Interface implemented in MOAB which provides memory for mesh reading utilities. More...

#include <WriteUtilIface.hpp>

Inheritance diagram for moab::WriteUtilIface:

Public Types
enum	EntityListType { CONTENTS = 0 , CHILDREN = 1 , PARENTS = 2 , TOPOLOGICAL = 1 }

Public Member Functions
	WriteUtilIface ()
	Constructor. More...

virtual	~WriteUtilIface ()
	Destructor. More...

virtual ErrorCode	check_doesnt_exist (const char *file_name)=0
	Check if the specified file already exists. Returns MB_SUCCESS if file does not exist, MB_ALREADY_ALLOCATED if file does exist, or MB_FAILURE for some other error condition. More...

virtual ErrorCode	gather_entities (Range &all_ents, const EntityHandle *ent_sets=NULL, int num_sets=0)=0
	Gather all entities in the mesh, or in the sets specified. More...

virtual ErrorCode	get_node_coords (const int num_arrays, const int num_nodes, const Range &entities, Tag node_id_tag, const int start_node_id, std::vector< double * > &arrays)=0
	Given information about the nodes to be written, and pointers to memory to which coordinates will be written, writes coordinate data there, and also assigns global ids to nodes & writes to a tag, if a tag is specified. More...

virtual ErrorCode	get_node_coords (const int which_array, Range::const_iterator begin, const Range::const_iterator &end, const size_t output_size, double *const output_array)=0

virtual ErrorCode	get_element_connect (const int num_elements, const int verts_per_element, Tag node_id_tag, const Range &entities, Tag element_id_tag, int start_element_id, int *array, bool add_sizes=false)=0
	Given information about elements to be written and a pointer to memory where connectivity for those elements should be written, writes connectivity to that memory; uses node ids stored in a tag during call to get_node_coords function. More...

virtual ErrorCode	get_element_connect (Range::const_iterator begin, const Range::const_iterator &end, const int vertices_per_elem, Tag node_id_tag, const size_t array_size, int *const element_array, bool add_sizes=false)=0

virtual ErrorCode	get_element_connect (Range::const_iterator begin, const Range::const_iterator &end, const int vertices_per_elem, const size_t array_size, EntityHandle *const element_array)=0

virtual ErrorCode	get_poly_connect_size (Range::const_iterator begin, const Range::const_iterator &end, int &connectivity_size)=0

virtual ErrorCode	get_poly_connect (Range::const_iterator &iter, const Range::const_iterator &end, const Tag node_id_tag, size_t &element_array_len, int const element_array, size_t &index_array_len, int const index_array, int &index_offset)=0

virtual ErrorCode	gather_nodes_from_elements (const Range &elements, const Tag node_bit_mark_tag, Range &nodes)=0
	Given elements to be written, gather all the nodes which define those elements. More...

virtual ErrorCode	assign_ids (Range &elements, Tag id_tag, const int start_id)=0
	assign ids to input entities starting with start_id, written to id_tag if id_tag is zero, assigns to GLOBAL_ID_TAG_NAME More...

virtual ErrorCode	get_adjacencies (EntityHandle entity, Tag id_tag, std::vector< int > &adj)=0

virtual ErrorCode	get_adjacencies (EntityHandle entity, const EntityHandle *&adj_array, int &num_adj)=0

virtual ErrorCode	get_tag_list (std::vector< Tag > &result_list, const Tag *user_tag_list=0, int user_tag_list_length=0, bool include_variable_length_tags=true)=0
	Get list of tags to write. More...

virtual ErrorCode	get_entity_list_pointers (Range::const_iterator query_begin, Range::const_iterator query_end, EntityHandle const *output_pointer_array, EntityListType relation=CONTENTS, int lengths=0, unsigned char *flags=0)=0

virtual ErrorCode	get_entity_list_pointers (EntityHandle const entities, int num_entities, EntityHandle const output_pointer_array, EntityListType relation=CONTENTS, int lengths=0, unsigned char *flags=0)=0

Static Public Member Functions
template<typename T >
static void	reorder (const int order, T conn, int num_elem, int node_per_elem)
	Re-order outgoing element connectivity. More...

Detailed Description

Interface implemented in MOAB which provides memory for mesh reading utilities.

Definition at line 27 of file WriteUtilIface.hpp.

Member Enumeration Documentation

◆ EntityListType

enum moab::WriteUtilIface::EntityListType

Enumerator
CONTENTS
CHILDREN
PARENTS
TOPOLOGICAL

Definition at line 307 of file WriteUtilIface.hpp.

     {
         CONTENTS    = 0,
         CHILDREN    = 1,
         PARENTS     = 2,
         TOPOLOGICAL = 1
     };

Constructor & Destructor Documentation

◆ WriteUtilIface()

moab::WriteUtilIface::WriteUtilIface ( )

inline

Constructor.

Definition at line 31 of file WriteUtilIface.hpp.

31 {}

◆ ~WriteUtilIface()

virtual moab::WriteUtilIface::~WriteUtilIface ( )

inlinevirtual

Destructor.

Definition at line 34 of file WriteUtilIface.hpp.

34 {}

Member Function Documentation

◆ assign_ids()

virtual ErrorCode moab::WriteUtilIface::assign_ids	(	Range &	elements,
		Tag	id_tag,
		const int	start_id
	)

pure virtual

assign ids to input entities starting with start_id, written to id_tag if id_tag is zero, assigns to GLOBAL_ID_TAG_NAME

Parameters

elements	Entities to be written
id_tag	Tag used to store entity id
start_id	Starting value for entity ids

Returns: status Return status

Implemented in moab::WriteUtil.

Referenced by moab::WriteGMV::local_write_mesh(), moab::WriteCCMIO::write_cells_and_faces(), and moab::WriteCCMIO::write_file().

◆ check_doesnt_exist()

virtual ErrorCode moab::WriteUtilIface::check_doesnt_exist ( const char * file_name )

pure virtual

Check if the specified file already exists. Returns MB_SUCCESS if file does not exist, MB_ALREADY_ALLOCATED if file does exist, or MB_FAILURE for some other error condition.

Implemented in moab::WriteUtil.

Referenced by moab::WriteCGNS::write_file(), moab::WriteGmsh::write_file(), moab::WriteSmf::write_file(), and moab::WriteVtk::write_file().

◆ gather_entities()

virtual ErrorCode moab::WriteUtilIface::gather_entities	(	Range &	all_ents,
		const EntityHandle *	ent_sets = `NULL`,
		int	num_sets = `0`
	)

pure virtual

Gather all entities in the mesh, or in the sets specified.

Parameters

all_ents	range in which entities are returned
ent_sets	entity sets whose contents are to be gathered
num_sets	number of sets in list

Implemented in moab::WriteUtil.

Referenced by moab::WriteDamsel::write_file().

◆ gather_nodes_from_elements()

virtual ErrorCode moab::WriteUtilIface::gather_nodes_from_elements	(	const Range &	elements,
		const Tag	node_bit_mark_tag,
		Range &	nodes
	)

pure virtual

Given elements to be written, gather all the nodes which define those elements.

Parameters

elements	Range of elements to be written
node_bit_mark_tag	Bit tag to use to identify nodes
nodes	Range of nodes gathered from elements (returned)

Returns: status Return status

Implemented in moab::WriteUtil.

Referenced by moab::WriteCCMIO::gather_matset_info(), moab::WriteHDF5::gather_mesh_info(), moab::WriteNCDF::gather_mesh_information(), moab::WriteSLAC::gather_mesh_information(), and moab::WriteTemplate::gather_mesh_information().

◆ get_adjacencies() [1/2]

virtual ErrorCode moab::WriteUtilIface::get_adjacencies	(	EntityHandle	entity,
		const EntityHandle *&	adj_array,
		int &	num_adj
	)

pure virtual

Implemented in moab::WriteUtil.

◆ get_adjacencies() [2/2]

virtual ErrorCode moab::WriteUtilIface::get_adjacencies	(	EntityHandle	entity,
		Tag	id_tag,
		std::vector< int > &	adj
	)

pure virtual

Get explicit adjacencies

Get explicit adjacences stored in database. Does not create any explicit adjacencies or search for implicit ones.

Parameters

entity	The entity to retrieve adjacencies for.
id_tag	The global ID tag
adj	The output list of global IDs of adjacent entities.

Author: Jason Kraftcheck

Implemented in moab::WriteUtil.

Referenced by moab::WriteHDF5::get_adjacencies().

◆ get_element_connect() [1/3]

virtual ErrorCode moab::WriteUtilIface::get_element_connect	(	const int	num_elements,
		const int	verts_per_element,
		Tag	node_id_tag,
		const Range &	entities,
		Tag	element_id_tag,
		int	start_element_id,
		int *	array,
		bool	add_sizes = `false`
	)

pure virtual

Given information about elements to be written and a pointer to memory where connectivity for those elements should be written, writes connectivity to that memory; uses node ids stored in a tag during call to get_node_coords function.

Parameters

num_elements	Number of elements to be written
verts_per_element	Number of vertices per element
node_id_tag	Tag used to store node ids
entities	Range of elements to be written
element_id_tag	Tag which should be used to store element ids
start_element_id	Starting value for element ids
array	Pointer to memory where connectivity data will be written

Returns: status Return status

Implemented in moab::WriteUtil.

Referenced by moab::WriteGMV::local_write_mesh(), moab::WriteNCDF::write_elementblocks(), moab::WriteHDF5::write_elems(), and moab::WriteCCMIO::write_external_faces().

◆ get_element_connect() [2/3]

virtual ErrorCode moab::WriteUtilIface::get_element_connect	(	Range::const_iterator	begin,
		const Range::const_iterator &	end,
		const int	vertices_per_elem,
		const size_t	array_size,
		EntityHandle *const	element_array
	)

pure virtual

Get connectivity for elements

Get the connectivity list for a range of elements.

Failure cases:

Passed range is empty (begin == end).
vertices_per_elem is less than one
element_array is null.
The range contains invalid handles (non-existent entities, not an element, etc.)
Insufficient space in passed array.

Parameters

begin	The first element handle
end	One past the last element handle
vertices_per_elem	Number of vertices to retrieve for each element. If the element has more vertices, the element connectivity will be truncated. If `vertices_per_elem` is greater than the number of nodes for an element, the data will be padded with zeros.
array_size	The length of `element_array`
element_array	The memory location at which to store the connectivity list.

Author: Jason Kraftcheck

Implemented in moab::WriteUtil.

◆ get_element_connect() [3/3]

virtual ErrorCode moab::WriteUtilIface::get_element_connect	(	Range::const_iterator	begin,
		const Range::const_iterator &	end,
		const int	vertices_per_elem,
		Tag	node_id_tag,
		const size_t	array_size,
		int *const	element_array,
		bool	add_sizes = `false`
	)

pure virtual

Get connectivity for elements

Get the connectivity list for a range of elements.

Failure cases:

Passed range is empty (begin == end).
vertices_per_elem is less than one
element_array is null.
The range contains invalid handles (non-existent entities, not an element, etc.)
Retrieving ID tag for an entity failed.
Insufficient space in passed array.

Parameters

begin	The first element handle
end	One past the last element handle
vertices_per_elem	Number of vertices to retrieve for each element. If the element has more vertices, the element connectivity will be truncated. If `vertices_per_elem` is greater than the number of nodes for an element, the data will be padded with zeros.
node_id_tag	A tag with integer values.
array_size	The length of `element_array`
element_array	The memory location at which to store the connectivity list.
add_sizes	If true, writes size of connect array before connectivity in array

Author: Jason Kraftcheck

Implemented in moab::WriteUtil.

◆ get_entity_list_pointers() [1/2]

virtual ErrorCode moab::WriteUtilIface::get_entity_list_pointers	(	EntityHandle const *	entities,
		int	num_entities,
		EntityHandle const **	output_pointer_array,
		EntityListType	relation = `CONTENTS`,
		int *	lengths = `0`,
		unsigned char *	flags = `0`
	)

pure virtual

Implemented in moab::WriteUtil.

◆ get_entity_list_pointers() [2/2]

virtual ErrorCode moab::WriteUtilIface::get_entity_list_pointers	(	Range::const_iterator	query_begin,
		Range::const_iterator	query_end,
		EntityHandle const **	output_pointer_array,
		EntityListType	relation = `CONTENTS`,
		int *	lengths = `0`,
		unsigned char *	flags = `0`
	)

pure virtual

Implemented in moab::WriteUtil.

Referenced by moab::WriteHDF5Parallel::pack_set(), and moab::WriteHDF5::write_set_data().

◆ get_node_coords() [1/2]

virtual ErrorCode moab::WriteUtilIface::get_node_coords	(	const int	num_arrays,
		const int	num_nodes,
		const Range &	entities,
		Tag	node_id_tag,
		const int	start_node_id,
		std::vector< double * > &	arrays
	)

pure virtual

Given information about the nodes to be written, and pointers to memory to which coordinates will be written, writes coordinate data there, and also assigns global ids to nodes & writes to a tag, if a tag is specified.

Parameters

num_arrays	Number of coordinate arrays requested
num_nodes	Number of nodes to be written
entities	Range of nodes to be written
node_id_tag	Tag used to write ids to nodes
start_node_id	Starting value for node ids
arrays	Pointers to memory where coordinate data will be written

Returns: status Return status

Implemented in moab::WriteUtil.

Referenced by moab::WriteGMV::local_write_mesh(), moab::WriteHDF5::write_nodes(), moab::WriteCCMIO::write_nodes(), moab::WriteSLAC::write_nodes(), moab::WriteTemplate::write_nodes(), and moab::WriteNCDF::write_nodes().

◆ get_node_coords() [2/2]

virtual ErrorCode moab::WriteUtilIface::get_node_coords	(	const int	which_array,
		Range::const_iterator	begin,
		const Range::const_iterator &	end,
		const size_t	output_size,
		double *const	output_array
	)

pure virtual

Get array of coordinate values for nodes

Given a range of node handles, retrieve a single or multiple coordinate value(s) for each.

Failure conditions:

invalid entity handles (not vertices, non-existent entity, etc.)
range is empty (iter == end)
output_array is null
insufficient space in output_array

Parameters

which_array	The coordinate to retrieve (0->X, 1->Y, 2->Z, -1->all)
begin	The first node handle.
end	One past the last node handle.
output_size	The size of `output_array`.
output_array	The memory in which to write the node coordinates.

Author: Jason Kraftcheck

Implemented in moab::WriteUtil.

◆ get_poly_connect()

virtual ErrorCode moab::WriteUtilIface::get_poly_connect	(	Range::const_iterator &	iter,
		const Range::const_iterator &	end,
		const Tag	node_id_tag,
		size_t &	element_array_len,
		int *const	element_array,
		size_t &	index_array_len,
		int *const	index_array,
		int &	index_offset
	)

pure virtual

Get poly (polygon or polyhedron) connectivity.

Connectivity is returned in two arrays. The first is an array of global IDs that is the concatenation of the connectivity for the entire range of polys. The second is the last index of the connectivity data for each poly in the global ID array.

This function will add as many polys as possible to the passed arrays given the sizes of those arrays. It will then pass back position at which it stopped and the sizes of the data written to the arrays.

Failure cases:

Passed range is empty (begin == end).
element_array or index_array is null.
The range contains invalid handles (non-existent entities, not an poly, etc.)
Retrieving ID tag for an entity failed.

Parameters

iter	As input, the first element handle. As output, one past the last element handle for which data was written to the arrays.
end	The iterator at which to stop.
node_id_tag	A tag with integer values.
element_array_len	As input, length of `element_array`. As output, the number of entries written in that array.
element_array	The memory location at which to store the connectivity list.
index_array_len	As input, the length of `index_array`. As output, the number of entries written in that array.
index_array	The memory location at which to store offsets.
index_offset	Value to offset (add to) index values. As output the input value plus the amount of data written to the element array. (The value you presumably want to pass to the next call.)

Author: Jason Kraftcheck

Implemented in moab::WriteUtil.

◆ get_poly_connect_size()

virtual ErrorCode moab::WriteUtilIface::get_poly_connect_size	(	Range::const_iterator	begin,
		const Range::const_iterator &	end,
		int &	connectivity_size
	)

pure virtual

Get poly (polygon or polyhedron) connectivity size

Parameters

begin	First iterator in range of poly
end	One past last in range of poly.
connectivity_size	The length of the connectivity list For the specified range of polyhedra.

Author: Jason Kraftcheck

Implemented in moab::WriteUtil.

◆ get_tag_list()

virtual ErrorCode moab::WriteUtilIface::get_tag_list	(	std::vector< Tag > &	result_list,
		const Tag *	user_tag_list = `0`,
		int	user_tag_list_length = `0`,
		bool	include_variable_length_tags = `true`
	)

pure virtual

Get list of tags to write.

Get the list of tags to write to the file, possibly using an optional user-specified tag list. This function consolidates some common code for file writers to use to figure out what tag data to write to the file. It provides the following features: o filter list based on user-specified array of tag handles o filter internal tags (those for which the name is prefixed with two underscore characters) o filter anonymous tags o optionally filter variable-length tags.

Author: Jason Kraftcheck

Parameters

result_list	List of tag handles for which to write data
user_tag_list	Optional array of tag handles passed by user to write to file.
include_variable_length_tags	If false, return only fixed-length tags.

Implemented in moab::WriteUtil.

Referenced by moab::WriteHDF5::gather_tags(), and moab::WriteVtk::write_tags().

◆ reorder()

template<typename T >

void moab::WriteUtilIface::reorder	(	const int *	order,
		T *	conn,
		int	num_elem,
		int	node_per_elem
	)

inlinestatic

Re-order outgoing element connectivity.

Permute the connectivity of each element such that the node order is that of the target file format rather than that of MBCN.

Parameters

order	The permutation to use. Must be an array of 'node_per_elem' integers and be a permutation of the values [0..node_per_elem-1]. Such that for a single element: target_conn[i] == mbcn_conn[order[i]]
conn	The connectivity array to re-order
num_elem	The number of elements in the connectivity array
node_per_elem	The number of nodes in each element's connectivity list.

Definition at line 375 of file WriteUtilIface.hpp.

 {
     std::vector< T > elem( node_per_elem );
     T* const end = conn + num_elem * node_per_elem;
     while( conn != end )
     {
         std::copy( conn, conn + node_per_elem, elem.begin() );
         for( int j = 0; j < node_per_elem; ++j, ++conn )
             *conn = elem[order[j]];
     }
 }

Referenced by moab::WriteNCDF::write_elementblocks().

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

WriteUtilIface.hpp

Public Types

Public Member Functions

Static Public Member Functions

Detailed Description

Member Enumeration Documentation

◆ EntityListType

Constructor & Destructor Documentation

◆ WriteUtilIface()

◆ ~WriteUtilIface()

Member Function Documentation

◆ assign_ids()

◆ check_doesnt_exist()

◆ gather_entities()

◆ gather_nodes_from_elements()

◆ get_adjacencies() [1/2]

◆ get_adjacencies() [2/2]

◆ get_element_connect() [1/3]

◆ get_element_connect() [2/3]

◆ get_element_connect() [3/3]

◆ get_entity_list_pointers() [1/2]

◆ get_entity_list_pointers() [2/2]

◆ get_node_coords() [1/2]

◆ get_node_coords() [2/2]

◆ get_poly_connect()

◆ get_poly_connect_size()

◆ get_tag_list()

◆ reorder()