October 2010 - moab-dev - mailman3.cels.anl.gov

NAME_TAG_SIZE value?
by Rajeev Jain 11 Nov '10

11 Nov '10

Why is the NAME_TAG_SIZE variable in MBTagConventions.hpp is set to 32? This caused mbsize to fail in Tqdcfr::parse_acis_attribs when I was reading a .cub file. It fails around memcpy step in Tqdcfr:2264. On increasing NAME_TAG_SIZE to 64 the mbsize/mbconvert works. The .cub file is at /homes/jain/MeshKit-acis/rgg/Justin/fc33.cub. I need to make this work, so that mbsize/mbconvert doesn't seg-fault with this .cub file. Rajeev

4 8

r4242 - MOAB/trunk/src/io
by jain＠mcs.anl.gov 26 Oct '10

26 Oct '10

Author: jain Date: 2010-10-26 16:54:15 -0500 (Tue, 26 Oct 2010) New Revision: 4242 Modified: MOAB/trunk/src/io/WriteCCMIO.cpp Log: o Fix bug when writing material names (this is now read in Tqdcfr) to .ccm file. Modified: MOAB/trunk/src/io/WriteCCMIO.cpp =================================================================== --- MOAB/trunk/src/io/WriteCCMIO.cpp 2010-10-26 20:04:04 UTC (rev 4241) +++ MOAB/trunk/src/io/WriteCCMIO.cpp 2010-10-26 21:54:15 UTC (rev 4242) @@ -471,6 +471,10 @@ if (!matset_data[i].setName.empty()){ CCMIONewIndexedEntity(&error, problemID, kCCMIOCellType, matset_data[i].matsetId, matset_data[i].setName.c_str(), &id); + CHKCCMERR(error, "Failure creating celltype node."); + + CCMIOWriteOptstr(&error, id, "MaterialType", matset_data[i].setName.c_str()); + CHKCCMERR(error, "Error assigning material name."); } else{ char dum_name[NAME_TAG_SIZE];

1 0

r4241 - MOAB/trunk/src/moab
by sjackson＠cae.wisc.edu 26 Oct '10

26 Oct '10

Author: sjackson Date: 2010-10-26 15:04:04 -0500 (Tue, 26 Oct 2010) New Revision: 4241 Modified: MOAB/trunk/src/moab/OrientedBoxTreeTool.hpp Log: Fix issue where a TrvStats object used an uninitialized value for count of ray/triangle tests. This bug was asymptomatic in ray_fire_test, but only because I was lucky. Yikes. Modified: MOAB/trunk/src/moab/OrientedBoxTreeTool.hpp =================================================================== --- MOAB/trunk/src/moab/OrientedBoxTreeTool.hpp 2010-10-26 17:20:50 UTC (rev 4240) +++ MOAB/trunk/src/moab/OrientedBoxTreeTool.hpp 2010-10-26 20:04:04 UTC (rev 4241) @@ -160,6 +160,8 @@ //! print the contents of this structure to given stream void print( std::ostream& str ) const ; + TrvStats() : ray_tri_tests_count(0) {} + private: std::vector< unsigned > nodes_visited_count;

1 0

r4240 - MOAB/trunk/tools/mbcoupler
by smithrm＠mcs.anl.gov 26 Oct '10

26 Oct '10

Author: smithrm Date: 2010-10-26 12:20:50 -0500 (Tue, 26 Oct 2010) New Revision: 4240 Modified: MOAB/trunk/tools/mbcoupler/ElemUtil.cpp MOAB/trunk/tools/mbcoupler/ElemUtil.hpp Log: ElemUtil.hpp o Added evaluate_scalar_field and integrate_scalar_field as virtual functions to Element::Map. o Changed Element::Map::set_vertices to a virtual function. ElemUtil.cpp o Removed extraneous code I had added a while ago. Modified: MOAB/trunk/tools/mbcoupler/ElemUtil.cpp =================================================================== --- MOAB/trunk/tools/mbcoupler/ElemUtil.cpp 2010-10-26 14:27:13 UTC (rev 4239) +++ MOAB/trunk/tools/mbcoupler/ElemUtil.cpp 2010-10-26 17:20:50 UTC (rev 4240) @@ -116,55 +116,7 @@ return J *= 0.125; } -/**\brief Shape function for linear tetrahedron */ -class LinearTetMap : public VolMap { - public: - LinearTetMap( const CartVect* corner_coords ) : corners(corner_coords) {} - virtual CartVect center_xi() const; - virtual CartVect evaluate( const CartVect& xi ) const; - virtual Matrix3 jacobian( const CartVect& xi ) const; - private: - const CartVect* corners; - static const double corner_xi[8][3]; -}; -const double LinearTetMap::corner_xi[8][3] = { { -1, -1, -1 }, - { 1, -1, -1 }, - { 0, 1, -1 }, - { 0, 1, -1 }, - { 0, 0, 1 }, - { 0, 0, 1 }, - { 0, 0, 1 }, - { 0, 0, 1 } }; -CartVect LinearTetMap::center_xi() const - { return CartVect(0.0); } - -CartVect LinearTetMap::evaluate( const CartVect& xi ) const -{ - CartVect x(0.0); - for (unsigned i = 0; i < 8; ++i) { - const double N_i = (1 + xi[0]*corner_xi[i][0]) - * (1 + xi[1]*corner_xi[i][1]) - * (1 + xi[2]*corner_xi[i][2]); - - if ((i == 0) || (i == 1)) - x += N_i * corners[i]; - else if (i == 2) - x += N_i * corners[2]; - else - x += N_i * corners[3]; - } - x *= 0.125; - return x; -} - -Matrix3 LinearTetMap::jacobian( const CartVect& xi ) const

1 0

MOAB API cleanup : get_connectivity
by Jason Kraftcheck 25 Oct '10

25 Oct '10

I think that, before the release, we should remove the following functions from MBInterface: virtual ErrorCode get_connectivity(const EntityHandle *entity_handles, const int num_handles, Range &connectivity, bool topological_connectivity = false) const; virtual ErrorCode get_connectivity( const Range& entity_handles, Range &connectivity, bool topological_connectivity = false) const; Both of these are mostly redundant because get_adjacencies can be used for exactly the same thing. The only time they would differ is if the input list contained a mixture of polyhedra and other elements. But in that case, the behavior of get_adjacencies is probably both less confusing and more useful. Further, this function should accept an optional vector in which offsets into the connectivity vector are stored: virtual ErrorCode get_connectivity(const EntityHandle *entity_handles, const int num_handles, std::vector<EntityHandle> &connectivity, bool topological_connectivity = false) const; While the offset vector isn't that important when getting only topological connectivity (verts per ent can be determined from only the type), if the complete node list is requested for higher-order elements then this function isn't so useful without returning an offset list. Alternately, the final optional argument could be removed and the function renamed as 'get_topolgocial_connectivity'. - jason

3 4

r4237 - MOAB/trunk/itaps/imesh
by jvporter＠wisc.edu 22 Oct '10

22 Oct '10

Author: jvporter Date: 2010-10-22 15:28:40 -0500 (Fri, 22 Oct 2010) New Revision: 4237 Modified: MOAB/trunk/itaps/imesh/iMesh_MOAB.cpp Log: The iMesh spec says entities aren't adjacent to themselves, so let's obey that. Modified: MOAB/trunk/itaps/imesh/iMesh_MOAB.cpp =================================================================== --- MOAB/trunk/itaps/imesh/iMesh_MOAB.cpp 2010-10-22 18:53:00 UTC (rev 4236) +++ MOAB/trunk/itaps/imesh/iMesh_MOAB.cpp 2010-10-22 20:28:40 UTC (rev 4237) @@ -643,6 +643,8 @@ if (iBase_VERTEX == entity_type_requested && TYPE_FROM_HANDLE(*entity_iter) != MBPOLYHEDRON) { + if (CN::Dimension(TYPE_FROM_HANDLE(*entity_iter)) == 0) + continue; result = MBI->get_connectivity(*entity_iter, connect, num_connect, false, &conn_storage); if (MB_SUCCESS != result) { if (allocated_array) @@ -666,6 +668,8 @@ num_connect = adj_ents.size(); } else { + if (CN::Dimension(TYPE_FROM_HANDLE(*entity_iter)) == entity_type_requested) + continue; adj_ents.clear(); result = MBI->get_adjacencies( entity_iter, 1, entity_type_requested, false, adj_ents );

1 0

Changing adjacency behavior
by James Porter 22 Oct '10

22 Oct '10

Last month, the ITAPS list discussed[1] how adjacency should work, specifically whether an entity is adjacent to itself. Everyone seemed to agree that an entity is not adjacent to itself and that a call to iMesh_getEntAdj where the source dimension is the same as the target dimension should return an empty list. Currently, MOAB returns an error for vertex-vertex adjacency, and the entity itself for higher dimensions. I have a patch to change the behavior to the expected ITAPS way, but I wanted to make sure no one needed the old way before I got rid of it. If someone does have a use for this, let me know and I'll make it optional. - Jim [1] http://lists.mcs.anl.gov/pipermail/tstt-interface/2010-September/000250.html

2 6

r4236 - in MOAB/trunk: MeshFiles/unittest/io src/io test/io
by kraftche＠cae.wisc.edu 22 Oct '10

22 Oct '10

Author: kraftche Date: 2010-10-22 13:53:00 -0500 (Fri, 22 Oct 2010) New Revision: 4236 Added: MOAB/trunk/MeshFiles/unittest/io/hex_2x2x2_ss.exo Modified: MOAB/trunk/MeshFiles/unittest/io/Makefile.am MOAB/trunk/src/io/ReadNCDF.cpp MOAB/trunk/test/io/exodus_test.cc Log: incorporate fixes from Rao Garimella for exodus files with alternate coordinate format and exodus files w/out elem_map Modified: MOAB/trunk/MeshFiles/unittest/io/Makefile.am =================================================================== --- MOAB/trunk/MeshFiles/unittest/io/Makefile.am 2010-10-22 16:45:02 UTC (rev 4235) +++ MOAB/trunk/MeshFiles/unittest/io/Makefile.am 2010-10-22 18:53:00 UTC (rev 4236) @@ -4,6 +4,7 @@ cubtest12.cub \ cubtest.jou \ gmsh2.msh \ + hex_2x2x2_ss.exo \ ho_test.g \ ho_test.cub \ test.cub \ Added: MOAB/trunk/MeshFiles/unittest/io/hex_2x2x2_ss.exo =================================================================== (Binary files differ) Property changes on: MOAB/trunk/MeshFiles/unittest/io/hex_2x2x2_ss.exo ___________________________________________________________________ Added: svn:mime-type + application/octet-stream Modified: MOAB/trunk/src/io/ReadNCDF.cpp =================================================================== --- MOAB/trunk/src/io/ReadNCDF.cpp 2010-10-22 16:45:02 UTC (rev 4235) +++ MOAB/trunk/src/io/ReadNCDF.cpp 2010-10-22 18:53:00 UTC (rev 4236) @@ -430,7 +430,6 @@ ErrorCode ReadNCDF::read_nodes(const Tag* file_id_tag) { - // read the nodes into memory assert(NULL != ncFile); @@ -446,46 +445,49 @@ vertexOffset = ID_FROM_HANDLE( node_handle ) - MB_START_ID; // read in the coordinates - NcBool status; - NcVar *coords = ncFile->get_var("coord"); - if (NULL == coords || !coords->is_valid()) { - readMeshIface->report_error("ReadNCDF:: Problem getting coords variable."); - return MB_FAILURE; - } - status = coords->get(arrays[0], 1, numberNodes_loading); - if (0 == status) { - readMeshIface->report_error("ReadNCDF:: Problem getting x coord array."); - return MB_FAILURE; - } - status = coords->set_cur(1, 0);

1 0

r4233 - MOAB/trunk
by kraftche＠cae.wisc.edu 22 Oct '10

22 Oct '10

Author: kraftche Date: 2010-10-22 11:13:20 -0500 (Fri, 22 Oct 2010) New Revision: 4233 Modified: MOAB/trunk/configure.ac Log: fix configure bug where we need libtool during configure but it isn't created until end of script for libtool 2.x.x Modified: MOAB/trunk/configure.ac =================================================================== --- MOAB/trunk/configure.ac 2010-10-22 13:02:07 UTC (rev 4232) +++ MOAB/trunk/configure.ac 2010-10-22 16:13:20 UTC (rev 4233) @@ -233,7 +233,16 @@ fi AC_DEFINE_UNQUOTED(MB_VERSION_STRING,"${VERSION_STRING}",[MOAB Version String]) +################################################################################ +# Create libtool script +################################################################################ +# We need the libtool script both for the calls to the ITAPS_LIBTOOL_VAR +# macro and for us in testing for ACIS libraries. If we're using a newer +# version of libtool, the script normally isn't generated until AC_OUTPUT +# at the end of the configure script. Ask that it be created now instead. +m4_ifdef([LT_OUTPUT],[LT_OUTPUT]) + ################################################################################ # Extract libtool config ################################################################################

1 0

r4232 - MOAB/trunk/MeshFiles/unittest/io
by kraftche＠cae.wisc.edu 22 Oct '10

22 Oct '10

Author: kraftche Date: 2010-10-22 08:02:07 -0500 (Fri, 22 Oct 2010) New Revision: 4232 Modified: MOAB/trunk/MeshFiles/unittest/io/Makefile.am Log: fix failing dist-check Modified: MOAB/trunk/MeshFiles/unittest/io/Makefile.am =================================================================== --- MOAB/trunk/MeshFiles/unittest/io/Makefile.am 2010-10-21 03:49:33 UTC (rev 4231) +++ MOAB/trunk/MeshFiles/unittest/io/Makefile.am 2010-10-22 13:02:07 UTC (rev 4232) @@ -1,6 +1,8 @@ EXTRA_DIST = brick_cubit10.1.cub \ brick_cubit10.2.cub \ brick_cubit10.cub \ + cubtest12.cub \ + cubtest.jou \ gmsh2.msh \ ho_test.g \ ho_test.cub \

1 0