Data collection with Sidre routines following the Conduit mesh blueprint specification. More...

#include <sidredatacollection.hpp>

Inheritance diagram for mfem::SidreDataCollection:

Collaboration diagram for mfem::SidreDataCollection:

Public Types
typedef NamedFieldsMap< Array< int > >	AttributeFieldMap

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

Public Member Functions
	SidreDataCollection (const std::string &collection_name, Mesh *the_mesh=NULL, bool owns_mesh_data=false)
	Constructor that allocates and initializes a Sidre DataStore.

	SidreDataCollection (const std::string &collection_name, axom::sidre::Group bp_index_grp, axom::sidre::Group domain_grp, bool owns_mesh_data=false)
	Constructor that links to an external Sidre DataStore.

void	SetComm (MPI_Comm comm)
	Associate an MPI communicator with the collection.

virtual void	RegisterField (const std::string &field_name, GridFunction *gf)
	Register a GridFunction in the Sidre DataStore.

void	RegisterField (const std::string &field_name, GridFunction *gf, const std::string &buffer_name, axom::sidre::IndexType offset)
	Register a GridFunction in the Sidre DataStore.

void	RegisterAttributeField (const std::string &name, bool is_bdry)
	Registers an attribute field in the Sidre DataStore.

void	DeregisterAttributeField (const std::string &name)

Array< int > *	GetAttributeField (const std::string &field_name) const

bool	HasAttributeField (const std::string &field_name) const

bool	HasBoundaryMesh () const

void	SetMeshNodesName (const std::string &nodes_name)
	Set the name of the mesh nodes field.

virtual void	DeregisterField (const std::string &field_name)
	De-register field_name from the SidreDataCollection.

virtual	~SidreDataCollection ()
	Delete all owned data.

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

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

void	SetGroupPointers (axom::sidre::Group global_grp, axom::sidre::Group domain_grp)
	Reset the domain and global datastore group pointers.

axom::sidre::Group *	GetBPGroup ()

axom::sidre::Group *	GetBPIndexGroup ()

virtual void	PrepareToSave ()
	Prepare the DataStore for writing.

virtual void	Save ()
	Save the collection to file.

void	Save (const std::string &filename, const std::string &protocol)
	Save the collection to filename.

void	Load (const std::string &path, const std::string &protocol)
	Load the Sidre DataStore from file.

virtual void	Load (int cycle_=0)
	Load SidreDataCollection from file.

void	LoadExternalData (const std::string &path)
	Load external data after registering externally owned fields.

void	UpdateStateFromDS ()
	Updates the DataCollection's cycle, time, and time-step variables with the values from the data store.

void	UpdateStateToDS ()
	Updates the data store's cycle, time, and time-step variables with the values from the SidreDataCollection.

Methods for named buffer access and manipulation.
axom::sidre::View *	GetNamedBuffer (const std::string &buffer_name) const
	Get a pointer to the sidre::View holding the named buffer for buffer_name.

axom::sidre::View *	AllocNamedBuffer (const std::string &buffer_name, axom::sidre::IndexType sz, axom::sidre::TypeID type=axom::sidre::DOUBLE_ID)
	Return newly allocated or existing named buffer for buffer_name.

void	FreeNamedBuffer (const std::string &buffer_name)
	Deallocate the named buffer buffer_name.

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	RegisterQField (const std::string &q_field_name, QuadratureFunction *qf)
	Add a QuadratureFunction to 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	SetPadDigits (int digits)
	Set the number of digits used for both the cycle and the MPI rank.

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.

Public Attributes
AttributeFieldMap	attr_map

Protected Member Functions
axom::sidre::Group *	named_buffers_grp () const

axom::sidre::View *	alloc_view (axom::sidre::Group *grp, const std::string &view_name)

axom::sidre::View *	alloc_view (axom::sidre::Group *grp, const std::string &view_name, const axom::sidre::DataType &dtype)

axom::sidre::Group *	alloc_group (axom::sidre::Group *grp, const std::string &group_name)

std::string	get_file_path (const std::string &filename) const

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.

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

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.

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 Sidre routines following the Conduit mesh blueprint specification.

SidreDataCollection provides an HDF5-based file format for visualization or restart capability. This functionality is aimed primarily at customers of LLNL's axom project that run problems at extreme scales.

For more information, see:

Sidre component of LLNL's axom project (to be open-sourced), http://goo.gl/cZyJdn
LLNL conduit/blueprint library, https://github.com/LLNL/conduit
HDF5 library, https://support.hdfgroup.org/HDF5

The layout created in the Sidre DataStore is: ("──" denote groups, "─•" denote views, "─>" denote links, i.e. shallow-copy view)

<root>
 ├── <collection-name>_global          (global group)
 │    └── blueprint_index
 │         └── <collection-name>       (bp_index group)
 │              ├── state
 │              │    ├─• cycle
 │              │    ├─• time
 │              │    └─• number_of_domains = <mesh-mpi-comm-size>
 │              ├── coordsets
 │              │    └── coords
 │              │         ├─• path = "<bp-path>/coordsets/coords"
 │              │         ├─• type ─> <bp-grp>/coordsets/coords/type = "explicit"
 │              │         └─• coord_system = "x"|"xy"|"xyz"
 │              ├── topologies
 │              │    ├── mesh
 │              │    │    ├─• path = "<bp-path>/topologies/mesh"
 │              │    │    ├─• type              ─> <bp-grp>/topologies/mesh/type = "unstructured"
 │              │    │    ├─• coordset          ─> <bp-grp>/topologies/mesh/coordset = "coords"
 │              │    │    ├─• grid_function     ─> <bp-grp>/topologies/mesh/grid_function = "<nodes-field-name>"
 │              │    │    └─• boundary_topology ─> <bp-grp>/topologies/mesh/boundary_topology = "boundary"
 │              │    └── boundary
 │              │         ├─• path = "<bp-path>/topologies/mesh"
 │              │         ├─• type     ─> <bp-grp>/topologies/boundary/type = "unstructured"
 │              │         └─• coordset ─> <bp-grp>/topologies/boundary/coordset = "coords"
 │              └── fields
 │                   ├── mesh_material_attribute
 │                   │    ├─• path = "<bp-path>/fields/mesh_material_attribute"
 │                   │    ├─• association ─> <bp-grp>/fields/mesh_material_attribute/association = "element"
 │                   │    ├─• topology    ─> <bp-grp>/fields/mesh_material_attribute/topology = "mesh"
 │                   │    └─• number_of_components = 1
 │                   ├── boundary_material_attribute
 │                   │    ├─• path = "<bp-path>/fields/boundary_material_attribute"
 │                   │    ├─• association ─> <bp-grp>/fields/boundary_material_attribute/association = "element"
 │                   │    ├─• topology    ─> <bp-grp>/fields/boundary_material_attribute/topology = "boundary"
 │                   │    └─• number_of_components = 1
 │                   ├── grid-function-1
 │                   │    ├─• path = "<bp-path>/fields/grid-function-1"
 │                   │    ├─• basis    ─> <bp-grp>/fields/grid-function-1/basis = "<fe-coll-name>"
 │                   │    ├─• topology ─> <bp-grp>/fields/grid-function-1/topology = "mesh"
 │                   │    └─• number_of_components = gf1->VectorDim()
 │                   ├── grid-function-2
 │                   │    ├─• path = "<bp-path>/fields/grid-function-2"
 │                   │    ├─• basis    ─> <bp-grp>/fields/grid-function-2/basis = "<fe-coll-name>"
 │                   │    ├─• topology ─> <bp-grp>/fields/grid-function-2/topology = "mesh"
 │                   │    └─• number_of_components = gf2->VectorDim()
 │                   ├── ...
 │                  ...
 └── <collection-name>                 (domain group)
      ├── blueprint                    (blueprint group)
      │    ├── state
      │    │    ├─• cycle
      │    │    ├─• time
      │    │    ├─• domain = <mesh-mpi-rank>
      │    │    └─• time_step
      │    ├── coordsets
      │    │    └── coords
      │    │         ├─• type = "explicit"
      │    │         └── values
      │    │              ├─• x = view in <vertex-coords-buffer>/<ext-double-data>
      │    │              ├─• y = view in <vertex-coords-buffer>/<ext-double-data>
      │    │              └─• z = view in <vertex-coords-buffer>/<ext-double-data>
      │    ├── topologies
      │    │    ├── mesh
      │    │    │    ├─• type = "unstructured"
      │    │    │    ├── elements
      │    │    │    │    ├─• shape = "points"|"lines"|...
      │    │    │    │    └─• connectivity = <vert-idx-array>
      │    │    │    ├─• coordset = "coords"
      │    │    │    ├─• grid_function = "<nodes-field-name>"
      │    │    │    └─• boundary_topology = "boundary"
      │    │    └── boundary
      │    │         ├─• type = "unstructured"
      │    │         ├── elements
      │    │         │    ├─• shape = "points"|"lines"|...
      │    │         │    └─• connectivity = <vert-idx-array>
      │    │         └─• coordset = "coords"
      │    └── fields
      │         ├── mesh_material_attribute
      │         │    ├─• association = "element"
      │         │    ├─• topology = "mesh"
      │         │    └─• values = <attr-array>
      │         ├── boundary_material_attribute
      │         │    ├─• association = "element"
      │         │    ├─• topology = "boundary"
      │         │    └─• values = <attr-array>
      │         ├── grid-function-1   (name can include path)
      │         │    ├─• basis = "<fe-coll-name>"
      │         │    ├─• topology = "mesh"
      │         │    └─• values = <ext-double-array>/<named-buffer> (vdim == 1)
      │         ├── grid-function-2   (name can include path)
      │         │    ├─• basis = "<fe-coll-name>"
      │         │    ├─• topology = "mesh"
      │         │    └── values   (vdim > 1)
      │         │         ├─• x0 = view into <ext-double-array>/<named-buffer>
      │         │         ├─• x1 = view into <ext-double-array>/<named-buffer>
      │         │         └─• x2 = view into <ext-double-array>/<named-buffer>
      │         ├── ...
      │        ...
      └── named_buffers                (named_buffers group)
           ├─• vertex_coords = <double-array>
           ├─• grid-function-1 = <double-array>
           ├─• grid-function-2 = <double-array>
          ...

Note: blueprint_index is used both in serial and in parallel. In parallel, only rank 0 will add entries to the blueprint index.; QuadratureFunctions (q-fields) are not supported.; SidreDataCollection does not manage the FiniteElementSpaces and FiniteElementCollections associated with registered GridFunctions. Therefore, field registration is left to the user of SidreDataCollection and there are no methods that automatically register GridFunctions using just the content of the Sidre DataStore. Such capabilities can be implemented in a derived class, adding any desired object management routines.

Warning: This class is still experimental, meaning that in future releases, it may not be backward compatible, and the output files generated by the current version may become unreadable.

Definition at line 172 of file sidredatacollection.hpp.

Member Typedef Documentation

◆ AttributeFieldMap

typedef NamedFieldsMap< Array<int> > mfem::SidreDataCollection::AttributeFieldMap

Definition at line 175 of file sidredatacollection.hpp.

Constructor & Destructor Documentation

◆ SidreDataCollection() [1/2]

mfem::SidreDataCollection::SidreDataCollection	(	const std::string &	collection_name,
		Mesh *	the_mesh = NULL,
		bool	owns_mesh_data = false )

Constructor that allocates and initializes a Sidre DataStore.

Parameters

[in]	collection_name	Name of the collection used as a file name when saving
[in]	the_mesh	Mesh shared by all grid functions in the collection (can be NULL)
[in]	owns_mesh_data	Does the SidreDC own the mesh vertices?

With this constructor, the SidreDataCollection owns the allocated Sidre DataStore.

Definition at line 32 of file sidredatacollection.cpp.

◆ SidreDataCollection() [2/2]

mfem::SidreDataCollection::SidreDataCollection	(	const std::string &	collection_name,
		axom::sidre::Group *	bp_index_grp,
		axom::sidre::Group *	domain_grp,
		bool	owns_mesh_data = false )

Constructor that links to an external Sidre DataStore.

Specifically, the global and domain groups can be at arbitrary paths.

Parameters

[in]	collection_name	Name of the collection used as a file name when saving
[in]	bp_index_grp	Pointer to the blueprint index group in the datastore, see the above schematic
[in]	domain_grp	Pointer to the domain group in the datastore, see the above schematic
[in]	owns_mesh_data	Does the SidreDC own the mesh vertices?

With this constructor, the SidreDataCollection does not own the Sidre DataStore.

Note: No mesh or fields are read from the given Groups. The mesh has to be set with SetMesh() and fields registered with RegisterField().

Definition at line 70 of file sidredatacollection.cpp.

◆ ~SidreDataCollection()

mfem::SidreDataCollection::~SidreDataCollection ( )

virtual

Delete all owned data.

Definition at line 90 of file sidredatacollection.cpp.

Member Function Documentation

◆ alloc_group()

axom::sidre::Group * mfem::SidreDataCollection::alloc_group	(	axom::sidre::Group *	grp,
		const std::string &	group_name )

protected

Definition at line 166 of file sidredatacollection.cpp.

◆ alloc_view() [1/2]

axom::sidre::View * mfem::SidreDataCollection::alloc_view	(	axom::sidre::Group *	grp,
		const std::string &	view_name )

protected

Definition at line 121 of file sidredatacollection.cpp.

◆ alloc_view() [2/2]

axom::sidre::View * mfem::SidreDataCollection::alloc_view	(	axom::sidre::Group *	grp,
		const std::string &	view_name,
		const axom::sidre::DataType &	dtype )

protected

Definition at line 143 of file sidredatacollection.cpp.

◆ AllocNamedBuffer()

axom::sidre::View * mfem::SidreDataCollection::AllocNamedBuffer	(	const std::string &	buffer_name,
		axom::sidre::IndexType	sz,
		axom::sidre::TypeID	type = axom::sidre::DOUBLE_ID )

Return newly allocated or existing named buffer for buffer_name.

The buffer is stored in the named_buffers group. If the currently allocated buffer size is smaller than sz, then the buffer is reallocated with size sz, destroying its contents.

Note: To access the underlying pointer, use View::getData().

Definition at line 204 of file sidredatacollection.cpp.

◆ DeregisterAttributeField()

void mfem::SidreDataCollection::DeregisterAttributeField ( const std::string & name )

Definition at line 1155 of file sidredatacollection.cpp.

◆ DeregisterField()

void mfem::SidreDataCollection::DeregisterField ( const std::string & field_name )

virtual

De-register field_name from the SidreDataCollection.

The field is removed from the field_map and the DataStore, including deleting it from the named_buffers group, if allocated.

Reimplemented from mfem::DataCollection.

Definition at line 1208 of file sidredatacollection.cpp.

◆ FreeNamedBuffer()

void mfem::SidreDataCollection::FreeNamedBuffer ( const std::string & buffer_name )

inline

Deallocate the named buffer buffer_name.

Definition at line 395 of file sidredatacollection.hpp.

◆ get_file_path()

std::string mfem::SidreDataCollection::get_file_path ( const std::string & filename ) const

protected

Definition at line 187 of file sidredatacollection.cpp.

◆ GetAttributeField()

Array< int > * mfem::SidreDataCollection::GetAttributeField ( const std::string & field_name ) const

inline

Returns a pointer to the attribute field associated with field_name, or NULL when there is no associated field

Definition at line 264 of file sidredatacollection.hpp.

◆ GetBPGroup()

axom::sidre::Group * mfem::SidreDataCollection::GetBPGroup ( )

inline

Definition at line 314 of file sidredatacollection.hpp.

◆ GetBPIndexGroup()

axom::sidre::Group * mfem::SidreDataCollection::GetBPIndexGroup ( )

inline

Definition at line 315 of file sidredatacollection.hpp.

◆ GetNamedBuffer()

axom::sidre::View * mfem::SidreDataCollection::GetNamedBuffer ( const std::string & buffer_name ) const

inline

Get a pointer to the sidre::View holding the named buffer for buffer_name.

If such named buffer is not allocated, the method returns NULL.

Note: To access the underlying pointer, use View::getData().; To query the size of the buffer, use View::getNumElements().

Definition at line 375 of file sidredatacollection.hpp.

◆ HasAttributeField()

bool mfem::SidreDataCollection::HasAttributeField ( const std::string & field_name ) const

inline

Checks if there is an attribute field associated with field_name

Definition at line 268 of file sidredatacollection.hpp.

◆ HasBoundaryMesh()

bool mfem::SidreDataCollection::HasBoundaryMesh ( ) const

Checks if any rank in the mesh has boundary elements

Definition at line 561 of file sidredatacollection.cpp.

◆ Load() [1/2]

void mfem::SidreDataCollection::Load	(	const std::string &	path,
		const std::string &	protocol )

Load the Sidre DataStore from file.

No mesh or fields are read from the loaded DataStore.

If the data collection created the datastore, it knows the layout of where the domain and global groups are, and can restore them after the Load().

If, however, the data collection does not own the datastore (e.g. it did not create the datastore), the host code must reset these pointers after the load operation, using SetGroupPointers(), and also reset the state variables, using UpdateStateFromDS().

Definition at line 698 of file sidredatacollection.cpp.

◆ Load() [2/2]

virtual void mfem::SidreDataCollection::Load ( int cycle_ = 0 )

inlinevirtual

Load SidreDataCollection from file.

The used file path is based on the current prefix path, collection name, and the given cycle_. The protocol is "sidre_hdf5".

See also: Load(const std::string &path, const std::string &protocol).

Reimplemented from mfem::DataCollection.

Definition at line 348 of file sidredatacollection.hpp.

◆ LoadExternalData()

void mfem::SidreDataCollection::LoadExternalData ( const std::string & path )

Load external data after registering externally owned fields.

Definition at line 731 of file sidredatacollection.cpp.

◆ named_buffers_grp()

sidre::Group * mfem::SidreDataCollection::named_buffers_grp ( ) const

protected

Definition at line 111 of file sidredatacollection.cpp.

◆ PrepareToSave()

void mfem::SidreDataCollection::PrepareToSave ( )

virtual

Prepare the DataStore for writing.

Definition at line 766 of file sidredatacollection.cpp.

◆ RegisterAttributeField()

void mfem::SidreDataCollection::RegisterAttributeField	(	const std::string &	name,
		bool	is_bdry )

Registers an attribute field in the Sidre DataStore.

The registration process is similar to that of RegisterField() The attribute field is associated with the elements of the mesh when is_bdry is false, and with the boundary elements, when is_bdry is true.

See also: RegisterField()

Definition at line 1087 of file sidredatacollection.cpp.

◆ RegisterField() [1/2]

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

inlinevirtual

Register a GridFunction in the Sidre DataStore.

This method is a shortcut for the call RegisterField(field_name, gf, field_name, 0).

Reimplemented from mfem::DataCollection.

Definition at line 227 of file sidredatacollection.hpp.

◆ RegisterField() [2/2]

void mfem::SidreDataCollection::RegisterField	(	const std::string &	field_name,
		GridFunction *	gf,
		const std::string &	buffer_name,
		axom::sidre::IndexType	offset )

Register a GridFunction in the Sidre DataStore.

The registration procedure is as follows:

if (gf's data is NULL), allocate named buffer with the name buffer_name with size offset + gf->FESpace()->GetVSize() and use its data (plus the given offset) to set gf's data;
else, if (DataStore has a named buffer buffer_name), replace gf's data array with that named buffer plus the given offset;
else, use gf's data as external data associated with field_name in the DataStore;
register field_name in field_map.

Both the field_name and buffer_name can contain a path prefix.

Note: If field_name or buffer_name is empty, the method does nothing.; If the GridFunction pointer gf or it's FiniteElementSpace pointer are NULL, the method does nothing.

Definition at line 1011 of file sidredatacollection.cpp.

◆ Save() [1/2]

void mfem::SidreDataCollection::Save ( )

virtual

Save the collection to file.

This method calls Save(collection_name, "sidre_hdf5").

Reimplemented from mfem::DataCollection.

Definition at line 772 of file sidredatacollection.cpp.

◆ Save() [2/2]

void mfem::SidreDataCollection::Save	(	const std::string &	filename,
		const std::string &	protocol )

Save the collection to filename.

The collection path prefix is prepended to the filename and the current cycle is appended, if cycle >= 0.

Definition at line 780 of file sidredatacollection.cpp.

◆ SetComm()

void mfem::SidreDataCollection::SetComm ( MPI_Comm comm )

Associate an MPI communicator with the collection.

If no mesh was associated with the collection, this method should be called before using any of the Load() methods to read parallel data.

Definition at line 100 of file sidredatacollection.cpp.

◆ SetGroupPointers()

void mfem::SidreDataCollection::SetGroupPointers	(	axom::sidre::Group *	global_grp,
		axom::sidre::Group *	domain_grp )

Reset the domain and global datastore group pointers.

These are set in the constructor, but if a host code changes the datastore contents ( such as wiping out the datastore and loading in new contents from a file, i.e. a restart ) these pointers will need to be reset to valid groups in the datastore.

See also: Load(const std::string &path, const std::string &protocol).

Definition at line 686 of file sidredatacollection.cpp.

◆ SetMesh() [1/2]

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

virtual

Set/change the mesh associated with the collection.

Uses the field name "mesh_nodes" or the value set by SetMeshNodesName() to register the mesh nodes GridFunction, if the mesh uses nodes.

Reimplemented from mfem::DataCollection.

Definition at line 582 of file sidredatacollection.cpp.

◆ SetMesh() [2/2]

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

virtual

Set/change the mesh associated with the collection.

Uses the field name "mesh_nodes" or the value set by SetMeshNodesName() to register the mesh nodes GridFunction, if the mesh uses nodes.

Reimplemented from mfem::DataCollection.

Definition at line 675 of file sidredatacollection.cpp.

◆ SetMeshNodesName()

void mfem::SidreDataCollection::SetMeshNodesName ( const std::string & nodes_name )

inline

Set the name of the mesh nodes field.

This name will be used by SetMesh() to register the mesh nodes, if not already registered. Also, this method should be called if the mesh nodes GridFunction was or will be registered directly by the user. The default value for the name is "mesh_nodes".

Definition at line 279 of file sidredatacollection.hpp.

◆ UpdateStateFromDS()

void mfem::SidreDataCollection::UpdateStateFromDS ( )

Updates the DataCollection's cycle, time, and time-step variables with the values from the data store.

Definition at line 746 of file sidredatacollection.cpp.

◆ UpdateStateToDS()

void mfem::SidreDataCollection::UpdateStateToDS ( )

Updates the data store's cycle, time, and time-step variables with the values from the SidreDataCollection.

Definition at line 753 of file sidredatacollection.cpp.

Member Data Documentation

◆ attr_map

AttributeFieldMap mfem::SidreDataCollection::attr_map

Definition at line 176 of file sidredatacollection.hpp.

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

fem/sidredatacollection.hpp
fem/sidredatacollection.cpp

Public Types

Public Member Functions

Public Attributes

Protected Member Functions

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ AttributeFieldMap

Constructor & Destructor Documentation

◆ SidreDataCollection() [1/2]

◆ SidreDataCollection() [2/2]

◆ ~SidreDataCollection()

Member Function Documentation

◆ alloc_group()

◆ alloc_view() [1/2]

◆ alloc_view() [2/2]

◆ AllocNamedBuffer()

◆ DeregisterAttributeField()

◆ DeregisterField()

◆ FreeNamedBuffer()

◆ get_file_path()

◆ GetAttributeField()

◆ GetBPGroup()

◆ GetBPIndexGroup()

◆ GetNamedBuffer()

◆ HasAttributeField()

◆ HasBoundaryMesh()

◆ Load() [1/2]

◆ Load() [2/2]

◆ LoadExternalData()

◆ named_buffers_grp()

◆ PrepareToSave()

◆ RegisterAttributeField()

◆ RegisterField() [1/2]

◆ RegisterField() [2/2]

◆ Save() [1/2]

◆ Save() [2/2]

◆ SetComm()

◆ SetGroupPointers()

◆ SetMesh() [1/2]

◆ SetMesh() [2/2]

◆ SetMeshNodesName()

◆ UpdateStateFromDS()

◆ UpdateStateToDS()

Member Data Documentation

◆ attr_map