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

question about OBB
by Iulian Grindeanu 02 May '11

02 May '11

Hello, I have a question about OBB; When we use it in geom topo tool, the default constructor is called for obb: GeomTopoTool::GeomTopoTool(Interface *impl, bool find_geoments) : mdbImpl(impl), sense2Tag(0), senseNEntsTag(0), senseNSensesTag(0), geomTag(0), gidTag(0), obbTree(impl), contiguous(true), oneVolRootSet(0) This means that the obb sets are not deleted, even after GeomTopoTool is deleted. The third argument is by default false, (OrientedBoxTreeTool( Interface* i, const char* tag_name = 0, bool destroy_created_trees = false )) (if we would use obbTree(impl, 0, true), the OBB sets will be deleted when GeomTopoTool is deleted) Or is there another way to "clean" after the OBB? I am not quite sure about the lifecycle of OBB / and its sets Thanks, Iulian

3 7

r4785 - MOAB/trunk/itaps/imesh
by jvporter＠wisc.edu 28 Apr '11

28 Apr '11

Author: jvporter Date: 2011-04-28 18:15:21 -0500 (Thu, 28 Apr 2011) New Revision: 4785 Modified: MOAB/trunk/itaps/imesh/iMesh_MOAB.cpp Log: Fix some error handling in iMesh_createEnt (note that this doesn't fix any failures in the unit tests) Modified: MOAB/trunk/itaps/imesh/iMesh_MOAB.cpp =================================================================== --- MOAB/trunk/itaps/imesh/iMesh_MOAB.cpp 2011-04-28 22:47:22 UTC (rev 4784) +++ MOAB/trunk/itaps/imesh/iMesh_MOAB.cpp 2011-04-28 23:15:21 UTC (rev 4785) @@ -1991,19 +1991,23 @@ CONST_HANDLE_ARRAY_PTR(lower_order_entity_handles), lower_order_entity_handles_size, tmp_ent); - if (MB_SUCCESS != result) - *status = iBase_CREATION_FAILED; - else - *status = iBase_SUCCESS; - *new_entity_handle = reinterpret_cast<iBase_EntityHandle>(tmp_ent); + if (MB_SUCCESS == result) { + *new_entity_handle = reinterpret_cast<iBase_EntityHandle>(tmp_ent); + *status = iBase_NEW; - *err = *status; + if (MBIMESHI->AdjTable[5] || MBIMESHI->AdjTable[10]) { + Range set_ents; + set_ents.insert( tmp_ent ); + create_int_ents(MBIMESHI, set_ents); + } - if (MB_SUCCESS == result && (MBIMESHI->AdjTable[5] || MBIMESHI->AdjTable[10])) { - Range set_ents; - set_ents.insert( tmp_ent ); - create_int_ents(MBIMESHI, set_ents); + RETURN(iBase_SUCCESS); } + else { + *new_entity_handle = 0; + *status = iBase_CREATION_FAILED; + ERROR(result, "iMesh_createEnt: couldn't create entity"); + } } void iMesh_deleteEnt(iMesh_Instance instance,

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r4784 - MOAB/trunk/itaps/imesh
by jvporter＠wisc.edu 28 Apr '11

28 Apr '11

Author: jvporter Date: 2011-04-28 17:47:22 -0500 (Thu, 28 Apr 2011) New Revision: 4784 Modified: MOAB/trunk/itaps/imesh/iMesh.h Log: Update iMesh.h to most recent ITAPS version Modified: MOAB/trunk/itaps/imesh/iMesh.h =================================================================== --- MOAB/trunk/itaps/imesh/iMesh.h 2011-04-28 17:04:52 UTC (rev 4783) +++ MOAB/trunk/itaps/imesh/iMesh.h 2011-04-28 22:47:22 UTC (rev 4784) @@ -4,10 +4,14 @@ /* iMesh Interface Specification Major Release Number */ #define IMESH_VERSION_MAJOR 1 +/* maintain backward compatibility with old name for this symbol */ +#define IMESH_MAJOR_VERSION IMESH_VERSION_MAJOR /* iMesh Interface Specification Minor Release Number */ #define IMESH_VERSION_MINOR 3 +/* maintain backward compatibility with old name for this symbol */ +#define IMESH_MINOR_VERSION IMESH_VERSION_MINOR /* iMesh Interface Specification Patch Release Number * @@ -20,6 +24,8 @@ * digit for iMesh. */ #define IMESH_VERSION_PATCH 0 +/* maintain backward compatibility with old name for this symbol */ +#define IMESH_PATCH_VERSION IMESH_VERSION_PATCH /** \mainpage The ITAPS Mesh Interface iMesh * @@ -320,8 +326,9 @@ /**\brief Get the error type returned from the last iMesh function * - * Get the error type returned from the last iMesh function. Value - * returned is a member of the iBase_ErrorType enumeration. + * Get the error type returned from the last iMesh function among those + * that return an 'int *err' argument. The value returned is a member of + * the iBase_ErrorType enumeration. * \param instance iMesh instance handle * \param *error_type Error type returned from last iMesh function */ @@ -331,6 +338,7 @@ /**\brief Get a description of the error returned from the last iMesh function * * Get a description of the error returned from the last iMesh function + * among those that return an 'int *err' argument. * \param instance iMesh instance handle * \param descr Pointer to a character string to be filled with a * description of the error from the last iMesh function

1 0

r4783 - MOAB/trunk/itaps/igeom
by iulian＠mcs.anl.gov 28 Apr '11

28 Apr '11

Author: iulian Date: 2011-04-28 12:04:52 -0500 (Thu, 28 Apr 2011) New Revision: 4783 Modified: MOAB/trunk/itaps/igeom/iGeom.h MOAB/trunk/itaps/igeom/iGeom_MOAB.cpp MOAB/trunk/itaps/igeom/testSmooth.cc MOAB/trunk/itaps/igeom/testgeom.cc Log: align iGeom.h from MOAB with the one from CGM (r4778) (note: this is not built by default) Modified: MOAB/trunk/itaps/igeom/iGeom.h =================================================================== --- MOAB/trunk/itaps/igeom/iGeom.h 2011-04-28 16:53:43 UTC (rev 4782) +++ MOAB/trunk/itaps/igeom/iGeom.h 2011-04-28 17:04:52 UTC (rev 4783) @@ -75,12 +75,10 @@ * \param instance iGeom instance handle * \param descr Pointer to a character string to be filled with a * description of the error from the last iGeom function - * \param *err Pointer to error type returned from function * \param descr_len Length of the character string pointed to by descr */ void iGeom_getDescription( iGeom_Instance instance, char* descr, - int* err, int descr_len ); /**\brief Get the error type returned from the last iGeom function @@ -89,11 +87,9 @@ * returned is a member of the iBase_ErrorType enumeration. * \param instance iGeom instance handle * \param *error_type Error type returned from last iGeom function - * \param *err Pointer to error type returned from function */ void iGeom_getErrorType( iGeom_Instance instance, - /*out*/ int *error_type, - int *err ); + /*out*/ int *error_type ); /**\brief Construct a new iGeom instance * Modified: MOAB/trunk/itaps/igeom/iGeom_MOAB.cpp =================================================================== --- MOAB/trunk/itaps/igeom/iGeom_MOAB.cpp 2011-04-28 16:53:43 UTC (rev 4782) +++ MOAB/trunk/itaps/igeom/iGeom_MOAB.cpp 2011-04-28 17:04:52 UTC (rev 4783) @@ -226,20 +226,20 @@ return true; } -void iGeom_getDescription(iGeom_Instance instance, char* descr, int* err, +void iGeom_getDescription(iGeom_Instance instance, char* descr, int descr_len) { unsigned int len = MIN(strlen(iGeom_LAST_ERROR.description), ((unsigned int) descr_len)); strncpy(descr, iGeom_LAST_ERROR.description, len); descr[len] = '\0'; - RETURN(iBase_SUCCESS); + return; }

1 0

r4781 - in MOAB/trunk: itaps/imesh src src/io src/parallel src/parallel/moab tools/refiner
by tautges＠mcs.anl.gov 27 Apr '11

27 Apr '11

Author: tautges Date: 2011-04-27 19:36:18 -0500 (Wed, 27 Apr 2011) New Revision: 4781 Modified: MOAB/trunk/itaps/imesh/iMesh_MOAB.cpp MOAB/trunk/src/BSPTreePoly.cpp MOAB/trunk/src/Core.cpp MOAB/trunk/src/DualTool.cpp MOAB/trunk/src/Matrix3.hpp MOAB/trunk/src/io/WriteHDF5.cpp MOAB/trunk/src/parallel/ParallelMergeMesh.cpp MOAB/trunk/src/parallel/WriteHDF5Parallel.cpp MOAB/trunk/src/parallel/WriteHDF5Parallel.hpp MOAB/trunk/src/parallel/moab/ProcConfig.hpp MOAB/trunk/tools/refiner/RefinerTagManager.cpp MOAB/trunk/tools/refiner/test_mesh_refiner.cpp Log: - remove use of USE_MPI from public API headers, so that MOAB applications aren't required to define this; in most cases, this won't force any changes in applications, except for those including ParallelComm.hpp or ProcConfig.hpp, which will have to be compiled with an mpi-enabled compiler or with -I options that allow them to resolve mpi.h. - adding an error check to Interface::load_file, where if a non-NULL entity set pointer is passed in as the set handle pointer should point to a valid entity set - adding various checks for error conditions indicated from a static analysis of MOAB code from LLNL - fixed a few bugs in the refiner that were preventing that test from passing the unit test Passes make check in parallel and serial. Modified: MOAB/trunk/itaps/imesh/iMesh_MOAB.cpp =================================================================== --- MOAB/trunk/itaps/imesh/iMesh_MOAB.cpp 2011-04-26 22:45:44 UTC (rev 4780) +++ MOAB/trunk/itaps/imesh/iMesh_MOAB.cpp 2011-04-28 00:36:18 UTC (rev 4781) @@ -1464,6 +1464,9 @@ /*out*/ int* status_size, int *err) { // for now, throw an error if lower order entity handles aren't vertices + if (iMesh_POINT > new_entity_topology || iMesh_SEPTAHEDRON < new_entity_topology) { + ERROR(iBase_INVALID_ARGUMENT, "iMesh_createEntArr: invalid topology."); + } EntityType this_type = mb_topology_table[new_entity_topology]; int num_ents = 0, num_verts; const EntityHandle *lower_ents; Modified: MOAB/trunk/src/BSPTreePoly.cpp =================================================================== --- MOAB/trunk/src/BSPTreePoly.cpp 2011-04-26 22:45:44 UTC (rev 4780) +++ MOAB/trunk/src/BSPTreePoly.cpp 2011-04-28 00:36:18 UTC (rev 4781) @@ -668,6 +668,7 @@ co_edge = co_edge->nextPtr; } while (co_edge && co_edge != face->usePtr); } + if (!edge_ptr) return false; // Constuct new face and first CoEdge faceList = new Face( faceList ); Modified: MOAB/trunk/src/Core.cpp =================================================================== --- MOAB/trunk/src/Core.cpp 2011-04-26 22:45:44 UTC (rev 4780) +++ MOAB/trunk/src/Core.cpp 2011-04-28 00:36:18 UTC (rev 4781) @@ -459,6 +459,12 @@ ErrorCode rval; ReaderIface::IDTag t = { set_tag_name, set_tag_vals, num_set_tag_vals }; ReaderIface::SubsetList sl = { &t, 1, 0, 0 }; + + assert(!file_set || (*file_set && is_valid(*file_set))); + if (file_set && !*file_set) { + mError->set_last_error( "Non-NULL file set pointer should point to non-NULL set.\n" ); + return MB_FAILURE; + } // if reading in parallel, call a different reader std::string parallel_opt; Modified: MOAB/trunk/src/DualTool.cpp =================================================================== --- MOAB/trunk/src/DualTool.cpp 2011-04-26 22:45:44 UTC (rev 4780) +++ MOAB/trunk/src/DualTool.cpp 2011-04-28 00:36:18 UTC (rev 4781) @@ -1946,6 +1946,7 @@

1 0

r4777 - MOAB/trunk/itaps/imesh
by jvporter＠wisc.edu 26 Apr '11

26 Apr '11

Author: jvporter Date: 2011-04-26 17:43:09 -0500 (Tue, 26 Apr 2011) New Revision: 4777 Modified: MOAB/trunk/itaps/imesh/iMesh.h MOAB/trunk/itaps/imesh/iMesh_MOAB.cpp Log: Update iMesh.h to be in sync with ITAPS repo Modified: MOAB/trunk/itaps/imesh/iMesh.h =================================================================== --- MOAB/trunk/itaps/imesh/iMesh.h 2011-04-26 18:57:10 UTC (rev 4776) +++ MOAB/trunk/itaps/imesh/iMesh.h 2011-04-26 22:43:09 UTC (rev 4777) @@ -1,25 +1,25 @@ #ifndef _ITAPS_iMesh #define _ITAPS_iMesh - /**\brief iMesh Interface Specification Major Release Number + /* iMesh Interface Specification Major Release Number */ -#define IMESH_MAJOR_VERSION 1 +#define IMESH_VERSION_MAJOR 1 - /**\brief iMesh Interface Specification Minor Release Number + /* iMesh Interface Specification Minor Release Number */ -#define IMESH_MINOR_VERSION 1 +#define IMESH_VERSION_MINOR 3 - /**\brief iMesh Interface Specification Patch Release Number + /* iMesh Interface Specification Patch Release Number * * Technically speaking, there is not much practical value in * a 'patch' digit for an interface specification. A 'patch' * release is typically only used for bug fix releases. That * is unlikely to apply to an interface specification such as - * iMesh. Nonetheless, there is non-technical value in having - * a bit finer grained control over version numbers that a patch - * digit affords. So, we define one for iMesh. + * iMesh. On the other hand, there are indeed ways of interpreting + * some interface changes as bug fixes. So, we define a patch + * digit for iMesh. */ -#define IMESH_PATCH_VERSION 0 +#define IMESH_VERSION_PATCH 0 /** \mainpage The ITAPS Mesh Interface iMesh * @@ -30,9 +30,9 @@ * to this interface, for example mesh smoothing, adaptive mesh refinement, * and parallel mesh support. * - * \section ITAPS Data Model + * \section iMesh Data Model * - * The ITAPS interfaces use a data model composed of four basic data types: \n + * The iMesh interface use a data model composed of four basic data types: \n * \em Entity: basic topological entities in a mesh, e.g. vertices, * triangles, hexahedra. \n * \em Entity \em Set: arbitrary grouping of other entities and sets.

1 0

r4776 - MOAB/trunk/doc
by tautges＠mcs.anl.gov 26 Apr '11

26 Apr '11

Author: tautges Date: 2011-04-26 13:57:10 -0500 (Tue, 26 Apr 2011) New Revision: 4776 Modified: MOAB/trunk/doc/metadata_info.doc Log: Additions documenting tags for climate data. Modified: MOAB/trunk/doc/metadata_info.doc =================================================================== (Binary files differ)

1 0

A PDE example with MOAB.
by Vijay S. Mahadevan 25 Apr '11

25 Apr '11

All, I was wondering whether there is a simple example on the usage of MOAB or iMesh for solving a PDE. This could be as trivial as a finite differenced, 1-d poisson equation but I just wanted to have a look at a working example in action in order to extend the ideas to more practical problems. I could not find any such tutorial in the MOAB repository and so thought that maybe someone in the list can point me to one. Also, if there is a different forum for such questions, I would appreciate it if you can redirect me to it. Thanks, Vijay

3 12

buildbot failure in moab-par: failed test
by moab-dev＠mcs.anl.gov 23 Apr '11

23 Apr '11

2 1

r4774 - MOAB/trunk/test
by iulian＠mcs.anl.gov 23 Apr '11

23 Apr '11

Author: iulian Date: 2011-04-23 00:15:17 -0500 (Sat, 23 Apr 2011) New Revision: 4774 Modified: MOAB/trunk/test/mbfacet_test.cpp Log: the latest and greatest test introduced fails on a 64-bit desktop need to investigate more, it is not ready for prime time comment it out for the time being :( This line, and those below, will be ignored-- M mbfacet_test.cpp Modified: MOAB/trunk/test/mbfacet_test.cpp =================================================================== --- MOAB/trunk/test/mbfacet_test.cpp 2011-04-23 05:04:45 UTC (rev 4773) +++ MOAB/trunk/test/mbfacet_test.cpp 2011-04-23 05:15:17 UTC (rev 4774) @@ -147,7 +147,7 @@ // split_test_across std::cout << " split across test: "; - rval = split_test_across(); + //rval = split_test_across(); handle_error_code(rval, number_tests_failed, number_tests_successful); std::cout << "\n";

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