_N.nodes will be converted to cmgui format and put in the output directory given in the constructor.

Definition at line 212 of file CmguiDeformedSolutionsWriter.cpp.

References EXCEPTION.

◆ GetNumNodes()

template<unsigned DIM>

unsigned CmguiDeformedSolutionsWriter< DIM >::GetNumNodes ( )

inlineprivatevirtual

Overloaded GetNumNodes().

Returns: either mpQuadraticMesh->GetNumVertices() for linear visualisation or mpQuadraticMesh->GetNumNodes() for quadratic visualisation

Reimplemented from AbstractMeshWriter< ELEMENT_DIM, SPACE_DIM >.

Definition at line 91 of file CmguiDeformedSolutionsWriter.hpp.

References CmguiDeformedSolutionsWriter< DIM >::mNumNodesToUse.

◆ WriteCmguiScript()

template<unsigned DIM>

void CmguiDeformedSolutionsWriter< DIM >::WriteCmguiScript	(	std::string	fieldBaseName = `""`,
		std::string	undeformedBaseName = `""`
	)

Writes a small cmgui script called LoadSolutions.com, for loading the output that has been written. Assumes the output was solution_0.exnode .. solution_N.exnode, where N is the counter that was given in the last call to WriteDeformationPositions()

Parameters

fieldBaseName	If there is a field to visualise on top of the deforming mesh, give it's path (relative to the cmgui deformation directory), and filename prefix. Leave empty if no field to visualise. For example, WriteCmguiScript("../../electrics/cmgui_output/voltage_mechanics_mesh"); for the script to read files voltage_mechanics_mesh_0.exnode .. voltage_mechanics_mesh_N.exnode.
undeformedBaseName	is assumed to be "solution_0.exnode" and .exelem unless this optional parameter is given. Depends on what parameters were given to WriteInitialMesh(). If undeformedBaseName the time given to plot the undeformed shape is set to -1, otherwise it is set to 0.

Definition at line 173 of file CmguiDeformedSolutionsWriter.cpp.

Referenced by AbstractNonlinearElasticitySolver< DIM >::CreateCmguiOutput(), and CardiacElectroMechanicsProblem< DIM, ELEC_PROB_DIM >::Solve().

◆ WriteDeformationPositions()

template<unsigned DIM>

void CmguiDeformedSolutionsWriter< DIM >::WriteDeformationPositions	(	std::vector< c_vector< double, DIM > > &	rDeformedPositions,
		unsigned	counter
	)

Write [basename]_i.exnode using the given deformed positions

Parameters

rDeformedPositions	std::vector of deformed positions to be used, must have size equal to number of nodes in the mesh
counter	the value "i" in "[basename]_i.exnode" to be used.

Definition at line 142 of file CmguiDeformedSolutionsWriter.cpp.

References EXCEPTION.

Referenced by AbstractNonlinearElasticitySolver< DIM >::CreateCmguiOutput(), and CardiacElectroMechanicsProblem< DIM, ELEC_PROB_DIM >::Solve().

◆ WriteInitialMesh()

template<unsigned DIM>

void CmguiDeformedSolutionsWriter< DIM >::WriteInitialMesh ( std::string fileName = "" )

Write [basename]_0.exnode, [basename]_0.exelem using the quadratic mesh If the optional argument fileName is given, writes [fileName].exnode and [fileName].exelem instead

Parameters

fileName Optional file name (stem).

Definition at line 126 of file CmguiDeformedSolutionsWriter.cpp.

Referenced by AbstractNonlinearElasticitySolver< DIM >::CreateCmguiOutput(), and CardiacElectroMechanicsProblem< DIM, ELEC_PROB_DIM >::Solve().

Member Data Documentation

◆ mFinalCounter

template<unsigned DIM>

unsigned CmguiDeformedSolutionsWriter< DIM >::mFinalCounter

private

A counter is given whenever WriteDeformationPositions() is called, this variable stores the last one used

Definition at line 78 of file CmguiDeformedSolutionsWriter.hpp.

◆ mNumNodesToUse

template<unsigned DIM>

unsigned CmguiDeformedSolutionsWriter< DIM >::mNumNodesToUse

private

Number of nodes to output - either mpQuadraticMesh->GetNumVertices() (linear visualisation) mpQuadraticMesh->GetNumNodes() (quadratic visualisation)

Definition at line 84 of file CmguiDeformedSolutionsWriter.hpp.

Referenced by CmguiDeformedSolutionsWriter< DIM >::CmguiDeformedSolutionsWriter(), and CmguiDeformedSolutionsWriter< DIM >::GetNumNodes().

◆ mpQuadraticMesh

template<unsigned DIM>

AbstractTetrahedralMesh<DIM,DIM>* CmguiDeformedSolutionsWriter< DIM >::mpQuadraticMesh

private

The quadratic mesh used in the mechanics simulation. solution_0.exnode and solution_0.exelem (the only exelem file written) will be written using this mesh

Definition at line 72 of file CmguiDeformedSolutionsWriter.hpp.

Referenced by CmguiDeformedSolutionsWriter< DIM >::CmguiDeformedSolutionsWriter().

The documentation for this class was generated from the following files:

mesh/src/writer/CmguiDeformedSolutionsWriter.hpp
mesh/src/writer/CmguiDeformedSolutionsWriter.cpp

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ CmguiDeformedSolutionsWriter()

Member Function Documentation

◆ ConvertOutput()

◆ GetNumNodes()

◆ WriteCmguiScript()

◆ WriteDeformationPositions()

◆ WriteInitialMesh()

Member Data Documentation

◆ mFinalCounter

◆ mNumNodesToUse

◆ mpQuadraticMesh