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

r5042 - MOAB/trunk/tools/vtkMOABReader
by iulian＠mcs.anl.gov 30 Jun '11

30 Jun '11

Author: iulian Date: 2011-06-30 17:31:50 -0500 (Thu, 30 Jun 2011) New Revision: 5042 Modified: MOAB/trunk/tools/vtkMOABReader/vtkMOABReader.cxx Log: with this change, loading the file MOAB/MeshFiles/unittest/3k-tri-cube.h5m will not result in an abort of paraview. This file has a set of geom dimension -1, which is probably wrong. Modified: MOAB/trunk/tools/vtkMOABReader/vtkMOABReader.cxx =================================================================== --- MOAB/trunk/tools/vtkMOABReader/vtkMOABReader.cxx 2011-06-29 21:30:53 UTC (rev 5041) +++ MOAB/trunk/tools/vtkMOABReader/vtkMOABReader.cxx 2011-06-30 22:31:50 UTC (rev 5042) @@ -1217,11 +1217,11 @@ // geom id static const char *lnames[] = {"Vertex", "Curve", "Surface", "Volume"}; - if (gidTag) { + if (gdimTag) { int gdim; rval = mbImpl->tag_get_data(gdimTag, &eset, 1, &gdim); - if (MB_SUCCESS == rval) { - assert(0 <= gdim && gdim <= 3); + if (MB_SUCCESS == rval && (0 <= gdim && gdim <= 3) ) { + //assert(0 <= gdim && gdim <= 3); os << lnames[gdim] << id << '\0'; cat_name = os.str(); return MB_SUCCESS;

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r5040 - in MOAB/trunk: . tools/vtkMOABReader
by tautges＠mcs.anl.gov 29 Jun '11

29 Jun '11

Author: tautges Date: 2011-06-29 13:43:25 -0500 (Wed, 29 Jun 2011) New Revision: 5040 Added: MOAB/trunk/tools/vtkMOABReader/CMakeLists.txt.in Modified: MOAB/trunk/configure.ac MOAB/trunk/tools/vtkMOABReader/README Log: Changing paraview plugin build process to execute from the build directory, not the source directory. Modified: MOAB/trunk/configure.ac =================================================================== --- MOAB/trunk/configure.ac 2011-06-27 21:38:09 UTC (rev 5039) +++ MOAB/trunk/configure.ac 2011-06-29 18:43:25 UTC (rev 5040) @@ -1139,6 +1139,7 @@ tools/qvdual/Makefile tools/vtkMOABReader/Makefile tools/dagmc/Makefile + tools/vtkMOABReader/CMakeLists.txt doc/Makefile doc/user.dox examples/Makefile Added: MOAB/trunk/tools/vtkMOABReader/CMakeLists.txt.in =================================================================== --- MOAB/trunk/tools/vtkMOABReader/CMakeLists.txt.in (rev 0) +++ MOAB/trunk/tools/vtkMOABReader/CMakeLists.txt.in 2011-06-29 18:43:25 UTC (rev 5040) @@ -0,0 +1,13 @@ +SET(MOAB_DIR "@abs_builddir@/../.." CACHE PATH "MOAB base directory") +if (MOAB_DIR) + INCLUDE_DIRECTORIES(${MOAB_DIR}/include @srcdir@) + LINK_DIRECTORIES(${MOAB_DIR}/lib) + LINK_LIBRARIES(MOAB) +CMAKE_MINIMUM_REQUIRED(VERSION 2.6.3) +FIND_PACKAGE(ParaView REQUIRED) +INCLUDE(${PARAVIEW_USE_FILE}) + ADD_PARAVIEW_PLUGIN(vtkMOABReader "4.0" + SERVER_MANAGER_XML @srcdir@/vtkMOABReader.xml + SERVER_MANAGER_SOURCES @srcdir@/vtkMOABReader.cxx + GUI_RESOURCE_FILES @srcdir@/vtkMOABReaderGUI.xml) +endif (MOAB_DIR) Modified: MOAB/trunk/tools/vtkMOABReader/README =================================================================== --- MOAB/trunk/tools/vtkMOABReader/README 2011-06-27 21:38:09 UTC (rev 5039) +++ MOAB/trunk/tools/vtkMOABReader/README 2011-06-29 18:43:25 UTC (rev 5040) @@ -2,18 +2,19 @@ - build your version of MOAB; YOU MUST ENABLE SHARED LIBS IN MOAB, since running a paraview plugin requires a shared lib and some of MOAB's dependencies (e.g. hdf5) should be the same ones used by Paraview. (Note, I haven't tested this, but maybe you can get away with building MOAB static but the plugin shared) +- install MOAB (needed so the cmake-based build can file MOAB's header files and libs) - download and build Paraview from www.paraview.org; for my build, I turn on python (PARAVIEW_ENABLE_PYTHON=ON), point hdf5 to the same one used with MOAB (HDF5_INCLUDE_DIR=/usr/include, HDF5_LIBRARY=/usr/lib/libhdf5.so), and the rest of the settings the default ones. -- In this directory, run 'ccmake .'; point MOAB_DIR to the MOAB install location, and ParaView_DIR to - THE PARAVIEW BUILD DIRECTORY (NOT the ParaView source directory); specifically, this is - the directory containing the ParaViewConfig.cmake file. Configure, then generate. +- In the <build_dir>/tools/vtkMOABReader directory, run 'ccmake .'; point MOAB_DIR to the MOAB install + location, and ParaView_DIR to THE PARAVIEW BUILD DIRECTORY (NOT the ParaView source directory); + specifically, this is the directory containing the ParaViewConfig.cmake file. Configure, then generate. - run make; this should compile a 'libvtkMOABReader.so' shared library file, which serves

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(no subject)
by lk58p＠udcf.gla.ac.uk 28 Jun '11

28 Jun '11

On 28 Jun 2011, at 14:56, Iulian Grindeanu wrote: ----- Original Message ----- Hello, I modelling crack propagation where some entities are created and removed. I work with parallel meshes and have problem how to clean remove ents and resolve shared entities. When I remove entity I get error, Reason: Entity should be shared but isn't. Tri 62: Adjacencies: Vertex 56, Vertex 48, Vertex 102 Edge 103, Edge 101, Edge 104 Tet 361 Can you advise me how to solve this problem? I am not sure I understand your problem. If entities are in a set, you should remove them from the set, before deleting the entities. If this is too hard, when you create the set you should use the MESHSET_TRACK_OWNER flag. In that case, removing from the set is managed automatically when you delete the entity (this takes more memory, and it is not turned on by default). Do you create sets? I am not sure about the sharing part, but I think that you would need to manage that yourself; the distribution/sharing is resolved at the beginning; Still, what is the scenario? Best Regards, Iulian Thanks Iulian, I have problem with sharing part. To make it work I had to create pcomm for meshset after entities were removed. Now I have to solve problem how to write parallel file and force moab to use new pcomm (f.e. index 1 instead 0). Regards, Lukasz ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program.

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delete entities & shared data
by lk58p＠udcf.gla.ac.uk 28 Jun '11

28 Jun '11

Hello, I modelling crack propagation where some entities are created and removed. I work with parallel meshes and have problem how to clean remove ents and resolve shared entities. When I remove entity I get error, Reason: Entity should be shared but isn't. Tri 62: Adjacencies: Vertex 56, Vertex 48, Vertex 102 Edge 103, Edge 101, Edge 104 Tet 361 Can you advise me how to solve this problem? Regards, Lukasz Kaczmarczyk web: http://people.civil.gla.ac.uk/~kaczmarczyk ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program.

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r5039 - in MOAB/trunk: examples src src/moab
by iulian＠mcs.anl.gov 27 Jun '11

27 Jun '11

Author: iulian Date: 2011-06-27 16:38:09 -0500 (Mon, 27 Jun 2011) New Revision: 5039 Modified: MOAB/trunk/examples/README.FileReader MOAB/trunk/src/FBEngine.cpp MOAB/trunk/src/SmoothCurve.cpp MOAB/trunk/src/SmoothCurve.hpp MOAB/trunk/src/moab/FBEngine.hpp Log: in order to support variable mesh size along an edge, tangents at points are needed, for Newton-Raphson iteration. The iteration finds a parameter u at which the current edge size is close to the target (variable) mesh size at that point. So, expose the tangent for smooth edges. Modified: MOAB/trunk/examples/README.FileReader =================================================================== --- MOAB/trunk/examples/README.FileReader 2011-06-24 22:37:53 UTC (rev 5038) +++ MOAB/trunk/examples/README.FileReader 2011-06-27 21:38:09 UTC (rev 5039) @@ -2,13 +2,11 @@ Reading a mesh often involves importing large sets of data, for example coordinates of all the nodes in the mesh. Normally, this process would involve reading data from the file into a temporary data buffer, then copying data from there into its destination in MOAB. To avoid the expense of copying data, MOAB has implemented a reader/writer interface that provides direct access to blocks of memory used to represent mesh. The reader interface, declared in MBReadUtilIface, is used to request blocks of memory for storing coordinate positions and element connectivity. The pointers returned from these functions point to the actual memory used to represent those data in MOAB. Once data is written to that memory, no further copying is done. This not only saves time, but it also eliminates the need to allocate a large memory buffer for intermediate storage of these data. -In this example, Triangle output files are read into MOAB. The database is saved into a file specified by the user, extension decides the type of the file. +In this example, Triangle output files are read into MOAB. The database is saved into a file specified by the user, as the second argument usage -fread <triangle_file_base> <output_file> +FileRead <triangle_file_base> <output_file> example provided -$> fread A.1 out.vtk +$> FileRead A.1 out.vtk -It is assumed that the <>.node file and <>.ele files are existing. - - +It is assumed that the <>.node file and <>.ele files are existing. Modified: MOAB/trunk/src/FBEngine.cpp =================================================================== --- MOAB/trunk/src/FBEngine.cpp 2011-06-24 22:37:53 UTC (rev 5038) +++ MOAB/trunk/src/FBEngine.cpp 2011-06-27 21:38:09 UTC (rev 5039) @@ -1051,6 +1051,21 @@ smoothCurve -> position_from_u(u, x, y, z); return MB_SUCCESS; } + +ErrorCode FBEngine::getEntTgntU( EntityHandle edge, + double u, + double& i, double& j, double& k ) +{ + SmoothCurve * smoothCurve = _edges[edge];// this is a map + // now, call smoothCurve methods + double tg[3]; + double x, y, z; + smoothCurve -> position_from_u(u, x, y, z, tg); + i = tg[0]; + j = tg[1]; + k = tg[2]; + return MB_SUCCESS; +} ErrorCode FBEngine::isEntAdj(EntityHandle entity1, EntityHandle entity2, bool& adjacent_out) { Modified: MOAB/trunk/src/SmoothCurve.cpp

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r5038 - MOAB/trunk/tools/mbzoltan
by hongjun＠mcs.anl.gov 24 Jun '11

24 Jun '11

Author: hongjun Date: 2011-06-24 17:37:53 -0500 (Fri, 24 Jun 2011) New Revision: 5038 Modified: MOAB/trunk/tools/mbzoltan/mbpart.cpp Log: o GeometryQueryTool::import(export)_solid_model" functions are changed to CubitCompat functions o Passes make check Modified: MOAB/trunk/tools/mbzoltan/mbpart.cpp =================================================================== --- MOAB/trunk/tools/mbzoltan/mbpart.cpp 2011-06-24 22:36:43 UTC (rev 5037) +++ MOAB/trunk/tools/mbzoltan/mbpart.cpp 2011-06-24 22:37:53 UTC (rev 5038) @@ -5,6 +5,7 @@ #ifdef CGM #include "InitCGMA.hpp" +#include "CubitCompat.hpp" #endif #include <iostream> @@ -270,8 +271,7 @@ int junk; DLIList<RefEntity*> ref_entity_list; - CubitStatus status = GeometryQueryTool::instance()-> - export_solid_model(ref_entity_list, + CubitStatus status = CubitCompat_export_solid_model(ref_entity_list, tmp_output_file.str().c_str(), file_type, junk, CubitString(__FILE__));

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r5035 - MOAB/trunk/itaps/imesh
by jvporter＠wisc.edu 24 Jun '11

24 Jun '11

Author: jvporter Date: 2011-06-24 14:11:03 -0500 (Fri, 24 Jun 2011) New Revision: 5035 Modified: MOAB/trunk/itaps/imesh/iMesh.h MOAB/trunk/itaps/imesh/iMesh_MOAB.cpp Log: Update to use latest revision of iMesh.h and make a stub for iMesh_optimize Modified: MOAB/trunk/itaps/imesh/iMesh.h =================================================================== --- MOAB/trunk/itaps/imesh/iMesh.h 2011-06-23 15:59:08 UTC (rev 5034) +++ MOAB/trunk/itaps/imesh/iMesh.h 2011-06-24 19:11:03 UTC (rev 5035) @@ -263,10 +263,9 @@ * \brief Set geometric dimension of vertex coordinates * * Set the geometric dimension of the mesh. Note: An application - * should not expect this function to succeed unless the mesh database - * is empty (no vertices created, no files read, etc.) - * - * \pre iMesh instance must be <em>empty</em>; no vertex entities + * should not expect this function to succeed unless the mesh instance + * is empty. An empty mesh instance is any mesh instance in which there are + * no vertex entities. ******************************************************************************/ void iMesh_setGeometricDimension( @@ -416,24 +415,36 @@ /***************************************************************************//** * \ingroup MeshModification - * \brief Check if entity handles have changed since last reset or instance - * construction + * \brief Permit implementation to 'optimize' the mesh instance * - * Return whether entity handles have changed since last reset or since - * instance construction. If non-zero value is returned, it is not - * guaranteed that a handle from before the last call to this function - * represents the same entity as the same handle value does now. If - * doReset is non-zero, resets the starting point for this function. + * Its concievable that after a series of operations modifying the mesh + * instance, the implementation's internal representation of the mesh may + * include data and tie up memory resources that could be 'optimized' away. + * For example, if the implementation only marks removed entities for deletion + * but does not actually free up memory resources associated those entities, + * a call to this function gives the implementation the 'ok' to go ahead and + * free up such memory. + * + * Depending on the implementation as well as the amount and kind of changes + * to the mesh that have been made prior to calling it, this call may be + * very expensive in time complexity. On the other hand, it is also perfectly + * acceptable that an implementation basically treat this operation as a no-op. + * + * In any event, any entity, entity set, iterator or tag handle obtained prior + * to calling this method will may be invalidated as a result of this call. In + * that case, the caller must re-acquire handles after making this call. A + * return argument indicates if handles have been invalidated. ******************************************************************************/ -void iMesh_areEHValid(

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r5034 - MOAB/trunk/src
by kraftche＠cae.wisc.edu 23 Jun '11

23 Jun '11

Author: kraftche Date: 2011-06-23 10:59:08 -0500 (Thu, 23 Jun 2011) New Revision: 5034 Modified: MOAB/trunk/src/moab_mpe.h Log: deleted one too many lines in previous commit Modified: MOAB/trunk/src/moab_mpe.h =================================================================== --- MOAB/trunk/src/moab_mpe.h 2011-06-23 15:57:16 UTC (rev 5033) +++ MOAB/trunk/src/moab_mpe.h 2011-06-23 15:59:08 UTC (rev 5034) @@ -1,4 +1,5 @@ #ifndef MOAB_MPE_H +#define MOAB_MPE_H #ifdef USE_MPE # include "moab_mpi.h"

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r5033 - in MOAB/trunk/src: . io
by kraftche＠cae.wisc.edu 23 Jun '11

23 Jun '11

Author: kraftche Date: 2011-06-23 10:57:16 -0500 (Thu, 23 Jun 2011) New Revision: 5033 Removed: MOAB/trunk/src/moab_mpe.c Modified: MOAB/trunk/src/Makefile.am MOAB/trunk/src/io/ReadHDF5Dataset.cpp MOAB/trunk/src/moab_mpe.h Log: Remove MOAB's MPE_Allocate_event: MPE already provides MPE_Log_get_event_nubmer to do the same thing Modified: MOAB/trunk/src/Makefile.am =================================================================== --- MOAB/trunk/src/Makefile.am 2011-06-21 21:12:14 UTC (rev 5032) +++ MOAB/trunk/src/Makefile.am 2011-06-23 15:57:16 UTC (rev 5033) @@ -131,8 +131,7 @@ VertexSequence.cpp \ WriteUtil.cpp \ WriteUtil.hpp \ - moab_mpe.h \ - moab_mpe.c + moab_mpe.h # The list of header files which are to be installed nobase_libMOAB_la_include_HEADERS = \ Modified: MOAB/trunk/src/io/ReadHDF5Dataset.cpp =================================================================== --- MOAB/trunk/src/io/ReadHDF5Dataset.cpp 2011-06-21 21:12:14 UTC (rev 5032) +++ MOAB/trunk/src/io/ReadHDF5Dataset.cpp 2011-06-23 15:57:16 UTC (rev 5033) @@ -38,8 +38,8 @@ static std::pair<int,int> allocate_mpe_state( const char* name, const char* color ) { std::pair<int,int> result; - result.first = MPE_Allocate_event(); - result.second = MPE_Allocate_event(); + result.first = MPE_Log_get_event_number(); + result.second = MPE_Log_get_event_number(); MPE_Describe_state( result.first, result.second, name, color ); return result; } Deleted: MOAB/trunk/src/moab_mpe.c =================================================================== --- MOAB/trunk/src/moab_mpe.c 2011-06-21 21:12:14 UTC (rev 5032) +++ MOAB/trunk/src/moab_mpe.c 2011-06-23 15:57:16 UTC (rev 5033) @@ -1,7 +0,0 @@ -#include "moab_mpe.h" - -int MPE_Allocate_event() -{ - static int counter = MOAB_MPE_FIRST_EVENT; - return counter++; -} Modified: MOAB/trunk/src/moab_mpe.h =================================================================== --- MOAB/trunk/src/moab_mpe.h 2011-06-21 21:12:14 UTC (rev 5032) +++ MOAB/trunk/src/moab_mpe.h 2011-06-23 15:57:16 UTC (rev 5033) @@ -1,17 +1,5 @@ #ifndef MOAB_MPE_H -#define MOAB_MPE_H

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r5025 - in MOAB/trunk/src: . moab
by iulian＠mcs.anl.gov 21 Jun '11

21 Jun '11

Author: iulian Date: 2011-06-21 00:18:44 -0500 (Tue, 21 Jun 2011) New Revision: 5025 Modified: MOAB/trunk/src/FBEngine.cpp MOAB/trunk/src/moab/FBEngine.hpp Log: set unique neumann tags for all faces, after volume creation used mostly to extract faces with mbconvert later Modified: MOAB/trunk/src/FBEngine.cpp =================================================================== --- MOAB/trunk/src/FBEngine.cpp 2011-06-20 17:22:00 UTC (rev 5024) +++ MOAB/trunk/src/FBEngine.cpp 2011-06-21 05:18:44 UTC (rev 5025) @@ -2847,6 +2847,9 @@ MBERRORR(rval, "can't set lateral face sense to the volume"); } + rval = set_default_neumann_tags(); + MBERRORR(rval, "can't set new neumann tags"); + return MB_SUCCESS; } @@ -3133,6 +3136,34 @@ // return MB_SUCCESS; } +// this will be used during creation of the volume, to set unique +// tags on all surfaces +// it is changing original tags, so do not use it if you want to preserve +// initial neumann tags +ErrorCode FBEngine::set_default_neumann_tags() +{ + // these are for debugging purposes only + // check the initial tag, then + Tag ntag; + ErrorCode rval = _mbImpl->tag_get_handle(NEUMANN_SET_TAG_NAME, 1, MB_TYPE_INTEGER, ntag); + MBERRORR(rval, "can't get tag handle"); + // get all surfaces in the model now + Range sets[4]; + rval = _my_geomTopoTool->find_geomsets(sets); + MBERRORR(rval, "can't get geo sets"); + int nfaces = (int)sets[2].size(); + int * vals = new int [nfaces]; + for (int i=0; i<nfaces; i++) + { + vals[i] = i+1; + } + rval = _mbImpl->tag_set_data(ntag, sets[2], (void*)vals); + MBERRORR(rval, "can't set tag values for neumann sets"); + + delete [] vals; + + return MB_SUCCESS; +} } // namespace moab Modified: MOAB/trunk/src/moab/FBEngine.hpp

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