mesh_data_transfer.cpp File Reference

Transfer data from source mesh to target mesh. More...

#include <MoFEM.hpp>
#include <mbcoupler/Coupler.hpp>

Go to the source code of this file.

Functions
int	main (int argc, char *argv[])

Variables
static char	help [] = "...\n\n"

Detailed Description

Transfer data from source mesh to target mesh.

The data is transferred from tags on 3D elements of the source mesh to tags on 3D elements in the target mesh. This code uses MBCoupler functionality of MOAB and is based on mbcoupler_test.cpp from MOAB.

For this tool to work, source and target files should be partitioned using mbpart tool from MOAB, e.g. mbpart -z PHG -t 4 sslv116_hex.cub sslv116_hex_4mp.h5m

Definition in file mesh_data_transfer.cpp.

Function Documentation

main()

int main	(	int	argc,
		char *	argv[]
	)

Definition at line 21 of file mesh_data_transfer.cpp.

                                 {
  MoFEM::Core::Initialize(&argc, &argv, (char *)0, help);
 
  try {
 
    moab::Core mb_instance;
    moab::Interface &moab = mb_instance;
 
    // Create MoFEM database
    MoFEM::Core core(moab);
    MoFEM::Interface &m_field = core;
 
    char mesh_source_file[255] = "source.h5m";
    char mesh_target_file[255] = "target.h5m";
    char mesh_out_file[255] = "out.h5m";
    char iterp_tag_name[255] = "INTERNAL_STRESS";
 
    int interp_order = 1;
 
    PetscBool use_target_verts = PETSC_TRUE;
 
    int atom_test = 0;
 
    double toler = 5.e-10;
 
    PetscOptionsBegin(m_field.get_comm(), "", "mesh data transfer tool",
                             "none");
    CHKERR PetscOptionsString("-source_file", "source mesh file name", "",
                              "source.h5m", mesh_source_file, 255, PETSC_NULLPTR);
    CHKERR PetscOptionsString("-target_file", "target mesh file name", "",
                              "target.h5m", mesh_target_file, 255, PETSC_NULLPTR);
    CHKERR PetscOptionsString("-output_file", "output mesh file name", "",
                              "out.h5m", mesh_out_file, 255, PETSC_NULLPTR);
    CHKERR PetscOptionsString("-interp_tag", "interpolation tag name", "",
                              "INTERNAL_STRESS", iterp_tag_name, 255,
                              PETSC_NULLPTR);
    CHKERR PetscOptionsInt("-interp_order", "interpolation order", "", 0,
                           &interp_order, PETSC_NULLPTR);
    CHKERR PetscOptionsBool("-use_target_verts",
                            "use target vertices for interpolation", "",
                            use_target_verts, &use_target_verts, PETSC_NULLPTR);
    CHKERR PetscOptionsInt("-atom_test", "atom test number", "", 0, &atom_test,
                           PETSC_NULLPTR);
 
    PetscOptionsEnd();
 
    MOFEM_LOG_CHANNEL("WORLD");
    MOFEM_LOG_TAG("WORLD", "mesh_data_transfer");
 
    Coupler::Method method;
    switch (interp_order) {
    case 0:
      method = Coupler::CONSTANT;
      break;
    case 1:
      method = Coupler::LINEAR_FE;
      break;
    default:
      SETERRQ(PETSC_COMM_WORLD, MOFEM_NOT_IMPLEMENTED,
              "Unsupported interpolation order");
    }
 
    std::vector<std::string> mesh_files(2);
    mesh_files[0] = string(mesh_source_file);
    mesh_files[1] = string(mesh_target_file);
 
    int nprocs, rank;
    ierr = MPI_Comm_size(MPI_COMM_WORLD, &nprocs);
    CHKERRQ(ierr);
    ierr = MPI_Comm_rank(MPI_COMM_WORLD, &rank);
    CHKERRQ(ierr);
 
    std::string read_opts, write_opts;
    read_opts = "PARALLEL=READ_PART;PARTITION=PARALLEL_PARTITION;PARTITION_"
                "DISTRIBUTE;PARALLEL_RESOLVE_SHARED_ENTS";
    if (nprocs > 1)
      read_opts += ";PARALLEL_GHOSTS=3.0.1";
    write_opts = (nprocs > 1) ? "PARALLEL=WRITE_PART" : "";
 
    std::vector<ParallelComm *> pcs(mesh_files.size());
    std::vector<EntityHandle> roots(mesh_files.size());
 
    for (unsigned int i = 0; i < mesh_files.size(); i++) {
      pcs[i] = new ParallelComm(&moab, MPI_COMM_WORLD);
      int index = pcs[i]->get_id();
      std::string newread_opts;
      std::ostringstream extra_opt;
      extra_opt << ";PARALLEL_COMM=" << index;
      newread_opts = read_opts + extra_opt.str();
 
      CHKERR moab.create_meshset(MESHSET_SET, roots[i]);
 
      CHKERR moab.load_file(mesh_files[i].c_str(), &roots[i],
                            newread_opts.c_str());
    }
 
    Range src_elems, targ_elems, targ_verts;
    CHKERR pcs[0]->get_part_entities(src_elems, 3);
 
    Tag interp_tag;
    CHKERR moab.tag_get_handle(iterp_tag_name, interp_tag);
 
    int interp_tag_len;
    CHKERR moab.tag_get_length(interp_tag, interp_tag_len);
 
    if (interp_tag_len != 1 && interp_tag_len != 3 && interp_tag_len != 9) {
      SETERRQ(PETSC_COMM_WORLD, MOFEM_NOT_IMPLEMENTED,
               "Unsupported interpolation tag length: %d", interp_tag_len);
    }
 
    Coupler mbc(&moab, pcs[0], src_elems, 0, true);
 
    std::vector<double> vpos; // the positions we are interested in
    int num_pts = 0;
 
    Range tmp_verts;
 
    // First get all vertices adj to partition entities in target mesh
    CHKERR pcs[1]->get_part_entities(targ_elems, 3);
    if (!use_target_verts) {
      targ_verts = targ_elems;
    } else {
      CHKERR moab.get_adjacencies(targ_elems, 0, false, targ_verts,
                                  moab::Interface::UNION);
    }
 
    // Then get non-owned verts and subtract
    CHKERR pcs[1]->get_pstatus_entities(0, PSTATUS_NOT_OWNED, tmp_verts);
    targ_verts = subtract(targ_verts, tmp_verts);
 
    // get position of these entities; these are the target points
    num_pts = (int)targ_verts.size();
    vpos.resize(3 * targ_verts.size());
    CHKERR moab.get_coords(targ_verts, &vpos[0]);
 
    // Locate those points in the source mesh
    CHKERR mbc.locate_points(&vpos[0], num_pts, 0, toler);
 
    std::vector<double> source_data(interp_tag_len * src_elems.size(), 0.0);
    std::vector<double> target_data(interp_tag_len * num_pts, 0.0);
 
    CHKERR moab.tag_get_data(interp_tag, src_elems, &source_data[0]);
 
    Tag scalar_tag, adj_count_tag;
    double def_scl = 0;
    string scalar_tag_name = string(iterp_tag_name) + "_COMP";
    CHKERR moab.tag_get_handle(scalar_tag_name.c_str(), 1, MB_TYPE_DOUBLE,
                               scalar_tag, MB_TAG_CREAT | MB_TAG_DENSE,
                               &def_scl);
 
    string adj_count_tag_name = "ADJ_COUNT";
    double def_adj = 0;
    CHKERR moab.tag_get_handle(adj_count_tag_name.c_str(), 1, MB_TYPE_DOUBLE,
                               adj_count_tag, MB_TAG_CREAT | MB_TAG_DENSE,
                               &def_adj);
 
    std::vector<double> source_data_scalar(src_elems.size());
 
    // MBCoupler functionality supports only scalar meshes. For the case of
    // vector or tensor tags we need to save each component as a scalar tag
    for (int itag = 0; itag < interp_tag_len; itag++) {
 
      for (int ielem = 0; ielem < src_elems.size(); ielem++) {
        source_data_scalar[ielem] = source_data[itag + ielem * interp_tag_len];
      }
 
      CHKERR moab.tag_set_data(scalar_tag, src_elems, &source_data_scalar[0]);
 
      if (interp_order == 1) {
        // In case of linear interpolation, data needs to be saved on source
        // mesh vertices. Here we compute average value of the data on the
        // vertices from all adjacent 3D elements
 
        Range src_verts;
        CHKERR moab.get_connectivity(src_elems, src_verts, true);
 
        CHKERR moab.tag_clear_data(scalar_tag, src_verts, &def_scl);
        CHKERR moab.tag_clear_data(adj_count_tag, src_verts, &def_adj);
 
        for (auto &tet : src_elems) {
          double tet_data = 0;
          CHKERR moab.tag_get_data(scalar_tag, &tet, 1, &tet_data);
 
          Range adj_verts;
          CHKERR moab.get_connectivity(&tet, 1, adj_verts, true);
 
          std::vector<double> adj_vert_data(adj_verts.size(), 0.0);
          std::vector<double> adj_vert_count(adj_verts.size(), 0.0);
 
          CHKERR moab.tag_get_data(scalar_tag, adj_verts, &adj_vert_data[0]);
          CHKERR moab.tag_get_data(adj_count_tag, adj_verts,
                                   &adj_vert_count[0]);
 
          for (int ivert = 0; ivert < adj_verts.size(); ivert++) {
            adj_vert_data[ivert] += tet_data;
            adj_vert_count[ivert] += 1;
          }
 
          CHKERR moab.tag_set_data(scalar_tag, adj_verts, &adj_vert_data[0]);
          CHKERR moab.tag_set_data(adj_count_tag, adj_verts,
                                   &adj_vert_count[0]);
        }
 
        // We need to reduce tags for the parallel case
        std::vector<Tag> tags;
        tags.push_back(scalar_tag);
        tags.push_back(adj_count_tag);
        pcs[0]->reduce_tags(tags, tags, MPI_SUM, src_verts);
 
        std::vector<double> src_vert_data(src_verts.size(), 0.0);
        std::vector<double> src_vert_adj_count(src_verts.size(), 0.0);
 
        CHKERR moab.tag_get_data(scalar_tag, src_verts, &src_vert_data[0]);
        CHKERR moab.tag_get_data(adj_count_tag, src_verts,
                                 &src_vert_adj_count[0]);
 
        for (int ivert = 0; ivert < src_verts.size(); ivert++) {
          src_vert_data[ivert] /= src_vert_adj_count[ivert];
        }
        CHKERR moab.tag_set_data(scalar_tag, src_verts, &src_vert_data[0]);
      }
 
      std::vector<double> target_data_scalar(num_pts, 0.0);
      CHKERR mbc.interpolate(method, scalar_tag_name, &target_data_scalar[0]);
 
      for (int ielem = 0; ielem < num_pts; ielem++) {
        target_data[itag + ielem * interp_tag_len] = target_data_scalar[ielem];
      }
    }
 
    CHKERR moab.tag_delete(scalar_tag);
    CHKERR moab.tag_delete(adj_count_tag);
 
    // Use original tag
    CHKERR moab.tag_set_data(interp_tag, targ_verts, &target_data[0]);
 
    if (use_target_verts) {
      // If the data was interpolated to target mesh vertices, we need to
      // average the vertex values for each 3D element and save on its tag
 
      // We need to reduce tags for the parallel case
      std::vector<Tag> tags;
      tags.push_back(interp_tag);
      pcs[1]->reduce_tags(tags, tags, MPI_SUM, targ_verts);
 
      for (auto &tet : targ_elems) {
        Range adj_verts;
        CHKERR moab.get_connectivity(&tet, 1, adj_verts, true);
 
        std::vector<double> adj_vert_data(adj_verts.size() * interp_tag_len,
                                          0.0);
        CHKERR moab.tag_get_data(interp_tag, adj_verts, &adj_vert_data[0]);
 
        std::vector<double> tet_data(interp_tag_len, 0.0);
        for (int itag = 0; itag < interp_tag_len; itag++) {
          for (int i = 0; i < adj_verts.size(); i++) {
            tet_data[itag] += adj_vert_data[i * interp_tag_len + itag];
          }
          tet_data[itag] /= adj_verts.size();
        }
        CHKERR moab.tag_set_data(interp_tag, &tet, 1, &tet_data[0]);
      }
    }
 
    if (atom_test == 1 || atom_test == 2) {
      // Check the integrated stress for the SSLV116 test
 
      std::vector<double> data_integ(interp_tag_len, 0.0);
      for (auto &tet : targ_elems) {
 
        std::vector<double> tet_data(interp_tag_len, 0.0);
        CHKERR moab.tag_get_data(interp_tag, &tet, 1, &tet_data[0]);
 
        const EntityHandle *vert_conn;
        int vert_num;
        CHKERR moab.get_connectivity(tet, vert_conn, vert_num, true);
        std::vector<double> vpos(3 * vert_num);
        CHKERR moab.get_coords(vert_conn, vert_num, &vpos[0]);
        double vol = Tools::tetVolume(vpos.data());
 
        for (int itag = 0; itag < interp_tag_len; itag++) {
          data_integ[itag] += tet_data[itag] * vol;
        }
      }
 
      std::vector<double> global_data_integ(interp_tag_len, 0.0);
      MPI_Allreduce(&data_integ[0], &global_data_integ[0], interp_tag_len,
                    MPI_DOUBLE, MPI_SUM, m_field.get_comm());
 
      std::string temp = "Integrated stress for sslv116 test: ";
      for (int i = 0; i < 9; ++i) {
        std::stringstream ss;
        ss << std::scientific << std::setprecision(3) << global_data_integ[i];
        temp += ss.str() + " ";
      }
      MOFEM_LOG("WORLD", Sev::inform) << temp;
 
      double non_zero_val = 1.655e12;
      double non_zero_tol = 5.1e-2;
      if (interp_order == 1) {
        non_zero_tol = 1e-3;
      }
      std::vector<int> non_zero_inds(3);
      std::vector<int> zero_inds(6);
      if (atom_test == 1) {
        non_zero_inds = {0, 4, 8};
        zero_inds = {1, 2, 3, 5, 6, 7};
      } else {
        non_zero_inds = {0, 1, 2};
        zero_inds = {3, 4, 5, 6, 7, 8};
      }
      bool non_zero_check =
          all_of(begin(non_zero_inds), end(non_zero_inds), [&](int i) {
            return abs(global_data_integ[i] - non_zero_val) / non_zero_val <
                   non_zero_tol;
          });
      bool zero_check = all_of(begin(zero_inds), end(zero_inds), [&](int i) {
        return abs(global_data_integ[i]) < 1e-12;
      });
      if (!non_zero_check || !zero_check) {
        SETERRQ(PETSC_COMM_WORLD, MOFEM_ATOM_TEST_INVALID,
                "Wrong value of the integrated stress");
      }
    } else if (atom_test) {
      SETERRQ(PETSC_COMM_WORLD, MOFEM_NOT_IMPLEMENTED,
               "Unknown test number: %d", atom_test);
    }
 
    Range part_sets;
    // Only save the target mesh
    part_sets.insert(roots[1]);
    std::string new_write_opts;
    std::ostringstream extra_opt;
    if (nprocs > 1) {
      int index = pcs[1]->get_id();
      extra_opt << ";PARALLEL_COMM=" << index;
    }
    new_write_opts = write_opts + extra_opt.str();
    CHKERR moab.write_file(mesh_out_file, NULL, new_write_opts.c_str(),
                           part_sets);
    if (0 == rank) {
      MOFEM_LOG("WORLD", Sev::inform) << "Wrote file " << mesh_out_file;
    }
 
    for (unsigned int i = 0; i < mesh_files.size(); i++)
      delete pcs[i];
  }
  CATCH_ERRORS;
 
  MoFEM::Core::Finalize();
 
  return 0;
}

Variable Documentation

help

char help[] = "...\n\n"

static

Definition at line 19 of file mesh_data_transfer.cpp.