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

r4021 - MOAB/trunk/src/io
by jain＠mcs.anl.gov 29 Jun '10

29 Jun '10

Author: jain Date: 2010-06-29 17:01:33 -0500 (Tue, 29 Jun 2010) New Revision: 4021 Modified: MOAB/trunk/src/io/WriteCCMIO.cpp Log: o Appending numeric extension 'i' to Cell Type[i] label "Material" Modified: MOAB/trunk/src/io/WriteCCMIO.cpp =================================================================== --- MOAB/trunk/src/io/WriteCCMIO.cpp 2010-06-29 21:52:12 UTC (rev 4020) +++ MOAB/trunk/src/io/WriteCCMIO.cpp 2010-06-29 22:01:33 UTC (rev 4021) @@ -330,8 +330,8 @@ // to call CCMIOCompress() here to ensure that the file is as small as // possible. Please see the Core API documentation for caveats on its // usage. - CCMIOCompress(&error, const_cast<char*>(filename)); - CHKCCMERR(error, "Error compressing file."); + // CCMIOCompress(&error, const_cast<char*>(filename)); + // CHKCCMERR(error, "Error compressing file."); return MB_SUCCESS; } @@ -468,14 +468,22 @@ // write material types and other info for (unsigned int i = 0; i < matset_data.size(); i++) { - if (!matset_data[i].setName.empty()) + if (!matset_data[i].setName.empty()){ CCMIONewIndexedEntity(&error, problemID, kCCMIOCellType, matset_data[i].matsetId, matset_data[i].setName.c_str(), &id); - else + } + else{ + char dum_name[NAME_TAG_SIZE]; + std::ostringstream os; + std::string mat_name = "Material", temp_str; + os << mat_name << (i+1); + temp_str = os.str(); + strcpy(dum_name,temp_str.c_str()); CCMIONewIndexedEntity(&error, problemID, kCCMIOCellType, matset_data[i].matsetId, - "Material", &id); - CHKCCMERR(error, "Failure creating celltype node."); - + dum_name, &id); + CHKCCMERR(error, "Failure creating celltype node."); + os.str(""); + } rval = write_int_option("MaterialId", matset_data[i].setHandle, mMaterialIdTag, id); CHKERR(rval, "Trouble writing MaterialId option.");

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r4020 - MOAB/trunk/tools/dagmc
by sjackson＠cae.wisc.edu 29 Jun '10

29 Jun '10

Author: sjackson Date: 2010-06-29 16:52:12 -0500 (Tue, 29 Jun 2010) New Revision: 4020 Modified: MOAB/trunk/tools/dagmc/DagMC.cpp MOAB/trunk/tools/dagmc/DagMC.hpp Log: Move DagMC version reporting functions out of DagMC.hpp header file. There was no good reason for these static functions to be inline: they certainly don't need to be fast. Modified: MOAB/trunk/tools/dagmc/DagMC.cpp =================================================================== --- MOAB/trunk/tools/dagmc/DagMC.cpp 2010-06-25 22:41:23 UTC (rev 4019) +++ MOAB/trunk/tools/dagmc/DagMC.cpp 2010-06-29 21:52:12 UTC (rev 4020) @@ -66,6 +66,25 @@ } +float DagMC::version(std::string *version_string) +{ + if (NULL != version_string) + *version_string = std::string("DagMC version ") + std::string(DAGMC_VERSION_STRING); + return DAGMC_VERSION; +} + +unsigned int DagMC::interface_revision() +{ + unsigned int result = 0; + const char* interface_string = DAGMC_INTERFACE_REVISION; + if( strlen(interface_string) >= 5 ){ + // start looking for the revision number after "$Rev: " + result = strtol( interface_string+5, NULL, 10 ); + } + return result; +} + + const bool debug = false; DagMC::DagMC(Interface *mb_impl) : mbImpl(mb_impl), obbTree(mb_impl), have_cgm_geom(false) Modified: MOAB/trunk/tools/dagmc/DagMC.hpp =================================================================== --- MOAB/trunk/tools/dagmc/DagMC.hpp 2010-06-25 22:41:23 UTC (rev 4019) +++ MOAB/trunk/tools/dagmc/DagMC.hpp 2010-06-29 21:52:12 UTC (rev 4020) @@ -7,8 +7,6 @@ #include <vector> #include <string> #include <assert.h> -#include <stdlib.h> -#include <string.h> #include "moab/OrientedBoxTreeTool.hpp" @@ -398,25 +396,6 @@ return instance_; } -inline float DagMC::version(std::string *version_string) -{ - if (NULL != version_string)

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r4019 - MOAB/trunk/src/io
by jain＠mcs.anl.gov 25 Jun '10

25 Jun '10

Author: jain Date: 2010-06-25 17:41:23 -0500 (Fri, 25 Jun 2010) New Revision: 4019 Modified: MOAB/trunk/src/io/WriteCCMIO.cpp Log: o Opening compress again.. o Filtering out the faces with 2 adjacent elements before calling write_external_faces Modified: MOAB/trunk/src/io/WriteCCMIO.cpp =================================================================== --- MOAB/trunk/src/io/WriteCCMIO.cpp 2010-06-25 19:22:48 UTC (rev 4018) +++ MOAB/trunk/src/io/WriteCCMIO.cpp 2010-06-25 22:41:23 UTC (rev 4019) @@ -330,8 +330,8 @@ // to call CCMIOCompress() here to ensure that the file is as small as // possible. Please see the Core API documentation for caveats on its // usage. - // CCMIOCompress(&error, const_cast<char*>(filename)); - // CHKCCMERR(error, "Error compressing file."); + CCMIOCompress(&error, const_cast<char*>(filename)); + CHKCCMERR(error, "Error compressing file."); return MB_SUCCESS; } @@ -968,9 +968,31 @@ // write external faces //================================================ for (unsigned int i = 0; i < neuset_data.size(); i++) { - result = write_external_faces(rootID, topologyID, neuset_data[i].neusetId, - neuset_data[i].elems); + Range::reverse_iterator rit; + unsigned char cmarks[2]; + Range ext_faces; + std::vector<EntityHandle> cells; + // removing the faces connected to two regions + for (rit = neuset_data[i].elems.rbegin(); rit != neuset_data[i].elems.rend(); ++rit) { + cells.clear(); + result = mbImpl->get_adjacencies(&(*rit), 1, mDimension, false, cells); + CHKERR(result, "Trouble getting bounding cells."); + + result = mbImpl->tag_get_data(mEntityMark, &cells[0], cells.size(), cmarks); + CHKERR(result, "Trouble getting mark tags on cells bounding facets."); + + if( cells.size() == 2 && (mWholeMesh || (cmarks[0] && cmarks[1]))) { + } + else{ + // external face + ext_faces.insert(*rit); + } + } + if (ext_faces.size() != 0) + result = write_external_faces(rootID, topologyID, neuset_data[i].neusetId, + ext_faces); CHKERR(result, "Trouble writing Neumann set facets."); + ext_faces.clear (); } if (!skin_facets.empty()) { @@ -1203,10 +1225,6 @@ CCMIONewEntity(&error, rootID, kCCMIOMap, NULL, &mapID);

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r4018 - MOAB/trunk/src/io
by jain＠mcs.anl.gov 25 Jun '10

25 Jun '10

Author: jain Date: 2010-06-25 14:22:48 -0500 (Fri, 25 Jun 2010) New Revision: 4018 Modified: MOAB/trunk/src/io/WriteCCMIO.cpp Log: o Commented CCMIOCompress o Skipping empty neumann sets when writing external faces o Commented the check for internal faces in write_external_faces function, since neumann sets can have internal faces Modified: MOAB/trunk/src/io/WriteCCMIO.cpp =================================================================== --- MOAB/trunk/src/io/WriteCCMIO.cpp 2010-06-24 11:31:05 UTC (rev 4017) +++ MOAB/trunk/src/io/WriteCCMIO.cpp 2010-06-25 19:22:48 UTC (rev 4018) @@ -330,8 +330,8 @@ // to call CCMIOCompress() here to ensure that the file is as small as // possible. Please see the Core API documentation for caveats on its // usage. - CCMIOCompress(&error, const_cast<char*>(filename)); - CHKCCMERR(error, "Error compressing file."); + // CCMIOCompress(&error, const_cast<char*>(filename)); + // CHKCCMERR(error, "Error compressing file."); return MB_SUCCESS; } @@ -1203,6 +1203,10 @@ CCMIONewEntity(&error, rootID, kCCMIOMap, NULL, &mapID); CHKCCMERR(error, "Problem creating face id map."); + // ignoring an empty neuset, just return + if(facets.size()==0) + return MB_SUCCESS; + CCMIOWriteMap(&error, mapID, CCMIOSIZEC(facets.size()), CCMIOSIZEC(maxid), gids, CCMIOINDEXC(kCCMIOStart), CCMIOINDEXC(kCCMIOEnd)); @@ -1254,8 +1258,9 @@ result = mbImpl->tag_get_data(mEntityMark, &cells[0], cells.size(), cmarks); CHKERR(result, "Trouble getting mark tags on cells bounding facets."); if (cells.size() == 2 && (mWholeMesh || (cmarks[0] && cmarks[1]))) { - result = MB_FILE_WRITE_ERROR; - CHKERR(result, "External facet with two output bounding cells."); + // commenting since neuset_data can have internal faces + // result = MB_FILE_WRITE_ERROR; + // CHKERR(result, "External facet with two output bounding cells."); } else if (1 == cells.size() && !mWholeMesh && !cmarks[0]) { result = MB_FILE_WRITE_ERROR;

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r4016 - MOAB/trunk/tools/dagmc
by sjackson＠cae.wisc.edu 24 Jun '10

24 Jun '10

Author: sjackson Date: 2010-06-23 14:44:46 -0500 (Wed, 23 Jun 2010) New Revision: 4016 Modified: MOAB/trunk/tools/dagmc/DagMC.hpp Log: Fix a very old, but recently symptomatic, bug in DagMC. When MOAB is built with CGM, the macro "CGM" is defined. Until now, this caused an extra data member to be included in the DagMC class. However, client code compiling against DagMC does not define the CGM macro (the macro is not exported to moab.make). This means a client compiling against DagMC.hpp can wind up with an incorrect map of the data members in a DagMC object. This hasn't surfaced as a problem before because the conditionally- included data member was declared *after* all other client-facing data members. The reordering of data members in r4006 exposed the problem. The easy solution (which I've taken) is to simply remove the checks from the header file. If CGM is not available, the extra declarations are harmless (and DagMC gets one extra unused std::vector). Moral: Beware of #ifdefs in public headers, particularly if they check for macros that client code may not know about. Modified: MOAB/trunk/tools/dagmc/DagMC.hpp =================================================================== --- MOAB/trunk/tools/dagmc/DagMC.hpp 2010-06-22 18:15:50 UTC (rev 4015) +++ MOAB/trunk/tools/dagmc/DagMC.hpp 2010-06-23 19:44:46 UTC (rev 4016) @@ -12,9 +12,7 @@ #include "moab/OrientedBoxTreeTool.hpp" -#ifdef CGM class RefEntity; -#endif namespace moab { @@ -349,10 +347,8 @@ // entity index (contiguous 1-N indices) indexed like rootSets are std::vector<int> entIndices; -#ifdef CGM // corresponding geometric entities indexed like rootSets are std::vector<RefEntity *> geomEntities; -#endif // metadata Tag matTag, densTag, bcTag, impTag, tallyTag;

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Fwd: MOAB Help
by Tim Tautges 24 Jun '10

24 Jun '10

[Forwarding to moab-dev, could someone help Paul with this? Thanks.] Paul, in the future, please send general help requests like this to moab-dev instead of to me, you'll probably get more timely response. - tim -------- Original Message -------- Subject: MOAB Help Date: Tue, 22 Jun 2010 09:31:02 -0600 From: Stanfield, Paul <pstanfi(a)sandia.gov> To: 'Tim Tautges' <tautges(a)mcs.anl.gov> I was trying to create a tag and I am having some trouble. It doesn't seem to like the inputs I'm giving it. --------------------------------------------------------------------------------------------------------- moab::Core moab; moab::Interface& mb = moab; moab::ErrorCode rval; moab::Tag energy; double def_val = 1.00; double new_val=10.00; rval=mb.tag_create("ENERGY", int(sizeof(double)), MB_TAG_DENSE, MB_TYPE_DOUBLE, energy, &def_val); /*( const char* name, const int size, const TagType storage, const DataType data, Tag& handle, const void* def_val, bool use_existing = false ) = 0; */ KDMain.C(66): error: no instance of overloaded function "moab::Interface::tag_create" matches the argument list argument types are: (const char [7], int, TagType, DataType, moab::Tag, double *) object type is: moab::Interface rval=mb.tag_create("ENERGY", int(sizeof(double)), MB_TAG_DENSE, MB_TYPE_DOUBLE, energy, &def_val); --------------------------------------------------------------------------------------------------------- I was trying to follow the format of the example given in the manual: --------------------------------------------------------------------------------------------------------- // load a file using MOAB and get the vertices MBErrorCode rval = moab->load_file("fname.vtk"); MBRange verts; rval = moab->get_entities_by_dimension(file_set, 0, verts); // create a tag called "TEMPERATURE" MBTag temperature; double def_val = -1.0d-300, new_val = 273.0; rval = moab->tag_create("TEMPERATURE", sizeof(double), MB_TAG_DENSE, MB_TYPE_DOUBLE, temperature, &def_val); // assign a value to vertices for (MBRange::iterator vit = verts.begin(); vit != verts.end(); vit++) rval = moab->tag_set_data(temperature, &(*rit), 1, &new_val); ---------------------------------------------------------------------------------------------------------

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r4017 - MOAB/trunk/tools/dagmc
by wilsonp＠engr.wisc.edu 24 Jun '10

24 Jun '10

Author: wilsonp Date: 2010-06-24 06:31:05 -0500 (Thu, 24 Jun 2010) New Revision: 4017 Modified: MOAB/trunk/tools/dagmc/DagMC.cpp MOAB/trunk/tools/dagmc/DagMC.hpp Log: Add support for Tripoli4 v7. Primary changes are to provide more access to metadata and/or support different metadata. A method was added to get all the metadata for a volume, but this probably needs to be replaced by a more generic lightweight access to tags across the DAGMC interface. Added support for "composition" definitions that are different from MCNP materials: cubit group "comp_COMPNAME" (Note: the implicit complement is assigned a material with "comp_COMPNAME_comp".) Added support for testing whether a specific surface has a specular or white reflecting boundary condition and whether a specific volume is part of the graveyard. Changed the order of the definition of discard_ and add_ tolerance so that the add_tolerance can be defined as 100*discard_tolerance as default. Modified: MOAB/trunk/tools/dagmc/DagMC.cpp =================================================================== --- MOAB/trunk/tools/dagmc/DagMC.cpp 2010-06-23 19:44:46 UTC (rev 4016) +++ MOAB/trunk/tools/dagmc/DagMC.cpp 2010-06-24 11:31:05 UTC (rev 4017) @@ -34,19 +34,23 @@ #endif #define MB_OBB_TREE_TAG_NAME "OBB_TREE" +#define FACETING_TOL_TAG_NAME "FACETING_TOL" #define CATEGORY_TAG_LENGTH 32 +#define COMP_NAME_TAG_LENGTH 64 #define MAT_GROUP 0 #define BC_SPEC 1 #define BC_WHITE 2 #define IMP_ZERO 3 #define TALLY_GROUP 4 +#define COMP_GROUP 5 #define MATERIAL_TAG_NAME "DAGMC_MATERIAL_ID" #define DENSITY_TAG_NAME "DAGMC_MATERIAL_DENSITY" #define BC_TAG_NAME "DAGMC_BOUNDARY_CONDITION" #define IMP_TAG_NAME "DAGMC_IMPORTANCE" #define TALLY_TAG_NAME "DAGMC_TALLY" +#define COMP_TAG_NAME "DAGMC_COMPOSITION" #define MBI moab_instance() @@ -93,6 +97,8 @@ geomTag = get_tag( GEOM_DIMENSION_TAG_NAME, sizeof(int), MB_TAG_DENSE, MB_TYPE_INTEGER ); obbTag = get_tag( MB_OBB_TREE_TAG_NAME, sizeof(EntityHandle), MB_TAG_DENSE, MB_TYPE_HANDLE ); + + facetingTolTag = get_tag(FACETING_TOL_TAG_NAME, sizeof(double), MB_TAG_SPARSE, MB_TYPE_DOUBLE ); // get sense of surfaces wrt volumes senseTag = get_tag( "GEOM_SENSE_2", 2*sizeof(EntityHandle), MB_TAG_DENSE, MB_TYPE_HANDLE ); @@ -101,6 +107,7 @@ const void *def_matid = &matid; matTag = get_tag(MATERIAL_TAG_NAME, sizeof(int), MB_TAG_DENSE, MB_TYPE_INTEGER, def_matid ); densTag = get_tag(DENSITY_TAG_NAME, sizeof(double), MB_TAG_DENSE, MB_TYPE_DOUBLE ); + compTag = get_tag(COMP_TAG_NAME, COMP_NAME_TAG_LENGTH, MB_TAG_SPARSE, MB_TYPE_OPAQUE ); bcTag = get_tag(BC_TAG_NAME, sizeof(int), MB_TAG_SPARSE, MB_TYPE_INTEGER); double imp_one = 1; @@ -119,6 +126,8 @@ const double facet_tolerance) { ErrorCode rval; + + std::cout << "Requested faceting tolerance: " << facet_tolerance << std::endl;

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test
by Tim Tautges 24 Jun '10

24 Jun '10

just testing, please disregard. -- ================================================================ "You will keep in perfect peace him whose mind is steadfast, because he trusts in you." Isaiah 26:3 Tim Tautges Argonne National Laboratory (tautges(a)mcs.anl.gov) (telecommuting from UW-Madison) phone: (608) 263-8485 1500 Engineering Dr. fax: (608) 263-4499 Madison, WI 53706

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r4015 - MOAB/trunk/tools/dagmc
by sjackson＠cae.wisc.edu 22 Jun '10

22 Jun '10

Author: sjackson Date: 2010-06-22 13:15:50 -0500 (Tue, 22 Jun 2010) New Revision: 4015 Modified: MOAB/trunk/tools/dagmc/DagMC.hpp MOAB/trunk/tools/dagmc/ray_fire_test.cc Log: Fix DagMC's broken interface_revision() function Modified: MOAB/trunk/tools/dagmc/DagMC.hpp =================================================================== --- MOAB/trunk/tools/dagmc/DagMC.hpp 2010-06-21 20:48:31 UTC (rev 4014) +++ MOAB/trunk/tools/dagmc/DagMC.hpp 2010-06-22 18:15:50 UTC (rev 4015) @@ -7,7 +7,8 @@ #include <vector> #include <string> #include <assert.h> -#include <stdio.h> +#include <stdlib.h> +#include <string.h> #include "moab/OrientedBoxTreeTool.hpp" @@ -31,7 +32,7 @@ ~DagMC(); /** Return the version of this library */ - float version(std::string *version_string = NULL); /* PPHW: should this be static? */ + static float version(std::string *version_string = NULL); /** Get subversion revision of this file (DagMC.hpp) */ static unsigned int interface_revision(); @@ -395,7 +396,11 @@ inline unsigned int DagMC::interface_revision() { unsigned int result = 0; - sscanf( DAGMC_INTERFACE_REVISION, "$Rev$\n", &result ); + const char* interface_string = DAGMC_INTERFACE_REVISION; + if( strlen(interface_string) >= 5 ){ + // start looking for the revision number after "$Rev: " + result = strtol( interface_string+5, NULL, 10 ); + } return result; } Modified: MOAB/trunk/tools/dagmc/ray_fire_test.cc =================================================================== --- MOAB/trunk/tools/dagmc/ray_fire_test.cc 2010-06-21 20:48:31 UTC (rev 4014) +++ MOAB/trunk/tools/dagmc/ray_fire_test.cc 2010-06-22 18:15:50 UTC (rev 4015) @@ -233,6 +233,9 @@ } } + std::cout << "DagMC Version: " << DagMC::version() + << ", svn revision: " << DagMC::interface_revision() << std::endl; + if( !filename ){ usage("No filename specified", 0, argv[0] ); }

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r4014 - in MOAB/trunk: src src/moab tools/dagmc
by sjackson＠cae.wisc.edu 21 Jun '10

21 Jun '10

Author: sjackson Date: 2010-06-21 15:48:31 -0500 (Mon, 21 Jun 2010) New Revision: 4014 Modified: MOAB/trunk/src/OrientedBoxTreeTool.cpp MOAB/trunk/src/moab/OrientedBoxTreeTool.hpp MOAB/trunk/tools/dagmc/ray_fire_test.cc Log: As part of OBBTree traversal statistics, count the number of ray- triangle intersection tests that are performed within the OrientedBoxTreeTool. Also record this data from DagMC's ray_fire_test. Modified: MOAB/trunk/src/OrientedBoxTreeTool.cpp =================================================================== --- MOAB/trunk/src/OrientedBoxTreeTool.cpp 2010-06-21 15:55:57 UTC (rev 4013) +++ MOAB/trunk/src/OrientedBoxTreeTool.cpp 2010-06-21 20:48:31 UTC (rev 4014) @@ -676,6 +676,7 @@ const double tol; Range& boxes; + public: RayIntersector( OrientedBoxTreeTool* tool_ptr, const double* ray_point, @@ -713,7 +714,8 @@ double tolerance, const double ray_point[3], const double unit_ray_dir[3], - const double* ray_length ) + const double* ray_length, + unsigned int* raytri_test_count ) { ErrorCode rval; intersection_distances_out.clear(); @@ -761,6 +763,8 @@ if (MB_SUCCESS != rval) return rval; + if( raytri_test_count ) *raytri_test_count += 1; + double td; if (GeomUtil::ray_tri_intersect( coords, point, dir, tolerance, td, ray_length )) intersection_distances_out.push_back(td); @@ -786,7 +790,9 @@ if (MB_SUCCESS != rval) return rval; - return ray_intersect_triangles( intersection_distances_out, boxes, tolerance, ray_point, unit_ray_dir, ray_length ); + return ray_intersect_triangles( intersection_distances_out, boxes, + tolerance, ray_point, unit_ray_dir, ray_length, + accum ? &(accum->ray_tri_tests_count) : NULL ); } ErrorCode OrientedBoxTreeTool::ray_intersect_boxes( @@ -837,6 +843,7 @@ std::vector<double>& intersections; std::vector<EntityHandle>& sets; std::vector<EntityHandle>& facets; + unsigned int* raytri_test_count; EntityHandle lastSet; int lastSetDepth; @@ -852,12 +859,13 @@

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