March 2014 - moab-dev - mailman3.cels.anl.gov

commit/MOAB: danwu: Fix merge conflicts in .gitignore
by commits-noreply＠bitbucket.org 13 Mar '14

13 Mar '14

1 new commit in MOAB: https://bitbucket.org/fathomteam/moab/commits/2e44578b75a6/ Changeset: 2e44578b75a6 Branch: error_handling_enhancement User: danwu Date: 2014-03-13 22:08:46 Summary: Fix merge conflicts in .gitignore Affected #: 1 file diff --git a/.gitignore b/.gitignore index 41d33aa..94df472 100644 --- a/.gitignore +++ b/.gitignore @@ -58,9 +58,6 @@ examples/SetsNTags examples/SkinMesh examples/structuredmesh examples/StructuredMeshSimple -examples/SurfArea -examples/TestErrorHandling -examples/TestErrorHandlingPar examples/TestExodusII history??.jou hpctoolkit-* Repository URL: https://bitbucket.org/fathomteam/moab/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/MOAB: danwu: Adding and deleting a few ignore items.
by commits-noreply＠bitbucket.org 13 Mar '14

13 Mar '14

1 new commit in MOAB: https://bitbucket.org/fathomteam/moab/commits/b93d30421f6c/ Changeset: b93d30421f6c Branch: master User: danwu Date: 2014-03-13 21:55:20 Summary: Adding and deleting a few ignore items. Affected #: 1 file diff --git a/.gitignore b/.gitignore index eb99939..c80a80a 100644 --- a/.gitignore +++ b/.gitignore @@ -31,14 +31,13 @@ doc/config.tex doc/dev.dox doc/user/* doc/user.dox +examples/CrystalRouterExample examples/DeformMeshRemap examples/DirectAccessNoHoles examples/DirectAccessNoHolesF90 examples/DirectAccessWithHoles examples/examples.make examples/freem.mod -examples/FileRead -examples/GeomSetHierarchy examples/GetEntities examples/*.h5m examples/HelloMOAB @@ -48,17 +47,14 @@ examples/itaps/ListSetsNTagsCXX examples/itaps/ListSetsNTagsF90 examples/itaps/TagIterateC examples/itaps/TagIterateF -examples/KDTree examples/LloydRelaxation -examples/ObbTree +examples/LoadPartial examples/point_in_elem_search examples/PushParMeshIntoMoabF90 examples/ReduceExchangeTags examples/SetsNTags -examples/SkinMesh examples/structuredmesh examples/StructuredMeshSimple -examples/SurfArea examples/TestExodusII history??.jou hpctoolkit-* Repository URL: https://bitbucket.org/fathomteam/moab/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/MOAB: danwu: Updated macro-based error handling interface.
by commits-noreply＠bitbucket.org 13 Mar '14

13 Mar '14

1 new commit in MOAB: https://bitbucket.org/fathomteam/moab/commits/fcc05cd64a00/ Changeset: fcc05cd64a00 Branch: error_handling_enhancement User: danwu Date: 2014-03-13 21:13:08 Summary: Updated macro-based error handling interface. Affected #: 1 file diff --git a/src/moab/ErrorHandler.hpp b/src/moab/ErrorHandler.hpp index 42c1758..2adc868 100644 --- a/src/moab/ErrorHandler.hpp +++ b/src/moab/ErrorHandler.hpp @@ -120,121 +120,186 @@ ErrorCode MBError(int line, const char* func, const char* file, const char* dir, #endif #ifdef USE_ERROR_INFO_CLASS +//! Set a new error with passed error code and passed error message string #define SET_ERR(err_code, err_msg) \ return MBError(__LINE__, __func__, __FILENAME__, __SDIR__, ErrorInfo(err_code, err_msg), MB_ERROR_TYPE_NEW_LOCAL) -#define SET_ERR1(err_info) \ - return MBError(__LINE__, __func__, __FILENAME__, __SDIR__, err_info, MB_ERROR_TYPE_NEW_LOCAL) - +//! Set a new error with passed error code and passed error message string stream #define SET_ERR_STR(err_code, err_msg_str) \ - ErrorInfo err_info; \ - err_info << err_msg_str; \ - return MBError(__LINE__, __func__, __FILENAME__, __SDIR__, err_info, MB_ERROR_TYPE_NEW_LOCAL) + do { \ + ErrorInfo err_info(err_code); \ + err_info << err_msg_str; \ + return MBError(__LINE__, __func__, __FILENAME__, __SDIR__, err_info, MB_ERROR_TYPE_NEW_LOCAL); \ + } while (false) +//! Set a new global error with passed error code and passed error message string #define SET_GLB_ERR(err_code, err_msg) \ return MBError(__LINE__, __func__, __FILENAME__, __SDIR__, ErrorInfo(err_code, err_msg), MB_ERROR_TYPE_NEW_GLOBAL) -#define SET_GLB_ERR1(err_info) \ - return MBError(__LINE__, __func__, __FILENAME__, __SDIR__, err_info, MB_ERROR_TYPE_NEW_GLOBAL) - +//! Set a new global error with passed error code and passed error message string stream #define SET_GLB_ERR_STR(err_code, err_msg_str) \ - ErrorInfo err_info; \ - err_info << err_msg_str; \ - return MBError(__LINE__, __func__, __FILENAME__, __SDIR__, err_info, MB_ERROR_TYPE_NEW_GLOBAL) + do { \ + ErrorInfo err_info(err_code); \ + err_info << err_msg_str; \ + return MBError(__LINE__, __func__, __FILENAME__, __SDIR__, err_info, MB_ERROR_TYPE_NEW_GLOBAL); \ + } while (false) +//! Check returned error code against MB_SUCCESS #define CHK_ERR(err_info) \ do { \ if (MB_SUCCESS != err_info) \ return MBError(__LINE__, __func__, __FILENAME__, __SDIR__, err_info, MB_ERROR_TYPE_EXISTING); \ } while (false) +//! Check returned error code against MB_SUCCESS +//! Set a new error with the returned error code and passed error message string #define CHK_ERR1(err_info, err_msg_to_set) \ do { \ if (MB_SUCCESS != err_info) { \ - err_info.set_error_msg(err_msg_to_set); \ - SET_ERR(err_info); \ + ErrorCode err_code = err_info.get_error_code(); \ + SET_ERR(err_code, err_msg_to_set); \ } \ } while (false) -#define CHK_ERR2(err_info, err_code_to_set, err_msg_to_set) \ +//! Check returned error code against MB_SUCCESS +//! Set a new error with the returned error code and passed error message string stream +#define CHK_ERR1_STR(err_info, err_msg_str_to_set) \ do { \ if (MB_SUCCESS != err_info) { \ - err_info.set_error_code(err_code_to_set); \ - err_info.set_error_msg(err_msg_to_set); \ - SET_ERR(err_info); \ + ErrorCode err_code = err_info.get_error_code(); \ + SET_ERR_STR(err_code, err_msg_str_to_set); \ } \ } while (false) +//! Check returned error code against MB_SUCCESS +//! Set a new error with passed error code and passed error message string +#define CHK_ERR2(err_info, err_code_to_set, err_msg_to_set) \ + do { \ + if (MB_SUCCESS != err_info) \ + SET_ERR(err_code_to_set, err_msg_to_set); \ + } while (false) + +//! Check returned error code against MB_SUCCESS +//! Set a new error with passed error code and passed error message string stream +#define CHK_ERR2_STR(err_info, err_code_to_set, err_msg_str_to_set) \ + do { \ + if (MB_SUCCESS != err_info) \ + SET_ERR_STR(err_code_to_set, err_msg_str_to_set); \ + } while (false) + +//! Check returned error code against an expected one +//! Set a new error with default error code and default error message string #define CHK_EQL(err_info, exp_err_code) \ do { \ - if (exp_err_code != err_info) { \ - err_info.set_error_code(MB_FAILURE); \ - err_info.set_error_msg("Returned error code is not expected"); \ - SET_ERR(err_info); \ - } \ + if (exp_err_code != err_info) \ + SET_ERR(MB_FAILURE, "Returned error code is not expected"); \ } while (false) +//! Check returned error code against an expected one +//! Set a new error with default error code and passed error message string #define CHK_EQL1(err_info, exp_err_code, err_msg_to_set) \ do { \ - if (exp_err_code != err_info) { \ - err_info.set_error_code(MB_FAILURE); \ - err_info.set_error_msg(err_msg_to_set); \ - SET_ERR(err_info); \ - } \ + if (exp_err_code != err_info) \ + SET_ERR(MB_FAILURE, err_msg_to_set); \ + } while (false) + +//! Check returned error code against an expected one +//! Set a new error with default error code and passed error message string stream +#define CHK_EQL1_STR(err_info, exp_err_code, err_msg_str_to_set) \ + do { \ + if (exp_err_code != err_info) \ + SET_ERR_STR(MB_FAILURE, err_msg_str_to_set); \ } while (false) +//! Check returned error code against an expected one +//! Set a new error with passed error code and passed error message string #define CHK_EQL2(err_info, exp_err_code, err_code_to_set, err_msg_to_set) \ do { \ - if (exp_err_code != err_info) { \ - err_info.set_error_code(err_code_to_set); \ - err_info.set_error_msg(err_msg_to_set); \ - SET_ERR(err_info); \ - } \ + if (exp_err_code != err_info) \ + SET_ERR(err_code_to_set, err_msg_to_set); \ + } while (false) + +//! Check returned error code against an expected one +//! Set a new error with passed error code and passed error message string stream +#define CHK_EQL2_STR(err_info, exp_err_code, err_code_to_set, err_msg_str_to_set) \ + do { \ + if (exp_err_code != err_info) \ + SET_ERR_STR(err_code_to_set, err_msg_str_to_set); \ } while (false) #else +//! Set a new error with passed error code and passed error message string #define SET_ERR(err_code, err_msg) \ return MBError(__LINE__, __func__, __FILENAME__, __SDIR__, err_code, err_msg, MB_ERROR_TYPE_NEW_LOCAL) +//! Set a new error with passed error code and passed error message string stream #define SET_ERR_STR(err_code, err_msg_str) \ - std::ostringstream ostr; \ - ostr << err_msg_str; \ - return MBError(__LINE__, __func__, __FILENAME__, __SDIR__, err_code, ostr.str().c_str(), MB_ERROR_TYPE_NEW_LOCAL) + do { \ + std::ostringstream ostr; \ + ostr << err_msg_str; \ + return MBError(__LINE__, __func__, __FILENAME__, __SDIR__, err_code, ostr.str().c_str(), MB_ERROR_TYPE_NEW_LOCAL); \ + } while (false) +//! Set a new global error with passed error code and passed error message string #define SET_GLB_ERR(err_code, err_msg) \ return MBError(__LINE__, __func__, __FILENAME__, __SDIR__, err_code, err_msg, MB_ERROR_TYPE_NEW_GLOBAL) +//! Set a new global error with passed error code and passed error message string stream #define SET_GLB_ERR_STR(err_code, err_msg_str) \ - std::ostringstream ostr; \ - ostr << err_msg_str; \ - return MBError(__LINE__, __func__, __FILENAME__, __SDIR__, err_code, ostr.str().c_str(), MB_ERROR_TYPE_NEW_GLOBAL) + do { \ + std::ostringstream ostr; \ + ostr << err_msg_str; \ + return MBError(__LINE__, __func__, __FILENAME__, __SDIR__, err_code, ostr.str().c_str(), MB_ERROR_TYPE_NEW_GLOBAL); \ + } while (false) +//! Check returned error code against MB_SUCCESS #define CHK_ERR(err_code) \ do { \ if (MB_SUCCESS != err_code) \ return MBError(__LINE__, __func__, __FILENAME__, __SDIR__, err_code, "", MB_ERROR_TYPE_EXISTING); \ } while (false) +//! Check returned error code against MB_SUCCESS +//! Set a new error with the returned error code and passed error message string #define CHK_ERR1(err_code, err_msg_to_set) \ do { \ - if (MB_SUCCESS != err_code) { \ + if (MB_SUCCESS != err_code) \ SET_ERR(err_code, err_msg_to_set); \ - } \ } while (false) +//! Check returned error code against MB_SUCCESS +//! Set a new error with the returned error code and passed error message string stream +#define CHK_ERR1_STR(err_code, err_msg_str_to_set) \ + do { \ + if (MB_SUCCESS != err_code) \ + SET_ERR_STR(err_code, err_msg_str_to_set); \ + } while (false) + +//! Check returned error code against MB_SUCCESS +//! Set a new error with passed error code and passed error message string #define CHK_ERR2(err_code, err_code_to_set, err_msg_to_set) \ do { \ - if (MB_SUCCESS != err_code) { \ + if (MB_SUCCESS != err_code) \ SET_ERR(err_code_to_set, err_msg_to_set); \ - } \ } while (false) +//! Check returned error code against MB_SUCCESS +//! Set a new error with passed error code and passed error message string stream +#define CHK_ERR2_STR(err_code, err_code_to_set, err_msg_str_to_set) \ + do { \ + if (MB_SUCCESS != err_code) \ + SET_ERR_STR(err_code_to_set, err_msg_str_to_set); \ + } while (false) + +//! Check returned error code against an expected one +//! Set a new error with default error code and default error message string #define CHK_EQL(err_code, exp_err_code) \ do { \ - if (exp_err_code != err_code) { \ + if (exp_err_code != err_code) \ SET_ERR(MB_FAILURE, "Returned error code is not expected"); \ - } \ } while (false) +//! Check returned error code against an expected one +//! Set a new error with default error code and passed error message string #define CHK_EQL1(err_code, exp_err_code, err_msg_to_set) \ do { \ if (exp_err_code != err_code) { \ @@ -242,11 +307,28 @@ ErrorCode MBError(int line, const char* func, const char* file, const char* dir, } \ } while (false) +//! Check returned error code against an expected one +//! Set a new error with default error code and passed error message string stream +#define CHK_EQL1_STR(err_code, exp_err_code, err_msg_str_to_set) \ + do { \ + if (exp_err_code != err_code) \ + SET_ERR_STR(MB_FAILURE, err_msg_str_to_set); \ + } while (false) + +//! Check returned error code against an expected one +//! Set a new error with passed error code and passed error message string #define CHK_EQL2(err_code, exp_err_code, err_code_to_set, err_msg_to_set) \ do { \ - if (exp_err_code != err_code) { \ + if (exp_err_code != err_code) \ SET_ERR(err_code_to_set, err_msg_to_set); \ - } \ + } while (false) + +//! Check returned error code against an expected one +//! Set a new error with passed error code and passed error message string stream +#define CHK_EQL2_STR(err_code, exp_err_code, err_code_to_set, err_msg_str_to_set) \ + do { \ + if (exp_err_code != err_code) \ + SET_ERR_STR(err_code_to_set, err_msg_str_to_set); \ } while (false) #endif Repository URL: https://bitbucket.org/fathomteam/moab/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/MOAB: iulian07: enable mbcslam should work in serial builds too
by commits-noreply＠bitbucket.org 12 Mar '14

12 Mar '14

1 new commit in MOAB: https://bitbucket.org/fathomteam/moab/commits/6694ba1ab8f8/ Changeset: 6694ba1ab8f8 Branch: master User: iulian07 Date: 2014-03-13 03:52:37 Summary: enable mbcslam should work in serial builds too the parallel tests are disabled, and USE_MPI define is used as a guard for parallel specific code some rearranging was needed Affected #: 4 files diff --git a/tools/mbcslam/Intx2Mesh.cpp b/tools/mbcslam/Intx2Mesh.cpp index e055beb..b17cc33 100644 --- a/tools/mbcslam/Intx2Mesh.cpp +++ b/tools/mbcslam/Intx2Mesh.cpp @@ -5,8 +5,9 @@ */ #include "Intx2Mesh.hpp" -//#include "Coupler.hpp" +#ifdef USE_MPI #include "moab/ParallelComm.hpp" +#endif /* USE_MPI */ #include "moab/AdaptiveKDTree.hpp" #include "MBParallelConventions.h" #include "MBTagConventions.hpp" @@ -18,7 +19,10 @@ namespace moab { -Intx2Mesh::Intx2Mesh(Interface * mbimpl): mb(mbimpl), parcomm(NULL), remote_cells(NULL) +Intx2Mesh::Intx2Mesh(Interface * mbimpl): mb(mbimpl) +#ifdef USE_MPI + , parcomm(NULL), remote_cells(NULL) +#endif { dbg_1=0; box_error=0; @@ -33,11 +37,13 @@ Intx2Mesh::Intx2Mesh(Interface * mbimpl): mb(mbimpl), parcomm(NULL), remote_cell Intx2Mesh::~Intx2Mesh() { // TODO Auto-generated destructor stub +#ifdef USE_MPI if (remote_cells) { delete remote_cells; remote_cells=NULL; } +#endif } void Intx2Mesh::createTags() { @@ -404,11 +410,13 @@ ErrorCode Intx2Mesh::intersect_meshes(EntityHandle mbset1, EntityHandle mbset2, // before cleaning up , we need to settle the position of the intersection points // on the boundary edges // this needs to be collective, so we should maybe wait something +#ifdef USE_MPI rval = correct_intersection_points_positions(); if (rval!=MB_SUCCESS) { std::cout << "can't correct position, Intx2Mesh.cpp \n"; } +#endif clean(); return MB_SUCCESS; } @@ -438,7 +446,38 @@ void Intx2Mesh::clean() localEnts.clear();*/ } - +// this method will reduce number of nodes, collapse edges that are of length 0 + // so a polygon like 428 431 431 will become a line 428 431 + // or something like 428 431 431 531 -> 428 431 531 +void Intx2Mesh::correct_polygon(EntityHandle * nodes, int & nP) +{ + int i = 0; + while(i<nP) + { + int nextIndex = (i+1)%nP; + if (nodes[i]==nodes[nextIndex]) + { + // we need to reduce nP, and collapse nodes + if (dbg_1) + { + std::cout<<" nodes duplicated in list: " ; + for (int j=0; j<nP; j++) + std::cout<<nodes[j] << " " ; + std::cout<<"\n"; + std::cout<<" node " << nodes[i] << " at index " << i << " is duplicated" << "\n"; + } + // this will work even if we start from 1 2 3 1; when i is 3, we find nextIndex is 0, then next thing does nothing + // (nP-1 is 3, so k is already >= nP-1); it will result in nodes -> 1, 2, 3 + for (int k=i; k<nP-1; k++) + nodes[k] = nodes[k+1]; + nP--; // decrease the number of nodes; also, decrease i, just if we may need to check again + i--; + } + i++; + } + return; +} +#if USE_MPI ErrorCode Intx2Mesh::build_processor_euler_boxes(EntityHandle euler_set, Range & local_verts) { localEnts.clear(); @@ -1119,37 +1158,6 @@ ErrorCode Intx2Mesh::create_departure_mesh_3rd_alg(EntityHandle & lagr_set, return MB_SUCCESS; //end copy } -// this method will reduce number of nodes, collapse edges that are of length 0 - // so a polygon like 428 431 431 will become a line 428 431 - // or something like 428 431 431 531 -> 428 431 531 -void Intx2Mesh::correct_polygon(EntityHandle * nodes, int & nP) -{ - int i = 0; - while(i<nP) - { - int nextIndex = (i+1)%nP; - if (nodes[i]==nodes[nextIndex]) - { - // we need to reduce nP, and collapse nodes - if (dbg_1) - { - std::cout<<" nodes duplicated in list: " ; - for (int j=0; j<nP; j++) - std::cout<<nodes[j] << " " ; - std::cout<<"\n"; - std::cout<<" node " << nodes[i] << " at index " << i << " is duplicated" << "\n"; - } - // this will work even if we start from 1 2 3 1; when i is 3, we find nextIndex is 0, then next thing does nothing - // (nP-1 is 3, so k is already >= nP-1); it will result in nodes -> 1, 2, 3 - for (int k=i; k<nP-1; k++) - nodes[k] = nodes[k+1]; - nP--; // decrease the number of nodes; also, decrease i, just if we may need to check again - i--; - } - i++; - } - return; -} ErrorCode Intx2Mesh::correct_intersection_points_positions() { @@ -1169,4 +1177,5 @@ ErrorCode Intx2Mesh::correct_intersection_points_positions() } return MB_SUCCESS; } +#endif /* USE_MPI */ } /* namespace moab */ diff --git a/tools/mbcslam/Intx2Mesh.hpp b/tools/mbcslam/Intx2Mesh.hpp index d54b0b5..528ab7e 100644 --- a/tools/mbcslam/Intx2Mesh.hpp +++ b/tools/mbcslam/Intx2Mesh.hpp @@ -32,9 +32,11 @@ namespace moab { #define ERRORV(rval, str) \ if (MB_SUCCESS != rval) {std::cout << str << "\n"; return ;} +#ifdef USE_MPI // forward declarations class ParallelComm; class TupleList; +#endif class Intx2Mesh { @@ -93,9 +95,9 @@ public: ErrorCode build_processor_euler_boxes(EntityHandle euler_set, Range & local_verts); void correct_polygon(EntityHandle * foundIds, int & nP); - +#ifdef USE_MPI ErrorCode correct_intersection_points_positions(); - +#endif void enable_debug() {dbg_1 = 1;} void disable_debug() {dbg_1 = 0;} protected: // so it can be accessed in derived classes, InPlane and OnSphere @@ -141,20 +143,21 @@ protected: // so it can be accessed in derived classes, InPlane and OnSphere double epsilon_1; double epsilon_area; - ParallelComm * parcomm; - std::vector<double> allBoxes; double box_error; /* \brief Local root of the kdtree */ EntityHandle localRoot; Range localEnts;// this range is for local elements of interest, euler cells - unsigned int my_rank; - int max_edges; // maximum number of edges in the euler set - +#ifdef USE_MPI + ParallelComm * parcomm; TupleList * remote_cells; std::map<int, EntityHandle> globalID_to_eh;// needed for parallel, mostly +#endif + int max_edges; // maximum number of edges in the euler set + + }; diff --git a/tools/mbcslam/Intx2MeshOnSphere.cpp b/tools/mbcslam/Intx2MeshOnSphere.cpp index ac33e91..5b7a88a 100644 --- a/tools/mbcslam/Intx2MeshOnSphere.cpp +++ b/tools/mbcslam/Intx2MeshOnSphere.cpp @@ -7,8 +7,10 @@ #include "Intx2MeshOnSphere.hpp" #include "moab/GeomUtil.hpp" #include "MBTagConventions.hpp" -#include "moab/ParallelComm.hpp" #include <queue> +#ifdef USE_MPI +#include "moab/ParallelComm.hpp" +#endif namespace moab { @@ -481,6 +483,7 @@ ErrorCode Intx2MeshOnSphere::update_tracer_data(EntityHandle out_set, Tag & tagE rval = mb->tag_get_data(corrTag, &blue, 1, &redArr); if (0==redArr || MB_TAG_NOT_FOUND==rval) { +#ifdef USE_MPI if (!remote_cells) ERRORR( MB_FAILURE, "no remote cells, failure\n"); // maybe the element is remote, from another processor @@ -492,6 +495,7 @@ ErrorCode Intx2MeshOnSphere::update_tracer_data(EntityHandle out_set, Tag & tagE if (index_in_remote==-1) ERRORR( MB_FAILURE, "can't find the global id element in remote cells\n"); remote_cells->vr_wr[index_in_remote] += currentVals[redIndex]*areap; +#endif } else if (MB_SUCCESS==rval) { @@ -506,6 +510,7 @@ ErrorCode Intx2MeshOnSphere::update_tracer_data(EntityHandle out_set, Tag & tagE } // now, send back the remote_cells to the processors they came from, with the updated values for // the tracer mass in a cell +#ifdef USE_MPI if (remote_cells) { // so this means that some cells will be sent back with tracer info to the procs they were sent from @@ -522,7 +527,7 @@ ErrorCode Intx2MeshOnSphere::update_tracer_data(EntityHandle out_set, Tag & tagE newValues[arrRedIndex] += remote_cells->vr_rd[j]; } } - +#endif /* USE_MPI */ // now divide by red area (current) int j=0; Range::iterator iter = rs2.begin(); @@ -543,6 +548,8 @@ ErrorCode Intx2MeshOnSphere::update_tracer_data(EntityHandle out_set, Tag & tagE rval = mb->tag_set_data(tagElem, rs2, &newValues[0]); ERRORR(rval, "can't set new values tag"); + +#ifdef USE_MPI double total_mass=0.; double total_intx_area =0; int mpi_err = MPI_Reduce(&total_mass_local, &total_mass, 1, MPI_DOUBLE, MPI_SUM, 0, MPI_COMM_WORLD); @@ -553,7 +560,7 @@ ErrorCode Intx2MeshOnSphere::update_tracer_data(EntityHandle out_set, Tag & tagE if (my_rank==0) { std::cout <<"total mass now:" << total_mass << "\n"; - std::cout <<"check: total intersection area: (4 * M_PI * R^2): " << total_intx_area << "\n"; + std::cout <<"check: total intersection area: (4 * M_PI * R^2): " << 4 * M_PI * R*R << " " << total_intx_area << "\n"; } if (remote_cells) @@ -561,6 +568,10 @@ ErrorCode Intx2MeshOnSphere::update_tracer_data(EntityHandle out_set, Tag & tagE delete remote_cells; remote_cells=NULL; } +#else + std::cout <<"total mass now:" << total_mass_local << "\n"; + std::cout <<"check: total intersection area: (4 * M_PI * R^2): " << 4 * M_PI * R*R << " " << check_intx_area << "\n"; +#endif return MB_SUCCESS; } } /* namespace moab */ diff --git a/tools/mbcslam/Makefile.am b/tools/mbcslam/Makefile.am index 0dac164..ffc3dff 100644 --- a/tools/mbcslam/Makefile.am +++ b/tools/mbcslam/Makefile.am @@ -24,7 +24,11 @@ LDADD = libmbcslam.la $(top_builddir)/src/libMOAB.la libmbcslam_la_SOURCES = \ Intx2Mesh.cpp Intx2Mesh.hpp Intx2MeshOnSphere.cpp Intx2MeshOnSphere.hpp \ - CslamUtils.cpp CslamUtils.hpp Intx2MeshInPlane.cpp Intx2MeshInPlane.hpp wrap_intx.cpp + CslamUtils.cpp CslamUtils.hpp Intx2MeshInPlane.cpp Intx2MeshInPlane.hpp + +if PARALLEL + libmbcslam_la_SOURCES += wrap_intx.cpp +endif # these will be installed libmbcslam_la_include_HEADERS = @@ -38,24 +42,36 @@ libmbcslam_la_includedir = $(includedir) cfgdir = $(libdir) TESTS = intx_on_sphere_test intx_in_plane_test spherical_area_test \ - case1_test intx_mpas -noinst_PROGRAMS = cslam_par_test diffusion proj1 intx_imesh create_dp advection + case1_test +if PARALLEL + TESTS+=intx_mpas +endif + +noinst_PROGRAMS = proj1 create_dp +if PARALLEL + noinst_PROGRAMS +=cslam_par_test diffusion intx_imesh advection +endif check_PROGRAMS = $(TESTS) + intx_on_sphere_test_SOURCES = intx_on_sphere_test.cpp -diffusion_SOURCES = diffusion.cpp + intx_in_plane_test_SOURCES = intx_in_plane_test.cpp # spec_visu_test_SOURCES = spec_visu_test.cpp spherical_area_test_SOURCES = spherical_area_test.cpp case1_test_SOURCES = case1_test.cpp -intx_mpas_SOURCES = intx_mpas.cpp -cslam_par_test_SOURCES = cslam_par_test.cpp proj1_SOURCES = proj1.cpp -intx_imesh_SOURCES = intx_imesh.cpp -intx_imesh_LDADD = $(LDADD) $(top_builddir)/itaps/imesh/libiMesh.la create_dp_SOURCES = create_dp.cpp -advection_SOURCES = advection.F90 -advection_LDADD = $(LDADD) $(top_builddir)/itaps/imesh/libiMesh.la + +if PARALLEL + diffusion_SOURCES = diffusion.cpp + intx_imesh_SOURCES = intx_imesh.cpp + intx_imesh_LDADD = $(LDADD) $(top_builddir)/itaps/imesh/libiMesh.la + cslam_par_test_SOURCES = cslam_par_test.cpp + intx_mpas_SOURCES = intx_mpas.cpp + advection_SOURCES = advection.F90 + advection_LDADD = $(LDADD) $(top_builddir)/itaps/imesh/libiMesh.la +endif EXTRA_DIST = lagrangeHomme.vtk \ eulerHomme.vtk \ Repository URL: https://bitbucket.org/fathomteam/moab/ -- This is a commit notification from bitbucket.org. 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commit/MOAB: danwu: Replaced ERRORR and ERRORS macros with new error handling macros in NCHelper.cpp.
by commits-noreply＠bitbucket.org 12 Mar '14

12 Mar '14

1 new commit in MOAB: https://bitbucket.org/fathomteam/moab/commits/252454a23db6/ Changeset: 252454a23db6 Branch: error_handling_enhancement User: danwu Date: 2014-03-13 00:56:29 Summary: Replaced ERRORR and ERRORS macros with new error handling macros in NCHelper.cpp. Affected #: 1 file diff --git a/src/io/NCHelper.cpp b/src/io/NCHelper.cpp index a83284b..85afdba 100644 --- a/src/io/NCHelper.cpp +++ b/src/io/NCHelper.cpp @@ -9,12 +9,6 @@ #include "moab/ReadUtilIface.hpp" #include "MBTagConventions.hpp" -#define ERRORR(rval, str) \ - if (MB_SUCCESS != rval) {_readNC->readMeshIface->report_error("%s", str); return rval;} - -#define ERRORS(err, str) \ - if (err) {_readNC->readMeshIface->report_error("%s", str); return MB_FAILURE;} - namespace moab { NCHelper* NCHelper::get_nc_helper(ReadNC* readNC, int fileId, const FileOptions& opts, EntityHandle fileSet) @@ -74,10 +68,10 @@ ErrorCode NCHelper::create_conventional_tags(const std::vector<int>& tstep_nums) Tag numDimsTag = 0; tag_name = "__NUM_DIMS"; int numDims = dimNames.size(); - rval = mbImpl->tag_get_handle(tag_name.c_str(), 1, MB_TYPE_INTEGER, numDimsTag, MB_TAG_SPARSE | MB_TAG_CREAT); - ERRORR(rval, "Trouble creating __NUM_DIMS tag."); - rval = mbImpl->tag_set_data(numDimsTag, &_fileSet, 1, &numDims); - ERRORR(rval, "Trouble setting data for __NUM_DIMS tag."); + rval = mbImpl->tag_get_handle(tag_name.c_str(), 1, MB_TYPE_INTEGER, numDimsTag, MB_TAG_SPARSE | MB_TAG_CREAT); \ + CHK_ERR1(rval, "Trouble creating __NUM_DIMS tag"); + rval = mbImpl->tag_set_data(numDimsTag, &_fileSet, 1, &numDims); \ + CHK_ERR1(rval, "Trouble setting data for __NUM_DIMS tag"); if (MB_SUCCESS == rval) dbgOut.tprintf(2, "Tag created for variable %s\n", tag_name.c_str()); @@ -85,10 +79,10 @@ ErrorCode NCHelper::create_conventional_tags(const std::vector<int>& tstep_nums) Tag numVarsTag = 0; tag_name = "__NUM_VARS"; int numVars = varInfo.size(); - rval = mbImpl->tag_get_handle(tag_name.c_str(), 1, MB_TYPE_INTEGER, numVarsTag, MB_TAG_SPARSE | MB_TAG_CREAT); - ERRORR(rval, "Trouble creating __NUM_VARS tag."); - rval = mbImpl->tag_set_data(numVarsTag, &_fileSet, 1, &numVars); - ERRORR(rval, "Trouble setting data for __NUM_VARS tag."); + rval = mbImpl->tag_get_handle(tag_name.c_str(), 1, MB_TYPE_INTEGER, numVarsTag, MB_TAG_SPARSE | MB_TAG_CREAT); \ + CHK_ERR1(rval, "Trouble creating __NUM_VARS tag"); + rval = mbImpl->tag_set_data(numVarsTag, &_fileSet, 1, &numVars); \ + CHK_ERR1(rval, "Trouble setting data for __NUM_VARS tag"); if (MB_SUCCESS == rval) dbgOut.tprintf(2, "Tag created for variable %s\n", tag_name.c_str()); @@ -102,11 +96,11 @@ ErrorCode NCHelper::create_conventional_tags(const std::vector<int>& tstep_nums) dimnames.push_back('\0'); } int dimnamesSz = dimnames.size(); - rval = mbImpl->tag_get_handle(tag_name.c_str(), 0, MB_TYPE_OPAQUE, dimNamesTag, MB_TAG_CREAT | MB_TAG_SPARSE | MB_TAG_VARLEN); - ERRORR(rval, "Trouble creating __DIM_NAMES tag."); + rval = mbImpl->tag_get_handle(tag_name.c_str(), 0, MB_TYPE_OPAQUE, dimNamesTag, MB_TAG_CREAT | MB_TAG_SPARSE | MB_TAG_VARLEN); \ + CHK_ERR1(rval, "Trouble creating __DIM_NAMES tag"); const void* ptr = dimnames.c_str(); - rval = mbImpl->tag_set_by_ptr(dimNamesTag, &_fileSet, 1, &ptr, &dimnamesSz); - ERRORR(rval, "Trouble setting data for __DIM_NAMES tag."); + rval = mbImpl->tag_set_by_ptr(dimNamesTag, &_fileSet, 1, &ptr, &dimnamesSz); \ + CHK_ERR1(rval, "Trouble setting data for __DIM_NAMES tag"); if (MB_SUCCESS == rval) dbgOut.tprintf(2, "Tag created for variable %s\n", tag_name.c_str()); @@ -114,11 +108,11 @@ ErrorCode NCHelper::create_conventional_tags(const std::vector<int>& tstep_nums) Tag dimLensTag = 0; tag_name = "__DIM_LENS"; int dimLensSz = dimLens.size(); - rval = mbImpl->tag_get_handle(tag_name.c_str(), 0, MB_TYPE_INTEGER, dimLensTag, MB_TAG_CREAT | MB_TAG_SPARSE | MB_TAG_VARLEN); - ERRORR(rval, "Trouble creating __DIM_LENS tag."); + rval = mbImpl->tag_get_handle(tag_name.c_str(), 0, MB_TYPE_INTEGER, dimLensTag, MB_TAG_CREAT | MB_TAG_SPARSE | MB_TAG_VARLEN); \ + CHK_ERR1(rval, "Trouble creating __DIM_LENS tag"); ptr = &(dimLens[0]); - rval = mbImpl->tag_set_by_ptr(dimLensTag, &_fileSet, 1, &ptr, &dimLensSz); - ERRORR(rval, "Trouble setting data for __DIM_LENS tag."); + rval = mbImpl->tag_set_by_ptr(dimLensTag, &_fileSet, 1, &ptr, &dimLensSz); \ + CHK_ERR1(rval, "Trouble setting data for __DIM_LENS tag"); if (MB_SUCCESS == rval) dbgOut.tprintf(2, "Tag created for variable %s\n", tag_name.c_str()); @@ -132,11 +126,11 @@ ErrorCode NCHelper::create_conventional_tags(const std::vector<int>& tstep_nums) varnames.push_back('\0'); } int varnamesSz = varnames.size(); - rval = mbImpl->tag_get_handle(tag_name.c_str(), 0, MB_TYPE_OPAQUE, varNamesTag, MB_TAG_CREAT | MB_TAG_SPARSE | MB_TAG_VARLEN); - ERRORR(rval, "Trouble creating __VAR_NAMES tag."); + rval = mbImpl->tag_get_handle(tag_name.c_str(), 0, MB_TYPE_OPAQUE, varNamesTag, MB_TAG_CREAT | MB_TAG_SPARSE | MB_TAG_VARLEN); \ + CHK_ERR1(rval, "Trouble creating __VAR_NAMES tag"); ptr = varnames.c_str(); - rval = mbImpl->tag_set_by_ptr(varNamesTag, &_fileSet, 1, &ptr, &varnamesSz); - ERRORR(rval, "Trouble setting data for __VAR_NAMES tag."); + rval = mbImpl->tag_set_by_ptr(varNamesTag, &_fileSet, 1, &ptr, &varnamesSz); \ + CHK_ERR1(rval, "Trouble setting data for __VAR_NAMES tag"); if (MB_SUCCESS == rval) dbgOut.tprintf(2, "Tag created for variable %s\n", tag_name.c_str()); @@ -150,10 +144,10 @@ ErrorCode NCHelper::create_conventional_tags(const std::vector<int>& tstep_nums) std::vector<int> val(2, 0); val[0] = 0; val[1] = nTimeSteps - 1; - rval = mbImpl->tag_get_handle(tag_name.c_str(), 2, MB_TYPE_INTEGER, tagh, MB_TAG_SPARSE | MB_TAG_CREAT); - ERRORR(rval, "Trouble creating __<dim_name>_LOC_MINMAX tag."); - rval = mbImpl->tag_set_data(tagh, &_fileSet, 1, &val[0]); - ERRORR(rval, "Trouble setting data for __<dim_name>_LOC_MINMAX tag."); + rval = mbImpl->tag_get_handle(tag_name.c_str(), 2, MB_TYPE_INTEGER, tagh, MB_TAG_SPARSE | MB_TAG_CREAT); \ + CHK_ERR1(rval, "Trouble creating __<dim_name>_LOC_MINMAX tag"); + rval = mbImpl->tag_set_data(tagh, &_fileSet, 1, &val[0]); \ + CHK_ERR1(rval, "Trouble setting data for __<dim_name>_LOC_MINMAX tag"); if (MB_SUCCESS == rval) dbgOut.tprintf(2, "Tag created for variable %s\n", tag_name.c_str()); } @@ -174,10 +168,10 @@ ErrorCode NCHelper::create_conventional_tags(const std::vector<int>& tstep_nums) std::stringstream ss_tag_name; ss_tag_name << "__" << dimNames[i] << "_LOC_VALS"; tag_name = ss_tag_name.str(); - rval = mbImpl->tag_get_handle(tag_name.c_str(), val.size(), MB_TYPE_INTEGER, tagh, MB_TAG_SPARSE | MB_TAG_CREAT); - ERRORR(rval, "Trouble creating __<dim_name>_LOC_VALS tag."); - rval = mbImpl->tag_set_data(tagh, &_fileSet, 1, &val[0]); - ERRORR(rval, "Trouble setting data for __<dim_name>_LOC_VALS tag."); + rval = mbImpl->tag_get_handle(tag_name.c_str(), val.size(), MB_TYPE_INTEGER, tagh, MB_TAG_SPARSE | MB_TAG_CREAT); \ + CHK_ERR1(rval, "Trouble creating __<dim_name>_LOC_VALS tag"); + rval = mbImpl->tag_set_data(tagh, &_fileSet, 1, &val[0]); \ + CHK_ERR1(rval, "Trouble setting data for __<dim_name>_LOC_VALS tag"); if (MB_SUCCESS == rval) dbgOut.tprintf(2, "Tag created for variable %s\n", tag_name.c_str()); } @@ -199,10 +193,10 @@ ErrorCode NCHelper::create_conventional_tags(const std::vector<int>& tstep_nums) mbImpl->tag_get_handle(tmptagname.c_str(), 0, MB_TYPE_OPAQUE, tmptag, MB_TAG_ANY); varInfo[mapIter->first].varTags[i] = tmptag; } - rval = mbImpl->tag_get_handle(tag_name.c_str(), varDimSz, MB_TYPE_HANDLE, varNamesDimsTag, MB_TAG_SPARSE | MB_TAG_CREAT); - ERRORR(rval, "Trouble creating __<var_name>_DIMS tag."); - rval = mbImpl->tag_set_data(varNamesDimsTag, &_fileSet, 1, &(varInfo[mapIter->first].varTags[0])); - ERRORR(rval, "Trouble setting data for __<var_name>_DIMS tag."); + rval = mbImpl->tag_get_handle(tag_name.c_str(), varDimSz, MB_TYPE_HANDLE, varNamesDimsTag, MB_TAG_SPARSE | MB_TAG_CREAT); \ + CHK_ERR1(rval, "Trouble creating __<var_name>_DIMS tag"); + rval = mbImpl->tag_set_data(varNamesDimsTag, &_fileSet, 1, &(varInfo[mapIter->first].varTags[0])); \ + CHK_ERR1(rval, "Trouble setting data for __<var_name>_DIMS tag"); if (MB_SUCCESS == rval) dbgOut.tprintf(2, "Tag created for variable %s\n", tag_name.c_str()); } @@ -210,25 +204,25 @@ ErrorCode NCHelper::create_conventional_tags(const std::vector<int>& tstep_nums) // <PARTITION_METHOD> Tag part_tag = scdi->part_method_tag(); if (!part_tag) - ERRORR(MB_FAILURE, "Trouble getting partition method tag."); - rval = mbImpl->tag_set_data(part_tag, &_fileSet, 1, &partMethod); - ERRORR(rval, "Trouble setting data for PARTITION_METHOD tag."); + SET_ERR(MB_FAILURE, "Trouble getting partition method tag"); + rval = mbImpl->tag_set_data(part_tag, &_fileSet, 1, &partMethod); \ + CHK_ERR1(rval, "Trouble setting data for PARTITION_METHOD tag"); if (MB_SUCCESS == rval) dbgOut.tprintf(2, "Tag created for variable %s\n", tag_name.c_str()); // <__GLOBAL_ATTRIBS> tag_name = "__GLOBAL_ATTRIBS"; Tag globalAttTag = 0; - rval = mbImpl->tag_get_handle(tag_name.c_str(), 0, MB_TYPE_OPAQUE, globalAttTag, MB_TAG_CREAT | MB_TAG_SPARSE | MB_TAG_VARLEN); - ERRORR(rval, "Trouble creating __GLOBAL_ATTRIBS tag."); + rval = mbImpl->tag_get_handle(tag_name.c_str(), 0, MB_TYPE_OPAQUE, globalAttTag, MB_TAG_CREAT | MB_TAG_SPARSE | MB_TAG_VARLEN); \ + CHK_ERR1(rval, "Trouble creating __GLOBAL_ATTRIBS tag"); std::string gattVal; std::vector<int> gattLen; - rval = create_attrib_string(globalAtts, gattVal, gattLen); - ERRORR(rval, "Trouble creating attribute strings."); + rval = create_attrib_string(globalAtts, gattVal, gattLen); \ + CHK_ERR1(rval, "Trouble creating attribute strings"); const void* gattptr = gattVal.c_str(); int globalAttSz = gattVal.size(); - rval = mbImpl->tag_set_by_ptr(globalAttTag, &_fileSet, 1, &gattptr, &globalAttSz); - ERRORR(rval, "Trouble setting data for __GLOBAL_ATTRIBS tag."); + rval = mbImpl->tag_set_by_ptr(globalAttTag, &_fileSet, 1, &gattptr, &globalAttSz); \ + CHK_ERR1(rval, "Trouble setting data for __GLOBAL_ATTRIBS tag"); if (MB_SUCCESS == rval) dbgOut.tprintf(2, "Tag created for variable %s\n", tag_name.c_str()); @@ -237,10 +231,10 @@ ErrorCode NCHelper::create_conventional_tags(const std::vector<int>& tstep_nums) Tag globalAttLenTag = 0; if (gattLen.size() == 0) gattLen.push_back(0); - rval = mbImpl->tag_get_handle(tag_name.c_str(), gattLen.size(), MB_TYPE_INTEGER, globalAttLenTag, MB_TAG_SPARSE | MB_TAG_CREAT); - ERRORR(rval, "Trouble creating __GLOBAL_ATTRIBS_LEN tag."); - rval = mbImpl->tag_set_data(globalAttLenTag, &_fileSet, 1, &gattLen[0]); - ERRORR(rval, "Trouble setting data for __GLOBAL_ATTRIBS_LEN tag."); + rval = mbImpl->tag_get_handle(tag_name.c_str(), gattLen.size(), MB_TYPE_INTEGER, globalAttLenTag, MB_TAG_SPARSE | MB_TAG_CREAT); \ + CHK_ERR1(rval, "Trouble creating __GLOBAL_ATTRIBS_LEN tag"); + rval = mbImpl->tag_set_data(globalAttLenTag, &_fileSet, 1, &gattLen[0]); \ + CHK_ERR1(rval, "Trouble setting data for __GLOBAL_ATTRIBS_LEN tag"); if (MB_SUCCESS == rval) dbgOut.tprintf(2, "Tag created for variable %s\n", tag_name.c_str()); @@ -250,16 +244,16 @@ ErrorCode NCHelper::create_conventional_tags(const std::vector<int>& tstep_nums) ssTagName << "__" << mapIter->first << "_ATTRIBS"; tag_name = ssTagName.str(); Tag varAttTag = 0; - rval = mbImpl->tag_get_handle(tag_name.c_str(), 0, MB_TYPE_OPAQUE, varAttTag, MB_TAG_CREAT | MB_TAG_SPARSE | MB_TAG_VARLEN); - ERRORR(rval, "Trouble creating __<var_name>_ATTRIBS tag."); + rval = mbImpl->tag_get_handle(tag_name.c_str(), 0, MB_TYPE_OPAQUE, varAttTag, MB_TAG_CREAT | MB_TAG_SPARSE | MB_TAG_VARLEN); \ + CHK_ERR1(rval, "Trouble creating __<var_name>_ATTRIBS tag"); std::string varAttVal; std::vector<int> varAttLen; - rval = create_attrib_string(mapIter->second.varAtts, varAttVal, varAttLen); - ERRORR(rval, "Trouble creating attribute strings."); + rval = create_attrib_string(mapIter->second.varAtts, varAttVal, varAttLen); \ + CHK_ERR1(rval, "Trouble creating attribute strings"); const void* varAttPtr = varAttVal.c_str(); int varAttSz = varAttVal.size(); - rval = mbImpl->tag_set_by_ptr(varAttTag, &_fileSet, 1, &varAttPtr, &varAttSz); - ERRORR(rval, "Trouble setting data for __<var_name>_ATTRIBS tag."); + rval = mbImpl->tag_set_by_ptr(varAttTag, &_fileSet, 1, &varAttPtr, &varAttSz); \ + CHK_ERR1(rval, "Trouble setting data for __<var_name>_ATTRIBS tag"); if (MB_SUCCESS == rval) dbgOut.tprintf(2, "Tag created for variable %s\n", tag_name.c_str()); if (varAttLen.size() == 0) @@ -267,10 +261,10 @@ ErrorCode NCHelper::create_conventional_tags(const std::vector<int>& tstep_nums) ssTagName << "_LEN"; tag_name = ssTagName.str(); Tag varAttLenTag = 0; - rval = mbImpl->tag_get_handle(tag_name.c_str(), varAttLen.size(), MB_TYPE_INTEGER, varAttLenTag, MB_TAG_SPARSE | MB_TAG_CREAT); - ERRORR(rval, "Trouble creating __<var_name>_ATTRIBS_LEN tag."); - rval = mbImpl->tag_set_data(varAttLenTag, &_fileSet, 1, &varAttLen[0]); - ERRORR(rval, "Trouble setting data for __<var_name>_ATTRIBS_LEN tag."); + rval = mbImpl->tag_get_handle(tag_name.c_str(), varAttLen.size(), MB_TYPE_INTEGER, varAttLenTag, MB_TAG_SPARSE | MB_TAG_CREAT); \ + CHK_ERR1(rval, "Trouble creating __<var_name>_ATTRIBS_LEN tag"); + rval = mbImpl->tag_set_data(varAttLenTag, &_fileSet, 1, &varAttLen[0]); \ + CHK_ERR1(rval, "Trouble setting data for __<var_name>_ATTRIBS_LEN tag"); if (MB_SUCCESS == rval) dbgOut.tprintf(2, "Tag created for variable %s\n", tag_name.c_str()); } @@ -280,13 +274,13 @@ ErrorCode NCHelper::create_conventional_tags(const std::vector<int>& tstep_nums) Tag varNamesLocsTag = 0; std::vector<int> varNamesLocs(varInfo.size()); rval = mbImpl->tag_get_handle(tag_name.c_str(), varNamesLocs.size(), MB_TYPE_INTEGER, varNamesLocsTag, MB_TAG_CREAT - | MB_TAG_SPARSE); - ERRORR(rval, "Trouble creating __VAR_NAMES_LOCATIONS tag."); + | MB_TAG_SPARSE); \ + CHK_ERR1(rval, "Trouble creating __VAR_NAMES_LOCATIONS tag"); for (mapIter = varInfo.begin(); mapIter != varInfo.end(); ++mapIter) { varNamesLocs[std::distance(varInfo.begin(), mapIter)] = mapIter->second.entLoc; } - rval = mbImpl->tag_set_data(varNamesLocsTag, &_fileSet, 1, &varNamesLocs[0]); - ERRORR(rval, "Trouble setting data for __VAR_NAMES_LOCATIONS tag."); + rval = mbImpl->tag_set_data(varNamesLocsTag, &_fileSet, 1, &varNamesLocs[0]); \ + CHK_ERR1(rval, "Trouble setting data for __VAR_NAMES_LOCATIONS tag"); if (MB_SUCCESS == rval) dbgOut.tprintf(2, "Tag created for variable %s\n", tag_name.c_str()); @@ -295,12 +289,12 @@ ErrorCode NCHelper::create_conventional_tags(const std::vector<int>& tstep_nums) tag_name = "__MESH_TYPE"; std::string meshTypeName = get_mesh_type_name(); - rval = mbImpl->tag_get_handle(tag_name.c_str(), 0, MB_TYPE_OPAQUE, meshTypeTag, MB_TAG_CREAT | MB_TAG_SPARSE | MB_TAG_VARLEN); - ERRORR(rval, "Trouble creating __MESH_TYPE tag."); + rval = mbImpl->tag_get_handle(tag_name.c_str(), 0, MB_TYPE_OPAQUE, meshTypeTag, MB_TAG_CREAT | MB_TAG_SPARSE | MB_TAG_VARLEN); \ + CHK_ERR1(rval, "Trouble creating __MESH_TYPE tag"); ptr = meshTypeName.c_str(); int leng = meshTypeName.size(); - rval = mbImpl->tag_set_by_ptr(meshTypeTag, &_fileSet, 1, &ptr, &leng); - ERRORR(rval, "Trouble setting data for __MESH_TYPE tag."); + rval = mbImpl->tag_set_by_ptr(meshTypeTag, &_fileSet, 1, &ptr, &leng); \ + CHK_ERR1(rval, "Trouble setting data for __MESH_TYPE tag"); if (MB_SUCCESS == rval) dbgOut.tprintf(2, "Tag created for variable %s\n", tag_name.c_str()); @@ -347,7 +341,7 @@ ErrorCode NCHelper::read_variable_setup(std::vector<std::string>& var_names, std vdatas.push_back(vd); } else { - ERRORR(MB_FAILURE, "Couldn't find variable."); + SET_ERR_STR(MB_FAILURE, "Couldn't find variable " << var_names[i]); } } } @@ -392,11 +386,11 @@ ErrorCode NCHelper::read_variable_to_set(std::vector<ReadNC::VarData>& vdatas, s Interface*& mbImpl = _readNC->mbImpl; DebugOutput& dbgOut = _readNC->dbgOut; - ErrorCode rval = read_variable_to_set_allocate(vdatas, tstep_nums); - ERRORR(rval, "Trouble allocating read variables to set."); + ErrorCode rval = read_variable_to_set_allocate(vdatas, tstep_nums); \ + CHK_ERR1(rval, "Trouble allocating space to read set variables"); // Finally, read into that space - int success; + int success = 0; for (unsigned int i = 0; i < vdatas.size(); i++) { // Note, for set variables without timesteps, loop one time and then break for (unsigned int t = 0; t < tstep_nums.size(); t++) { @@ -413,42 +407,44 @@ ErrorCode NCHelper::read_variable_to_set(std::vector<ReadNC::VarData>& vdatas, s case NC_CHAR: success = NCFUNCAG(_vara_text)(_fileId, vdatas[i].varId, &vdatas[i].readStarts[0], &vdatas[i].readCounts[0], (char*) data); - ERRORS(success, "Failed to read char data."); + if (success) + SET_ERR(MB_FAILURE, "Failed to read char data"); break; case NC_DOUBLE: success = NCFUNCAG(_vara_double)(_fileId, vdatas[i].varId, &vdatas[i].readStarts[0], &vdatas[i].readCounts[0], (double*) data); - ERRORS(success, "Failed to read double data."); + if (success) + SET_ERR(MB_FAILURE, "Failed to read double data"); break; case NC_FLOAT: success = NCFUNCAG(_vara_float)(_fileId, vdatas[i].varId, &vdatas[i].readStarts[0], &vdatas[i].readCounts[0], (float*) data); - ERRORS(success, "Failed to read float data."); + if (success) + SET_ERR(MB_FAILURE, "Failed to read float data"); break; case NC_INT: success = NCFUNCAG(_vara_int)(_fileId, vdatas[i].varId, &vdatas[i].readStarts[0], &vdatas[i].readCounts[0], (int*) data); - ERRORS(success, "Failed to read int data."); + if (success) + SET_ERR(MB_FAILURE, "Failed to read int data"); break; case NC_SHORT: success = NCFUNCAG(_vara_short)(_fileId, vdatas[i].varId, &vdatas[i].readStarts[0], &vdatas[i].readCounts[0], (short*) data); - ERRORS(success, "Failed to read short data."); + if (success) + SET_ERR(MB_FAILURE, "Failed to read short data"); break; default: - success = 1; + SET_ERR_STR(MB_FAILURE, "Unrecognized data type for set variable " << vdatas[i].varName); } - if (success) - ERRORR(MB_FAILURE, "Trouble reading variable."); - dbgOut.tprintf(2, "Converting variable %s, time step %d\n", vdatas[i].varName.c_str(), tstep_nums[t]); - rval = convert_variable(vdatas[i], t); - ERRORR(rval, "Failed to convert variable."); + rval = convert_variable(vdatas[i], t); \ + CHK_ERR1(rval, "Failed to convert variable"); dbgOut.tprintf(2, "Setting data for variable %s, time step %d\n", vdatas[i].varName.c_str(), tstep_nums[t]); - rval = mbImpl->tag_set_by_ptr(vdatas[i].varTags[t], &_fileSet, 1, &data, &vdatas[i].sz); - ERRORR(rval, "Failed to set data for variable."); + rval = mbImpl->tag_set_by_ptr(vdatas[i].varTags[t], &_fileSet, 1, &data, &vdatas[i].sz); \ + CHK_ERR1(rval, "Failed to set data for variable"); // Memory pointed by pointer data can be deleted, as tag_set_by_ptr() has already copied the tag values switch (vdatas[i].varDataType) { @@ -498,7 +494,6 @@ ErrorCode NCHelper::convert_variable(ReadNC::VarData& var_data, int tstep_num) assert(sz > 0); // Finally, read into that space - int success = 0; int* idata; double* ddata; float* fdata; @@ -520,10 +515,10 @@ ErrorCode NCHelper::convert_variable(ReadNC::VarData& var_data, int tstep_num) idata[i] = sdata[i]; break; default: - success = 1; + break; } - if (2 <= dbgOut.get_verbosity() && !success) { + if (2 <= dbgOut.get_verbosity()) { double dmin, dmax; int imin, imax; switch (var_data.varDataType) { @@ -557,12 +552,8 @@ ErrorCode NCHelper::convert_variable(ReadNC::VarData& var_data, int tstep_num) } dbgOut.tprintf(2, "Variable %s (int): min = %d, max = %d\n", var_data.varName.c_str(), imin, imax); break; - case NC_NAT: - case NC_BYTE: - case NC_CHAR: + default: break; - default: // Default case added to remove compiler warnings - success = 1; } } @@ -573,14 +564,15 @@ ErrorCode NCHelper::read_coordinate(const char* var_name, int lmin, int lmax, st { std::map<std::string, ReadNC::VarData>& varInfo = _readNC->varInfo; std::map<std::string, ReadNC::VarData>::iterator vmit = varInfo.find(var_name); - if (varInfo.end() == vmit) - return MB_FAILURE; + if (varInfo.end() == vmit) { + SET_ERR_STR(MB_FAILURE, "Couldn't find variable " << var_name); + } assert(lmin >= 0 && lmax >= lmin); NCDF_SIZE tstart = lmin; NCDF_SIZE tcount = lmax - lmin + 1; NCDF_DIFF dum_stride = 1; - int fail; + int success = 0; // Check size if ((std::size_t)tcount != cvals.size()) @@ -588,19 +580,19 @@ ErrorCode NCHelper::read_coordinate(const char* var_name, int lmin, int lmax, st // Check to make sure it's a float or double if (NC_DOUBLE == (*vmit).second.varDataType) { - fail = NCFUNCAG(_vars_double)(_fileId, (*vmit).second.varId, &tstart, &tcount, &dum_stride, &cvals[0]); - if (fail) - ERRORS(MB_FAILURE, "Failed to get coordinate values."); + success = NCFUNCAG(_vars_double)(_fileId, (*vmit).second.varId, &tstart, &tcount, &dum_stride, &cvals[0]); + if (success) + SET_ERR(MB_FAILURE, "Failed to get coordinate values"); } else if (NC_FLOAT == (*vmit).second.varDataType) { std::vector<float> tcvals(tcount); - fail = NCFUNCAG(_vars_float)(_fileId, (*vmit).second.varId, &tstart, &tcount, &dum_stride, &tcvals[0]); - if (fail) - ERRORS(MB_FAILURE, "Failed to get coordinate values."); + success = NCFUNCAG(_vars_float)(_fileId, (*vmit).second.varId, &tstart, &tcount, &dum_stride, &tcvals[0]); + if (success) + SET_ERR(MB_FAILURE, "Failed to get coordinate values"); std::copy(tcvals.begin(), tcvals.end(), cvals.begin()); } else { - ERRORR(MB_FAILURE, "Wrong data type for coordinate variable."); + SET_ERR(MB_FAILURE, "Wrong data type for coordinate variable"); } return MB_SUCCESS; @@ -633,8 +625,7 @@ ErrorCode NCHelper::get_tag_to_set(ReadNC::VarData& var_data, int tstep_num, Tag rval = mbImpl->tag_get_handle(tag_name.str().c_str(), 0, MB_TYPE_INTEGER, tagh, MB_TAG_CREAT | MB_TAG_SPARSE | MB_TAG_VARLEN); break; default: - std::cerr << "Unrecognized data type for tag " << tag_name << std::endl; - rval = MB_FAILURE; + SET_ERR_STR(MB_FAILURE, "Unrecognized data type for tag " << tag_name.str()); } if (MB_SUCCESS == rval) @@ -667,8 +658,7 @@ ErrorCode NCHelper::get_tag_to_nonset(ReadNC::VarData& var_data, int tstep_num, rval = mbImpl->tag_get_handle(tag_name.str().c_str(), num_lev, MB_TYPE_INTEGER, tagh, MB_TAG_DENSE | MB_TAG_CREAT); break; default: - std::cerr << "Unrecognized data type for tag " << tag_name.str() << std::endl; - rval = MB_FAILURE; + SET_ERR_STR(MB_FAILURE, "Unrecognized data type for tag " << tag_name.str()); } if (MB_SUCCESS == rval) @@ -679,7 +669,7 @@ ErrorCode NCHelper::get_tag_to_nonset(ReadNC::VarData& var_data, int tstep_num, ErrorCode NCHelper::create_attrib_string(const std::map<std::string, ReadNC::AttData>& attMap, std::string& attVal, std::vector<int>& attLen) { - int success; + int success = 0; std::stringstream ssAtt; unsigned int sz = 0; std::map<std::string, ReadNC::AttData>::const_iterator attIt = attMap.begin(); @@ -693,39 +683,44 @@ ErrorCode NCHelper::create_attrib_string(const std::map<std::string, ReadNC::Att sz = attIt->second.attLen; attData = (char *) malloc(sz); success = NCFUNC(get_att_text)(_fileId, attIt->second.attVarId, attIt->second.attName.c_str(), (char*) attData); - ERRORS(success, "Failed to read attribute char data."); + if (success) + SET_ERR(MB_FAILURE, "Failed to read attribute char data"); ssAtt << "char;"; break; case NC_DOUBLE: sz = attIt->second.attLen * sizeof(double); attData = (double *) malloc(sz); success = NCFUNC(get_att_double)(_fileId, attIt->second.attVarId, attIt->second.attName.c_str(), (double*) attData); - ERRORS(success, "Failed to read attribute double data."); + if (success) + SET_ERR(MB_FAILURE, "Failed to read attribute double data"); ssAtt << "double;"; break; case NC_FLOAT: sz = attIt->second.attLen * sizeof(float); attData = (float *) malloc(sz); success = NCFUNC(get_att_float)(_fileId, attIt->second.attVarId, attIt->second.attName.c_str(), (float*) attData); - ERRORS(success, "Failed to read attribute float data."); + if (success) + SET_ERR(MB_FAILURE, "Failed to read attribute float data"); ssAtt << "float;"; break; case NC_INT: sz = attIt->second.attLen * sizeof(int); attData = (int *) malloc(sz); success = NCFUNC(get_att_int)(_fileId, attIt->second.attVarId, attIt->second.attName.c_str(), (int*) attData); - ERRORS(success, "Failed to read attribute int data."); + if (success) + SET_ERR(MB_FAILURE, "Failed to read attribute int data"); ssAtt << "int;"; break; case NC_SHORT: sz = attIt->second.attLen * sizeof(short); attData = (short *) malloc(sz); success = NCFUNC(get_att_short)(_fileId, attIt->second.attVarId, attIt->second.attName.c_str(), (short*) attData); - ERRORS(success, "Failed to read attribute short data."); + if (success) + SET_ERR(MB_FAILURE, "Failed to read attribute short data"); ssAtt << "short;"; break; default: - success = 1; + SET_ERR_STR(MB_FAILURE, "Unrecognized data type for attribute " << attIt->second.attName); } char* tmpc = (char *) attData; for (unsigned int counter = 0; counter != sz; ++counter) @@ -773,15 +768,15 @@ ErrorCode NCHelper::create_dummy_variables() // Create a corresponding sparse tag Tag tagh; ErrorCode rval = mbImpl->tag_get_handle(dimNames[i].c_str(), 0, MB_TYPE_INTEGER, tagh, - MB_TAG_CREAT | MB_TAG_SPARSE | MB_TAG_VARLEN); - ERRORR(rval, "Failed to create tag for a dummy dimension variable."); + MB_TAG_CREAT | MB_TAG_SPARSE | MB_TAG_VARLEN); \ + CHK_ERR1(rval, "Failed to create tag for a dummy dimension variable"); // Tag value is the dimension length const void* ptr = &dimLens[i]; // Tag size is 1 int size = 1; - rval = mbImpl->tag_set_by_ptr(tagh, &_fileSet, 1, &ptr, &size); - ERRORR(rval, "Failed to set data for dimension tag."); + rval = mbImpl->tag_set_by_ptr(tagh, &_fileSet, 1, &ptr, &size); \ + CHK_ERR1(rval, "Failed to set data for dimension tag"); dbgOut.tprintf(2, "Sparse tag created for dimension %s\n", dimNames[i].c_str()); } @@ -804,7 +799,7 @@ ErrorCode NCHelper::read_variable_to_set_allocate(std::vector<ReadNC::VarData>& vdatas[i].readCounts.push_back(1); // Next: other dimensions - for (unsigned int idx = 1; idx != vdatas[i].varDims.size(); idx++){ + for (unsigned int idx = 1; idx != vdatas[i].varDims.size(); idx++) { vdatas[i].readStarts.push_back(0); vdatas[i].readCounts.push_back(dimLens[vdatas[i].varDims[idx]]); } @@ -816,7 +811,7 @@ ErrorCode NCHelper::read_variable_to_set_allocate(std::vector<ReadNC::VarData>& vdatas[i].readCounts.push_back(1); } else { - for (unsigned int idx = 0; idx != vdatas[i].varDims.size(); idx++){ + for (unsigned int idx = 0; idx != vdatas[i].varDims.size(); idx++) { vdatas[i].readStarts.push_back(0); vdatas[i].readCounts.push_back(dimLens[vdatas[i].varDims[idx]]); } @@ -833,13 +828,13 @@ ErrorCode NCHelper::read_variable_to_set_allocate(std::vector<ReadNC::VarData>& dbgOut.tprintf(2, "Reading variable %s, time step %d\n", vdatas[i].varName.c_str(), tstep_nums[t]); if (tstep_nums[t] >= dimLens[tDim]) { - ERRORR(MB_INDEX_OUT_OF_RANGE, "Wrong value for a timestep number."); + SET_ERR(MB_INDEX_OUT_OF_RANGE, "Wrong value for a timestep number"); } // Get the tag to read into if (!vdatas[i].varTags[t]) { - rval = get_tag_to_set(vdatas[i], tstep_nums[t], vdatas[i].varTags[t]); - ERRORR(rval, "Trouble getting tag for a set variable."); + rval = get_tag_to_set(vdatas[i], tstep_nums[t], vdatas[i].varTags[t]); \ + CHK_ERR1(rval, "Trouble getting tag for a set variable"); } switch (vdatas[i].varDataType) { @@ -856,8 +851,7 @@ ErrorCode NCHelper::read_variable_to_set_allocate(std::vector<ReadNC::VarData>& vdatas[i].varDatas[t] = new int[vdatas[i].sz]; break; default: - std::cerr << "Unrecognized data type for set variable tag values" << std::endl; - rval = MB_FAILURE; + SET_ERR_STR(MB_FAILURE, "Unrecognized data type for tag values of set variable " << vdatas[i].varName); } // Loop continues only for set variables with timesteps, e.g. xtime(Time, StrLen) @@ -874,8 +868,8 @@ ErrorCode ScdNCHelper::check_existing_mesh() { // Get the number of vertices int num_verts; - ErrorCode rval = mbImpl->get_number_entities_by_dimension(_fileSet, 0, num_verts); - ERRORR(rval, "Trouble getting number of vertices."); + ErrorCode rval = mbImpl->get_number_entities_by_dimension(_fileSet, 0, num_verts); \ + CHK_ERR1(rval, "Trouble getting number of vertices"); /* // Check against parameters @@ -883,15 +877,15 @@ ErrorCode ScdNCHelper::check_existing_mesh() { if (num_verts > 0) { int expected_verts = (lDims[3] - lDims[0] + 1) * (lDims[4] - lDims[1] + 1) * (-1 == lDims[2] ? 1 : lDims[5] - lDims[2] + 1); if (num_verts != expected_verts) { - ERRORR(MB_FAILURE, "Number of vertices doesn't match."); + SET_ERR(MB_FAILURE, "Number of vertices doesn't match"); } } */ // Check the number of elements too int num_elems; - rval = mbImpl->get_number_entities_by_dimension(_fileSet, (-1 == lCDims[2] ? 2 : 3), num_elems); - ERRORR(rval, "Trouble getting number of elements."); + rval = mbImpl->get_number_entities_by_dimension(_fileSet, (-1 == lCDims[2] ? 2 : 3), num_elems); \ + CHK_ERR1(rval, "Trouble getting number of elements"); /* // Check against parameters @@ -899,7 +893,7 @@ ErrorCode ScdNCHelper::check_existing_mesh() { if (num_elems > 0) { int expected_elems = (lCDims[3] - lCDims[0] + 1) * (lCDims[4] - lCDims[1] + 1) * (-1 == lCDims[2] ? 1 : (lCDims[5] - lCDims[2] + 1)); if (num_elems != expected_elems) { - ERRORR(MB_FAILURE, "Number of elements doesn't match."); + SET_ERR(MB_FAILURE, "Number of elements doesn't match"); } } */ @@ -920,8 +914,8 @@ ErrorCode ScdNCHelper::create_mesh(Range& faces) ScdBox* scd_box; ErrorCode rval = scdi->construct_box(HomCoord(lDims[0], lDims[1], lDims[2], 1), HomCoord(lDims[3], lDims[4], lDims[5], 1), - NULL, 0, scd_box, locallyPeriodic, &parData, true); - ERRORR(rval, "Trouble creating scd vertex sequence."); + NULL, 0, scd_box, locallyPeriodic, &parData, true); \ + CHK_ERR1(rval, "Trouble creating scd vertex sequence"); // Add verts to tmp_range first, so we can duplicate global ids in vertex ids tmp_range.insert(scd_box->start_vertex(), scd_box->start_vertex() + scd_box->num_vertices() - 1); @@ -929,12 +923,12 @@ ErrorCode ScdNCHelper::create_mesh(Range& faces) if (mpFileIdTag) { int count; void* data; - rval = mbImpl->tag_iterate(*mpFileIdTag, tmp_range.begin(), tmp_range.end(), count, data); - ERRORR(rval, "Failed to get tag iterator on file id tag."); + rval = mbImpl->tag_iterate(*mpFileIdTag, tmp_range.begin(), tmp_range.end(), count, data); \ + CHK_ERR1(rval, "Failed to get tag iterator on file id tag"); assert(count == scd_box->num_vertices()); int* fid_data = (int*) data; - rval = mbImpl->tag_iterate(mGlobalIdTag, tmp_range.begin(), tmp_range.end(), count, data); - ERRORR(rval, "Failed to get tag iterator on global id tag."); + rval = mbImpl->tag_iterate(mGlobalIdTag, tmp_range.begin(), tmp_range.end(), count, data); \ + CHK_ERR1(rval, "Failed to get tag iterator on global id tag"); assert(count == scd_box->num_vertices()); int* gid_data = (int*) data; for (int i = 0; i < count; i++) @@ -944,22 +938,22 @@ ErrorCode ScdNCHelper::create_mesh(Range& faces) // Then add box set and elements to the range, then to the file set tmp_range.insert(scd_box->start_element(), scd_box->start_element() + scd_box->num_elements() - 1); tmp_range.insert(scd_box->box_set()); - rval = mbImpl->add_entities(_fileSet, tmp_range); - ERRORR(rval, "Couldn't add new vertices to file set."); + rval = mbImpl->add_entities(_fileSet, tmp_range); \ + CHK_ERR1(rval, "Couldn't add new vertices to file set"); dbgOut.tprintf(1, "scdbox %d quads, %d vertices\n", scd_box->num_elements(), scd_box->num_vertices()); // Set the vertex coordinates double *xc, *yc, *zc; - rval = scd_box->get_coordinate_arrays(xc, yc, zc); - ERRORR(rval, "Couldn't get vertex coordinate arrays."); + rval = scd_box->get_coordinate_arrays(xc, yc, zc); \ + CHK_ERR1(rval, "Couldn't get vertex coordinate arrays"); int i, j, k, il, jl, kl; int dil = lDims[3] - lDims[0] + 1; int djl = lDims[4] - lDims[1] + 1; assert(dil == (int)ilVals.size() && djl == (int)jlVals.size() && (-1 == lDims[2] || lDims[5] - lDims[2] + 1 == (int)levVals.size())); -//#define INDEX(i, j, k) () + for (kl = lDims[2]; kl <= lDims[5]; kl++) { k = kl - lDims[2]; for (jl = lDims[1]; jl <= lDims[4]; jl++) { @@ -973,14 +967,13 @@ ErrorCode ScdNCHelper::create_mesh(Range& faces) } } } -//#undef INDEX #ifndef NDEBUG int num_verts = (lDims[3] - lDims[0] + 1) * (lDims[4] - lDims[1] + 1) * (-1 == lDims[2] ? 1 : lDims[5] - lDims[2] + 1); std::vector<int> gids(num_verts); Range verts(scd_box->start_vertex(), scd_box->start_vertex() + scd_box->num_vertices() - 1); - rval = mbImpl->tag_get_data(mGlobalIdTag, verts, &gids[0]); - ERRORR(rval, "Trouble getting gid values."); + rval = mbImpl->tag_get_data(mGlobalIdTag, verts, &gids[0]); \ + CHK_ERR1(rval, "Trouble getting gid values"); int vmin = *(std::min_element(gids.begin(), gids.end())), vmax = *(std::max_element(gids.begin(), gids.end())); dbgOut.tprintf(1, "Vertex gids %d-%d\n", vmin, vmax); #endif @@ -991,15 +984,15 @@ ErrorCode ScdNCHelper::create_mesh(Range& faces) if (2 <= dbgOut.get_verbosity()) { assert(scd_box->boundary_complete()); EntityHandle dum_ent = scd_box->start_element(); - rval = mbImpl->list_entities(&dum_ent, 1); - ERRORR(rval, "Trouble listing first hex."); + rval = mbImpl->list_entities(&dum_ent, 1); \ + CHK_ERR1(rval, "Trouble listing first hex"); std::vector<EntityHandle> connect; - rval = mbImpl->get_connectivity(&dum_ent, 1, connect); - ERRORR(rval, "Trouble getting connectivity."); + rval = mbImpl->get_connectivity(&dum_ent, 1, connect); \ + CHK_ERR1(rval, "Trouble getting connectivity"); - rval = mbImpl->list_entities(&connect[0], connect.size()); - ERRORR(rval, "Trouble listing element connectivity."); + rval = mbImpl->list_entities(&connect[0], connect.size()); \ + CHK_ERR1(rval, "Trouble listing element connectivity"); } Range edges; @@ -1013,16 +1006,16 @@ ErrorCode ScdNCHelper::read_variables(std::vector<std::string>& var_names, std:: std::vector<ReadNC::VarData> vdatas; std::vector<ReadNC::VarData> vsetdatas; - ErrorCode rval = read_variable_setup(var_names, tstep_nums, vdatas, vsetdatas); - ERRORR(rval, "Trouble setting up read variable."); + ErrorCode rval = read_variable_setup(var_names, tstep_nums, vdatas, vsetdatas); \ + CHK_ERR1(rval, "Trouble setting up read variable"); // Create COORDS tag for quads - rval = create_quad_coordinate_tag(); - ERRORR(rval, "Trouble creating coordinate tags to entities quads"); + rval = create_quad_coordinate_tag(); \ + CHK_ERR1(rval, "Trouble creating coordinate tags to entities quads"); if (!vsetdatas.empty()) { - rval = read_variable_to_set(vsetdatas, tstep_nums); - ERRORR(rval, "Trouble read variables to set."); + rval = read_variable_to_set(vsetdatas, tstep_nums); \ + CHK_ERR1(rval, "Trouble read variables to set"); } if (!vdatas.empty()) { @@ -1046,19 +1039,19 @@ ErrorCode ScdNCHelper::read_scd_variable_to_nonset_allocate(std::vector<ReadNC:: // Get vertices in set Range verts; - rval = mbImpl->get_entities_by_dimension(_fileSet, 0, verts); - ERRORR(rval, "Trouble getting vertices in set."); + rval = mbImpl->get_entities_by_dimension(_fileSet, 0, verts); \ + CHK_ERR1(rval, "Trouble getting vertices in set"); assert("Should only have a single vertex subrange, since they were read in one shot" && verts.psize() == 1); Range edges; - rval = mbImpl->get_entities_by_dimension(_fileSet, 1, edges); - ERRORR(rval, "Trouble getting edges in set."); + rval = mbImpl->get_entities_by_dimension(_fileSet, 1, edges); \ + CHK_ERR1(rval, "Trouble getting edges in set"); // Get faces in set Range faces; - rval = mbImpl->get_entities_by_dimension(_fileSet, 2, faces); - ERRORR(rval, "Trouble getting faces in set."); + rval = mbImpl->get_entities_by_dimension(_fileSet, 2, faces); \ + CHK_ERR1(rval, "Trouble getting faces in set"); assert("Should only have a single face subrange, since they were read in one shot" && faces.psize() == 1); @@ -1067,8 +1060,8 @@ ErrorCode ScdNCHelper::read_scd_variable_to_nonset_allocate(std::vector<ReadNC:: bool& isParallel = _readNC->isParallel; if (isParallel) { ParallelComm*& myPcomm = _readNC->myPcomm; - rval = myPcomm->filter_pstatus(faces, PSTATUS_NOT_OWNED, PSTATUS_NOT, -1, &faces_owned); - ERRORR(rval, "Trouble getting owned faces in set."); + rval = myPcomm->filter_pstatus(faces, PSTATUS_NOT_OWNED, PSTATUS_NOT, -1, &faces_owned); \ + CHK_ERR1(rval, "Trouble getting owned faces in set"); } else faces_owned = faces; // Not running in parallel, but still with MPI @@ -1122,28 +1115,27 @@ ErrorCode ScdNCHelper::read_scd_variable_to_nonset_allocate(std::vector<ReadNC:: // Set break; default: - ERRORR(MB_FAILURE, "Unrecognized entity location type."); - break; + SET_ERR(MB_FAILURE, "Unrecognized entity location type"); } for (unsigned int t = 0; t < tstep_nums.size(); t++) { dbgOut.tprintf(2, "Reading variable %s, time step %d\n", vdatas[i].varName.c_str(), tstep_nums[t]); if (tstep_nums[t] >= dimLens[tDim]) { - ERRORR(MB_INDEX_OUT_OF_RANGE, "Wrong value for a timestep number."); + SET_ERR(MB_INDEX_OUT_OF_RANGE, "Wrong value for a timestep number"); } // Get the tag to read into if (!vdatas[i].varTags[t]) { - rval = get_tag_to_nonset(vdatas[i], tstep_nums[t], vdatas[i].varTags[t], vdatas[i].numLev); - ERRORR(rval, "Trouble getting tag."); + rval = get_tag_to_nonset(vdatas[i], tstep_nums[t], vdatas[i].varTags[t], vdatas[i].numLev); \ + CHK_ERR1(rval, "Trouble getting tag"); } // Get ptr to tag space void* data; int count; - rval = mbImpl->tag_iterate(vdatas[i].varTags[t], range->begin(), range->end(), count, data); - ERRORR(rval, "Failed to get tag iterator."); + rval = mbImpl->tag_iterate(vdatas[i].varTags[t], range->begin(), range->end(), count, data); \ + CHK_ERR1(rval, "Failed to get tag iterator"); assert((unsigned)count == range->size()); vdatas[i].varDatas[t] = data; } @@ -1161,12 +1153,11 @@ ErrorCode ScdNCHelper::read_scd_variable_to_nonset(std::vector<ReadNC::VarData>& { DebugOutput& dbgOut = _readNC->dbgOut; - ErrorCode rval = read_scd_variable_to_nonset_allocate(vdatas, tstep_nums); - if (MB_SUCCESS != rval) - SET_ERR(rval, "Trouble allocating space to read variables"); + ErrorCode rval = read_scd_variable_to_nonset_allocate(vdatas, tstep_nums); \ + CHK_ERR1(rval, "Trouble allocating space to read non-set variables"); // Finally, read into that space - int success; + int success = 0; for (unsigned int i = 0; i < vdatas.size(); i++) { std::size_t sz = vdatas[i].sz; @@ -1196,7 +1187,8 @@ ErrorCode ScdNCHelper::read_scd_variable_to_nonset(std::vector<ReadNC::VarData>& for (std::size_t idx = 0; idx != tmpchardata.size(); idx++) ((char*) data)[idx] = tmpchardata[idx]; } - ERRORS(success, "Failed to read char data."); + if (success) + SET_ERR(MB_FAILURE, "Failed to read char data"); break; } case NC_DOUBLE: { @@ -1210,7 +1202,8 @@ ErrorCode ScdNCHelper::read_scd_variable_to_nonset(std::vector<ReadNC::VarData>& for (std::size_t idx = 0; idx != tmpdoubledata.size(); idx++) ((double*) data)[idx] = tmpdoubledata[idx]; } - ERRORS(success, "Failed to read double data."); + if (success) + SET_ERR(MB_FAILURE, "Failed to read double data"); break; } case NC_FLOAT: { @@ -1224,7 +1217,8 @@ ErrorCode ScdNCHelper::read_scd_variable_to_nonset(std::vector<ReadNC::VarData>& for (std::size_t idx = 0; idx != tmpfloatdata.size(); idx++) ((float*) data)[idx] = tmpfloatdata[idx]; } - ERRORS(success, "Failed to read float data."); + if (success) + SET_ERR(MB_FAILURE, "Failed to read float data"); break; } case NC_INT: { @@ -1238,7 +1232,8 @@ ErrorCode ScdNCHelper::read_scd_variable_to_nonset(std::vector<ReadNC::VarData>& for (std::size_t idx = 0; idx != tmpintdata.size(); idx++) ((int*) data)[idx] = tmpintdata[idx]; } - ERRORS(success, "Failed to read int data."); + if (success) + SET_ERR(MB_FAILURE, "Failed to read int data"); break; } case NC_SHORT: { @@ -1252,24 +1247,20 @@ ErrorCode ScdNCHelper::read_scd_variable_to_nonset(std::vector<ReadNC::VarData>& for (std::size_t idx = 0; idx != tmpshortdata.size(); idx++) ((short*) data)[idx] = tmpshortdata[idx]; } - ERRORS(success, "Failed to read short data."); + if (success) + SET_ERR(MB_FAILURE, "Failed to read short data"); break; } default: - success = 1; + SET_ERR_STR(MB_FAILURE, "Unrecognized data type for non-set variable " << vdatas[i].varName); } - - if (success) - ERRORR(MB_FAILURE, "Trouble reading variable."); } } for (unsigned int i = 0; i < vdatas.size(); i++) { for (unsigned int t = 0; t < tstep_nums.size(); t++) { dbgOut.tprintf(2, "Converting variable %s, time step %d\n", vdatas[i].varName.c_str(), tstep_nums[t]); - ErrorCode tmp_rval = convert_variable(vdatas[i], t); - if (MB_SUCCESS != tmp_rval) - rval = tmp_rval; + rval = convert_variable(vdatas[i], t);CHK_ERR(rval); } } @@ -1288,8 +1279,8 @@ ErrorCode ScdNCHelper::create_quad_coordinate_tag() { Interface*& mbImpl = _readNC->mbImpl; Range ents; - ErrorCode rval = mbImpl->get_entities_by_type(_fileSet, moab::MBQUAD, ents); - ERRORR(rval, "Trouble getting QUAD entity."); + ErrorCode rval = mbImpl->get_entities_by_type(_fileSet, moab::MBQUAD, ents); \ + CHK_ERR1(rval, "Trouble getting QUAD entity"); std::size_t numOwnedEnts = 0; #ifdef USE_MPI @@ -1297,12 +1288,11 @@ ErrorCode ScdNCHelper::create_quad_coordinate_tag() { bool& isParallel = _readNC->isParallel; if (isParallel) { ParallelComm*& myPcomm = _readNC->myPcomm; - rval = myPcomm->filter_pstatus(ents, PSTATUS_NOT_OWNED, PSTATUS_NOT, -1, &ents_owned); - ERRORR(rval, "Trouble getting owned QUAD entity."); + rval = myPcomm->filter_pstatus(ents, PSTATUS_NOT_OWNED, PSTATUS_NOT, -1, &ents_owned); \ + CHK_ERR1(rval, "Trouble getting owned QUAD entity"); numOwnedEnts = ents_owned.size(); } - else - { + else { numOwnedEnts = ents.size(); ents_owned = ents; } @@ -1326,17 +1316,18 @@ ErrorCode ScdNCHelper::create_quad_coordinate_tag() { } std::string tag_name = "COORDS"; Tag tagh = 0; - rval = mbImpl->tag_get_handle(tag_name.c_str(), 3, MB_TYPE_DOUBLE, tagh, MB_TAG_DENSE | MB_TAG_CREAT); - ERRORR(rval, "Trouble creating COORDS tag."); + rval = mbImpl->tag_get_handle(tag_name.c_str(), 3, MB_TYPE_DOUBLE, tagh, MB_TAG_DENSE | MB_TAG_CREAT); \ + CHK_ERR1(rval, "Trouble creating COORDS tag"); void *data; int count; #ifdef USE_MPI - rval = mbImpl->tag_iterate(tagh, ents_owned.begin(), ents_owned.end(), count, data); + rval = mbImpl->tag_iterate(tagh, ents_owned.begin(), ents_owned.end(), count, data); \ + CHK_ERR1(rval, "Failed to get COORDS tag iterator"); #else - rval = mbImpl->tag_iterate(tagh, ents.begin(), ents.end(), count, data); + rval = mbImpl->tag_iterate(tagh, ents.begin(), ents.end(), count, data); \ + CHK_ERR1(rval, "Failed to get COORDS tag iterator"); #endif - ERRORR(rval, "Failed to get COORDS tag iterator."); assert(count == (int)numOwnedEnts); double* quad_data = (double*) data; std::copy(coords.begin(), coords.end(), quad_data); @@ -1349,23 +1340,24 @@ ErrorCode UcdNCHelper::read_variables(std::vector<std::string>& var_names, std:: std::vector<ReadNC::VarData> vdatas; std::vector<ReadNC::VarData> vsetdatas; - ErrorCode rval = read_variable_setup(var_names, tstep_nums, vdatas, vsetdatas); - ERRORR(rval, "Trouble setting up read variable."); + ErrorCode rval = read_variable_setup(var_names, tstep_nums, vdatas, vsetdatas); \ + CHK_ERR1(rval, "Trouble setting up to read variables"); if (!vsetdatas.empty()) { - rval = read_variable_to_set(vsetdatas, tstep_nums); - ERRORR(rval, "Trouble read variables to set."); + rval = read_variable_to_set(vsetdatas, tstep_nums); \ + CHK_ERR1(rval, "Trouble reading variables to set"); } if (!vdatas.empty()) { #ifdef PNETCDF_FILE // With pnetcdf support, we will use async read - rval = read_ucd_variable_to_nonset_async(vdatas, tstep_nums); + rval = read_ucd_variable_to_nonset_async(vdatas, tstep_nums); \ + CHK_ERR1(rval, "Trouble reading variables to entities verts/edges/faces"); #else // Without pnetcdf support, we will use old read - rval = read_ucd_variable_to_nonset(vdatas, tstep_nums); + rval = read_ucd_variable_to_nonset(vdatas, tstep_nums); \ + CHK_ERR1(rval, "Trouble reading variables to entities verts/edges/faces"); #endif - ERRORR(rval, "Trouble read variables to entities verts/edges/faces."); } return MB_SUCCESS; Repository URL: https://bitbucket.org/fathomteam/moab/ -- This is a commit notification from bitbucket.org. 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commit/MOAB: tautges: Merged deformed-mesh-remap into master
by commits-noreply＠bitbucket.org 12 Mar '14

12 Mar '14

1 new commit in MOAB: https://bitbucket.org/fathomteam/moab/commits/0c6bff4ac382/ Changeset: 0c6bff4ac382 Branch: master User: tautges Date: 2014-03-12 17:07:54 Summary: Merged deformed-mesh-remap into master Affected #: 19 files diff --git a/examples/DeformMeshRemap.cpp b/examples/DeformMeshRemap.cpp index 5442d1d..55dac45 100644 --- a/examples/DeformMeshRemap.cpp +++ b/examples/DeformMeshRemap.cpp @@ -12,6 +12,7 @@ #include "moab/Core.hpp" #include "moab/Range.hpp" +#include "moab/Skinner.hpp" #include "moab/LloydSmoother.hpp" #include "moab/ProgOptions.hpp" #include "moab/BoundBox.hpp" @@ -19,6 +20,10 @@ #include "MBTagConventions.hpp" #include "DataCoupler.hpp" +#define IS_BUILDING_MB +#include "moab/Error.hpp" +#undef IS_BUILDING_MB + #ifdef USE_MPI # include "moab/ParallelComm.hpp" #endif @@ -69,13 +74,13 @@ public: ErrorCode execute(); //! add a set number - ErrorCode add_set_no(int fluid_or_solid, int set_no); + ErrorCode add_set_no(int m_or_s, int fluid_or_solid, int set_no); //! remove a set number - ErrorCode remove_set_no(int fluid_or_solid, int set_no); + ErrorCode remove_set_no(int m_or_s, int fluid_or_solid, int set_no); //! get the set numbers - ErrorCode get_set_nos(int fluid_or_solid, std::set<int> &set_nos) const; + ErrorCode get_set_nos(int m_or_s, int fluid_or_solid, std::set<int> &set_nos) const; //! get the xNew tag handle inline Tag x_new() const {return xNew;} @@ -91,6 +96,10 @@ public: //! get/set the file name void set_file_name(int m_or_s, const std::string &name); + + //! get/set the x displacement tag names + std::string xdisp_name(int idx = 0); + void xdisp_name(const std::string &nm, int idx = 0); private: //! apply a known deformation to the solid elements, putting the results in the xNew tag; also @@ -101,24 +110,32 @@ private: ErrorCode read_file(int m_or_s, string &fname, EntityHandle &seth); //! write the input tag to the coordinates for the vertices in the input elems - ErrorCode write_to_coords(Range &elems, Tag tagh); + //! if non-zero tmp_tag is input, save coords to tmp_tag before over-writing with tag value + ErrorCode write_to_coords(Range &elems, Tag tagh, Tag tmp_tag = 0); //! write the tag to the vertices, then save to the specified file - ErrorCode write_and_save(Range &ents, EntityHandle seth, Tag tagh, const char *filename); + //! if restore_coords is true, coords are restored to their initial state after file is written + ErrorCode write_and_save(Range &ents, EntityHandle seth, Tag tagh, const char *filename, + bool restore_coords = false); + //! find fluid/solid sets from complement of solid/fluid sets + ErrorCode find_other_sets(int m_or_s, EntityHandle file_set); + //! moab interface Interface *mbImpl; + Error *mError; + #ifdef USE_MPI //! ParallelComm for master, slave meshes ParallelComm *pcMaster, *pcSlave; #endif - //! material set numbers for fluid materials - std::set<int> fluidSetNos; + //! material set numbers for fluid materials, for master/slave + std::set<int> fluidSetNos[2]; - //! material set numbers for solid materials - std::set<int> solidSetNos; + //! material set numbers for solid materials, for master/slave + std::set<int> solidSetNos[2]; //! sets defining master/slave meshes EntityHandle masterSet, slaveSet; @@ -132,22 +149,31 @@ private: //! filenames for master/slave meshes std::string masterFileName, slaveFileName; + //! tag from file, might be 3 + Tag xDisp[3]; + //! tag used for new positions Tag xNew; + //! tag name used to read disps from file + std::string xDispNames[3]; + //! tag name used for new positions std::string xNewName; }; //! add a set number -inline ErrorCode DeformMeshRemap::add_set_no(int f_or_s, int set_no) +inline ErrorCode DeformMeshRemap::add_set_no(int m_or_s, int f_or_s, int set_no) { std::set<int> *this_set; + assert ((m_or_s == MASTER || m_or_s == SLAVE) && "m_or_s should be MASTER or SLAVE."); + if (m_or_s != MASTER && m_or_s != SLAVE) return MB_INDEX_OUT_OF_RANGE; + switch (f_or_s) { case FLUID: - this_set = &fluidSetNos; break; + this_set = &fluidSetNos[m_or_s]; break; case SOLID: - this_set = &solidSetNos; break; + this_set = &solidSetNos[m_or_s]; break; default: assert(false && "f_or_s should be FLUID or SOLID."); return MB_FAILURE; @@ -159,14 +185,16 @@ inline ErrorCode DeformMeshRemap::add_set_no(int f_or_s, int set_no) } //! remove a set number -inline ErrorCode DeformMeshRemap::remove_set_no(int f_or_s, int set_no) +inline ErrorCode DeformMeshRemap::remove_set_no(int m_or_s, int f_or_s, int set_no) { std::set<int> *this_set; + assert ((m_or_s == MASTER || m_or_s == SLAVE) && "m_or_s should be MASTER or SLAVE."); + if (m_or_s != MASTER && m_or_s != SLAVE) return MB_INDEX_OUT_OF_RANGE; switch (f_or_s) { case FLUID: - this_set = &fluidSetNos; break; + this_set = &fluidSetNos[m_or_s]; break; case SOLID: - this_set = &solidSetNos; break; + this_set = &solidSetNos[m_or_s]; break; default: assert(false && "f_or_s should be FLUID or SOLID."); return MB_FAILURE; @@ -181,14 +209,16 @@ inline ErrorCode DeformMeshRemap::remove_set_no(int f_or_s, int set_no) } //! get the set numbers -inline ErrorCode DeformMeshRemap::get_set_nos(int f_or_s, std::set<int> &set_nos) const +inline ErrorCode DeformMeshRemap::get_set_nos(int m_or_s, int f_or_s, std::set<int> &set_nos) const { const std::set<int> *this_set; + assert ((m_or_s == MASTER || m_or_s == SLAVE) && "m_or_s should be MASTER or SLAVE."); + if (m_or_s != MASTER && m_or_s != SLAVE) return MB_INDEX_OUT_OF_RANGE; switch (f_or_s) { case FLUID: - this_set = &fluidSetNos; break; + this_set = &fluidSetNos[m_or_s]; break; case SOLID: - this_set = &solidSetNos; break; + this_set = &solidSetNos[m_or_s]; break; default: assert(false && "f_or_s should be FLUID or SOLID."); return MB_FAILURE; @@ -199,56 +229,108 @@ inline ErrorCode DeformMeshRemap::get_set_nos(int f_or_s, std::set<int> &set_nos return MB_SUCCESS; } +inline std::string DeformMeshRemap::xdisp_name(int idx) +{ + return xDispNames[idx]; +} + +void DeformMeshRemap::xdisp_name(const std::string &nm, int idx) +{ + xDispNames[idx] = nm; +} + ErrorCode DeformMeshRemap::execute() { // read master/slave files and get fluid/solid material sets ErrorCode rval = read_file(MASTER, masterFileName, masterSet); if (MB_SUCCESS != rval) return rval; - - rval = read_file(SLAVE, slaveFileName, slaveSet); - if (MB_SUCCESS != rval) return rval; + if (solidSetNos[MASTER].empty() || fluidSetNos[MASTER].empty()) { + rval = find_other_sets(MASTER, masterSet); RR("Failed to find other sets in master mesh."); + } + + bool have_slave = !(slaveFileName == "none"); + if (have_slave) { + rval = read_file(SLAVE, slaveFileName, slaveSet); + if (MB_SUCCESS != rval) return rval; + + if (solidSetNos[SLAVE].empty() || fluidSetNos[SLAVE].empty()) { + rval = find_other_sets(SLAVE, slaveSet); RR("Failed to find other sets in slave mesh."); + } + } + + if (debug) std::cout << "Constructing data coupler/search tree on master mesh..." << std::endl; + Range src_elems = solidElems[MASTER]; src_elems.merge(fluidElems[MASTER]); - // locate slave vertices in master, orig coords; do this with a data coupler, so you can - // later interpolate - Range tgt_verts, tmp_range = solidElems[SLAVE]; - tmp_range.merge(fluidElems[SLAVE]); - rval = mbImpl->get_adjacencies(tmp_range, 0, false, tgt_verts, Interface::UNION); - RR("Failed to get target verts."); - // initialize data coupler on source elements - DataCoupler dc_master(mbImpl, NULL, src_elems, 0); - - // locate slave vertices, caching results in dc - rval = dc_master.locate_points(tgt_verts); RR("Point location of tgt verts failed."); - int num_located = dc_master.spatial_locator()->local_num_located(); - if (num_located != (int)tgt_verts.size()) { - rval = MB_FAILURE; - std::cout << "Only " << num_located << " out of " << tgt_verts.size() << " target points successfully located." << std::endl; - return rval; + DataCoupler dc_master(mbImpl, src_elems, 0, NULL); + + Range tgt_verts; + if (have_slave) { + // locate slave vertices in master, orig coords; do this with a data coupler, so you can + // later interpolate + Range tmp_range = solidElems[SLAVE]; + tmp_range.merge(fluidElems[SLAVE]); + rval = mbImpl->get_adjacencies(tmp_range, 0, false, tgt_verts, Interface::UNION); + RR("Failed to get target verts."); + + // locate slave vertices, caching results in dc + if (debug) std::cout << "Locating slave vertices in master mesh..." << std::endl; + rval = dc_master.locate_points(tgt_verts); RR("Point location of tgt verts failed."); + int num_located = dc_master.spatial_locator()->local_num_located(); + if (num_located != (int)tgt_verts.size()) { + rval = MB_FAILURE; + std::cout << "Only " << num_located << " out of " << tgt_verts.size() << " target points successfully located." << std::endl; + return rval; + } } - + // deform the master's solid mesh, put results in a new tag + if (debug) std::cout << "Deforming fluid elements in master mesh..." << std::endl; rval = deform_master(fluidElems[MASTER], solidElems[MASTER], "xnew"); RR(""); { // to isolate the lloyd smoother & delete when done + if (debug) { + // output the skin of smoothed elems, as a check + // get the skin; get facets, because we might need to filter on shared entities + Skinner skinner(mbImpl); + Range skin; + rval = skinner.find_skin(0, fluidElems[MASTER], false, skin); RR("Unable to find skin."); + EntityHandle skin_set; + std::cout << "Writing skin_mesh.g and fluid_mesh.g." << std::endl; + rval = mbImpl->create_meshset(MESHSET_SET, skin_set); RR("Failed to create skin set."); + rval = mbImpl->add_entities(skin_set, skin); RR("Failed to add skin entities to set."); + rval = mbImpl->write_file("skin_mesh.vtk", NULL, NULL, &skin_set, 1); RR("Failure to write skin set."); + rval = mbImpl->remove_entities(skin_set, skin); RR("Failed to remove skin entities from set."); + rval = mbImpl->add_entities(skin_set, fluidElems[MASTER]); RR("Failed to add fluid entities to set."); + rval = mbImpl->write_file("fluid_mesh.vtk", NULL, NULL, &skin_set, 1); RR("Failure to write fluid set."); + rval = mbImpl->delete_entities(&skin_set, 1); RR("Failed to delete skin set."); + } // smooth the master mesh + if (debug) std::cout << "Smoothing fluid elements in master mesh..." << std::endl; LloydSmoother ll(mbImpl, NULL, fluidElems[MASTER], xNew); rval = ll.perform_smooth(); RR("Failed in lloyd smoothing."); cout << "Lloyd smoothing required " << ll.num_its() << " iterations." << endl; } - - // map new locations to slave - // interpolate xNew to slave points - rval = dc_master.interpolate((int)DataCoupler::VOLUME, "xnew"); RR("Failed to interpolate target solution."); - // transfer xNew to coords, for master and slave + // transfer xNew to coords, for master + if (debug) std::cout << "Transferring coords tag to vertex coordinates in master mesh..." << std::endl; + rval = write_to_coords(solidElems[MASTER], xNew); RR("Failed writing tag to master fluid verts."); rval = write_to_coords(fluidElems[MASTER], xNew); RR("Failed writing tag to master fluid verts."); - rval = write_to_coords(tgt_verts, xNew); RR("Failed writing tag to slave verts."); + + if (have_slave) { + // map new locations to slave + // interpolate xNew to slave points + if (debug) std::cout << "Interpolating new coordinates to slave vertices..." << std::endl; + rval = dc_master.interpolate((int)DataCoupler::VOLUME, "xnew"); RR("Failed to interpolate target solution."); + // transfer xNew to coords, for slave + if (debug) std::cout << "Transferring coords tag to vertex coordinates in slave mesh..." << std::endl; + rval = write_to_coords(tgt_verts, xNew); RR("Failed writing tag to slave verts."); + } if (debug) { std::string str; @@ -256,14 +338,22 @@ ErrorCode DeformMeshRemap::execute() if (pcMaster && pcMaster->size() > 1) str = "PARALLEL=WRITE_PART"; #endif - rval = mbImpl->write_file("smoothed_master.vtk", NULL, str.c_str(), &masterSet, 1); + if (debug) std::cout << "Writing smoothed_master.h5m..." << std::endl; + rval = mbImpl->write_file("smoothed_master.h5m", NULL, str.c_str(), &masterSet, 1); + + if (have_slave) { #ifdef USE_MPI - str.clear(); - if (pcSlave && pcSlave->size() > 1) - str = "PARALLEL=WRITE_PART"; + str.clear(); + if (pcSlave && pcSlave->size() > 1) + str = "PARALLEL=WRITE_PART"; #endif - rval = mbImpl->write_file("slave_interp.vtk", NULL, str.c_str(), &slaveSet, 1); - } + if (debug) std::cout << "Writing slave_interp.h5m..." << std::endl; + rval = mbImpl->write_file("slave_interp.h5m", NULL, str.c_str(), &slaveSet, 1); + } // if have_slave + } // if debug + + if (debug) + dc_master.spatial_locator()->get_tree()->tree_stats().print(); return MB_SUCCESS; } @@ -296,14 +386,16 @@ void DeformMeshRemap::set_file_name(int m_or_s, const std::string &name) DeformMeshRemap::DeformMeshRemap(Interface *impl, ParallelComm *master, ParallelComm *slave) : mbImpl(impl), pcMaster(master), pcSlave(slave), masterSet(0), slaveSet(0), xNew(0), xNewName("xnew") { + mbImpl->query_interface(mError); + xDisp[0] = xDisp[1] = xDisp[2] = 0; + if (!pcSlave && pcMaster) pcSlave = pcMaster; } DeformMeshRemap::~DeformMeshRemap() { - // delete the tag - mbImpl->tag_delete(xNew); + mbImpl->release_interface(mError); } int main(int argc, char **argv) { @@ -312,14 +404,16 @@ int main(int argc, char **argv) { ProgOptions po("Deformed mesh options"); po.addOpt<std::string> ("master,m", "Specify the master meshfile name" ); - po.addOpt<std::string> ("slave,s", "Specify the slave meshfile name" ); + po.addOpt<std::string> ("worker,w", "Specify the slave/worker meshfile name, or 'none' (no quotes) if master only" ); + po.addOpt<std::string> ("d1,", "Tag name for displacement x or xyz" ); + po.addOpt<std::string> ("d2,", "Tag name for displacement y" ); + po.addOpt<std::string> ("d3,", "Tag name for displacement z" ); + po.addOpt<int> ("fm,", "Specify master fluid material set number(s). If none specified, fluid sets derived from complement of solid sets."); + po.addOpt<int> ("fs,", "Specify master solid material set number(s). If none specified, solid sets derived from complement of fluid sets."); + po.addOpt<int> ("sm,", "Specify slave fluid material set number(s). If none specified, fluid sets derived from complement of solid sets."); + po.addOpt<int> ("ss,", "Specify slave solid material set number(s). If none specified, solid sets derived from complement of fluid sets."); + po.parseCommandLine(argc, argv); - std::string foo; - string masterf, slavef; - if(!po.getOpt("master", &masterf)) - masterf = string(MESH_DIR) + string("/rodquad.g"); - if(!po.getOpt("slave", &slavef)) - slavef = string(MESH_DIR) + string("/rodtri.g"); mb = new Core(); @@ -330,10 +424,46 @@ int main(int argc, char **argv) { #else dfr = new DeformMeshRemap(mb); #endif + + + std::string masterf, slavef; + if(!po.getOpt("master", &masterf)) + masterf = string(MESH_DIR) + string("/rodquad.g"); dfr->set_file_name(DeformMeshRemap::MASTER, masterf); + + if(!po.getOpt("worker", &slavef)) + slavef = string(MESH_DIR) + string("/rodtri.g"); dfr->set_file_name(DeformMeshRemap::SLAVE, slavef); - rval = dfr->add_set_no(DeformMeshRemap::SOLID, SOLID_SETNO); RR("Failed to add solid set no."); - rval = dfr->add_set_no(DeformMeshRemap::FLUID, FLUID_SETNO); RR("Failed to add fluid set no."); + if (slavef.empty()) { + std::cerr << "Empty slave file name; if no slave, use filename 'none' (no quotes)." << std::endl; + return 1; + } + + std::vector<int> set_nos; + po.getOptAllArgs("fm", set_nos); + for (std::vector<int>::iterator vit = set_nos.begin(); vit != set_nos.end(); vit++) + dfr->add_set_no(DeformMeshRemap::MASTER, DeformMeshRemap::FLUID, *vit); + set_nos.clear(); + + po.getOptAllArgs("fs", set_nos); + for (std::vector<int>::iterator vit = set_nos.begin(); vit != set_nos.end(); vit++) + dfr->add_set_no(DeformMeshRemap::SLAVE, DeformMeshRemap::FLUID, *vit); + set_nos.clear(); + + po.getOptAllArgs("sm", set_nos); + for (std::vector<int>::iterator vit = set_nos.begin(); vit != set_nos.end(); vit++) + dfr->add_set_no(DeformMeshRemap::MASTER, DeformMeshRemap::SOLID, *vit); + + po.getOptAllArgs("ss", set_nos); + for (std::vector<int>::iterator vit = set_nos.begin(); vit != set_nos.end(); vit++) + dfr->add_set_no(DeformMeshRemap::SLAVE, DeformMeshRemap::SOLID, *vit); + + std::string tnames[3]; + po.getOpt("d1", &tnames[0]); + po.getOpt("d2", &tnames[1]); + po.getOpt("d3", &tnames[2]); + for (int i = 0; i < 3; i++) + if (!tnames[i].empty()) dfr->xdisp_name(tnames[i], i); rval = dfr->execute(); @@ -343,20 +473,38 @@ int main(int argc, char **argv) { return rval; } -ErrorCode DeformMeshRemap::write_and_save(Range &ents, EntityHandle seth, Tag tagh, const char *filename) +ErrorCode DeformMeshRemap::write_and_save(Range &ents, EntityHandle seth, Tag tagh, const char *filename, + bool restore_coords) { - ErrorCode rval = write_to_coords(ents, tagh); RR(""); + Tag tmp_tag = 0; + ErrorCode rval; + if (restore_coords) + rval = mbImpl->tag_get_handle("", 3, MB_TYPE_DOUBLE, tmp_tag, MB_TAG_CREAT|MB_TAG_DENSE); + + rval = write_to_coords(ents, tagh, tmp_tag); RR(""); rval = mbImpl->write_file(filename, NULL, NULL, &seth, 1); RR(""); + if (restore_coords) { + rval = write_to_coords(ents, tmp_tag); RR(""); + rval = mbImpl->tag_delete(tmp_tag); + } + return rval; } -ErrorCode DeformMeshRemap::write_to_coords(Range &elems, Tag tagh) +ErrorCode DeformMeshRemap::write_to_coords(Range &elems, Tag tagh, Tag tmp_tag) { // write the tag to coordinates Range verts; ErrorCode rval = mbImpl->get_adjacencies(elems, 0, false, verts, Interface::UNION); RR("Failed to get adj vertices."); std::vector<double> coords(3*verts.size()); + + if (tmp_tag) { + // save the coords to tmp_tag first + rval = mbImpl->get_coords(verts, &coords[0]); RR("Failed to get tmp copy of coords."); + rval = mbImpl->tag_set_data(tmp_tag, verts, &coords[0]); RR("Failed to save tmp copy of coords."); + } + rval = mbImpl->tag_get_data(tagh, verts, &coords[0]); RR("Failed to get tag data."); rval = mbImpl->set_coords(verts, &coords[0]); @@ -376,7 +524,6 @@ void deform_func(const BoundBox &bbox, double *xold, double *xnew) xnew[0] = xold[0] + yfrac * delx; xnew[1] = xold[1] + yfrac * (1.0 + xfrac) * 0.05; */ - /* Deformation function based on fraction of bounding box dimension in each direction */ double frac = 0.01; // taken from approximate relative deformation from LLNL Diablo of XX09 assys CartVect *xo = reinterpret_cast<CartVect*>(xold), *xn = reinterpret_cast<CartVect*>(xnew); @@ -387,40 +534,95 @@ void deform_func(const BoundBox &bbox, double *xold, double *xnew) ErrorCode DeformMeshRemap::deform_master(Range &fluid_elems, Range &solid_elems, const char *tag_name) { // deform elements with an analytic function + ErrorCode rval; - // create the tag - ErrorCode rval = mbImpl->tag_get_handle((tag_name ? tag_name : ""), 3, MB_TYPE_DOUBLE, xNew, MB_TAG_CREAT|MB_TAG_DENSE); - RR("Failed to create xnew tag."); - - // get all the vertices and coords in the fluid, set xnew to them - Range verts; - rval = mbImpl->get_adjacencies(fluid_elems, 0, false, verts, Interface::UNION); + // get all the vertices and coords in the solid + Range solid_verts, fluid_verts; + rval = mbImpl->get_adjacencies(solid_elems, 0, false, solid_verts, Interface::UNION); RR("Failed to get vertices."); - std::vector<double> coords(3*verts.size(), 0.0); - rval = mbImpl->get_coords(verts, &coords[0]); + std::vector<double> coords(3*solid_verts.size()), new_coords(3*solid_verts.size()); + rval = mbImpl->get_coords(solid_verts, &coords[0]); RR("Failed to get vertex coords."); - rval = mbImpl->tag_set_data(xNew, verts, &coords[0]); - RR("Failed to set xnew tag on fluid verts."); + unsigned int num_verts = solid_verts.size(); + + // get or create the tag + if (!xDispNames[0].empty() && !xDispNames[1].empty() && !xDispNames[2].empty()) { + // 3 tags, specifying xyz individual data, integrate into one tag + rval = mbImpl->tag_get_handle((tag_name ? tag_name : ""), 3, MB_TYPE_DOUBLE, xNew, MB_TAG_CREAT|MB_TAG_DENSE); + RR("Failed to create xnew tag."); + std::vector<double> disps(num_verts); + for (int i = 0; i < 3; i++) { + rval = mbImpl->tag_get_handle(xDispNames[0].c_str(), 1, MB_TYPE_DOUBLE, xDisp[i]); + RR("Failed to get xDisp tag."); + rval = mbImpl->tag_get_data(xDisp[i], solid_verts, &disps[0]); + RR("Failed to get xDisp tag values."); + for (unsigned int j = 0; j < num_verts; j++) + new_coords[3*j+i] = coords[3*j+i] + disps[j]; + } + } + else if (!xDispNames[0].empty()) { + rval = mbImpl->tag_get_handle(xDispNames[0].c_str(), 3, MB_TYPE_DOUBLE, xDisp[0]); + RR("Failed to get first xDisp tag."); + xNew = xDisp[0]; + std::vector<double> disps(3*num_verts); + rval = mbImpl->tag_get_data(xDisp[0], solid_verts, &disps[0]); + for (unsigned int j = 0; j < 3*num_verts; j++) + new_coords[j] = coords[j] + disps[j]; + } + else { + // get the bounding box of the solid mesh + BoundBox bbox; + bbox.update(*mbImpl, solid_elems); + + for (unsigned int j = 0; j < num_verts; j++) + deform_func(bbox, &coords[3*j], &new_coords[3*j]); + } - // get the bounding box of the solid mesh - BoundBox bbox; - bbox.update(*mbImpl, solid_elems); + if (debug) { + double len = 0.0; + for (unsigned int i = 0; i < num_verts; i++) { + CartVect dx = CartVect(&new_coords[3*i]) - CartVect(&coords[3*i]); + double tmp_len = dx.length_squared(); + if (tmp_len > len) len = tmp_len; + } + Range tmp_elems(fluid_elems); + tmp_elems.merge(solid_elems); + BoundBox box; + box.update(*mbImpl, tmp_elems); + double max_len = std::max(box.bMax[2]-box.bMin[2], std::max(box.bMax[1]-box.bMin[1], box.bMax[0]-box.bMin[0])); + + std::cout << "Max displacement = " << len << " (" << 100.0 * len / max_len << "% of max box length)" << std::endl; + } - // get all the vertices and coords in the solid - verts.clear(); - rval = mbImpl->get_adjacencies(solid_elems, 0, false, verts, Interface::UNION); - RR("Failed to get vertices."); - coords.resize(3*verts.size(), 0.0); - rval = mbImpl->get_coords(verts, &coords[0]); - RR("Failed to get vertex coords."); - unsigned int num_verts = verts.size(); - for (unsigned int i = 0; i < num_verts; i++) - deform_func(bbox, &coords[3*i], &coords[3*i]); + if (!xNew) { + rval = mbImpl->tag_get_handle((tag_name ? tag_name : ""), 3, MB_TYPE_DOUBLE, + xDisp[0], MB_TAG_CREAT|MB_TAG_DENSE); + RR("Failed to get xNew tag."); + xNew = xDisp[0]; + } // set the new tag to those coords - rval = mbImpl->tag_set_data(xNew, verts, &coords[0]); + rval = mbImpl->tag_set_data(xNew, solid_verts, &new_coords[0]); RR("Failed to set tag data."); + // get all the vertices and coords in the fluid, set xnew to them + rval = mbImpl->get_adjacencies(fluid_elems, 0, false, fluid_verts, Interface::UNION); + RR("Failed to get vertices."); + fluid_verts = subtract(fluid_verts, solid_verts); + + if (coords.size() < 3*fluid_verts.size()) coords.resize(3*fluid_verts.size()); + rval = mbImpl->get_coords(fluid_verts, &coords[0]); + RR("Failed to get vertex coords."); + rval = mbImpl->tag_set_data(xNew, fluid_verts, &coords[0]); + RR("Failed to set xnew tag on fluid verts."); + + if (debug) { + // save deformed mesh coords to new file for visualizing + Range tmp_range(fluidElems[MASTER]); + tmp_range.merge(solidElems[MASTER]); + rval = write_and_save(tmp_range, masterSet, xNew, "deformed_master.h5m", true); RR(""); + } + return MB_SUCCESS; } @@ -441,17 +643,22 @@ ErrorCode DeformMeshRemap::read_file(int m_or_s, string &fname, EntityHandle &se rval = mbImpl->load_file(fname.c_str(), &seth, ostr.str().c_str()); RR("Couldn't load master/slave mesh."); + if (*solidSetNos[m_or_s].begin() == -1 || *fluidSetNos[m_or_s].begin() == -1) return MB_SUCCESS; + // get material sets for solid/fluid Tag tagh; rval = mbImpl->tag_get_handle(MATERIAL_SET_TAG_NAME, tagh); RR("Couldn't get material set tag name."); - for (std::set<int>::iterator sit = solidSetNos.begin(); sit != solidSetNos.end(); sit++) { + for (std::set<int>::iterator sit = solidSetNos[m_or_s].begin(); sit != solidSetNos[m_or_s].end(); sit++) { Range sets; int set_no = *sit; const void *setno_ptr = &set_no; - rval = mbImpl->get_entities_by_type_and_tag(seth, MBENTITYSET, &tagh, &setno_ptr, 1, sets); - if (sets.empty()) rval = MB_FAILURE; - RR("Couldn't get any solid sets."); - solidSets[m_or_s].merge(sets); + ErrorCode tmp_rval = mbImpl->get_entities_by_type_and_tag(seth, MBENTITYSET, &tagh, &setno_ptr, 1, sets); + if (sets.empty() || MB_SUCCESS != tmp_rval) { + rval = MB_FAILURE; + mError->set_last_error("Couldn't find solid set #%d.\n", *sit); + } + else + solidSets[m_or_s].merge(sets); } // get solid entities, and dimension @@ -460,19 +667,26 @@ ErrorCode DeformMeshRemap::read_file(int m_or_s, string &fname, EntityHandle &se rval = mbImpl->get_entities_by_handle(*rit, tmp_range, true); RR("Failed to get entities in solid."); } - int dim = mbImpl->dimension_from_handle(*tmp_range.rbegin()); - assert(dim > 0 && dim < 4); - - solidElems[m_or_s] = tmp_range.subset_by_dimension(dim); + if (!tmp_range.empty()) { + int dim = mbImpl->dimension_from_handle(*tmp_range.rbegin()); + assert(dim > 0 && dim < 4); + solidElems[m_or_s] = tmp_range.subset_by_dimension(dim); + } + + if (debug) + std::cout << "Read " << solidElems[m_or_s].size() << " solid elements from " << solidSets[m_or_s].size() << " sets in " << (m_or_s == MASTER ? "master" : "slave") << " mesh." << std::endl; - for (std::set<int>::iterator sit = fluidSetNos.begin(); sit != fluidSetNos.end(); sit++) { + for (std::set<int>::iterator sit = fluidSetNos[m_or_s].begin(); sit != fluidSetNos[m_or_s].end(); sit++) { Range sets; int set_no = *sit; const void *setno_ptr = &set_no; - rval = mbImpl->get_entities_by_type_and_tag(seth, MBENTITYSET, &tagh, &setno_ptr, 1, sets); - if (sets.empty()) rval = MB_FAILURE; - RR("Couldn't get any fluid sets."); - fluidSets[m_or_s].merge(sets); + ErrorCode tmp_rval = mbImpl->get_entities_by_type_and_tag(seth, MBENTITYSET, &tagh, &setno_ptr, 1, sets); + if (sets.empty() || MB_SUCCESS != tmp_rval) { + rval = MB_FAILURE; + mError->set_last_error("Couldn't find fluid set #%d.\n", *sit); + } + else + fluidSets[m_or_s].merge(sets); } // get fluid entities, and dimension @@ -481,8 +695,66 @@ ErrorCode DeformMeshRemap::read_file(int m_or_s, string &fname, EntityHandle &se rval = mbImpl->get_entities_by_handle(*rit, tmp_range, true); RR("Failed to get entities in fluid."); } + if (!tmp_range.empty()) { + int dim = mbImpl->dimension_from_handle(*tmp_range.rbegin()); + assert(dim > 0 && dim < 4); + fluidElems[m_or_s] = tmp_range.subset_by_dimension(dim); + } + + if (debug) + std::cout << "Read " << fluidElems[m_or_s].size() << " fluid elements from " << fluidSets[m_or_s].size() << " sets in " << (m_or_s == MASTER ? "master" : "slave") << " mesh." << std::endl; + + return rval; +} + +ErrorCode DeformMeshRemap::find_other_sets(int m_or_s, EntityHandle file_set) +{ + // solid or fluid sets are missing; find the other + Range *filled_sets = NULL, *unfilled_sets = NULL, *unfilled_elems = NULL; + + if (fluidSets[m_or_s].empty() && !solidSets[m_or_s].empty()) { + unfilled_sets = &fluidSets[m_or_s]; + filled_sets = &solidSets[m_or_s]; + unfilled_elems = &fluidElems[m_or_s]; + if (debug) + std::cout << "Finding unspecified fluid elements in " << (m_or_s == MASTER ? "master" : "slave") << " mesh..."; + } + else if (!fluidSets[m_or_s].empty() && solidSets[m_or_s].empty()) { + filled_sets = &fluidSets[m_or_s]; + unfilled_sets = &solidSets[m_or_s]; + unfilled_elems = &solidElems[m_or_s]; + if (debug) + std::cout << "Finding unspecified solid elements in " << (m_or_s == MASTER ? "master" : "slave") << " mesh..."; + } - fluidElems[m_or_s] = tmp_range.subset_by_dimension(dim); + // ok, we know the filled sets, now fill the unfilled sets, and the elems from those + Tag tagh; + ErrorCode rval = mbImpl->tag_get_handle(MATERIAL_SET_TAG_NAME, tagh); RR("Couldn't get material set tag name."); + Range matsets; + rval = mbImpl->get_entities_by_type_and_tag(file_set, MBENTITYSET, &tagh, NULL, 1, matsets); + if (matsets.empty()) rval = MB_FAILURE; + RR("Couldn't get any material sets."); + *unfilled_sets = subtract(matsets, *filled_sets); + if (unfilled_sets->empty()) { + rval = MB_FAILURE; + RR("Failed to find any unfilled material sets."); + } + Range tmp_range; + for (Range::iterator rit = unfilled_sets->begin(); rit != unfilled_sets->end(); rit++) { + rval = mbImpl->get_entities_by_handle(*rit, tmp_range, true); + RR("Failed to get entities in unfilled set."); + } + int dim = mbImpl->dimension_from_handle(*tmp_range.rbegin()); + assert(dim > 0 && dim < 4); + *unfilled_elems = tmp_range.subset_by_dimension(dim); + if (unfilled_elems->empty()) { + rval = MB_FAILURE; + RR("Failed to find any unfilled set entities."); + } + + if (debug) + std::cout << "found " << unfilled_sets->size() << " sets and " << unfilled_elems->size() << " elements." << std::endl; return MB_SUCCESS; } + diff --git a/src/AdaptiveKDTree.cpp b/src/AdaptiveKDTree.cpp index 1324c30..8aafdd1 100644 --- a/src/AdaptiveKDTree.cpp +++ b/src/AdaptiveKDTree.cpp @@ -176,7 +176,6 @@ namespace moab { else { rval = iter.step(); if (MB_ENTITY_NOT_FOUND == rval) { - treeStats.reset(); rval = treeStats.compute_stats(mbImpl, myRoot); treeStats.initTime = cp.time_elapsed(); return rval; // at end @@ -807,8 +806,7 @@ namespace moab { t_enter, t_exit ); } - static ErrorCode intersect_children_with_elems( - AdaptiveKDTree* tool, + ErrorCode AdaptiveKDTree::intersect_children_with_elems( const Range& elems, AdaptiveKDTree::Plane plane, double eps, @@ -823,15 +821,16 @@ namespace moab { right_tris.clear(); both_tris.clear(); CartVect coords[16]; - Interface *const moab = tool->moab(); // get extents of boxes for left and right sides - CartVect right_min( box_min ), left_max( box_max ); - right_min[plane.norm] = left_max[plane.norm] = plane.coord; - const CartVect left_cen = 0.5*(left_max + box_min); - const CartVect left_dim = 0.5*(left_max - box_min); - const CartVect right_cen = 0.5*(box_max + right_min); - const CartVect right_dim = 0.5*(box_max - right_min); + BoundBox left_box(box_min, box_max), right_box(box_min, box_max); + right_box.bMin = box_min; + left_box.bMax = box_max; + right_box.bMin[plane.norm] = left_box.bMax[plane.norm] = plane.coord; + const CartVect left_cen = 0.5*(left_box.bMax + box_min); + const CartVect left_dim = 0.5*(left_box.bMax - box_min); + const CartVect right_cen = 0.5*(box_max + right_box.bMin); + const CartVect right_dim = 0.5*(box_max - right_box.bMin); const CartVect dim = box_max - box_min; const double max_tol = std::max(dim[0], std::max(dim[1], dim[2]))/10; @@ -851,8 +850,8 @@ namespace moab { // vertices for (i = elems.begin(); i != elem_begin; ++i) { - tool->tree_stats().leafObjectTests++; - rval = moab->get_coords( &*i, 1, coords[0].array() ); + tree_stats().leafObjectTests++; + rval = moab()->get_coords( &*i, 1, coords[0].array() ); if (MB_SUCCESS != rval) return rval; @@ -873,13 +872,13 @@ namespace moab { // non-polyhedron elements std::vector<EntityHandle> dum_vector; for (i = elem_begin; i != poly_begin; ++i) { - tool->tree_stats().leafObjectTests++; - rval = moab->get_connectivity( *i, conn, count, true, &dum_vector); + tree_stats().leafObjectTests++; + rval = moab()->get_connectivity( *i, conn, count, true, &dum_vector); if (MB_SUCCESS != rval) return rval; if (count > (int)(sizeof(coords)/sizeof(coords[0]))) return MB_FAILURE; - rval = moab->get_coords( &conn[0], count, coords[0].array() ); + rval = moab()->get_coords( &conn[0], count, coords[0].array() ); if (MB_SUCCESS != rval) return rval; bool lo = false, ro = false; @@ -894,12 +893,16 @@ namespace moab { // identified that leaf, then we're done. If triangle is on both // sides of plane, do more precise test to ensure that it is really // in both. +// BoundBox box; +// box.update(*moab(), *i); if (lo && ro) { double tol = eps; lo = ro = false; while (!lo && !ro && tol <= max_tol) { - lo = GeomUtil::box_elem_overlap( coords, TYPE_FROM_HANDLE(*i), left_cen, left_dim+CartVect(tol) ); - ro = GeomUtil::box_elem_overlap( coords, TYPE_FROM_HANDLE(*i),right_cen,right_dim+CartVect(tol) ); + tree_stats().boxElemTests+= 2; + lo = GeomUtil::box_elem_overlap( coords, TYPE_FROM_HANDLE(*i), left_cen, left_dim+CartVect(tol)); + ro = GeomUtil::box_elem_overlap( coords, TYPE_FROM_HANDLE(*i), right_cen, right_dim+CartVect(tol)); + tol *= 10.0; } } @@ -913,20 +916,20 @@ namespace moab { // polyhedra for (i = poly_begin; i != set_begin; ++i) { - tool->tree_stats().leafObjectTests++; - rval = moab->get_connectivity( *i, conn, count, true ); + tree_stats().leafObjectTests++; + rval = moab()->get_connectivity( *i, conn, count, true ); if (MB_SUCCESS != rval) return rval; // just check the bounding box of the polyhedron bool lo = false, ro = false; for (int j = 0; j < count; ++j) { - rval = moab->get_connectivity( conn[j], conn2, count2, true ); + rval = moab()->get_connectivity( conn[j], conn2, count2, true ); if (MB_SUCCESS != rval) return rval; for (int k = 0; k < count2; ++k) { - rval = moab->get_coords( conn2 + k, 1, coords[0].array() ); + rval = moab()->get_coords( conn2 + k, 1, coords[0].array() ); if (MB_SUCCESS != rval) return rval; if (coords[0][plane.norm] <= plane.coord) @@ -947,8 +950,8 @@ namespace moab { // sets BoundBox tbox; for (i = set_begin; i != elems.end(); ++i) { - tool->tree_stats().leafObjectTests++; - rval = tbox.update(*tool->moab(), *i); + tree_stats().leafObjectTests++; + rval = tbox.update(*moab(), *i); if (MB_SUCCESS != rval) return rval; @@ -1005,8 +1008,7 @@ namespace moab { AdaptiveKDTree::Plane plane = { box_min[axis] + (p/(1.0+plane_count)) * diff[axis], axis }; Range left, right, both; double val; - r = intersect_children_with_elems( iter.tool(), - entities, plane, eps, + r = intersect_children_with_elems( entities, plane, eps, box_min, box_max, left, right, both, val ); @@ -1057,32 +1059,38 @@ namespace moab { if (MB_SUCCESS != r) return r; - tmp_data.resize( vertices.size() ); + unsigned int nverts = vertices.size(); + tmp_data.resize( 3*nverts); + r = iter.tool()->moab()->get_coords( vertices, &tmp_data[0], &tmp_data[nverts], &tmp_data[2*nverts] ); + if (MB_SUCCESS != r) + return r; + for (int axis = 0; axis < 3; ++axis) { int plane_count = num_planes; + + // if num_planes results in width < eps, reset the plane count if ((num_planes+1)*eps >= diff[axis]) plane_count = (int)(diff[axis] / eps) - 1; - double *ptrs[] = { 0, 0, 0 }; - ptrs[axis] = &tmp_data[0]; - r = iter.tool()->moab()->get_coords( vertices, ptrs[0], ptrs[1], ptrs[2] ); - if (MB_SUCCESS != r) - return r; - for (int p = 1; p <= plane_count; ++p) { + + // coord of this plane on axis double coord = box_min[axis] + (p/(1.0+plane_count)) * diff[axis]; - double closest_coord = tmp_data[0]; - for (unsigned i = 1; i < tmp_data.size(); ++i) - if (fabs(coord-tmp_data[i]) < fabs(coord-closest_coord)) - closest_coord = tmp_data[i]; + + // find closest vertex coordinate to this plane position + unsigned int istrt = axis*nverts; + double closest_coord = tmp_data[istrt]; + for (unsigned i = 1; i < nverts; ++i) + if (fabs(coord-tmp_data[istrt+i]) < fabs(coord-closest_coord)) + closest_coord = tmp_data[istrt+i]; if (closest_coord - box_min[axis] <= eps || box_max[axis] - closest_coord <= eps) continue; + // seprate elems into left/right/both, and compute separating metric AdaptiveKDTree::Plane plane = { closest_coord, axis }; Range left, right, both; double val; - r = intersect_children_with_elems( iter.tool(), - entities, plane, eps, + r = intersect_children_with_elems( entities, plane, eps, box_min, box_max, left, right, both, val ); @@ -1160,8 +1168,7 @@ namespace moab { AdaptiveKDTree::Plane plane = { *citer, axis }; Range left, right, both; double val; - r = intersect_children_with_elems( iter.tool(), - entities, plane, eps, + r = intersect_children_with_elems( entities, plane, eps, box_min, box_max, left, right, both, val ); @@ -1276,8 +1283,7 @@ namespace moab { AdaptiveKDTree::Plane plane = { coords[indices[p]], axis }; Range left, right, both; double val; - r = intersect_children_with_elems( iter.tool(), - entities, plane, eps, + r = intersect_children_with_elems( entities, plane, eps, box_min, box_max, left, right, both, val ); diff --git a/src/BVHTree.cpp b/src/BVHTree.cpp index d54e24d..e2592fb 100644 --- a/src/BVHTree.cpp +++ b/src/BVHTree.cpp @@ -48,7 +48,7 @@ namespace moab #ifndef NDEBUG for(std::vector<HandleData>::const_iterator i = handle_data_vec.begin(); i != handle_data_vec.end(); ++i) { - if(!boundBox.contains_box(i->myBox, 0)){ + if(!boundBox.intersects_box(i->myBox, 0)){ std::cerr << "BB:" << boundBox << "EB:" << i->myBox << std::endl; return MB_FAILURE; } @@ -168,16 +168,16 @@ namespace moab for (unsigned int dim = 0; dim < 3; ++dim){ const unsigned int index = Bucket::bucket_index(splitsPerDir, box, interval, dim); Bucket &bucket = buckets[dim][index]; - if(!bucket.boundingBox.contains_box(box)) + if(!bucket.boundingBox.intersects_box(box)) std::cerr << "Buckets not covering elements!" << std::endl; } } - if(!elt_union.contains_box(interval) ){ + if(!elt_union.intersects_box(interval) ){ std::cout << "element union: " << std::endl << elt_union; std::cout << "intervals: " << std::endl << interval; std::cout << "union of elts does not contain original box!" << std::endl; } - if (!interval.contains_box(elt_union) ){ + if (!interval.intersects_box(elt_union) ){ std::cout << "original box does not contain union of elts" << std::endl; std::cout << interval << std::endl << elt_union << std::endl; } @@ -193,9 +193,9 @@ namespace moab for(unsigned int i = 0; i < nonempty.size(); ++i) test_box.update(buckets_[nonempty[i]].boundingBox); - if(!test_box.contains_box(interval) ) + if(!test_box.intersects_box(interval) ) std::cout << "union of buckets in dimension: " << d << "does not contain original box!" << std::endl; - if (!interval.contains_box(test_box) ) { + if (!interval.intersects_box(test_box) ) { std::cout << "original box does " << "not contain union of buckets" << "in dimension: " << d << std::endl; std::cout << interval << std::endl << test_box << std::endl; @@ -234,7 +234,7 @@ namespace moab s != splits_end; ++s, ++left_end) { BoundBox test_box = s->leftBox; test_box.update(s->rightBox); - if(!data.boundingBox.contains_box(test_box)) { + if(!data.boundingBox.intersects_box(test_box)) { std::cout << "nr: " << s->nr << std::endl; std::cout << "Test box: " << std::endl << test_box; @@ -247,7 +247,7 @@ namespace moab std::cout << "Split boxes larger than bb" << std::endl; } - if(!test_box.contains_box(data.boundingBox)) { + if(!test_box.intersects_box(data.boundingBox)) { std::cout << "bb larger than union of split boxes" << std::endl; } } @@ -288,7 +288,7 @@ namespace moab data.Lmax = data.leftBox.bMax[data.dim]; #ifndef NDEBUG BoundBox test_box(data.rightBox); - if(!data.boundingBox.contains_box(test_box)) { + if(!data.boundingBox.intersects_box(test_box)) { std::cerr << "MEDIAN: BB Does not contain splits" << std::endl; std::cerr << "test_box: " << test_box << std::endl; std::cerr << "data.boundingBox: " << data.boundingBox << std::endl; @@ -335,7 +335,7 @@ namespace moab else { right_box.update(i->myBox); } - if(!right_box.contains_box(i->myBox)) { + if(!right_box.intersects_box(i->myBox)) { if(!issue) { std::cerr << "Bounding right box issue!" << std::endl; @@ -352,7 +352,7 @@ namespace moab else { left_box.update(i->myBox); } - if(!data.leftBox.contains_box(i->myBox)) { + if(!data.leftBox.intersects_box(i->myBox)) { if(!issue) { std::cerr << "Bounding left box issue!" << std::endl; @@ -367,13 +367,13 @@ namespace moab } } } - if(!left_box.contains_box(data.leftBox)) + if(!left_box.intersects_box(data.leftBox)) std::cout << "left elts do not contain left box" << std::endl; - if(!data.leftBox.contains_box(left_box)) + if(!data.leftBox.intersects_box(left_box)) std::cout << "left box does not contain left elts" << std::endl; - if(!right_box.contains_box(data.rightBox)) + if(!right_box.intersects_box(data.rightBox)) std::cout << "right elts do not contain right box" << std::endl; - if(!data.rightBox.contains_box(right_box)) + if(!data.rightBox.intersects_box(right_box)) std::cout << "right box do not contain right elts" << std::endl; if(count_left != data.nl || count_right != data.nr) { @@ -400,7 +400,7 @@ namespace moab { #ifndef NDEBUG for(HandleDataVec::const_iterator i = begin; i != end; ++i) { - if(!box.contains_box(i->myBox, 0)) { + if(!box.intersects_box(i->myBox, 0)) { std::cerr << "depth: " << depth << std::endl; std::cerr << "BB:" << box << "EB:" << i->myBox << std::endl; std::exit(-1); diff --git a/src/LloydSmoother.cpp b/src/LloydSmoother.cpp index b1614d2..ba8169a 100644 --- a/src/LloydSmoother.cpp +++ b/src/LloydSmoother.cpp @@ -39,6 +39,17 @@ ErrorCode LloydSmoother::perform_smooth() { ErrorCode rval; + if (myElems.empty()) { + rval = MB_FAILURE; + RR("No elements specified to Lloyd smoother."); + } + else if (mbImpl->dimension_from_handle(*myElems.begin()) != mbImpl->dimension_from_handle(*myElems.rbegin())) { + rval = MB_FAILURE; + RR("Elements of unequal dimension specified to Lloyd smoother."); + } + + int dim = mbImpl->dimension_from_handle(*myElems.begin()); + // first figure out tolerance to use if (0 > absTol) { // no tolerance set - get one relative to bounding box around elements @@ -140,7 +151,7 @@ ErrorCode LloydSmoother::perform_smooth() if (fix_tag[v]) continue; // vertex centroid = sum(cell centroids)/ncells adj_elems.clear(); - rval = mbImpl->get_adjacencies(&(*vit), 1, 2, false, adj_elems); RR("Failed getting adjs."); + rval = mbImpl->get_adjacencies(&(*vit), 1, dim, false, adj_elems); RR("Failed getting adjs."); rval = mbImpl->tag_get_data(centroid, &adj_elems[0], adj_elems.size(), &fcentroids[0]); RR("Failed to get elem centroid."); double vnew[] = {0.0, 0.0, 0.0}; @@ -221,7 +232,7 @@ ErrorCode LloydSmoother::initialize() RR("Trouble getting vertices."); // mark them fixed - std::vector<unsigned char> marks(skin.size(), 0x1); + std::vector<unsigned char> marks(skin_verts.size(), 0x1); rval = mbImpl->tag_set_data(fixedTag, skin_verts, &marks[0]); RR("Unable to set tag on skin."); } diff --git a/src/LocalDiscretization/moab/ElemEvaluator.hpp b/src/LocalDiscretization/moab/ElemEvaluator.hpp index 866388c..6a1efd0 100644 --- a/src/LocalDiscretization/moab/ElemEvaluator.hpp +++ b/src/LocalDiscretization/moab/ElemEvaluator.hpp @@ -339,8 +339,13 @@ namespace moab { std::vector<EntityHandle> dum_vec; ErrorCode rval = mbImpl->get_connectivity(ent, vertHandles, numVerts, false, &dum_vec); if (MB_SUCCESS != rval) return rval; + + if (!evalSets[entType].evalFcn) + EvalSet::get_eval_set(entType, numVerts, evalSets[entType]); + rval = mbImpl->get_coords(vertHandles, numVerts, vertPos[0].array()); if (MB_SUCCESS != rval) return rval; + if (tagHandle) { rval = set_tag_handle(tagHandle); if (MB_SUCCESS != rval) return rval; diff --git a/src/SpatialLocator.cpp b/src/SpatialLocator.cpp index f976ae7..702399e 100644 --- a/src/SpatialLocator.cpp +++ b/src/SpatialLocator.cpp @@ -2,6 +2,7 @@ #include "moab/Interface.hpp" #include "moab/ElemEvaluator.hpp" #include "moab/AdaptiveKDTree.hpp" +#include "moab/BVHTree.hpp" // include ScdInterface for box partitioning #include "moab/ScdInterface.hpp" @@ -18,10 +19,8 @@ namespace moab SpatialLocator::SpatialLocator(Interface *impl, Range &elems, Tree *tree, ElemEvaluator *eval) : mbImpl(impl), myElems(elems), myDim(-1), myTree(tree), elemEval(eval), iCreatedTree(false) { - if (!myTree) { - myTree = new AdaptiveKDTree(impl); - iCreatedTree = true; - } + create_tree(); + if (!elems.empty()) { myDim = mbImpl->dimension_from_handle(*elems.rbegin()); ErrorCode rval = myTree->build_tree(myElems); @@ -32,6 +31,20 @@ namespace moab } } + void SpatialLocator::create_tree() + { + if (myTree) return; + + if (myElems.empty() || mbImpl->type_from_handle(*myElems.rbegin()) == MBVERTEX) + // create a kdtree if only vertices + myTree = new AdaptiveKDTree(mbImpl); + else + // otherwise a BVHtree, since it performs better for elements + myTree = new BVHTree(mbImpl); + + iCreatedTree = true; + } + ErrorCode SpatialLocator::add_elems(Range &elems) { if (elems.empty() || @@ -40,7 +53,9 @@ namespace moab myDim = mbImpl->dimension_from_handle(*elems.begin()); myElems = elems; - return MB_SUCCESS; + + ErrorCode rval = myTree->build_tree(myElems); + return rval; } #ifdef USE_MPI @@ -352,90 +367,29 @@ namespace moab // relative epsilon given, translate to absolute epsilon using box dimensions tmp_abs_iter_tol = rel_iter_tol * localBox.diagonal_length(); } - - EntityHandle closest_leaf; - std::vector<double> dists; - std::vector<EntityHandle> leaves; - ErrorCode rval = MB_SUCCESS; + if (elemEval && myTree->get_eval() != elemEval) + myTree->set_eval(elemEval); + + ErrorCode rval = MB_SUCCESS; for (int i = 0; i < num_points; i++) { int i3 = 3*i; - ents[i] = 0; - if (tmp_abs_iter_tol) { - rval = myTree->distance_search(pos+i3, tmp_abs_iter_tol, leaves, tmp_abs_iter_tol, inside_tol, &dists); - if (MB_SUCCESS != rval) return rval; - if (!leaves.empty()) { - // get closest leaf - double min_dist = *dists.begin(); - closest_leaf = *leaves.begin(); - std::vector<EntityHandle>::iterator vit = leaves.begin()+1; - std::vector<double>::iterator dit = dists.begin()+1; - for (; vit != leaves.end() && min_dist; vit++, dit++) { - if (*dit < min_dist) { - min_dist = *dit; - closest_leaf = *vit; - } - } - dists.clear(); - leaves.clear(); - } - } - else { - rval = myTree->point_search(pos+i3, closest_leaf); - if (MB_ENTITY_NOT_FOUND == rval) closest_leaf = 0; - else if (MB_SUCCESS != rval) return rval; - } - - // if no ElemEvaluator, just return the box - if (!elemEval) { - ents[i] = closest_leaf; - params[i3] = params[i3+1] = params[i3+2] = -2; - if (is_inside && closest_leaf) is_inside[i] = true; + ErrorCode tmp_rval = myTree->point_search(pos+i3, ents[i], abs_iter_tol, inside_tol, NULL, NULL, + (CartVect*)(params+i3)); + if (MB_SUCCESS != tmp_rval) { + rval = tmp_rval; continue; } - - // find natural coordinates of point in element(s) in that leaf - CartVect tmp_nat_coords; - Range range_leaf; - rval = mbImpl->get_entities_by_dimension(closest_leaf, myDim, range_leaf, false); - if(rval != MB_SUCCESS) return rval; - - // loop over the range_leaf - int tmp_inside; - int *is_ptr = (is_inside ? is_inside+i : &tmp_inside); - *is_ptr = false; - EntityHandle ent = 0; - for(Range::iterator rit = range_leaf.begin(); rit != range_leaf.end(); rit++) - { - rval = elemEval->set_ent_handle(*rit); - if (MB_SUCCESS != rval) return rval; - rval = elemEval->reverse_eval(pos+i3, tmp_abs_iter_tol, inside_tol, params+i3, is_ptr); - if (MB_SUCCESS != rval) return rval; - if (*is_ptr) { - ent = *rit; - break; - } - } - if (debug && !ent) { + + if (debug && !ents[i]) { std::cout << "Point " << i << " not found; point: (" << pos[i3] << "," << pos[i3+1] << "," << pos[i3+2] << ")" << std::endl; - std::cout << "Source element candidates: " << std::endl; - range_leaf.print(" "); - for(Range::iterator rit = range_leaf.begin(); rit != range_leaf.end(); rit++) - { - std::cout << "Candidate " << CN::EntityTypeName(mbImpl->type_from_handle(*rit)) << " " << mbImpl->id_from_handle(*rit) << ": "; - rval = elemEval->set_ent_handle(*rit); - if (MB_SUCCESS != rval) return rval; - rval = elemEval->reverse_eval(pos+i3, tmp_abs_iter_tol, inside_tol, params+i3, is_ptr); - if (MB_SUCCESS != rval) return rval; - std::cout << "Parameters: (" << params[i3] << "," << params[i3+1] << "," << params[i3+2] << ")" - << " inside = " << *is_ptr << std::endl; - } } - ents[i] = ent; - } - return MB_SUCCESS; + if (is_inside) is_inside[i] = (ents[i] ? true : false); + } + + return rval; } /* Count the number of located points in locTable diff --git a/src/moab/AdaptiveKDTree.hpp b/src/moab/AdaptiveKDTree.hpp index c77bdbc..e4c5078 100644 --- a/src/moab/AdaptiveKDTree.hpp +++ b/src/moab/AdaptiveKDTree.hpp @@ -38,6 +38,13 @@ namespace moab { ~AdaptiveKDTree(); + /** \brief Parse options for tree creation + * \param options Options passed in by application + * \return Failure is returned if any options were passed in and not interpreted; could mean + * inappropriate options for a particular tree type + */ + ErrorCode parse_options(FileOptions &options); + /** Build the tree * Build a tree with the entities input. If a non-NULL tree_root_set pointer is input, * use the pointed-to set as the root of this tree (*tree_root_set!=0) otherwise construct @@ -251,16 +258,8 @@ namespace moab { virtual ErrorCode print(); private: - friend class AdaptiveKDTreeIter; - /** \brief Parse options for tree creation - * \param options Options passed in by application - * \return Failure is returned if any options were passed in and not interpreted; could mean - * inappropriate options for a particular tree type - */ - ErrorCode parse_options(FileOptions &options); - ErrorCode init(); /**\brief find a triangle near the input point */ @@ -273,7 +272,18 @@ namespace moab { DataType type, int count, void* default_val, Tag& tag_handle, std::vector<Tag>& created_tags ); - static ErrorCode best_subdivision_snap_plane( int num_planes, + ErrorCode intersect_children_with_elems( + const Range& elems, + AdaptiveKDTree::Plane plane, + double eps, + CartVect box_min, + CartVect box_max, + Range& left_tris, + Range& right_tris, + Range& both_tris, + double& metric_value ); + + ErrorCode best_subdivision_snap_plane( int num_planes, const AdaptiveKDTreeIter& iter, Range& best_left, Range& best_right, @@ -282,7 +292,7 @@ namespace moab { std::vector<double>& tmp_data, double eps ); - static ErrorCode best_subdivision_plane( int num_planes, + ErrorCode best_subdivision_plane( int num_planes, const AdaptiveKDTreeIter& iter, Range& best_left, Range& best_right, @@ -290,7 +300,7 @@ namespace moab { AdaptiveKDTree::Plane& best_plane, double eps ); - static ErrorCode best_vertex_median_plane( int num_planes, + ErrorCode best_vertex_median_plane( int num_planes, const AdaptiveKDTreeIter& iter, Range& best_left, Range& best_right, @@ -299,7 +309,7 @@ namespace moab { std::vector<double>& coords, double eps); - static ErrorCode best_vertex_sample_plane( int num_planes, + ErrorCode best_vertex_sample_plane( int num_planes, const AdaptiveKDTreeIter& iter, Range& best_left, Range& best_right, diff --git a/src/moab/BVHTree.hpp b/src/moab/BVHTree.hpp index d435ebf..354d3a1 100644 --- a/src/moab/BVHTree.hpp +++ b/src/moab/BVHTree.hpp @@ -272,7 +272,6 @@ namespace moab { Range entityHandles; std::vector<TreeNode> myTree; - ElemEvaluator *myEval; int splitsPerDir; EntityHandle startSetHandle; static const char *treeName; @@ -305,7 +304,7 @@ namespace moab { } inline BVHTree::BVHTree(Interface *impl) : - Tree(impl), myEval(NULL), splitsPerDir(3), startSetHandle(0) {boxTagName = treeName;} + Tree(impl), splitsPerDir(3), startSetHandle(0) {boxTagName = treeName;} inline unsigned int BVHTree::set_interval(BoundBox &interval, std::vector<Bucket>::const_iterator begin, diff --git a/src/moab/BoundBox.hpp b/src/moab/BoundBox.hpp index 3e525ac..c74707a 100644 --- a/src/moab/BoundBox.hpp +++ b/src/moab/BoundBox.hpp @@ -17,7 +17,7 @@ namespace moab { ~BoundBox() {} bool contains_point(const double *point, const double tol = 0.0) const; - bool contains_box(const BoundBox &b, const double tol = 0.0) const; + bool intersects_box(const BoundBox &b, const double tol = 0.0) const; void compute_center(CartVect &center); void update(const BoundBox &other_box); void update(const double *coords); @@ -75,10 +75,10 @@ namespace moab { else return true; } - inline bool BoundBox::contains_box(const BoundBox &b, const double tol) const { - if (b.bMin[0] < bMin[0]-tol || b.bMax[0] > bMax[0]+tol || - b.bMin[1] < bMin[1]-tol || b.bMax[1] > bMax[1]+tol || - b.bMin[2] < bMin[2]-tol || b.bMax[2] > bMax[2]+tol) + inline bool BoundBox::intersects_box(const BoundBox &b, const double tol) const { + if (b.bMax[0] < bMin[0]-tol || b.bMin[0] > bMax[0]+tol || + b.bMax[1] < bMin[1]-tol || b.bMin[1] > bMax[1]+tol || + b.bMax[2] < bMin[2]-tol || b.bMin[2] > bMax[2]+tol) return false; else return true; diff --git a/src/moab/SpatialLocator.hpp b/src/moab/SpatialLocator.hpp index 3d29c55..2690058 100644 --- a/src/moab/SpatialLocator.hpp +++ b/src/moab/SpatialLocator.hpp @@ -193,6 +193,12 @@ namespace moab { ErrorCode register_src_with_intermediate_procs(ParallelComm *pc, double abs_iter_tol, TupleList &TLreg_o); #endif + + /** Create a tree + * Tree type depends on what's in myElems: if empty or all vertices, creates a kdtree, + * otherwise creates a BVHTree. + */ + void create_tree(); /* MOAB instance */ Interface* mbImpl; diff --git a/src/moab/Tree.hpp b/src/moab/Tree.hpp index 4d2694a..0a995b4 100644 --- a/src/moab/Tree.hpp +++ b/src/moab/Tree.hpp @@ -236,7 +236,7 @@ namespace moab { inline Tree::Tree(Interface* iface) : mbImpl(iface), maxPerLeaf(6), maxDepth(30), treeDepth(-1), minWidth(1.0e-10), - meshsetFlags(0), cleanUp(true), myRoot(0), boxTag(0) + meshsetFlags(0), cleanUp(true), myRoot(0), boxTag(0), myEval(0) {} inline Tree::~Tree() @@ -264,6 +264,14 @@ namespace moab { if (!boxTag && create_if_missing) { assert(boxTagName.length() > 0); ErrorCode rval = moab()->tag_get_handle(boxTagName.c_str(), 6, MB_TYPE_DOUBLE, boxTag, MB_TAG_CREAT | MB_TAG_SPARSE); + if (MB_INVALID_SIZE == rval) { + // delete the tag and get it again, legacy file... + rval = moab()->tag_delete(boxTag); + if (MB_SUCCESS != rval) return 0; + boxTag = 0; + return get_box_tag(true); + } + if (MB_SUCCESS != rval) return 0; } diff --git a/src/moab/TreeStats.hpp b/src/moab/TreeStats.hpp index be619a5..4ae685b 100644 --- a/src/moab/TreeStats.hpp +++ b/src/moab/TreeStats.hpp @@ -59,6 +59,7 @@ namespace moab unsigned int leavesVisited; unsigned int numTraversals; unsigned int leafObjectTests; + unsigned int boxElemTests; private: ErrorCode traverse(Interface *impl, EntityHandle node, unsigned int &depth); @@ -68,6 +69,8 @@ namespace moab inline ErrorCode TreeStats::compute_stats(Interface *impl, EntityHandle root_node) { maxDepth = 0; + numNodes = 0; + numLeaves = 0; return traverse(impl, root_node, maxDepth); } @@ -111,21 +114,27 @@ namespace moab leavesVisited = 0; numTraversals = 0; leafObjectTests = 0; + boxElemTests = 0; } inline void TreeStats::print() const { std::cout << "Tree initialization time = " << initTime << " seconds" << std::endl; + std::cout << "Num nodes = " << numNodes << std::endl; + std::cout << "Num leaves = " << numLeaves << std::endl; + std::cout << "Max depth = " << maxDepth << std::endl << std::endl; + std::cout << "NodesVisited = " << nodesVisited << std::endl; std::cout << "LeavesVisited = " << leavesVisited << std::endl; std::cout << "Num Traversals = " << numTraversals << std::endl; std::cout << "Leaf Object Tests = " << leafObjectTests << std::endl; + std::cout << "Box-Element Tests = " << boxElemTests << std::endl; } inline void TreeStats::output() const { - std::cout << initTime << " " << nodesVisited << " " << leavesVisited << " " << numTraversals << " " << leafObjectTests - << " # initTime, nodesVisited, leavesVisited, numTraversals, leafObjectTests" << std::endl; + std::cout << initTime << " " << nodesVisited << " " << leavesVisited << " " << numTraversals << " " << leafObjectTests << " " << boxElemTests + << " # initTime, nodesVisited, leavesVisited, numTraversals, leafObjectTests, boxElemTests" << std::endl; } } diff --git a/test/parallel/par_coupler_test.cpp b/test/parallel/par_coupler_test.cpp index 6ec3143..b0d7c06 100644 --- a/test/parallel/par_coupler_test.cpp +++ b/test/parallel/par_coupler_test.cpp @@ -139,8 +139,8 @@ int main(int argc, char **argv) if (!dbgFile.empty()) { std::stringstream dfname; dfname << dbgFile << rank << ".txt"; - std::freopen(dfname.str().c_str(), "a", stdout); - std::freopen(dfname.str().c_str(), "a", stderr); + if (!std::freopen(dfname.str().c_str(), "a", stdout)) return false; + if (!std::freopen(dfname.str().c_str(), "a", stderr)) return false; } // create MOAB instance based on that diff --git a/test/spatial_locator_test.cpp b/test/spatial_locator_test.cpp index 0171bf9..404e668 100644 --- a/test/spatial_locator_test.cpp +++ b/test/spatial_locator_test.cpp @@ -4,7 +4,9 @@ #include "moab/HomXform.hpp" #include "moab/ScdInterface.hpp" #include "moab/CartVect.hpp" +#include "moab/AdaptiveKDTree.hpp" #include "moab/BVHTree.hpp" +#include "moab/ElemEvaluator.hpp" #include "moab/ProgOptions.hpp" #include "moab/CpuTimer.hpp" @@ -69,11 +71,21 @@ void test_kd_tree() Range elems; rval = create_hex_mesh(mb, elems, ints, 3); CHECK_ERR(rval); - // initialize spatial locator with the elements and the default tree type - SpatialLocator *sl = new SpatialLocator(&mb, elems); + // initialize spatial locator with the elements and KDtree + AdaptiveKDTree kd(&mb); + std::ostringstream opts; + opts << "MAX_DEPTH=" << max_depth << ";MAX_PER_LEAF=" << leaf; + FileOptions fo(opts.str().c_str()); + rval = kd.parse_options(fo); + SpatialLocator *sl = new SpatialLocator(&mb, elems, &kd); test_locator(sl); + // test with an evaluator + ElemEvaluator eval(&mb); + kd.set_eval(&eval); + test_locator(sl); + // destroy spatial locator, and tree along with it delete sl; } @@ -96,6 +108,11 @@ void test_bvh_tree() SpatialLocator *sl = new SpatialLocator(&mb, elems, &bvh); test_locator(sl); + // test with an evaluator + ElemEvaluator eval(&mb); + bvh.set_eval(&eval); + test_locator(sl); + // destroy spatial locator, and tree along with it delete sl; } diff --git a/test/test_boundbox.cpp b/test/test_boundbox.cpp index 9fe0357..b089972 100644 --- a/test/test_boundbox.cpp +++ b/test/test_boundbox.cpp @@ -35,7 +35,7 @@ void test_bound_box() // test for contains point failure bool result = box.contains_point(vec.array(), tol); CHECK(!result); - result = box.contains_box(other_box, tol); + result = box.intersects_box(other_box, tol); CHECK(!result); box = other_box; @@ -44,7 +44,7 @@ void test_bound_box() // test for success result = box.contains_point(&vals[0], tol); CHECK(result); - result = box.contains_box(other_box, tol); + result = box.intersects_box(other_box, tol); CHECK(result); // check update functions @@ -54,9 +54,9 @@ void test_bound_box() CHECK(result); result = box.contains_point((three*1.1).array(), tol); CHECK(!result); - result = box.contains_box(BoundBox(three, three), tol); + result = box.intersects_box(BoundBox(three, three), tol); CHECK(result); - result = box.contains_box(BoundBox(three, 1.1*three), tol); + result = box.intersects_box(BoundBox(1.1*three, 3.0*three), tol); CHECK(!result); CartVect negthree(-3.0); @@ -65,9 +65,9 @@ void test_bound_box() CHECK(result); result = box.contains_point((negthree*1.1).array(), tol); CHECK(!result); - result = box.contains_box(BoundBox(negthree, negthree), tol); + result = box.intersects_box(BoundBox(negthree, negthree), tol); CHECK(result); - result = box.contains_box(BoundBox(1.1*negthree, negthree), tol); + result = box.intersects_box(BoundBox(3.0*negthree, 1.1*negthree), tol); CHECK(!result); for (int i = 0; i < 3; i++) { @@ -78,9 +78,9 @@ void test_bound_box() CHECK(result); result = box.contains_point((CartVect(&vals[0])*1.1).array(), tol); CHECK(!result); - result = box.contains_box(BoundBox(&vals[0]), tol); + result = box.intersects_box(BoundBox(&vals[0]), tol); CHECK(result); - result = box.contains_box(BoundBox(1.1*CartVect(&vals[0]), CartVect(&vals[3])), tol); + result = box.intersects_box(BoundBox(1.2*CartVect(&vals[0]), 1.1*CartVect(&vals[0])), tol); CHECK(!result); // check length functions diff --git a/tools/mbcoupler/DataCoupler.cpp b/tools/mbcoupler/DataCoupler.cpp index a5a3ec1..06a8564 100644 --- a/tools/mbcoupler/DataCoupler.cpp +++ b/tools/mbcoupler/DataCoupler.cpp @@ -1,24 +1,27 @@ #include "DataCoupler.hpp" -#include "moab/ParallelComm.hpp" #include "moab/Tree.hpp" #include "moab/TupleList.hpp" #include "moab/SpatialLocator.hpp" #include "moab/ElemEvaluator.hpp" #include "moab/Error.hpp" +#ifdef USE_MPI +#include "moab/ParallelComm.hpp" +#endif + #include "iostream" -#include <stdio.h> #include <algorithm> #include <sstream> +#include <stdio.h> #include "assert.h" namespace moab { DataCoupler::DataCoupler(Interface *impl, - ParallelComm *pc, Range &source_ents, int coupler_id, + ParallelComm *pc, bool init_locator, int dim) : mbImpl(impl), myPcomm(pc), myId(coupler_id), myDim(dim) @@ -64,7 +67,12 @@ ErrorCode DataCoupler::locate_points(Range &targ_ents, const double inside_tol) { targetEnts = targ_ents; - + +#ifdef USE_MPI + if (myPcomm && myPcomm->size() > 1) + return myLocator->par_locate_points(myPcomm, targ_ents, rel_iter_tol, abs_iter_tol, inside_tol); +#endif + return myLocator->locate_points(targ_ents, rel_iter_tol, abs_iter_tol, inside_tol); } @@ -72,6 +80,11 @@ ErrorCode DataCoupler::locate_points(double *xyz, int num_points, const double rel_iter_tol, const double abs_iter_tol, const double inside_tol) { +#ifdef USE_MPI + if (myPcomm && myPcomm->size() > 1) + return myLocator->par_locate_points(myPcomm, xyz, num_points, rel_iter_tol, abs_iter_tol, inside_tol); +#endif + return myLocator->locate_points(xyz, num_points, rel_iter_tol, abs_iter_tol, inside_tol); } @@ -95,7 +108,7 @@ ErrorCode DataCoupler::interpolate(/*DataCoupler::Method*/ int method, return interpolate(method, tag, interp_vals, point_indices, normalize); } -ErrorCode DataCoupler::interpolate(/*DataCoupler::Method*/ int *methods, +ErrorCode DataCoupler::interpolate(/*DataCoupler::Method*/ int */* methods */, Tag *tags, int *points_per_method, int num_methods, @@ -111,7 +124,12 @@ ErrorCode DataCoupler::interpolate(/*DataCoupler::Method*/ int *methods, for (int i = 0; i < num_methods; i++) pts_total += (points_per_method ? points_per_method[i] : targetEnts.size()); unsigned int num_indices = (point_indices ? point_indices->size() : targetEnts.size()); + // # points and indices should be identical + if (pts_total != num_indices) + return MB_FAILURE; + // since each tuple contains one interpolated tag, if we're interpolating multiple tags, every tuple + // needs to be able to store up to max tag size int max_tsize = -1; for (int i = 0; i < num_methods; i++) { int tmp_tsize; @@ -120,75 +138,82 @@ ErrorCode DataCoupler::interpolate(/*DataCoupler::Method*/ int *methods, max_tsize = std::max(max_tsize, tmp_tsize); } - // if tl was passed in non-NULL, just have those points, otherwise have targetPts plus - // locally mapped pts - if (pts_total != num_indices) - return MB_FAILURE; - - if (myPcomm) { - // TL to send interpolation indices to target procs - // Tuple structure: (pto_i, ridx_i, lidx_i, meth_i, tagidx_i, interp_val[max_tsize]_d) - TupleList tinterp; - tinterp.initialize(5, 0, 0, max_tsize, num_indices); - int t = 0; - tinterp.enableWriteAccess(); - for (int i = 0; i < num_methods; i++) { - int num_points = (points_per_method ? points_per_method[i] : targetEnts.size()); + if (myPcomm && myPcomm->size() > 1) { + // build up the tuple list to distribute from my target points; assume that + // all procs use same method/tag input + TupleList TLob; // TLob structure: (pto_i, ridx_i, lidx_i, meth_tagidx_i) + TLob.initialize(4, 0, 0, 0, num_indices); + int tn = 0; // the tuple number we're currently on + TLob.enableWriteAccess(); + for (int m = 0; m < num_methods; m++) { + int num_points = (points_per_method ? points_per_method[m] : targetEnts.size()); for (int j = 0; j < num_points; j++) { - int idx = (point_indices ? (*point_indices)[j] : j); + int idx = (point_indices ? (*point_indices)[j] : j); // the index in my targetEnts for this interpolation point // remote proc/idx from myLocator->parLocTable - tinterp.vi_wr[5*t] = myLocator->par_loc_table().vi_rd[2*idx]; // proc - tinterp.vi_wr[5*t+1] = myLocator->par_loc_table().vi_rd[2*idx+1]; // remote idx + TLob.vi_wr[4*tn] = myLocator->par_loc_table().vi_rd[2*idx]; // proc + TLob.vi_wr[4*tn+1] = myLocator->par_loc_table().vi_rd[2*idx+1]; // remote idx // local entity index, tag/method index from my data - tinterp.vi_wr[5*t+2] = idx; - tinterp.vi_wr[5*t+3] = methods[i]; - tinterp.vi_wr[5*t+4] = i; - tinterp.inc_n(); - t++; + TLob.vi_wr[4*tn+2] = idx; + TLob.vi_wr[4*tn+3] = m; + TLob.inc_n(); + tn++; } } // scatter/gather interpolation points - myPcomm->proc_config().crystal_router()->gs_transfer(1, tinterp, 0); - - // perform interpolation on local source mesh; put results into - // tinterp.vr_wr - - for (unsigned int i = 0; i < tinterp.get_n(); i++) { - int lidx = tinterp.vi_rd[5*i+1]; -// /*Method*/ int method = (/*Method*/ int)tinterp.vi_rd[5*i+3]; - Tag tag = tags[tinterp.vi_rd[5*i+4]]; - + myPcomm->proc_config().crystal_router()->gs_transfer(1, TLob, 0); + + // perform interpolation on local source mesh; put results into TLinterp + TupleList TLinterp; // TLinterp structure: (pto_i, ridx_i, vals[max_tsize]_d) + TLinterp.initialize(2, 0, 0, max_tsize, TLob.get_n()); + TLinterp.set_n(TLob.get_n()); // set the size right away + TLinterp.enableWriteAccess(); + + for (unsigned int i = 0; i < TLob.get_n(); i++) { + int lidx = TLob.vi_rd[4*i+1]; // index into myLocator's local table + // method and tag indexed with same index +// /*Method*/ int method = methods[TLob.vi_rd[4*i+3]]; + Tag tag = tags[TLob.vi_rd[4*i+3]]; + // copy proc/remote index from TLob + TLinterp.vi_wr[2*i] = TLob.vi_rd[4*i]; + TLinterp.vi_wr[2*i+1] = TLob.vi_rd[4*i+2]; + + // set up the evaluator for the tag and entity, then interpolate, putting result in TLinterp myLocator->elem_eval()->set_tag_handle(tag); myLocator->elem_eval()->set_ent_handle(myLocator->loc_table().vul_rd[lidx]); - result = myLocator->elem_eval()->eval(myLocator->loc_table().vr_rd+3*lidx, tinterp.vr_rd+i*max_tsize); + result = myLocator->elem_eval()->eval(myLocator->loc_table().vr_rd+3*lidx, TLinterp.vr_rd+i*max_tsize); if (MB_SUCCESS != result) return result; } // scatter/gather interpolation data - myPcomm->proc_config().crystal_router()->gs_transfer(1, tinterp, 0); + myPcomm->proc_config().crystal_router()->gs_transfer(1, TLinterp, 0); // copy the interpolated field as a unit - std::copy(tinterp.vr_rd, tinterp.vr_rd+tinterp.get_n()*max_tsize, interp_vals); + std::copy(TLinterp.vr_rd, TLinterp.vr_rd+TLinterp.get_n()*max_tsize, interp_vals); } else { + // if called serially, interpolate directly from local locations/entities, + // into either interp_vals or by setting data directly on tags on those entities std::vector<double> tmp_vals; std::vector<EntityHandle> tmp_ents; double *tmp_dbl = interp_vals; for (int i = 0; i < num_methods; i++) { int num_points = (points_per_method ? points_per_method[i] : targetEnts.size()); - // interpolated data is tsize long, which is either max size (if data passed back to caller in tinterp) + // interpolated data is tsize long, which is either max size (if data passed back to caller in interp_vals) // or tag size (if data will be set on entities, in which case it shouldn't have padding) + // set sizes here, inside loop over methods, to reduce memory usage int tsize = max_tsize, tsize_bytes = 0; if (!interp_vals) { tmp_vals.resize(num_points*max_tsize); tmp_dbl = &tmp_vals[0]; tmp_ents.resize(num_points); result = mbImpl->tag_get_length(tags[i], tsize); + if (MB_SUCCESS != result) return result; result = mbImpl->tag_get_bytes(tags[i], tsize_bytes); + if (MB_SUCCESS != result) return result; } for (int j = 0; j < num_points; j++) { @@ -206,7 +231,7 @@ ErrorCode DataCoupler::interpolate(/*DataCoupler::Method*/ int *methods, result = myLocator->elem_eval()->eval(myLocator->loc_table().vr_rd+3*lidx, tmp_dbl); tmp_dbl += tsize; if (MB_SUCCESS != result) return result; - } // for j + } // for j over points if (!interp_vals) { // set tags on tmp_ents; data is already w/o padding, due to tsize setting above @@ -214,7 +239,7 @@ ErrorCode DataCoupler::interpolate(/*DataCoupler::Method*/ int *methods, if (MB_SUCCESS != result) return result; } - } // for i + } // for i over methods } // if myPcomm // done diff --git a/tools/mbcoupler/DataCoupler.hpp b/tools/mbcoupler/DataCoupler.hpp index bfe2ba5..a9d6f5e 100644 --- a/tools/mbcoupler/DataCoupler.hpp +++ b/tools/mbcoupler/DataCoupler.hpp @@ -39,21 +39,23 @@ class DataCoupler { public: + enum Method {CONSTANT, LINEAR_FE, QUADRATIC_FE, SPECTRAL} ; + enum IntegType {VOLUME}; /* constructor * Constructor, which also optionally initializes the coupler + * \param source_ents Elements in the source mesh + * \param coupler_id Id of this coupler, should be the same over all procs * \param pc ParallelComm object to be used with this coupler, representing the union * of processors containing source and target meshes - * \param source_elems Elements in the source mesh - * \param coupler_id Id of this coupler, should be the same over all procs * \param init_locator If true, initializes a spatial locator inside the constructor * \param dim Dimension of entities to be coupled; if -1, get from source_elems */ DataCoupler(Interface *impl, - ParallelComm *pc, Range &source_ents, int coupler_id, + ParallelComm *pc = NULL, bool init_locator = true, int dim = -1); diff --git a/tools/mbcoupler/Makefile.am b/tools/mbcoupler/Makefile.am index ea32ff9..8114a52 100644 --- a/tools/mbcoupler/Makefile.am +++ b/tools/mbcoupler/Makefile.am @@ -40,7 +40,8 @@ libmbcoupler_la_includedir = $(includedir) # check that only libraries are going in $(libdir) cfgdir = $(libdir) -TESTS = elem_util_test element_test +TESTS = elem_util_test element_test datacoupler_test +datacoupler_test_SOURCES = datacoupler_test.cpp check_PROGRAMS = $(TESTS) elem_util_test_SOURCES = ElemUtilTest.cpp element_test_SOURCES = ElementTest.cpp This diff is so big that we needed to truncate the remainder. Repository URL: https://bitbucket.org/fathomteam/moab/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/MOAB: tautges: Removing compiler warnings.
by commits-noreply＠bitbucket.org 12 Mar '14

12 Mar '14

1 new commit in MOAB: https://bitbucket.org/fathomteam/moab/commits/f253c376259a/ Changeset: f253c376259a Branch: deformed-mesh-remap User: tautges Date: 2014-03-12 17:06:53 Summary: Removing compiler warnings. Affected #: 2 files diff --git a/test/parallel/par_coupler_test.cpp b/test/parallel/par_coupler_test.cpp index 6ec3143..b0d7c06 100644 --- a/test/parallel/par_coupler_test.cpp +++ b/test/parallel/par_coupler_test.cpp @@ -139,8 +139,8 @@ int main(int argc, char **argv) if (!dbgFile.empty()) { std::stringstream dfname; dfname << dbgFile << rank << ".txt"; - std::freopen(dfname.str().c_str(), "a", stdout); - std::freopen(dfname.str().c_str(), "a", stderr); + if (!std::freopen(dfname.str().c_str(), "a", stdout)) return false; + if (!std::freopen(dfname.str().c_str(), "a", stderr)) return false; } // create MOAB instance based on that diff --git a/tools/mbcoupler/datacoupler_test.cpp b/tools/mbcoupler/datacoupler_test.cpp index b39ca0e..35b7810 100644 --- a/tools/mbcoupler/datacoupler_test.cpp +++ b/tools/mbcoupler/datacoupler_test.cpp @@ -148,8 +148,8 @@ int main(int argc, char **argv) if (!dbgFile.empty()) { std::stringstream dfname; dfname << dbgFile << rank << ".txt"; - std::freopen(dfname.str().c_str(), "a", stdout); - std::freopen(dfname.str().c_str(), "a", stderr); + if (!std::freopen(dfname.str().c_str(), "a", stdout)) return false; + if (!std::freopen(dfname.str().c_str(), "a", stderr)) return false; } // create MOAB instance based on that @@ -546,17 +546,17 @@ ErrorCode get_file_options(int argc, char **argv, ErrorCode test_interpolation(Interface *mbImpl, DataCoupler::Method method, std::string &interpTag, - std::string &gNormTag, - std::string &ssNormTag, - std::vector<const char *> &ssTagNames, - std::vector<const char *> &ssTagValues, - iBase_EntitySetHandle *roots, + std::string &/*gNormTag*/, + std::string &/*ssNormTag*/, + std::vector<const char *> &/*ssTagNames*/, + std::vector<const char *> &/*ssTagValues*/, + iBase_EntitySetHandle */*roots*/, std::vector<ParallelComm *> &pcs, double &instant_time, double &pointloc_time, double &interp_time, - double &gnorm_time, - double &ssnorm_time, + double &/*gnorm_time*/, + double &/*ssnorm_time*/, double & toler) { assert(method >= DataCoupler::CONSTANT && method <= DataCoupler::SPECTRAL); @@ -572,7 +572,7 @@ ErrorCode test_interpolation(Interface *mbImpl, DataCoupler dc(mbImpl, src_elems, 0, pcs[0]); // initialize spectral elements, if they exist - bool specSou=false, specTar = false; + // bool specSou=false, specTar = false; // result = mbc.initialize_spectral_elements((EntityHandle)roots[0], (EntityHandle)roots[1], specSou, specTar); instant_time = timer.time_since_birth(); Repository URL: https://bitbucket.org/fathomteam/moab/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/MOAB: 24 new changesets
by commits-noreply＠bitbucket.org 12 Mar '14

12 Mar '14

24 new commits in MOAB: https://bitbucket.org/fathomteam/moab/commits/e0c608b42e90/ Changeset: e0c608b42e90 Branch: None User: tautges Date: 2014-03-12 16:51:41 Summary: Changes to allow specification of existing displacement tag(s), which can be either single name corresponding to xyz[3] or 3 names x, y, z. Handle either case in deform_master. Affected #: 1 file diff --git a/examples/DeformMeshRemap.cpp b/examples/DeformMeshRemap.cpp index 5442d1d..23ad554 100644 --- a/examples/DeformMeshRemap.cpp +++ b/examples/DeformMeshRemap.cpp @@ -91,6 +91,10 @@ public: //! get/set the file name void set_file_name(int m_or_s, const std::string &name); + + //! get/set the x displacement tag names + std::string xdisp_name(int idx = 0); + void xdisp_name(const std::string &nm, int idx = 0); private: //! apply a known deformation to the solid elements, putting the results in the xNew tag; also @@ -132,9 +136,15 @@ private: //! filenames for master/slave meshes std::string masterFileName, slaveFileName; + //! tag from file, might be 3 + Tag xDisp[3]; + //! tag used for new positions Tag xNew; + //! tag name used to read disps from file + std::string xDispNames[3]; + //! tag name used for new positions std::string xNewName; }; @@ -199,6 +209,16 @@ inline ErrorCode DeformMeshRemap::get_set_nos(int f_or_s, std::set<int> &set_nos return MB_SUCCESS; } +inline std::string DeformMeshRemap::xdisp_name(int idx) +{ + return xDispNames[idx]; +} + +void DeformMeshRemap::xdisp_name(const std::string &nm, int idx) +{ + xDispNames[idx] = nm; +} + ErrorCode DeformMeshRemap::execute() { // read master/slave files and get fluid/solid material sets @@ -296,14 +316,14 @@ void DeformMeshRemap::set_file_name(int m_or_s, const std::string &name) DeformMeshRemap::DeformMeshRemap(Interface *impl, ParallelComm *master, ParallelComm *slave) : mbImpl(impl), pcMaster(master), pcSlave(slave), masterSet(0), slaveSet(0), xNew(0), xNewName("xnew") { + xDisp[0] = xDisp[1] = xDisp[2] = 0; + if (!pcSlave && pcMaster) pcSlave = pcMaster; } DeformMeshRemap::~DeformMeshRemap() { - // delete the tag - mbImpl->tag_delete(xNew); } int main(int argc, char **argv) { @@ -312,14 +332,14 @@ int main(int argc, char **argv) { ProgOptions po("Deformed mesh options"); po.addOpt<std::string> ("master,m", "Specify the master meshfile name" ); - po.addOpt<std::string> ("slave,s", "Specify the slave meshfile name" ); + po.addOpt<std::string> ("worker,w", "Specify the slave/worker meshfile name" ); + po.addOpt<std::string> ("d1,", "Tag name for displacement x or xyz" ); + po.addOpt<std::string> ("d2,", "Tag name for displacement y" ); + po.addOpt<std::string> ("d3,", "Tag name for displacement z" ); + po.addOpt<int> ("fluid,f", "Specify fluid material set number(s)."); + po.addOpt<int> ("solid,s", "Specify fluid material set number(s)."); + po.parseCommandLine(argc, argv); - std::string foo; - string masterf, slavef; - if(!po.getOpt("master", &masterf)) - masterf = string(MESH_DIR) + string("/rodquad.g"); - if(!po.getOpt("slave", &slavef)) - slavef = string(MESH_DIR) + string("/rodtri.g"); mb = new Core(); @@ -330,10 +350,43 @@ int main(int argc, char **argv) { #else dfr = new DeformMeshRemap(mb); #endif + + + std::string masterf, slavef; + if(!po.getOpt("master", &masterf)) + masterf = string(MESH_DIR) + string("/rodquad.g"); dfr->set_file_name(DeformMeshRemap::MASTER, masterf); + + if(!po.getOpt("worker", &slavef)) + slavef = string(MESH_DIR) + string("/rodtri.g"); dfr->set_file_name(DeformMeshRemap::SLAVE, slavef); - rval = dfr->add_set_no(DeformMeshRemap::SOLID, SOLID_SETNO); RR("Failed to add solid set no."); - rval = dfr->add_set_no(DeformMeshRemap::FLUID, FLUID_SETNO); RR("Failed to add fluid set no."); + + std::vector<int> set_nos; + po.getOptAllArgs("fluid", set_nos); + if (set_nos.empty()) { + rval = dfr->add_set_no(DeformMeshRemap::FLUID, FLUID_SETNO); RR("Failed to add solid set no."); + } + else { + for (std::vector<int>::iterator vit = set_nos.begin(); vit != set_nos.end(); vit++) + dfr->add_set_no(DeformMeshRemap::FLUID, *vit); + } + set_nos.clear(); + + po.getOptAllArgs("solid", set_nos); + if (set_nos.empty()) { + rval = dfr->add_set_no(DeformMeshRemap::SOLID, SOLID_SETNO); RR("Failed to add solid set no."); + } + else { + for (std::vector<int>::iterator vit = set_nos.begin(); vit != set_nos.end(); vit++) + dfr->add_set_no(DeformMeshRemap::SOLID, *vit); + } + + std::string tnames[3]; + po.getOpt("d1", &tnames[0]); + po.getOpt("d2", &tnames[1]); + po.getOpt("d3", &tnames[2]); + for (int i = 0; i < 3; i++) + if (!tnames[i].empty()) dfr->xdisp_name(tnames[i], i); rval = dfr->execute(); @@ -387,40 +440,71 @@ void deform_func(const BoundBox &bbox, double *xold, double *xnew) ErrorCode DeformMeshRemap::deform_master(Range &fluid_elems, Range &solid_elems, const char *tag_name) { // deform elements with an analytic function + ErrorCode rval; - // create the tag - ErrorCode rval = mbImpl->tag_get_handle((tag_name ? tag_name : ""), 3, MB_TYPE_DOUBLE, xNew, MB_TAG_CREAT|MB_TAG_DENSE); - RR("Failed to create xnew tag."); - - // get all the vertices and coords in the fluid, set xnew to them - Range verts; - rval = mbImpl->get_adjacencies(fluid_elems, 0, false, verts, Interface::UNION); - RR("Failed to get vertices."); - std::vector<double> coords(3*verts.size(), 0.0); - rval = mbImpl->get_coords(verts, &coords[0]); - RR("Failed to get vertex coords."); - rval = mbImpl->tag_set_data(xNew, verts, &coords[0]); - RR("Failed to set xnew tag on fluid verts."); - - // get the bounding box of the solid mesh - BoundBox bbox; - bbox.update(*mbImpl, solid_elems); - // get all the vertices and coords in the solid - verts.clear(); + Range verts; rval = mbImpl->get_adjacencies(solid_elems, 0, false, verts, Interface::UNION); RR("Failed to get vertices."); - coords.resize(3*verts.size(), 0.0); + std::vector<double> coords(3*verts.size()); rval = mbImpl->get_coords(verts, &coords[0]); RR("Failed to get vertex coords."); unsigned int num_verts = verts.size(); - for (unsigned int i = 0; i < num_verts; i++) - deform_func(bbox, &coords[3*i], &coords[3*i]); + + // get or create the tag + + if (!xDispNames[0].empty() && !xDispNames[1].empty() && !xDispNames[2].empty()) { + // 3 tags, specifying xyz individual data, integrate into one tag + rval = mbImpl->tag_get_handle((tag_name ? tag_name : ""), 3, MB_TYPE_DOUBLE, xNew, MB_TAG_CREAT|MB_TAG_DENSE); + RR("Failed to create xnew tag."); + std::vector<double> disps(num_verts); + for (int i = 0; i < 3; i++) { + rval = mbImpl->tag_get_handle(xDispNames[0].c_str(), 1, MB_TYPE_DOUBLE, xDisp[i]); + RR("Failed to get xDisp tag."); + rval = mbImpl->tag_get_data(xDisp[i], verts, &disps[0]); + RR("Failed to get xDisp tag values."); + for (unsigned int j = 0; j < num_verts; j++) + coords[3*j+i] = disps[j]; + } + } + else if (!xDispNames[0].empty()) { + rval = mbImpl->tag_get_handle(xDispNames[0].c_str(), 3, MB_TYPE_DOUBLE, xDisp[0]); + RR("Failed to get first xDisp tag."); + xNew = xDisp[0]; + std::vector<double> disps(3*num_verts); + rval = mbImpl->tag_get_data(xDisp[0], verts, &disps[0]); + for (unsigned int j = 0; j < 3*num_verts; j++) + coords[j] += disps[j]; + } + else { + // get the bounding box of the solid mesh + BoundBox bbox; + bbox.update(*mbImpl, solid_elems); + + for (unsigned int j = 0; j < num_verts; j++) + deform_func(bbox, &coords[3*j], &coords[3*j]); + } + + if (!xNew) { + rval = mbImpl->tag_get_handle((tag_name ? tag_name : ""), 3, MB_TYPE_DOUBLE, + xDisp[0], MB_TAG_CREAT|MB_TAG_DENSE); + RR("Failed to get xNew tag."); + } // set the new tag to those coords rval = mbImpl->tag_set_data(xNew, verts, &coords[0]); RR("Failed to set tag data."); + // get all the vertices and coords in the fluid, set xnew to them + verts.clear(); + rval = mbImpl->get_adjacencies(fluid_elems, 0, false, verts, Interface::UNION); + RR("Failed to get vertices."); + coords.resize(3*verts.size()); + rval = mbImpl->get_coords(verts, &coords[0]); + RR("Failed to get vertex coords."); + rval = mbImpl->tag_set_data(xNew, verts, &coords[0]); + RR("Failed to set xnew tag on fluid verts."); + return MB_SUCCESS; } https://bitbucket.org/fathomteam/moab/commits/37f2b44c6262/ Changeset: 37f2b44c6262 Branch: None User: tautges Date: 2014-03-12 16:53:02 Summary: - add ability to specify master and slave mesh solid/fluid set numbers separately, so set numbers don't need to agree - add ability to specify only fluid or solid sets, with other sets derived from that and all material sets in a file - add DeformMeshRemap to list of examples in makefile Affected #: 1 file diff --git a/examples/DeformMeshRemap.cpp b/examples/DeformMeshRemap.cpp index 23ad554..b92d994 100644 --- a/examples/DeformMeshRemap.cpp +++ b/examples/DeformMeshRemap.cpp @@ -69,13 +69,13 @@ public: ErrorCode execute(); //! add a set number - ErrorCode add_set_no(int fluid_or_solid, int set_no); + ErrorCode add_set_no(int m_or_s, int fluid_or_solid, int set_no); //! remove a set number - ErrorCode remove_set_no(int fluid_or_solid, int set_no); + ErrorCode remove_set_no(int m_or_s, int fluid_or_solid, int set_no); //! get the set numbers - ErrorCode get_set_nos(int fluid_or_solid, std::set<int> &set_nos) const; + ErrorCode get_set_nos(int m_or_s, int fluid_or_solid, std::set<int> &set_nos) const; //! get the xNew tag handle inline Tag x_new() const {return xNew;} @@ -110,6 +110,9 @@ private: //! write the tag to the vertices, then save to the specified file ErrorCode write_and_save(Range &ents, EntityHandle seth, Tag tagh, const char *filename); + //! find fluid/solid sets from complement of solid/fluid sets + ErrorCode find_other_sets(int m_or_s, EntityHandle file_set); + //! moab interface Interface *mbImpl; @@ -118,11 +121,11 @@ private: ParallelComm *pcMaster, *pcSlave; #endif - //! material set numbers for fluid materials - std::set<int> fluidSetNos; + //! material set numbers for fluid materials, for master/slave + std::set<int> fluidSetNos[2]; - //! material set numbers for solid materials - std::set<int> solidSetNos; + //! material set numbers for solid materials, for master/slave + std::set<int> solidSetNos[2]; //! sets defining master/slave meshes EntityHandle masterSet, slaveSet; @@ -150,14 +153,17 @@ private: }; //! add a set number -inline ErrorCode DeformMeshRemap::add_set_no(int f_or_s, int set_no) +inline ErrorCode DeformMeshRemap::add_set_no(int m_or_s, int f_or_s, int set_no) { std::set<int> *this_set; + assert ((m_or_s == MASTER || m_or_s == SLAVE) && "m_or_s should be MASTER or SLAVE."); + if (m_or_s != MASTER && m_or_s != SLAVE) return MB_INDEX_OUT_OF_RANGE; + switch (f_or_s) { case FLUID: - this_set = &fluidSetNos; break; + this_set = &fluidSetNos[m_or_s]; break; case SOLID: - this_set = &solidSetNos; break; + this_set = &solidSetNos[m_or_s]; break; default: assert(false && "f_or_s should be FLUID or SOLID."); return MB_FAILURE; @@ -169,14 +175,16 @@ inline ErrorCode DeformMeshRemap::add_set_no(int f_or_s, int set_no) } //! remove a set number -inline ErrorCode DeformMeshRemap::remove_set_no(int f_or_s, int set_no) +inline ErrorCode DeformMeshRemap::remove_set_no(int m_or_s, int f_or_s, int set_no) { std::set<int> *this_set; + assert ((m_or_s == MASTER || m_or_s == SLAVE) && "m_or_s should be MASTER or SLAVE."); + if (m_or_s != MASTER && m_or_s != SLAVE) return MB_INDEX_OUT_OF_RANGE; switch (f_or_s) { case FLUID: - this_set = &fluidSetNos; break; + this_set = &fluidSetNos[m_or_s]; break; case SOLID: - this_set = &solidSetNos; break; + this_set = &solidSetNos[m_or_s]; break; default: assert(false && "f_or_s should be FLUID or SOLID."); return MB_FAILURE; @@ -191,14 +199,16 @@ inline ErrorCode DeformMeshRemap::remove_set_no(int f_or_s, int set_no) } //! get the set numbers -inline ErrorCode DeformMeshRemap::get_set_nos(int f_or_s, std::set<int> &set_nos) const +inline ErrorCode DeformMeshRemap::get_set_nos(int m_or_s, int f_or_s, std::set<int> &set_nos) const { const std::set<int> *this_set; + assert ((m_or_s == MASTER || m_or_s == SLAVE) && "m_or_s should be MASTER or SLAVE."); + if (m_or_s != MASTER && m_or_s != SLAVE) return MB_INDEX_OUT_OF_RANGE; switch (f_or_s) { case FLUID: - this_set = &fluidSetNos; break; + this_set = &fluidSetNos[m_or_s]; break; case SOLID: - this_set = &solidSetNos; break; + this_set = &solidSetNos[m_or_s]; break; default: assert(false && "f_or_s should be FLUID or SOLID."); return MB_FAILURE; @@ -224,10 +234,18 @@ ErrorCode DeformMeshRemap::execute() // read master/slave files and get fluid/solid material sets ErrorCode rval = read_file(MASTER, masterFileName, masterSet); if (MB_SUCCESS != rval) return rval; + + if (*solidSetNos[MASTER].begin() == -1 || *fluidSetNos[MASTER].begin() == -1) { + rval = find_other_sets(MASTER, masterSet); RR("Failed to find other sets in master mesh."); + } rval = read_file(SLAVE, slaveFileName, slaveSet); if (MB_SUCCESS != rval) return rval; + if (*solidSetNos[SLAVE].begin() == -1 || *fluidSetNos[SLAVE].begin() == -1) { + rval = find_other_sets(SLAVE, slaveSet); RR("Failed to find other sets in slave mesh."); + } + Range src_elems = solidElems[MASTER]; src_elems.merge(fluidElems[MASTER]); // locate slave vertices in master, orig coords; do this with a data coupler, so you can @@ -288,6 +306,50 @@ ErrorCode DeformMeshRemap::execute() return MB_SUCCESS; } +ErrorCode DeformMeshRemap::find_other_sets(int m_or_s, EntityHandle file_set) +{ + // solid or fluid sets are missing; find the other + Range *filled_sets = NULL, *unfilled_sets = NULL, *unfilled_elems = NULL; + + if (fluidSets[m_or_s].empty() && !solidSets[m_or_s].empty()) { + unfilled_sets = &fluidSets[m_or_s]; + filled_sets = &solidSets[m_or_s]; + unfilled_elems = &fluidElems[m_or_s]; + } + else if (!fluidSets[m_or_s].empty() && solidSets[m_or_s].empty()) { + filled_sets = &fluidSets[m_or_s]; + unfilled_sets = &solidSets[m_or_s]; + unfilled_elems = &solidElems[m_or_s]; + } + + // ok, we know the filled sets, now fill the unfilled sets, and the elems from those + Tag tagh; + ErrorCode rval = mbImpl->tag_get_handle(MATERIAL_SET_TAG_NAME, tagh); RR("Couldn't get material set tag name."); + Range matsets; + rval = mbImpl->get_entities_by_type_and_tag(file_set, MBENTITYSET, &tagh, NULL, 1, matsets); + if (matsets.empty()) rval = MB_FAILURE; + RR("Couldn't get any material sets."); + *unfilled_sets = subtract(matsets, *filled_sets); + if (unfilled_sets->empty()) { + rval = MB_FAILURE; + RR("Failed to find any unfilled material sets."); + } + Range tmp_range; + for (Range::iterator rit = unfilled_sets->begin(); rit != unfilled_sets->end(); rit++) { + rval = mbImpl->get_entities_by_handle(*rit, tmp_range, true); + RR("Failed to get entities in unfilled set."); + } + int dim = mbImpl->dimension_from_handle(*tmp_range.rbegin()); + assert(dim > 0 && dim < 4); + *unfilled_elems = tmp_range.subset_by_dimension(dim); + if (unfilled_elems->empty()) { + rval = MB_FAILURE; + RR("Failed to find any unfilled set entities."); + } + + return MB_SUCCESS; +} + std::string DeformMeshRemap::get_file_name(int m_or_s) const { switch (m_or_s) { @@ -336,8 +398,10 @@ int main(int argc, char **argv) { po.addOpt<std::string> ("d1,", "Tag name for displacement x or xyz" ); po.addOpt<std::string> ("d2,", "Tag name for displacement y" ); po.addOpt<std::string> ("d3,", "Tag name for displacement z" ); - po.addOpt<int> ("fluid,f", "Specify fluid material set number(s)."); - po.addOpt<int> ("solid,s", "Specify fluid material set number(s)."); + po.addOpt<int> ("fm,", "Specify master fluid material set number(s). If -1 specified, fluid sets derived from complement of solid sets."); + po.addOpt<int> ("fs,", "Specify master solid material set number(s). If -1 specified, fluid sets derived from complement of solid sets."); + po.addOpt<int> ("sm,", "Specify slave fluid material set number(s). If -1 specified, fluid sets derived from complement of solid sets."); + po.addOpt<int> ("ss,", "Specify slave solid material set number(s). If -1 specified, fluid sets derived from complement of solid sets."); po.parseCommandLine(argc, argv); @@ -362,23 +426,44 @@ int main(int argc, char **argv) { dfr->set_file_name(DeformMeshRemap::SLAVE, slavef); std::vector<int> set_nos; - po.getOptAllArgs("fluid", set_nos); + po.getOptAllArgs("fm", set_nos); if (set_nos.empty()) { - rval = dfr->add_set_no(DeformMeshRemap::FLUID, FLUID_SETNO); RR("Failed to add solid set no."); + rval = dfr->add_set_no(DeformMeshRemap::MASTER, DeformMeshRemap::FLUID, FLUID_SETNO); + RR("Failed to add solid set no."); } else { for (std::vector<int>::iterator vit = set_nos.begin(); vit != set_nos.end(); vit++) - dfr->add_set_no(DeformMeshRemap::FLUID, *vit); + dfr->add_set_no(DeformMeshRemap::MASTER, DeformMeshRemap::FLUID, *vit); } set_nos.clear(); - po.getOptAllArgs("solid", set_nos); + po.getOptAllArgs("fs", set_nos); if (set_nos.empty()) { - rval = dfr->add_set_no(DeformMeshRemap::SOLID, SOLID_SETNO); RR("Failed to add solid set no."); + rval = dfr->add_set_no(DeformMeshRemap::SLAVE, DeformMeshRemap::FLUID, FLUID_SETNO); + RR("Failed to add solid set no."); } else { for (std::vector<int>::iterator vit = set_nos.begin(); vit != set_nos.end(); vit++) - dfr->add_set_no(DeformMeshRemap::SOLID, *vit); + dfr->add_set_no(DeformMeshRemap::SLAVE, DeformMeshRemap::FLUID, *vit); + } + set_nos.clear(); + + po.getOptAllArgs("sm", set_nos); + if (set_nos.empty()) { + rval = dfr->add_set_no(DeformMeshRemap::MASTER, DeformMeshRemap::SOLID, SOLID_SETNO); RR("Failed to add solid set no."); + } + else { + for (std::vector<int>::iterator vit = set_nos.begin(); vit != set_nos.end(); vit++) + dfr->add_set_no(DeformMeshRemap::MASTER, DeformMeshRemap::SOLID, *vit); + } + + po.getOptAllArgs("ss", set_nos); + if (set_nos.empty()) { + rval = dfr->add_set_no(DeformMeshRemap::SLAVE, DeformMeshRemap::SOLID, SOLID_SETNO); RR("Failed to add solid set no."); + } + else { + for (std::vector<int>::iterator vit = set_nos.begin(); vit != set_nos.end(); vit++) + dfr->add_set_no(DeformMeshRemap::SLAVE, DeformMeshRemap::SOLID, *vit); } std::string tnames[3]; @@ -489,6 +574,7 @@ ErrorCode DeformMeshRemap::deform_master(Range &fluid_elems, Range &solid_elems, rval = mbImpl->tag_get_handle((tag_name ? tag_name : ""), 3, MB_TYPE_DOUBLE, xDisp[0], MB_TAG_CREAT|MB_TAG_DENSE); RR("Failed to get xNew tag."); + xNew = xDisp[0]; } // set the new tag to those coords @@ -525,10 +611,12 @@ ErrorCode DeformMeshRemap::read_file(int m_or_s, string &fname, EntityHandle &se rval = mbImpl->load_file(fname.c_str(), &seth, ostr.str().c_str()); RR("Couldn't load master/slave mesh."); + if (*solidSetNos[m_or_s].begin() == -1 || *fluidSetNos[m_or_s].begin() == -1) return MB_SUCCESS; + // get material sets for solid/fluid Tag tagh; rval = mbImpl->tag_get_handle(MATERIAL_SET_TAG_NAME, tagh); RR("Couldn't get material set tag name."); - for (std::set<int>::iterator sit = solidSetNos.begin(); sit != solidSetNos.end(); sit++) { + for (std::set<int>::iterator sit = solidSetNos[m_or_s].begin(); sit != solidSetNos[m_or_s].end(); sit++) { Range sets; int set_no = *sit; const void *setno_ptr = &set_no; @@ -549,7 +637,7 @@ ErrorCode DeformMeshRemap::read_file(int m_or_s, string &fname, EntityHandle &se solidElems[m_or_s] = tmp_range.subset_by_dimension(dim); - for (std::set<int>::iterator sit = fluidSetNos.begin(); sit != fluidSetNos.end(); sit++) { + for (std::set<int>::iterator sit = fluidSetNos[m_or_s].begin(); sit != fluidSetNos[m_or_s].end(); sit++) { Range sets; int set_no = *sit; const void *setno_ptr = &set_no; https://bitbucket.org/fathomteam/moab/commits/a93cd6825b14/ Changeset: a93cd6825b14 Branch: None User: tautges Date: 2014-03-12 16:53:02 Summary: Adding the ability to compute on master only. Affected #: 1 file diff --git a/examples/DeformMeshRemap.cpp b/examples/DeformMeshRemap.cpp index b92d994..ac3ca39 100644 --- a/examples/DeformMeshRemap.cpp +++ b/examples/DeformMeshRemap.cpp @@ -238,36 +238,42 @@ ErrorCode DeformMeshRemap::execute() if (*solidSetNos[MASTER].begin() == -1 || *fluidSetNos[MASTER].begin() == -1) { rval = find_other_sets(MASTER, masterSet); RR("Failed to find other sets in master mesh."); } - - rval = read_file(SLAVE, slaveFileName, slaveSet); - if (MB_SUCCESS != rval) return rval; - if (*solidSetNos[SLAVE].begin() == -1 || *fluidSetNos[SLAVE].begin() == -1) { - rval = find_other_sets(SLAVE, slaveSet); RR("Failed to find other sets in slave mesh."); + bool have_slave = !(slaveFileName == "none"); + if (have_slave) { + rval = read_file(SLAVE, slaveFileName, slaveSet); + if (MB_SUCCESS != rval) return rval; + + if (*solidSetNos[SLAVE].begin() == -1 || *fluidSetNos[SLAVE].begin() == -1) { + rval = find_other_sets(SLAVE, slaveSet); RR("Failed to find other sets in slave mesh."); + } } Range src_elems = solidElems[MASTER]; src_elems.merge(fluidElems[MASTER]); - // locate slave vertices in master, orig coords; do this with a data coupler, so you can - // later interpolate - Range tgt_verts, tmp_range = solidElems[SLAVE]; - tmp_range.merge(fluidElems[SLAVE]); - rval = mbImpl->get_adjacencies(tmp_range, 0, false, tgt_verts, Interface::UNION); - RR("Failed to get target verts."); - // initialize data coupler on source elements DataCoupler dc_master(mbImpl, NULL, src_elems, 0); - - // locate slave vertices, caching results in dc - rval = dc_master.locate_points(tgt_verts); RR("Point location of tgt verts failed."); - int num_located = dc_master.spatial_locator()->local_num_located(); - if (num_located != (int)tgt_verts.size()) { - rval = MB_FAILURE; - std::cout << "Only " << num_located << " out of " << tgt_verts.size() << " target points successfully located." << std::endl; - return rval; - } + Range tgt_verts; + if (have_slave) { + // locate slave vertices in master, orig coords; do this with a data coupler, so you can + // later interpolate + Range tmp_range = solidElems[SLAVE]; + tmp_range.merge(fluidElems[SLAVE]); + rval = mbImpl->get_adjacencies(tmp_range, 0, false, tgt_verts, Interface::UNION); + RR("Failed to get target verts."); + + // locate slave vertices, caching results in dc + rval = dc_master.locate_points(tgt_verts); RR("Point location of tgt verts failed."); + int num_located = dc_master.spatial_locator()->local_num_located(); + if (num_located != (int)tgt_verts.size()) { + rval = MB_FAILURE; + std::cout << "Only " << num_located << " out of " << tgt_verts.size() << " target points successfully located." << std::endl; + return rval; + } + } + // deform the master's solid mesh, put results in a new tag rval = deform_master(fluidElems[MASTER], solidElems[MASTER], "xnew"); RR(""); @@ -279,14 +285,17 @@ ErrorCode DeformMeshRemap::execute() RR("Failed in lloyd smoothing."); cout << "Lloyd smoothing required " << ll.num_its() << " iterations." << endl; } - - // map new locations to slave - // interpolate xNew to slave points - rval = dc_master.interpolate((int)DataCoupler::VOLUME, "xnew"); RR("Failed to interpolate target solution."); - // transfer xNew to coords, for master and slave + // transfer xNew to coords, for master rval = write_to_coords(fluidElems[MASTER], xNew); RR("Failed writing tag to master fluid verts."); - rval = write_to_coords(tgt_verts, xNew); RR("Failed writing tag to slave verts."); + + if (have_slave) { + // map new locations to slave + // interpolate xNew to slave points + rval = dc_master.interpolate((int)DataCoupler::VOLUME, "xnew"); RR("Failed to interpolate target solution."); + // transfer xNew to coords, for slave + rval = write_to_coords(tgt_verts, xNew); RR("Failed writing tag to slave verts."); + } if (debug) { std::string str; @@ -295,13 +304,16 @@ ErrorCode DeformMeshRemap::execute() str = "PARALLEL=WRITE_PART"; #endif rval = mbImpl->write_file("smoothed_master.vtk", NULL, str.c_str(), &masterSet, 1); + + if (have_slave) { #ifdef USE_MPI - str.clear(); - if (pcSlave && pcSlave->size() > 1) - str = "PARALLEL=WRITE_PART"; + str.clear(); + if (pcSlave && pcSlave->size() > 1) + str = "PARALLEL=WRITE_PART"; #endif - rval = mbImpl->write_file("slave_interp.vtk", NULL, str.c_str(), &slaveSet, 1); - } + rval = mbImpl->write_file("slave_interp.vtk", NULL, str.c_str(), &slaveSet, 1); + } // if have_slave + } // if debug return MB_SUCCESS; } @@ -394,7 +406,7 @@ int main(int argc, char **argv) { ProgOptions po("Deformed mesh options"); po.addOpt<std::string> ("master,m", "Specify the master meshfile name" ); - po.addOpt<std::string> ("worker,w", "Specify the slave/worker meshfile name" ); + po.addOpt<std::string> ("worker,w", "Specify the slave/worker meshfile name, or 'none' (no quotes) if master only" ); po.addOpt<std::string> ("d1,", "Tag name for displacement x or xyz" ); po.addOpt<std::string> ("d2,", "Tag name for displacement y" ); po.addOpt<std::string> ("d3,", "Tag name for displacement z" ); https://bitbucket.org/fathomteam/moab/commits/8d9ccfdea33f/ Changeset: 8d9ccfdea33f Branch: None User: tautges Date: 2014-03-12 16:53:02 Summary: Better error handling & debug printing. In Tree, handle legacy tag on tree root by deleting and re-creating (legacy files have old-sized tag). Affected #: 2 files diff --git a/examples/DeformMeshRemap.cpp b/examples/DeformMeshRemap.cpp index ac3ca39..afb4d9d 100644 --- a/examples/DeformMeshRemap.cpp +++ b/examples/DeformMeshRemap.cpp @@ -19,6 +19,10 @@ #include "MBTagConventions.hpp" #include "DataCoupler.hpp" +#define IS_BUILDING_MB +#include "moab/Error.hpp" +#undef IS_BUILDING_MB + #ifdef USE_MPI # include "moab/ParallelComm.hpp" #endif @@ -116,6 +120,8 @@ private: //! moab interface Interface *mbImpl; + Error *mError; + #ifdef USE_MPI //! ParallelComm for master, slave meshes ParallelComm *pcMaster, *pcSlave; @@ -235,7 +241,7 @@ ErrorCode DeformMeshRemap::execute() ErrorCode rval = read_file(MASTER, masterFileName, masterSet); if (MB_SUCCESS != rval) return rval; - if (*solidSetNos[MASTER].begin() == -1 || *fluidSetNos[MASTER].begin() == -1) { + if (solidSetNos[MASTER].empty() || fluidSetNos[MASTER].empty()) { rval = find_other_sets(MASTER, masterSet); RR("Failed to find other sets in master mesh."); } @@ -244,7 +250,7 @@ ErrorCode DeformMeshRemap::execute() rval = read_file(SLAVE, slaveFileName, slaveSet); if (MB_SUCCESS != rval) return rval; - if (*solidSetNos[SLAVE].begin() == -1 || *fluidSetNos[SLAVE].begin() == -1) { + if (solidSetNos[SLAVE].empty() || fluidSetNos[SLAVE].empty()) { rval = find_other_sets(SLAVE, slaveSet); RR("Failed to find other sets in slave mesh."); } } @@ -318,50 +324,6 @@ ErrorCode DeformMeshRemap::execute() return MB_SUCCESS; } -ErrorCode DeformMeshRemap::find_other_sets(int m_or_s, EntityHandle file_set) -{ - // solid or fluid sets are missing; find the other - Range *filled_sets = NULL, *unfilled_sets = NULL, *unfilled_elems = NULL; - - if (fluidSets[m_or_s].empty() && !solidSets[m_or_s].empty()) { - unfilled_sets = &fluidSets[m_or_s]; - filled_sets = &solidSets[m_or_s]; - unfilled_elems = &fluidElems[m_or_s]; - } - else if (!fluidSets[m_or_s].empty() && solidSets[m_or_s].empty()) { - filled_sets = &fluidSets[m_or_s]; - unfilled_sets = &solidSets[m_or_s]; - unfilled_elems = &solidElems[m_or_s]; - } - - // ok, we know the filled sets, now fill the unfilled sets, and the elems from those - Tag tagh; - ErrorCode rval = mbImpl->tag_get_handle(MATERIAL_SET_TAG_NAME, tagh); RR("Couldn't get material set tag name."); - Range matsets; - rval = mbImpl->get_entities_by_type_and_tag(file_set, MBENTITYSET, &tagh, NULL, 1, matsets); - if (matsets.empty()) rval = MB_FAILURE; - RR("Couldn't get any material sets."); - *unfilled_sets = subtract(matsets, *filled_sets); - if (unfilled_sets->empty()) { - rval = MB_FAILURE; - RR("Failed to find any unfilled material sets."); - } - Range tmp_range; - for (Range::iterator rit = unfilled_sets->begin(); rit != unfilled_sets->end(); rit++) { - rval = mbImpl->get_entities_by_handle(*rit, tmp_range, true); - RR("Failed to get entities in unfilled set."); - } - int dim = mbImpl->dimension_from_handle(*tmp_range.rbegin()); - assert(dim > 0 && dim < 4); - *unfilled_elems = tmp_range.subset_by_dimension(dim); - if (unfilled_elems->empty()) { - rval = MB_FAILURE; - RR("Failed to find any unfilled set entities."); - } - - return MB_SUCCESS; -} - std::string DeformMeshRemap::get_file_name(int m_or_s) const { switch (m_or_s) { @@ -390,6 +352,8 @@ void DeformMeshRemap::set_file_name(int m_or_s, const std::string &name) DeformMeshRemap::DeformMeshRemap(Interface *impl, ParallelComm *master, ParallelComm *slave) : mbImpl(impl), pcMaster(master), pcSlave(slave), masterSet(0), slaveSet(0), xNew(0), xNewName("xnew") { + mbImpl->query_interface(mError); + xDisp[0] = xDisp[1] = xDisp[2] = 0; if (!pcSlave && pcMaster) @@ -398,6 +362,7 @@ DeformMeshRemap::DeformMeshRemap(Interface *impl, ParallelComm *master, Parallel DeformMeshRemap::~DeformMeshRemap() { + mbImpl->release_interface(mError); } int main(int argc, char **argv) { @@ -436,47 +401,29 @@ int main(int argc, char **argv) { if(!po.getOpt("worker", &slavef)) slavef = string(MESH_DIR) + string("/rodtri.g"); dfr->set_file_name(DeformMeshRemap::SLAVE, slavef); + if (slavef.empty()) { + std::cerr << "Empty slave file name; if no slave, use filename 'none' (no quotes)." << std::endl; + return 1; + } std::vector<int> set_nos; po.getOptAllArgs("fm", set_nos); - if (set_nos.empty()) { - rval = dfr->add_set_no(DeformMeshRemap::MASTER, DeformMeshRemap::FLUID, FLUID_SETNO); - RR("Failed to add solid set no."); - } - else { - for (std::vector<int>::iterator vit = set_nos.begin(); vit != set_nos.end(); vit++) - dfr->add_set_no(DeformMeshRemap::MASTER, DeformMeshRemap::FLUID, *vit); - } + for (std::vector<int>::iterator vit = set_nos.begin(); vit != set_nos.end(); vit++) + dfr->add_set_no(DeformMeshRemap::MASTER, DeformMeshRemap::FLUID, *vit); set_nos.clear(); po.getOptAllArgs("fs", set_nos); - if (set_nos.empty()) { - rval = dfr->add_set_no(DeformMeshRemap::SLAVE, DeformMeshRemap::FLUID, FLUID_SETNO); - RR("Failed to add solid set no."); - } - else { - for (std::vector<int>::iterator vit = set_nos.begin(); vit != set_nos.end(); vit++) - dfr->add_set_no(DeformMeshRemap::SLAVE, DeformMeshRemap::FLUID, *vit); - } + for (std::vector<int>::iterator vit = set_nos.begin(); vit != set_nos.end(); vit++) + dfr->add_set_no(DeformMeshRemap::SLAVE, DeformMeshRemap::FLUID, *vit); set_nos.clear(); po.getOptAllArgs("sm", set_nos); - if (set_nos.empty()) { - rval = dfr->add_set_no(DeformMeshRemap::MASTER, DeformMeshRemap::SOLID, SOLID_SETNO); RR("Failed to add solid set no."); - } - else { - for (std::vector<int>::iterator vit = set_nos.begin(); vit != set_nos.end(); vit++) - dfr->add_set_no(DeformMeshRemap::MASTER, DeformMeshRemap::SOLID, *vit); - } + for (std::vector<int>::iterator vit = set_nos.begin(); vit != set_nos.end(); vit++) + dfr->add_set_no(DeformMeshRemap::MASTER, DeformMeshRemap::SOLID, *vit); po.getOptAllArgs("ss", set_nos); - if (set_nos.empty()) { - rval = dfr->add_set_no(DeformMeshRemap::SLAVE, DeformMeshRemap::SOLID, SOLID_SETNO); RR("Failed to add solid set no."); - } - else { - for (std::vector<int>::iterator vit = set_nos.begin(); vit != set_nos.end(); vit++) - dfr->add_set_no(DeformMeshRemap::SLAVE, DeformMeshRemap::SOLID, *vit); - } + for (std::vector<int>::iterator vit = set_nos.begin(); vit != set_nos.end(); vit++) + dfr->add_set_no(DeformMeshRemap::SLAVE, DeformMeshRemap::SOLID, *vit); std::string tnames[3]; po.getOpt("d1", &tnames[0]); @@ -632,10 +579,13 @@ ErrorCode DeformMeshRemap::read_file(int m_or_s, string &fname, EntityHandle &se Range sets; int set_no = *sit; const void *setno_ptr = &set_no; - rval = mbImpl->get_entities_by_type_and_tag(seth, MBENTITYSET, &tagh, &setno_ptr, 1, sets); - if (sets.empty()) rval = MB_FAILURE; - RR("Couldn't get any solid sets."); - solidSets[m_or_s].merge(sets); + ErrorCode tmp_rval = mbImpl->get_entities_by_type_and_tag(seth, MBENTITYSET, &tagh, &setno_ptr, 1, sets); + if (sets.empty() || MB_SUCCESS != tmp_rval) { + rval = MB_FAILURE; + mError->set_last_error("Couldn't find solid set #%d.\n", *sit); + } + else + solidSets[m_or_s].merge(sets); } // get solid entities, and dimension @@ -644,19 +594,26 @@ ErrorCode DeformMeshRemap::read_file(int m_or_s, string &fname, EntityHandle &se rval = mbImpl->get_entities_by_handle(*rit, tmp_range, true); RR("Failed to get entities in solid."); } - int dim = mbImpl->dimension_from_handle(*tmp_range.rbegin()); - assert(dim > 0 && dim < 4); - - solidElems[m_or_s] = tmp_range.subset_by_dimension(dim); + if (!tmp_range.empty()) { + int dim = mbImpl->dimension_from_handle(*tmp_range.rbegin()); + assert(dim > 0 && dim < 4); + solidElems[m_or_s] = tmp_range.subset_by_dimension(dim); + } + + if (debug) + std::cout << "Read " << solidElems[m_or_s].size() << " solid elements from " << solidSets[m_or_s].size() << " sets in " << (m_or_s == MASTER ? "master" : "slave") << " mesh." << std::endl; for (std::set<int>::iterator sit = fluidSetNos[m_or_s].begin(); sit != fluidSetNos[m_or_s].end(); sit++) { Range sets; int set_no = *sit; const void *setno_ptr = &set_no; - rval = mbImpl->get_entities_by_type_and_tag(seth, MBENTITYSET, &tagh, &setno_ptr, 1, sets); - if (sets.empty()) rval = MB_FAILURE; - RR("Couldn't get any fluid sets."); - fluidSets[m_or_s].merge(sets); + ErrorCode tmp_rval = mbImpl->get_entities_by_type_and_tag(seth, MBENTITYSET, &tagh, &setno_ptr, 1, sets); + if (sets.empty() || MB_SUCCESS != tmp_rval) { + rval = MB_FAILURE; + mError->set_last_error("Couldn't find fluid set #%d.\n", *sit); + } + else + fluidSets[m_or_s].merge(sets); } // get fluid entities, and dimension @@ -665,8 +622,66 @@ ErrorCode DeformMeshRemap::read_file(int m_or_s, string &fname, EntityHandle &se rval = mbImpl->get_entities_by_handle(*rit, tmp_range, true); RR("Failed to get entities in fluid."); } + if (!tmp_range.empty()) { + int dim = mbImpl->dimension_from_handle(*tmp_range.rbegin()); + assert(dim > 0 && dim < 4); + fluidElems[m_or_s] = tmp_range.subset_by_dimension(dim); + } - fluidElems[m_or_s] = tmp_range.subset_by_dimension(dim); + if (debug) + std::cout << "Read " << fluidElems[m_or_s].size() << " fluid elements from " << fluidSets[m_or_s].size() << " sets in " << (m_or_s == MASTER ? "master" : "slave") << " mesh." << std::endl; + + return rval; +} + +ErrorCode DeformMeshRemap::find_other_sets(int m_or_s, EntityHandle file_set) +{ + // solid or fluid sets are missing; find the other + Range *filled_sets = NULL, *unfilled_sets = NULL, *unfilled_elems = NULL; + + if (fluidSets[m_or_s].empty() && !solidSets[m_or_s].empty()) { + unfilled_sets = &fluidSets[m_or_s]; + filled_sets = &solidSets[m_or_s]; + unfilled_elems = &fluidElems[m_or_s]; + if (debug) + std::cout << "Finding unspecified fluid elements in " << (m_or_s == MASTER ? "master" : "slave") << " mesh..."; + } + else if (!fluidSets[m_or_s].empty() && solidSets[m_or_s].empty()) { + filled_sets = &fluidSets[m_or_s]; + unfilled_sets = &solidSets[m_or_s]; + unfilled_elems = &solidElems[m_or_s]; + if (debug) + std::cout << "Finding unspecified solid elements in " << (m_or_s == MASTER ? "master" : "slave") << " mesh..."; + } + + // ok, we know the filled sets, now fill the unfilled sets, and the elems from those + Tag tagh; + ErrorCode rval = mbImpl->tag_get_handle(MATERIAL_SET_TAG_NAME, tagh); RR("Couldn't get material set tag name."); + Range matsets; + rval = mbImpl->get_entities_by_type_and_tag(file_set, MBENTITYSET, &tagh, NULL, 1, matsets); + if (matsets.empty()) rval = MB_FAILURE; + RR("Couldn't get any material sets."); + *unfilled_sets = subtract(matsets, *filled_sets); + if (unfilled_sets->empty()) { + rval = MB_FAILURE; + RR("Failed to find any unfilled material sets."); + } + Range tmp_range; + for (Range::iterator rit = unfilled_sets->begin(); rit != unfilled_sets->end(); rit++) { + rval = mbImpl->get_entities_by_handle(*rit, tmp_range, true); + RR("Failed to get entities in unfilled set."); + } + int dim = mbImpl->dimension_from_handle(*tmp_range.rbegin()); + assert(dim > 0 && dim < 4); + *unfilled_elems = tmp_range.subset_by_dimension(dim); + if (unfilled_elems->empty()) { + rval = MB_FAILURE; + RR("Failed to find any unfilled set entities."); + } + + if (debug) + std::cout << "found " << unfilled_sets->size() << " sets and " << unfilled_elems->size() << " elements." << std::endl; return MB_SUCCESS; } + diff --git a/src/moab/Tree.hpp b/src/moab/Tree.hpp index 4d2694a..67b67f9 100644 --- a/src/moab/Tree.hpp +++ b/src/moab/Tree.hpp @@ -264,6 +264,14 @@ namespace moab { if (!boxTag && create_if_missing) { assert(boxTagName.length() > 0); ErrorCode rval = moab()->tag_get_handle(boxTagName.c_str(), 6, MB_TYPE_DOUBLE, boxTag, MB_TAG_CREAT | MB_TAG_SPARSE); + if (MB_INVALID_SIZE == rval) { + // delete the tag and get it again, legacy file... + rval = moab()->tag_delete(boxTag); + if (MB_SUCCESS != rval) return 0; + boxTag = 0; + return get_box_tag(true); + } + if (MB_SUCCESS != rval) return 0; } https://bitbucket.org/fathomteam/moab/commits/863998bd5433/ Changeset: 863998bd5433 Branch: None User: tautges Date: 2014-03-12 16:53:02 Summary: Adding progress-type debug messages. Was assuming faces in Lloyd smoother, now getting dimension from elements. Affected #: 2 files diff --git a/examples/DeformMeshRemap.cpp b/examples/DeformMeshRemap.cpp index afb4d9d..6357df9 100644 --- a/examples/DeformMeshRemap.cpp +++ b/examples/DeformMeshRemap.cpp @@ -254,6 +254,8 @@ ErrorCode DeformMeshRemap::execute() rval = find_other_sets(SLAVE, slaveSet); RR("Failed to find other sets in slave mesh."); } } + + if (debug) std::cout << "Constructing data coupler/search tree on master mesh..." << std::endl; Range src_elems = solidElems[MASTER]; src_elems.merge(fluidElems[MASTER]); @@ -271,6 +273,7 @@ ErrorCode DeformMeshRemap::execute() RR("Failed to get target verts."); // locate slave vertices, caching results in dc + if (debug) std::cout << "Locating slave vertices in master mesh..." << std::endl; rval = dc_master.locate_points(tgt_verts); RR("Point location of tgt verts failed."); int num_located = dc_master.spatial_locator()->local_num_located(); if (num_located != (int)tgt_verts.size()) { @@ -281,11 +284,13 @@ ErrorCode DeformMeshRemap::execute() } // deform the master's solid mesh, put results in a new tag + if (debug) std::cout << "Deforming fluid elements in master mesh..." << std::endl; rval = deform_master(fluidElems[MASTER], solidElems[MASTER], "xnew"); RR(""); { // to isolate the lloyd smoother & delete when done // smooth the master mesh + if (debug) std::cout << "Smoothing fluid elements in master mesh..." << std::endl; LloydSmoother ll(mbImpl, NULL, fluidElems[MASTER], xNew); rval = ll.perform_smooth(); RR("Failed in lloyd smoothing."); @@ -293,13 +298,16 @@ ErrorCode DeformMeshRemap::execute() } // transfer xNew to coords, for master + if (debug) std::cout << "Transferring coords tag to vertex coordinates in master mesh..." << std::endl; rval = write_to_coords(fluidElems[MASTER], xNew); RR("Failed writing tag to master fluid verts."); if (have_slave) { // map new locations to slave // interpolate xNew to slave points + if (debug) std::cout << "Interpolating new coordinates to slave vertices..." << std::endl; rval = dc_master.interpolate((int)DataCoupler::VOLUME, "xnew"); RR("Failed to interpolate target solution."); // transfer xNew to coords, for slave + if (debug) std::cout << "Transferring coords tag to vertex coordinates in slave mesh..." << std::endl; rval = write_to_coords(tgt_verts, xNew); RR("Failed writing tag to slave verts."); } @@ -309,6 +317,7 @@ ErrorCode DeformMeshRemap::execute() if (pcMaster && pcMaster->size() > 1) str = "PARALLEL=WRITE_PART"; #endif + if (debug) std::cout << "Writing smoothed_master.vtk..." << std::endl; rval = mbImpl->write_file("smoothed_master.vtk", NULL, str.c_str(), &masterSet, 1); if (have_slave) { @@ -317,6 +326,7 @@ ErrorCode DeformMeshRemap::execute() if (pcSlave && pcSlave->size() > 1) str = "PARALLEL=WRITE_PART"; #endif + if (debug) std::cout << "Writing slave_interp.vtk..." << std::endl; rval = mbImpl->write_file("slave_interp.vtk", NULL, str.c_str(), &slaveSet, 1); } // if have_slave } // if debug diff --git a/src/LloydSmoother.cpp b/src/LloydSmoother.cpp index b1614d2..e9cce82 100644 --- a/src/LloydSmoother.cpp +++ b/src/LloydSmoother.cpp @@ -39,6 +39,17 @@ ErrorCode LloydSmoother::perform_smooth() { ErrorCode rval; + if (myElems.empty()) { + rval = MB_FAILURE; + RR("No elements specified to Lloyd smoother."); + } + else if (mbImpl->dimension_from_handle(*myElems.begin()) != mbImpl->dimension_from_handle(*myElems.rbegin())) { + rval = MB_FAILURE; + RR("Elements of unequal dimension specified to Lloyd smoother."); + } + + int dim = mbImpl->dimension_from_handle(*myElems.begin()); + // first figure out tolerance to use if (0 > absTol) { // no tolerance set - get one relative to bounding box around elements @@ -140,7 +151,7 @@ ErrorCode LloydSmoother::perform_smooth() if (fix_tag[v]) continue; // vertex centroid = sum(cell centroids)/ncells adj_elems.clear(); - rval = mbImpl->get_adjacencies(&(*vit), 1, 2, false, adj_elems); RR("Failed getting adjs."); + rval = mbImpl->get_adjacencies(&(*vit), 1, dim, false, adj_elems); RR("Failed getting adjs."); rval = mbImpl->tag_get_data(centroid, &adj_elems[0], adj_elems.size(), &fcentroids[0]); RR("Failed to get elem centroid."); double vnew[] = {0.0, 0.0, 0.0}; https://bitbucket.org/fathomteam/moab/commits/bd2eb5c6475b/ Changeset: bd2eb5c6475b Branch: None User: tautges Date: 2014-03-12 16:53:02 Summary: DeformMeshRemap: more debugging output, and handle coord displacements properly (add to prev coords) LloydSmoother: fix a bug with fixed tag entity handles size SpatialLocator: if an element range is specified, build the tree too Affected #: 3 files diff --git a/examples/DeformMeshRemap.cpp b/examples/DeformMeshRemap.cpp index 6357df9..f0d55fa 100644 --- a/examples/DeformMeshRemap.cpp +++ b/examples/DeformMeshRemap.cpp @@ -12,6 +12,7 @@ #include "moab/Core.hpp" #include "moab/Range.hpp" +#include "moab/Skinner.hpp" #include "moab/LloydSmoother.hpp" #include "moab/ProgOptions.hpp" #include "moab/BoundBox.hpp" @@ -288,6 +289,22 @@ ErrorCode DeformMeshRemap::execute() rval = deform_master(fluidElems[MASTER], solidElems[MASTER], "xnew"); RR(""); { // to isolate the lloyd smoother & delete when done + if (debug) { + // output the skin of smoothed elems, as a check + // get the skin; get facets, because we might need to filter on shared entities + Skinner skinner(mbImpl); + Range skin; + rval = skinner.find_skin(0, fluidElems[MASTER], false, skin); RR("Unable to find skin."); + EntityHandle skin_set; + std::cout << "Writing skin_mesh.g and fluid_mesh.g." << std::endl; + rval = mbImpl->create_meshset(MESHSET_SET, skin_set); RR("Failed to create skin set."); + rval = mbImpl->add_entities(skin_set, skin); RR("Failed to add skin entities to set."); + rval = mbImpl->write_file("skin_mesh.vtk", NULL, NULL, &skin_set, 1); RR("Failure to write skin set."); + rval = mbImpl->remove_entities(skin_set, skin); RR("Failed to remove skin entities from set."); + rval = mbImpl->add_entities(skin_set, fluidElems[MASTER]); RR("Failed to add fluid entities to set."); + rval = mbImpl->write_file("fluid_mesh.vtk", NULL, NULL, &skin_set, 1); RR("Failure to write fluid set."); + rval = mbImpl->delete_entities(&skin_set, 1); RR("Failed to delete skin set."); + } // smooth the master mesh if (debug) std::cout << "Smoothing fluid elements in master mesh..." << std::endl; @@ -385,10 +402,10 @@ int main(int argc, char **argv) { po.addOpt<std::string> ("d1,", "Tag name for displacement x or xyz" ); po.addOpt<std::string> ("d2,", "Tag name for displacement y" ); po.addOpt<std::string> ("d3,", "Tag name for displacement z" ); - po.addOpt<int> ("fm,", "Specify master fluid material set number(s). If -1 specified, fluid sets derived from complement of solid sets."); - po.addOpt<int> ("fs,", "Specify master solid material set number(s). If -1 specified, fluid sets derived from complement of solid sets."); - po.addOpt<int> ("sm,", "Specify slave fluid material set number(s). If -1 specified, fluid sets derived from complement of solid sets."); - po.addOpt<int> ("ss,", "Specify slave solid material set number(s). If -1 specified, fluid sets derived from complement of solid sets."); + po.addOpt<int> ("fm,", "Specify master fluid material set number(s). If none specified, fluid sets derived from complement of solid sets."); + po.addOpt<int> ("fs,", "Specify master solid material set number(s). If none specified, solid sets derived from complement of fluid sets."); + po.addOpt<int> ("sm,", "Specify slave fluid material set number(s). If none specified, fluid sets derived from complement of solid sets."); + po.addOpt<int> ("ss,", "Specify slave solid material set number(s). If none specified, solid sets derived from complement of fluid sets."); po.parseCommandLine(argc, argv); @@ -500,7 +517,7 @@ ErrorCode DeformMeshRemap::deform_master(Range &fluid_elems, Range &solid_elems, Range verts; rval = mbImpl->get_adjacencies(solid_elems, 0, false, verts, Interface::UNION); RR("Failed to get vertices."); - std::vector<double> coords(3*verts.size()); + std::vector<double> coords(3*verts.size()), new_coords(3*verts.size()); rval = mbImpl->get_coords(verts, &coords[0]); RR("Failed to get vertex coords."); unsigned int num_verts = verts.size(); @@ -512,13 +529,14 @@ ErrorCode DeformMeshRemap::deform_master(Range &fluid_elems, Range &solid_elems, rval = mbImpl->tag_get_handle((tag_name ? tag_name : ""), 3, MB_TYPE_DOUBLE, xNew, MB_TAG_CREAT|MB_TAG_DENSE); RR("Failed to create xnew tag."); std::vector<double> disps(num_verts); + for (int i = 0; i < 3; i++) { rval = mbImpl->tag_get_handle(xDispNames[0].c_str(), 1, MB_TYPE_DOUBLE, xDisp[i]); RR("Failed to get xDisp tag."); rval = mbImpl->tag_get_data(xDisp[i], verts, &disps[0]); RR("Failed to get xDisp tag values."); for (unsigned int j = 0; j < num_verts; j++) - coords[3*j+i] = disps[j]; + new_coords[3*j+i] = coords[3*j+i] + disps[j]; } } else if (!xDispNames[0].empty()) { @@ -528,7 +546,7 @@ ErrorCode DeformMeshRemap::deform_master(Range &fluid_elems, Range &solid_elems, std::vector<double> disps(3*num_verts); rval = mbImpl->tag_get_data(xDisp[0], verts, &disps[0]); for (unsigned int j = 0; j < 3*num_verts; j++) - coords[j] += disps[j]; + new_coords[j] = coords[j] + disps[j]; } else { // get the bounding box of the solid mesh @@ -536,9 +554,19 @@ ErrorCode DeformMeshRemap::deform_master(Range &fluid_elems, Range &solid_elems, bbox.update(*mbImpl, solid_elems); for (unsigned int j = 0; j < num_verts; j++) - deform_func(bbox, &coords[3*j], &coords[3*j]); + deform_func(bbox, &coords[3*j], &new_coords[3*j]); } + if (debug) { + double len = 0.0; + for (unsigned int i = 0; i < num_verts; i++) { + CartVect dx = CartVect(&new_coords[3*i]) - CartVect(&coords[3*i]); + double tmp_len = dx.length_squared(); + if (tmp_len > len) len = tmp_len; + } + std::cout << "Max displacement = " << len << std::endl; + } + if (!xNew) { rval = mbImpl->tag_get_handle((tag_name ? tag_name : ""), 3, MB_TYPE_DOUBLE, xDisp[0], MB_TAG_CREAT|MB_TAG_DENSE); diff --git a/src/LloydSmoother.cpp b/src/LloydSmoother.cpp index e9cce82..ba8169a 100644 --- a/src/LloydSmoother.cpp +++ b/src/LloydSmoother.cpp @@ -232,7 +232,7 @@ ErrorCode LloydSmoother::initialize() RR("Trouble getting vertices."); // mark them fixed - std::vector<unsigned char> marks(skin.size(), 0x1); + std::vector<unsigned char> marks(skin_verts.size(), 0x1); rval = mbImpl->tag_set_data(fixedTag, skin_verts, &marks[0]); RR("Unable to set tag on skin."); } diff --git a/src/SpatialLocator.cpp b/src/SpatialLocator.cpp index f976ae7..b2dc8e3 100644 --- a/src/SpatialLocator.cpp +++ b/src/SpatialLocator.cpp @@ -40,7 +40,9 @@ namespace moab myDim = mbImpl->dimension_from_handle(*elems.begin()); myElems = elems; - return MB_SUCCESS; + + ErrorCode rval = myTree->build_tree(myElems); + return rval; } #ifdef USE_MPI https://bitbucket.org/fathomteam/moab/commits/7d59aad7b01d/ Changeset: 7d59aad7b01d Branch: None User: tautges Date: 2014-03-12 16:53:02 Summary: Adding % change to max displacement debug output. Affected #: 1 file diff --git a/examples/DeformMeshRemap.cpp b/examples/DeformMeshRemap.cpp index f0d55fa..667904b 100644 --- a/examples/DeformMeshRemap.cpp +++ b/examples/DeformMeshRemap.cpp @@ -564,7 +564,13 @@ ErrorCode DeformMeshRemap::deform_master(Range &fluid_elems, Range &solid_elems, double tmp_len = dx.length_squared(); if (tmp_len > len) len = tmp_len; } - std::cout << "Max displacement = " << len << std::endl; + Range tmp_elems(fluid_elems); + tmp_elems.merge(solid_elems); + BoundBox box; + box.update(*mbImpl, tmp_elems); + double max_len = std::max(box.bMax[2]-box.bMin[2], std::max(box.bMax[1]-box.bMin[1], box.bMax[0]-box.bMin[0])); + + std::cout << "Max displacement = " << len << " (" << 100.0 * len / max_len << "% of max box length)" << std::endl; } if (!xNew) { https://bitbucket.org/fathomteam/moab/commits/cd923766bcc7/ Changeset: cd923766bcc7 Branch: None User: tautges Date: 2014-03-12 16:53:41 Summary: DeformMeshRemap: add some tree statistics output AdaptiveKDTree: make several functions non-static so they show up in profiling; also use BoundBox a bit more BVHTree: account for BoundBox change SpatialLocator: choose tree type based on contents of myElems, and move tree construction to a separate function BoundBox: change name of contains_box to intersects_box, and fix logic that was broken there TreeStats.hpp: improve statistics output test_boundbox: fix tests for changes to BoundBox Affected #: 8 files diff --git a/examples/DeformMeshRemap.cpp b/examples/DeformMeshRemap.cpp index 667904b..f752b4e 100644 --- a/examples/DeformMeshRemap.cpp +++ b/examples/DeformMeshRemap.cpp @@ -348,6 +348,9 @@ ErrorCode DeformMeshRemap::execute() } // if have_slave } // if debug + if (debug) + dc_master.spatial_locator()->get_tree()->tree_stats().print(); + return MB_SUCCESS; } diff --git a/src/AdaptiveKDTree.cpp b/src/AdaptiveKDTree.cpp index 1324c30..8aafdd1 100644 --- a/src/AdaptiveKDTree.cpp +++ b/src/AdaptiveKDTree.cpp @@ -176,7 +176,6 @@ namespace moab { else { rval = iter.step(); if (MB_ENTITY_NOT_FOUND == rval) { - treeStats.reset(); rval = treeStats.compute_stats(mbImpl, myRoot); treeStats.initTime = cp.time_elapsed(); return rval; // at end @@ -807,8 +806,7 @@ namespace moab { t_enter, t_exit ); } - static ErrorCode intersect_children_with_elems( - AdaptiveKDTree* tool, + ErrorCode AdaptiveKDTree::intersect_children_with_elems( const Range& elems, AdaptiveKDTree::Plane plane, double eps, @@ -823,15 +821,16 @@ namespace moab { right_tris.clear(); both_tris.clear(); CartVect coords[16]; - Interface *const moab = tool->moab(); // get extents of boxes for left and right sides - CartVect right_min( box_min ), left_max( box_max ); - right_min[plane.norm] = left_max[plane.norm] = plane.coord; - const CartVect left_cen = 0.5*(left_max + box_min); - const CartVect left_dim = 0.5*(left_max - box_min); - const CartVect right_cen = 0.5*(box_max + right_min); - const CartVect right_dim = 0.5*(box_max - right_min); + BoundBox left_box(box_min, box_max), right_box(box_min, box_max); + right_box.bMin = box_min; + left_box.bMax = box_max; + right_box.bMin[plane.norm] = left_box.bMax[plane.norm] = plane.coord; + const CartVect left_cen = 0.5*(left_box.bMax + box_min); + const CartVect left_dim = 0.5*(left_box.bMax - box_min); + const CartVect right_cen = 0.5*(box_max + right_box.bMin); + const CartVect right_dim = 0.5*(box_max - right_box.bMin); const CartVect dim = box_max - box_min; const double max_tol = std::max(dim[0], std::max(dim[1], dim[2]))/10; @@ -851,8 +850,8 @@ namespace moab { // vertices for (i = elems.begin(); i != elem_begin; ++i) { - tool->tree_stats().leafObjectTests++; - rval = moab->get_coords( &*i, 1, coords[0].array() ); + tree_stats().leafObjectTests++; + rval = moab()->get_coords( &*i, 1, coords[0].array() ); if (MB_SUCCESS != rval) return rval; @@ -873,13 +872,13 @@ namespace moab { // non-polyhedron elements std::vector<EntityHandle> dum_vector; for (i = elem_begin; i != poly_begin; ++i) { - tool->tree_stats().leafObjectTests++; - rval = moab->get_connectivity( *i, conn, count, true, &dum_vector); + tree_stats().leafObjectTests++; + rval = moab()->get_connectivity( *i, conn, count, true, &dum_vector); if (MB_SUCCESS != rval) return rval; if (count > (int)(sizeof(coords)/sizeof(coords[0]))) return MB_FAILURE; - rval = moab->get_coords( &conn[0], count, coords[0].array() ); + rval = moab()->get_coords( &conn[0], count, coords[0].array() ); if (MB_SUCCESS != rval) return rval; bool lo = false, ro = false; @@ -894,12 +893,16 @@ namespace moab { // identified that leaf, then we're done. If triangle is on both // sides of plane, do more precise test to ensure that it is really // in both. +// BoundBox box; +// box.update(*moab(), *i); if (lo && ro) { double tol = eps; lo = ro = false; while (!lo && !ro && tol <= max_tol) { - lo = GeomUtil::box_elem_overlap( coords, TYPE_FROM_HANDLE(*i), left_cen, left_dim+CartVect(tol) ); - ro = GeomUtil::box_elem_overlap( coords, TYPE_FROM_HANDLE(*i),right_cen,right_dim+CartVect(tol) ); + tree_stats().boxElemTests+= 2; + lo = GeomUtil::box_elem_overlap( coords, TYPE_FROM_HANDLE(*i), left_cen, left_dim+CartVect(tol)); + ro = GeomUtil::box_elem_overlap( coords, TYPE_FROM_HANDLE(*i), right_cen, right_dim+CartVect(tol)); + tol *= 10.0; } } @@ -913,20 +916,20 @@ namespace moab { // polyhedra for (i = poly_begin; i != set_begin; ++i) { - tool->tree_stats().leafObjectTests++; - rval = moab->get_connectivity( *i, conn, count, true ); + tree_stats().leafObjectTests++; + rval = moab()->get_connectivity( *i, conn, count, true ); if (MB_SUCCESS != rval) return rval; // just check the bounding box of the polyhedron bool lo = false, ro = false; for (int j = 0; j < count; ++j) { - rval = moab->get_connectivity( conn[j], conn2, count2, true ); + rval = moab()->get_connectivity( conn[j], conn2, count2, true ); if (MB_SUCCESS != rval) return rval; for (int k = 0; k < count2; ++k) { - rval = moab->get_coords( conn2 + k, 1, coords[0].array() ); + rval = moab()->get_coords( conn2 + k, 1, coords[0].array() ); if (MB_SUCCESS != rval) return rval; if (coords[0][plane.norm] <= plane.coord) @@ -947,8 +950,8 @@ namespace moab { // sets BoundBox tbox; for (i = set_begin; i != elems.end(); ++i) { - tool->tree_stats().leafObjectTests++; - rval = tbox.update(*tool->moab(), *i); + tree_stats().leafObjectTests++; + rval = tbox.update(*moab(), *i); if (MB_SUCCESS != rval) return rval; @@ -1005,8 +1008,7 @@ namespace moab { AdaptiveKDTree::Plane plane = { box_min[axis] + (p/(1.0+plane_count)) * diff[axis], axis }; Range left, right, both; double val; - r = intersect_children_with_elems( iter.tool(), - entities, plane, eps, + r = intersect_children_with_elems( entities, plane, eps, box_min, box_max, left, right, both, val ); @@ -1057,32 +1059,38 @@ namespace moab { if (MB_SUCCESS != r) return r; - tmp_data.resize( vertices.size() ); + unsigned int nverts = vertices.size(); + tmp_data.resize( 3*nverts); + r = iter.tool()->moab()->get_coords( vertices, &tmp_data[0], &tmp_data[nverts], &tmp_data[2*nverts] ); + if (MB_SUCCESS != r) + return r; + for (int axis = 0; axis < 3; ++axis) { int plane_count = num_planes; + + // if num_planes results in width < eps, reset the plane count if ((num_planes+1)*eps >= diff[axis]) plane_count = (int)(diff[axis] / eps) - 1; - double *ptrs[] = { 0, 0, 0 }; - ptrs[axis] = &tmp_data[0]; - r = iter.tool()->moab()->get_coords( vertices, ptrs[0], ptrs[1], ptrs[2] ); - if (MB_SUCCESS != r) - return r; - for (int p = 1; p <= plane_count; ++p) { + + // coord of this plane on axis double coord = box_min[axis] + (p/(1.0+plane_count)) * diff[axis]; - double closest_coord = tmp_data[0]; - for (unsigned i = 1; i < tmp_data.size(); ++i) - if (fabs(coord-tmp_data[i]) < fabs(coord-closest_coord)) - closest_coord = tmp_data[i]; + + // find closest vertex coordinate to this plane position + unsigned int istrt = axis*nverts; + double closest_coord = tmp_data[istrt]; + for (unsigned i = 1; i < nverts; ++i) + if (fabs(coord-tmp_data[istrt+i]) < fabs(coord-closest_coord)) + closest_coord = tmp_data[istrt+i]; if (closest_coord - box_min[axis] <= eps || box_max[axis] - closest_coord <= eps) continue; + // seprate elems into left/right/both, and compute separating metric AdaptiveKDTree::Plane plane = { closest_coord, axis }; Range left, right, both; double val; - r = intersect_children_with_elems( iter.tool(), - entities, plane, eps, + r = intersect_children_with_elems( entities, plane, eps, box_min, box_max, left, right, both, val ); @@ -1160,8 +1168,7 @@ namespace moab { AdaptiveKDTree::Plane plane = { *citer, axis }; Range left, right, both; double val; - r = intersect_children_with_elems( iter.tool(), - entities, plane, eps, + r = intersect_children_with_elems( entities, plane, eps, box_min, box_max, left, right, both, val ); @@ -1276,8 +1283,7 @@ namespace moab { AdaptiveKDTree::Plane plane = { coords[indices[p]], axis }; Range left, right, both; double val; - r = intersect_children_with_elems( iter.tool(), - entities, plane, eps, + r = intersect_children_with_elems( entities, plane, eps, box_min, box_max, left, right, both, val ); diff --git a/src/BVHTree.cpp b/src/BVHTree.cpp index d54e24d..e2592fb 100644 --- a/src/BVHTree.cpp +++ b/src/BVHTree.cpp @@ -48,7 +48,7 @@ namespace moab #ifndef NDEBUG for(std::vector<HandleData>::const_iterator i = handle_data_vec.begin(); i != handle_data_vec.end(); ++i) { - if(!boundBox.contains_box(i->myBox, 0)){ + if(!boundBox.intersects_box(i->myBox, 0)){ std::cerr << "BB:" << boundBox << "EB:" << i->myBox << std::endl; return MB_FAILURE; } @@ -168,16 +168,16 @@ namespace moab for (unsigned int dim = 0; dim < 3; ++dim){ const unsigned int index = Bucket::bucket_index(splitsPerDir, box, interval, dim); Bucket &bucket = buckets[dim][index]; - if(!bucket.boundingBox.contains_box(box)) + if(!bucket.boundingBox.intersects_box(box)) std::cerr << "Buckets not covering elements!" << std::endl; } } - if(!elt_union.contains_box(interval) ){ + if(!elt_union.intersects_box(interval) ){ std::cout << "element union: " << std::endl << elt_union; std::cout << "intervals: " << std::endl << interval; std::cout << "union of elts does not contain original box!" << std::endl; } - if (!interval.contains_box(elt_union) ){ + if (!interval.intersects_box(elt_union) ){ std::cout << "original box does not contain union of elts" << std::endl; std::cout << interval << std::endl << elt_union << std::endl; } @@ -193,9 +193,9 @@ namespace moab for(unsigned int i = 0; i < nonempty.size(); ++i) test_box.update(buckets_[nonempty[i]].boundingBox); - if(!test_box.contains_box(interval) ) + if(!test_box.intersects_box(interval) ) std::cout << "union of buckets in dimension: " << d << "does not contain original box!" << std::endl; - if (!interval.contains_box(test_box) ) { + if (!interval.intersects_box(test_box) ) { std::cout << "original box does " << "not contain union of buckets" << "in dimension: " << d << std::endl; std::cout << interval << std::endl << test_box << std::endl; @@ -234,7 +234,7 @@ namespace moab s != splits_end; ++s, ++left_end) { BoundBox test_box = s->leftBox; test_box.update(s->rightBox); - if(!data.boundingBox.contains_box(test_box)) { + if(!data.boundingBox.intersects_box(test_box)) { std::cout << "nr: " << s->nr << std::endl; std::cout << "Test box: " << std::endl << test_box; @@ -247,7 +247,7 @@ namespace moab std::cout << "Split boxes larger than bb" << std::endl; } - if(!test_box.contains_box(data.boundingBox)) { + if(!test_box.intersects_box(data.boundingBox)) { std::cout << "bb larger than union of split boxes" << std::endl; } } @@ -288,7 +288,7 @@ namespace moab data.Lmax = data.leftBox.bMax[data.dim]; #ifndef NDEBUG BoundBox test_box(data.rightBox); - if(!data.boundingBox.contains_box(test_box)) { + if(!data.boundingBox.intersects_box(test_box)) { std::cerr << "MEDIAN: BB Does not contain splits" << std::endl; std::cerr << "test_box: " << test_box << std::endl; std::cerr << "data.boundingBox: " << data.boundingBox << std::endl; @@ -335,7 +335,7 @@ namespace moab else { right_box.update(i->myBox); } - if(!right_box.contains_box(i->myBox)) { + if(!right_box.intersects_box(i->myBox)) { if(!issue) { std::cerr << "Bounding right box issue!" << std::endl; @@ -352,7 +352,7 @@ namespace moab else { left_box.update(i->myBox); } - if(!data.leftBox.contains_box(i->myBox)) { + if(!data.leftBox.intersects_box(i->myBox)) { if(!issue) { std::cerr << "Bounding left box issue!" << std::endl; @@ -367,13 +367,13 @@ namespace moab } } } - if(!left_box.contains_box(data.leftBox)) + if(!left_box.intersects_box(data.leftBox)) std::cout << "left elts do not contain left box" << std::endl; - if(!data.leftBox.contains_box(left_box)) + if(!data.leftBox.intersects_box(left_box)) std::cout << "left box does not contain left elts" << std::endl; - if(!right_box.contains_box(data.rightBox)) + if(!right_box.intersects_box(data.rightBox)) std::cout << "right elts do not contain right box" << std::endl; - if(!data.rightBox.contains_box(right_box)) + if(!data.rightBox.intersects_box(right_box)) std::cout << "right box do not contain right elts" << std::endl; if(count_left != data.nl || count_right != data.nr) { @@ -400,7 +400,7 @@ namespace moab { #ifndef NDEBUG for(HandleDataVec::const_iterator i = begin; i != end; ++i) { - if(!box.contains_box(i->myBox, 0)) { + if(!box.intersects_box(i->myBox, 0)) { std::cerr << "depth: " << depth << std::endl; std::cerr << "BB:" << box << "EB:" << i->myBox << std::endl; std::exit(-1); diff --git a/src/SpatialLocator.cpp b/src/SpatialLocator.cpp index b2dc8e3..2903155 100644 --- a/src/SpatialLocator.cpp +++ b/src/SpatialLocator.cpp @@ -2,6 +2,7 @@ #include "moab/Interface.hpp" #include "moab/ElemEvaluator.hpp" #include "moab/AdaptiveKDTree.hpp" +#include "moab/BVHTree.hpp" // include ScdInterface for box partitioning #include "moab/ScdInterface.hpp" @@ -18,10 +19,8 @@ namespace moab SpatialLocator::SpatialLocator(Interface *impl, Range &elems, Tree *tree, ElemEvaluator *eval) : mbImpl(impl), myElems(elems), myDim(-1), myTree(tree), elemEval(eval), iCreatedTree(false) { - if (!myTree) { - myTree = new AdaptiveKDTree(impl); - iCreatedTree = true; - } + create_tree(); + if (!elems.empty()) { myDim = mbImpl->dimension_from_handle(*elems.rbegin()); ErrorCode rval = myTree->build_tree(myElems); @@ -32,6 +31,20 @@ namespace moab } } + void SpatialLocator::create_tree() + { + if (myTree) return; + + if (myElems.empty() || mbImpl->type_from_handle(*myElems.rbegin()) == MBVERTEX) + // create a kdtree if only vertices + myTree = new AdaptiveKDTree(mbImpl); + else + // otherwise a BVHtree, since it performs better for elements + myTree = new BVHTree(mbImpl); + + iCreatedTree = true; + } + ErrorCode SpatialLocator::add_elems(Range &elems) { if (elems.empty() || diff --git a/src/moab/AdaptiveKDTree.hpp b/src/moab/AdaptiveKDTree.hpp index c77bdbc..450a418 100644 --- a/src/moab/AdaptiveKDTree.hpp +++ b/src/moab/AdaptiveKDTree.hpp @@ -251,7 +251,6 @@ namespace moab { virtual ErrorCode print(); private: - friend class AdaptiveKDTreeIter; /** \brief Parse options for tree creation @@ -273,7 +272,18 @@ namespace moab { DataType type, int count, void* default_val, Tag& tag_handle, std::vector<Tag>& created_tags ); - static ErrorCode best_subdivision_snap_plane( int num_planes, + ErrorCode intersect_children_with_elems( + const Range& elems, + AdaptiveKDTree::Plane plane, + double eps, + CartVect box_min, + CartVect box_max, + Range& left_tris, + Range& right_tris, + Range& both_tris, + double& metric_value ); + + ErrorCode best_subdivision_snap_plane( int num_planes, const AdaptiveKDTreeIter& iter, Range& best_left, Range& best_right, @@ -282,7 +292,7 @@ namespace moab { std::vector<double>& tmp_data, double eps ); - static ErrorCode best_subdivision_plane( int num_planes, + ErrorCode best_subdivision_plane( int num_planes, const AdaptiveKDTreeIter& iter, Range& best_left, Range& best_right, @@ -290,7 +300,7 @@ namespace moab { AdaptiveKDTree::Plane& best_plane, double eps ); - static ErrorCode best_vertex_median_plane( int num_planes, + ErrorCode best_vertex_median_plane( int num_planes, const AdaptiveKDTreeIter& iter, Range& best_left, Range& best_right, @@ -299,7 +309,7 @@ namespace moab { std::vector<double>& coords, double eps); - static ErrorCode best_vertex_sample_plane( int num_planes, + ErrorCode best_vertex_sample_plane( int num_planes, const AdaptiveKDTreeIter& iter, Range& best_left, Range& best_right, diff --git a/src/moab/BoundBox.hpp b/src/moab/BoundBox.hpp index 3e525ac..c74707a 100644 --- a/src/moab/BoundBox.hpp +++ b/src/moab/BoundBox.hpp @@ -17,7 +17,7 @@ namespace moab { ~BoundBox() {} bool contains_point(const double *point, const double tol = 0.0) const; - bool contains_box(const BoundBox &b, const double tol = 0.0) const; + bool intersects_box(const BoundBox &b, const double tol = 0.0) const; void compute_center(CartVect &center); void update(const BoundBox &other_box); void update(const double *coords); @@ -75,10 +75,10 @@ namespace moab { else return true; } - inline bool BoundBox::contains_box(const BoundBox &b, const double tol) const { - if (b.bMin[0] < bMin[0]-tol || b.bMax[0] > bMax[0]+tol || - b.bMin[1] < bMin[1]-tol || b.bMax[1] > bMax[1]+tol || - b.bMin[2] < bMin[2]-tol || b.bMax[2] > bMax[2]+tol) + inline bool BoundBox::intersects_box(const BoundBox &b, const double tol) const { + if (b.bMax[0] < bMin[0]-tol || b.bMin[0] > bMax[0]+tol || + b.bMax[1] < bMin[1]-tol || b.bMin[1] > bMax[1]+tol || + b.bMax[2] < bMin[2]-tol || b.bMin[2] > bMax[2]+tol) return false; else return true; diff --git a/src/moab/TreeStats.hpp b/src/moab/TreeStats.hpp index be619a5..4ae685b 100644 --- a/src/moab/TreeStats.hpp +++ b/src/moab/TreeStats.hpp @@ -59,6 +59,7 @@ namespace moab unsigned int leavesVisited; unsigned int numTraversals; unsigned int leafObjectTests; + unsigned int boxElemTests; private: ErrorCode traverse(Interface *impl, EntityHandle node, unsigned int &depth); @@ -68,6 +69,8 @@ namespace moab inline ErrorCode TreeStats::compute_stats(Interface *impl, EntityHandle root_node) { maxDepth = 0; + numNodes = 0; + numLeaves = 0; return traverse(impl, root_node, maxDepth); } @@ -111,21 +114,27 @@ namespace moab leavesVisited = 0; numTraversals = 0; leafObjectTests = 0; + boxElemTests = 0; } inline void TreeStats::print() const { std::cout << "Tree initialization time = " << initTime << " seconds" << std::endl; + std::cout << "Num nodes = " << numNodes << std::endl; + std::cout << "Num leaves = " << numLeaves << std::endl; + std::cout << "Max depth = " << maxDepth << std::endl << std::endl; + std::cout << "NodesVisited = " << nodesVisited << std::endl; std::cout << "LeavesVisited = " << leavesVisited << std::endl; std::cout << "Num Traversals = " << numTraversals << std::endl; std::cout << "Leaf Object Tests = " << leafObjectTests << std::endl; + std::cout << "Box-Element Tests = " << boxElemTests << std::endl; } inline void TreeStats::output() const { - std::cout << initTime << " " << nodesVisited << " " << leavesVisited << " " << numTraversals << " " << leafObjectTests - << " # initTime, nodesVisited, leavesVisited, numTraversals, leafObjectTests" << std::endl; + std::cout << initTime << " " << nodesVisited << " " << leavesVisited << " " << numTraversals << " " << leafObjectTests << " " << boxElemTests + << " # initTime, nodesVisited, leavesVisited, numTraversals, leafObjectTests, boxElemTests" << std::endl; } } diff --git a/test/test_boundbox.cpp b/test/test_boundbox.cpp index 9fe0357..b089972 100644 --- a/test/test_boundbox.cpp +++ b/test/test_boundbox.cpp @@ -35,7 +35,7 @@ void test_bound_box() // test for contains point failure bool result = box.contains_point(vec.array(), tol); CHECK(!result); - result = box.contains_box(other_box, tol); + result = box.intersects_box(other_box, tol); CHECK(!result); box = other_box; @@ -44,7 +44,7 @@ void test_bound_box() // test for success result = box.contains_point(&vals[0], tol); CHECK(result); - result = box.contains_box(other_box, tol); + result = box.intersects_box(other_box, tol); CHECK(result); // check update functions @@ -54,9 +54,9 @@ void test_bound_box() CHECK(result); result = box.contains_point((three*1.1).array(), tol); CHECK(!result); - result = box.contains_box(BoundBox(three, three), tol); + result = box.intersects_box(BoundBox(three, three), tol); CHECK(result); - result = box.contains_box(BoundBox(three, 1.1*three), tol); + result = box.intersects_box(BoundBox(1.1*three, 3.0*three), tol); CHECK(!result); CartVect negthree(-3.0); @@ -65,9 +65,9 @@ void test_bound_box() CHECK(result); result = box.contains_point((negthree*1.1).array(), tol); CHECK(!result); - result = box.contains_box(BoundBox(negthree, negthree), tol); + result = box.intersects_box(BoundBox(negthree, negthree), tol); CHECK(result); - result = box.contains_box(BoundBox(1.1*negthree, negthree), tol); + result = box.intersects_box(BoundBox(3.0*negthree, 1.1*negthree), tol); CHECK(!result); for (int i = 0; i < 3; i++) { @@ -78,9 +78,9 @@ void test_bound_box() CHECK(result); result = box.contains_point((CartVect(&vals[0])*1.1).array(), tol); CHECK(!result); - result = box.contains_box(BoundBox(&vals[0]), tol); + result = box.intersects_box(BoundBox(&vals[0]), tol); CHECK(result); - result = box.contains_box(BoundBox(1.1*CartVect(&vals[0]), CartVect(&vals[3])), tol); + result = box.intersects_box(BoundBox(1.2*CartVect(&vals[0]), 1.1*CartVect(&vals[0])), tol); CHECK(!result); // check length functions https://bitbucket.org/fathomteam/moab/commits/da1daa3012a9/ Changeset: da1daa3012a9 Branch: None User: tautges Date: 2014-03-12 16:54:58 Summary: Changes to allow specification of existing displacement tag(s), which can be either single name corresponding to xyz[3] or 3 names x, y, z. Handle either case in deform_master. Affected #: 1 file diff --git a/examples/DeformMeshRemap.cpp b/examples/DeformMeshRemap.cpp index f752b4e..109fd3b 100644 --- a/examples/DeformMeshRemap.cpp +++ b/examples/DeformMeshRemap.cpp @@ -532,7 +532,6 @@ ErrorCode DeformMeshRemap::deform_master(Range &fluid_elems, Range &solid_elems, rval = mbImpl->tag_get_handle((tag_name ? tag_name : ""), 3, MB_TYPE_DOUBLE, xNew, MB_TAG_CREAT|MB_TAG_DENSE); RR("Failed to create xnew tag."); std::vector<double> disps(num_verts); - for (int i = 0; i < 3; i++) { rval = mbImpl->tag_get_handle(xDispNames[0].c_str(), 1, MB_TYPE_DOUBLE, xDisp[i]); RR("Failed to get xDisp tag."); https://bitbucket.org/fathomteam/moab/commits/173e849acfb2/ Changeset: 173e849acfb2 Branch: None User: tautges Date: 2014-03-12 16:56:11 Summary: - add ability to specify master and slave mesh solid/fluid set numbers separately, so set numbers don't need to agree - add ability to specify only fluid or solid sets, with other sets derived from that and all material sets in a file - add DeformMeshRemap to list of examples in makefile Affected #: 1 file diff --git a/examples/DeformMeshRemap.cpp b/examples/DeformMeshRemap.cpp index 109fd3b..0292cf7 100644 --- a/examples/DeformMeshRemap.cpp +++ b/examples/DeformMeshRemap.cpp @@ -354,6 +354,50 @@ ErrorCode DeformMeshRemap::execute() return MB_SUCCESS; } +ErrorCode DeformMeshRemap::find_other_sets(int m_or_s, EntityHandle file_set) +{ + // solid or fluid sets are missing; find the other + Range *filled_sets = NULL, *unfilled_sets = NULL, *unfilled_elems = NULL; + + if (fluidSets[m_or_s].empty() && !solidSets[m_or_s].empty()) { + unfilled_sets = &fluidSets[m_or_s]; + filled_sets = &solidSets[m_or_s]; + unfilled_elems = &fluidElems[m_or_s]; + } + else if (!fluidSets[m_or_s].empty() && solidSets[m_or_s].empty()) { + filled_sets = &fluidSets[m_or_s]; + unfilled_sets = &solidSets[m_or_s]; + unfilled_elems = &solidElems[m_or_s]; + } + + // ok, we know the filled sets, now fill the unfilled sets, and the elems from those + Tag tagh; + ErrorCode rval = mbImpl->tag_get_handle(MATERIAL_SET_TAG_NAME, tagh); RR("Couldn't get material set tag name."); + Range matsets; + rval = mbImpl->get_entities_by_type_and_tag(file_set, MBENTITYSET, &tagh, NULL, 1, matsets); + if (matsets.empty()) rval = MB_FAILURE; + RR("Couldn't get any material sets."); + *unfilled_sets = subtract(matsets, *filled_sets); + if (unfilled_sets->empty()) { + rval = MB_FAILURE; + RR("Failed to find any unfilled material sets."); + } + Range tmp_range; + for (Range::iterator rit = unfilled_sets->begin(); rit != unfilled_sets->end(); rit++) { + rval = mbImpl->get_entities_by_handle(*rit, tmp_range, true); + RR("Failed to get entities in unfilled set."); + } + int dim = mbImpl->dimension_from_handle(*tmp_range.rbegin()); + assert(dim > 0 && dim < 4); + *unfilled_elems = tmp_range.subset_by_dimension(dim); + if (unfilled_elems->empty()) { + rval = MB_FAILURE; + RR("Failed to find any unfilled set entities."); + } + + return MB_SUCCESS; +} + std::string DeformMeshRemap::get_file_name(int m_or_s) const { switch (m_or_s) { https://bitbucket.org/fathomteam/moab/commits/cf1c8106890e/ Changeset: cf1c8106890e Branch: None User: tautges Date: 2014-03-12 16:57:08 Summary: Better error handling & debug printing. In Tree, handle legacy tag on tree root by deleting and re-creating (legacy files have old-sized tag). Affected #: 1 file diff --git a/examples/DeformMeshRemap.cpp b/examples/DeformMeshRemap.cpp index 0292cf7..109fd3b 100644 --- a/examples/DeformMeshRemap.cpp +++ b/examples/DeformMeshRemap.cpp @@ -354,50 +354,6 @@ ErrorCode DeformMeshRemap::execute() return MB_SUCCESS; } -ErrorCode DeformMeshRemap::find_other_sets(int m_or_s, EntityHandle file_set) -{ - // solid or fluid sets are missing; find the other - Range *filled_sets = NULL, *unfilled_sets = NULL, *unfilled_elems = NULL; - - if (fluidSets[m_or_s].empty() && !solidSets[m_or_s].empty()) { - unfilled_sets = &fluidSets[m_or_s]; - filled_sets = &solidSets[m_or_s]; - unfilled_elems = &fluidElems[m_or_s]; - } - else if (!fluidSets[m_or_s].empty() && solidSets[m_or_s].empty()) { - filled_sets = &fluidSets[m_or_s]; - unfilled_sets = &solidSets[m_or_s]; - unfilled_elems = &solidElems[m_or_s]; - } - - // ok, we know the filled sets, now fill the unfilled sets, and the elems from those - Tag tagh; - ErrorCode rval = mbImpl->tag_get_handle(MATERIAL_SET_TAG_NAME, tagh); RR("Couldn't get material set tag name."); - Range matsets; - rval = mbImpl->get_entities_by_type_and_tag(file_set, MBENTITYSET, &tagh, NULL, 1, matsets); - if (matsets.empty()) rval = MB_FAILURE; - RR("Couldn't get any material sets."); - *unfilled_sets = subtract(matsets, *filled_sets); - if (unfilled_sets->empty()) { - rval = MB_FAILURE; - RR("Failed to find any unfilled material sets."); - } - Range tmp_range; - for (Range::iterator rit = unfilled_sets->begin(); rit != unfilled_sets->end(); rit++) { - rval = mbImpl->get_entities_by_handle(*rit, tmp_range, true); - RR("Failed to get entities in unfilled set."); - } - int dim = mbImpl->dimension_from_handle(*tmp_range.rbegin()); - assert(dim > 0 && dim < 4); - *unfilled_elems = tmp_range.subset_by_dimension(dim); - if (unfilled_elems->empty()) { - rval = MB_FAILURE; - RR("Failed to find any unfilled set entities."); - } - - return MB_SUCCESS; -} - std::string DeformMeshRemap::get_file_name(int m_or_s) const { switch (m_or_s) { https://bitbucket.org/fathomteam/moab/commits/96b0903bde31/ Changeset: 96b0903bde31 Branch: None User: tautges Date: 2014-03-12 16:57:32 Summary: DeformMeshRemap: more debugging output, and handle coord displacements properly (add to prev coords) LloydSmoother: fix a bug with fixed tag entity handles size SpatialLocator: if an element range is specified, build the tree too Affected #: 1 file diff --git a/examples/DeformMeshRemap.cpp b/examples/DeformMeshRemap.cpp index 109fd3b..f752b4e 100644 --- a/examples/DeformMeshRemap.cpp +++ b/examples/DeformMeshRemap.cpp @@ -532,6 +532,7 @@ ErrorCode DeformMeshRemap::deform_master(Range &fluid_elems, Range &solid_elems, rval = mbImpl->tag_get_handle((tag_name ? tag_name : ""), 3, MB_TYPE_DOUBLE, xNew, MB_TAG_CREAT|MB_TAG_DENSE); RR("Failed to create xnew tag."); std::vector<double> disps(num_verts); + for (int i = 0; i < 3; i++) { rval = mbImpl->tag_get_handle(xDispNames[0].c_str(), 1, MB_TYPE_DOUBLE, xDisp[i]); RR("Failed to get xDisp tag."); https://bitbucket.org/fathomteam/moab/commits/661a70a4dda5/ Changeset: 661a70a4dda5 Branch: None User: tautges Date: 2014-03-12 16:57:32 Summary: DeformMeshRemap: add some tree statistics output AdaptiveKDTree: make several functions non-static so they show up in profiling; also use BoundBox a bit more BVHTree: account for BoundBox change SpatialLocator: choose tree type based on contents of myElems, and move tree construction to a separate function BoundBox: change name of contains_box to intersects_box, and fix logic that was broken there TreeStats.hpp: improve statistics output test_boundbox: fix tests for changes to BoundBox Affected #: 1 file diff --git a/src/moab/SpatialLocator.hpp b/src/moab/SpatialLocator.hpp index 3d29c55..2690058 100644 --- a/src/moab/SpatialLocator.hpp +++ b/src/moab/SpatialLocator.hpp @@ -193,6 +193,12 @@ namespace moab { ErrorCode register_src_with_intermediate_procs(ParallelComm *pc, double abs_iter_tol, TupleList &TLreg_o); #endif + + /** Create a tree + * Tree type depends on what's in myElems: if empty or all vertices, creates a kdtree, + * otherwise creates a BVHTree. + */ + void create_tree(); /* MOAB instance */ Interface* mbImpl; https://bitbucket.org/fathomteam/moab/commits/e0f9f1e46ca6/ Changeset: e0f9f1e46ca6 Branch: None User: tautges Date: 2014-03-12 16:57:32 Summary: DeformMeshRemap.cpp: Write more intermediate files if compiled with local debug flag true; change some of the functions for moving coords to tags and vice versa to facilitate this. SpatialLocator.cpp: Back out change that automatically chose BVH tree for non-vertex entities, there's a bug in point location there currently... Affected #: 2 files diff --git a/examples/DeformMeshRemap.cpp b/examples/DeformMeshRemap.cpp index f752b4e..a8a0e10 100644 --- a/examples/DeformMeshRemap.cpp +++ b/examples/DeformMeshRemap.cpp @@ -110,10 +110,13 @@ private: ErrorCode read_file(int m_or_s, string &fname, EntityHandle &seth); //! write the input tag to the coordinates for the vertices in the input elems - ErrorCode write_to_coords(Range &elems, Tag tagh); + //! if non-zero tmp_tag is input, save coords to tmp_tag before over-writing with tag value + ErrorCode write_to_coords(Range &elems, Tag tagh, Tag tmp_tag = 0); //! write the tag to the vertices, then save to the specified file - ErrorCode write_and_save(Range &ents, EntityHandle seth, Tag tagh, const char *filename); + //! if restore_coords is true, coords are restored to their initial state after file is written + ErrorCode write_and_save(Range &ents, EntityHandle seth, Tag tagh, const char *filename, + bool restore_coords = false); //! find fluid/solid sets from complement of solid/fluid sets ErrorCode find_other_sets(int m_or_s, EntityHandle file_set); @@ -262,7 +265,7 @@ ErrorCode DeformMeshRemap::execute() src_elems.merge(fluidElems[MASTER]); // initialize data coupler on source elements - DataCoupler dc_master(mbImpl, NULL, src_elems, 0); + DataCoupler dc_master(mbImpl, src_elems, 0, NULL); Range tgt_verts; if (have_slave) { @@ -316,6 +319,7 @@ ErrorCode DeformMeshRemap::execute() // transfer xNew to coords, for master if (debug) std::cout << "Transferring coords tag to vertex coordinates in master mesh..." << std::endl; + rval = write_to_coords(solidElems[MASTER], xNew); RR("Failed writing tag to master fluid verts."); rval = write_to_coords(fluidElems[MASTER], xNew); RR("Failed writing tag to master fluid verts."); if (have_slave) { @@ -334,8 +338,8 @@ ErrorCode DeformMeshRemap::execute() if (pcMaster && pcMaster->size() > 1) str = "PARALLEL=WRITE_PART"; #endif - if (debug) std::cout << "Writing smoothed_master.vtk..." << std::endl; - rval = mbImpl->write_file("smoothed_master.vtk", NULL, str.c_str(), &masterSet, 1); + if (debug) std::cout << "Writing smoothed_master.h5m..." << std::endl; + rval = mbImpl->write_file("smoothed_master.h5m", NULL, str.c_str(), &masterSet, 1); if (have_slave) { #ifdef USE_MPI @@ -343,8 +347,8 @@ ErrorCode DeformMeshRemap::execute() if (pcSlave && pcSlave->size() > 1) str = "PARALLEL=WRITE_PART"; #endif - if (debug) std::cout << "Writing slave_interp.vtk..." << std::endl; - rval = mbImpl->write_file("slave_interp.vtk", NULL, str.c_str(), &slaveSet, 1); + if (debug) std::cout << "Writing slave_interp.h5m..." << std::endl; + rval = mbImpl->write_file("slave_interp.h5m", NULL, str.c_str(), &slaveSet, 1); } // if have_slave } // if debug @@ -470,20 +474,38 @@ int main(int argc, char **argv) { return rval; } -ErrorCode DeformMeshRemap::write_and_save(Range &ents, EntityHandle seth, Tag tagh, const char *filename) +ErrorCode DeformMeshRemap::write_and_save(Range &ents, EntityHandle seth, Tag tagh, const char *filename, + bool restore_coords) { - ErrorCode rval = write_to_coords(ents, tagh); RR(""); + Tag tmp_tag = 0; + ErrorCode rval; + if (restore_coords) + rval = mbImpl->tag_get_handle("", 3, MB_TYPE_DOUBLE, tmp_tag, MB_TAG_CREAT|MB_TAG_DENSE); + + rval = write_to_coords(ents, tagh, tmp_tag); RR(""); rval = mbImpl->write_file(filename, NULL, NULL, &seth, 1); RR(""); + if (restore_coords) { + rval = write_to_coords(ents, tmp_tag); RR(""); + rval = mbImpl->tag_delete(tmp_tag); + } + return rval; } -ErrorCode DeformMeshRemap::write_to_coords(Range &elems, Tag tagh) +ErrorCode DeformMeshRemap::write_to_coords(Range &elems, Tag tagh, Tag tmp_tag) { // write the tag to coordinates Range verts; ErrorCode rval = mbImpl->get_adjacencies(elems, 0, false, verts, Interface::UNION); RR("Failed to get adj vertices."); std::vector<double> coords(3*verts.size()); + + if (tmp_tag) { + // save the coords to tmp_tag first + rval = mbImpl->get_coords(verts, &coords[0]); RR("Failed to get tmp copy of coords."); + rval = mbImpl->tag_set_data(tmp_tag, verts, &coords[0]); RR("Failed to save tmp copy of coords."); + } + rval = mbImpl->tag_get_data(tagh, verts, &coords[0]); RR("Failed to get tag data."); rval = mbImpl->set_coords(verts, &coords[0]); @@ -503,7 +525,6 @@ void deform_func(const BoundBox &bbox, double *xold, double *xnew) xnew[0] = xold[0] + yfrac * delx; xnew[1] = xold[1] + yfrac * (1.0 + xfrac) * 0.05; */ - /* Deformation function based on fraction of bounding box dimension in each direction */ double frac = 0.01; // taken from approximate relative deformation from LLNL Diablo of XX09 assys CartVect *xo = reinterpret_cast<CartVect*>(xold), *xn = reinterpret_cast<CartVect*>(xnew); @@ -517,13 +538,13 @@ ErrorCode DeformMeshRemap::deform_master(Range &fluid_elems, Range &solid_elems, ErrorCode rval; // get all the vertices and coords in the solid - Range verts; - rval = mbImpl->get_adjacencies(solid_elems, 0, false, verts, Interface::UNION); + Range solid_verts, fluid_verts; + rval = mbImpl->get_adjacencies(solid_elems, 0, false, solid_verts, Interface::UNION); RR("Failed to get vertices."); - std::vector<double> coords(3*verts.size()), new_coords(3*verts.size()); - rval = mbImpl->get_coords(verts, &coords[0]); + std::vector<double> coords(3*solid_verts.size()), new_coords(3*solid_verts.size()); + rval = mbImpl->get_coords(solid_verts, &coords[0]); RR("Failed to get vertex coords."); - unsigned int num_verts = verts.size(); + unsigned int num_verts = solid_verts.size(); // get or create the tag @@ -536,7 +557,7 @@ ErrorCode DeformMeshRemap::deform_master(Range &fluid_elems, Range &solid_elems, for (int i = 0; i < 3; i++) { rval = mbImpl->tag_get_handle(xDispNames[0].c_str(), 1, MB_TYPE_DOUBLE, xDisp[i]); RR("Failed to get xDisp tag."); - rval = mbImpl->tag_get_data(xDisp[i], verts, &disps[0]); + rval = mbImpl->tag_get_data(xDisp[i], solid_verts, &disps[0]); RR("Failed to get xDisp tag values."); for (unsigned int j = 0; j < num_verts; j++) new_coords[3*j+i] = coords[3*j+i] + disps[j]; @@ -547,7 +568,7 @@ ErrorCode DeformMeshRemap::deform_master(Range &fluid_elems, Range &solid_elems, RR("Failed to get first xDisp tag."); xNew = xDisp[0]; std::vector<double> disps(3*num_verts); - rval = mbImpl->tag_get_data(xDisp[0], verts, &disps[0]); + rval = mbImpl->tag_get_data(xDisp[0], solid_verts, &disps[0]); for (unsigned int j = 0; j < 3*num_verts; j++) new_coords[j] = coords[j] + disps[j]; } @@ -584,18 +605,26 @@ ErrorCode DeformMeshRemap::deform_master(Range &fluid_elems, Range &solid_elems, } // set the new tag to those coords - rval = mbImpl->tag_set_data(xNew, verts, &coords[0]); + rval = mbImpl->tag_set_data(xNew, solid_verts, &new_coords[0]); RR("Failed to set tag data."); // get all the vertices and coords in the fluid, set xnew to them - verts.clear(); - rval = mbImpl->get_adjacencies(fluid_elems, 0, false, verts, Interface::UNION); + rval = mbImpl->get_adjacencies(fluid_elems, 0, false, fluid_verts, Interface::UNION); RR("Failed to get vertices."); - coords.resize(3*verts.size()); - rval = mbImpl->get_coords(verts, &coords[0]); + fluid_verts = subtract(fluid_verts, solid_verts); + + if (coords.size() < 3*fluid_verts.size()) coords.resize(3*fluid_verts.size()); + rval = mbImpl->get_coords(fluid_verts, &coords[0]); RR("Failed to get vertex coords."); - rval = mbImpl->tag_set_data(xNew, verts, &coords[0]); + rval = mbImpl->tag_set_data(xNew, fluid_verts, &coords[0]); RR("Failed to set xnew tag on fluid verts."); + + if (debug) { + // save deformed mesh coords to new file for visualizing + Range tmp_range(fluidElems[MASTER]); + tmp_range.merge(solidElems[MASTER]); + rval = write_and_save(tmp_range, masterSet, xNew, "deformed_master.h5m", true); RR(""); + } return MB_SUCCESS; } diff --git a/src/SpatialLocator.cpp b/src/SpatialLocator.cpp index 2903155..63c2fdc 100644 --- a/src/SpatialLocator.cpp +++ b/src/SpatialLocator.cpp @@ -35,12 +35,12 @@ namespace moab { if (myTree) return; - if (myElems.empty() || mbImpl->type_from_handle(*myElems.rbegin()) == MBVERTEX) +// if (myElems.empty() || mbImpl->type_from_handle(*myElems.rbegin()) == MBVERTEX) // create a kdtree if only vertices myTree = new AdaptiveKDTree(mbImpl); - else +// else // otherwise a BVHtree, since it performs better for elements - myTree = new BVHTree(mbImpl); +// myTree = new BVHTree(mbImpl); iCreatedTree = true; } https://bitbucket.org/fathomteam/moab/commits/b7b7922b5372/ Changeset: b7b7922b5372 Branch: None User: tautges Date: 2014-03-12 16:57:32 Summary: Various smallish bug fixes and minor changes, improving the use of SpatialLocator. ElemEvaluator: in set_ent_handle, if there's no evalSet for that entity type, call EvalSet::get_eval_set SpatialLocator: set the evaluator on the tree if it's not the same as what's on SpatialLocator; also, replace find_point logic (that used distance_search for some reason) with call to Tree::point_search. AdaptiveKDTree: move parse_options to public function, as it is in Tree BVHTree: fixed bug, where BVHTree had its own myEval shadowing the one declared in Tree Tree: fixed bug, initialize myEval to NULL in constructor spatial_locator_test: test trees with and without evaluators DataCoupler: improving comments a bit, and move ParallelComm down in arg list for constructor; also, some improved comments datacoupler_test: adding test Passes make check in parallel. Affected #: 10 files diff --git a/src/LocalDiscretization/moab/ElemEvaluator.hpp b/src/LocalDiscretization/moab/ElemEvaluator.hpp index 866388c..6a1efd0 100644 --- a/src/LocalDiscretization/moab/ElemEvaluator.hpp +++ b/src/LocalDiscretization/moab/ElemEvaluator.hpp @@ -339,8 +339,13 @@ namespace moab { std::vector<EntityHandle> dum_vec; ErrorCode rval = mbImpl->get_connectivity(ent, vertHandles, numVerts, false, &dum_vec); if (MB_SUCCESS != rval) return rval; + + if (!evalSets[entType].evalFcn) + EvalSet::get_eval_set(entType, numVerts, evalSets[entType]); + rval = mbImpl->get_coords(vertHandles, numVerts, vertPos[0].array()); if (MB_SUCCESS != rval) return rval; + if (tagHandle) { rval = set_tag_handle(tagHandle); if (MB_SUCCESS != rval) return rval; diff --git a/src/SpatialLocator.cpp b/src/SpatialLocator.cpp index 63c2fdc..702399e 100644 --- a/src/SpatialLocator.cpp +++ b/src/SpatialLocator.cpp @@ -35,12 +35,12 @@ namespace moab { if (myTree) return; -// if (myElems.empty() || mbImpl->type_from_handle(*myElems.rbegin()) == MBVERTEX) + if (myElems.empty() || mbImpl->type_from_handle(*myElems.rbegin()) == MBVERTEX) // create a kdtree if only vertices myTree = new AdaptiveKDTree(mbImpl); -// else + else // otherwise a BVHtree, since it performs better for elements -// myTree = new BVHTree(mbImpl); + myTree = new BVHTree(mbImpl); iCreatedTree = true; } @@ -367,90 +367,29 @@ namespace moab // relative epsilon given, translate to absolute epsilon using box dimensions tmp_abs_iter_tol = rel_iter_tol * localBox.diagonal_length(); } - - EntityHandle closest_leaf; - std::vector<double> dists; - std::vector<EntityHandle> leaves; - ErrorCode rval = MB_SUCCESS; + if (elemEval && myTree->get_eval() != elemEval) + myTree->set_eval(elemEval); + + ErrorCode rval = MB_SUCCESS; for (int i = 0; i < num_points; i++) { int i3 = 3*i; - ents[i] = 0; - if (tmp_abs_iter_tol) { - rval = myTree->distance_search(pos+i3, tmp_abs_iter_tol, leaves, tmp_abs_iter_tol, inside_tol, &dists); - if (MB_SUCCESS != rval) return rval; - if (!leaves.empty()) { - // get closest leaf - double min_dist = *dists.begin(); - closest_leaf = *leaves.begin(); - std::vector<EntityHandle>::iterator vit = leaves.begin()+1; - std::vector<double>::iterator dit = dists.begin()+1; - for (; vit != leaves.end() && min_dist; vit++, dit++) { - if (*dit < min_dist) { - min_dist = *dit; - closest_leaf = *vit; - } - } - dists.clear(); - leaves.clear(); - } - } - else { - rval = myTree->point_search(pos+i3, closest_leaf); - if (MB_ENTITY_NOT_FOUND == rval) closest_leaf = 0; - else if (MB_SUCCESS != rval) return rval; - } - - // if no ElemEvaluator, just return the box - if (!elemEval) { - ents[i] = closest_leaf; - params[i3] = params[i3+1] = params[i3+2] = -2; - if (is_inside && closest_leaf) is_inside[i] = true; + ErrorCode tmp_rval = myTree->point_search(pos+i3, ents[i], abs_iter_tol, inside_tol, NULL, NULL, + (CartVect*)(params+i3)); + if (MB_SUCCESS != tmp_rval) { + rval = tmp_rval; continue; } - - // find natural coordinates of point in element(s) in that leaf - CartVect tmp_nat_coords; - Range range_leaf; - rval = mbImpl->get_entities_by_dimension(closest_leaf, myDim, range_leaf, false); - if(rval != MB_SUCCESS) return rval; - - // loop over the range_leaf - int tmp_inside; - int *is_ptr = (is_inside ? is_inside+i : &tmp_inside); - *is_ptr = false; - EntityHandle ent = 0; - for(Range::iterator rit = range_leaf.begin(); rit != range_leaf.end(); rit++) - { - rval = elemEval->set_ent_handle(*rit); - if (MB_SUCCESS != rval) return rval; - rval = elemEval->reverse_eval(pos+i3, tmp_abs_iter_tol, inside_tol, params+i3, is_ptr); - if (MB_SUCCESS != rval) return rval; - if (*is_ptr) { - ent = *rit; - break; - } - } - if (debug && !ent) { + + if (debug && !ents[i]) { std::cout << "Point " << i << " not found; point: (" << pos[i3] << "," << pos[i3+1] << "," << pos[i3+2] << ")" << std::endl; - std::cout << "Source element candidates: " << std::endl; - range_leaf.print(" "); - for(Range::iterator rit = range_leaf.begin(); rit != range_leaf.end(); rit++) - { - std::cout << "Candidate " << CN::EntityTypeName(mbImpl->type_from_handle(*rit)) << " " << mbImpl->id_from_handle(*rit) << ": "; - rval = elemEval->set_ent_handle(*rit); - if (MB_SUCCESS != rval) return rval; - rval = elemEval->reverse_eval(pos+i3, tmp_abs_iter_tol, inside_tol, params+i3, is_ptr); - if (MB_SUCCESS != rval) return rval; - std::cout << "Parameters: (" << params[i3] << "," << params[i3+1] << "," << params[i3+2] << ")" - << " inside = " << *is_ptr << std::endl; - } } - ents[i] = ent; - } - return MB_SUCCESS; + if (is_inside) is_inside[i] = (ents[i] ? true : false); + } + + return rval; } /* Count the number of located points in locTable diff --git a/src/moab/AdaptiveKDTree.hpp b/src/moab/AdaptiveKDTree.hpp index 450a418..e4c5078 100644 --- a/src/moab/AdaptiveKDTree.hpp +++ b/src/moab/AdaptiveKDTree.hpp @@ -38,6 +38,13 @@ namespace moab { ~AdaptiveKDTree(); + /** \brief Parse options for tree creation + * \param options Options passed in by application + * \return Failure is returned if any options were passed in and not interpreted; could mean + * inappropriate options for a particular tree type + */ + ErrorCode parse_options(FileOptions &options); + /** Build the tree * Build a tree with the entities input. If a non-NULL tree_root_set pointer is input, * use the pointed-to set as the root of this tree (*tree_root_set!=0) otherwise construct @@ -253,13 +260,6 @@ namespace moab { private: friend class AdaptiveKDTreeIter; - /** \brief Parse options for tree creation - * \param options Options passed in by application - * \return Failure is returned if any options were passed in and not interpreted; could mean - * inappropriate options for a particular tree type - */ - ErrorCode parse_options(FileOptions &options); - ErrorCode init(); /**\brief find a triangle near the input point */ diff --git a/src/moab/BVHTree.hpp b/src/moab/BVHTree.hpp index d435ebf..354d3a1 100644 --- a/src/moab/BVHTree.hpp +++ b/src/moab/BVHTree.hpp @@ -272,7 +272,6 @@ namespace moab { Range entityHandles; std::vector<TreeNode> myTree; - ElemEvaluator *myEval; int splitsPerDir; EntityHandle startSetHandle; static const char *treeName; @@ -305,7 +304,7 @@ namespace moab { } inline BVHTree::BVHTree(Interface *impl) : - Tree(impl), myEval(NULL), splitsPerDir(3), startSetHandle(0) {boxTagName = treeName;} + Tree(impl), splitsPerDir(3), startSetHandle(0) {boxTagName = treeName;} inline unsigned int BVHTree::set_interval(BoundBox &interval, std::vector<Bucket>::const_iterator begin, diff --git a/src/moab/Tree.hpp b/src/moab/Tree.hpp index 67b67f9..0a995b4 100644 --- a/src/moab/Tree.hpp +++ b/src/moab/Tree.hpp @@ -236,7 +236,7 @@ namespace moab { inline Tree::Tree(Interface* iface) : mbImpl(iface), maxPerLeaf(6), maxDepth(30), treeDepth(-1), minWidth(1.0e-10), - meshsetFlags(0), cleanUp(true), myRoot(0), boxTag(0) + meshsetFlags(0), cleanUp(true), myRoot(0), boxTag(0), myEval(0) {} inline Tree::~Tree() diff --git a/test/spatial_locator_test.cpp b/test/spatial_locator_test.cpp index 0171bf9..404e668 100644 --- a/test/spatial_locator_test.cpp +++ b/test/spatial_locator_test.cpp @@ -4,7 +4,9 @@ #include "moab/HomXform.hpp" #include "moab/ScdInterface.hpp" #include "moab/CartVect.hpp" +#include "moab/AdaptiveKDTree.hpp" #include "moab/BVHTree.hpp" +#include "moab/ElemEvaluator.hpp" #include "moab/ProgOptions.hpp" #include "moab/CpuTimer.hpp" @@ -69,11 +71,21 @@ void test_kd_tree() Range elems; rval = create_hex_mesh(mb, elems, ints, 3); CHECK_ERR(rval); - // initialize spatial locator with the elements and the default tree type - SpatialLocator *sl = new SpatialLocator(&mb, elems); + // initialize spatial locator with the elements and KDtree + AdaptiveKDTree kd(&mb); + std::ostringstream opts; + opts << "MAX_DEPTH=" << max_depth << ";MAX_PER_LEAF=" << leaf; + FileOptions fo(opts.str().c_str()); + rval = kd.parse_options(fo); + SpatialLocator *sl = new SpatialLocator(&mb, elems, &kd); test_locator(sl); + // test with an evaluator + ElemEvaluator eval(&mb); + kd.set_eval(&eval); + test_locator(sl); + // destroy spatial locator, and tree along with it delete sl; } @@ -96,6 +108,11 @@ void test_bvh_tree() SpatialLocator *sl = new SpatialLocator(&mb, elems, &bvh); test_locator(sl); + // test with an evaluator + ElemEvaluator eval(&mb); + bvh.set_eval(&eval); + test_locator(sl); + // destroy spatial locator, and tree along with it delete sl; } diff --git a/tools/mbcoupler/DataCoupler.cpp b/tools/mbcoupler/DataCoupler.cpp index a5a3ec1..06a8564 100644 --- a/tools/mbcoupler/DataCoupler.cpp +++ b/tools/mbcoupler/DataCoupler.cpp @@ -1,24 +1,27 @@ #include "DataCoupler.hpp" -#include "moab/ParallelComm.hpp" #include "moab/Tree.hpp" #include "moab/TupleList.hpp" #include "moab/SpatialLocator.hpp" #include "moab/ElemEvaluator.hpp" #include "moab/Error.hpp" +#ifdef USE_MPI +#include "moab/ParallelComm.hpp" +#endif + #include "iostream" -#include <stdio.h> #include <algorithm> #include <sstream> +#include <stdio.h> #include "assert.h" namespace moab { DataCoupler::DataCoupler(Interface *impl, - ParallelComm *pc, Range &source_ents, int coupler_id, + ParallelComm *pc, bool init_locator, int dim) : mbImpl(impl), myPcomm(pc), myId(coupler_id), myDim(dim) @@ -64,7 +67,12 @@ ErrorCode DataCoupler::locate_points(Range &targ_ents, const double inside_tol) { targetEnts = targ_ents; - + +#ifdef USE_MPI + if (myPcomm && myPcomm->size() > 1) + return myLocator->par_locate_points(myPcomm, targ_ents, rel_iter_tol, abs_iter_tol, inside_tol); +#endif + return myLocator->locate_points(targ_ents, rel_iter_tol, abs_iter_tol, inside_tol); } @@ -72,6 +80,11 @@ ErrorCode DataCoupler::locate_points(double *xyz, int num_points, const double rel_iter_tol, const double abs_iter_tol, const double inside_tol) { +#ifdef USE_MPI + if (myPcomm && myPcomm->size() > 1) + return myLocator->par_locate_points(myPcomm, xyz, num_points, rel_iter_tol, abs_iter_tol, inside_tol); +#endif + return myLocator->locate_points(xyz, num_points, rel_iter_tol, abs_iter_tol, inside_tol); } @@ -95,7 +108,7 @@ ErrorCode DataCoupler::interpolate(/*DataCoupler::Method*/ int method, return interpolate(method, tag, interp_vals, point_indices, normalize); } -ErrorCode DataCoupler::interpolate(/*DataCoupler::Method*/ int *methods, +ErrorCode DataCoupler::interpolate(/*DataCoupler::Method*/ int */* methods */, Tag *tags, int *points_per_method, int num_methods, @@ -111,7 +124,12 @@ ErrorCode DataCoupler::interpolate(/*DataCoupler::Method*/ int *methods, for (int i = 0; i < num_methods; i++) pts_total += (points_per_method ? points_per_method[i] : targetEnts.size()); unsigned int num_indices = (point_indices ? point_indices->size() : targetEnts.size()); + // # points and indices should be identical + if (pts_total != num_indices) + return MB_FAILURE; + // since each tuple contains one interpolated tag, if we're interpolating multiple tags, every tuple + // needs to be able to store up to max tag size int max_tsize = -1; for (int i = 0; i < num_methods; i++) { int tmp_tsize; @@ -120,75 +138,82 @@ ErrorCode DataCoupler::interpolate(/*DataCoupler::Method*/ int *methods, max_tsize = std::max(max_tsize, tmp_tsize); } - // if tl was passed in non-NULL, just have those points, otherwise have targetPts plus - // locally mapped pts - if (pts_total != num_indices) - return MB_FAILURE; - - if (myPcomm) { - // TL to send interpolation indices to target procs - // Tuple structure: (pto_i, ridx_i, lidx_i, meth_i, tagidx_i, interp_val[max_tsize]_d) - TupleList tinterp; - tinterp.initialize(5, 0, 0, max_tsize, num_indices); - int t = 0; - tinterp.enableWriteAccess(); - for (int i = 0; i < num_methods; i++) { - int num_points = (points_per_method ? points_per_method[i] : targetEnts.size()); + if (myPcomm && myPcomm->size() > 1) { + // build up the tuple list to distribute from my target points; assume that + // all procs use same method/tag input + TupleList TLob; // TLob structure: (pto_i, ridx_i, lidx_i, meth_tagidx_i) + TLob.initialize(4, 0, 0, 0, num_indices); + int tn = 0; // the tuple number we're currently on + TLob.enableWriteAccess(); + for (int m = 0; m < num_methods; m++) { + int num_points = (points_per_method ? points_per_method[m] : targetEnts.size()); for (int j = 0; j < num_points; j++) { - int idx = (point_indices ? (*point_indices)[j] : j); + int idx = (point_indices ? (*point_indices)[j] : j); // the index in my targetEnts for this interpolation point // remote proc/idx from myLocator->parLocTable - tinterp.vi_wr[5*t] = myLocator->par_loc_table().vi_rd[2*idx]; // proc - tinterp.vi_wr[5*t+1] = myLocator->par_loc_table().vi_rd[2*idx+1]; // remote idx + TLob.vi_wr[4*tn] = myLocator->par_loc_table().vi_rd[2*idx]; // proc + TLob.vi_wr[4*tn+1] = myLocator->par_loc_table().vi_rd[2*idx+1]; // remote idx // local entity index, tag/method index from my data - tinterp.vi_wr[5*t+2] = idx; - tinterp.vi_wr[5*t+3] = methods[i]; - tinterp.vi_wr[5*t+4] = i; - tinterp.inc_n(); - t++; + TLob.vi_wr[4*tn+2] = idx; + TLob.vi_wr[4*tn+3] = m; + TLob.inc_n(); + tn++; } } // scatter/gather interpolation points - myPcomm->proc_config().crystal_router()->gs_transfer(1, tinterp, 0); - - // perform interpolation on local source mesh; put results into - // tinterp.vr_wr - - for (unsigned int i = 0; i < tinterp.get_n(); i++) { - int lidx = tinterp.vi_rd[5*i+1]; -// /*Method*/ int method = (/*Method*/ int)tinterp.vi_rd[5*i+3]; - Tag tag = tags[tinterp.vi_rd[5*i+4]]; - + myPcomm->proc_config().crystal_router()->gs_transfer(1, TLob, 0); + + // perform interpolation on local source mesh; put results into TLinterp + TupleList TLinterp; // TLinterp structure: (pto_i, ridx_i, vals[max_tsize]_d) + TLinterp.initialize(2, 0, 0, max_tsize, TLob.get_n()); + TLinterp.set_n(TLob.get_n()); // set the size right away + TLinterp.enableWriteAccess(); + + for (unsigned int i = 0; i < TLob.get_n(); i++) { + int lidx = TLob.vi_rd[4*i+1]; // index into myLocator's local table + // method and tag indexed with same index +// /*Method*/ int method = methods[TLob.vi_rd[4*i+3]]; + Tag tag = tags[TLob.vi_rd[4*i+3]]; + // copy proc/remote index from TLob + TLinterp.vi_wr[2*i] = TLob.vi_rd[4*i]; + TLinterp.vi_wr[2*i+1] = TLob.vi_rd[4*i+2]; + + // set up the evaluator for the tag and entity, then interpolate, putting result in TLinterp myLocator->elem_eval()->set_tag_handle(tag); myLocator->elem_eval()->set_ent_handle(myLocator->loc_table().vul_rd[lidx]); - result = myLocator->elem_eval()->eval(myLocator->loc_table().vr_rd+3*lidx, tinterp.vr_rd+i*max_tsize); + result = myLocator->elem_eval()->eval(myLocator->loc_table().vr_rd+3*lidx, TLinterp.vr_rd+i*max_tsize); if (MB_SUCCESS != result) return result; } // scatter/gather interpolation data - myPcomm->proc_config().crystal_router()->gs_transfer(1, tinterp, 0); + myPcomm->proc_config().crystal_router()->gs_transfer(1, TLinterp, 0); // copy the interpolated field as a unit - std::copy(tinterp.vr_rd, tinterp.vr_rd+tinterp.get_n()*max_tsize, interp_vals); + std::copy(TLinterp.vr_rd, TLinterp.vr_rd+TLinterp.get_n()*max_tsize, interp_vals); } else { + // if called serially, interpolate directly from local locations/entities, + // into either interp_vals or by setting data directly on tags on those entities std::vector<double> tmp_vals; std::vector<EntityHandle> tmp_ents; double *tmp_dbl = interp_vals; for (int i = 0; i < num_methods; i++) { int num_points = (points_per_method ? points_per_method[i] : targetEnts.size()); - // interpolated data is tsize long, which is either max size (if data passed back to caller in tinterp) + // interpolated data is tsize long, which is either max size (if data passed back to caller in interp_vals) // or tag size (if data will be set on entities, in which case it shouldn't have padding) + // set sizes here, inside loop over methods, to reduce memory usage int tsize = max_tsize, tsize_bytes = 0; if (!interp_vals) { tmp_vals.resize(num_points*max_tsize); tmp_dbl = &tmp_vals[0]; tmp_ents.resize(num_points); result = mbImpl->tag_get_length(tags[i], tsize); + if (MB_SUCCESS != result) return result; result = mbImpl->tag_get_bytes(tags[i], tsize_bytes); + if (MB_SUCCESS != result) return result; } for (int j = 0; j < num_points; j++) { @@ -206,7 +231,7 @@ ErrorCode DataCoupler::interpolate(/*DataCoupler::Method*/ int *methods, result = myLocator->elem_eval()->eval(myLocator->loc_table().vr_rd+3*lidx, tmp_dbl); tmp_dbl += tsize; if (MB_SUCCESS != result) return result; - } // for j + } // for j over points if (!interp_vals) { // set tags on tmp_ents; data is already w/o padding, due to tsize setting above @@ -214,7 +239,7 @@ ErrorCode DataCoupler::interpolate(/*DataCoupler::Method*/ int *methods, if (MB_SUCCESS != result) return result; } - } // for i + } // for i over methods } // if myPcomm // done diff --git a/tools/mbcoupler/DataCoupler.hpp b/tools/mbcoupler/DataCoupler.hpp index bfe2ba5..a9d6f5e 100644 --- a/tools/mbcoupler/DataCoupler.hpp +++ b/tools/mbcoupler/DataCoupler.hpp @@ -39,21 +39,23 @@ class DataCoupler { public: + enum Method {CONSTANT, LINEAR_FE, QUADRATIC_FE, SPECTRAL} ; + enum IntegType {VOLUME}; /* constructor * Constructor, which also optionally initializes the coupler + * \param source_ents Elements in the source mesh + * \param coupler_id Id of this coupler, should be the same over all procs * \param pc ParallelComm object to be used with this coupler, representing the union * of processors containing source and target meshes - * \param source_elems Elements in the source mesh - * \param coupler_id Id of this coupler, should be the same over all procs * \param init_locator If true, initializes a spatial locator inside the constructor * \param dim Dimension of entities to be coupled; if -1, get from source_elems */ DataCoupler(Interface *impl, - ParallelComm *pc, Range &source_ents, int coupler_id, + ParallelComm *pc = NULL, bool init_locator = true, int dim = -1); diff --git a/tools/mbcoupler/Makefile.am b/tools/mbcoupler/Makefile.am index ea32ff9..8114a52 100644 --- a/tools/mbcoupler/Makefile.am +++ b/tools/mbcoupler/Makefile.am @@ -40,7 +40,8 @@ libmbcoupler_la_includedir = $(includedir) # check that only libraries are going in $(libdir) cfgdir = $(libdir) -TESTS = elem_util_test element_test +TESTS = elem_util_test element_test datacoupler_test +datacoupler_test_SOURCES = datacoupler_test.cpp check_PROGRAMS = $(TESTS) elem_util_test_SOURCES = ElemUtilTest.cpp element_test_SOURCES = ElementTest.cpp diff --git a/tools/mbcoupler/datacoupler_test.cpp b/tools/mbcoupler/datacoupler_test.cpp new file mode 100644 index 0000000..b39ca0e --- /dev/null +++ b/tools/mbcoupler/datacoupler_test.cpp @@ -0,0 +1,682 @@ +#include "moab/Core.hpp" +#include "moab/CpuTimer.hpp" +#include "DataCoupler.hpp" +#include "ElemUtil.hpp" +#include "iMesh.h" +#include "MBiMesh.hpp" + +#include <iostream> +#include <iomanip> +#include <sstream> +#include <assert.h> + +#ifdef USE_MPI +#include "moab/ParallelComm.hpp" +#include "MBParallelConventions.h" +#endif + +using namespace moab; + +#define STRINGIFY_(A) #A +#define STRINGIFY(A) STRINGIFY_(A) +#ifdef MESHDIR +std::string TestDir( STRINGIFY(MESHDIR) ); +#else +std::string TestDir("."); +#endif + +#define RRA(a) if (MB_SUCCESS != result) {\ + std::string tmp_str; mbImpl->get_last_error(tmp_str);\ + tmp_str.append("\n"); tmp_str.append(a);\ + dynamic_cast<Core*>(mbImpl)->get_error_handler()->set_last_error(tmp_str.c_str()); \ + return result;} + +#define PRINT_LAST_ERROR \ + if (MB_SUCCESS != result) {\ + std::string tmp_str;\ + std::cout << "Failure; message:" << std::endl;\ + mbImpl->get_last_error(tmp_str);\ + std::cout << tmp_str << std::endl;\ + MPI_Abort(MPI_COMM_WORLD, result); \ + return result;\ + } + +#define PRINT_LAST_ERR \ + if (iBase_SUCCESS != err) {\ + std::string tmp_str;\ + std::cout << "Failure; message:" << std::endl;\ + mbImpl->get_last_error(tmp_str);\ + std::cout << tmp_str << std::endl;\ + MPI_Abort(MPI_COMM_WORLD, result); \ + return result;\ + } + +void print_usage(char **argv); + +ErrorCode get_file_options(int argc, char **argv, + std::vector<std::string> &meshFiles, + DataCoupler::Method &method, + std::string &interpTag, + std::string &gNormTag, + std::string &ssNormTag, + std::vector<const char *> &ssTagNames, + std::vector<const char *> &ssTagValues, + std::string &readOpts, + std::string &outFile, + std::string &writeOpts, + std::string &dbgFile, + bool &help, + double & epsilon); + +// ErrorCode get_file_options(int argc, char **argv, +// std::vector<const char *> &filenames, +// std::string &tag_name, +// std::string &out_fname, +// std::string &opts); + +#ifdef USE_MPI +ErrorCode report_iface_ents(Interface *mbImpl, + std::vector<ParallelComm *> &pcs, + bool print_results); +#endif + +ErrorCode test_interpolation(Interface *mbImpl, + DataCoupler::Method method, + std::string &interpTag, + std::string &gNormTag, + std::string &ssNormTag, + std::vector<const char *> &ssTagNames, + std::vector<const char *> &ssTagValues, + iBase_EntitySetHandle *roots, + std::vector<ParallelComm *> &pcs, + double &instant_time, + double &pointloc_time, + double &interp_time, + double &gnorm_time, + double &ssnorm_time, + double & toler); + +void reduceMax(double &v){ + double buf; + + MPI_Barrier(MPI_COMM_WORLD); + MPI_Allreduce( &v, &buf, 1, MPI_DOUBLE, MPI_MAX, MPI_COMM_WORLD); + + v=buf; +} + + +int main(int argc, char **argv) +{ + + int err; + +#ifdef USE_MPI + // need to init MPI first, to tell how many procs and rank + err = MPI_Init(&argc, &argv); +#endif + + std::vector<const char *> ssTagNames, ssTagValues; + std::vector<std::string> meshFiles; + std::string interpTag, gNormTag, ssNormTag, readOpts, outFile, writeOpts, dbgFile; + DataCoupler::Method method = DataCoupler::CONSTANT; + + ErrorCode result = MB_SUCCESS; + bool help = false; + double toler = 5.e-10; + result = get_file_options(argc, argv, meshFiles, method, interpTag, + gNormTag, ssNormTag, ssTagNames, ssTagValues, + readOpts, outFile, writeOpts, dbgFile, help, toler); + + if (result != MB_SUCCESS || help) { + print_usage(argv); +#ifdef USE_MPI + err = MPI_Finalize(); +#endif + return 1; + } + + int nprocs = 1, rank = 0; + +#ifdef USE_MPI + err = MPI_Comm_size(MPI_COMM_WORLD, &nprocs); + err = MPI_Comm_rank(MPI_COMM_WORLD, &rank); + std::vector<ParallelComm *> pcs(meshFiles.size()); +#endif + + // redirect stdout and stderr if dbgFile is not null + if (!dbgFile.empty()) { + std::stringstream dfname; + dfname << dbgFile << rank << ".txt"; + std::freopen(dfname.str().c_str(), "a", stdout); + std::freopen(dfname.str().c_str(), "a", stderr); + } + + // create MOAB instance based on that + Interface *mbImpl = new Core(); + if (NULL == mbImpl) return 1; + + iMesh_Instance iMeshInst = reinterpret_cast<iMesh_Instance>( new MBiMesh(mbImpl) ); + + // read in mesh(es) + + // Create root sets for each mesh using the iMesh API. Then pass these + // to the load_file functions to be populated. + iBase_EntitySetHandle *roots = (iBase_EntitySetHandle *) malloc(sizeof(iBase_EntitySetHandle) * meshFiles.size()); + + for (unsigned int i = 0; i < meshFiles.size(); i++) { + std::string newReadopts; + std::ostringstream extraOpt; +#ifdef USE_MPI + pcs[i] = new ParallelComm(mbImpl, MPI_COMM_WORLD); + int index = pcs[i]->get_id(); + extraOpt << ";PARALLEL_COMM=" << index; + newReadopts = readOpts+extraOpt.str(); +#endif + + iMesh_createEntSet(iMeshInst, 0, &(roots[i]), &err); + result = mbImpl->load_file( meshFiles[i].c_str(), (EntityHandle *)&roots[i], newReadopts.c_str() ); + PRINT_LAST_ERROR; + } + +#ifdef USE_MPI + result = report_iface_ents(mbImpl, pcs, true); + PRINT_LAST_ERROR; +#endif + + double instant_time=0.0, pointloc_time=0.0, interp_time=0.0, gnorm_time=0.0, ssnorm_time=0.0; + // test interpolation and global normalization and subset normalization + + result = test_interpolation(mbImpl, method, interpTag, gNormTag, ssNormTag, + ssTagNames, ssTagValues, roots, pcs, + instant_time, pointloc_time, interp_time, + gnorm_time, ssnorm_time, toler); + PRINT_LAST_ERROR; + + + reduceMax(instant_time); + reduceMax(pointloc_time); + reduceMax(interp_time); + + if(0==rank) + printf("\nMax time : %g %g %g (inst loc interp -- %d procs )\n", instant_time, + pointloc_time, interp_time, nprocs); + + // output mesh + if (!outFile.empty()) { + Range partSets; + // only save the target mesh + partSets.insert((EntityHandle)roots[1]); + std::string newwriteOpts = writeOpts; + std::ostringstream extraOpt; +#ifdef USE_MPI + extraOpt << ";PARALLEL_COMM=" << 1; + newwriteOpts += extraOpt.str(); +#endif + result = mbImpl->write_file(outFile.c_str(), NULL, newwriteOpts.c_str(), partSets); + PRINT_LAST_ERROR; + std::cout << "Wrote " << outFile << std::endl; + std::cout << "mbcoupler_test complete." << std::endl; + } + +#ifdef USE_MPI + for (unsigned int i = 0; i < meshFiles.size(); i++) { + delete pcs[i]; + } +#endif + + delete mbImpl; + //may be leaking iMeshInst, don't care since it's end of program. Remove above deletes? + +#ifdef USE_MPI + err = MPI_Finalize(); +#endif + + return 0; +} + +#ifdef USE_MPI +ErrorCode report_iface_ents(Interface *mbImpl, + std::vector<ParallelComm *> &pcs, + const bool print_results) +{ + Range iface_ents[6]; + ErrorCode result = MB_SUCCESS, tmp_result; + + // now figure out which vertices are shared + for (unsigned int p = 0; p < pcs.size(); p++) { + for (int i = 0; i < 4; i++) { + tmp_result = pcs[p]->get_iface_entities(-1, i, iface_ents[i]); + + if (MB_SUCCESS != tmp_result) { + std::cerr << "get_iface_entities returned error on proc " + << pcs[p]->proc_config().proc_rank() << "; message: " << std::endl; + std::string last_error; + result = mbImpl->get_last_error(last_error); + if (last_error.empty()) std::cerr << "(none)" << std::endl; + else std::cerr << last_error << std::endl; + result = tmp_result; + } + if (0 != i) iface_ents[4].merge(iface_ents[i]); + } + } + + // report # iface entities + result = mbImpl->get_adjacencies(iface_ents[4], 0, false, iface_ents[5], + Interface::UNION); + + int rank; + MPI_Comm_rank(MPI_COMM_WORLD, &rank); + + if (print_results || iface_ents[0].size() != iface_ents[5].size()) { + std::cerr << "Proc " << rank << " iface entities: " << std::endl; + for (int i = 0; i < 4; i++) + std::cerr << " " << iface_ents[i].size() << " " + << i << "d iface entities." << std::endl; + std::cerr << " (" << iface_ents[5].size() + << " verts adj to other iface ents)" << std::endl; + } + + return result; +} +#endif + +// Print usage +void print_usage(char **argv) { + std::cerr << "Usage: "; + std::cerr << argv[0] << " -meshes <source_mesh><target_mesh> -itag <interp_tag> [-gnorm <gnorm_tag>] [-ssnorm <ssnorm_tag><ssnorm_selection>] [-ropts <roptions>] [-outfile <out_file> [-wopts <woptions>]] [-dbgout [<dbg_file>]]" << std::endl; + std::cerr << " -meshes" << std::endl; + std::cerr << " Read in mesh files <source_mesh> and <target_mesh>." << std::endl; + std::cerr << " -itag" << std::endl; + std::cerr << " Interpolate tag <interp_tag> from source mesh to target mesh." << std::endl; + std::cerr << " -gnorm" << std::endl; + std::cerr << " Normalize the value of tag <gnorm_tag> over then entire mesh and save to" << std::endl; + std::cerr << " tag \"<gnorm_tag>_normf\" on the mesh set. Do this for all meshes." << std::endl; + std::cerr << " -ssnorm" << std::endl; + std::cerr << " Normalize the value of tag <ssnorm_tag> over subsets of a mesh and save to" << std::endl; + std::cerr << " tag \"<ssnorm_tag>_normf\" on the Entity Set for each subset. Subsets are selected" << std::endl; + std::cerr << " using criteria in <ssnorm_selection>. Do this for all meshes." << std::endl; + std::cerr << " -ropts" << std::endl; + std::cerr << " Read in the mesh files using options in <roptions>." << std::endl; + std::cerr << " -outfile" << std::endl; + std::cerr << " Write out target mesh to <out_file>." << std::endl; + std::cerr << " -wopts" << std::endl; + std::cerr << " Write out mesh files using options in <woptions>." << std::endl; + std::cerr << " -dbgout" << std::endl; + std::cerr << " Write stdout and stderr streams to the file \'<dbg_file>.txt\'." << std::endl; + std::cerr << " -eps" << std::endl; + std::cerr << " epsilon" << std::endl; + std::cerr << " -meth <method> (0=CONSTANT, 1=LINEAR_FE, 2=QUADRATIC_FE, 3=SPECTRAL)" << std::endl; +} + +// Check first character for a '-'. +// Return true if one is found. False otherwise. +bool check_for_flag(const char *str) { + if (str[0] == '-') + return true; + else + return false; +} + +// New get_file_options() function with added possibilities for mbcoupler_test. +ErrorCode get_file_options(int argc, char **argv, + std::vector<std::string> &meshFiles, + DataCoupler::Method &method, + std::string &interpTag, + std::string &gNormTag, + std::string &ssNormTag, + std::vector<const char *> &ssTagNames, + std::vector<const char *> &ssTagValues, + std::string &readOpts, + std::string &outFile, + std::string &writeOpts, + std::string &dbgFile, + bool &help, + double & epsilon) +{ + // Initialize some of the outputs to null values indicating not present + // in the argument list. + gNormTag = ""; + ssNormTag = ""; + readOpts = "PARALLEL=READ_PART;PARTITION=PARALLEL_PARTITION;PARTITION_DISTRIBUTE;PARALLEL_RESOLVE_SHARED_ENTS;PARALLEL_GHOSTS=3.0.1;CPUTIME"; + outFile = ""; + writeOpts = "PARALLEL=WRITE_PART;CPUTIME"; + dbgFile = ""; + std::string defaultDbgFile = argv[0]; // The executable name will be the default debug output file. + + // These will indicate if we've gotten our required parameters at the end of parsing. + bool haveMeshes = false; + bool haveInterpTag = false; + + // Loop over the values in argv pulling out an parsing each one + int npos = 1; + + if (argc > 1 && argv[1] == std::string("-h")) { + help = true; + return MB_SUCCESS; + } + + while (npos < argc) { + if (argv[npos] == std::string("-meshes")) { + // Parse out the mesh filenames + npos++; + int numFiles = 2; + meshFiles.resize(numFiles); + for (int i = 0; i < numFiles; i++) { + if ((npos < argc) && (!check_for_flag(argv[npos]))) + meshFiles[i] = argv[npos++]; + else { + std::cerr << " ERROR - missing correct number of mesh filenames" << std::endl; + return MB_FAILURE; + } + } + + haveMeshes = true; + } + else if (argv[npos] == std::string("-itag")) { + // Parse out the interpolation tag + npos++; + if ((npos < argc) && (!check_for_flag(argv[npos]))) + interpTag = argv[npos++]; + else { + std::cerr << " ERROR - missing <interp_tag>" << std::endl; + return MB_FAILURE; + } + + haveInterpTag = true; + } + else if (argv[npos] == std::string("-meth")) { + // Parse out the interpolation tag + npos++; + if (argv[npos][0] == '0') method = DataCoupler::CONSTANT; + else if (argv[npos][0] == '1') method = DataCoupler::LINEAR_FE; + else if (argv[npos][0] == '2') method = DataCoupler::QUADRATIC_FE; + else if (argv[npos][0] == '3') method = DataCoupler::SPECTRAL; + else { + std::cerr << " ERROR - unrecognized method number " << method << std::endl; + return MB_FAILURE; + } + npos++; + } + else if (argv[npos] == std::string("-eps")) { + // Parse out the tolerance + npos++; + if ((npos < argc) && (!check_for_flag(argv[npos]))) + epsilon = atof(argv[npos++]); + else { + std::cerr << " ERROR - missing <epsilon>" << std::endl; + return MB_FAILURE; + } + } + else if (argv[npos] == std::string("-gnorm")) { + // Parse out the global normalization tag + npos++; + if ((npos < argc) && (!check_for_flag(argv[npos]))) + gNormTag = argv[npos++]; + else { + std::cerr << " ERROR - missing <gnorm_tag>" << std::endl; + return MB_FAILURE; + } + } + else if (argv[npos] == std::string("-ssnorm")) { + // Parse out the subset normalization tag and selection criteria + npos++; + if ((npos < argc) && (!check_for_flag(argv[npos]))) + ssNormTag = argv[npos++]; + else { + std::cerr << " ERROR - missing <ssnorm_tag>" << std::endl; + return MB_FAILURE; + } + + if ((npos < argc) && (!check_for_flag(argv[npos]))) { + char* opts = argv[npos++]; + char sep1[1] = {';'}; + char sep2[1] = {'='}; + bool end_vals_seen = false; + std::vector<char *> tmpTagOpts; + + // first get the options + for (char* i = strtok(opts, sep1); i; i = strtok(0, sep1)) { + tmpTagOpts.push_back(i); + } + + // parse out the name and val or just name. + for (unsigned int j = 0; j < tmpTagOpts.size(); j++) { + char* e = strtok(tmpTagOpts[j], sep2); + ssTagNames.push_back(e); + e = strtok(0, sep2); + if (e != NULL) { + // We have a value + if (end_vals_seen) { + // ERROR we should not have a value after none are seen + std::cerr << " ERROR - new value seen after end of values in <ssnorm_selection>" << std::endl; + return MB_FAILURE; + } + // Otherwise get the value string from e and convert it to an int + int *valp = new int; + *valp = atoi(e); + ssTagValues.push_back((const char *) valp); + } + else { + // Otherwise there is no '=' so push a null on the list + end_vals_seen = true; + ssTagValues.push_back((const char *) 0); + } + } + } + else { + std::cerr << " ERROR - missing <ssnorm_selection>" << std::endl; + return MB_FAILURE; + } + } + else if (argv[npos] == std::string("-ropts")) { + // Parse out the mesh file read options + npos++; + if ((npos < argc) && (!check_for_flag(argv[npos]))) + readOpts = argv[npos++]; + else { + std::cerr << " ERROR - missing <roptions>" << std::endl; + return MB_FAILURE; + } + } + else if (argv[npos] == std::string("-outfile")) { + // Parse out the output file name + npos++; + if ((npos < argc) && (!check_for_flag(argv[npos]))) + outFile = argv[npos++]; + else { + std::cerr << " ERROR - missing <out_file>" << std::endl; + return MB_FAILURE; + } + } + else if (argv[npos] == std::string("-wopts")) { + // Parse out the output file write options + npos++; + if ((npos < argc) && (!check_for_flag(argv[npos]))) + writeOpts = argv[npos++]; + else { + std::cerr << " ERROR - missing <woptions>" << std::endl; + return MB_FAILURE; + } + } + else if (argv[npos] == std::string("-dbgout")) { + // Parse out the debug output file name. + // If no name then use the default. + npos++; + if ((npos < argc) && (!check_for_flag(argv[npos]))) + dbgFile = argv[npos++]; + else + dbgFile = defaultDbgFile; + } + else { + // Unrecognized parameter. Skip it and move along. + std::cerr << " ERROR - Unrecognized parameter:" << argv[npos] << std::endl; + std::cerr << " Skipping..." << std::endl; + npos++; + } + } + + if (!haveMeshes) { + meshFiles.resize(2); + meshFiles[0] = std::string(TestDir + "/64bricks_1khex.h5m"); + meshFiles[1] = std::string(TestDir + "/64bricks_12ktet.h5m"); + std::cout << "Mesh files not entered; using default files " + << meshFiles[0] << " and " << meshFiles[1] << std::endl; + } + + if (!haveInterpTag) { + interpTag = "vertex_field"; + std::cout << "Interpolation field name not given, using default of " << interpTag << std::endl; + } + +#ifdef HDF5_FILE + if (1 == argc) { + std::cout << "No arguments given; using output file dum.h5m." << std::endl; + outFile = "dum.h5m"; + } +#endif + + return MB_SUCCESS; +} + + +// End new get_file_options() + + +ErrorCode test_interpolation(Interface *mbImpl, + DataCoupler::Method method, + std::string &interpTag, + std::string &gNormTag, + std::string &ssNormTag, + std::vector<const char *> &ssTagNames, + std::vector<const char *> &ssTagValues, + iBase_EntitySetHandle *roots, + std::vector<ParallelComm *> &pcs, + double &instant_time, + double &pointloc_time, + double &interp_time, + double &gnorm_time, + double &ssnorm_time, + double & toler) +{ + assert(method >= DataCoupler::CONSTANT && method <= DataCoupler::SPECTRAL); + + // source is 1st mesh, target is 2nd + Range src_elems, targ_elems, targ_verts; + ErrorCode result = pcs[0]->get_part_entities(src_elems, 3); + PRINT_LAST_ERROR; + + CpuTimer timer; + + // instantiate a coupler, which also initializes the tree + DataCoupler dc(mbImpl, src_elems, 0, pcs[0]); + + // initialize spectral elements, if they exist + bool specSou=false, specTar = false; +// result = mbc.initialize_spectral_elements((EntityHandle)roots[0], (EntityHandle)roots[1], specSou, specTar); + + instant_time = timer.time_since_birth(); + + // get points from the target mesh to interpolate + // we have to treat differently the case when the target is a spectral mesh + // in that case, the points of interest are the GL points, not the vertex nodes + std::vector<double> vpos; // this will have the positions we are interested in + int numPointsOfInterest = 0; +#ifdef USE_MPI + result = pcs[1]->get_part_entities(targ_elems, 3); +#else + result = mbImpl->get_entities_by_dimension((EntityHandle)roots[1], 3); +#endif + PRINT_LAST_ERROR; + + // first get all vertices adj to partition entities in target mesh + if (DataCoupler::CONSTANT == method) + targ_verts = targ_elems; + else + result = mbImpl->get_adjacencies(targ_elems, 0, false, targ_verts, + Interface::UNION); + PRINT_LAST_ERROR; + +#ifdef USE_MPI + // then get non-owned verts and subtract + Range tmp_verts; + result = pcs[1]->get_pstatus_entities(0, PSTATUS_NOT_OWNED, tmp_verts); + PRINT_LAST_ERROR; + targ_verts = subtract( targ_verts, tmp_verts); +#endif + // get position of these entities; these are the target points + numPointsOfInterest = (int)targ_verts.size(); + vpos.resize(3*targ_verts.size()); + result = mbImpl->get_coords(targ_verts, &vpos[0]); + PRINT_LAST_ERROR; + + // locate those points in the source mesh +#ifdef USE_MPI + std::cout << "rank "<< pcs[0]->proc_config().proc_rank(); +#endif + std::cout << " points of interest: " << numPointsOfInterest << "\n"; + result = dc.locate_points(&vpos[0], numPointsOfInterest, toler); + PRINT_LAST_ERROR; + + pointloc_time = timer.time_elapsed(); + + // now interpolate tag onto target points + std::vector<double> field(numPointsOfInterest); + + result = dc.interpolate(method, interpTag, &field[0]); + PRINT_LAST_ERROR; + + interp_time = timer.time_elapsed(); + +/* + // do global normalization if specified + if (!gNormTag.empty()) { + int err; + + // Normalize the source mesh + err = dc.normalize_mesh(roots[0], gNormTag.c_str(), DataCoupler::VOLUME, 4); + PRINT_LAST_ERR; + + // Normalize the target mesh + err = dc.normalize_mesh(roots[1], gNormTag.c_str(), DataCoupler::VOLUME, 4); + PRINT_LAST_ERR; + } + + gnorm_time = timer.time_elapsed(); + + // do subset normalization if specified + + if (!ssNormTag.empty()) { + int err; + + err = dc.normalize_subset(roots[0], + ssNormTag.c_str(), + &ssTagNames[0], + ssTagNames.size(), + &ssTagValues[0], + DataCoupler::VOLUME, + 4); + PRINT_LAST_ERR; + + err = dc.normalize_subset(roots[1], + ssNormTag.c_str(), + &ssTagNames[0], + ssTagNames.size(), + &ssTagValues[0], + DataCoupler::VOLUME, + 4); + PRINT_LAST_ERR; + } + + ssnorm_time = timer.time_elapsed(); +*/ + // set field values as tag on target vertices + // use original tag + Tag tag; + result = mbImpl->tag_get_handle(interpTag.c_str(), 1, MB_TYPE_DOUBLE, tag); PRINT_LAST_ERROR; + result = mbImpl->tag_set_data(tag, targ_verts, &field[0]); + PRINT_LAST_ERROR; + + // done + return MB_SUCCESS; +} https://bitbucket.org/fathomteam/moab/commits/cfbad175c3f5/ Changeset: cfbad175c3f5 Branch: None User: tautges Date: 2014-03-12 16:59:30 Summary: - add ability to specify master and slave mesh solid/fluid set numbers separately, so set numbers don't need to agree - add ability to specify only fluid or solid sets, with other sets derived from that and all material sets in a file - add DeformMeshRemap to list of examples in makefile Affected #: 1 file diff --git a/examples/DeformMeshRemap.cpp b/examples/DeformMeshRemap.cpp index a8a0e10..c5e2452 100644 --- a/examples/DeformMeshRemap.cpp +++ b/examples/DeformMeshRemap.cpp @@ -358,6 +358,50 @@ ErrorCode DeformMeshRemap::execute() return MB_SUCCESS; } +ErrorCode DeformMeshRemap::find_other_sets(int m_or_s, EntityHandle file_set) +{ + // solid or fluid sets are missing; find the other + Range *filled_sets = NULL, *unfilled_sets = NULL, *unfilled_elems = NULL; + + if (fluidSets[m_or_s].empty() && !solidSets[m_or_s].empty()) { + unfilled_sets = &fluidSets[m_or_s]; + filled_sets = &solidSets[m_or_s]; + unfilled_elems = &fluidElems[m_or_s]; + } + else if (!fluidSets[m_or_s].empty() && solidSets[m_or_s].empty()) { + filled_sets = &fluidSets[m_or_s]; + unfilled_sets = &solidSets[m_or_s]; + unfilled_elems = &solidElems[m_or_s]; + } + + // ok, we know the filled sets, now fill the unfilled sets, and the elems from those + Tag tagh; + ErrorCode rval = mbImpl->tag_get_handle(MATERIAL_SET_TAG_NAME, tagh); RR("Couldn't get material set tag name."); + Range matsets; + rval = mbImpl->get_entities_by_type_and_tag(file_set, MBENTITYSET, &tagh, NULL, 1, matsets); + if (matsets.empty()) rval = MB_FAILURE; + RR("Couldn't get any material sets."); + *unfilled_sets = subtract(matsets, *filled_sets); + if (unfilled_sets->empty()) { + rval = MB_FAILURE; + RR("Failed to find any unfilled material sets."); + } + Range tmp_range; + for (Range::iterator rit = unfilled_sets->begin(); rit != unfilled_sets->end(); rit++) { + rval = mbImpl->get_entities_by_handle(*rit, tmp_range, true); + RR("Failed to get entities in unfilled set."); + } + int dim = mbImpl->dimension_from_handle(*tmp_range.rbegin()); + assert(dim > 0 && dim < 4); + *unfilled_elems = tmp_range.subset_by_dimension(dim); + if (unfilled_elems->empty()) { + rval = MB_FAILURE; + RR("Failed to find any unfilled set entities."); + } + + return MB_SUCCESS; +} + std::string DeformMeshRemap::get_file_name(int m_or_s) const { switch (m_or_s) { https://bitbucket.org/fathomteam/moab/commits/321ee0341127/ Changeset: 321ee0341127 Branch: None User: tautges Date: 2014-03-12 17:00:26 Summary: Better error handling & debug printing. In Tree, handle legacy tag on tree root by deleting and re-creating (legacy files have old-sized tag). Affected #: 1 file diff --git a/examples/DeformMeshRemap.cpp b/examples/DeformMeshRemap.cpp index c5e2452..a8a0e10 100644 --- a/examples/DeformMeshRemap.cpp +++ b/examples/DeformMeshRemap.cpp @@ -358,50 +358,6 @@ ErrorCode DeformMeshRemap::execute() return MB_SUCCESS; } -ErrorCode DeformMeshRemap::find_other_sets(int m_or_s, EntityHandle file_set) -{ - // solid or fluid sets are missing; find the other - Range *filled_sets = NULL, *unfilled_sets = NULL, *unfilled_elems = NULL; - - if (fluidSets[m_or_s].empty() && !solidSets[m_or_s].empty()) { - unfilled_sets = &fluidSets[m_or_s]; - filled_sets = &solidSets[m_or_s]; - unfilled_elems = &fluidElems[m_or_s]; - } - else if (!fluidSets[m_or_s].empty() && solidSets[m_or_s].empty()) { - filled_sets = &fluidSets[m_or_s]; - unfilled_sets = &solidSets[m_or_s]; - unfilled_elems = &solidElems[m_or_s]; - } - - // ok, we know the filled sets, now fill the unfilled sets, and the elems from those - Tag tagh; - ErrorCode rval = mbImpl->tag_get_handle(MATERIAL_SET_TAG_NAME, tagh); RR("Couldn't get material set tag name."); - Range matsets; - rval = mbImpl->get_entities_by_type_and_tag(file_set, MBENTITYSET, &tagh, NULL, 1, matsets); - if (matsets.empty()) rval = MB_FAILURE; - RR("Couldn't get any material sets."); - *unfilled_sets = subtract(matsets, *filled_sets); - if (unfilled_sets->empty()) { - rval = MB_FAILURE; - RR("Failed to find any unfilled material sets."); - } - Range tmp_range; - for (Range::iterator rit = unfilled_sets->begin(); rit != unfilled_sets->end(); rit++) { - rval = mbImpl->get_entities_by_handle(*rit, tmp_range, true); - RR("Failed to get entities in unfilled set."); - } - int dim = mbImpl->dimension_from_handle(*tmp_range.rbegin()); - assert(dim > 0 && dim < 4); - *unfilled_elems = tmp_range.subset_by_dimension(dim); - if (unfilled_elems->empty()) { - rval = MB_FAILURE; - RR("Failed to find any unfilled set entities."); - } - - return MB_SUCCESS; -} - std::string DeformMeshRemap::get_file_name(int m_or_s) const { switch (m_or_s) { https://bitbucket.org/fathomteam/moab/commits/7c68d61d2b8f/ Changeset: 7c68d61d2b8f Branch: None User: tautges Date: 2014-03-12 17:01:17 Summary: Changes to allow specification of existing displacement tag(s), which can be either single name corresponding to xyz[3] or 3 names x, y, z. Handle either case in deform_master. Affected #: 1 file diff --git a/examples/DeformMeshRemap.cpp b/examples/DeformMeshRemap.cpp index a8a0e10..344565a 100644 --- a/examples/DeformMeshRemap.cpp +++ b/examples/DeformMeshRemap.cpp @@ -387,7 +387,6 @@ DeformMeshRemap::DeformMeshRemap(Interface *impl, ParallelComm *master, Parallel : mbImpl(impl), pcMaster(master), pcSlave(slave), masterSet(0), slaveSet(0), xNew(0), xNewName("xnew") { mbImpl->query_interface(mError); - xDisp[0] = xDisp[1] = xDisp[2] = 0; if (!pcSlave && pcMaster) @@ -553,7 +552,7 @@ ErrorCode DeformMeshRemap::deform_master(Range &fluid_elems, Range &solid_elems, rval = mbImpl->tag_get_handle((tag_name ? tag_name : ""), 3, MB_TYPE_DOUBLE, xNew, MB_TAG_CREAT|MB_TAG_DENSE); RR("Failed to create xnew tag."); std::vector<double> disps(num_verts); - + for (int i = 0; i < 3; i++) { rval = mbImpl->tag_get_handle(xDispNames[0].c_str(), 1, MB_TYPE_DOUBLE, xDisp[i]); RR("Failed to get xDisp tag."); https://bitbucket.org/fathomteam/moab/commits/fbad7648f20f/ Changeset: fbad7648f20f Branch: None User: tautges Date: 2014-03-12 17:01:17 Summary: - add ability to specify master and slave mesh solid/fluid set numbers separately, so set numbers don't need to agree - add ability to specify only fluid or solid sets, with other sets derived from that and all material sets in a file - add DeformMeshRemap to list of examples in makefile Affected #: 1 file diff --git a/examples/DeformMeshRemap.cpp b/examples/DeformMeshRemap.cpp index 344565a..59e4469 100644 --- a/examples/DeformMeshRemap.cpp +++ b/examples/DeformMeshRemap.cpp @@ -358,6 +358,50 @@ ErrorCode DeformMeshRemap::execute() return MB_SUCCESS; } +ErrorCode DeformMeshRemap::find_other_sets(int m_or_s, EntityHandle file_set) +{ + // solid or fluid sets are missing; find the other + Range *filled_sets = NULL, *unfilled_sets = NULL, *unfilled_elems = NULL; + + if (fluidSets[m_or_s].empty() && !solidSets[m_or_s].empty()) { + unfilled_sets = &fluidSets[m_or_s]; + filled_sets = &solidSets[m_or_s]; + unfilled_elems = &fluidElems[m_or_s]; + } + else if (!fluidSets[m_or_s].empty() && solidSets[m_or_s].empty()) { + filled_sets = &fluidSets[m_or_s]; + unfilled_sets = &solidSets[m_or_s]; + unfilled_elems = &solidElems[m_or_s]; + } + + // ok, we know the filled sets, now fill the unfilled sets, and the elems from those + Tag tagh; + ErrorCode rval = mbImpl->tag_get_handle(MATERIAL_SET_TAG_NAME, tagh); RR("Couldn't get material set tag name."); + Range matsets; + rval = mbImpl->get_entities_by_type_and_tag(file_set, MBENTITYSET, &tagh, NULL, 1, matsets); + if (matsets.empty()) rval = MB_FAILURE; + RR("Couldn't get any material sets."); + *unfilled_sets = subtract(matsets, *filled_sets); + if (unfilled_sets->empty()) { + rval = MB_FAILURE; + RR("Failed to find any unfilled material sets."); + } + Range tmp_range; + for (Range::iterator rit = unfilled_sets->begin(); rit != unfilled_sets->end(); rit++) { + rval = mbImpl->get_entities_by_handle(*rit, tmp_range, true); + RR("Failed to get entities in unfilled set."); + } + int dim = mbImpl->dimension_from_handle(*tmp_range.rbegin()); + assert(dim > 0 && dim < 4); + *unfilled_elems = tmp_range.subset_by_dimension(dim); + if (unfilled_elems->empty()) { + rval = MB_FAILURE; + RR("Failed to find any unfilled set entities."); + } + + return MB_SUCCESS; +} + std::string DeformMeshRemap::get_file_name(int m_or_s) const { switch (m_or_s) { https://bitbucket.org/fathomteam/moab/commits/8c76f8fc316e/ Changeset: 8c76f8fc316e Branch: None User: tautges Date: 2014-03-12 17:01:17 Summary: Better error handling & debug printing. In Tree, handle legacy tag on tree root by deleting and re-creating (legacy files have old-sized tag). Affected #: 1 file diff --git a/examples/DeformMeshRemap.cpp b/examples/DeformMeshRemap.cpp index 59e4469..344565a 100644 --- a/examples/DeformMeshRemap.cpp +++ b/examples/DeformMeshRemap.cpp @@ -358,50 +358,6 @@ ErrorCode DeformMeshRemap::execute() return MB_SUCCESS; } -ErrorCode DeformMeshRemap::find_other_sets(int m_or_s, EntityHandle file_set) -{ - // solid or fluid sets are missing; find the other - Range *filled_sets = NULL, *unfilled_sets = NULL, *unfilled_elems = NULL; - - if (fluidSets[m_or_s].empty() && !solidSets[m_or_s].empty()) { - unfilled_sets = &fluidSets[m_or_s]; - filled_sets = &solidSets[m_or_s]; - unfilled_elems = &fluidElems[m_or_s]; - } - else if (!fluidSets[m_or_s].empty() && solidSets[m_or_s].empty()) { - filled_sets = &fluidSets[m_or_s]; - unfilled_sets = &solidSets[m_or_s]; - unfilled_elems = &solidElems[m_or_s]; - } - - // ok, we know the filled sets, now fill the unfilled sets, and the elems from those - Tag tagh; - ErrorCode rval = mbImpl->tag_get_handle(MATERIAL_SET_TAG_NAME, tagh); RR("Couldn't get material set tag name."); - Range matsets; - rval = mbImpl->get_entities_by_type_and_tag(file_set, MBENTITYSET, &tagh, NULL, 1, matsets); - if (matsets.empty()) rval = MB_FAILURE; - RR("Couldn't get any material sets."); - *unfilled_sets = subtract(matsets, *filled_sets); - if (unfilled_sets->empty()) { - rval = MB_FAILURE; - RR("Failed to find any unfilled material sets."); - } - Range tmp_range; - for (Range::iterator rit = unfilled_sets->begin(); rit != unfilled_sets->end(); rit++) { - rval = mbImpl->get_entities_by_handle(*rit, tmp_range, true); - RR("Failed to get entities in unfilled set."); - } - int dim = mbImpl->dimension_from_handle(*tmp_range.rbegin()); - assert(dim > 0 && dim < 4); - *unfilled_elems = tmp_range.subset_by_dimension(dim); - if (unfilled_elems->empty()) { - rval = MB_FAILURE; - RR("Failed to find any unfilled set entities."); - } - - return MB_SUCCESS; -} - std::string DeformMeshRemap::get_file_name(int m_or_s) const { switch (m_or_s) { https://bitbucket.org/fathomteam/moab/commits/12bd6aeace15/ Changeset: 12bd6aeace15 Branch: None User: tautges Date: 2014-03-12 17:01:17 Summary: DeformMeshRemap: more debugging output, and handle coord displacements properly (add to prev coords) LloydSmoother: fix a bug with fixed tag entity handles size SpatialLocator: if an element range is specified, build the tree too Affected #: 1 file diff --git a/examples/DeformMeshRemap.cpp b/examples/DeformMeshRemap.cpp index 344565a..fee03b8 100644 --- a/examples/DeformMeshRemap.cpp +++ b/examples/DeformMeshRemap.cpp @@ -552,7 +552,6 @@ ErrorCode DeformMeshRemap::deform_master(Range &fluid_elems, Range &solid_elems, rval = mbImpl->tag_get_handle((tag_name ? tag_name : ""), 3, MB_TYPE_DOUBLE, xNew, MB_TAG_CREAT|MB_TAG_DENSE); RR("Failed to create xnew tag."); std::vector<double> disps(num_verts); - for (int i = 0; i < 3; i++) { rval = mbImpl->tag_get_handle(xDispNames[0].c_str(), 1, MB_TYPE_DOUBLE, xDisp[i]); RR("Failed to get xDisp tag."); https://bitbucket.org/fathomteam/moab/commits/854a59211ad5/ Changeset: 854a59211ad5 Branch: None User: tautges Date: 2014-03-12 17:01:17 Summary: DeformMeshRemap.cpp: Write more intermediate files if compiled with local debug flag true; change some of the functions for moving coords to tags and vice versa to facilitate this. SpatialLocator.cpp: Back out change that automatically chose BVH tree for non-vertex entities, there's a bug in point location there currently... Affected #: 1 file diff --git a/src/SpatialLocator.cpp b/src/SpatialLocator.cpp index 702399e..6046fb2 100644 --- a/src/SpatialLocator.cpp +++ b/src/SpatialLocator.cpp @@ -35,12 +35,12 @@ namespace moab { if (myTree) return; - if (myElems.empty() || mbImpl->type_from_handle(*myElems.rbegin()) == MBVERTEX) +// if (myElems.empty() || mbImpl->type_from_handle(*myElems.rbegin()) == MBVERTEX) // create a kdtree if only vertices myTree = new AdaptiveKDTree(mbImpl); - else +// else // otherwise a BVHtree, since it performs better for elements - myTree = new BVHTree(mbImpl); +// myTree = new BVHTree(mbImpl); iCreatedTree = true; } https://bitbucket.org/fathomteam/moab/commits/1fa59bf61d07/ Changeset: 1fa59bf61d07 Branch: None User: tautges Date: 2014-03-12 17:01:17 Summary: Various smallish bug fixes and minor changes, improving the use of SpatialLocator. ElemEvaluator: in set_ent_handle, if there's no evalSet for that entity type, call EvalSet::get_eval_set SpatialLocator: set the evaluator on the tree if it's not the same as what's on SpatialLocator; also, replace find_point logic (that used distance_search for some reason) with call to Tree::point_search. AdaptiveKDTree: move parse_options to public function, as it is in Tree BVHTree: fixed bug, where BVHTree had its own myEval shadowing the one declared in Tree Tree: fixed bug, initialize myEval to NULL in constructor spatial_locator_test: test trees with and without evaluators DataCoupler: improving comments a bit, and move ParallelComm down in arg list for constructor; also, some improved comments datacoupler_test: adding test Passes make check in parallel. Affected #: 1 file Diff not available. https://bitbucket.org/fathomteam/moab/commits/9c9c716a8e6b/ Changeset: 9c9c716a8e6b Branch: deformed-mesh-remap User: tautges Date: 2014-03-12 17:05:39 Summary: Merge branch 'deformed-mesh-remap' of bitbucket.org:fathomteam/moab into deformed-mesh-remap Conflicts: examples/DeformMeshRemap.cpp Affected #: 1 file Diff not available. Repository URL: https://bitbucket.org/fathomteam/moab/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/MOAB: tautges: Adding a few files to be removed after testing. Make distcheck now passes for parallel.
by commits-noreply＠bitbucket.org 12 Mar '14

12 Mar '14

1 new commit in MOAB: https://bitbucket.org/fathomteam/moab/commits/076e26039749/ Changeset: 076e26039749 Branch: master User: tautges Date: 2014-03-12 16:50:08 Summary: Adding a few files to be removed after testing. Make distcheck now passes for parallel. Affected #: 1 file diff --git a/test/parallel/Makefile.am b/test/parallel/Makefile.am index 2ac73fa..dde3a87 100644 --- a/test/parallel/Makefile.am +++ b/test/parallel/Makefile.am @@ -115,4 +115,6 @@ MOSTLYCLEANFILES = mhdf_ll.h5m tmp0.h5m tmp1.h5m tmp2.h5m tmp3.h5m \ initial1.vtk \ test_mpas.h5m \ dum.h5m \ - test_mpas_no_mixed_elements.h5m + test_mpas_no_mixed_elements.h5m \ + test_mpas_rcbzoltan.h5m \ + test_mpas_rcbzoltan_no_mixed_elements.h5m Repository URL: https://bitbucket.org/fathomteam/moab/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/MOAB: tautges: Removing some warnings.
by commits-noreply＠bitbucket.org 12 Mar '14

12 Mar '14

1 new commit in MOAB: https://bitbucket.org/fathomteam/moab/commits/76a83e8282fc/ Changeset: 76a83e8282fc Branch: master User: tautges Date: 2014-03-12 16:32:09 Summary: Removing some warnings. Affected #: 7 files diff --git a/src/io/Tqdcfr.cpp b/src/io/Tqdcfr.cpp index 701ff15..7416164 100644 --- a/src/io/Tqdcfr.cpp +++ b/src/io/Tqdcfr.cpp @@ -959,7 +959,7 @@ ErrorCode Tqdcfr::read_block(const unsigned int blindex, FREADD(blockh->attribOrder); num_read += sizeof(double); void const* tag_data[] = { &dbl_buf[0] }; - int tag_sizes[] = { blockh->attribOrder }; + int tag_sizes[] = { static_cast<int>(blockh->attribOrder) }; result = mdbImpl->tag_set_by_ptr(block_attribs,&(blockh->setHandle),1,tag_data,tag_sizes); if (MB_SUCCESS != result) return result; } @@ -1932,7 +1932,8 @@ ErrorCode Tqdcfr::BlockHeader::read_info_header(const double data_version, result = instance->mdbImpl->tag_get_handle(BLOCK_HEADER,3*sizeof(unsigned int),MB_TYPE_INTEGER, bhTag_header,MB_TAG_CREAT|MB_TAG_SPARSE|MB_TAG_BYTES,&def_uint_zero[0]); if (MB_SUCCESS != result) return result; - int block_header_data[] = { block_headers[i].blockCol, block_headers[i].blockMat, block_headers[i].blockDim }; + int block_header_data[] = { static_cast<int>(block_headers[i].blockCol), static_cast<int>(block_headers[i].blockMat), + static_cast<int>(block_headers[i].blockDim) }; result = instance->mdbImpl->tag_set_data(bhTag_header,&(block_headers[i].setHandle), 1, block_header_data); } diff --git a/src/parallel/WriteHDF5Parallel.cpp b/src/parallel/WriteHDF5Parallel.cpp index 20a36a3..be692ba 100644 --- a/src/parallel/WriteHDF5Parallel.cpp +++ b/src/parallel/WriteHDF5Parallel.cpp @@ -118,6 +118,7 @@ const char* mpi_err_str( int errorcode ) { template <typename T> inline void VALGRIND_MAKE_VEC_UNDEFINED( std::vector<T>& v ) { + if (v.size()) {} VALGRIND_MAKE_MEM_UNDEFINED( &v[0], v.size() * sizeof(T) ); } diff --git a/tools/mbcoupler/Coupler.cpp b/tools/mbcoupler/Coupler.cpp index b496441..afee8af 100644 --- a/tools/mbcoupler/Coupler.cpp +++ b/tools/mbcoupler/Coupler.cpp @@ -483,10 +483,13 @@ ErrorCode Coupler::test_local_box(double *xyz, { std::vector<EntityHandle> entities; std::vector<CartVect> nat_coords; - bool canWrite; + bool canWrite = false; if (tl) { canWrite = tl->get_writeEnabled(); - if(!canWrite) tl->enableWriteAccess(); + if(!canWrite) { + tl->enableWriteAccess(); + canWrite = true; + } } if (rel_eps && !abs_eps) { @@ -833,7 +836,7 @@ ErrorCode Coupler::interp_field(EntityHandle elem, else { double vfields[27]; // will work for linear hex, quadratic hex or Tets - moab::Element::Map *elemMap; + moab::Element::Map *elemMap = NULL; int num_verts = 0; // get the EntityType // get the tag values at the vertices @@ -1533,7 +1536,7 @@ int Coupler::get_group_integ_vals(std::vector< std::vector<iBase_EntityHandle> > iMesh_getEntTopo(iMeshInst, (*iter_j), &topo_type, &err); ERRORR("Failed to get topology for entity.", err); - moab::Element::Map *elemMap; + moab::Element::Map *elemMap = NULL; int num_verts = 0; if (topo_type == iMesh_HEXAHEDRON) { elemMap = new moab::Element::LinearHex(); diff --git a/tools/mbcoupler/mbcoupler_test.cpp b/tools/mbcoupler/mbcoupler_test.cpp index c5c826f..20be50d 100644 --- a/tools/mbcoupler/mbcoupler_test.cpp +++ b/tools/mbcoupler/mbcoupler_test.cpp @@ -131,8 +131,8 @@ int main(int argc, char **argv) if (!dbgFile.empty()) { std::stringstream dfname; dfname << dbgFile << rank << ".txt"; - std::freopen(dfname.str().c_str(), "a", stdout); - std::freopen(dfname.str().c_str(), "a", stderr); + if (!std::freopen(dfname.str().c_str(), "a", stdout)) return false; + if (!std::freopen(dfname.str().c_str(), "a", stderr)) return false; } // create MOAB instance based on that diff --git a/tools/mbcoupler/ssn_test.cpp b/tools/mbcoupler/ssn_test.cpp index 21adf72..a7e4188 100644 --- a/tools/mbcoupler/ssn_test.cpp +++ b/tools/mbcoupler/ssn_test.cpp @@ -102,8 +102,8 @@ int main(int argc, char **argv) { // Create an ofstream to write output. One file each for each proc. std::stringstream fname; fname << argv[0] << rank << ".out"; - std::freopen(fname.str().c_str(), "a", stdout); - std::freopen(fname.str().c_str(), "a", stderr); + if (!std::freopen(fname.str().c_str(), "a", stdout)) return false; + if (!std::freopen(fname.str().c_str(), "a", stderr)) return false; // Create the moab instance Interface *mbi = new Core(); diff --git a/tools/mbcslam/Intx2Mesh.cpp b/tools/mbcslam/Intx2Mesh.cpp index 9859d00..e055beb 100644 --- a/tools/mbcslam/Intx2Mesh.cpp +++ b/tools/mbcslam/Intx2Mesh.cpp @@ -782,7 +782,7 @@ ErrorCode Intx2Mesh::create_departure_mesh_2nd_alg(EntityHandle & euler_set, Ent { // construct the conn quad EntityHandle new_conn[MAXEDGES]; - int nnodes; + int nnodes = -1; for (int j=0; j<max_edges; j++) { int vgid = TLq.vi_rd[sizeTuple*i+2+j];// vertex global ID @@ -1072,7 +1072,7 @@ ErrorCode Intx2Mesh::create_departure_mesh_3rd_alg(EntityHandle & lagr_set, { // construct the conn quad EntityHandle new_conn[MAXEDGES]; - int nnodes; + int nnodes = -1; for (int j = 0; j < max_edges; j++) { int vgid = TLq.vi_rd[sizeTuple * i + 2 + j]; // vertex global ID diff --git a/tools/mcnpmit/main.cpp b/tools/mcnpmit/main.cpp index eca4b85..cc2d19a 100644 --- a/tools/mcnpmit/main.cpp +++ b/tools/mcnpmit/main.cpp @@ -136,7 +136,7 @@ int main(int argc, char **argv) { char line[10000]; // Used only when reading a mesh file to get vertex info - double *cfd_coords; + double *cfd_coords = NULL; moab::Range::iterator cfd_iter; moab::EntityHandle meshset; Repository URL: https://bitbucket.org/fathomteam/moab/ -- This is a commit notification from bitbucket.org. 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