Data collection with VisIt I/O routines. More...

#include <datacollection.hpp>

Inheritance diagram for mfem::VisItDataCollection:

Collaboration diagram for mfem::VisItDataCollection:

Public Member Functions
	VisItDataCollection (const std::string &collection_name, Mesh *mesh_=NULL)
	Constructor. The collection name is used when saving the data.

	VisItDataCollection (MPI_Comm comm, const std::string &collection_name, Mesh *mesh_=NULL)
	Construct a parallel VisItDataCollection to be loaded from files.

virtual void	SetMesh (Mesh *new_mesh) override
	Set/change the mesh associated with the collection.

virtual void	SetMesh (MPI_Comm comm, Mesh *new_mesh) override
	Set/change the mesh associated with the collection.

virtual void	RegisterField (const std::string &field_name, GridFunction *gf) override
	Add a grid function to the collection and update the root file.

virtual void	RegisterQField (const std::string &q_field_name, QuadratureFunction *qf) override
	Add a quadrature function to the collection and update the root file.

virtual void	SetPadDigits (int digits) override

void	SetLevelsOfDetail (int levels_of_detail)
	Set VisIt parameter: default levels of detail for the MultiresControl.

void	SetMaxLevelsOfDetail (int max_levels_of_detail)
	Set VisIt parameter: maximum levels of detail for the MultiresControl.

void	DeleteAll ()
	Delete all data owned by VisItDataCollection including field data information.

virtual void	Save () override
	Save the collection and a VisIt root file.

void	SaveRootFile ()
	Save a VisIt root file for the collection.

virtual void	Load (int cycle_=0) override
	Load the collection based on its VisIt data (described in its root file)

virtual	~VisItDataCollection ()
	We will delete the mesh and fields if we own them.

Public Member Functions inherited from mfem::DataCollection
	DataCollection (const std::string &collection_name, Mesh *mesh_=NULL)
	Initialize the collection with its name and Mesh.

virtual void	DeregisterField (const std::string &field_name)
	Remove a grid function from the collection.

virtual void	DeregisterQField (const std::string &field_name)
	Remove a QuadratureFunction from the collection.

bool	HasField (const std::string &field_name) const
	Check if a grid function is part of the collection.

GridFunction *	GetField (const std::string &field_name)
	Get a pointer to a grid function in the collection.

MPI_Comm	GetComm () const
	Return the associated MPI communicator or MPI_COMM_NULL.

ParGridFunction *	GetParField (const std::string &field_name)
	Get a pointer to a parallel grid function in the collection.

bool	HasQField (const std::string &q_field_name) const
	Check if a QuadratureFunction with the given name is in the collection.

QuadratureFunction *	GetQField (const std::string &q_field_name)
	Get a pointer to a QuadratureFunction in the collection.

const FieldMapType &	GetFieldMap () const
	Get a const reference to the internal field map.

const QFieldMapType &	GetQFieldMap () const
	Get a const reference to the internal q-field map.

Mesh *	GetMesh ()
	Get a pointer to the mesh in the collection.

void	SetCycle (int c)
	Set time cycle (for time-dependent simulations)

void	SetTime (real_t t)
	Set physical time (for time-dependent simulations)

void	SetTimeStep (real_t ts)
	Set the simulation time step (for time-dependent simulations)

int	GetCycle () const
	Get time cycle (for time-dependent simulations)

real_t	GetTime () const
	Get physical time (for time-dependent simulations)

real_t	GetTimeStep () const
	Get the simulation time step (for time-dependent simulations)

const std::string &	GetCollectionName () const
	Get the name of the collection.

void	SetOwnData (bool o)
	Set the ownership of collection data.

void	SetPrecision (int prec)
	Set the precision (number of digits) used for the text output of doubles.

virtual void	SetPadDigitsCycle (int digits)
	Set the number of digits used for the cycle.

virtual void	SetPadDigitsRank (int digits)
	Set the number of digits used for the MPI rank in filenames.

virtual void	SetFormat (int fmt)
	Set the desired output mesh and data format.

virtual void	SetCompression (bool comp)
	Set the flag for use of gz compressed files.

void	SetPrefixPath (const std::string &prefix)
	Set the path where the DataCollection will be saved.

const std::string &	GetPrefixPath () const
	Get the path where the DataCollection will be saved.

virtual void	SaveMesh ()
	Save the mesh, creating the collection directory.

virtual void	SaveField (const std::string &field_name)
	Save one field, assuming the collection directory already exists.

virtual void	SaveQField (const std::string &q_field_name)
	Save one q-field, assuming the collection directory already exists.

virtual	~DataCollection ()
	Delete the mesh and fields if owned by the collection.

int	Error () const
	Get the current error state.

void	ResetError (int err_state=No_Error)
	Reset the error state.

Protected Types
typedef std::map< std::string, VisItFieldInfo >::iterator	FieldInfoMapIterator

Protected Member Functions
std::string	GetVisItRootString ()
	Prepare the VisIt root file in JSON format for the current collection.

void	ParseVisItRootString (const std::string &json)
	Read in a VisIt root file in JSON format.

void	UpdateMeshInfo ()

void	LoadVisItRootFile (const std::string &root_name)

void	LoadMesh ()

void	LoadFields ()

Protected Member Functions inherited from mfem::DataCollection
void	DeleteData ()
	Delete data owned by the DataCollection keeping field information.

void	DeleteAll ()
	Delete data owned by the DataCollection including field information.

std::string	GetMeshShortFileName () const

std::string	GetMeshFileName () const

std::string	GetFieldFileName (const std::string &field_name) const

void	SaveOneField (const FieldMapIterator &it)
	Save one field to disk, assuming the collection directory exists.

void	SaveOneQField (const QFieldMapIterator &it)
	Save one q-field to disk, assuming the collection directory exists.

Protected Attributes
int	spatial_dim

int	topo_dim

int	visit_levels_of_detail

int	visit_max_levels_of_detail

std::map< std::string, VisItFieldInfo >	field_info_map

Protected Attributes inherited from mfem::DataCollection
std::string	name
	Name of the collection, used as a directory name when saving.

std::string	prefix_path
	A path where the directory with results is saved. If not empty, it has '/' at the end.

GFieldMap	field_map

QFieldMap	q_field_map

Mesh *	mesh
	The (common) mesh for the collected fields.

int	cycle
	Time cycle; for time-dependent simulations cycle >= 0, otherwise = -1.

real_t	time
	Physical time (for time-dependent simulations)

real_t	time_step
	Time step i.e. delta_t (for time-dependent simulations)

bool	serial
	Serial or parallel run? False iff mesh is a ParMesh.

bool	appendRankToFileName
	Append rank to any output file names.

int	myid
	MPI rank (in parallel)

int	num_procs
	Number of MPI ranks (in parallel)

MPI_Comm	m_comm
	Associated MPI communicator.

int	precision
	Precision (number of digits) used for the text output of doubles.

int	pad_digits_cycle
	Number of digits used for the cycle and MPI rank in filenames.

int	pad_digits_rank

int	format
	Output mesh format: see the Format enumeration.

int	compression

bool	own_data
	Should the collection delete its mesh and fields.

int	error
	Error state.

Additional Inherited Members
Public Types inherited from mfem::DataCollection
enum	Format { SERIAL_FORMAT = 0 , PARALLEL_FORMAT = 1 }
	Format constants to be used with SetFormat(). More...

enum	{ NO_ERROR = 0 , No_Error = 0 , READ_ERROR = 1 , WRITE_ERROR = 2 }
	Errors returned by Error() More...

typedef GFieldMap::MapType	FieldMapType

typedef GFieldMap::iterator	FieldMapIterator

typedef GFieldMap::const_iterator	FieldMapConstIterator

typedef QFieldMap::MapType	QFieldMapType

typedef QFieldMap::iterator	QFieldMapIterator

typedef QFieldMap::const_iterator	QFieldMapConstIterator

Static Protected Member Functions inherited from mfem::DataCollection
static int	create_directory (const std::string &dir_name, const Mesh *mesh, int myid)

Static Protected Attributes inherited from mfem::DataCollection
static const int	precision_default = 6
	Default value for precision.

static const int	pad_digits_default = 6
	Default value for pad_digits_*.

Detailed Description

Data collection with VisIt I/O routines.

Definition at line 419 of file datacollection.hpp.

Member Typedef Documentation

◆ FieldInfoMapIterator

typedef std::map<std::string,VisItFieldInfo>::iterator mfem::VisItDataCollection::FieldInfoMapIterator

protected

Definition at line 428 of file datacollection.hpp.

Constructor & Destructor Documentation

◆ VisItDataCollection() [1/2]

mfem::VisItDataCollection::VisItDataCollection	(	const std::string &	collection_name,
		Mesh *	mesh_ = NULL )

Constructor. The collection name is used when saving the data.

If mesh_ is NULL, then the mesh can be set later by calling either SetMesh() or Load(). The latter works only in serial.

Definition at line 365 of file datacollection.cpp.

◆ VisItDataCollection() [2/2]

mfem::VisItDataCollection::VisItDataCollection	(	MPI_Comm	comm,
		const std::string &	collection_name,
		Mesh *	mesh_ = NULL )

Construct a parallel VisItDataCollection to be loaded from files.

Before loading the collection with Load(), some parameters in the collection can be adjusted, e.g. SetPadDigits(), SetPrefixPath(), etc.

Definition at line 379 of file datacollection.cpp.

◆ ~VisItDataCollection()

virtual mfem::VisItDataCollection::~VisItDataCollection ( )

inlinevirtual

We will delete the mesh and fields if we own them.

Definition at line 501 of file datacollection.hpp.

Member Function Documentation

◆ DeleteAll()

void mfem::VisItDataCollection::DeleteAll ( )

Delete all data owned by VisItDataCollection including field data information.

Definition at line 465 of file datacollection.cpp.

◆ GetVisItRootString()

std::string mfem::VisItDataCollection::GetVisItRootString ( )

protected

Prepare the VisIt root file in JSON format for the current collection.

Definition at line 652 of file datacollection.cpp.

◆ Load()

void mfem::VisItDataCollection::Load ( int cycle_ = 0 )

overridevirtual

Load the collection based on its VisIt data (described in its root file)

Reimplemented from mfem::DataCollection.

Definition at line 493 of file datacollection.cpp.

◆ LoadFields()

void mfem::VisItDataCollection::LoadFields ( )

protected

Definition at line 599 of file datacollection.cpp.

◆ LoadMesh()

void mfem::VisItDataCollection::LoadMesh ( )

protected

Definition at line 564 of file datacollection.cpp.

◆ LoadVisItRootFile()

void mfem::VisItDataCollection::LoadVisItRootFile ( const std::string & root_name )

protected

Definition at line 548 of file datacollection.cpp.

◆ ParseVisItRootString()

void mfem::VisItDataCollection::ParseVisItRootString ( const std::string & json )

protected

Read in a VisIt root file in JSON format.

Definition at line 699 of file datacollection.cpp.

◆ RegisterField()

void mfem::VisItDataCollection::RegisterField	(	const std::string &	field_name,
		GridFunction *	gf )

overridevirtual

Add a grid function to the collection and update the root file.

Reimplemented from mfem::DataCollection.

Definition at line 415 of file datacollection.cpp.

◆ RegisterQField()

void mfem::VisItDataCollection::RegisterQField	(	const std::string &	q_field_name,
		QuadratureFunction *	qf )

overridevirtual

Add a quadrature function to the collection and update the root file.

Visualization of quadrature function is not supported in VisIt(3.12). A patch has been sent to VisIt developers in June 2020.

Reimplemented from mfem::DataCollection.

Definition at line 436 of file datacollection.cpp.

◆ Save()

void mfem::VisItDataCollection::Save ( )

overridevirtual

Save the collection and a VisIt root file.

Reimplemented from mfem::DataCollection.

Definition at line 471 of file datacollection.cpp.

◆ SaveRootFile()

void mfem::VisItDataCollection::SaveRootFile ( )

Save a VisIt root file for the collection.

Definition at line 477 of file datacollection.cpp.

◆ SetLevelsOfDetail()

void mfem::VisItDataCollection::SetLevelsOfDetail ( int levels_of_detail )

Set VisIt parameter: default levels of detail for the MultiresControl.

Definition at line 455 of file datacollection.cpp.

◆ SetMaxLevelsOfDetail()

void mfem::VisItDataCollection::SetMaxLevelsOfDetail ( int max_levels_of_detail )

Set VisIt parameter: maximum levels of detail for the MultiresControl.

Definition at line 460 of file datacollection.cpp.

◆ SetMesh() [1/2]

void mfem::VisItDataCollection::SetMesh ( Mesh * new_mesh )

overridevirtual

Set/change the mesh associated with the collection.

Reimplemented from mfem::DataCollection.

Definition at line 397 of file datacollection.cpp.

◆ SetMesh() [2/2]

void mfem::VisItDataCollection::SetMesh	(	MPI_Comm	comm,
		Mesh *	new_mesh )

overridevirtual

Set/change the mesh associated with the collection.

Reimplemented from mfem::DataCollection.

Definition at line 405 of file datacollection.cpp.

◆ SetPadDigits()

virtual void mfem::VisItDataCollection::SetPadDigits ( int digits )

inlineoverridevirtual

Set the number of digits used for both the cycle and the MPI rank

Note: VisIt seems to require 6 pad digits for the MPI rank. Therefore, this function uses this default value. This behavior can be overridden by calling SetPadDigitsCycle() and SetPadDigitsRank() instead.

Reimplemented from mfem::DataCollection.

Definition at line 478 of file datacollection.hpp.

◆ UpdateMeshInfo()

void mfem::VisItDataCollection::UpdateMeshInfo ( )

protected

Definition at line 346 of file datacollection.cpp.

Member Data Documentation

◆ field_info_map

std::map<std::string, VisItFieldInfo> mfem::VisItDataCollection::field_info_map

protected

Definition at line 427 of file datacollection.hpp.

◆ spatial_dim

int mfem::VisItDataCollection::spatial_dim

protected

Definition at line 424 of file datacollection.hpp.

◆ topo_dim

int mfem::VisItDataCollection::topo_dim

protected

Definition at line 424 of file datacollection.hpp.

◆ visit_levels_of_detail

int mfem::VisItDataCollection::visit_levels_of_detail

protected

Definition at line 425 of file datacollection.hpp.

◆ visit_max_levels_of_detail

int mfem::VisItDataCollection::visit_max_levels_of_detail

protected

Definition at line 426 of file datacollection.hpp.

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

fem/datacollection.hpp
fem/datacollection.cpp

Public Member Functions

Protected Types

Protected Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ FieldInfoMapIterator

Constructor & Destructor Documentation

◆ VisItDataCollection() [1/2]

◆ VisItDataCollection() [2/2]

◆ ~VisItDataCollection()

Member Function Documentation

◆ DeleteAll()

◆ GetVisItRootString()

◆ Load()

◆ LoadFields()

◆ LoadMesh()

◆ LoadVisItRootFile()

◆ ParseVisItRootString()

◆ RegisterField()

◆ RegisterQField()

◆ Save()

◆ SaveRootFile()

◆ SetLevelsOfDetail()

◆ SetMaxLevelsOfDetail()

◆ SetMesh() [1/2]

◆ SetMesh() [2/2]

◆ SetPadDigits()

◆ UpdateMeshInfo()

Member Data Documentation

◆ field_info_map

◆ spatial_dim

◆ topo_dim

◆ visit_levels_of_detail

◆ visit_max_levels_of_detail