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

r5249 - MOAB/trunk/tools/mbcoupler
by tautges＠mcs.anl.gov 08 Dec '11

08 Dec '11

Author: tautges Date: 2011-12-08 16:04:21 -0600 (Thu, 08 Dec 2011) New Revision: 5249 Modified: MOAB/trunk/tools/mbcoupler/ElemUtil.cpp MOAB/trunk/tools/mbcoupler/ElemUtil.hpp Log: Fix a bug with Tet interpolation in the coupler. Modified: MOAB/trunk/tools/mbcoupler/ElemUtil.cpp =================================================================== --- MOAB/trunk/tools/mbcoupler/ElemUtil.cpp 2011-12-08 21:46:42 UTC (rev 5248) +++ MOAB/trunk/tools/mbcoupler/ElemUtil.cpp 2011-12-08 22:04:21 UTC (rev 5249) @@ -565,12 +565,12 @@ void LinearTet::set_vertices(const std::vector<CartVect>& v) { this->Map::set_vertices(v); - this->T = Matrix3(v[1][0]-v[0][0],v[1][0]-v[0][0],v[2][0]-v[0][0], - v[1][1]-v[0][1],v[1][1]-v[0][1],v[2][1]-v[0][1], - v[1][2]-v[0][2],v[1][2]-v[0][2],v[2][2]-v[0][2]); + this->T = Matrix3(v[1][0]-v[0][0],v[2][0]-v[0][0],v[3][0]-v[0][0], + v[1][1]-v[0][1],v[2][1]-v[0][1],v[3][1]-v[0][1], + v[1][2]-v[0][2],v[2][2]-v[0][2],v[3][2]-v[0][2]); this->T_inverse = this->T.inverse(); this->det_T = this->T.determinant(); - this->det_T_inverse = 1.0/this->det_T; + this->det_T_inverse = (0.0 == this->det_T ? HUGE : 1.0/this->det_T); }// LinearTet::set_vertices() Modified: MOAB/trunk/tools/mbcoupler/ElemUtil.hpp =================================================================== --- MOAB/trunk/tools/mbcoupler/ElemUtil.hpp 2011-12-08 21:46:42 UTC (rev 5248) +++ MOAB/trunk/tools/mbcoupler/ElemUtil.hpp 2011-12-08 22:04:21 UTC (rev 5249) @@ -61,7 +61,7 @@ class Map { public: /**\brief Construct a Map defined by the given std::vector of vertices. */ - Map(const std::vector<CartVect>& v) {this->vertex = v;}; + Map(const std::vector<CartVect>& v) {this->vertex.resize(v.size()); this->set_vertices(v);}; /**\brief Construct a Map defined by n vertices. */ Map(const unsigned int n) {this->vertex = std::vector<CartVect>(n);}; /**\brief Evaluate the map on \xi (calculate $\vec x = F($\vec \xi)$ )*/

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What's going on in this test?
by James Porter 08 Dec '11

08 Dec '11

In test/h5file/dump_sets.c, there's an uninitialized variable being used: <http://trac.mcs.anl.gov/projects/ITAPS/browser/MOAB/trunk/test/h5file/dump_…>. Does anyone know what's actually supposed to be happening here? - Jim

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r5248 - MOAB/trunk/test/h5file
by iulian＠mcs.anl.gov 08 Dec '11

08 Dec '11

Author: iulian Date: 2011-12-08 15:46:42 -0600 (Thu, 08 Dec 2011) New Revision: 5248 Modified: MOAB/trunk/test/h5file/dump_sets.c Log: it should be >=10 :) Modified: MOAB/trunk/test/h5file/dump_sets.c =================================================================== --- MOAB/trunk/test/h5file/dump_sets.c 2011-12-08 21:40:21 UTC (rev 5247) +++ MOAB/trunk/test/h5file/dump_sets.c 2011-12-08 21:46:42 UTC (rev 5248) @@ -35,7 +35,7 @@ file = mhdf_openFile( argv[1], 0, &max_id, -1, &status ); CHECK; WIDTH = 1; - while (max_id > 10) { + while (max_id >= 10) { max_id /= 10; ++WIDTH; }

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r5247 - MOAB/trunk/test/h5file
by iulian＠mcs.anl.gov 08 Dec '11

08 Dec '11

Author: iulian Date: 2011-12-08 15:40:21 -0600 (Thu, 08 Dec 2011) New Revision: 5247 Modified: MOAB/trunk/test/h5file/dump_sets.c Log: bug in determining the width for formatting the max_id is determined after the file is opened Modified: MOAB/trunk/test/h5file/dump_sets.c =================================================================== --- MOAB/trunk/test/h5file/dump_sets.c 2011-12-08 20:00:09 UTC (rev 5246) +++ MOAB/trunk/test/h5file/dump_sets.c 2011-12-08 21:40:21 UTC (rev 5247) @@ -32,13 +32,13 @@ return 1; } + file = mhdf_openFile( argv[1], 0, &max_id, -1, &status ); CHECK; + WIDTH = 1; while (max_id > 10) { max_id /= 10; ++WIDTH; } - - file = mhdf_openFile( argv[1], 0, &max_id, -1, &status ); CHECK; dump_sets( file ); mhdf_closeFile( file, &status ); CHECK; return 0;

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r5246 - MOAB/trunk/test
by jvporter＠wisc.edu 08 Dec '11

08 Dec '11

Author: jvporter Date: 2011-12-08 14:00:09 -0600 (Thu, 08 Dec 2011) New Revision: 5246 Modified: MOAB/trunk/test/TagTest.cpp Log: Eliminate some warnings Modified: MOAB/trunk/test/TagTest.cpp =================================================================== --- MOAB/trunk/test/TagTest.cpp 2011-12-08 19:40:25 UTC (rev 5245) +++ MOAB/trunk/test/TagTest.cpp 2011-12-08 20:00:09 UTC (rev 5246) @@ -187,7 +187,7 @@ int bytes; rval = mb.tag_get_bytes( tag, bytes ); CHECK_ERR(rval); - int exp_bytes; + int exp_bytes = 0; switch (type) { case MB_TYPE_INTEGER: exp_bytes = num_vals * sizeof(int); break; case MB_TYPE_DOUBLE: exp_bytes = num_vals * sizeof(double); break; @@ -375,7 +375,7 @@ CHECK_ERR(rval); CHECK( !entities.empty() ); - int bytes; + int bytes = 0; switch (type) { case MB_TYPE_INTEGER: bytes = vals_per_ent*sizeof(int); break; case MB_TYPE_DOUBLE : bytes = vals_per_ent*sizeof(double); break; @@ -1553,7 +1553,7 @@ CHECK_EQUAL( lengths[0], data_len ); CHECK( !memcmp( values[0], data_ptr, data_len ) ); - int typesize; + int typesize = 0; switch (type) { case MB_TYPE_INTEGER: typesize = sizeof(int); break; case MB_TYPE_DOUBLE: typesize = sizeof(double); break;

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r5245 - MOAB/trunk/itaps/imesh
by jvporter＠wisc.edu 08 Dec '11

08 Dec '11

Author: jvporter Date: 2011-12-08 13:40:25 -0600 (Thu, 08 Dec 2011) New Revision: 5245 Modified: MOAB/trunk/itaps/imesh/ScdMeshF90.F90 Log: I forgot to save this file... Modified: MOAB/trunk/itaps/imesh/ScdMeshF90.F90 =================================================================== --- MOAB/trunk/itaps/imesh/ScdMeshF90.F90 2011-12-08 19:23:50 UTC (rev 5244) +++ MOAB/trunk/itaps/imesh/ScdMeshF90.F90 2011-12-08 19:40:25 UTC (rev 5245) @@ -67,7 +67,7 @@ call iMesh_getNumOfType(%VAL(mesh), %VAL(root_set), %VAL(iBase_VERTEX), num_verts, ier); ERROR(ier); call iMesh_initEntArrIter(%VAL(mesh), %VAL(root_set), %VAL(iBase_FACE), %VAL(iMesh_QUADRILATERAL),%VAL(num_quads), & - iter, ier); ERROR(ier); + %VAL(0), iter, ier); ERROR(ier); call iMesh_createTagWithOptions(%VAL(mesh), "XM1", "moab:TAG_STORAGE_TYPE=DENSE; moab:TAG_DEFAULT_VALUE=0.0", & %VAL(5), %VAL(iBase_DOUBLE), tagh, ier); ERROR(ier);

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r5244 - in MOAB/trunk: examples/itaps itaps/imesh
by jvporter＠wisc.edu 08 Dec '11

08 Dec '11

Author: jvporter Date: 2011-12-08 13:23:50 -0600 (Thu, 08 Dec 2011) New Revision: 5244 Modified: MOAB/trunk/examples/itaps/TagIterateC.c MOAB/trunk/examples/itaps/TagIterateF.F MOAB/trunk/itaps/imesh/ScdMeshF77.F MOAB/trunk/itaps/imesh/iMeshP_MOAB.cpp Log: More updates for iMesh spec change (I wish tests worked on this machine...) Modified: MOAB/trunk/examples/itaps/TagIterateC.c =================================================================== --- MOAB/trunk/examples/itaps/TagIterateC.c 2011-12-08 19:03:19 UTC (rev 5243) +++ MOAB/trunk/examples/itaps/TagIterateC.c 2011-12-08 19:23:50 UTC (rev 5244) @@ -40,7 +40,7 @@ CHKERR(err, "Failed to get number of regions."); /* get an iterator to all regions in the model */ - iMesh_initEntArrIter( mesh, root_set, iBase_REGION, iMesh_ALL_TOPOLOGIES, num_regions, &iter, &err ); + iMesh_initEntArrIter( mesh, root_set, iBase_REGION, iMesh_ALL_TOPOLOGIES, num_regions, 0, &iter, &err ); CHKERR(err, "Failed to create iterator over regions."); /* create a tag to put on the regions */ Modified: MOAB/trunk/examples/itaps/TagIterateF.F =================================================================== --- MOAB/trunk/examples/itaps/TagIterateF.F 2011-12-08 19:03:19 UTC (rev 5243) +++ MOAB/trunk/examples/itaps/TagIterateF.F 2011-12-08 19:23:50 UTC (rev 5244) @@ -37,7 +37,7 @@ c get an iterator over regions call iMesh_initEntArrIter(%VAL(mesh), %VAL(root_set), 1 %VAL(iBase_REGION), %VAL(iMesh_ALL_TOPOLOGIES),%VAL(num_regions), - 1 iter, ierr) + 1 %VAL(0), iter, ierr) c create a tag to put on the regions call iMesh_createTagWithOptions(%VAL(mesh), "dumtag", Modified: MOAB/trunk/itaps/imesh/ScdMeshF77.F =================================================================== --- MOAB/trunk/itaps/imesh/ScdMeshF77.F 2011-12-08 19:03:19 UTC (rev 5243) +++ MOAB/trunk/itaps/imesh/ScdMeshF77.F 2011-12-08 19:23:50 UTC (rev 5244) @@ -81,7 +81,7 @@ call iMesh_initEntArrIter(%VAL(mesh), %VAL(root_set), 1 %VAL(iBase_FACE), %VAL(iMesh_QUADRILATERAL),%VAL(num_quads), - 1 iter, ier) + 1 %VAL(0), iter, ier) call iMesh_createTagWithOptions(%VAL(mesh), "XM1", 1 "moab:TAG_STORAGE_TYPE=DENSE; moab:TAG_DEFAULT_VALUE=0.0", Modified: MOAB/trunk/itaps/imesh/iMeshP_MOAB.cpp =================================================================== --- MOAB/trunk/itaps/imesh/iMeshP_MOAB.cpp 2011-12-08 19:03:19 UTC (rev 5243) +++ MOAB/trunk/itaps/imesh/iMeshP_MOAB.cpp 2011-12-08 19:23:50 UTC (rev 5244) @@ -1180,6 +1180,7 @@ requested_entity_type, requested_entity_topology, requested_array_size, + 0, // TODO: update this function for "resilient" arg

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r5243 - MOAB/trunk/itaps/imesh
by jvporter＠wisc.edu 08 Dec '11

08 Dec '11

Author: jvporter Date: 2011-12-08 13:03:19 -0600 (Thu, 08 Dec 2011) New Revision: 5243 Modified: MOAB/trunk/itaps/imesh/MOAB_iMesh_extensions_tests.cpp MOAB/trunk/itaps/imesh/testc_cbind.c Log: Fix tests for new ITAPS spec Modified: MOAB/trunk/itaps/imesh/MOAB_iMesh_extensions_tests.cpp =================================================================== --- MOAB/trunk/itaps/imesh/MOAB_iMesh_extensions_tests.cpp 2011-12-08 18:42:38 UTC (rev 5242) +++ MOAB/trunk/itaps/imesh/MOAB_iMesh_extensions_tests.cpp 2011-12-08 19:03:19 UTC (rev 5243) @@ -51,7 +51,8 @@ iBase_EntityArrIterator iter; int count, atend; double *data; - iMesh_initEntArrIter( mesh, root_set, iBase_ALL_TYPES, iMesh_ALL_TOPOLOGIES, 6, &iter, &err ); + iMesh_initEntArrIter( mesh, root_set, iBase_ALL_TYPES, iMesh_ALL_TOPOLOGIES, + 6, 0, &iter, &err ); CHECK_EQUAL( iBase_SUCCESS, err ); iMesh_tagIterate(mesh, tagh, iter, &data, &count, &err); CHECK_EQUAL( iBase_SUCCESS, err ); @@ -64,7 +65,8 @@ CHECK_EQUAL( iBase_SUCCESS, err ); /* get an iterator over the set with two subranges, and check tag iterator for that */ - iMesh_initEntArrIter( mesh, entset, iBase_ALL_TYPES, iMesh_ALL_TOPOLOGIES, 6, &iter, &err ); + iMesh_initEntArrIter( mesh, entset, iBase_ALL_TYPES, iMesh_ALL_TOPOLOGIES, 6, + 0, &iter, &err ); CHECK_EQUAL( iBase_SUCCESS, err ); iMesh_tagIterate(mesh, tagh, iter, &data, &count, &err); CHECK_EQUAL( iBase_SUCCESS, err ); Modified: MOAB/trunk/itaps/imesh/testc_cbind.c =================================================================== --- MOAB/trunk/itaps/imesh/testc_cbind.c 2011-12-08 18:42:38 UTC (rev 5242) +++ MOAB/trunk/itaps/imesh/testc_cbind.c 2011-12-08 19:03:19 UTC (rev 5243) @@ -2273,7 +2273,7 @@ int i, twice, has_data, result = iBase_SUCCESS, result2; iBase_EntityHandle value; - iMesh_initEntIter( mesh, set, type, topo, &iter, &result ); + iMesh_initEntIter( mesh, set, type, topo, 0, &iter, &result ); if (iBase_SUCCESS != result) { printf("%s:%d: Error %d initializing %s iterator for type %d/topo %d\n", __FILE__,__LINE__,result,info,(int)type,(int)topo); @@ -2354,7 +2354,7 @@ int values_size, values_alloc = array_size; values = (iBase_EntityHandle*)malloc( array_size * sizeof(iBase_EntityHandle) ); - iMesh_initEntArrIter( mesh, set, type, topo, array_size, &iter, &result ); + iMesh_initEntArrIter( mesh, set, type, topo, array_size, 0, &iter, &result ); if (iBase_SUCCESS != result) { printf("%s:%d: Error %d initializing %s array iterator for type %d/topo %d\n", __FILE__,__LINE__,result,info,(int)type,(int)topo);

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Faceting tolerances in OCC
by Steve Jackson 08 Dec '11

08 Dec '11

I am interested in two functions in CGM's OCCQueryEngine: get_graphics( Surface* ... ), and get_graphics( Curve* ... ). Both these functions take faceting tolerances as arguments, and then silently ignore them. This becomes confusing for users who convert CAD geometries to Moab meshes (e.g. using dag-mcnp5, dagmc_preproc, or mbconvert). When OCC is the CGM backend for a client of Moab's ReadCGM, all faceting tolerances are silently ignored. This behavior should be documented, at minimum; it may also be helpful if ReadCGM issues a warning that faceting tolerances are being ignored for an OCC-based backend. The ideal would be a fix to the OCCQueryEngine to support the faceting tolerance parameters. ~S

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r5241 - in MOAB/trunk/itaps: . imesh
by jvporter＠wisc.edu 08 Dec '11

08 Dec '11

Author: jvporter Date: 2011-12-08 12:39:44 -0600 (Thu, 08 Dec 2011) New Revision: 5241 Modified: MOAB/trunk/itaps/iBase.h MOAB/trunk/itaps/imesh/iMesh.h MOAB/trunk/itaps/imesh/iMesh_MOAB.cpp Log: Update spec Modified: MOAB/trunk/itaps/iBase.h =================================================================== --- MOAB/trunk/itaps/iBase.h 2011-12-08 18:37:56 UTC (rev 5240) +++ MOAB/trunk/itaps/iBase.h 2011-12-08 18:39:44 UTC (rev 5241) @@ -9,10 +9,10 @@ * Technically speaking, there is not much practical value in patch digit * for an interface specification. A patch release is typically only used * for bug fix releases. Although it is rare, sometimes a bug fix - * necessitates an API change. So, we define a patch digit for iMesh. + * necessitates an API change. So, we define a patch digit for iBase. * * Although each interface in ITAPS has been designed to support its own - * uniqe version numbers, apart from other ITAPS interfaces, as currently + * unique version numbers, apart from other ITAPS interfaces, as currently * used, we require all ITAPS interfaces to use the same ITAPS-wide version * number derived from the version number defined by these three digits. ******************************************************************************/ @@ -114,7 +114,7 @@ iBase_REGION, /**< A topological dimension 3 entity */ iBase_ALL_TYPES, - /**< used only in queires to request information about all types */ + /**< used only in queries to request information about all types */ iBase_EntityType_MAX = iBase_ALL_TYPES /**< facilitates iteration over all values */ }; @@ -409,6 +409,152 @@ * Note that iMesh itself currently does not define any options. In order * to discover options a given implementation defines, users are directed * to the developers of the respective implementations. + * + * \page resilient Resilient and Non-Resilient Iterators + * + * A resilient iterator is one that can deal with modifications to the container + * it is iterating over. + * + * A common concern about an iterator is how it behaves when the container + * over which it is iterating is modified. For example, in STL, iterators + * for std::set<> and std::map<> and std::list<> containers are guaranteed + * to work in the presence of modifications to the associated + * containers with one exception; they don't handle the case when the + * container member the iterator is currently pointed at is deleted. However, + * iterators for std::vector<> are not guaranteed to work under any kinds of + * modification. + * + * In the ITAPS interfaces, a resilient iterator is one that makes + * certain guarantees (described below) about how it behaves when the + * container being iterated is modified. On the other hand, a + * non-resilient is one that does not make such guarantees. + * + * In all cases, the container associated with an iterator in the

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