iMOAB.h File Reference

#include "moab/MOABConfig.h"
#include "moab/Types.hpp"
#include <stdio.h>
#include <assert.h>
#include <stdlib.h>

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Macros
#define	iMOAB_AppID   int*
#define	iMOAB_String   char*
#define	iMOAB_GlobalID   int
#define	iMOAB_LocalID   int
#define	ErrCode   int
#define	__PRETTY_FUNCTION__   __func__
#define	CHK_MPI_ERR(ierr)
#define	IMOAB_CHECKPOINTER(prmObj, position)
#define	IMOAB_THROW_ERROR(message, retval)
#define	IMOAB_ASSERT_RET(condition, message, retval)
#define	IMOAB_ASSERT(condition, message)   IMOAB_ASSERT_RET( condition, message, moab::MB_UNHANDLED_OPTION )

Enumerations
enum	MOAB_TAG_TYPE {   DENSE_INTEGER = 0 , DENSE_DOUBLE = 1 , DENSE_ENTITYHANDLE = 2 , SPARSE_INTEGER = 3 ,   SPARSE_DOUBLE = 4 , SPARSE_ENTITYHANDLE = 5 }
	MOAB tag types can be: dense/sparse, and of int/double/EntityHandle types. They can also be defined on both elements and vertices of the mesh. More...
enum	MOAB_TAG_OWNER_TYPE { TAG_VERTEX = 0 , TAG_EDGE = 1 , TAG_FACE = 2 , TAG_ELEMENT = 3 }
	Define MOAB tag ownership information i.e., the entity where the tag is primarily defined This is typically used to query the tag data and to set it back. More...

Functions
ErrCode	iMOAB_Initialize (int argc, iMOAB_String *argv)
	Initialize the iMOAB interface implementation. More...
ErrCode	iMOAB_InitializeFortran (void)
	Initialize the iMOAB interface implementation from Fortran driver. More...
ErrCode	iMOAB_Finalize (void)
	Finalize the iMOAB interface implementation. More...
ErrCode	iMOAB_RegisterApplication (const iMOAB_String app_name, int *compid, iMOAB_AppID pid)
	Register application - Create a unique application ID and bootstrap interfaces for further queries. More...
ErrCode	iMOAB_DeregisterApplication (iMOAB_AppID pid)
	De-Register application: delete mesh (set) associated with the application ID. More...
ErrCode	iMOAB_RegisterApplicationFortran (const iMOAB_String app_name, int *compid, iMOAB_AppID pid)
	Register a Fortran-based application - Create a unique application ID and bootstrap interfaces for further queries. More...
ErrCode	iMOAB_DeregisterApplicationFortran (iMOAB_AppID pid)
	De-Register the Fortran based application: delete mesh (set) associated with the application ID. More...
ErrCode	iMOAB_ReadHeaderInfo (const iMOAB_String filename, int *num_global_vertices, int *num_global_elements, int *num_dimension, int *num_parts)
	It should be called on master task only, and information obtained could be broadcasted by the user. It is a fast lookup in the header of the file. More...
ErrCode	iMOAB_LoadMesh (iMOAB_AppID pid, const iMOAB_String filename, const iMOAB_String read_options, int *num_ghost_layers)
	Load a MOAB mesh file in parallel and exchange ghost layers as requested. More...
ErrCode	iMOAB_CreateVertices (iMOAB_AppID pid, int *coords_len, int *dim, double *coordinates)
	Create vertices for an app; it assumes no other vertices. More...
ErrCode	iMOAB_CreateElements (iMOAB_AppID pid, int *num_elem, int *type, int *num_nodes_per_element, int *connectivity, int *block_ID)
	Create elements for an app; it assumes connectivity from local vertices, in order. More...
ErrCode	iMOAB_ResolveSharedEntities (iMOAB_AppID pid, int *num_verts, int *marker)
	Resolve shared entities using global markers on shared vertices. More...
ErrCode	iMOAB_DetermineGhostEntities (iMOAB_AppID pid, int *ghost_dim, int *num_ghost_layers, int *bridge_dim)
	Create the requested number of ghost layers for the parallel mesh. More...
ErrCode	iMOAB_WriteMesh (iMOAB_AppID pid, const iMOAB_String filename, const iMOAB_String write_options)
	Write a MOAB mesh along with the solution tags to a file. More...
ErrCode	iMOAB_WriteLocalMesh (iMOAB_AppID pid, iMOAB_String prefix)
	Write a local MOAB mesh copy. More...
ErrCode	iMOAB_UpdateMeshInfo (iMOAB_AppID pid)
	Update local mesh data structure, from file information. More...
ErrCode	iMOAB_GetMeshInfo (iMOAB_AppID pid, int *num_visible_vertices, int *num_visible_elements, int *num_visible_blocks, int *num_visible_surfaceBC, int *num_visible_vertexBC)
	Retrieve all the important mesh information related to vertices, elements, vertex and surface boundary conditions. More...
ErrCode	iMOAB_GetVertexID (iMOAB_AppID pid, int *vertices_length, iMOAB_GlobalID *global_vertex_ID)
	Get the global vertex IDs for all locally visible (owned and shared/ghosted) vertices. More...
ErrCode	iMOAB_GetVertexOwnership (iMOAB_AppID pid, int *vertices_length, int *visible_global_rank_ID)
	Get vertex ownership information. More...
ErrCode	iMOAB_GetVisibleVerticesCoordinates (iMOAB_AppID pid, int *coords_length, double *coordinates)
	Get vertex coordinates for all local (owned and ghosted) vertices. More...
ErrCode	iMOAB_GetBlockID (iMOAB_AppID pid, int *block_length, iMOAB_GlobalID *global_block_IDs)
	Get the global block IDs for all locally visible (owned and shared/ghosted) blocks. More...
ErrCode	iMOAB_GetBlockInfo (iMOAB_AppID pid, iMOAB_GlobalID *global_block_ID, int *vertices_per_element, int *num_elements_in_block)
	Get the global block information and number of visible elements of belonging to a block (MATERIAL SET). More...
ErrCode	iMOAB_GetVisibleElementsInfo (iMOAB_AppID pid, int *num_visible_elements, iMOAB_GlobalID *element_global_IDs, int *ranks, iMOAB_GlobalID *block_IDs)
	Get the visible elements information. More...
ErrCode	iMOAB_GetBlockElementConnectivities (iMOAB_AppID pid, iMOAB_GlobalID *global_block_ID, int *connectivity_length, int *element_connectivity)
	Get the connectivities for elements contained within a certain block. More...
ErrCode	iMOAB_GetElementConnectivity (iMOAB_AppID pid, iMOAB_LocalID *elem_index, int *connectivity_length, int *element_connectivity)
	Get the connectivity for one element only. More...
ErrCode	iMOAB_GetElementOwnership (iMOAB_AppID pid, iMOAB_GlobalID *global_block_ID, int *num_elements_in_block, int *element_ownership)
	Get the element ownership within a certain block i.e., processor ID of the element owner. More...
ErrCode	iMOAB_GetElementID (iMOAB_AppID pid, iMOAB_GlobalID *global_block_ID, int *num_elements_in_block, iMOAB_GlobalID *global_element_ID, iMOAB_LocalID *local_element_ID)
	Get the global IDs for all locally visible elements belonging to a particular block. More...
ErrCode	iMOAB_GetPointerToSurfaceBC (iMOAB_AppID pid, int *surface_BC_length, iMOAB_LocalID *local_element_ID, int *reference_surface_ID, int *boundary_condition_value)
	Get the surface boundary condition information. More...
ErrCode	iMOAB_GetPointerToVertexBC (iMOAB_AppID pid, int *vertex_BC_length, iMOAB_LocalID *local_vertex_ID, int *boundary_condition_value)
	Get the vertex boundary condition information. More...
ErrCode	iMOAB_DefineTagStorage (iMOAB_AppID pid, const iMOAB_String tag_storage_name, int *tag_type, int *components_per_entity, int *tag_index)
	Define a MOAB Tag corresponding to the application depending on requested types. More...
ErrCode	iMOAB_SetIntTagStorage (iMOAB_AppID pid, const iMOAB_String tag_storage_name, int *num_tag_storage_length, int *entity_type, int *tag_storage_data)
	Store the specified values in a MOAB integer Tag. More...
ErrCode	iMOAB_GetIntTagStorage (iMOAB_AppID pid, const iMOAB_String tag_storage_name, int *num_tag_storage_length, int *entity_type, int *tag_storage_data)
	Get the specified values in a MOAB integer Tag. More...
ErrCode	iMOAB_SetDoubleTagStorage (iMOAB_AppID pid, const iMOAB_String tag_storage_name, int *num_tag_storage_length, int *entity_type, double *tag_storage_data)
	Store the specified values in a MOAB double Tag. More...
ErrCode	iMOAB_SetDoubleTagStorageWithGid (iMOAB_AppID pid, const iMOAB_String tag_storage_names, int *num_tag_storage_length, int *entity_type, double *tag_storage_data, int *globalIds)
	Store the specified values in a MOAB double Tag, for given ids. More...
ErrCode	iMOAB_GetDoubleTagStorage (iMOAB_AppID pid, const iMOAB_String tag_storage_name, int *num_tag_storage_length, int *entity_type, double *tag_storage_data)
	Retrieve the specified values in a MOAB double Tag. More...
ErrCode	iMOAB_SynchronizeTags (iMOAB_AppID pid, int *num_tag, int *tag_indices, int *ent_type)
	Exchange tag values for the given tags across process boundaries. More...
ErrCode	iMOAB_ReduceTagsMax (iMOAB_AppID pid, int *tag_index, int *ent_type)
	Perform global reductions with the processes in the current applications communicator. Specifically this routine performs reductions on the maximum value of the tag indicated by tag_index. More...
ErrCode	iMOAB_GetNeighborElements (iMOAB_AppID pid, iMOAB_LocalID *local_index, int *num_adjacent_elements, iMOAB_LocalID *adjacent_element_IDs)
	Retrieve the adjacencies for the element entities. More...
ErrCode	iMOAB_GetNeighborVertices (iMOAB_AppID pid, iMOAB_LocalID *local_vertex_ID, int *num_adjacent_vertices, iMOAB_LocalID *adjacent_vertex_IDs)
	Get the adjacencies for the vertex entities. More...
ErrCode	iMOAB_SetGlobalInfo (iMOAB_AppID pid, int *num_global_verts, int *num_global_elems)
	Set global information for number of vertices and number of elements; It is usually available from the h5m file, or it can be computed with a MPI_Reduce. More...
ErrCode	iMOAB_GetGlobalInfo (iMOAB_AppID pid, int *num_global_verts, int *num_global_elems)
	Get global information about number of vertices and number of elements. More...

Detailed Description

iMOAB: a language-agnostic, lightweight interface to MOAB.

Supports usage from C/C++, Fortran (77/90/2003), Python.

Remarks

1) All data in the interface are exposed via POD-types.

2) Pass everything by reference, so we do not have to use VAL()

3) Arrays are allocated by the user code. No concerns about de-allocation of the data will be taken up by the interface.

4) Always pass the pointer to the start of array along with the total allocated size for the array.

5) Return the filled array requested by user along with optionally the actual length of the array that was filled. (for typical cases, should be the allocated length)

Definition in file iMOAB.h.

Macro Definition Documentation

__PRETTY_FUNCTION__

#define __PRETTY_FUNCTION__   __func__

Definition at line 65 of file iMOAB.h.

CHK_MPI_ERR

#define CHK_MPI_ERR

(

ierr

)

Value:

    {                                                \
        if( 0 != ( ierr ) ) return moab::MB_FAILURE; \
    }

Definition at line 95 of file iMOAB.h.

ErrCode

#define ErrCode   int

Definition at line 58 of file iMOAB.h.

iMOAB_AppID

#define iMOAB_AppID   int*

\Notes 1) Fortran MPI_Comm won't work. Take an integer argument and use MPI_F2C calls to get the C-Comm object 2) ReadHeaderInfo - Does it need the pid ? 3) Reuse the comm object from the registration for both load and write operations. Do not take comm objects again to avoid confusion and retain consistency. 4) Decipher the global comm object and the subset partioning for each application based on the comm object 5) GetMeshInfo - return separately the owned and ghosted vertices/elements – not together in visible_** but rather owned_** and ghosted_**. Make these arrays of size 2. 6) Should we sort the vertices after ghosting, such that the locally owned is first, and the ghosted appended next. 7) RCM only for the owned part of the mesh – do not screw with the ghosted layers 8) GetBlockID - identical to GetVertexID – return the global numbering for block 9) GetVertexID – remember that the order of vertices returned have an implicit numbering embedded in it. DO NOT CHANGE THIS ORDERING... 10) GetBlockInfo takes global Block ID; Remove blockname unless there is a separate use case for it.. 11) GetElementConnectivity - clarify whether we return global or local vertex numbering. Preferably local numbering else lot of deciphering for global.

Definition at line 51 of file iMOAB.h.

IMOAB_ASSERT

#define IMOAB_ASSERT	(		condition,
			message
	)		IMOAB_ASSERT_RET( condition, message, moab::MB_UNHANDLED_OPTION )

Definition at line 126 of file iMOAB.h.

IMOAB_ASSERT_RET

#define IMOAB_ASSERT_RET	(		condition,
			message,
			retval
	)

Value:

    {                                                                                                          \
        if( !( condition ) )                                                                                   \
        {                                                                                                      \
            printf( "iMOAB Error: %s.\n Failed condition: %s\n Location: %s in %s:%d.\n", message, #condition, \
                    __PRETTY_FUNCTION__, __FILE__, __LINE__ );                                                 \
            return retval;                                                                                     \
        }                                                                                                      \
    }

Definition at line 116 of file iMOAB.h.

IMOAB_CHECKPOINTER

#define IMOAB_CHECKPOINTER	(		prmObj,
			position
	)

Value:

    {                                                                                          \
        if( prmObj == nullptr )                                                                \
        {                                                                                      \
            printf( "InputParamError at %d: '%s' is invalid and null.\n", position, #prmObj ); \
            return moab::MB_UNHANDLED_OPTION;                                                  \
        }                                                                                      \
    }

Definition at line 100 of file iMOAB.h.

iMOAB_GlobalID

#define iMOAB_GlobalID   int

Definition at line 53 of file iMOAB.h.

iMOAB_LocalID

#define iMOAB_LocalID   int

Definition at line 54 of file iMOAB.h.

iMOAB_String

#define iMOAB_String   char*

Definition at line 52 of file iMOAB.h.

IMOAB_THROW_ERROR

#define IMOAB_THROW_ERROR	(		message,
			retval
	)

Value:

    {                                                                                                              \
        printf( "iMOAB Error: %s.\n Location: %s in %s:%d.\n", message, __PRETTY_FUNCTION__, __FILE__, __LINE__ ); \
        return retval;                                                                                             \
    }

Definition at line 109 of file iMOAB.h.

Enumeration Type Documentation

MOAB_TAG_OWNER_TYPE

enum MOAB_TAG_OWNER_TYPE

Define MOAB tag ownership information i.e., the entity where the tag is primarily defined This is typically used to query the tag data and to set it back.

Enumerator
TAG_VERTEX
TAG_EDGE
TAG_FACE
TAG_ELEMENT

Definition at line 87 of file iMOAB.h.

{
    TAG_VERTEX  = 0,
    TAG_EDGE    = 1,
    TAG_FACE    = 2,
    TAG_ELEMENT = 3
};

MOAB_TAG_TYPE

enum MOAB_TAG_TYPE

MOAB tag types can be: dense/sparse, and of int/double/EntityHandle types. They can also be defined on both elements and vertices of the mesh.

Enumerator
DENSE_INTEGER
DENSE_DOUBLE
DENSE_ENTITYHANDLE
SPARSE_INTEGER
SPARSE_DOUBLE
SPARSE_ENTITYHANDLE

Definition at line 73 of file iMOAB.h.

{
    DENSE_INTEGER       = 0,
    DENSE_DOUBLE        = 1,
    DENSE_ENTITYHANDLE  = 2,
    SPARSE_INTEGER      = 3,
    SPARSE_DOUBLE       = 4,
    SPARSE_ENTITYHANDLE = 5
};

Function Documentation

iMOAB_CreateElements()

ErrCode iMOAB_CreateElements	(	iMOAB_AppID	pid,
		int *	num_elem,
		int *	type,
		int *	num_nodes_per_element,
		int *	connectivity,
		int *	block_ID
	)

Create elements for an app; it assumes connectivity from local vertices, in order.

Note

Operations: Not collective

Parameters

[in]	pid	(iMOAB_AppID) The unique pointer to the application ID.
[in]	num_elem	(int*) Number of elements.
[in]	type	(int*) Type of element (moab type).
[in]	num_nodes_per_element	(int*) Number of nodes per element.
[in]	connectivity	(int *) Connectivity array, with respect to vertices (assumed contiguous).
[in]	block_ID	(int *) The local block identifier, which will now contain the elements.

Returns

ErrCode The error code indicating success or failure.

add the new ents to the clock set

Definition at line 2239 of file iMOAB.cpp.

{
    // Create elements
    appData& data = context.appDatas[*pid];
 
    ReadUtilIface* read_iface;
    ErrorCode rval = context.MBI->query_interface( read_iface );MB_CHK_ERR( rval );
 
    EntityType mbtype = (EntityType)( *type );
    EntityHandle actual_start_handle;
    EntityHandle* array = NULL;
    rval = read_iface->get_element_connect( *num_elem, *num_nodes_per_element, mbtype, 1, actual_start_handle, array );MB_CHK_ERR( rval );
 
    // fill up with actual connectivity from input; assume the vertices are in order, and start
    // vertex is the first in the current data vertex range
    EntityHandle firstVertex = data.local_verts[0];
 
    for( int j = 0; j < *num_elem * ( *num_nodes_per_element ); j++ )
    {
        array[j] = connectivity[j] + firstVertex - 1;
    }  // assumes connectivity uses 1 based array (from fortran, mostly)
 
    Range new_elems( actual_start_handle, actual_start_handle + *num_elem - 1 );
 
    rval = context.MBI->add_entities( data.file_set, new_elems );MB_CHK_ERR( rval );
 
    data.primary_elems.merge( new_elems );
 
    // add to adjacency
    rval = read_iface->update_adjacencies( actual_start_handle, *num_elem, *num_nodes_per_element, array );MB_CHK_ERR( rval );
    // organize all new elements in block, with the given block ID; if the block set is not
    // existing, create  a new mesh set;
    Range sets;
    int set_no            = *block_ID;
    const void* setno_ptr = &set_no;
    rval = context.MBI->get_entities_by_type_and_tag( data.file_set, MBENTITYSET, &context.material_tag, &setno_ptr, 1,
                                                      sets );
    EntityHandle block_set;
 
    if( MB_FAILURE == rval || sets.empty() )
    {
        // create a new set, with this block ID
        rval = context.MBI->create_meshset( MESHSET_SET, block_set );MB_CHK_ERR( rval );
 
        rval = context.MBI->tag_set_data( context.material_tag, &block_set, 1, &set_no );MB_CHK_ERR( rval );
 
        // add the material set to file set
        rval = context.MBI->add_entities( data.file_set, &block_set, 1 );MB_CHK_ERR( rval );
    }
    else
    {
        block_set = sets[0];
    }  // first set is the one we want
 
    /// add the new ents to the clock set
    rval = context.MBI->add_entities( block_set, new_elems );MB_CHK_ERR( rval );
 
    return moab::MB_SUCCESS;
}

References moab::Interface::add_entities(), GlobalContext::appDatas, context, moab::Interface::create_meshset(), moab::Range::empty(), ErrorCode, appData::file_set, moab::ReadUtilIface::get_element_connect(), moab::Interface::get_entities_by_type_and_tag(), appData::local_verts, GlobalContext::material_tag, MB_CHK_ERR, MB_SUCCESS, MBENTITYSET, GlobalContext::MBI, moab::Range::merge(), MESHSET_SET, appData::primary_elems, moab::Interface::query_interface(), moab::Interface::tag_set_data(), and moab::ReadUtilIface::update_adjacencies().

iMOAB_CreateVertices()

ErrCode iMOAB_CreateVertices	(	iMOAB_AppID	pid,
		int *	coords_len,
		int *	dim,
		double *	coordinates
	)

Create vertices for an app; it assumes no other vertices.

Note

Operations: Not collective

Parameters

[in]	pid	(iMOAB_AppID) The unique pointer to the application ID.
[in]	coords_len	(int*) Size of the coordinates array (nverts * dim).
[in]	dim	(int*) Dimension of the vertex coordinates (usually 3).
[in]	coordinates	(double*) Coordinates of all vertices, interleaved.

Returns

ErrCode The error code indicating success or failure.

Definition at line 2218 of file iMOAB.cpp.

{
    ErrorCode rval;
    appData& data = context.appDatas[*pid];
 
    if( !data.local_verts.empty() )  // we should have no vertices in the app
    {
        return moab::MB_FAILURE;
    }
 
    int nverts = *coords_len / *dim;
 
    rval = context.MBI->create_vertices( coordinates, nverts, data.local_verts );MB_CHK_ERR( rval );
 
    rval = context.MBI->add_entities( data.file_set, data.local_verts );MB_CHK_ERR( rval );
 
    // also add the vertices to the all_verts range
    data.all_verts.merge( data.local_verts );
    return moab::MB_SUCCESS;
}

References moab::Interface::add_entities(), appData::all_verts, GlobalContext::appDatas, context, moab::Interface::create_vertices(), dim, moab::Range::empty(), ErrorCode, appData::file_set, appData::local_verts, MB_CHK_ERR, MB_SUCCESS, GlobalContext::MBI, and moab::Range::merge().

iMOAB_DefineTagStorage()

ErrCode iMOAB_DefineTagStorage	(	iMOAB_AppID	pid,
		const iMOAB_String	tag_storage_name,
		int *	tag_type,
		int *	components_per_entity,
		int *	tag_index
	)

Define a MOAB Tag corresponding to the application depending on requested types.

Note

In MOAB, for most solution vectors, we only need to create a "Dense", "Double" Tag. A sparse tag can be created too. If the tag is already existing in the file, it will not be created. If it is a new tag, memory will be allocated when setting the values. Default values are 0 for for integer tags, 0.0 for double tags, 0 for entity handle tags.

Operations: Collective

Parameters

[in]	pid	(iMOAB_AppID) The unique pointer to the application ID.
[in]	tag_storage_name	(iMOAB_String) The tag name to store/retrieve the data in MOAB.
[in]	tag_type	(int*) The type of MOAB tag (Dense/Sparse, Double/Int/EntityHandle), enum MOAB_TAG_TYPE.
[in]	components_per_entity	(int*) The total size of vector dimension per entity for the tag (e.g., number of doubles per entity).
[out]	tag_index	(int*) The tag index which can be used as identifier in synchronize methods.

Returns

ErrCode The error code indicating success or failure.

Definition at line 1467 of file iMOAB.cpp.

{
    // see if the tag is already existing, and if yes, check the type, length
    if( *tag_type < 0 || *tag_type > 5 )
    {
        return moab::MB_FAILURE;
    }  // we have 6 types of tags supported so far
 
    DataType tagDataType;
    TagType tagType;
    void* defaultVal        = NULL;
    int* defInt             = new int[*components_per_entity];
    double* defDouble       = new double[*components_per_entity];
    EntityHandle* defHandle = new EntityHandle[*components_per_entity];
 
    for( int i = 0; i < *components_per_entity; i++ )
    {
        defInt[i]    = 0;
        defDouble[i] = -1e+10;
        defHandle[i] = (EntityHandle)0;
    }
 
    switch( *tag_type )
    {
        case 0:
            tagDataType = MB_TYPE_INTEGER;
            tagType     = MB_TAG_DENSE;
            defaultVal  = defInt;
            break;
 
        case 1:
            tagDataType = MB_TYPE_DOUBLE;
            tagType     = MB_TAG_DENSE;
            defaultVal  = defDouble;
            break;
 
        case 2:
            tagDataType = MB_TYPE_HANDLE;
            tagType     = MB_TAG_DENSE;
            defaultVal  = defHandle;
            break;
 
        case 3:
            tagDataType = MB_TYPE_INTEGER;
            tagType     = MB_TAG_SPARSE;
            defaultVal  = defInt;
            break;
 
        case 4:
            tagDataType = MB_TYPE_DOUBLE;
            tagType     = MB_TAG_SPARSE;
            defaultVal  = defDouble;
            break;
 
        case 5:
            tagDataType = MB_TYPE_HANDLE;
            tagType     = MB_TAG_SPARSE;
            defaultVal  = defHandle;
            break;
 
        default: {
            delete[] defInt;
            delete[] defDouble;
            delete[] defHandle;
            return moab::MB_FAILURE;
        }  // error
    }
 
    Tag tagHandle;
    // split storage names if separated list
 
    std::string tag_name( tag_storage_name );
 
    //  first separate the names of the tags
    // we assume that there are separators ":" between the tag names
    std::vector< std::string > tagNames;
    std::string separator( ":" );
    split_tag_names( tag_name, separator, tagNames );
 
    ErrorCode rval           = moab::MB_SUCCESS;  // assume success already :)
    appData& data            = context.appDatas[*pid];
    int already_defined_tags = 0;
 
    for( size_t i = 0; i < tagNames.size(); i++ )
    {
        rval = context.MBI->tag_get_handle( tagNames[i].c_str(), *components_per_entity, tagDataType, tagHandle,
                                            tagType | MB_TAG_EXCL | MB_TAG_CREAT, defaultVal );
 
        if( MB_ALREADY_ALLOCATED == rval )
        {
            std::map< std::string, Tag >& mTags        = data.tagMap;
            std::map< std::string, Tag >::iterator mit = mTags.find( tagNames[i].c_str() );
 
            if( mit == mTags.end() )
            {
                // add it to the map
                mTags[tagNames[i]] = tagHandle;
                // push it to the list of tags, too
                *tag_index = (int)data.tagList.size();
                data.tagList.push_back( tagHandle );
            }
            rval = MB_SUCCESS;
            already_defined_tags++;
        }
        else if( MB_SUCCESS == rval )
        {
            data.tagMap[tagNames[i]] = tagHandle;
            *tag_index               = (int)data.tagList.size();
            data.tagList.push_back( tagHandle );
        }
        else
        {
            rval = moab::MB_FAILURE;  // some tags were not created
        }
    }
    // we don't need default values anymore, avoid leaks
    int rankHere = 0;
#ifdef MOAB_HAVE_MPI
    ParallelComm* pco = context.pcomms[*pid];
    rankHere          = pco->rank();
#endif
    if( !rankHere && already_defined_tags )
        std::cout << " application with ID: " << *pid << " global id: " << data.global_id << " name: " << data.name
                  << " has " << already_defined_tags << " already defined tags out of " << tagNames.size()
                  << " tags \n";
    delete[] defInt;
    delete[] defDouble;
    delete[] defHandle;
    return rval;
}

References GlobalContext::appDatas, context, ErrorCode, appData::global_id, MB_ALREADY_ALLOCATED, MB_SUCCESS, MB_TAG_CREAT, MB_TAG_DENSE, MB_TAG_EXCL, MB_TAG_SPARSE, MB_TYPE_DOUBLE, MB_TYPE_HANDLE, MB_TYPE_INTEGER, GlobalContext::MBI, appData::name, moab::ParallelComm::rank(), split_tag_names(), moab::Interface::tag_get_handle(), appData::tagList, appData::tagMap, and TagType.

iMOAB_DeregisterApplication()

ErrCode iMOAB_DeregisterApplication

(

iMOAB_AppID

pid

)

De-Register application: delete mesh (set) associated with the application ID.

Note

The associated communicator will be released, and all associated mesh entities and sets will be deleted from the mesh data structure. Associated tag storage data will be freed too.

Operations: Collective

Parameters

[in]

pid

(iMOAB_AppID) The unique pointer to the application ID

Returns

ErrCode The error code indicating success or failure.

Definition at line 331 of file iMOAB.cpp.

{
    // the file set , parallel comm are all in vectors indexed by *pid
    // assume we did not delete anything yet
    // *pid will not be reused if we register another application
    appData& data = context.appDatas[*pid];
    int rankHere  = 0;
#ifdef MOAB_HAVE_MPI
    ParallelComm* pco = context.pcomms[*pid];
    rankHere          = pco->rank();
#endif
    if( !rankHere )
        std::cout << " application with ID: " << *pid << " global id: " << data.global_id << " name: " << data.name
                  << " is de-registered now \n";
 
    EntityHandle fileSet = data.file_set;
    // get all entities part of the file set
    Range fileents;
    ErrorCode rval = context.MBI->get_entities_by_handle( fileSet, fileents, /*recursive */ true );MB_CHK_ERR( rval );
 
    fileents.insert( fileSet );
 
    rval = context.MBI->get_entities_by_type( fileSet, MBENTITYSET, fileents );MB_CHK_ERR( rval );  // append all mesh sets
 
#ifdef MOAB_HAVE_TEMPESTREMAP
    if( data.tempestData.remapper ) delete data.tempestData.remapper;
    if( data.tempestData.weightMaps.size() ) data.tempestData.weightMaps.clear();
#endif
 
#ifdef MOAB_HAVE_MPI
 
    // we could get the pco also with
    // ParallelComm * pcomm = ParallelComm::get_pcomm(context.MBI, *pid);
 
    std::map< int, ParCommGraph* >& pargs = data.pgraph;
 
    // free the parallel comm graphs associated with this app
    for( std::map< int, ParCommGraph* >::iterator mt = pargs.begin(); mt != pargs.end(); mt++ )
    {
        ParCommGraph* pgr = mt->second;
        delete pgr;
        pgr = NULL;
    }
    if( pco ) delete pco;
#endif
 
    // delete first all except vertices
    Range vertices = fileents.subset_by_type( MBVERTEX );
    Range noverts  = subtract( fileents, vertices );
 
    rval = context.MBI->delete_entities( noverts );MB_CHK_ERR( rval );
    // now retrieve connected elements that still exist (maybe in other sets, pids?)
    Range adj_ents_left;
    rval = context.MBI->get_adjacencies( vertices, 1, false, adj_ents_left, Interface::UNION );MB_CHK_ERR( rval );
    rval = context.MBI->get_adjacencies( vertices, 2, false, adj_ents_left, Interface::UNION );MB_CHK_ERR( rval );
    rval = context.MBI->get_adjacencies( vertices, 3, false, adj_ents_left, Interface::UNION );MB_CHK_ERR( rval );
 
    if( !adj_ents_left.empty() )
    {
        Range conn_verts;
        rval = context.MBI->get_connectivity( adj_ents_left, conn_verts );MB_CHK_ERR( rval );
        vertices = subtract( vertices, conn_verts );
    }
 
    rval = context.MBI->delete_entities( vertices );MB_CHK_ERR( rval );
 
    std::map< std::string, int >::iterator mit;
 
    for( mit = context.appIdMap.begin(); mit != context.appIdMap.end(); mit++ )
    {
        int pidx = mit->second;
 
        if( *pid == pidx )
        {
            break;
        }
    }
 
    context.appIdMap.erase( mit );
    std::map< int, int >::iterator mit1;
 
    for( mit1 = context.appIdCompMap.begin(); mit1 != context.appIdCompMap.end(); mit1++ )
    {
        int pidx = mit1->second;
 
        if( *pid == pidx )
        {
            break;
        }
    }
 
    context.appIdCompMap.erase( mit1 );
 
    context.unused_pid--;  // we have to go backwards always TODO
    context.appDatas.pop_back();
#ifdef MOAB_HAVE_MPI
    context.pcomms.pop_back();
#endif
    return moab::MB_SUCCESS;
}

References GlobalContext::appDatas, GlobalContext::appIdCompMap, GlobalContext::appIdMap, context, moab::Interface::delete_entities(), moab::Range::empty(), ErrorCode, appData::file_set, moab::Interface::get_adjacencies(), moab::Interface::get_connectivity(), moab::Interface::get_entities_by_handle(), moab::Interface::get_entities_by_type(), appData::global_id, moab::Range::insert(), MB_CHK_ERR, MB_SUCCESS, MBENTITYSET, GlobalContext::MBI, MBVERTEX, appData::name, moab::ParallelComm::rank(), moab::Range::subset_by_type(), moab::subtract(), moab::Interface::UNION, and GlobalContext::unused_pid.

Referenced by iMOAB_DeregisterApplicationFortran().

iMOAB_DeregisterApplicationFortran()

ErrCode iMOAB_DeregisterApplicationFortran

(

iMOAB_AppID

pid

)

De-Register the Fortran based application: delete mesh (set) associated with the application ID.

Note

The associated communicator will be released, and all associated mesh entities and sets will be deleted from the mesh data structure. Associated tag storage data will be freed too.

Operations: Collective

Parameters

[in]

pid

(iMOAB_AppID) The unique pointer to the application ID

Returns

ErrCode The error code indicating success or failure.

Definition at line 432 of file iMOAB.cpp.

{
    // release any Fortran specific allocations here before we pass it on
    context.appDatas[*pid].is_fortran = false;
 
    // release all datastructure allocations
    return iMOAB_DeregisterApplication( pid );
}

References GlobalContext::appDatas, context, and iMOAB_DeregisterApplication().

iMOAB_DetermineGhostEntities()

ErrCode iMOAB_DetermineGhostEntities	(	iMOAB_AppID	pid,
		int *	ghost_dim,
		int *	num_ghost_layers,
		int *	bridge_dim
	)

Create the requested number of ghost layers for the parallel mesh.

Note

The routine assumes that the shared entities were resolved successfully, and that the mesh is properly distributed on separate tasks.

Operations: Collective.

Parameters

[in]	pid	(iMOAB_AppID) The unique pointer to the application ID.
[in]	ghost_dim	(int*) Desired ghost dimension (2 or 3, most of the time).
[in]	num_ghost_layers	(int*) Number of ghost layers requested.
[in]	bridge_dim	(int*) Bridge dimension (0 for vertices, 1 for edges, 2 for faces).

Returns

ErrCode The error code indicating success or failure.

iMOAB_Finalize()

ErrCode iMOAB_Finalize

(

void

)

Finalize the iMOAB interface implementation.

It will delete the internally reference counted MOAB instance, if the reference count reaches 0.

Operations: Collective

Returns

ErrCode The error code indicating success or failure.

Definition at line 187 of file iMOAB.cpp.

{
    context.refCountMB--;
 
    if( 0 == context.refCountMB )
    {
        delete context.MBI;
    }
 
    return MB_SUCCESS;
}

References context, MB_SUCCESS, GlobalContext::MBI, and GlobalContext::refCountMB.

iMOAB_GetBlockElementConnectivities()

ErrCode iMOAB_GetBlockElementConnectivities	(	iMOAB_AppID	pid,
		iMOAB_GlobalID *	global_block_ID,
		int *	connectivity_length,
		int *	element_connectivity
	)

Get the connectivities for elements contained within a certain block.

Note

input is the block ID. Should we change to visible block local index?

Operations: Not Collective

Parameters

[in]	pid	(iMOAB_AppID) The unique pointer to the application ID.
[in]	global_block_ID	(iMOAB_GlobalID*) The global block ID of the set being queried.
[in]	connectivity_length	(int*) The allocated size of array. (typical size := vertices_per_element*num_elements_in_block)
[out]	element_connectivity	(int*) The connectivity array to store element ordering in MOAB canonical numbering scheme (array allocated by user); array contains vertex indices in the local numbering order for vertices elements are in the same order as provided by GetElementOwnership and GetElementID.

Returns

ErrCode The error code indicating success or failure.

Definition at line 1159 of file iMOAB.cpp.

{
    assert( global_block_ID );      // ensure global block ID argument is not null
    assert( connectivity_length );  // ensure connectivity length argument is not null
 
    appData& data                     = context.appDatas[*pid];
    std::map< int, int >& matMap      = data.matIndex;
    std::map< int, int >::iterator it = matMap.find( *global_block_ID );
 
    if( it == matMap.end() )
    {
        return moab::MB_FAILURE;
    }  // error in finding block with id
 
    int blockIndex          = matMap[*global_block_ID];
    EntityHandle matMeshSet = data.mat_sets[blockIndex];
    std::vector< EntityHandle > elems;
 
    ErrorCode rval = context.MBI->get_entities_by_handle( matMeshSet, elems );MB_CHK_ERR( rval );
 
    if( elems.empty() )
    {
        return moab::MB_FAILURE;
    }
 
    std::vector< EntityHandle > vconnect;
    rval = context.MBI->get_connectivity( &elems[0], elems.size(), vconnect );MB_CHK_ERR( rval );
 
    if( *connectivity_length != (int)vconnect.size() )
    {
        return moab::MB_FAILURE;
    }  // mismatched sizes
 
    for( int i = 0; i < *connectivity_length; i++ )
    {
        int inx = data.all_verts.index( vconnect[i] );
 
        if( -1 == inx )
        {
            return moab::MB_FAILURE;
        }  // error, vertex not in local range
 
        element_connectivity[i] = inx;
    }
 
    return moab::MB_SUCCESS;
}

References appData::all_verts, GlobalContext::appDatas, context, ErrorCode, moab::Interface::get_connectivity(), moab::Interface::get_entities_by_handle(), moab::Range::index(), appData::mat_sets, appData::matIndex, MB_CHK_ERR, MB_SUCCESS, and GlobalContext::MBI.

iMOAB_GetBlockID()

ErrCode iMOAB_GetBlockID	(	iMOAB_AppID	pid,
		int *	block_length,
		iMOAB_GlobalID *	global_block_IDs
	)

Get the global block IDs for all locally visible (owned and shared/ghosted) blocks.

Note

Block IDs are corresponding to MATERIAL_SET tags for material sets. Usually the block ID is exported from Cubit as a unique integer value. First blocks are local, and next blocks are fully ghosted. First blocks have at least one owned cell/element, ghost blocks have only ghost cells. Internally, a block corresponds to a mesh set with a MATERIAL_SET tag value equal to the block ID.

Operations: Not Collective

Parameters

[in]	pid	(iMOAB_AppID) The unique pointer to the application ID.
[in]	block_length	(int*) The allocated size of array (typical size := num_visible_blocks).
[out]	global_block_IDs	(iMOAB_GlobalID*) The global IDs for all locally visible blocks (array allocated by user).

Returns

ErrCode The error code indicating success or failure.

Definition at line 1036 of file iMOAB.cpp.

{
    // local id blocks? they are counted from 0 to number of visible blocks ...
    // will actually return material set tag value for global
    Range& matSets = context.appDatas[*pid].mat_sets;
 
    if( *block_length != (int)matSets.size() )
    {
        return moab::MB_FAILURE;
    }
 
    // return material set tag gtags[0 is material set tag
    ErrorCode rval = context.MBI->tag_get_data( context.material_tag, matSets, global_block_IDs );MB_CHK_ERR( rval );
 
    // populate map with index
    std::map< int, int >& matIdx = context.appDatas[*pid].matIndex;
    for( unsigned i = 0; i < matSets.size(); i++ )
    {
        matIdx[global_block_IDs[i]] = i;
    }
 
    return moab::MB_SUCCESS;
}

References GlobalContext::appDatas, context, ErrorCode, GlobalContext::material_tag, MB_CHK_ERR, MB_SUCCESS, GlobalContext::MBI, moab::Range::size(), and moab::Interface::tag_get_data().

iMOAB_GetBlockInfo()

ErrCode iMOAB_GetBlockInfo	(	iMOAB_AppID	pid,
		iMOAB_GlobalID *	global_block_ID,
		int *	vertices_per_element,
		int *	num_elements_in_block
	)

Get the global block information and number of visible elements of belonging to a block (MATERIAL SET).

Note

A block has to be homogeneous, it can contain elements of a single type.

Operations: Not Collective

Parameters

[in]	pid	(iMOAB_AppID) The unique pointer to the application ID.
[in]	global_block_ID	(iMOAB_GlobalID) The global block ID of the set to be queried.
[out]	vertices_per_element	(int*) The number of vertices per element.
[out]	num_elements_in_block	(int*) The number of elements in block.

Returns

ErrCode The error code indicating success or failure.

Definition at line 1060 of file iMOAB.cpp.

{
    assert( global_block_ID );
 
    std::map< int, int >& matMap      = context.appDatas[*pid].matIndex;
    std::map< int, int >::iterator it = matMap.find( *global_block_ID );
 
    if( it == matMap.end() )
    {
        return moab::MB_FAILURE;
    }  // error in finding block with id
 
    int blockIndex          = matMap[*global_block_ID];
    EntityHandle matMeshSet = context.appDatas[*pid].mat_sets[blockIndex];
    Range blo_elems;
    ErrorCode rval = context.MBI->get_entities_by_handle( matMeshSet, blo_elems );
 
    if( MB_SUCCESS != rval || blo_elems.empty() )
    {
        return moab::MB_FAILURE;
    }
 
    EntityType type = context.MBI->type_from_handle( blo_elems[0] );
 
    if( !blo_elems.all_of_type( type ) )
    {
        return moab::MB_FAILURE;
    }  // not all of same  type
 
    const EntityHandle* conn = NULL;
    int num_verts            = 0;
    rval                     = context.MBI->get_connectivity( blo_elems[0], conn, num_verts );MB_CHK_ERR( rval );
 
    *vertices_per_element  = num_verts;
    *num_elements_in_block = (int)blo_elems.size();
 
    return moab::MB_SUCCESS;
}

References moab::Range::all_of_type(), GlobalContext::appDatas, context, moab::Range::empty(), ErrorCode, moab::Interface::get_connectivity(), moab::Interface::get_entities_by_handle(), MB_CHK_ERR, MB_SUCCESS, GlobalContext::MBI, moab::Range::size(), and moab::Interface::type_from_handle().

iMOAB_GetDoubleTagStorage()

ErrCode iMOAB_GetDoubleTagStorage	(	iMOAB_AppID	pid,
		const iMOAB_String	tag_storage_name,
		int *	num_tag_storage_length,
		int *	entity_type,
		double *	tag_storage_data
	)

Retrieve the specified values in a MOAB double Tag.

Note

Operations: Collective

Parameters

[in]	pid	(iMOAB_AppID) The unique pointer to the application ID.
[in]	tag_storage_name	(iMOAB_String) The tag names to retrieve the data in MOAB.
[in]	num_tag_storage_length	(int) The size of total tag storage data (e.g., num_visible_vertices*components_per_entity*num_tags or num_visible_elements*components_per_entity*num_tags)
[in]	entity_type	(int*) Type=0 for vertices, and Type=1 for primary elements.
[out]	tag_storage_data	(double*) The array data of type double to replace the internal tag memory; The data is assumed to be contiguous over the local set of visible entities (either vertices or elements). unrolled by tags

Returns

ErrCode The error code indicating success or failure.

Definition at line 2035 of file iMOAB.cpp.

{
    ErrorCode rval;
    // exactly the same code, except tag type check
    std::string tag_names( tag_storage_names );
    // exactly the same code as for int tag :) maybe should check the type of tag too
    std::vector< std::string > tagNames;
    std::vector< Tag > tagHandles;
    std::string separator( ":" );
    split_tag_names( tag_names, separator, tagNames );
 
    appData& data = context.appDatas[*pid];
 
    // set it on a subset of entities, based on type and length
    Range* ents_to_get = NULL;
 
    if( *ent_type == 0 )  // vertices
    {
        ents_to_get = &data.all_verts;
    }
    else if( *ent_type == 1 )
    {
        ents_to_get = &data.primary_elems;
    }
    int nents_to_get = (int)ents_to_get->size();
    int position     = 0;
    for( size_t i = 0; i < tagNames.size(); i++ )
    {
        if( data.tagMap.find( tagNames[i] ) == data.tagMap.end() )
        {
            return moab::MB_FAILURE;
        }  // tag not defined
 
        Tag tag = data.tagMap[tagNames[i]];
 
        int tagLength = 0;
        rval          = context.MBI->tag_get_length( tag, tagLength );MB_CHK_ERR( rval );
 
        DataType dtype;
        rval = context.MBI->tag_get_data_type( tag, dtype );MB_CHK_ERR( rval );
 
        if( dtype != MB_TYPE_DOUBLE )
        {
            return moab::MB_FAILURE;
        }
 
        if( position + nents_to_get * tagLength > *num_tag_storage_length )
            return moab::MB_FAILURE;  // too many entity values to get
 
        rval = context.MBI->tag_get_data( tag, *ents_to_get, &tag_storage_data[position] );MB_CHK_ERR( rval );
        position = position + nents_to_get * tagLength;
    }
 
    return moab::MB_SUCCESS;  // no error
}

References appData::all_verts, GlobalContext::appDatas, context, ErrorCode, MB_CHK_ERR, MB_SUCCESS, MB_TYPE_DOUBLE, GlobalContext::MBI, appData::primary_elems, moab::Range::size(), split_tag_names(), moab::Interface::tag_get_data(), moab::Interface::tag_get_data_type(), moab::Interface::tag_get_length(), and appData::tagMap.

iMOAB_GetElementConnectivity()

ErrCode iMOAB_GetElementConnectivity	(	iMOAB_AppID	pid,
		iMOAB_LocalID *	elem_index,
		int *	connectivity_length,
		int *	element_connectivity
	)

Get the connectivity for one element only.

Note

This is a convenience method and in general should not be used unless necessary. You should use colaesced calls for multiple elements for efficiency.

Operations: Not Collective

Parameters

[in]	pid	(iMOAB_AppID) The unique pointer to the application ID.
[in]	elem_index	(iMOAB_LocalID *) Local element index.
[in,out]	connectivity_length	(int *) On input, maximum length of connectivity. On output, actual length.
[out]	element_connectivity	(int*) The connectivity array to store connectivity in MOAB canonical numbering scheme. Array contains vertex indices in the local numbering order for vertices.

Returns

ErrCode The error code indicating success or failure.

Definition at line 1210 of file iMOAB.cpp.

{
    assert( elem_index );           // ensure element index argument is not null
    assert( connectivity_length );  // ensure connectivity length argument is not null
 
    appData& data = context.appDatas[*pid];
    assert( ( *elem_index >= 0 ) && ( *elem_index < (int)data.primary_elems.size() ) );
 
    int num_nodes;
    const EntityHandle* conn;
 
    EntityHandle eh = data.primary_elems[*elem_index];
 
    ErrorCode rval = context.MBI->get_connectivity( eh, conn, num_nodes );MB_CHK_ERR( rval );
 
    if( *connectivity_length < num_nodes )
    {
        return moab::MB_FAILURE;
    }  // wrong number of vertices
 
    for( int i = 0; i < num_nodes; i++ )
    {
        int index = data.all_verts.index( conn[i] );
 
        if( -1 == index )
        {
            return moab::MB_FAILURE;
        }
 
        element_connectivity[i] = index;
    }
 
    *connectivity_length = num_nodes;
 
    return moab::MB_SUCCESS;
}

References appData::all_verts, GlobalContext::appDatas, context, ErrorCode, moab::Interface::get_connectivity(), moab::Range::index(), MB_CHK_ERR, MB_SUCCESS, GlobalContext::MBI, appData::primary_elems, and moab::Range::size().

iMOAB_GetElementID()

ErrCode iMOAB_GetElementID	(	iMOAB_AppID	pid,
		iMOAB_GlobalID *	global_block_ID,
		int *	num_elements_in_block,
		iMOAB_GlobalID *	global_element_ID,
		iMOAB_LocalID *	local_element_ID
	)

Get the global IDs for all locally visible elements belonging to a particular block.

Note

The method will return also the local index of each element, in the local range that contains all visible elements.

Operations: Not Collective

Parameters

[in]	pid	(iMOAB_AppID) The unique pointer to the application ID.
[in]	global_block_ID	(iMOAB_GlobalID*) The global block ID of the set being queried.
[in]	num_elements_in_block	(int*) The allocated size of global element ID array, same as num_elements_in_block returned from GetBlockInfo().
[out]	global_element_ID	(iMOAB_GlobalID*) The global IDs for all locally visible elements (array allocated by user).
[out]	local_element_ID	(iMOAB_LocalID*) (Optional) The local IDs for all locally visible elements (index in the range of all primary elements in the rank)

Returns

ErrCode The error code indicating success or failure.

Definition at line 1300 of file iMOAB.cpp.

{
    assert( global_block_ID );        // ensure global block ID argument is not null
    assert( num_elements_in_block );  // ensure number of elements in block argument is not null
 
    appData& data                = context.appDatas[*pid];
    std::map< int, int >& matMap = data.matIndex;
 
    std::map< int, int >::iterator it = matMap.find( *global_block_ID );
 
    if( it == matMap.end() )
    {
        return moab::MB_FAILURE;
    }  // error in finding block with id
 
    int blockIndex          = matMap[*global_block_ID];
    EntityHandle matMeshSet = data.mat_sets[blockIndex];
    Range elems;
    ErrorCode rval = context.MBI->get_entities_by_handle( matMeshSet, elems );MB_CHK_ERR( rval );
 
    if( elems.empty() )
    {
        return moab::MB_FAILURE;
    }
 
    if( *num_elements_in_block != (int)elems.size() )
    {
        return moab::MB_FAILURE;
    }  // bad memory allocation
 
    rval = context.MBI->tag_get_data( context.globalID_tag, elems, global_element_ID );MB_CHK_ERR( rval );
 
    // check that elems are among primary_elems in data
    for( int i = 0; i < *num_elements_in_block; i++ )
    {
        local_element_ID[i] = data.primary_elems.index( elems[i] );
 
        if( -1 == local_element_ID[i] )
        {
            return moab::MB_FAILURE;
        }  // error, not in local primary elements
    }
 
    return moab::MB_SUCCESS;
}

References GlobalContext::appDatas, context, moab::Range::empty(), ErrorCode, moab::Interface::get_entities_by_handle(), GlobalContext::globalID_tag, moab::Range::index(), appData::mat_sets, appData::matIndex, MB_CHK_ERR, MB_SUCCESS, GlobalContext::MBI, appData::primary_elems, moab::Range::size(), and moab::Interface::tag_get_data().

iMOAB_GetElementOwnership()

ErrCode iMOAB_GetElementOwnership	(	iMOAB_AppID	pid,
		iMOAB_GlobalID *	global_block_ID,
		int *	num_elements_in_block,
		int *	element_ownership
	)

Get the element ownership within a certain block i.e., processor ID of the element owner.

Note

: Should we use local block index for input, instead of the global block ID ?

Operations: Not Collective

Parameters

[in]	pid	(iMOAB_AppID) The unique pointer to the application ID.
[in]	global_block_ID	(iMOAB_GlobalID) The global block ID of the set being queried.
[in]	num_elements_in_block	(int*) The allocated size of ownership array, same as num_elements_in_block returned from GetBlockInfo().
[out]	element_ownership	(int*) The ownership array to store processor ID for all elements (array allocated by user).

Returns

ErrCode The error code indicating success or failure.

Definition at line 1250 of file iMOAB.cpp.

{
    assert( global_block_ID );        // ensure global block ID argument is not null
    assert( num_elements_in_block );  // ensure number of elements in block argument is not null
 
    std::map< int, int >& matMap = context.appDatas[*pid].matIndex;
 
    std::map< int, int >::iterator it = matMap.find( *global_block_ID );
 
    if( it == matMap.end() )
    {
        return moab::MB_FAILURE;
    }  // error in finding block with id
 
    int blockIndex          = matMap[*global_block_ID];
    EntityHandle matMeshSet = context.appDatas[*pid].mat_sets[blockIndex];
    Range elems;
 
    ErrorCode rval = context.MBI->get_entities_by_handle( matMeshSet, elems );MB_CHK_ERR( rval );
 
    if( elems.empty() )
    {
        return moab::MB_FAILURE;
    }
 
    if( *num_elements_in_block != (int)elems.size() )
    {
        return moab::MB_FAILURE;
    }  // bad memory allocation
 
    int i = 0;
#ifdef MOAB_HAVE_MPI
    ParallelComm* pco = context.pcomms[*pid];
#endif
 
    for( Range::iterator vit = elems.begin(); vit != elems.end(); vit++, i++ )
    {
#ifdef MOAB_HAVE_MPI
        rval = pco->get_owner( *vit, element_ownership[i] );MB_CHK_ERR( rval );
#else
        element_ownership[i] = 0; /* owned by 0 */
#endif
    }
 
    return moab::MB_SUCCESS;
}

References GlobalContext::appDatas, moab::Range::begin(), context, moab::Range::empty(), moab::Range::end(), ErrorCode, moab::Interface::get_entities_by_handle(), moab::ParallelComm::get_owner(), MB_CHK_ERR, MB_SUCCESS, GlobalContext::MBI, and moab::Range::size().

iMOAB_GetGlobalInfo()

ErrCode iMOAB_GetGlobalInfo	(	iMOAB_AppID	pid,
		int *	num_global_verts,
		int *	num_global_elems
	)

Get global information about number of vertices and number of elements.

Parameters

[in]	pid	(iMOAB_AppID) The unique pointer to the application ID.
[in]	num_global_verts	(int*) The number of total vertices in the mesh.
[in]	num_global_elems	(MPI_Comm) The number of total elements in the mesh.

Returns

ErrCode The error code indicating success or failure.

Definition at line 2312 of file iMOAB.cpp.

{
    appData& data = context.appDatas[*pid];
    if( NULL != num_global_verts )
    {
        *num_global_verts = data.num_global_vertices;
    }
    if( NULL != num_global_elems )
    {
        *num_global_elems = data.num_global_elements;
    }
 
    return moab::MB_SUCCESS;
}

References GlobalContext::appDatas, context, MB_SUCCESS, appData::num_global_elements, and appData::num_global_vertices.

iMOAB_GetIntTagStorage()

ErrCode iMOAB_GetIntTagStorage	(	iMOAB_AppID	pid,
		const iMOAB_String	tag_storage_name,
		int *	num_tag_storage_length,
		int *	entity_type,
		int *	tag_storage_data
	)

Get the specified values in a MOAB integer Tag.

Note

Operations: Collective

Parameters

[in]	pid	(iMOAB_AppID) The unique pointer to the application ID.
[in]	tag_storage_name	(iMOAB_String) The tag name to store/retreive the data in MOAB.
[in]	num_tag_storage_length	(int*) The size of tag storage data (e.g., num_visible_vertices*components_per_entity or num_visible_elements*components_per_entity).
[in]	entity_type	(int*) Type=0 for vertices, and Type=1 for primary elements.
[out]	tag_storage_data	(int*) The array data of type int to be copied from the internal tag memory; The data is assumed to be contiguous over the local set of visible entities (either vertices or elements).

Returns

ErrCode The error code indicating success or failure.

Definition at line 1659 of file iMOAB.cpp.

{
    ErrorCode rval;
    std::string tag_name( tag_storage_name );
 
    appData& data = context.appDatas[*pid];
 
    if( data.tagMap.find( tag_name ) == data.tagMap.end() )
    {
        return moab::MB_FAILURE;
    }  // tag not defined
 
    Tag tag = data.tagMap[tag_name];
 
    int tagLength = 0;
    rval          = context.MBI->tag_get_length( tag, tagLength );MB_CHK_ERR( rval );
 
    DataType dtype;
    rval = context.MBI->tag_get_data_type( tag, dtype );MB_CHK_ERR( rval );
 
    if( dtype != MB_TYPE_INTEGER )
    {
        return moab::MB_FAILURE;
    }
 
    // set it on a subset of entities, based on type and length
    Range* ents_to_get;
 
    if( *ent_type == 0 )  // vertices
    {
        ents_to_get = &data.all_verts;
    }
    else  // if (*ent_type == 1)
    {
        ents_to_get = &data.primary_elems;
    }
 
    int nents_to_get = *num_tag_storage_length / tagLength;
 
    if( nents_to_get > (int)ents_to_get->size() || nents_to_get < 1 )
    {
        return moab::MB_FAILURE;
    }  // to many entities to get, or too little
 
    // restrict the range; everything is contiguous; or not?
    // Range contig_range ( * ( ents_to_get->begin() ), * ( ents_to_get->begin() + nents_to_get - 1
    // ) );
 
    rval = context.MBI->tag_get_data( tag, *ents_to_get, tag_storage_data );MB_CHK_ERR( rval );
 
    return moab::MB_SUCCESS;  // no error
}

References appData::all_verts, GlobalContext::appDatas, context, ErrorCode, MB_CHK_ERR, MB_SUCCESS, MB_TYPE_INTEGER, GlobalContext::MBI, appData::primary_elems, moab::Range::size(), moab::Interface::tag_get_data(), moab::Interface::tag_get_data_type(), moab::Interface::tag_get_length(), and appData::tagMap.

iMOAB_GetMeshInfo()

ErrCode iMOAB_GetMeshInfo	(	iMOAB_AppID	pid,
		int *	num_visible_vertices,
		int *	num_visible_elements,
		int *	num_visible_blocks,
		int *	num_visible_surfaceBC,
		int *	num_visible_vertexBC
	)

Retrieve all the important mesh information related to vertices, elements, vertex and surface boundary conditions.

Note

Number of visible vertices and cells include ghost entities. All arrays returned have size 3. Local entities are first, then ghost entities are next. Shared vertices can be owned in MOAB sense by different tasks. Ghost vertices and cells are always owned by other tasks.

Operations: Not Collective

Parameters

[in]	pid	(iMOAB_AppID) The unique pointer to the application ID.
[out]	num_visible_vertices	(int*) The number of vertices in the current partition/process arranged. as: owned/shared only, ghosted, total_visible (array allocated by user, size := 3).
[out]	num_visible_elements	(int*) The number of elements in current partition/process arranged as: owned only, ghosted/shared, total_visible (array allocated by user, size := 3).
[out]	num_visible_blocks	(int*) The number of material sets in local mesh in current partition/process arranged as: owned only, ghosted/shared, total_visible (array allocated by user, size := 3).
[out]	num_visible_surfaceBC	(int*) The number of mesh surfaces that have a NEUMANN_SET BC defined in local mesh in current partition/process arranged as: owned only, ghosted/shared, total_visible (array allocated by user, size := 3).
[out]	num_visible_vertexBC	(int*) The number of vertices that have a DIRICHLET_SET BC defined in local mesh in current partition/process arranged as: owned only, ghosted/shared, total_visible (array allocated by user, size := 3).

Returns

ErrCode The error code indicating success or failure.

Definition at line 878 of file iMOAB.cpp.

{
    ErrorCode rval;
    appData& data        = context.appDatas[*pid];
    EntityHandle fileSet = data.file_set;
 
    // this will include ghost elements
    // first clear all data ranges; this can be called after ghosting
    if( num_visible_elements )
    {
        num_visible_elements[2] = static_cast< int >( data.primary_elems.size() );
        // separate ghost and local/owned primary elements
        num_visible_elements[0] = static_cast< int >( data.owned_elems.size() );
        num_visible_elements[1] = static_cast< int >( data.ghost_elems.size() );
    }
    if( num_visible_vertices )
    {
        num_visible_vertices[2] = static_cast< int >( data.all_verts.size() );
        num_visible_vertices[1] = static_cast< int >( data.ghost_vertices.size() );
        // local are those that are not ghosts; they may include shared, not owned vertices
        num_visible_vertices[0] = num_visible_vertices[2] - num_visible_vertices[1];
    }
 
    if( num_visible_blocks )
    {
        rval = context.MBI->get_entities_by_type_and_tag( fileSet, MBENTITYSET, &( context.material_tag ), 0, 1,
                                                          data.mat_sets, Interface::UNION );MB_CHK_ERR( rval );
 
        num_visible_blocks[2] = data.mat_sets.size();
        num_visible_blocks[0] = num_visible_blocks[2];
        num_visible_blocks[1] = 0;
    }
 
    if( num_visible_surfaceBC )
    {
        rval = context.MBI->get_entities_by_type_and_tag( fileSet, MBENTITYSET, &( context.neumann_tag ), 0, 1,
                                                          data.neu_sets, Interface::UNION );MB_CHK_ERR( rval );
 
        num_visible_surfaceBC[2] = 0;
        // count how many faces are in each neu set, and how many regions are
        // adjacent to them;
        int numNeuSets = (int)data.neu_sets.size();
 
        for( int i = 0; i < numNeuSets; i++ )
        {
            Range subents;
            EntityHandle nset = data.neu_sets[i];
            rval              = context.MBI->get_entities_by_dimension( nset, data.dimension - 1, subents );MB_CHK_ERR( rval );
 
            for( Range::iterator it = subents.begin(); it != subents.end(); ++it )
            {
                EntityHandle subent = *it;
                Range adjPrimaryEnts;
                rval = context.MBI->get_adjacencies( &subent, 1, data.dimension, false, adjPrimaryEnts );MB_CHK_ERR( rval );
 
                num_visible_surfaceBC[2] += (int)adjPrimaryEnts.size();
            }
        }
 
        num_visible_surfaceBC[0] = num_visible_surfaceBC[2];
        num_visible_surfaceBC[1] = 0;
    }
 
    if( num_visible_vertexBC )
    {
        rval = context.MBI->get_entities_by_type_and_tag( fileSet, MBENTITYSET, &( context.dirichlet_tag ), 0, 1,
                                                          data.diri_sets, Interface::UNION );MB_CHK_ERR( rval );
 
        num_visible_vertexBC[2] = 0;
        int numDiriSets         = (int)data.diri_sets.size();
 
        for( int i = 0; i < numDiriSets; i++ )
        {
            Range verts;
            EntityHandle diset = data.diri_sets[i];
            rval               = context.MBI->get_entities_by_dimension( diset, 0, verts );MB_CHK_ERR( rval );
 
            num_visible_vertexBC[2] += (int)verts.size();
        }
 
        num_visible_vertexBC[0] = num_visible_vertexBC[2];
        num_visible_vertexBC[1] = 0;
    }
 
    return moab::MB_SUCCESS;
}

References appData::all_verts, GlobalContext::appDatas, moab::Range::begin(), context, appData::dimension, appData::diri_sets, GlobalContext::dirichlet_tag, moab::Range::end(), ErrorCode, appData::file_set, moab::Interface::get_adjacencies(), moab::Interface::get_entities_by_dimension(), moab::Interface::get_entities_by_type_and_tag(), appData::ghost_elems, appData::ghost_vertices, appData::mat_sets, GlobalContext::material_tag, MB_CHK_ERR, MB_SUCCESS, MBENTITYSET, GlobalContext::MBI, appData::neu_sets, GlobalContext::neumann_tag, appData::owned_elems, appData::primary_elems, moab::Range::size(), and moab::Interface::UNION.

iMOAB_GetNeighborElements()

ErrCode iMOAB_GetNeighborElements	(	iMOAB_AppID	pid,
		iMOAB_LocalID *	local_index,
		int *	num_adjacent_elements,
		iMOAB_LocalID *	adjacent_element_IDs
	)

Retrieve the adjacencies for the element entities.

Note

Operations: Not Collective

Parameters

[in]	pid	(iMOAB_AppID) The unique pointer to the application ID.
[in]	local_index	(iMOAB_LocalID*) The local element ID for which adjacency information is needed.
[out]	num_adjacent_elements	(int*) The total number of adjacent elements.
[out]	adjacent_element_IDs	(iMOAB_LocalID*) The local element IDs of all adjacent elements to the current one (typically, num_total_sides for internal elements or num_total_sides-num_sides_on_boundary for boundary elements).

Returns

ErrCode The error code indicating success or failure.

Definition at line 2180 of file iMOAB.cpp.

{
    ErrorCode rval;
 
    // one neighbor for each subentity of dimension-1
    MeshTopoUtil mtu( context.MBI );
    appData& data   = context.appDatas[*pid];
    EntityHandle eh = data.primary_elems[*local_index];
    Range adjs;
    rval = mtu.get_bridge_adjacencies( eh, data.dimension - 1, data.dimension, adjs );MB_CHK_ERR( rval );
 
    if( *num_adjacent_elements < (int)adjs.size() )
    {
        return moab::MB_FAILURE;
    }  // not dimensioned correctly
 
    *num_adjacent_elements = (int)adjs.size();
 
    for( int i = 0; i < *num_adjacent_elements; i++ )
    {
        adjacent_element_IDs[i] = data.primary_elems.index( adjs[i] );
    }
 
    return moab::MB_SUCCESS;
}

References GlobalContext::appDatas, context, appData::dimension, ErrorCode, moab::MeshTopoUtil::get_bridge_adjacencies(), moab::Range::index(), MB_CHK_ERR, MB_SUCCESS, GlobalContext::MBI, appData::primary_elems, and moab::Range::size().

iMOAB_GetNeighborVertices()

ErrCode iMOAB_GetNeighborVertices	(	iMOAB_AppID	pid,
		iMOAB_LocalID *	local_vertex_ID,
		int *	num_adjacent_vertices,
		iMOAB_LocalID *	adjacent_vertex_IDs
	)

Get the adjacencies for the vertex entities.

Note

Operations: Not Collective

Parameters

[in]	pid	(iMOAB_AppID) The unique pointer to the application ID.
[in]	local_vertex_ID	(iMOAB_LocalID*) The local vertex ID for which adjacency information is needed.
[out]	num_adjacent_vertices	(int*) The total number of adjacent vertices.
[out]	adjacent_vertex_IDs	(iMOAB_LocalID*) The local element IDs of all adjacent vertices to the current one (typically, num_total_sides for internal elements or num_total_sides-num_sides_on_boundary for boundary elements).

Returns

ErrCode The error code indicating success or failure.

iMOAB_GetPointerToSurfaceBC()

ErrCode iMOAB_GetPointerToSurfaceBC	(	iMOAB_AppID	pid,
		int *	surface_BC_length,
		iMOAB_LocalID *	local_element_ID,
		int *	reference_surface_ID,
		int *	boundary_condition_value
	)

Get the surface boundary condition information.

Note

Operations: Not Collective

Parameters

[in]	pid	(iMOAB_AppID) The unique pointer to the application ID.
[in]	surface_BC_length	(int*) The allocated size of surface boundary condition array, same as num_visible_surfaceBC returned by GetMeshInfo().
[out]	local_element_ID	(iMOAB_LocalID*) The local element IDs that contains the side with the surface BC.
[out]	reference_surface_ID	(int*) The surface number with the BC in the canonical reference element (e.g., 1 to 6 for HEX, 1-4 for TET).
[out]	boundary_condition_value	(int*) The boundary condition type as obtained from the mesh description (value of the NeumannSet defined on the element).

Returns

ErrCode The error code indicating success or failure.

Definition at line 1350 of file iMOAB.cpp.

{
    // we have to fill bc data for neumann sets;/
    ErrorCode rval;
 
    // it was counted above, in GetMeshInfo
    appData& data  = context.appDatas[*pid];
    int numNeuSets = (int)data.neu_sets.size();
 
    int index = 0;  // index [0, surface_BC_length) for the arrays returned
 
    for( int i = 0; i < numNeuSets; i++ )
    {
        Range subents;
        EntityHandle nset = data.neu_sets[i];
        rval              = context.MBI->get_entities_by_dimension( nset, data.dimension - 1, subents );MB_CHK_ERR( rval );
 
        int neuVal;
        rval = context.MBI->tag_get_data( context.neumann_tag, &nset, 1, &neuVal );MB_CHK_ERR( rval );
 
        for( Range::iterator it = subents.begin(); it != subents.end(); ++it )
        {
            EntityHandle subent = *it;
            Range adjPrimaryEnts;
            rval = context.MBI->get_adjacencies( &subent, 1, data.dimension, false, adjPrimaryEnts );MB_CHK_ERR( rval );
 
            // get global id of the primary ents, and side number of the quad/subentity
            // this is moab ordering
            for( Range::iterator pit = adjPrimaryEnts.begin(); pit != adjPrimaryEnts.end(); pit++ )
            {
                EntityHandle primaryEnt = *pit;
                // get global id
                /*int globalID;
                rval = context.MBI->tag_get_data(gtags[3], &primaryEnt, 1, &globalID);
                if (MB_SUCCESS!=rval)
                  return moab::MB_FAILURE;
                global_element_ID[index] = globalID;*/
 
                // get local element id
                local_element_ID[index] = data.primary_elems.index( primaryEnt );
 
                if( -1 == local_element_ID[index] )
                {
                    return moab::MB_FAILURE;
                }  // did not find the element locally
 
                int side_number, sense, offset;
                rval = context.MBI->side_number( primaryEnt, subent, side_number, sense, offset );MB_CHK_ERR( rval );
 
                reference_surface_ID[index]     = side_number + 1;  // moab is from 0 to 5, it needs 1 to 6
                boundary_condition_value[index] = neuVal;
                index++;
            }
        }
    }
 
    if( index != *surface_BC_length )
    {
        return moab::MB_FAILURE;
    }  // error in array allocations
 
    return moab::MB_SUCCESS;
}

References GlobalContext::appDatas, moab::Range::begin(), context, appData::dimension, moab::Range::end(), ErrorCode, moab::Interface::get_adjacencies(), moab::Interface::get_entities_by_dimension(), moab::Range::index(), MB_CHK_ERR, MB_SUCCESS, GlobalContext::MBI, appData::neu_sets, GlobalContext::neumann_tag, appData::primary_elems, moab::Interface::side_number(), moab::side_number(), moab::Range::size(), and moab::Interface::tag_get_data().

iMOAB_GetPointerToVertexBC()

ErrCode iMOAB_GetPointerToVertexBC	(	iMOAB_AppID	pid,
		int *	vertex_BC_length,
		iMOAB_LocalID *	local_vertex_ID,
		int *	boundary_condition_value
	)

Get the vertex boundary condition information.

Note

Operations: Not Collective

Parameters

[in]	pid	(iMOAB_AppID) The unique pointer to the application ID.
[in]	vertex_BC_length	(int) The allocated size of vertex boundary condition array, same as num_visible_vertexBC returned by GetMeshInfo().
[out]	local_vertex_ID	(iMOAB_LocalID*) The local vertex ID that has Dirichlet BC defined.
[out]	boundary_condition_value	(int*) The boundary condition type as obtained from the mesh description (value of the Dirichlet_Set tag defined on the vertex).

Returns

ErrCode The error code indicating success or failure.

Definition at line 1418 of file iMOAB.cpp.

{
    ErrorCode rval;
 
    // it was counted above, in GetMeshInfo
    appData& data   = context.appDatas[*pid];
    int numDiriSets = (int)data.diri_sets.size();
    int index       = 0;  // index [0, *vertex_BC_length) for the arrays returned
 
    for( int i = 0; i < numDiriSets; i++ )
    {
        Range verts;
        EntityHandle diset = data.diri_sets[i];
        rval               = context.MBI->get_entities_by_dimension( diset, 0, verts );MB_CHK_ERR( rval );
 
        int diriVal;
        rval = context.MBI->tag_get_data( context.dirichlet_tag, &diset, 1, &diriVal );MB_CHK_ERR( rval );
 
        for( Range::iterator vit = verts.begin(); vit != verts.end(); ++vit )
        {
            EntityHandle vt = *vit;
            /*int vgid;
            rval = context.MBI->tag_get_data(gtags[3], &vt, 1, &vgid);
            if (MB_SUCCESS!=rval)
              return moab::MB_FAILURE;
            global_vertext_ID[index] = vgid;*/
            local_vertex_ID[index] = data.all_verts.index( vt );
 
            if( -1 == local_vertex_ID[index] )
            {
                return moab::MB_FAILURE;
            }  // vertex was not found
 
            boundary_condition_value[index] = diriVal;
            index++;
        }
    }
 
    if( *vertex_BC_length != index )
    {
        return moab::MB_FAILURE;
    }  // array allocation issue
 
    return moab::MB_SUCCESS;
}

References appData::all_verts, GlobalContext::appDatas, moab::Range::begin(), context, appData::diri_sets, GlobalContext::dirichlet_tag, moab::Range::end(), ErrorCode, moab::Interface::get_entities_by_dimension(), moab::Range::index(), MB_CHK_ERR, MB_SUCCESS, GlobalContext::MBI, moab::Range::size(), and moab::Interface::tag_get_data().

iMOAB_GetVertexID()

ErrCode iMOAB_GetVertexID	(	iMOAB_AppID	pid,
		int *	vertices_length,
		iMOAB_GlobalID *	global_vertex_ID
	)

Get the global vertex IDs for all locally visible (owned and shared/ghosted) vertices.

Note

The array should be allocated by the user, sized with the total number of visible vertices from iMOAB_GetMeshInfo method.

Operations: Not collective

Parameters

[in]	pid	(iMOAB_AppID) The unique pointer to the application ID.
[in]	vertices_length	(int*) The allocated size of array (typical size := num_visible_vertices).
[out]	global_vertex_ID	(iMOAB_GlobalID*) The global IDs for all locally visible vertices (array allocated by user).

Returns

ErrCode The error code indicating success or failure.

Definition at line 970 of file iMOAB.cpp.

{
    IMOAB_CHECKPOINTER( vertices_length, 2 );
    IMOAB_CHECKPOINTER( global_vertex_ID, 3 );
 
    const Range& verts = context.appDatas[*pid].all_verts;
    // check for problems with array length
    IMOAB_ASSERT( *vertices_length == static_cast< int >( verts.size() ), "Invalid vertices length provided" );
 
    // global id tag is context.globalID_tag
    return context.MBI->tag_get_data( context.globalID_tag, verts, global_vertex_ID );
}

References GlobalContext::appDatas, context, GlobalContext::globalID_tag, IMOAB_ASSERT, IMOAB_CHECKPOINTER, GlobalContext::MBI, moab::Range::size(), and moab::Interface::tag_get_data().

iMOAB_GetVertexOwnership()

ErrCode iMOAB_GetVertexOwnership	(	iMOAB_AppID	pid,
		int *	vertices_length,
		int *	visible_global_rank_ID
	)

Get vertex ownership information.

For each vertex based on the local ID, return the process that owns the vertex (local, shared or ghost)

Note

Shared vertices could be owned by different tasks. Local and shared vertices are first, ghost vertices are next in the array. Ghost vertices are always owned by a different process ID. Array allocated by the user with total size of visible vertices.

Operations: Not Collective

Parameters

[in]	pid	(iMOAB_AppID) The unique pointer to the application ID.
[in]	vertices_length	(int*) The allocated size of array (typically size := num_visible_vertices).
[out]	visible_global_rank_ID	(int*) The processor rank owning each of the local vertices.

Returns

ErrCode The error code indicating success or failure.

Definition at line 983 of file iMOAB.cpp.

{
    assert( vertices_length && *vertices_length );
    assert( visible_global_rank_ID );
 
    Range& verts = context.appDatas[*pid].all_verts;
    int i        = 0;
#ifdef MOAB_HAVE_MPI
    ParallelComm* pco = context.pcomms[*pid];
 
    for( Range::iterator vit = verts.begin(); vit != verts.end(); vit++, i++ )
    {
        ErrorCode rval = pco->get_owner( *vit, visible_global_rank_ID[i] );MB_CHK_ERR( rval );
    }
 
    if( i != *vertices_length )
    {
        return moab::MB_FAILURE;
    }  // warning array allocation problem
 
#else
 
    /* everything owned by proc 0 */
    if( (int)verts.size() != *vertices_length )
    {
        return moab::MB_FAILURE;
    }  // warning array allocation problem
 
    for( Range::iterator vit = verts.begin(); vit != verts.end(); vit++, i++ )
    {
        visible_global_rank_ID[i] = 0;
    }  // all vertices are owned by processor 0, as this is serial run
 
#endif
 
    return moab::MB_SUCCESS;
}

References GlobalContext::appDatas, moab::Range::begin(), context, moab::Range::end(), ErrorCode, moab::ParallelComm::get_owner(), MB_CHK_ERR, MB_SUCCESS, and moab::Range::size().

iMOAB_GetVisibleElementsInfo()

ErrCode iMOAB_GetVisibleElementsInfo	(	iMOAB_AppID	pid,
		int *	num_visible_elements,
		iMOAB_GlobalID *	element_global_IDs,
		int *	ranks,
		iMOAB_GlobalID *	block_IDs
	)

Get the visible elements information.

Return for all visible elements the global IDs, ranks they belong to, block ids they belong to.

Note

Operations: Not Collective

Parameters

[in]	pid	(iMOAB_AppID) The unique pointer to the application ID.
[in]	num_visible_elements	(int*) The number of visible elements (returned by GetMeshInfo).
[out]	element_global_IDs	(iMOAB_GlobalID*) Element global ids to be added to the block.
[out]	ranks	(int*) The owning ranks of elements.
[out]	block_IDs	(iMOAB_GlobalID*) The block ids containing the elements.

Returns

ErrCode The error code indicating success or failure.

Definition at line 1102 of file iMOAB.cpp.

{
    appData& data = context.appDatas[*pid];
#ifdef MOAB_HAVE_MPI
    ParallelComm* pco = context.pcomms[*pid];
#endif
 
    ErrorCode rval = context.MBI->tag_get_data( context.globalID_tag, data.primary_elems, element_global_IDs );MB_CHK_ERR( rval );
 
    int i = 0;
 
    for( Range::iterator eit = data.primary_elems.begin(); eit != data.primary_elems.end(); ++eit, ++i )
    {
#ifdef MOAB_HAVE_MPI
        rval = pco->get_owner( *eit, ranks[i] );MB_CHK_ERR( rval );
 
#else
        /* everything owned by task 0 */
        ranks[i] = 0;
#endif
    }
 
    for( Range::iterator mit = data.mat_sets.begin(); mit != data.mat_sets.end(); ++mit )
    {
        EntityHandle matMeshSet = *mit;
        Range elems;
        rval = context.MBI->get_entities_by_handle( matMeshSet, elems );MB_CHK_ERR( rval );
 
        int valMatTag;
        rval = context.MBI->tag_get_data( context.material_tag, &matMeshSet, 1, &valMatTag );MB_CHK_ERR( rval );
 
        for( Range::iterator eit = elems.begin(); eit != elems.end(); ++eit )
        {
            EntityHandle eh = *eit;
            int index       = data.primary_elems.index( eh );
 
            if( -1 == index )
            {
                return moab::MB_FAILURE;
            }
 
            if( -1 >= *num_visible_elements )
            {
                return moab::MB_FAILURE;
            }
 
            block_IDs[index] = valMatTag;
        }
    }
 
    return moab::MB_SUCCESS;
}

References GlobalContext::appDatas, moab::Range::begin(), context, moab::Range::end(), ErrorCode, moab::Interface::get_entities_by_handle(), moab::ParallelComm::get_owner(), GlobalContext::globalID_tag, moab::Range::index(), appData::mat_sets, GlobalContext::material_tag, MB_CHK_ERR, MB_SUCCESS, GlobalContext::MBI, appData::primary_elems, and moab::Interface::tag_get_data().

iMOAB_GetVisibleVerticesCoordinates()

ErrCode iMOAB_GetVisibleVerticesCoordinates	(	iMOAB_AppID	pid,
		int *	coords_length,
		double *	coordinates
	)

Get vertex coordinates for all local (owned and ghosted) vertices.

Note

coordinates are returned in an array allocated by user, interleaved. (do need an option for blocked coordinates ?) size of the array is dimension times number of visible vertices. The local ordering is implicit, owned/shared vertices are first, then ghosts.

Operations: Not Collective

Parameters

[in]	pid	(iMOAB_AppID) The unique pointer to the application ID.
[in]	coords_length	(int*) The size of the allocated coordinate array (array allocated by user, size := 3*num_visible_vertices).
[out]	coordinates	(double*) The pointer to user allocated memory that will be filled with interleaved coordinates.

Returns

ErrCode The error code indicating success or failure.

Definition at line 1021 of file iMOAB.cpp.

{
    Range& verts = context.appDatas[*pid].all_verts;
 
    // interleaved coordinates, so that means deep copy anyway
    if( *coords_length != 3 * (int)verts.size() )
    {
        return moab::MB_FAILURE;
    }
 
    ErrorCode rval = context.MBI->get_coords( verts, coordinates );MB_CHK_ERR( rval );
 
    return moab::MB_SUCCESS;
}

References GlobalContext::appDatas, context, ErrorCode, moab::Interface::get_coords(), MB_CHK_ERR, MB_SUCCESS, GlobalContext::MBI, and moab::Range::size().

iMOAB_Initialize()

ErrCode iMOAB_Initialize	(	int	argc,
		iMOAB_String *	argv
	)

Initialize the iMOAB interface implementation.

Note

Will create the MOAB instance, if not created already (reference counted).

Operations: Collective

Parameters

[in]	argc	(int) Number of command line arguments
[in]	argv	(iMOAB_String*) Command line arguments

Returns

ErrCode

Definition at line 136 of file iMOAB.cpp.

{
    if( argc ) IMOAB_CHECKPOINTER( argv, 1 );
 
    context.iArgc = argc;
    context.iArgv = argv;  // shallow copy
 
    if( 0 == context.refCountMB )
    {
        context.MBI = new( std::nothrow ) moab::Core;
        // retrieve the default tags
        const char* const shared_set_tag_names[] = { MATERIAL_SET_TAG_NAME, NEUMANN_SET_TAG_NAME,
                                                     DIRICHLET_SET_TAG_NAME, GLOBAL_ID_TAG_NAME };
        // blocks, visible surfaceBC(neumann), vertexBC (Dirichlet), global id, parallel partition
        Tag gtags[4];
 
        for( int i = 0; i < 4; i++ )
        {
 
            ErrorCode rval =
                context.MBI->tag_get_handle( shared_set_tag_names[i], 1, MB_TYPE_INTEGER, gtags[i], MB_TAG_ANY );MB_CHK_ERR( rval );
        }
 
        context.material_tag  = gtags[0];
        context.neumann_tag   = gtags[1];
        context.dirichlet_tag = gtags[2];
        context.globalID_tag  = gtags[3];
    }
 
    context.MPI_initialized = false;
#ifdef MOAB_HAVE_MPI
    int flagInit;
    MPI_Initialized( &flagInit );
 
    if( flagInit && !context.MPI_initialized )
    {
        MPI_Comm_size( MPI_COMM_WORLD, &context.worldprocs );
        MPI_Comm_rank( MPI_COMM_WORLD, &context.globalrank );
        context.MPI_initialized = true;
    }
#endif
 
    context.refCountMB++;
    return moab::MB_SUCCESS;
}

References context, DIRICHLET_SET_TAG_NAME, GlobalContext::dirichlet_tag, ErrorCode, GLOBAL_ID_TAG_NAME, GlobalContext::globalID_tag, GlobalContext::globalrank, GlobalContext::iArgc, GlobalContext::iArgv, IMOAB_CHECKPOINTER, MATERIAL_SET_TAG_NAME, GlobalContext::material_tag, MB_CHK_ERR, MB_SUCCESS, MB_TAG_ANY, MB_TYPE_INTEGER, GlobalContext::MBI, GlobalContext::MPI_initialized, NEUMANN_SET_TAG_NAME, GlobalContext::neumann_tag, GlobalContext::refCountMB, moab::Interface::tag_get_handle(), and GlobalContext::worldprocs.

Referenced by iMOAB_InitializeFortran().

iMOAB_InitializeFortran()

ErrCode iMOAB_InitializeFortran

(

void

)

Initialize the iMOAB interface implementation from Fortran driver.

It will create the MOAB instance, if not created already (reference counted).

Operations: Collective

Returns

ErrCode The error code indicating success or failure.

Definition at line 182 of file iMOAB.cpp.

{
    return iMOAB_Initialize( 0, 0 );
}

References iMOAB_Initialize().

iMOAB_LoadMesh()

ErrCode iMOAB_LoadMesh	(	iMOAB_AppID	pid,
		const iMOAB_String	filename,
		const iMOAB_String	read_options,
		int *	num_ghost_layers
	)

Load a MOAB mesh file in parallel and exchange ghost layers as requested.

Note

All communication is MPI-based, and read options include parallel loading information, resolving shared entities. Local MOAB instance is populated with mesh cells and vertices in the corresponding local partitions.

This will also exchange ghost cells and vertices, as requested. The default bridge dimension is 0 (vertices), and all additional lower dimensional sub-entities are exchanged (mesh edges and faces). The tags in the file are not exchanged by default. Default tag information for GLOBAL_ID, MATERIAL_SET, NEUMANN_SET and DIRICHLET_SET is exchanged. Global ID tag is exchanged for all cells and vertices. Material sets, Neumann sets and Dirichlet sets are all augmented with the ghost entities.

Operations: Collective

Parameters

[in]	pid	(iMOAB_AppID) The unique pointer to the application ID.
[in]	filename	(iMOAB_String) The MOAB mesh file (H5M) to load onto the internal application mesh set.
[in]	read_options	(iMOAB_String) Additional options for reading the MOAB mesh file in parallel.
[in]	num_ghost_layers	(int*) The total number of ghost layers to exchange during mesh loading.

Returns

ErrCode The error code indicating success or failure.

Definition at line 607 of file iMOAB.cpp.

{
    IMOAB_CHECKPOINTER( filename, 2 );
    IMOAB_ASSERT( strlen( filename ), "Invalid filename length." );
    IMOAB_CHECKPOINTER( num_ghost_layers, 4 );
 
    // make sure we use the file set and pcomm associated with the *pid
    std::ostringstream newopts;
    if( read_options ) newopts << read_options;
 
#ifdef MOAB_HAVE_MPI
 
    if( context.MPI_initialized )
    {
        if( context.worldprocs > 1 )
        {
            std::string opts( ( read_options ? read_options : "" ) );
            std::string pcid( "PARALLEL_COMM=" );
            std::size_t found = opts.find( pcid );
 
            if( found != std::string::npos )
            {
                std::cerr << " cannot specify PARALLEL_COMM option, it is implicit \n";
                return moab::MB_FAILURE;
            }
 
            // in serial, apply PARALLEL_COMM option only for h5m files; it does not work for .g
            // files (used in test_remapping)
            std::string filen( filename );
            std::string::size_type idx = filen.rfind( '.' );
 
            if( idx != std::string::npos )
            {
                std::string extension = filen.substr( idx + 1 );
                if( ( extension == std::string( "h5m" ) ) || ( extension == std::string( "nc" ) ) )
                    newopts << ";;PARALLEL_COMM=" << *pid;
            }
 
            if( *num_ghost_layers >= 1 )
            {
                // if we want ghosts, we will want additional entities, the last .1
                // because the addl ents can be edges, faces that are part of the neumann sets
                std::string pcid2( "PARALLEL_GHOSTS=" );
                std::size_t found2 = opts.find( pcid2 );
 
                if( found2 != std::string::npos )
                {
                    std::cout << " PARALLEL_GHOSTS option is already specified, ignore passed "
                                 "number of layers \n";
                }
                else
                {
                    // dimension of primary entities is 3 here, but it could be 2 for climate
                    // meshes; we would need to pass PARALLEL_GHOSTS explicitly for 2d meshes, for
                    // example:  ";PARALLEL_GHOSTS=2.0.1"
                    newopts << ";PARALLEL_GHOSTS=3.0." << *num_ghost_layers << ".3";
                }
            }
        }
    }
#else
    IMOAB_ASSERT( *num_ghost_layers == 0, "Cannot provide ghost layers in serial." );
#endif
 
    // Now let us actually load the MOAB file with the appropriate read options
    ErrorCode rval = context.MBI->load_file( filename, &context.appDatas[*pid].file_set, newopts.str().c_str() );MB_CHK_ERR( rval );
 
#ifdef VERBOSE
    // some debugging stuff
    std::ostringstream outfile;
#ifdef MOAB_HAVE_MPI
    int rank   = context.pcomms[*pid]->rank();
    int nprocs = context.pcomms[*pid]->size();
    outfile << "TaskMesh_n" << nprocs << "." << rank << ".h5m";
#else
    outfile << "TaskMesh_n1.0.h5m";
#endif
    // the mesh contains ghosts too, but they are not part of mat/neumann set
    // write in serial the file, to see what tags are missing
    rval = context.MBI->write_file( outfile.str().c_str() );MB_CHK_ERR( rval );  // everything on current task, written in serial
#endif
 
    // Update ghost layer information
    context.appDatas[*pid].num_ghost_layers = *num_ghost_layers;
 
    // Update mesh information
    return iMOAB_UpdateMeshInfo( pid );
}

References GlobalContext::appDatas, context, ErrorCode, IMOAB_ASSERT, IMOAB_CHECKPOINTER, iMOAB_UpdateMeshInfo(), moab::Interface::load_file(), MB_CHK_ERR, GlobalContext::MBI, GlobalContext::MPI_initialized, GlobalContext::worldprocs, and moab::Interface::write_file().

iMOAB_ReadHeaderInfo()

ErrCode iMOAB_ReadHeaderInfo	(	const iMOAB_String	filename,
		int *	num_global_vertices,
		int *	num_global_elements,
		int *	num_dimension,
		int *	num_parts
	)

It should be called on master task only, and information obtained could be broadcasted by the user. It is a fast lookup in the header of the file.

Note

Operations: Not collective

Parameters

[in]	filename	(iMOAB_String) The MOAB mesh file (H5M) to probe for header information.
[out]	num_global_vertices	(int*) The total number of vertices in the mesh file.
[out]	num_global_elements	(int*) The total number of elements (of highest dimension only).
[out]	num_dimension	(int*) The highest dimension of elements in the mesh (Edge=1, Tri/Quad=2, Tet/Hex/Prism/Pyramid=3).
[out]	num_parts	(int*) The total number of partitions available in the mesh file, typically partitioned with mbpart during pre-processing.

Returns

ErrCode The error code indicating success or failure.

Definition at line 463 of file iMOAB.cpp.

{
    IMOAB_CHECKPOINTER( filename, 1 );
    IMOAB_ASSERT( strlen( filename ), "Invalid filename length." );
 
#ifdef MOAB_HAVE_HDF5
    std::string filen( filename );
 
    int edges   = 0;
    int faces   = 0;
    int regions = 0;
    if( num_global_vertices ) *num_global_vertices = 0;
    if( num_global_elements ) *num_global_elements = 0;
    if( num_dimension ) *num_dimension = 0;
    if( num_parts ) *num_parts = 0;
 
    mhdf_FileHandle file;
    mhdf_Status status;
    unsigned long max_id;
    struct mhdf_FileDesc* data;
 
    file = mhdf_openFile( filen.c_str(), 0, &max_id, -1, &status );
 
    if( mhdf_isError( &status ) )
    {
        fprintf( stderr, "%s: %s\n", filename, mhdf_message( &status ) );
        return moab::MB_FAILURE;
    }
 
    data = mhdf_getFileSummary( file, H5T_NATIVE_ULONG, &status,
                                1 );  // will use extra set info; will get parallel partition tag info too!
 
    if( mhdf_isError( &status ) )
    {
        fprintf( stderr, "%s: %s\n", filename, mhdf_message( &status ) );
        return moab::MB_FAILURE;
    }
 
    if( num_dimension ) *num_dimension = data->nodes.vals_per_ent;
    if( num_global_vertices ) *num_global_vertices = (int)data->nodes.count;
 
    for( int i = 0; i < data->num_elem_desc; i++ )
    {
        struct mhdf_ElemDesc* el_desc = &( data->elems[i] );
        struct mhdf_EntDesc* ent_d    = &( el_desc->desc );
 
        if( 0 == strcmp( el_desc->type, mhdf_EDGE_TYPE_NAME ) )
        {
            edges += ent_d->count;
        }
 
        if( 0 == strcmp( el_desc->type, mhdf_TRI_TYPE_NAME ) )
        {
            faces += ent_d->count;
        }
 
        if( 0 == strcmp( el_desc->type, mhdf_QUAD_TYPE_NAME ) )
        {
            faces += ent_d->count;
        }
 
        if( 0 == strcmp( el_desc->type, mhdf_POLYGON_TYPE_NAME ) )
        {
            faces += ent_d->count;
        }
 
        if( 0 == strcmp( el_desc->type, mhdf_TET_TYPE_NAME ) )
        {
            regions += ent_d->count;
        }
 
        if( 0 == strcmp( el_desc->type, mhdf_PYRAMID_TYPE_NAME ) )
        {
            regions += ent_d->count;
        }
 
        if( 0 == strcmp( el_desc->type, mhdf_PRISM_TYPE_NAME ) )
        {
            regions += ent_d->count;
        }
 
        if( 0 == strcmp( el_desc->type, mdhf_KNIFE_TYPE_NAME ) )
        {
            regions += ent_d->count;
        }
 
        if( 0 == strcmp( el_desc->type, mdhf_HEX_TYPE_NAME ) )
        {
            regions += ent_d->count;
        }
 
        if( 0 == strcmp( el_desc->type, mhdf_POLYHEDRON_TYPE_NAME ) )
        {
            regions += ent_d->count;
        }
 
        if( 0 == strcmp( el_desc->type, mhdf_SEPTAHEDRON_TYPE_NAME ) )
        {
            regions += ent_d->count;
        }
    }
 
    if( num_parts ) *num_parts = data->numEntSets[0];
 
    // is this required?
    if( edges > 0 )
    {
        if( num_dimension ) *num_dimension = 1;  // I don't think it will ever return 1
        if( num_global_elements ) *num_global_elements = edges;
    }
 
    if( faces > 0 )
    {
        if( num_dimension ) *num_dimension = 2;
        if( num_global_elements ) *num_global_elements = faces;
    }
 
    if( regions > 0 )
    {
        if( num_dimension ) *num_dimension = 3;
        if( num_global_elements ) *num_global_elements = regions;
    }
 
    mhdf_closeFile( file, &status );
 
    free( data );
 
#else
    std::cout << filename
              << ": Please reconfigure with HDF5. Cannot retrieve header information for file "
                 "formats other than a h5m file.\n";
    if( num_global_vertices ) *num_global_vertices = 0;
    if( num_global_elements ) *num_global_elements = 0;
    if( num_dimension ) *num_dimension = 0;
    if( num_parts ) *num_parts = 0;
#endif
 
    return moab::MB_SUCCESS;
}

References mhdf_EntDesc::count, mhdf_ElemDesc::desc, mhdf_FileDesc::elems, IMOAB_ASSERT, IMOAB_CHECKPOINTER, MB_SUCCESS, mdhf_HEX_TYPE_NAME, mdhf_KNIFE_TYPE_NAME, mhdf_closeFile(), mhdf_EDGE_TYPE_NAME, mhdf_getFileSummary(), mhdf_isError(), mhdf_message(), mhdf_openFile(), mhdf_POLYGON_TYPE_NAME, mhdf_POLYHEDRON_TYPE_NAME, mhdf_PRISM_TYPE_NAME, mhdf_PYRAMID_TYPE_NAME, mhdf_QUAD_TYPE_NAME, mhdf_SEPTAHEDRON_TYPE_NAME, mhdf_TET_TYPE_NAME, mhdf_TRI_TYPE_NAME, mhdf_FileDesc::nodes, mhdf_FileDesc::num_elem_desc, mhdf_FileDesc::numEntSets, mhdf_ElemDesc::type, and mhdf_EntDesc::vals_per_ent.

iMOAB_ReduceTagsMax()

ErrCode iMOAB_ReduceTagsMax	(	iMOAB_AppID	pid,
		int *	tag_index,
		int *	ent_type
	)

Perform global reductions with the processes in the current applications communicator. Specifically this routine performs reductions on the maximum value of the tag indicated by tag_index.

Note

Operations: Collective

Parameters

[in]	pid	(iMOAB_AppID) The unique pointer to the application ID.
[in]	tag_index	(int*) The tag index of interest.
[in]	ent_type	(int*) The type of entity for tag reduction operation (vertices = 0, elements = 1)

Returns

ErrCode The error code indicating success or failure.

Definition at line 2140 of file iMOAB.cpp.

{
#ifdef MOAB_HAVE_MPI
    appData& data = context.appDatas[*pid];
    Range ent_exchange;
 
    if( *tag_index < 0 || *tag_index >= (int)data.tagList.size() )
    {
        return moab::MB_FAILURE;
    }  // error in tag index
 
    Tag tagh = data.tagList[*tag_index];
 
    if( *ent_type == 0 )
    {
        ent_exchange = data.all_verts;
    }
    else if( *ent_type == 1 )
    {
        ent_exchange = data.primary_elems;
    }
    else
    {
        return moab::MB_FAILURE;
    }  // unexpected type
 
    ParallelComm* pco = context.pcomms[*pid];
    // we could do different MPI_Op; do not bother now, we will call from fortran
    ErrorCode rval = pco->reduce_tags( tagh, MPI_MAX, ent_exchange );MB_CHK_ERR( rval );
 
#else
    /* do nothing if serial */
    // just silence the warning
    // do not call sync tags in serial!
    int k = *pid + *tag_index + *ent_type;
    k++;  // just do junk, to avoid complaints
#endif
    return moab::MB_SUCCESS;
}

References appData::all_verts, GlobalContext::appDatas, context, ErrorCode, MB_CHK_ERR, MB_SUCCESS, appData::primary_elems, moab::ParallelComm::reduce_tags(), and appData::tagList.

iMOAB_RegisterApplication()

ErrCode iMOAB_RegisterApplication	(	const iMOAB_String	app_name,
		int *	compid,
		iMOAB_AppID	pid
	)

Register application - Create a unique application ID and bootstrap interfaces for further queries.

Note

Internally, a mesh set will be associated with the application ID and all subsequent queries on the MOAB instance will be directed to this mesh/file set.

Operations: Collective

Parameters

[in]	app_name	(iMOAB_String) Application name (PROTEUS, NEK5000, etc)
[in]	comm	(MPI_Comm*) MPI communicator to be used for all mesh-related queries originating from this application
[in]	compid	(int*) The unique external component identifier
[out]	pid	(iMOAB_AppID) The unique pointer to the application ID

Returns

ErrCode The error code indicating success or failure.

Definition at line 199 of file iMOAB.cpp.

{
    IMOAB_CHECKPOINTER( app_name, 1 );
#ifdef MOAB_HAVE_MPI
    IMOAB_CHECKPOINTER( comm, 2 );
    IMOAB_CHECKPOINTER( compid, 3 );
#else
    IMOAB_CHECKPOINTER( compid, 2 );
#endif
 
    // will create a parallel comm for this application too, so there will be a
    // mapping from *pid to file set and to parallel comm instances
    std::string name( app_name );
 
    if( context.appIdMap.find( name ) != context.appIdMap.end() )
    {
        std::cout << " application " << name << " already registered \n";
        return moab::MB_FAILURE;
    }
 
    *pid                   = context.unused_pid++;
    context.appIdMap[name] = *pid;
    int rankHere           = 0;
#ifdef MOAB_HAVE_MPI
    MPI_Comm_rank( *comm, &rankHere );
#endif
    if( !rankHere ) std::cout << " application " << name << " with ID = " << *pid << " is registered now \n";
    if( *compid <= 0 )
    {
        std::cout << " convention for external application is to have its id positive \n";
        return moab::MB_FAILURE;
    }
 
    if( context.appIdCompMap.find( *compid ) != context.appIdCompMap.end() )
    {
        std::cout << " external application with comp id " << *compid << " is already registered\n";
        return moab::MB_FAILURE;
    }
 
    context.appIdCompMap[*compid] = *pid;
 
    // now create ParallelComm and a file set for this application
#ifdef MOAB_HAVE_MPI
    if( *comm )
    {
        ParallelComm* pco = new ParallelComm( context.MBI, *comm );
 
#ifndef NDEBUG
        int index = pco->get_id();  // it could be useful to get app id from pcomm instance ...
        assert( index == *pid );
        // here, we assert the the pid is the same as the id of the ParallelComm instance
        // useful for writing in parallel
#endif
        context.pcomms.push_back( pco );
    }
    else
    {
        context.pcomms.push_back( 0 );
    }
#endif
 
    // create now the file set that will be used for loading the model in
    EntityHandle file_set;
    ErrorCode rval = context.MBI->create_meshset( MESHSET_SET, file_set );MB_CHK_ERR( rval );
 
    appData app_data;
    app_data.file_set  = file_set;
    app_data.global_id = *compid;  // will be used mostly for par comm graph
    app_data.name      = name;     // save the name of application
 
#ifdef MOAB_HAVE_TEMPESTREMAP
    app_data.tempestData.remapper = NULL;  // Only allocate as needed
#endif
 
    app_data.num_ghost_layers = 0;
    app_data.point_cloud      = false;
    app_data.is_fortran       = false;
 
    context.appDatas.push_back(
        app_data );  // it will correspond to app_FileSets[*pid] will be the file set of interest
    return moab::MB_SUCCESS;
}

References GlobalContext::appDatas, GlobalContext::appIdCompMap, GlobalContext::appIdMap, context, moab::Interface::create_meshset(), ErrorCode, appData::file_set, moab::ParallelComm::get_id(), appData::global_id, IMOAB_CHECKPOINTER, appData::is_fortran, MB_CHK_ERR, MB_SUCCESS, GlobalContext::MBI, MESHSET_SET, appData::name, appData::num_ghost_layers, appData::point_cloud, and GlobalContext::unused_pid.

Referenced by iMOAB_RegisterApplicationFortran().

iMOAB_RegisterApplicationFortran()

ErrCode iMOAB_RegisterApplicationFortran	(	const iMOAB_String	app_name,
		int *	compid,
		iMOAB_AppID	pid
	)

Register a Fortran-based application - Create a unique application ID and bootstrap interfaces for further queries.

Note

Internally, the comm object, usually a 32 bit integer in Fortran, will be converted using MPI_Comm_f2c and stored as MPI_Comm. A mesh set will be associated with the application ID and all subsequent queries on the MOAB instance will be directed to this mesh/file set.

Operations: Collective

Parameters

[in]	app_name	(iMOAB_String) Application name ("MySolver", "E3SM", "DMMoab", "PROTEUS", "NEK5000", etc)
[in]	communicator	(int*) Fortran MPI communicator to be used for all mesh-related queries originating from this application.
[in]	compid	(int*) External component id, (A const unique identifier).
[out]	pid	(iMOAB_AppID) The unique pointer to the application ID.

Returns

ErrCode The error code indicating success or failure.

Definition at line 287 of file iMOAB.cpp.

{
    IMOAB_CHECKPOINTER( app_name, 1 );
#ifdef MOAB_HAVE_MPI
    IMOAB_CHECKPOINTER( comm, 2 );
    IMOAB_CHECKPOINTER( compid, 3 );
#else
    IMOAB_CHECKPOINTER( compid, 2 );
#endif
 
    ErrCode err;
    assert( app_name != nullptr );
    std::string name( app_name );
 
#ifdef MOAB_HAVE_MPI
    MPI_Comm ccomm;
    if( comm )
    {
        // convert from Fortran communicator to a C communicator
        // see transfer of handles
        // http://www.mpi-forum.org/docs/mpi-2.2/mpi22-report/node361.htm
        ccomm = MPI_Comm_f2c( (MPI_Fint)*comm );
    }
#endif
 
    // now call C style registration function:
    err = iMOAB_RegisterApplication( app_name,
#ifdef MOAB_HAVE_MPI
                                     &ccomm,
#endif
                                     compid, pid );
 
    // Now that we have created the application context, store that
    // the application being registered is from a Fortran context
    context.appDatas[*pid].is_fortran = true;
 
    return err;
}

References GlobalContext::appDatas, context, ErrCode, IMOAB_CHECKPOINTER, and iMOAB_RegisterApplication().

iMOAB_ResolveSharedEntities()

ErrCode iMOAB_ResolveSharedEntities	(	iMOAB_AppID	pid,
		int *	num_verts,
		int *	marker
	)

Resolve shared entities using global markers on shared vertices.

Note

Global markers can be a global node id, for example, or a global DoF number (as for HOMME)

Operations: Collective .

Parameters

[in]	pid	(iMOAB_AppID) The unique pointer to the application ID.
[in]	num_verts	(int*) Number of vertices.
[in]	marker	(int*) Resolving marker (global id marker).

Returns

ErrCode The error code indicating success or failure.

iMOAB_SetDoubleTagStorage()

ErrCode iMOAB_SetDoubleTagStorage	(	iMOAB_AppID	pid,
		const iMOAB_String	tag_storage_name,
		int *	num_tag_storage_length,
		int *	entity_type,
		double *	tag_storage_data
	)

Store the specified values in a MOAB double Tag.

Note

Operations: Collective

Parameters

[in]	pid	(iMOAB_AppID) The unique pointer to the application ID.
[in]	tag_storage_name	(iMOAB_String) The tag names, separated, to store the data.
[in]	num_tag_storage_length	(int*) The size of total tag storage data (e.g., num_visible_vertices*components_per_entity or num_visible_elements*components_per_entity*num_tags).
[in]	entity_type	(int*) Type=0 for vertices, and Type=1 for primary elements.
[out]	tag_storage_data	(double*) The array data of type double to replace the internal tag memory; The data is assumed to be contiguous over the local set of visible entities (either vertices or elements). unrolled by tags

Returns

ErrCode The error code indicating success or failure.

Definition at line 1716 of file iMOAB.cpp.

{
    ErrorCode rval;
    std::string tag_names( tag_storage_names );
    // exactly the same code as for int tag :) maybe should check the type of tag too
    std::vector< std::string > tagNames;
    std::vector< Tag > tagHandles;
    std::string separator( ":" );
    split_tag_names( tag_names, separator, tagNames );
 
    appData& data      = context.appDatas[*pid];
    Range* ents_to_set = NULL;
 
    if( *ent_type == 0 )  // vertices
    {
        ents_to_set = &data.all_verts;
    }
    else if( *ent_type == 1 )
    {
        ents_to_set = &data.primary_elems;
    }
 
    int nents_to_be_set = (int)( *ents_to_set ).size();
    int position        = 0;
 
    for( size_t i = 0; i < tagNames.size(); i++ )
    {
        if( data.tagMap.find( tagNames[i] ) == data.tagMap.end() )
        {
            return moab::MB_FAILURE;
        }  // some tag not defined yet in the app
 
        Tag tag = data.tagMap[tagNames[i]];
 
        int tagLength = 0;
        rval          = context.MBI->tag_get_length( tag, tagLength );MB_CHK_ERR( rval );
 
        DataType dtype;
        rval = context.MBI->tag_get_data_type( tag, dtype );MB_CHK_ERR( rval );
 
        if( dtype != MB_TYPE_DOUBLE )
        {
            return moab::MB_FAILURE;
        }
 
        // set it on the subset of entities, based on type and length
        if( position + tagLength * nents_to_be_set > *num_tag_storage_length )
            return moab::MB_FAILURE;  // too many entity values to be set
 
        rval = context.MBI->tag_set_data( tag, *ents_to_set, &tag_storage_data[position] );MB_CHK_ERR( rval );
        // increment position to next tag
        position = position + tagLength * nents_to_be_set;
    }
    return moab::MB_SUCCESS;  // no error
}

References appData::all_verts, GlobalContext::appDatas, context, ErrorCode, MB_CHK_ERR, MB_SUCCESS, MB_TYPE_DOUBLE, GlobalContext::MBI, appData::primary_elems, moab::Range::size(), split_tag_names(), moab::Interface::tag_get_data_type(), moab::Interface::tag_get_length(), moab::Interface::tag_set_data(), and appData::tagMap.

iMOAB_SetDoubleTagStorageWithGid()

ErrCode iMOAB_SetDoubleTagStorageWithGid	(	iMOAB_AppID	pid,
		const iMOAB_String	tag_storage_names,
		int *	num_tag_storage_length,
		int *	entity_type,
		double *	tag_storage_data,
		int *	globalIds
	)

Store the specified values in a MOAB double Tag, for given ids.

Note

Operations: Collective

Parameters

[in]	pid	(iMOAB_AppID) The unique pointer to the application ID.
[in]	tag_storage_name	(iMOAB_String) The tag names, separated, to store the data.
[in]	num_tag_storage_length	(int*) The size of total tag storage data (e.g., num_visible_vertices*components_per_entity or num_visible_elements*components_per_entity*num_tags).
[in]	entity_type	(int*) Type=0 for vertices, and Type=1 for primary elements.
[in]	tag_storage_data	(double*) The array data of type double to replace the internal tag memory; The data is assumed to be permuted over the local set of visible entities (either vertices or elements). unrolled by tags in parallel, might be different order, or different entities on the task
[in]	globalIds	global ids of the cells to be set;

Returns

ErrCode The error code indicating success or failure.

Definition at line 1776 of file iMOAB.cpp.

{
    ErrorCode rval;
    std::string tag_names( tag_storage_names );
    // exactly the same code as for int tag :) maybe should check the type of tag too
    std::vector< std::string > tagNames;
    std::vector< Tag > tagHandles;
    std::string separator( ":" );
    split_tag_names( tag_names, separator, tagNames );
 
    appData& data      = context.appDatas[*pid];
    Range* ents_to_set = NULL;
 
    if( *ent_type == 0 )  // vertices
    {
        ents_to_set = &data.all_verts;
    }
    else if( *ent_type == 1 )
    {
        ents_to_set = &data.primary_elems;
    }
 
    int nents_to_be_set = (int)( *ents_to_set ).size();
 
    Tag gidTag = context.MBI->globalId_tag();
    std::vector< int > gids;
    gids.resize( nents_to_be_set );
    rval = context.MBI->tag_get_data( gidTag, *ents_to_set, &gids[0] );MB_CHK_ERR( rval );
 
    // so we will need to set the tags according to the global id passed;
    // so the order in tag_storage_data is the same as the order in globalIds, but the order
    // in local range is gids
    std::map< int, EntityHandle > eh_by_gid;
    int i = 0;
    for( Range::iterator it = ents_to_set->begin(); it != ents_to_set->end(); ++it, ++i )
    {
        eh_by_gid[gids[i]] = *it;
    }
 
    std::vector< int > tagLengths( tagNames.size() );
    std::vector< Tag > tagList;
    size_t total_tag_len = 0;
    for( size_t i = 0; i < tagNames.size(); i++ )
    {
        if( data.tagMap.find( tagNames[i] ) == data.tagMap.end() )
        {
            MB_SET_ERR( moab::MB_FAILURE, "tag missing" );
        }  // some tag not defined yet in the app
 
        Tag tag = data.tagMap[tagNames[i]];
        tagList.push_back( tag );
 
        int tagLength = 0;
        rval          = context.MBI->tag_get_length( tag, tagLength );MB_CHK_ERR( rval );
 
        total_tag_len += tagLength;
        tagLengths[i] = tagLength;
        DataType dtype;
        rval = context.MBI->tag_get_data_type( tag, dtype );MB_CHK_ERR( rval );
 
        if( dtype != MB_TYPE_DOUBLE )
        {
            MB_SET_ERR( moab::MB_FAILURE, "tag not double type" );
        }
    }
    bool serial = true;
#ifdef MOAB_HAVE_MPI
    ParallelComm* pco  = context.pcomms[*pid];
    unsigned num_procs = pco->size();
    if( num_procs > 1 ) serial = false;
#endif
 
    if( serial )
    {
        // we do not assume anymore that the number of entities has to match
        // we will set only what matches, and skip entities that do not have corresponding global ids
        //assert( total_tag_len * nents_to_be_set - *num_tag_storage_length == 0 );
        // tags are unrolled, we loop over global ids first, then careful about tags
        for( int i = 0; i < nents_to_be_set; i++ )
        {
            int gid                                       = globalIds[i];
            std::map< int, EntityHandle >::iterator mapIt = eh_by_gid.find( gid );
            if( mapIt == eh_by_gid.end() ) continue;
            EntityHandle eh = mapIt->second;
            // now loop over tags
            int indexInTagValues = 0;  //
            for( size_t j = 0; j < tagList.size(); j++ )
            {
                indexInTagValues += i * tagLengths[j];
                rval = context.MBI->tag_set_data( tagList[j], &eh, 1, &tag_storage_data[indexInTagValues] );MB_CHK_ERR( rval );
                // advance the pointer/index
                indexInTagValues += ( nents_to_be_set - i ) * tagLengths[j];  // at the end of tag data
            }
        }
    }
#ifdef MOAB_HAVE_MPI
    else  // it can be not serial only if pco->size() > 1, parallel
    {
        // in this case, we have to use 2 crystal routers, to send data to the processor that needs it
        // we will create first a tuple to rendevous points, then from there send to the processor that requested it
        // it is a 2-hop global gather scatter
        // TODO: allow for tags of different length; this is wrong
        int nbLocalVals = *num_tag_storage_length / ( (int)tagNames.size() );  // assumes all tags have the same length?
        // we do not expect the sizes to match
        //assert( nbLocalVals * tagNames.size() - *num_tag_storage_length == 0 );
        TupleList TLsend;
        TLsend.initialize( 2, 0, 0, total_tag_len, nbLocalVals );  //  to proc, marker(gid), total_tag_len doubles
        TLsend.enableWriteAccess();
        // the processor id that processes global_id is global_id / num_ents_per_proc
 
        int indexInRealLocal = 0;
        for( int i = 0; i < nbLocalVals; i++ )
        {
            // to proc, marker, element local index, index in el
            int marker              = globalIds[i];
            int to_proc             = marker % num_procs;
            int n                   = TLsend.get_n();
            TLsend.vi_wr[2 * n]     = to_proc;  // send to processor
            TLsend.vi_wr[2 * n + 1] = marker;
            int indexInTagValues    = 0;
            // tag data collect by number of tags
            for( size_t j = 0; j < tagList.size(); j++ )
            {
                indexInTagValues += i * tagLengths[j];
                for( int k = 0; k < tagLengths[j]; k++ )
                {
                    TLsend.vr_wr[indexInRealLocal++] = tag_storage_data[indexInTagValues + k];
                }
                indexInTagValues += ( nbLocalVals - i ) * tagLengths[j];
            }
            TLsend.inc_n();
        }
 
        //assert( nbLocalVals * total_tag_len - indexInRealLocal == 0 );
        // send now requests, basically inform the rendez-vous point who needs a particular global id
        // send the data to the other processors:
        ( pco->proc_config().crystal_router() )->gs_transfer( 1, TLsend, 0 );
        TupleList TLreq;
        TLreq.initialize( 2, 0, 0, 0, nents_to_be_set );
        TLreq.enableWriteAccess();
        for( int i = 0; i < nents_to_be_set; i++ )
        {
            // to proc, marker
            int marker             = gids[i];
            int to_proc            = marker % num_procs;
            int n                  = TLreq.get_n();
            TLreq.vi_wr[2 * n]     = to_proc;  // send to processor
            TLreq.vi_wr[2 * n + 1] = marker;
            // tag data collect by number of tags
            TLreq.inc_n();
        }
        ( pco->proc_config().crystal_router() )->gs_transfer( 1, TLreq, 0 );
 
        // we know now that process TLreq.vi_wr[2 * n] needs tags for gid TLreq.vi_wr[2 * n + 1]
        // we should first order by global id, and then build the new TL with send to proc, global id and
        // tags for it
        // sort by global ids the tuple lists
        moab::TupleList::buffer sort_buffer;
        sort_buffer.buffer_init( TLreq.get_n() );
        TLreq.sort( 1, &sort_buffer );
        sort_buffer.reset();
        sort_buffer.buffer_init( TLsend.get_n() );
        TLsend.sort( 1, &sort_buffer );
        sort_buffer.reset();
        // now send the tag values to the proc that requested it
        // in theory, for a full  partition, TLreq  and TLsend should have the same size, and
        // each dof should have exactly one target proc. Is that true or not in general ?
        // how do we plan to use this? Is it better to store the comm graph for future
 
        // start copy from comm graph settle
        TupleList TLBack;
        TLBack.initialize( 3, 0, 0, total_tag_len, 0 );  // to proc, marker, tag from proc , tag values
        TLBack.enableWriteAccess();
 
        int n1 = TLreq.get_n();
        int n2 = TLsend.get_n();
 
        int indexInTLreq  = 0;
        int indexInTLsend = 0;  // advance both, according to the marker
        if( n1 > 0 && n2 > 0 )
        {
 
            while( indexInTLreq < n1 && indexInTLsend < n2 )  // if any is over, we are done
            {
                int currentValue1 = TLreq.vi_rd[2 * indexInTLreq + 1];
                int currentValue2 = TLsend.vi_rd[2 * indexInTLsend + 1];
                if( currentValue1 < currentValue2 )
                {
                    // we have a big problem; basically, we are saying that
                    // dof currentValue is on one model and not on the other
                    // std::cout << " currentValue1:" << currentValue1 << " missing in comp2" << "\n";
                    indexInTLreq++;
                    continue;
                }
                if( currentValue1 > currentValue2 )
                {
                    // std::cout << " currentValue2:" << currentValue2 << " missing in comp1" << "\n";
                    indexInTLsend++;
                    continue;
                }
                int size1 = 1;
                int size2 = 1;
                while( indexInTLreq + size1 < n1 && currentValue1 == TLreq.vi_rd[2 * ( indexInTLreq + size1 ) + 1] )
                    size1++;
                while( indexInTLsend + size2 < n2 && currentValue2 == TLsend.vi_rd[2 * ( indexInTLsend + size2 ) + 1] )
                    size2++;
                // must be found in both lists, find the start and end indices
                for( int i1 = 0; i1 < size1; i1++ )
                {
                    for( int i2 = 0; i2 < size2; i2++ )
                    {
                        // send the info back to components
                        int n = TLBack.get_n();
                        TLBack.reserve();
                        TLBack.vi_wr[3 * n] = TLreq.vi_rd[2 * ( indexInTLreq + i1 )];  // send back to the proc marker
                                                                                       // came from, info from comp2
                        TLBack.vi_wr[3 * n + 1] = currentValue1;  // initial value (resend, just for verif ?)
                        TLBack.vi_wr[3 * n + 2] = TLsend.vi_rd[2 * ( indexInTLsend + i2 )];  // from proc on comp2
                        // also fill tag values
                        for( size_t k = 0; k < total_tag_len; k++ )
                        {
                            TLBack.vr_rd[total_tag_len * n + k] =
                                TLsend.vr_rd[total_tag_len * indexInTLsend + k];  // deep copy of tag values
                        }
                    }
                }
                indexInTLreq += size1;
                indexInTLsend += size2;
            }
        }
        ( pco->proc_config().crystal_router() )->gs_transfer( 1, TLBack, 0 );
        // end copy from comm graph
        // after we are done sending, we need to set those tag values, in a reverse process compared to send
        n1             = TLBack.get_n();
        double* ptrVal = &TLBack.vr_rd[0];  //
        for( int i = 0; i < n1; i++ )
        {
            int gid                                       = TLBack.vi_rd[3 * i + 1];  // marker
            std::map< int, EntityHandle >::iterator mapIt = eh_by_gid.find( gid );
            if( mapIt == eh_by_gid.end() ) continue;
            EntityHandle eh = mapIt->second;
            // now loop over tags
 
            for( size_t j = 0; j < tagList.size(); j++ )
            {
                rval = context.MBI->tag_set_data( tagList[j], &eh, 1, (void*)ptrVal );MB_CHK_ERR( rval );
                // advance the pointer/index
                ptrVal += tagLengths[j];  // at the end of tag data per call
            }
        }
    }
#endif
    return MB_SUCCESS;
}

References appData::all_verts, GlobalContext::appDatas, moab::Range::begin(), context, moab::ProcConfig::crystal_router(), moab::TupleList::enableWriteAccess(), moab::Range::end(), ErrorCode, moab::TupleList::get_n(), moab::Interface::globalId_tag(), moab::TupleList::inc_n(), moab::TupleList::initialize(), MB_CHK_ERR, MB_SET_ERR, MB_SUCCESS, MB_TYPE_DOUBLE, GlobalContext::MBI, appData::primary_elems, moab::ParallelComm::proc_config(), moab::TupleList::reserve(), moab::TupleList::buffer::reset(), moab::Range::size(), moab::ParallelComm::size(), moab::TupleList::sort(), split_tag_names(), moab::Interface::tag_get_data(), moab::Interface::tag_get_data_type(), moab::Interface::tag_get_length(), moab::Interface::tag_set_data(), appData::tagMap, moab::TupleList::vi_rd, moab::TupleList::vi_wr, moab::TupleList::vr_rd, and moab::TupleList::vr_wr.

iMOAB_SetGlobalInfo()

ErrCode iMOAB_SetGlobalInfo	(	iMOAB_AppID	pid,
		int *	num_global_verts,
		int *	num_global_elems
	)

Set global information for number of vertices and number of elements; It is usually available from the h5m file, or it can be computed with a MPI_Reduce.

Parameters

[in]	pid	(iMOAB_AppID) The unique pointer to the application ID.
[in]	num_global_verts	(int*) The number of total vertices in the mesh.
[in]	num_global_elems	(MPI_Comm) The number of total elements in the mesh.

Returns

ErrCode The error code indicating success or failure.

Definition at line 2304 of file iMOAB.cpp.

{
    appData& data            = context.appDatas[*pid];
    data.num_global_vertices = *num_global_verts;
    data.num_global_elements = *num_global_elems;
    return moab::MB_SUCCESS;
}

References GlobalContext::appDatas, context, MB_SUCCESS, appData::num_global_elements, and appData::num_global_vertices.

Referenced by iMOAB_UpdateMeshInfo().

iMOAB_SetIntTagStorage()

ErrCode iMOAB_SetIntTagStorage	(	iMOAB_AppID	pid,
		const iMOAB_String	tag_storage_name,
		int *	num_tag_storage_length,
		int *	entity_type,
		int *	tag_storage_data
	)

Store the specified values in a MOAB integer Tag.

Values are set on vertices or elements, depending on entity_type

Note

we could change the api to accept as input the tag index, as returned by iMOAB_DefineTagStorage.

Operations: Collective

Parameters

[in]	pid	(iMOAB_AppID) The unique pointer to the application ID.
[in]	tag_storage_name	(iMOAB_String) The tag name to store/retreive the data in MOAB.
[in]	num_tag_storage_length	(int*) The size of tag storage data (e.g., num_visible_vertices*components_per_entity or num_visible_elements*components_per_entity).
[in]	entity_type	(int*) Type=0 for vertices, and Type=1 for primary elements.
[out]	tag_storage_data	(int*) The array data of type int to replace the internal tag memory; The data is assumed to be contiguous over the local set of visible entities (either vertices or elements).

Returns

ErrCode The error code indicating success or failure.

Definition at line 1602 of file iMOAB.cpp.

{
    std::string tag_name( tag_storage_name );
 
    // Get the application data
    appData& data = context.appDatas[*pid];
 
    if( data.tagMap.find( tag_name ) == data.tagMap.end() )
    {
        return moab::MB_FAILURE;
    }  // tag not defined
 
    Tag tag = data.tagMap[tag_name];
 
    int tagLength  = 0;
    ErrorCode rval = context.MBI->tag_get_length( tag, tagLength );MB_CHK_ERR( rval );
 
    DataType dtype;
    rval = context.MBI->tag_get_data_type( tag, dtype );
 
    if( MB_SUCCESS != rval || dtype != MB_TYPE_INTEGER )
    {
        return moab::MB_FAILURE;
    }
 
    // set it on a subset of entities, based on type and length
    Range* ents_to_set;
 
    if( *ent_type == 0 )  // vertices
    {
        ents_to_set = &data.all_verts;
    }
    else  // if (*ent_type == 1) // *ent_type can be 0 (vertices) or 1 (elements)
    {
        ents_to_set = &data.primary_elems;
    }
 
    int nents_to_be_set = *num_tag_storage_length / tagLength;
 
    if( nents_to_be_set > (int)ents_to_set->size() || nents_to_be_set < 1 )
    {
        return moab::MB_FAILURE;
    }  // to many entities to be set or too few
 
    // restrict the range; everything is contiguous; or not?
 
    // Range contig_range ( * ( ents_to_set->begin() ), * ( ents_to_set->begin() + nents_to_be_set -
    // 1 ) );
    rval = context.MBI->tag_set_data( tag, *ents_to_set, tag_storage_data );MB_CHK_ERR( rval );
 
    return moab::MB_SUCCESS;  // no error
}

References appData::all_verts, GlobalContext::appDatas, context, ErrorCode, MB_CHK_ERR, MB_SUCCESS, MB_TYPE_INTEGER, GlobalContext::MBI, appData::primary_elems, moab::Range::size(), moab::Interface::tag_get_data_type(), moab::Interface::tag_get_length(), moab::Interface::tag_set_data(), and appData::tagMap.

iMOAB_SynchronizeTags()

ErrCode iMOAB_SynchronizeTags	(	iMOAB_AppID	pid,
		int *	num_tag,
		int *	tag_indices,
		int *	ent_type
	)

Exchange tag values for the given tags across process boundaries.

Note

Operations: Collective

Parameters

[in]	pid	(iMOAB_AppID) The unique pointer to the application ID.
[in]	num_tags	(int*) Number of tags to exchange.
[in]	tag_indices	(int*) Array with tag indices of interest (size = *num_tags).
[in]	ent_type	(int*) The type of entity for tag exchange.

Returns

ErrCode The error code indicating success or failure.

Definition at line 2095 of file iMOAB.cpp.

{
#ifdef MOAB_HAVE_MPI
    appData& data = context.appDatas[*pid];
    Range ent_exchange;
    std::vector< Tag > tags;
 
    for( int i = 0; i < *num_tag; i++ )
    {
        if( tag_indices[i] < 0 || tag_indices[i] >= (int)data.tagList.size() )
        {
            return moab::MB_FAILURE;
        }  // error in tag index
 
        tags.push_back( data.tagList[tag_indices[i]] );
    }
 
    if( *ent_type == 0 )
    {
        ent_exchange = data.all_verts;
    }
    else if( *ent_type == 1 )
    {
        ent_exchange = data.primary_elems;
    }
    else
    {
        return moab::MB_FAILURE;
    }  // unexpected type
 
    ParallelComm* pco = context.pcomms[*pid];
 
    ErrorCode rval = pco->exchange_tags( tags, tags, ent_exchange );MB_CHK_ERR( rval );
 
#else
    /* do nothing if serial */
    // just silence the warning
    // do not call sync tags in serial!
    int k = *pid + *num_tag + *tag_indices + *ent_type;
    k++;
#endif
 
    return moab::MB_SUCCESS;
}

References appData::all_verts, GlobalContext::appDatas, context, ErrorCode, moab::ParallelComm::exchange_tags(), MB_CHK_ERR, MB_SUCCESS, appData::primary_elems, and appData::tagList.

iMOAB_UpdateMeshInfo()

ErrCode iMOAB_UpdateMeshInfo

(

iMOAB_AppID

pid

)

Update local mesh data structure, from file information.

Note

The method should be called after mesh modifications, for example reading a file or creating mesh in memory

Operations: Collective

Parameters

[in]

pid

(iMOAB_AppID) The unique pointer to the application ID.

Returns

ErrCode The error code indicating success or failure.

Definition at line 778 of file iMOAB.cpp.

{
    // this will include ghost elements info
    appData& data        = context.appDatas[*pid];
    EntityHandle fileSet = data.file_set;
 
    // first clear all data ranges; this can be called after ghosting
    data.all_verts.clear();
    data.primary_elems.clear();
    data.local_verts.clear();
    data.owned_verts.clear();
    data.ghost_vertices.clear();
    data.owned_elems.clear();
    data.ghost_elems.clear();
    data.mat_sets.clear();
    data.neu_sets.clear();
    data.diri_sets.clear();
 
    // Let us get all the vertex entities
    ErrorCode rval = context.MBI->get_entities_by_type( fileSet, MBVERTEX, data.all_verts, true );MB_CHK_ERR( rval );  // recursive
 
    // Let us check first entities of dimension = 3
    data.dimension = 3;
    rval           = context.MBI->get_entities_by_dimension( fileSet, data.dimension, data.primary_elems, true );MB_CHK_ERR( rval );  // recursive
 
    if( data.primary_elems.empty() )
    {
        // Now 3-D elements. Let us check entities of dimension = 2
        data.dimension = 2;
        rval           = context.MBI->get_entities_by_dimension( fileSet, data.dimension, data.primary_elems, true );MB_CHK_ERR( rval );  // recursive
 
        if( data.primary_elems.empty() )
        {
            // Now 3-D/2-D elements. Let us check entities of dimension = 1
            data.dimension = 1;
            rval = context.MBI->get_entities_by_dimension( fileSet, data.dimension, data.primary_elems, true );MB_CHK_ERR( rval );  // recursive
 
            if( data.primary_elems.empty() )
            {
                // no elements of dimension 1 or 2 or 3; it could happen for point clouds
                data.dimension = 0;
            }
        }
    }
 
    // check if the current mesh is just a point cloud
    data.point_cloud = ( ( data.primary_elems.size() == 0 && data.all_verts.size() > 0 ) || data.dimension == 0 );
 
#ifdef MOAB_HAVE_MPI
 
    if( context.MPI_initialized )
    {
        ParallelComm* pco = context.pcomms[*pid];
 
        // filter ghost vertices, from local
        rval = pco->filter_pstatus( data.all_verts, PSTATUS_GHOST, PSTATUS_NOT, -1, &data.local_verts );MB_CHK_ERR( rval );
 
        // Store handles for all ghosted entities
        data.ghost_vertices = subtract( data.all_verts, data.local_verts );
 
        // filter ghost elements, from local
        rval = pco->filter_pstatus( data.primary_elems, PSTATUS_GHOST, PSTATUS_NOT, -1, &data.owned_elems );MB_CHK_ERR( rval );
 
        data.ghost_elems = subtract( data.primary_elems, data.owned_elems );
        // now update global number of primary cells and global number of vertices
        // determine first number of owned vertices
        // Get local owned vertices
        rval = pco->filter_pstatus( data.all_verts, PSTATUS_NOT_OWNED, PSTATUS_NOT, -1, &data.owned_verts );MB_CHK_ERR( rval );
        int local[2], global[2];
        local[0] = data.owned_verts.size();
        local[1] = data.owned_elems.size();
        MPI_Allreduce( local, global, 2, MPI_INT, MPI_SUM, pco->comm() );
        rval = iMOAB_SetGlobalInfo( pid, &( global[0] ), &( global[1] ) );MB_CHK_ERR( rval );
    }
    else
    {
        data.local_verts = data.all_verts;
        data.owned_elems = data.primary_elems;
    }
 
#else
 
    data.local_verts = data.all_verts;
    data.owned_elems = data.primary_elems;
 
#endif
 
    // Get the references for some standard internal tags such as material blocks, BCs, etc
    rval = context.MBI->get_entities_by_type_and_tag( fileSet, MBENTITYSET, &( context.material_tag ), 0, 1,
                                                      data.mat_sets, Interface::UNION );MB_CHK_ERR( rval );
 
    rval = context.MBI->get_entities_by_type_and_tag( fileSet, MBENTITYSET, &( context.neumann_tag ), 0, 1,
                                                      data.neu_sets, Interface::UNION );MB_CHK_ERR( rval );
 
    rval = context.MBI->get_entities_by_type_and_tag( fileSet, MBENTITYSET, &( context.dirichlet_tag ), 0, 1,
                                                      data.diri_sets, Interface::UNION );MB_CHK_ERR( rval );
 
    return moab::MB_SUCCESS;
}

References appData::all_verts, GlobalContext::appDatas, moab::Range::clear(), moab::ParallelComm::comm(), context, appData::dimension, appData::diri_sets, GlobalContext::dirichlet_tag, moab::Range::empty(), ErrorCode, appData::file_set, moab::ParallelComm::filter_pstatus(), moab::Interface::get_entities_by_dimension(), moab::Interface::get_entities_by_type(), moab::Interface::get_entities_by_type_and_tag(), appData::ghost_elems, appData::ghost_vertices, iMOAB_SetGlobalInfo(), appData::local_verts, appData::mat_sets, GlobalContext::material_tag, MB_CHK_ERR, MB_SUCCESS, MBENTITYSET, GlobalContext::MBI, MBVERTEX, GlobalContext::MPI_initialized, appData::neu_sets, GlobalContext::neumann_tag, appData::owned_elems, appData::owned_verts, appData::point_cloud, appData::primary_elems, PSTATUS_GHOST, PSTATUS_NOT, PSTATUS_NOT_OWNED, moab::Range::size(), moab::subtract(), and moab::Interface::UNION.

Referenced by iMOAB_LoadMesh().

iMOAB_WriteLocalMesh()

ErrCode iMOAB_WriteLocalMesh	(	iMOAB_AppID	pid,
		iMOAB_String	prefix
	)

Write a local MOAB mesh copy.

Note

The interface will write one file per task. Only the local mesh set and solution data associated to the application will be written to the file. Very convenient method used for debugging.

Operations: Not Collective (independent operation).

Parameters

[in]	pid	(iMOAB_AppID) The unique pointer to the application ID.
[in]	prefix	(iMOAB_String) The MOAB file prefix that will be used with task ID in parallel.

Returns

ErrCode The error code indicating success or failure.

Definition at line 760 of file iMOAB.cpp.

{
    IMOAB_CHECKPOINTER( prefix, 2 );
    IMOAB_ASSERT( strlen( prefix ), "Invalid prefix string length." );
 
    std::ostringstream file_name;
    int rank = 0, size = 1;
#ifdef MOAB_HAVE_MPI
    rank = context.pcomms[*pid]->rank();
    size = context.pcomms[*pid]->size();
#endif
    file_name << prefix << "_" << size << "_" << rank << ".h5m";
    // Now let us actually write the file to disk with appropriate options
    ErrorCode rval = context.MBI->write_file( file_name.str().c_str(), 0, 0, &context.appDatas[*pid].file_set, 1 );MB_CHK_ERR( rval );
 
    return moab::MB_SUCCESS;
}

References GlobalContext::appDatas, context, ErrorCode, IMOAB_ASSERT, IMOAB_CHECKPOINTER, MB_CHK_ERR, MB_SUCCESS, GlobalContext::MBI, size, and moab::Interface::write_file().

iMOAB_WriteMesh()

ErrCode iMOAB_WriteMesh	(	iMOAB_AppID	pid,
		const iMOAB_String	filename,
		const iMOAB_String	write_options
	)

Write a MOAB mesh along with the solution tags to a file.

Note

The interface will write one single file (H5M) and for serial files (VTK/Exodus), it will write one file per task. Write options include parallel write options, if needed. Only the mesh set and solution data associated to the application will be written to the file.

Operations: Collective for parallel write, non collective for serial write.

Parameters

[in]	pid	(iMOAB_AppID) The unique pointer to the application ID.
[in]	filename	(iMOAB_String) The MOAB mesh file (H5M) to write all the entities contained in the internal application mesh set.
[in]	write_options	(iMOAB_String) Additional options for writing the MOAB mesh in parallel.

Returns

ErrCode The error code indicating success or failure.

Definition at line 699 of file iMOAB.cpp.

{
    IMOAB_CHECKPOINTER( filename, 2 );
    IMOAB_ASSERT( strlen( filename ), "Invalid filename length." );
 
    appData& data        = context.appDatas[*pid];
    EntityHandle fileSet = data.file_set;
 
    std::ostringstream newopts;
#ifdef MOAB_HAVE_MPI
    std::string write_opts( ( write_options ? write_options : "" ) );
    std::string pcid( "PARALLEL_COMM=" );
    std::size_t found = write_opts.find( pcid );
 
    if( found != std::string::npos )
    {
        std::cerr << " cannot specify PARALLEL_COMM option, it is implicit \n";
        return moab::MB_FAILURE;
    }
 
    // if write in parallel, add pc option, to be sure about which ParallelComm instance is used
    std::string pw( "PARALLEL=WRITE_PART" );
    found = write_opts.find( pw );
 
    if( found != std::string::npos )
    {
        newopts << "PARALLEL_COMM=" << *pid << ";";
    }
 
#endif
 
    if( write_options ) newopts << write_options;
 
    std::vector< Tag > copyTagList = data.tagList;
    // append Global ID and Parallel Partition
    std::string gid_name_tag( "GLOBAL_ID" );
 
    // export global id tag, we need it always
    if( data.tagMap.find( gid_name_tag ) == data.tagMap.end() )
    {
        Tag gid = context.MBI->globalId_tag();
        copyTagList.push_back( gid );
    }
    // also Parallel_Partition PARALLEL_PARTITION
    std::string pp_name_tag( "PARALLEL_PARTITION" );
 
    // write parallel part tag too, if it exists
    if( data.tagMap.find( pp_name_tag ) == data.tagMap.end() )
    {
        Tag ptag;
        context.MBI->tag_get_handle( pp_name_tag.c_str(), ptag );
        if( ptag ) copyTagList.push_back( ptag );
    }
 
    // Now let us actually write the file to disk with appropriate options
    ErrorCode rval = context.MBI->write_file( filename, 0, newopts.str().c_str(), &fileSet, 1, &copyTagList[0],
                                              (int)copyTagList.size() );MB_CHK_ERR( rval );
 
    return moab::MB_SUCCESS;
}

References GlobalContext::appDatas, context, ErrorCode, appData::file_set, moab::Interface::globalId_tag(), IMOAB_ASSERT, IMOAB_CHECKPOINTER, MB_CHK_ERR, MB_SUCCESS, GlobalContext::MBI, moab::Interface::tag_get_handle(), appData::tagList, appData::tagMap, and moab::Interface::write_file().