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MOAB: Mesh Oriented datABase
(version 5.3.0)
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MOAB: Mesh Oriented datABase
(version 5.3.0)
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#include "moab/MOABConfig.h"#include "moab/iMOAB.h"#include "TestUtil.hpp"#include <cstdlib>#include <cstdio>#include <cstring>
Include dependency graph for imoab_test.cpp:Go to the source code of this file.
Defines | |
| #define | CHECKRC(rc, message) |
Functions | |
| int | main (int argc, char *argv[]) |
| #define CHECKRC | ( | rc, | |
| message | |||
| ) |
if( 0 != ( rc ) ) \ { \ printf( "%s", message ); \ return 1; \ }
Definition at line 15 of file imoab_test.cpp.
Referenced by main().
| int main | ( | int | argc, |
| char * | argv[] | ||
| ) |
Definition at line 22 of file imoab_test.cpp.
References CHECKRC, conn, DENSE_DOUBLE, DENSE_INTEGER, ErrCode, iMOAB_AppID, iMOAB_DefineTagStorage, iMOAB_DeregisterApplication, iMOAB_Finalize, iMOAB_GetBlockElementConnectivities, iMOAB_GetBlockID, iMOAB_GetBlockInfo, iMOAB_GetDoubleTagStorage, iMOAB_GetElementConnectivity, iMOAB_GetElementID, iMOAB_GetElementOwnership, iMOAB_GetIntTagStorage, iMOAB_GetMeshInfo, iMOAB_GetNeighborElements, iMOAB_GetPointerToSurfaceBC, iMOAB_GetPointerToVertexBC, iMOAB_GetVertexID, iMOAB_GetVertexOwnership, iMOAB_GetVisibleElementsInfo, iMOAB_GetVisibleVerticesCoordinates, iMOAB_GlobalID, iMOAB_Initialize(), iMOAB_LoadMesh, iMOAB_LocalID, iMOAB_ReadHeaderInfo, iMOAB_RegisterApplication(), iMOAB_SetGlobalInfo, iMOAB_SynchronizeTags, iMOAB_WriteMesh, MPI_COMM_WORLD, outputFile, and rank.
{
int nprocs = 1, rank = 0;
std::string filen;
#ifdef MOAB_HAVE_MPI
MPI_Init( &argc, &argv );
MPI_Comm comm = MPI_COMM_WORLD;
MPI_Comm_size( comm, &nprocs );
MPI_Comm_rank( comm, &rank );
#endif
#ifdef MOAB_HAVE_HDF5
filen = TestDir + "/io/p8ex1.h5m";
#endif
if( argc > 1 ) filen = std::string( argv[1] );
if( !filen.size() ) return 1;
/*
* MOAB needs to be initialized; A MOAB instance will be created, and will be used by each
* application in this framework. There is no parallel context yet.
*/
ErrCode rc = iMOAB_Initialize( argc, argv );
CHECKRC( rc, "failed to initialize MOAB" );
int num_global_vertices = 0, num_global_elements = 0, num_dimension = 0, num_parts = 0;
/*
* Header information is cheap to retrieve from an hdf5 file; it can be called by each process
* or can be called by one master task and broadcasted. The hdf5 file has to be in MOAB native
* format, and has to be partitioned in advance. There should be at least as many partitions in
* the file as number of tasks in the communicator.
*/
rc = iMOAB_ReadHeaderInfo( filen.c_str(), &num_global_vertices, &num_global_elements, &num_dimension, &num_parts,
(int)( filen.size() ) );
CHECKRC( rc, "failed to read header info" );
if( 0 == rank )
{
printf( "file %s has %d vertices, %d elements, %d parts in partition\n", filen.c_str(), num_global_vertices,
num_global_elements, num_parts );
}
int appID, appDupID;
iMOAB_AppID pid = &appID;
iMOAB_AppID pidDup = &appDupID;
/*
* Each application has to be registered once. A mesh set and a parallel communicator will be
* associated with each application. A unique application id will be returned, and will be used
* for all future mesh operations/queries.
*/
int compid = 11, compdupid = 12;
rc = iMOAB_RegisterApplication( "MBAPP",
#ifdef MOAB_HAVE_MPI
&comm,
#endif
&compid, pid );
CHECKRC( rc, "failed to register application" );
rc = iMOAB_RegisterApplication( "MBDUPAPP",
#ifdef MOAB_HAVE_MPI
&comm,
#endif
&compdupid, pidDup );
CHECKRC( rc, "failed to register duplicate application" );
#ifdef MOAB_HAVE_MPI
const char* read_opts = "PARALLEL=READ_PART;PARTITION=PARALLEL_PARTITION;PARALLEL_RESOLVE_SHARED_ENTS";
int num_ghost_layers[1] = { 1 };
#else
const char* read_opts = "";
int* num_ghost_layers = nullptr;
#endif
/*
* Loading the mesh is a parallel IO operation. Ghost layers can be exchanged too, and default
* MOAB sets are augmented with ghost elements. By convention, blocks correspond to MATERIAL_SET
* sets, side sets with NEUMANN_SET sets, node sets with DIRICHLET_SET sets. Each element and
* vertex entity should have a GLOBAL ID tag in the file, which will be available for visible
* entities
*/
rc = iMOAB_LoadMesh( pid, filen.c_str(), read_opts, num_ghost_layers, (int)( filen.size() ), strlen( read_opts ) );
CHECKRC( rc, "failed to load mesh" );
rc = iMOAB_LoadMesh( pidDup, filen.c_str(), read_opts, num_ghost_layers, (int)( filen.size() ),
strlen( read_opts ) );
CHECKRC( rc, "failed to load mesh" );
rc = iMOAB_SetGlobalInfo( pid, &num_global_vertices, &num_global_elements );
CHECKRC( rc, "failed to set global info" );
int nverts[3], nelem[3], nblocks[3], nsbc[3], ndbc[3];
/*
* Each process in the communicator will have access to a local mesh instance, which will
* contain the original cells in the local partition and ghost entities. Number of vertices,
* primary cells, visible blocks, number of sidesets and nodesets boundary conditions will be
* returned in size 3 arrays, for local, ghost and total numbers.
*/
rc = iMOAB_GetMeshInfo( pid, nverts, nelem, nblocks, nsbc, ndbc );
CHECKRC( rc, "failed to get mesh info" );
iMOAB_GlobalID* vGlobalID = (iMOAB_GlobalID*)malloc( nverts[2] * sizeof( iMOAB_GlobalID ) );
/*
* All visible vertices have a unique global ID. All arrays are allocated by client.
* Currently, global ID is a 32 bit integer, total number of visible vertices was returned by
* iMOAB_GetMeshInfo
*/
rc = iMOAB_GetVertexID( pid, &nverts[2], vGlobalID );
CHECKRC( rc, "failed to get vertex id info" );
int* vranks = (int*)malloc( nverts[2] * sizeof( int ) );
/*
* In MOAB terminology, a vertex can be owned, shared or ghost. An owned vertex will be
* owned by the current process. A shared vertex appears at the interface between partitions, it
* can be owned by another process, while a ghost vertex is owned by another process always. All
* vertex arrays have a natural local order, in which the ghost vertices are at the end of the
* arrays. The local index of the vertex will vary from 0 to number of visible vertices (in this
* example nverts[2]-1)
*/
rc = iMOAB_GetVertexOwnership( pid, &nverts[2], vranks );
CHECKRC( rc, "failed to get vertex ranks" );
double* coords = (double*)malloc( 3 * nverts[2] * sizeof( double ) );
int size_coords = 3 * nverts[2];
/*
* Coordinates are returned interleaved, for all visible vertices. Size is dimension times
* number of visible vertices
*/
rc = iMOAB_GetVisibleVerticesCoordinates( pid, &size_coords, coords );
CHECKRC( rc, "failed to get coordinates" );
/*
* Block IDs correspond to MATERIAL_SET tag values in hdf5 file
* They also correspond to block IDs in a Cubit model.
* Local visible blocks might contain ghost cells, owned by other
* processes.
* Inside MOAB, a block will correspond to a meshset with a MATERIAL_SET tag,
* with value the block ID.
* A MATERIAL_SET tag in moab if SPARSE and type INTEGER.
*/
iMOAB_GlobalID* gbIDs = (iMOAB_GlobalID*)malloc( nblocks[2] * sizeof( iMOAB_GlobalID ) );
rc = iMOAB_GetBlockID( pid, &nblocks[2], gbIDs );
CHECKRC( rc, "failed to get block info" );
/*
* The 2 tags used in this example exist in the file, already.
* If a user needs a new tag, it can be defined with the same call as this one
* this method, iMOAB_DefineTagStorage, will return a local index for the tag.
* The name of the tag is case sensitive.
* This method is collective.
*/
int tagIndex[2];
int entTypes[2] = { 0, 1 }; /* first is on vertex, second is on elements; */
int tagTypes[2] = { DENSE_INTEGER, DENSE_DOUBLE };
int num_components = 1;
rc = iMOAB_DefineTagStorage( pid, "INTFIELD", &tagTypes[0], &num_components, &tagIndex[0], strlen( "INTFIELD" ) );
CHECKRC( rc, "failed to get tag INTFIELD " );
rc = iMOAB_DefineTagStorage( pid, "DFIELD", &tagTypes[1], &num_components, &tagIndex[1], strlen( "DFIELD" ) );
CHECKRC( rc, "failed to get tag DFIELD " );
// synchronize one of the tags only, just to see what happens
int num_tags_to_sync = 1;
/*
* tags are not exchanged for ghost entities by default. The user has to explicitly
* synchronize them with a call like this one. The tags to synchronize are referenced by the
* index returned at their "definition" with iMOAB_DefineTagStorage method.
*/
rc = iMOAB_SynchronizeTags( pid, &num_tags_to_sync, &tagIndex[0], &tagTypes[0] );
CHECKRC( rc, "failed to sync tag INTFIELD " );
for( int irank = 0; irank < nprocs; irank++ )
{
if( irank == rank )
{
/* printf some of the block info */
printf( "on rank %d, there are \n"
" %3d visible vertices of which %3d local %3d ghost \n"
" %3d visible elements of which %3d owned %3d ghost \n"
" %3d visible blocks\n"
" %3d visible neumann BCs\n"
" %3d visible dirichlet BCs\n",
rank, nverts[2], nverts[0], nverts[1], nelem[2], nelem[0], nelem[1], nblocks[2], nsbc[2], ndbc[2] );
/* printf some of the vertex id infos */
int numToPrint = nverts[2];
printf( "on rank %d vertex info:\n", rank );
for( int i = 0; i < numToPrint; i++ )
printf( " vertex local id: %3d, rank ID:%d global ID: %3d coords: %g, %g, %g\n", i, vranks[i],
vGlobalID[i], coords[3 * i], coords[3 * i + 1], coords[3 * i + 2] );
iMOAB_GlobalID* element_global_IDs = (iMOAB_GlobalID*)malloc( nelem[2] * sizeof( iMOAB_GlobalID ) );
iMOAB_GlobalID* block_IDs = (iMOAB_GlobalID*)malloc( nelem[2] * sizeof( iMOAB_GlobalID ) );
int* ranks = (int*)malloc( nelem[2] * sizeof( int ) );
/*
* visible elements info is available for all visible elements, with this call. Similar
* information can be retrieved by looping over visible blocks
*/
rc = iMOAB_GetVisibleElementsInfo( pid, &nelem[2], element_global_IDs, ranks, block_IDs );
CHECKRC( rc, "failed to get all elem info" );
for( int i = 0; i < nelem[2]; i++ )
printf( " element local id: %3d, global ID: %3d rank:%d block ID: %2d \n", i, element_global_IDs[i],
ranks[i], block_IDs[i] );
free( element_global_IDs );
free( ranks );
free( block_IDs );
// get first element connectivity
int conn[27];
int nv = 27;
int eindex = 0;
/*
* element connectivity can be retrieved for a single element. Local vertex indices are
* returned.
*/
rc = iMOAB_GetElementConnectivity( pid, &eindex, &nv, conn );
CHECKRC( rc, "failed to get first element connectivity" );
printf( " conn for first element: \n" );
for( int i = 0; i < nv; i++ )
printf( " %3d", conn[i] );
printf( "\n" );
// test neighbors
int local_index = 0; // test element with local index 0
int num_adjacent_elements = 10; // we can have maximum 6 actually
iMOAB_LocalID adjacent_element_IDs[10];
/*
* Neighbor elements that share a face with current element can be determined with this
* call Elements are identified by their local index
*/
rc = iMOAB_GetNeighborElements( pid, &local_index, &num_adjacent_elements, adjacent_element_IDs );
CHECKRC( rc, "failed to get first element neighbors" );
printf( " neighbors for first element:\n" );
for( int i = 0; i < num_adjacent_elements; i++ )
{
printf( " %4d", adjacent_element_IDs[i] );
}
printf( "\n" );
for( int i = 0; i < nblocks[2]; i++ )
{
printf( " block index: %3d, block ID: %3d \n", i, gbIDs[i] );
int vertices_per_element, num_elements_in_block;
/*
* blocks should have the same type of primary elements. Number of elements in block
* and number of vertices per element are found with this call. The method refers
* only to the visible elements on the process. The block is identified with its
* block ID. Should it be identified with its local index in the list of visible
* blocks?
*/
rc = iMOAB_GetBlockInfo( pid, &gbIDs[i], &vertices_per_element, &num_elements_in_block );
CHECKRC( rc, "failed to elem block info" );
printf( " has %4d elements with %d vertices per element\n", num_elements_in_block,
vertices_per_element );
int size_conn = num_elements_in_block * vertices_per_element;
iMOAB_LocalID* element_connectivity = (iMOAB_LocalID*)malloc( sizeof( iMOAB_LocalID ) * size_conn );
/*
* Connectivity for all elements in the block can be determined with this method.
* Vertices are identified by their local index (from 0 to number of visible
* vertices -1)
*/
rc = iMOAB_GetBlockElementConnectivities( pid, &gbIDs[i], &size_conn, element_connectivity );
CHECKRC( rc, "failed to get block elem connectivity" );
int* element_ownership = (int*)malloc( sizeof( int ) * num_elements_in_block );
/*
* Each element is owned by a particular process. Ownership can be returned for all
* elements in a block with this call.
*/
rc = iMOAB_GetElementOwnership( pid, &gbIDs[i], &num_elements_in_block, element_ownership );
CHECKRC( rc, "failed to get block elem ownership" );
iMOAB_GlobalID* global_element_ID =
(iMOAB_GlobalID*)malloc( sizeof( iMOAB_GlobalID ) * num_elements_in_block );
iMOAB_LocalID* local_element_ID =
(iMOAB_LocalID*)malloc( sizeof( iMOAB_LocalID ) * num_elements_in_block );
/*
* Global element IDs are determined with this call. Local indices within the
* process are returned too.
*/
rc = iMOAB_GetElementID( pid, &gbIDs[i], &num_elements_in_block, global_element_ID, local_element_ID );
CHECKRC( rc, "failed to get block elem IDs" );
for( int j = 0; j < num_elements_in_block; j++ )
{
printf( " elem %3d owned by %d gid: %4d lid: %4d -- ", j, element_ownership[j],
global_element_ID[j], local_element_ID[j] );
for( int k = 0; k < vertices_per_element; k++ )
printf( " %5d", element_connectivity[j * vertices_per_element + k] );
printf( "\n" );
}
free( global_element_ID );
free( local_element_ID );
free( element_connectivity );
free( element_ownership );
}
/*
* query integer tag values on vertices
* this tag was synchronized (see iMOAB_SynchronizeTags above)
* Being a dense tag, all visible vertices have a value.
* As usual, the client allocates the returned array, which is filled with data with
* this call (deep copy)
*/
int* int_tag_vals = (int*)malloc( sizeof( int ) * nverts[2] ); // for all visible vertices on the rank
rc =
iMOAB_GetIntTagStorage( pid, "INTFIELD", &nverts[2], &entTypes[0], int_tag_vals, strlen( "INTFIELD" ) );
CHECKRC( rc, "failed to get INTFIELD tag" );
printf( "INTFIELD tag values:\n" );
for( int i = 0; i < nverts[2]; i++ )
{
printf( " %4d", int_tag_vals[i] );
if( i % 20 == 19 ) printf( "\n" );
}
printf( "\n" );
free( int_tag_vals );
/*
* query double tag values on elements
* This tag was not synchronized, so ghost elements have a default value of 0.
*/
double* double_tag_vals =
(double*)malloc( sizeof( double ) * nelem[2] ); // for all visible elements on the rank
rc = iMOAB_GetDoubleTagStorage( pid, "DFIELD", &nelem[2], &entTypes[1], double_tag_vals,
strlen( "DFIELD" ) );
CHECKRC( rc, "failed to get DFIELD tag" );
printf( "DFIELD tag values: (not exchanged) \n" );
for( int i = 0; i < nelem[2]; i++ )
{
printf( " %f", double_tag_vals[i] );
if( i % 8 == 7 ) printf( "\n" );
}
printf( "\n" );
free( double_tag_vals );
/* query surface BCs */
iMOAB_LocalID* surfBC_ID = (iMOAB_LocalID*)malloc( sizeof( iMOAB_LocalID ) * nsbc[2] );
int* ref_surf = (int*)malloc( sizeof( int ) * nsbc[2] );
int* bc_value = (int*)malloc( sizeof( int ) * nsbc[2] );
/*
* Surface boundary condition information is returned for all visible Neumann conditions
* the reference surfaces are indexed from 1 to 6 for hexahedrons, 1 to 4 to
* tetrahedrons, in the MOAB canonical ordering convention
*/
rc = iMOAB_GetPointerToSurfaceBC( pid, &nsbc[2], surfBC_ID, ref_surf, bc_value );
CHECKRC( rc, "failed to get surf boundary conditions" );
printf( " Surface boundary conditions:\n" );
for( int i = 0; i < nsbc[2]; i++ )
{
printf( " elem_localID %4d side:%d BC:%2d\n", surfBC_ID[i], ref_surf[i], bc_value[i] );
}
free( surfBC_ID );
free( ref_surf );
free( bc_value );
/* query vertex BCs */
iMOAB_LocalID* vertBC_ID = (iMOAB_LocalID*)malloc( sizeof( iMOAB_LocalID ) * ndbc[2] );
int* vertBC_value = (int*)malloc( sizeof( int ) * ndbc[2] );
rc = iMOAB_GetPointerToVertexBC( pid, &ndbc[2], vertBC_ID, vertBC_value );
CHECKRC( rc, "failed to get vertex boundary conditions" );
printf( " Vertex boundary conditions:\n" );
for( int i = 0; i < ndbc[2]; i++ )
{
printf( " vertex %4d BC:%2d\n", vertBC_ID[i], vertBC_value[i] );
}
free( vertBC_ID );
free( vertBC_value );
}
#ifdef MOAB_HAVE_MPI
MPI_Barrier( comm ); // to avoid printing problems, as we write all procs data
#endif
}
// free allocated data
free( coords );
free( vGlobalID );
free( vranks );
char outputFile[] = "fnew.h5m";
#ifdef MOAB_HAVE_MPI
char writeOptions[] = "PARALLEL=WRITE_PART";
#else
char writeOptions[] = "";
#endif
/*
* the file can be written in parallel, and it will contain additional tags defined by the user
* we may extend the method to write only desired tags to the file
*/
rc = iMOAB_WriteMesh( pid, outputFile, writeOptions, strlen( outputFile ), strlen( writeOptions ) );
/*
* deregistering application will delete all mesh entities associated with the application and
* will free allocated tag storage.
*/
rc = iMOAB_DeregisterApplication( pid );
CHECKRC( rc, "failed to de-register application" );
rc = iMOAB_DeregisterApplication( pidDup );
CHECKRC( rc, "failed to de-register application" );
/*
* this method will delete MOAB instance
*/
rc = iMOAB_Finalize();
CHECKRC( rc, "failed to finalize MOAB" );
#ifdef MOAB_HAVE_MPI
MPI_Finalize();
#endif
return 0;
}
1.7.6.1