July 2011 - moab-dev - mailman3.cels.anl.gov

r5074 - in MOAB/trunk: itaps/imesh src/parallel src/parallel/moab
by hongjun＠mcs.anl.gov 30 Jul '11

30 Jul '11

Author: hongjun Date: 2011-07-30 10:44:04 -0500 (Sat, 30 Jul 2011) New Revision: 5074 Modified: MOAB/trunk/itaps/imesh/MOAB_iMeshP_unit_tests.cpp MOAB/trunk/itaps/imesh/iMeshP_MOAB.cpp MOAB/trunk/src/parallel/ParallelComm.cpp MOAB/trunk/src/parallel/moab/ParallelComm.hpp Log: o "iMeshP::iMeshP_exchEntArrToPartsAll" is implemented o Exchanges entities to assigned parts o command_code and update_ghost options are not supported yet but will be o test code is added in MOAB_iMeshP_unit_tests.cpp o Passes make check Modified: MOAB/trunk/itaps/imesh/MOAB_iMeshP_unit_tests.cpp =================================================================== --- MOAB/trunk/itaps/imesh/MOAB_iMeshP_unit_tests.cpp 2011-07-29 20:08:15 UTC (rev 5073) +++ MOAB/trunk/itaps/imesh/MOAB_iMeshP_unit_tests.cpp 2011-07-30 15:44:04 UTC (rev 5074) @@ -212,6 +212,7 @@ int test_push_tag_data_iface( iMesh_Instance, iMeshP_PartitionHandle prtn, const PartMap& ); int test_push_tag_data_ghost( iMesh_Instance, iMeshP_PartitionHandle prtn, const PartMap& ); +int test_exchange_ents( iMesh_Instance imesh, iMeshP_PartitionHandle prtn, const PartMap& map ); /************************************************************************** Helper Funcions @@ -463,6 +464,7 @@ num_errors += RUN_TEST( test_push_tag_data_iface ); num_errors += RUN_TEST( test_push_tag_data_ghost ); num_errors += RUN_TEST( test_create_ghost_ents ); + num_errors += RUN_TEST( test_exchange_ents ); // wait until all procs are done before writing summary data std::cout.flush(); @@ -2529,6 +2531,63 @@ return iBase_SUCCESS; } +/**\brief Test exchange entities + * + * Test: + * - iMeshP_exchEntArrToPartsAll + */ +int test_exchange_ents( iMesh_Instance imesh, iMeshP_PartitionHandle prtn, const PartMap& map ) +{ + int ierr, rank, size; + int num_err = 0; + iMeshP_RequestHandle request; + MPI_Comm_rank( MPI_COMM_WORLD, &rank ); + MPI_Comm_size( MPI_COMM_WORLD, &size ); + + std::vector<iBase_EntityHandle> all_elems; + std::vector<iMeshP_Part> all_ids; + std::vector<iBase_EntityHandle> quads; + + // get local part handles and part ids + std::vector<iMeshP_PartHandle> local_handles; + std::vector<iMeshP_Part> local_ids; + ierr = get_local_parts( imesh, prtn, local_handles, &local_ids ); + PCHECK; + + // get loacal quads before exchange + quads.clear(); + ierr = get_entities( imesh, local_handles[0], iBase_FACE, iMesh_QUADRILATERAL, quads ); + CHKERR;

1 0

r5073 - MOAB/trunk/tools/mbzoltan
by hongjun＠mcs.anl.gov 29 Jul '11

29 Jul '11

Author: hongjun Date: 2011-07-29 15:08:15 -0500 (Fri, 29 Jul 2011) New Revision: 5073 Modified: MOAB/trunk/tools/mbzoltan/mbpart.cpp Log: o Loose facet tolerance is only applied to geometry partion Modified: MOAB/trunk/tools/mbzoltan/mbpart.cpp =================================================================== --- MOAB/trunk/tools/mbzoltan/mbpart.cpp 2011-07-28 16:23:45 UTC (rev 5072) +++ MOAB/trunk/tools/mbzoltan/mbpart.cpp 2011-07-29 20:08:15 UTC (rev 5073) @@ -138,8 +138,9 @@ std::string output_file = opts.getReqArg<std::string>("output_file"); clock_t t = clock(); - std::string options("FACET_DISTANCE_TOLERANCE=0.1"); - ErrorCode rval = mb.load_file( input_file.c_str(), 0, options.c_str() ); + const char* options = NULL; + if (part_geom) options = "FACET_DISTANCE_TOLERANCE=0.1"; + ErrorCode rval = mb.load_file( input_file.c_str(), 0, options ); if (MB_SUCCESS != rval) { std::cerr << input_file << " : failed to read file." << std::endl; std::cerr << " Error code: " << mb.get_error_string(rval) << " (" << rval << ")" << std::endl;

1 0

r5072 - MOAB/trunk/itaps
by jvporter＠wisc.edu 28 Jul '11

28 Jul '11

Author: jvporter Date: 2011-07-28 11:23:45 -0500 (Thu, 28 Jul 2011) New Revision: 5072 Modified: MOAB/trunk/itaps/iBase.h Log: Update iBase spec Modified: MOAB/trunk/itaps/iBase.h =================================================================== --- MOAB/trunk/itaps/iBase.h 2011-07-25 06:05:56 UTC (rev 5071) +++ MOAB/trunk/itaps/iBase.h 2011-07-28 16:23:45 UTC (rev 5072) @@ -331,6 +331,9 @@ * NOT include the null character and implementations must be coded to * accommodate this. This requirement is primarily due to differences in how * Fortran and C/C++ handle passing of strings as function arguments. + * Furthermore, because of the way Fortran clients pass strings (Fortran always + * passes the length of the string as declared in the source code), there + * may be trailing spaces in the string that need to be truncated. * * \page numhops Indirection in Set-Inclusion and Parent-Child structures *

1 0

r5071 - MOAB/trunk/src
by iulian＠mcs.anl.gov 25 Jul '11

25 Jul '11

Author: iulian Date: 2011-07-25 01:05:56 -0500 (Mon, 25 Jul 2011) New Revision: 5071 Modified: MOAB/trunk/src/GeomTopoTool.cpp Log: get senses filters the results using the model set the entities should belong to. initial filtering was introduced because after extracting with mbconvert, some sense tags values pointing to surfaces not extracted were set to 0. more filters are needed because the gentities could belong to a different model set altogether. Modified: MOAB/trunk/src/GeomTopoTool.cpp =================================================================== --- MOAB/trunk/src/GeomTopoTool.cpp 2011-07-22 21:39:30 UTC (rev 5070) +++ MOAB/trunk/src/GeomTopoTool.cpp 2011-07-25 06:05:56 UTC (rev 5071) @@ -728,16 +728,20 @@ // filter the results with the sets that are in the model at this time // this was introduced because extracting some sets (e.g. neumann set, with mbconvert) // from a model would leave some sense tags not defined correctly + // also, the geom ent set really needs to be part of the current model set unsigned int currentSize =0; - Range & possibleEntities = geomRanges[edim+1]; + for (unsigned int index=0; index<wrt_entities.size(); index++) { EntityHandle wrt_ent=wrt_entities[index]; - if (possibleEntities.find(wrt_ent)!=possibleEntities.end() ) + if (wrt_ent ) { - wrt_entities[currentSize] = wrt_entities[index]; - senses[currentSize] = senses[index]; - currentSize++; + if (mdbImpl->contains_entities(modelSet, &wrt_ent, 1)) + { + wrt_entities[currentSize] = wrt_entities[index]; + senses[currentSize] = senses[index]; + currentSize++; + } } } wrt_entities.resize(currentSize);

1 0

r5070 - MOAB/trunk/src/io/mhdf/src
by kraftche＠cae.wisc.edu 22 Jul '11

22 Jul '11

Author: kraftche Date: 2011-07-22 16:39:30 -0500 (Fri, 22 Jul 2011) New Revision: 5070 Modified: MOAB/trunk/src/io/mhdf/src/file-desc.c Log: fix SEGFAULT reading .h5m file with no tags (never actually happens because MOAB always creates GLOBAL_ID and a few others) Modified: MOAB/trunk/src/io/mhdf/src/file-desc.c =================================================================== --- MOAB/trunk/src/io/mhdf/src/file-desc.c 2011-07-21 19:09:54 UTC (rev 5069) +++ MOAB/trunk/src/io/mhdf/src/file-desc.c 2011-07-22 21:39:30 UTC (rev 5070) @@ -475,7 +475,7 @@ /* get tag list */ tag_names = mhdf_getTagNames( file_handle, &num_tag_names, status ); - if (tag_names == NULL) { + if (mhdf_isError(status)) { free( elem_handles ); free( result ); return NULL;

1 0

r5069 - MOAB/trunk/itaps/imesh
by iulian＠mcs.anl.gov 21 Jul '11

21 Jul '11

Author: iulian Date: 2011-07-21 14:09:54 -0500 (Thu, 21 Jul 2011) New Revision: 5069 Modified: MOAB/trunk/itaps/imesh/MOAB_iMesh_unit_tests.cpp MOAB/trunk/itaps/imesh/Makefile.am Log: define explicitly the path to the mesh files Modified: MOAB/trunk/itaps/imesh/MOAB_iMesh_unit_tests.cpp =================================================================== --- MOAB/trunk/itaps/imesh/MOAB_iMesh_unit_tests.cpp 2011-07-21 17:12:25 UTC (rev 5068) +++ MOAB/trunk/itaps/imesh/MOAB_iMesh_unit_tests.cpp 2011-07-21 19:09:54 UTC (rev 5069) @@ -424,10 +424,9 @@ // open a file with var len tags (sense tags) // they should be filtered out - char test_file[] = "../../MeshFiles/unittest/PB.h5m"; + std::string filename = STRINGIFY(MESHDIR) "/PB.h5m"; - iMesh_load(mesh, root_set, test_file, NULL, &err, strlen( - test_file), 0); + iMesh_load(mesh, root_set, filename.c_str(), NULL, &err, filename.length(), 0); CHECK_EQUAL( iBase_SUCCESS, err ); iBase_EntitySetHandle* contained_set_handles = NULL; Modified: MOAB/trunk/itaps/imesh/Makefile.am =================================================================== --- MOAB/trunk/itaps/imesh/Makefile.am 2011-07-21 17:12:25 UTC (rev 5068) +++ MOAB/trunk/itaps/imesh/Makefile.am 2011-07-21 19:09:54 UTC (rev 5069) @@ -1,13 +1,16 @@ BUILT_SOURCES = iMesh_protos.h iMeshP_protos.h iMesh_extensions_protos.h -AM_CPPFLAGS += -DSRCDIR=$(srcdir) \ +MESHDIR = $(top_srcdir)/MeshFiles/unittest + +AM_CPPFLAGS += -DSRCDIR=$(srcdir) \ + -DMESHDIR=$(MESHDIR) \ -I$(srcdir)/.. \ -I$(top_srcdir)/src \ -I$(top_builddir)/src \ -I$(top_srcdir)/test # stuff for c test program -check_PROGRAMS = testc_cbind MOAB_iMesh_unit_tests +check_PROGRAMS = testc_cbind MOAB_iMesh_unit_tests EXTRA_DIST = brick.vtk quad9.cub libiMesh_la_SOURCES = \

1 0

r5068 - MOAB/trunk/itaps/imesh
by iulian＠mcs.anl.gov 21 Jul '11

21 Jul '11

Author: iulian Date: 2011-07-21 12:12:25 -0500 (Thu, 21 Jul 2011) New Revision: 5068 Modified: MOAB/trunk/itaps/imesh/MOAB_iMesh_unit_tests.cpp MOAB/trunk/itaps/imesh/iMesh_MOAB.cpp Log: variable length tags were slipping through iMesh, so visit could not read files with edge sense tags in it Modified: MOAB/trunk/itaps/imesh/MOAB_iMesh_unit_tests.cpp =================================================================== --- MOAB/trunk/itaps/imesh/MOAB_iMesh_unit_tests.cpp 2011-07-21 16:19:03 UTC (rev 5067) +++ MOAB/trunk/itaps/imesh/MOAB_iMesh_unit_tests.cpp 2011-07-21 17:12:25 UTC (rev 5068) @@ -11,6 +11,7 @@ void test_getEntArrAdj_invalid_size(); void test_getEntArrAdj_none(); void test_existinterface(); +void test_tags_retrieval(); int main( int argc, char* argv[] ) { @@ -21,6 +22,7 @@ REGISTER_TEST( test_getEntArrAdj_invalid_size ); REGISTER_TEST( test_getEntArrAdj_none ); REGISTER_TEST( test_existinterface ); + REGISTER_TEST( test_tags_retrieval ); return RUN_TESTS( argc, argv ); } @@ -409,3 +411,59 @@ delete core; } +void test_tags_retrieval() +{ + iMesh_Instance mesh; + int err; + iMesh_newMesh("", &mesh, &err, 0); + CHECK_EQUAL( iBase_SUCCESS, err ); + + iBase_EntitySetHandle root_set; + iMesh_getRootSet(mesh, &root_set, &err); + CHECK_EQUAL( iBase_SUCCESS, err ); + + // open a file with var len tags (sense tags) + // they should be filtered out + char test_file[] = "../../MeshFiles/unittest/PB.h5m"; + + iMesh_load(mesh, root_set, test_file, NULL, &err, strlen( + test_file), 0); + CHECK_EQUAL( iBase_SUCCESS, err ); + + iBase_EntitySetHandle* contained_set_handles = NULL; + int contained_set_handles_allocated = 0; + int contained_set_handles_size; + // get all entity sets + iMesh_getEntSets(mesh, root_set, 1, + &contained_set_handles, + &contained_set_handles_allocated, + &contained_set_handles_size,

1 0

r5065 - MOAB/trunk/src/io/mhdf/example
by sjackson＠cae.wisc.edu 19 Jul '11

19 Jul '11

Author: sjackson Date: 2011-07-19 12:57:32 -0500 (Tue, 19 Jul 2011) New Revision: 5065 Modified: MOAB/trunk/src/io/mhdf/example/validate.c Log: Remove include of error.h, which is not portable on (at least) OSX. This program seems to compile fine on Linux without the include, but feel free to undo this change if it breaks MOAB on any production system. Modified: MOAB/trunk/src/io/mhdf/example/validate.c =================================================================== --- MOAB/trunk/src/io/mhdf/example/validate.c 2011-07-19 17:50:05 UTC (rev 5064) +++ MOAB/trunk/src/io/mhdf/example/validate.c 2011-07-19 17:57:32 UTC (rev 5065) @@ -3,7 +3,6 @@ #include <stdio.h> #include <string.h> #include <sys/stat.h> -#include <error.h> #include <H5Tpublic.h>

1 0

r5064 - MOAB/trunk/MeshFiles/unittest/iGeom
by iulian＠mcs.anl.gov 19 Jul '11

19 Jul '11

Author: iulian Date: 2011-07-19 12:50:05 -0500 (Tue, 19 Jul 2011) New Revision: 5064 Modified: MOAB/trunk/MeshFiles/unittest/iGeom/shell.h5m Log: correct the test file, it was missing some sense tags Modified: MOAB/trunk/MeshFiles/unittest/iGeom/shell.h5m =================================================================== (Binary files differ)

1 0

r5055 - MOAB/trunk/tools/dagmc
by sjackson＠cae.wisc.edu 13 Jul '11

13 Jul '11

Author: sjackson Date: 2011-07-13 14:53:02 -0500 (Wed, 13 Jul 2011) New Revision: 5055 Modified: MOAB/trunk/tools/dagmc/DagMC.cpp MOAB/trunk/tools/dagmc/DagMC.hpp Log: Allow the DagMC::get_angle function to accept an optional RayHistory, and operate upon its most recent entry if one is available. Modified: MOAB/trunk/tools/dagmc/DagMC.cpp =================================================================== --- MOAB/trunk/tools/dagmc/DagMC.cpp 2011-07-12 21:43:23 UTC (rev 5054) +++ MOAB/trunk/tools/dagmc/DagMC.cpp 2011-07-13 19:53:02 UTC (rev 5055) @@ -1111,15 +1111,24 @@ return MB_SUCCESS; } -ErrorCode DagMC::get_angle(EntityHandle surf, const double in_pt[3], double angle[3] ) +ErrorCode DagMC::get_angle(EntityHandle surf, const double in_pt[3], double angle[3], const RayHistory* history ) { EntityHandle root = rootSets[surf - setOffset]; + ErrorCode rval; std::vector<EntityHandle> facets; - ErrorCode rval = obbTree.closest_to_location( in_pt, root, numericalPrecision, facets ); - assert(MB_SUCCESS == rval); - if (MB_SUCCESS != rval) return rval; - + + // if no history or history empty, use nearby facets + if( !history || (history->prev_facets.size() == 0) ){ + rval = obbTree.closest_to_location( in_pt, root, numericalPrecision, facets ); + assert(MB_SUCCESS == rval); + if (MB_SUCCESS != rval) return rval; + } + // otherwise use most recent facet in history + else{ + facets.push_back( history->prev_facets.back() ); + } + CartVect coords[3], normal(0.0); const EntityHandle *conn; int len; Modified: MOAB/trunk/tools/dagmc/DagMC.hpp =================================================================== --- MOAB/trunk/tools/dagmc/DagMC.hpp 2011-07-12 21:43:23 UTC (rev 5054) +++ MOAB/trunk/tools/dagmc/DagMC.hpp 2011-07-13 19:53:02 UTC (rev 5055) @@ -234,9 +234,12 @@ * @param surf Surface on which to get normal * @param xyz Point on surf * @param angle Set to coordinates of surface normal nearest xyz - * + * @param history Optional ray history from a previous call to ray_fire(). + * If present and non-empty, return the normal + * of the most recently intersected facet, ignoring xyz. */ - ErrorCode get_angle(EntityHandle surf, const double xyz[3], double angle[3] ); + ErrorCode get_angle(EntityHandle surf, const double xyz[3], double angle[3], + const RayHistory* history = NULL );

1 0