CutMeshInterface.cpp File Reference

Cut mesh by surface. More...

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Namespaces
namespace	MoFEM
	implementation of Data Operators for Forces and Sources

Macros
#define	CutMeshFunctionBegin

Detailed Description

Cut mesh by surface.

Definition in file CutMeshInterface.cpp.

Macro Definition Documentation

CutMeshFunctionBegin

#define CutMeshFunctionBegin

Value:

  MoFEMFunctionBegin;                                                          \
  MOFEM_LOG_CHANNEL("WORLD");                                                  \
  MOFEM_LOG_FUNCTION();                                                        \
  MOFEM_LOG_TAG("WORLD", "CutMesh");

Definition at line 7 of file CutMeshInterface.cpp.

                {
 
MoFEMErrorCode
CutMeshInterface::query_interface(boost::typeindex::type_index type_index,
                                  UnknownInterface **iface) const {
  MoFEMFunctionBeginHot;
  *iface = const_cast<CutMeshInterface *>(this);
  MoFEMFunctionReturnHot(0);
}
 
CutMeshInterface::CutMeshInterface(const Core &core)
    : cOre(const_cast<Core &>(core)) {
  lineSearchSteps = 10;
  nbMaxMergingCycles = 200;
  projectEntitiesQualityTrashold = 0.5;
}
 
MoFEMErrorCode CutMeshInterface::clearMap() {
  MoFEMFunctionBegin;
  treeSurfPtr.reset();
  MoFEMFunctionReturn(0);
}
 
MoFEMErrorCode CutMeshInterface::setFront(const Range front) {
  MoFEMFunctionBeginHot;
  fRont = front;
  MoFEMFunctionReturnHot(0);
}
 
MoFEMErrorCode CutMeshInterface::setSurface(const Range surface) {
  MoFEMFunctionBeginHot;
  sUrface = surface;
  MoFEMFunctionReturnHot(0);
}
 
MoFEMErrorCode CutMeshInterface::copySurface(const Range surface, Tag th,
                                             double *shift, double *origin,
                                             double *transform,
                                             const std::string save_mesh) {
  CoreInterface &m_field = cOre;
  moab::Interface &moab = m_field.get_moab();
  MoFEMFunctionBegin;
  sUrface.clear();
  std::map<EntityHandle, EntityHandle> verts_map;
  for (Range::const_iterator tit = surface.begin(); tit != surface.end();
       tit++) {
    int num_nodes;
    const EntityHandle *conn;
    CHKERR moab.get_connectivity(*tit, conn, num_nodes, true);
    MatrixDouble coords(num_nodes, 3);
    if (th) {
      CHKERR moab.tag_get_data(th, conn, num_nodes, &coords(0, 0));
    } else {
      CHKERR moab.get_coords(conn, num_nodes, &coords(0, 0));
    }
    EntityHandle new_verts[num_nodes];
    for (int nn = 0; nn != num_nodes; nn++) {
      if (verts_map.find(conn[nn]) != verts_map.end()) {
        new_verts[nn] = verts_map[conn[nn]];
      } else {
        if (transform) {
          ublas::matrix_row<MatrixDouble> mr(coords, nn);
          if (origin) {
            VectorAdaptor vec_origin(
                3, ublas::shallow_array_adaptor<double>(3, origin));
            mr = mr - vec_origin;
          }
          MatrixAdaptor mat_transform = MatrixAdaptor(
              3, 3, ublas::shallow_array_adaptor<double>(9, transform));
          mr = prod(mat_transform, mr);
          if (origin) {
            VectorAdaptor vec_origin(
                3, ublas::shallow_array_adaptor<double>(3, origin));
            mr = mr + vec_origin;
          }
        }
        if (shift) {
          ublas::matrix_row<MatrixDouble> mr(coords, nn);
          VectorAdaptor vec_shift(
              3, ublas::shallow_array_adaptor<double>(3, shift));
          mr = mr + vec_shift;
        }
        CHKERR moab.create_vertex(&coords(nn, 0), new_verts[nn]);
        verts_map[conn[nn]] = new_verts[nn];
      }
    }
    EntityHandle ele;
    CHKERR moab.create_element(MBTRI, new_verts, num_nodes, ele);
    sUrface.insert(ele);
  }
  if (!save_mesh.empty())
    CHKERR SaveData(m_field.get_moab())(save_mesh, sUrface);
  MoFEMFunctionReturn(0);
}
 
MoFEMErrorCode CutMeshInterface::setVolume(const Range volume) {
  MoFEMFunctionBeginHot;
  vOlume = volume;
  MoFEMFunctionReturnHot(0);
}
 
MoFEMErrorCode CutMeshInterface::setConstrainSurface(const Range surf) {
  MoFEMFunctionBeginHot;
  constrainSurface = surf;
  MoFEMFunctionReturnHot(0);
}
 
MoFEMErrorCode CutMeshInterface::mergeSurface(const Range surface) {
  MoFEMFunctionBeginHot;
  sUrface.merge(surface);
  MoFEMFunctionReturnHot(0);
}
 
MoFEMErrorCode CutMeshInterface::mergeVolumes(const Range volume) {
  MoFEMFunctionBeginHot;
  vOlume.merge(volume);
  MoFEMFunctionReturnHot(0);
}
 
MoFEMErrorCode CutMeshInterface::snapSurfaceSkinToEdges(const Range fixed_edges,
                                                        const double rel_tol,
                                                        const double abs_tol,
                                                        Tag th,
                                                        const bool debug) {
  CoreInterface &m_field = cOre;
  moab::Interface &moab = m_field.get_moab();
  CutMeshFunctionBegin;
 
  // Get cutting surface skin
  Skinner skin(&moab);
  Range surface_skin;
  CHKERR skin.find_skin(0, sUrface, false, surface_skin);
 
  CHKERR snapSurfaceToEdges(surface_skin, fixed_edges, rel_tol, abs_tol, th,
                            debug);
 
  MoFEMFunctionReturn(0);
}
 
MoFEMErrorCode CutMeshInterface::snapSurfaceToEdges(const Range surface_edges,
                                                    const Range fixed_edges,
                                                    const double rel_tol,
                                                    const double abs_tol,
                                                    Tag th, const bool debug) {
  CoreInterface &m_field = cOre;
  moab::Interface &moab = m_field.get_moab();
  FTensor::Index<'i', 3> i;
  CutMeshFunctionBegin;
 
  map<EntityHandle, double> map_verts_length;
 
  for (auto f : surface_edges) {
    int num_nodes;
    const EntityHandle *conn_skin;
    CHKERR moab.get_connectivity(f, conn_skin, num_nodes, true);
    VectorDouble6 coords_skin(6);
    if (th)
      CHKERR moab.tag_get_data(th, conn_skin, num_nodes, &coords_skin[0]);
    else
      CHKERR moab.get_coords(conn_skin, num_nodes, &coords_skin[0]);
    FTensor::Tensor1<FTensor::PackPtr<double *, 3>, 3> t_n0(
        &coords_skin[0], &coords_skin[1], &coords_skin[2]);
    FTensor::Tensor1<FTensor::PackPtr<double *, 3>, 3> t_n1(
        &coords_skin[3], &coords_skin[4], &coords_skin[5]);
    FTensor::Tensor1<double, 3> t_skin_delta;
    t_skin_delta(i) = t_n1(i) - t_n0(i);
    const double skin_edge_length = sqrt(t_skin_delta(i) * t_skin_delta(i));
    for (int nn = 0; nn != 2; ++nn) {
      auto it = map_verts_length.find(conn_skin[nn]);
      if (it != map_verts_length.end())
        it->second = std::min(it->second, skin_edge_length);
      else
        map_verts_length[conn_skin[nn]] = skin_edge_length;
    }
  }
 
  for (auto m : map_verts_length) {
 
    FTensor::Tensor1<double, 3> t_n;
    if (th)
      CHKERR moab.tag_get_data(th, &m.first, 1, &t_n(0));
    else
      CHKERR moab.get_coords(&m.first, 1, &t_n(0));
 
    double min_dist = rel_tol * m.second;
    FTensor::Tensor1<double, 3> t_min_coords;
    CHKERR cOre.getInterface<Tools>()->findMinDistanceFromTheEdges(
        &t_n(0), 1, fixed_edges, &min_dist, &t_min_coords(0));
 
    if (min_dist < rel_tol * m.second || min_dist < abs_tol) {
      if (debug)
        MOFEM_LOG("WORLD", Sev::noisy) << "Snap " << min_dist;
      if (th)
        CHKERR moab.tag_set_data(th, &m.first, 1, &t_min_coords(0));
      else
        CHKERR moab.set_coords(&m.first, 1, &t_min_coords(0));
    }
  }
 
  MoFEMFunctionReturn(0);
}
 
MoFEMErrorCode CutMeshInterface::buildTree() {
  CoreInterface &m_field = cOre;
  moab::Interface &moab = m_field.get_moab();
  MoFEMFunctionBegin;
  treeSurfPtr = boost::shared_ptr<OrientedBoxTreeTool>(
      new OrientedBoxTreeTool(&moab, "ROOTSETSURF", true));
  CHKERR treeSurfPtr->build(sUrface, rootSetSurf);
  MoFEMFunctionReturn(0);
}
 
MoFEMErrorCode
CutMeshInterface::cutOnly(Range vol, const BitRefLevel cut_bit, Tag th,
                          const double tol_geometry, const double tol_cut_close,
                          Range *fixed_edges, Range *corner_nodes,
                          const bool update_meshsets, const bool debug) {
  CoreInterface &m_field = cOre;
  moab::Interface &moab = m_field.get_moab();
  CutMeshFunctionBegin;
 
  // cut mesh
  CHKERR findEdgesToCut(vol, QUIET, debug);
  CHKERR projectZeroDistanceEnts(fixed_edges, corner_nodes, tol_geometry,
                                 tol_cut_close, QUIET, debug);
  CHKERR cutEdgesInMiddle(cut_bit, cutNewVolumes, cutNewSurfaces,
                          cutNewVertices, debug);
 
  CHKERR cOre.getInterface<BitRefManager>()->updateRangeByChildren(constrainSurface,
                                                         constrainSurface);
  if (fixed_edges)
    CHKERR cOre.getInterface<BitRefManager>()->updateRangeByChildren(*fixed_edges,
                                                           *fixed_edges);
  if (corner_nodes)
    CHKERR cOre.getInterface<BitRefManager>()->updateRangeByChildren(*corner_nodes,
                                                           *corner_nodes);
  if (update_meshsets)
    CHKERR m_field.getInterface<MeshsetsManager>()
        ->updateAllMeshsetsByEntitiesChildren(cut_bit);
  CHKERR moveMidNodesOnCutEdges(th);
 
  if (debug) {
    CHKERR saveCutEdges();
    if (fixed_edges)
      CHKERR SaveData(moab)("out_cut_new_fixed_edges.vtk", *fixed_edges);
  }
 
  MoFEMFunctionReturn(0);
}
 
MoFEMErrorCode CutMeshInterface::trimOnly(const BitRefLevel trim_bit, Tag th,
                                          const double tol_trim_close,
                                          Range *fixed_edges,
                                          Range *corner_nodes,
                                          const bool update_meshsets,
                                          const bool debug) {
  CoreInterface &m_field = cOre;
  moab::Interface &moab = m_field.get_moab();
  CutMeshFunctionBegin;
 
  // trim mesh
  CHKERR findEdgesToTrim(fixed_edges, corner_nodes, th, tol_trim_close, debug);
  CHKERR trimEdgesInTheMiddle(trim_bit, debug);
 
  CHKERR cOre.getInterface<BitRefManager>()->updateRangeByChildren(constrainSurface,
                                                         constrainSurface);
  if (fixed_edges)
    CHKERR cOre.getInterface<BitRefManager>()->updateRangeByChildren(*fixed_edges,
                                                           *fixed_edges);
 
  if (corner_nodes)
    CHKERR cOre.getInterface<BitRefManager>()->updateRangeByChildren(*corner_nodes,
                                                           *corner_nodes);
 
  if (update_meshsets)
    CHKERR m_field.getInterface<MeshsetsManager>()
        ->updateAllMeshsetsByEntitiesChildren(trim_bit);
 
  // move nodes
  CHKERR moveMidNodesOnTrimmedEdges(th);
 
  // remove faces
  CHKERR trimSurface(fixed_edges, corner_nodes, tol_trim_close, th, debug);
 
  if (debug) {
    CHKERR saveTrimEdges();
    Range bit2_edges;
    CHKERR cOre.getInterface<BitRefManager>()->getEntitiesByTypeAndRefLevel(
        trim_bit, BitRefLevel().set(), MBEDGE, bit2_edges);
    CHKERR SaveData(moab)("trim_fixed_edges.vtk",
                          intersect(*fixed_edges, bit2_edges));
  }
 
  MoFEMFunctionReturn(0);
}
 
MoFEMErrorCode CutMeshInterface::cutAndTrim(
    int &first_bit, Tag th, const double tol_geometry,
    const double tol_cut_close, const double tol_trim_close, Range *fixed_edges,
    Range *corner_nodes, const bool update_meshsets, const bool debug) {
  CoreInterface &m_field = cOre;
  CutMeshFunctionBegin;
 
  std::vector<BitRefLevel> bit_levels;
 
  auto get_back_bit_levels = [&]() {
    bit_levels.push_back(BitRefLevel());
    bit_levels.back().set(first_bit + bit_levels.size() - 1);
    return bit_levels.back();
  };
 
  BitRefLevel cut_bit = get_back_bit_levels();
 
  CHKERR cutOnly(unite(cutSurfaceVolumes, cutFrontVolumes), cut_bit, th,
                 tol_geometry, tol_cut_close, fixed_edges, corner_nodes,
                 update_meshsets, debug);
 
  auto get_min_quality = [&m_field](const BitRefLevel bit, Tag th) {
    Range tets_level; // test at level
    CHKERR m_field.getInterface<BitRefManager>()->getEntitiesByTypeAndRefLevel(
        bit, BitRefLevel().set(), MBTET, tets_level);
    double min_q = 1;
    CHKERR m_field.getInterface<Tools>()->minTetsQuality(tets_level, min_q, th);
    return min_q;
  };
 
  MOFEM_LOG_C("WORLD", Sev::inform, "Min quality cut %6.4g",
              get_min_quality(cut_bit, th));
 
  Range starting_volume = cutNewVolumes;
  Range starting_volume_nodes;
  CHKERR m_field.get_moab().get_connectivity(starting_volume,
                                             starting_volume_nodes, true);
  std::vector<double> staring_volume_coords(3 * starting_volume_nodes.size());
  CHKERR m_field.get_moab().get_coords(starting_volume_nodes,
                                       &*staring_volume_coords.begin());
 
  if (th) {
    std::vector<double> staring_volume_th_coords(3 *
                                                 starting_volume_nodes.size());
    CHKERR m_field.get_moab().tag_get_data(th, starting_volume_nodes,
                                           &*staring_volume_th_coords.begin());
    CHKERR m_field.get_moab().set_coords(starting_volume_nodes,
                                         &*staring_volume_th_coords.begin());
  }
 
  if (th)
    CHKERR setTagData(th);
 
  BitRefLevel trim_bit = get_back_bit_levels();
 
  CHKERR trimOnly(trim_bit, th, tol_trim_close, fixed_edges, corner_nodes,
                  update_meshsets, debug);
 
  MOFEM_LOG_C("WORLD", Sev::inform, "Min quality trim %3.2g",
              get_min_quality(trim_bit, th));
 
  first_bit += bit_levels.size() - 1;
 
  if (th)
    CHKERR m_field.get_moab().set_coords(starting_volume_nodes,
                                         &*staring_volume_coords.begin());
 
  MoFEMFunctionReturn(0);
}
 
MoFEMErrorCode CutMeshInterface::cutTrimAndMerge(
    int &first_bit, const int fraction_level, Tag th, const double tol_geometry,
    const double tol_cut_close, const double tol_trim_close, Range &fixed_edges,
    Range &corner_nodes, const bool update_meshsets, const bool debug) {
  CoreInterface &m_field = cOre;
  CutMeshFunctionBegin;
 
  std::vector<BitRefLevel> bit_levels;
 
  auto get_back_bit_levels = [&]() {
    bit_levels.push_back(BitRefLevel());
    bit_levels.back().set(first_bit + bit_levels.size() - 1);
    return bit_levels.back();
  };
 
  if (debug) {
    CHKERR cOre.getInterface<BitRefManager>()->writeEntitiesNotInDatabase(
        "ents_not_in_database.vtk", "VTK", "");
  }
 
  CHKERR cutAndTrim(first_bit, th, tol_geometry, tol_cut_close, tol_trim_close,
                    &fixed_edges, &corner_nodes, update_meshsets, debug);
  if (debug)
    CHKERR cOre.getInterface<BitRefManager>()->writeEntitiesNotInDatabase(
        "cut_trim_ents_not_in_database.vtk", "VTK", "");
 
  BitRefLevel bit_level1 = BitRefLevel().set(first_bit - 1);
  BitRefLevel bit_level2 = get_back_bit_levels();
  BitRefLevel bit_level3 = get_back_bit_levels();
 
  CHKERR mergeBadEdges(fraction_level, bit_level1, bit_level2, bit_level3,
                       getNewTrimSurfaces(), fixed_edges, corner_nodes, th,
                       update_meshsets, debug);
 
  auto get_min_quality = [&m_field, debug](const BitRefLevel bit, Tag th) {
    Range tets_level; // test at level
    CHKERR m_field.getInterface<BitRefManager>()->getEntitiesByTypeAndRefLevel(
        bit, BitRefLevel().set(), MBTET, tets_level);
    double min_q = 1;
    CHKERR m_field.getInterface<Tools>()->minTetsQuality(tets_level, min_q, th);
    if (min_q < 0 && debug) {
      CHKERR m_field.getInterface<Tools>()->writeTetsWithQuality(
          "negative_tets.vtk", "VTK", "", tets_level, th);
    }
    return min_q;
  };
 
  MOFEM_LOG_C("WORLD", Sev::inform, "Min quality node merge %6.4g",
              get_min_quality(bit_level3, th));
 
  CHKERR cOre.getInterface<BitRefManager>()->updateRangeByChildren(constrainSurface,
                                                         constrainSurface);
  CHKERR cOre.getInterface<BitRefManager>()->updateRangeByChildren(fixed_edges,
                                                         fixed_edges);
  CHKERR cOre.getInterface<BitRefManager>()->updateRangeByChildren(corner_nodes,
                                                         corner_nodes);
 
  first_bit += bit_levels.size() - 1;
 
  if (debug) {
    CHKERR cOre.getInterface<BitRefManager>()->writeBitLevelByType(
        bit_level3, BitRefLevel().set(), MBTET, "out_tets_merged.vtk", "VTK",
        "");
    CHKERR cOre.getInterface<BitRefManager>()->writeEntitiesNotInDatabase(
        "cut_trim_merge_ents_not_in_database.vtk", "VTK", "");
    CHKERR SaveData(m_field.get_moab())("merged_surface.vtk", mergedSurfaces);
  }
 
  MoFEMFunctionReturn(0);
}
 
MoFEMErrorCode CutMeshInterface::makeFront(const bool debug) {
  CoreInterface &m_field = cOre;
  moab::Interface &moab = m_field.get_moab();
  CutMeshFunctionBegin;
  Skinner skin(&moab);
  Range tets_skin;
  CHKERR skin.find_skin(0, vOlume, false, tets_skin);
  Range tets_skin_edges;
  ErrorCode tmp_result;
  tmp_result = moab.get_adjacencies(tets_skin, 1, false, tets_skin_edges,
                                    moab::Interface::UNION);
 
  if (MB_SUCCESS != tmp_result)
    SETERRQ(PETSC_COMM_SELF, MOFEM_DATA_INCONSISTENCY,
            "Duplicated edges: most likely the source of error is comming from "
            "adding the vertices of the cracking "
            "volume to a BLOCKSET rather than NODESET (corresponding to the "
            "input parameter-vertex_block_set)");
 
  Range surface_skin;
  CHKERR skin.find_skin(0, sUrface, false, surface_skin);
  fRont = subtract(surface_skin, tets_skin_edges);
  if (debug)
    CHKERR SaveData(moab)("front.vtk", fRont);
  MoFEMFunctionReturn(0);
}
 
MoFEMErrorCode CutMeshInterface::createSurfaceLevelSets(int verb,
                                                        const bool debug) {
  CoreInterface &m_field = cOre;
  moab::Interface &moab = m_field.get_moab();
  CutMeshFunctionBegin;
  auto tools_interface = m_field.getInterface<Tools>();
 
  auto create_tag = [&](const std::string name, const int dim) {
    Tag th;
    rval = moab.tag_get_handle(name.c_str(), th);
    if (rval == MB_SUCCESS)
      return th;
    std::vector<double> def_val(dim, 0);
    CHKERR moab.tag_get_handle(name.c_str(), dim, MB_TYPE_DOUBLE, th,
                               MB_TAG_CREAT | MB_TAG_SPARSE, &*def_val.begin());
 
    return th;
  };
 
  auto set_vol = [&](const Range &vol_verts, std::vector<double> &coords,
                     std::vector<double> &dist_surface_vec,
                     std::vector<double> &dist_surface_normal_vec,
                     std::vector<double> &dist_surface_signed_dist_vec) {
    MoFEMFunctionBegin;
 
    coords.resize(3 * vol_verts.size());
    dist_surface_vec.resize(3 * vol_verts.size());
    dist_surface_normal_vec.resize(3 * vol_verts.size());
    dist_surface_signed_dist_vec.resize(vol_verts.size());
 
    CHKERR moab.get_coords(vol_verts, &*coords.begin());
    std::srand(0);
 
    for (auto v : vol_verts) {
 
      const int index = vol_verts.index(v);
      auto point_in = getVectorAdaptor(&coords[3 * index], 3);
      VectorDouble3 point_out(3);
      EntityHandle facets_out;
      CHKERR treeSurfPtr->closest_to_location(&point_in[0], rootSetSurf,
                                              &point_out[0], facets_out);
 
      VectorDouble3 delta = point_out - point_in;
      VectorDouble3 n_first(3);
      CHKERR tools_interface->getTriNormal(facets_out, &*n_first.begin());
 
      // Check of only triangle in proximity of point out is one triangle, if is
      // more than one, use normal of lager triangle to set orientation.
      auto check_triangle_orientation = [&](auto n) {
        int num_nodes;
        const EntityHandle *conn;
        CHKERR moab.get_connectivity(facets_out, conn, num_nodes, true);
        MatrixDouble3by3 coords(3, 3);
        CHKERR moab.get_coords(conn, 3, &coords(0, 0));
        VectorDouble3 center(3);
        center.clear();
        for (auto ii : {0, 1, 2})
          for (auto jj : {0, 1, 2})
            center(jj) += coords(ii, jj) / 3;
 
        std::vector<EntityHandle> triangles_out;
        std::vector<double> distance_out;
        auto a_max = norm_2(n);
        VectorDouble3 ray = -n / a_max;
        VectorDouble3 pt = center - ray * sqrt(a_max);
        const double ray_length = 2 * sqrt(a_max);
 
        CHKERR treeSurfPtr->ray_intersect_triangles(
            distance_out, triangles_out, rootSetSurf,
            std::numeric_limits<float>::epsilon(), &pt[0], &ray[0],
            &ray_length);
 
        if (triangles_out.size() > 1) {
          VectorDouble3 nt(3);
          for (auto t : triangles_out) {
            CHKERR tools_interface->getTriNormal(t, &*nt.begin());
            double at = norm_2(nt);
            if (at > a_max) {
              n = nt;
              a_max = at;
            }
          }
        }
 
        return n;
      };
 
      auto n = check_triangle_orientation(n_first);
      n /= norm_2(n);
      const double dot = inner_prod(delta, n);
 
 
      if (std::abs(dot) < std::numeric_limits<double>::epsilon()) {
        if (std::rand() % 2 == 0)
          delta += n * std::numeric_limits<double>::epsilon();
        else
          delta -= n * std::numeric_limits<double>::epsilon();
      }
 
      auto dist_vec = getVectorAdaptor(&dist_surface_vec[3 * index], 3);
      noalias(dist_vec) = delta;
 
      auto dist_normal_vec =
          getVectorAdaptor(&dist_surface_normal_vec[3 * index], 3);
 
      dist_surface_signed_dist_vec[index] = dot;
      noalias(dist_normal_vec) = dot * n;
    }
 
    MoFEMFunctionReturn(0);
  };
 
  std::vector<double> coords;
  std::vector<double> dist_surface_vec;
  std::vector<double> dist_surface_normal_vec;
  std::vector<double> dist_surface_signed_dist_vec;
  Range vol_verts;
  CHKERR moab.get_connectivity(vOlume, vol_verts, true);
 
  CHKERR set_vol(vol_verts, coords, dist_surface_vec, dist_surface_normal_vec,
                 dist_surface_signed_dist_vec);
 
  CHKERR moab.tag_set_data(create_tag("DIST_SURFACE_VECTOR", 3), vol_verts,
                           &*dist_surface_vec.begin());
  CHKERR moab.tag_set_data(create_tag("DIST_SURFACE_NORMAL_VECTOR", 3),
                           vol_verts, &*dist_surface_normal_vec.begin());
  CHKERR moab.tag_set_data(create_tag("DIST_SURFACE_NORMAL_SIGNED", 1),
                           vol_verts, &*dist_surface_signed_dist_vec.begin());
 
  MoFEMFunctionReturn(0);
}
 
MoFEMErrorCode CutMeshInterface::createFrontLevelSets(Range vol, Tag th,
                                                      int verb,
                                                      const bool debug) {
  CoreInterface &m_field = cOre;
  moab::Interface &moab = m_field.get_moab();
  CutMeshFunctionBegin;
 
  auto create_tag = [&](const std::string name, const int dim) {
    Tag th;
    rval = moab.tag_get_handle(name.c_str(), th);
    if (rval == MB_SUCCESS)
      return th;
    std::vector<double> def_val(dim, 0);
    CHKERR moab.tag_get_handle(name.c_str(), dim, MB_TYPE_DOUBLE, th,
                               MB_TAG_CREAT | MB_TAG_SPARSE, &*def_val.begin());
    return th;
  };
 
  Range vol_vertices;
  CHKERR moab.get_connectivity(vol, vol_vertices, true);
 
  std::vector<double> min_distances_from_front(vol_vertices.size(), -1);
  std::vector<double> points_on_edges(3 * vol_vertices.size(), 0);
  std::vector<EntityHandle> closest_edges(vol_vertices.size(), 0);
 
  std::vector<double> coords(3 * vol_vertices.size());
  if (th)
    CHKERR moab.tag_get_data(th, vol_vertices, &*coords.begin());
  else
    CHKERR moab.get_coords(vol_vertices, &*coords.begin());
 
  CHKERR cOre.getInterface<Tools>()->findMinDistanceFromTheEdges(
      &*coords.begin(), vol_vertices.size(), fRont,
      &*min_distances_from_front.begin(), &*points_on_edges.begin(),
      &*closest_edges.begin());
 
  if (!points_on_edges.empty()) {
    for (int i = 0; i != min_distances_from_front.size(); ++i) {
      Range faces;
      CHKERR moab.get_adjacencies(&closest_edges[0], 1, 2, false, faces);
      auto point_in = getVectorAdaptor(&coords[3 * i], 3);
      auto point_out = getVectorAdaptor(&points_on_edges[3 * i], 3);
      point_out -= point_in;
    }
  }
 
  auto th_dist_front_vec = create_tag("DIST_FRONT_VECTOR", 3);
  CHKERR moab.tag_set_data(th_dist_front_vec, vol_vertices,
                           &*points_on_edges.begin());
 
  MoFEMFunctionReturn(0);
}
 
MoFEMErrorCode CutMeshInterface::findLevelSetVolumes(
    Tag th, Range &vol_edges, const bool remove_adj_prims_edges, int verb,
    const bool debug, const std::string edges_file_name) {
  CoreInterface &m_field = cOre;
  moab::Interface &moab = m_field.get_moab();
  CutMeshFunctionBegin;
 
  auto get_tag_dim = [&](auto th) {
    int dim;
    CHKERR moab.tag_get_length(th, dim);
    return dim;
  };
  auto dim = get_tag_dim(th);
 
  auto get_tag_data = [&](auto th, auto conn) {
    const void *ptr;
    CHKERR moab.tag_get_by_ptr(th, &conn, 1, &ptr);
    return getVectorAdaptor(
        const_cast<double *>(static_cast<const double *>(ptr)), 3);
  };
 
  auto get_edge_ray = [&](auto conn) {
    VectorDouble6 coords(6);
    CHKERR moab.get_coords(conn, 2, &coords[0]);
    VectorAdaptor n0 = getVectorAdaptor(&coords[0], 3);
    VectorAdaptor n1 = getVectorAdaptor(&coords[3], 3);
    VectorDouble3 ray = n1 - n0;
    return ray;
  };
 
  Range edges;
  CHKERR moab.get_adjacencies(vOlume, 1, true, edges, moab::Interface::UNION);
 
  auto remove_prisms_edges = [&](Range &edges) {
    MoFEMFunctionBegin;
    Range prisms;
    CHKERR moab.get_adjacencies(edges, 3, false, prisms,
                                moab::Interface::UNION);
    prisms = prisms.subset_by_type(MBPRISM);
    Range prisms_verts;
    CHKERR moab.get_connectivity(prisms, prisms_verts, true);
    Range prism_edges;
    CHKERR moab.get_adjacencies(prisms_verts, 1, false, prism_edges,
                                moab::Interface::UNION);
    edges = subtract(edges, prism_edges);
    MoFEMFunctionReturn(0);
  };
  if (remove_adj_prims_edges)
    CHKERR remove_prisms_edges(edges);
 
  std::vector<EntityHandle> cut_edges;
  cut_edges.reserve(edges.size());
 
  auto get_cut_edges_vec = [&](auto th, auto &cut_edges, auto e, auto &&conn) {
    MoFEMFunctionBegin;
 
    auto ray = get_edge_ray(conn);
    const double length = norm_2(ray);
    ray /= length;
    const auto dist0 = get_tag_data(th, conn[0]);
    const auto dist1 = get_tag_data(th, conn[1]);
    const double max_dist = std::max(norm_2(dist0), norm_2(dist1));
    if (max_dist < length) {
      cut_edges.push_back(e);
    }
 
    MoFEMFunctionReturn(0);
  };
 
  auto get_cut_edges_signed_dist = [&](auto th, auto &cut_edges, auto e,
                                       auto &&conn) {
    MoFEMFunctionBegin;
    auto get_tag_signed_dist = [&](auto conn) {
      double dist;
      CHKERR moab.tag_get_data(th, &conn, 1, &dist);
      return dist;
    };
    const auto dist0 = get_tag_signed_dist(conn[0]);
    const auto dist1 = get_tag_signed_dist(conn[1]);
    const double opposite = dist0 * dist1;
    if (opposite <= 0)
      cut_edges.push_back(e);
    MoFEMFunctionReturn(0);
  };
 
  auto get_conn = [&](auto e) {
    int num_nodes;
    const EntityHandle *conn;
    CHKERR moab.get_connectivity(e, conn, num_nodes, true);
    return conn;
  };
 
  if (dim == 3)
    for (auto e : edges)
      CHKERR get_cut_edges_vec(th, cut_edges, e, get_conn(e));
  else
    for (auto e : edges)
      CHKERR get_cut_edges_signed_dist(th, cut_edges, e, get_conn(e));
 
  CHKERR moab.get_adjacencies(&*cut_edges.begin(), cut_edges.size(), 3, false,
                              vol_edges, moab::Interface::UNION);
  vol_edges = intersect(vol_edges, vOlume);
 
  auto convert_to_ranger = [](auto &v) {
    Range r;
    r.insert_list(v.begin(), v.end());
    return r;
  };
 
  if (debug && !edges_file_name.empty())
    CHKERR SaveData(m_field.get_moab())(edges_file_name,
                                        convert_to_ranger(cut_edges));
 
  MoFEMFunctionReturn(0);
}
 
MoFEMErrorCode CutMeshInterface::findLevelSetVolumes(int verb,
                                                     const bool debug) {
  CoreInterface &m_field = cOre;
  moab::Interface &moab = m_field.get_moab();
  CutMeshFunctionBegin;
 
  CHKERR createFrontLevelSets(vOlume, nullptr, verb, debug);
  Tag th_dist_front_vec;
  CHKERR moab.tag_get_handle("DIST_FRONT_VECTOR", th_dist_front_vec);
  CHKERR findLevelSetVolumes(th_dist_front_vec, cutFrontVolumes, true, verb,
                             debug, "cutFrontEdges.vtk");
 
  CHKERR createSurfaceLevelSets(verb, debug);
 
  Tag th_dist_surface_vec;
  CHKERR moab.tag_get_handle("DIST_SURFACE_VECTOR", th_dist_surface_vec);
  cutSurfaceVolumes.clear();
  CHKERR findLevelSetVolumes(th_dist_surface_vec, cutSurfaceVolumes, true, verb,
                             debug, "cutSurfaceEdges.vtk");
 
  if (debug)
    CHKERR SaveData(m_field.get_moab())("level_sets.vtk", vOlume);
  if (debug)
    CHKERR SaveData(m_field.get_moab())("cutSurfaceVolumes.vtk",
                                        cutSurfaceVolumes);
  if (debug)
    CHKERR SaveData(m_field.get_moab())("cutFrontVolumes.vtk", cutFrontVolumes);
 
  MoFEMFunctionReturn(0);
}
 
MoFEMErrorCode CutMeshInterface::refineMesh(const int init_bit_level,
                                            const int surf_levels,
                                            const int front_levels,
                                            Range *fixed_edges, int verb,
                                            const bool debug) {
  CoreInterface &m_field = cOre;
  moab::Interface &moab = m_field.get_moab();
  MeshRefinement *refiner;
  BitRefManager *bit_ref_manager;
  CutMeshFunctionBegin;
  CHKERR m_field.getInterface(refiner);
  CHKERR m_field.getInterface(bit_ref_manager);
 
  auto add_bit = [&](const int bit) {
    MoFEMFunctionBegin;
    CHKERR bit_ref_manager->addBitRefLevel(vOlume, BitRefLevel().set(bit),
                                           verb);
    Range adj_ents;
    for (auto d : {2, 1, 0}) {
      CHKERR moab.get_adjacencies(vOlume, d, true, adj_ents,
                                  moab::Interface::UNION);
      CHKERR bit_ref_manager->addBitRefLevel(adj_ents, BitRefLevel().set(bit),
                                             verb);
    }
    MoFEMFunctionReturn(0);
  };
  CHKERR add_bit(init_bit_level);
 
  auto update_range = [&](Range *r_ptr) {
    MoFEMFunctionBegin;
    if (r_ptr) {
      Range childs;
      CHKERR bit_ref_manager->updateRangeByChildren(*r_ptr, childs);
      r_ptr->merge(childs);
    }
    MoFEMFunctionReturn(0);
  };
 
  auto refine = [&](const BitRefLevel bit, const Range tets) {
    MoFEMFunctionBegin;
    Range verts;
    CHKERR moab.get_connectivity(tets, verts, true);
    Range ref_edges;
    CHKERR moab.get_adjacencies(verts, 1, true, ref_edges,
                                moab::Interface::UNION);
 
    CHKERR refiner->addVerticesInTheMiddleOfEdges(ref_edges, bit);
    CHKERR refiner->refineTets(vOlume, bit, verb);
 
    CHKERR update_range(fixed_edges);
    CHKERR update_range(&vOlume);
    CHKERR m_field.getInterface<MeshsetsManager>()
        ->updateAllMeshsetsByEntitiesChildren(bit);
 
    Range bit_tets;
    CHKERR m_field.getInterface<BitRefManager>()->getEntitiesByTypeAndRefLevel(
        bit, BitRefLevel().set(), MBTET, bit_tets);
    vOlume = intersect(vOlume, bit_tets);
 
    Range bit_edges;
    CHKERR m_field.getInterface<BitRefManager>()->getEntitiesByTypeAndRefLevel(
        bit, BitRefLevel().set(), MBEDGE, bit_edges);
    if (fixed_edges)
      *fixed_edges = intersect(*fixed_edges, bit_edges);
 
    MoFEMFunctionReturn(0);
  };
 
  for (int ll = init_bit_level; ll != init_bit_level + surf_levels; ++ll) {
    CHKERR findLevelSetVolumes(verb, debug);
    CHKERR refine(BitRefLevel().set(ll + 1),
                  unite(cutSurfaceVolumes, cutFrontVolumes));
  }
 
  for (int ll = init_bit_level + surf_levels;
       ll != init_bit_level + surf_levels + front_levels; ++ll) {
    CHKERR findLevelSetVolumes(verb, debug);
    CHKERR refine(BitRefLevel().set(ll + 1), cutFrontVolumes);
  }
 
  CHKERR findLevelSetVolumes(verb, debug);
 
  if (debug)
    CHKERR SaveData(m_field.get_moab())("refinedVolume.vtk", vOlume);
 
  MoFEMFunctionReturn(0);
}
 
MoFEMErrorCode CutMeshInterface::findEdgesToCut(Range vol, int verb,
                                                const bool debug) {
  CoreInterface &m_field = cOre;
  moab::Interface &moab = m_field.get_moab();
  CutMeshFunctionBegin;
 
  edgesToCut.clear();
  cutEdges.clear();
 
  Tag th_signed_dist;
  CHKERR moab.tag_get_handle("DIST_SURFACE_NORMAL_SIGNED", th_signed_dist);
 
  auto get_tag_edge_dist = [&](auto th, auto conn) {
    std::array<double, 2> r;
    CHKERR moab.tag_get_data(th, conn, 2, r.data());
    return r;
  };
 
  auto get_conn = [&](const auto e) {
    int num_nodes;
    const EntityHandle *conn;
    CHKERR moab.get_connectivity(e, conn, num_nodes, true);
    return conn;
  };
 
  auto get_adj = [&moab](const Range r, const int dim) {
    Range a;
    if (dim)
      CHKERR moab.get_adjacencies(r, dim, false, a, moab::Interface::UNION);
    else
      CHKERR moab.get_connectivity(r, a, true);
    return a;
  };
 
  auto vol_edges = get_adj(vol, 1);
 
  aveLength = 0;
  maxLength = 0;
  int nb_ave_length = 0;
  for (auto e : vol_edges) {
 
    auto conn = get_conn(e);
    auto dist = get_tag_edge_dist(th_signed_dist, conn);
    const auto dist_max = std::max(dist[0], dist[1]);
    const auto dist_min = std::min(dist[0], dist[1]);
    const auto dot = dist[0] * dist[1];
 
    VectorDouble6 coords(6);
    CHKERR moab.get_coords(conn, 2, &coords[0]);
    VectorAdaptor n0 = getVectorAdaptor(&coords[0], 3);
    VectorAdaptor n1 = getVectorAdaptor(&coords[3], 3);
    VectorDouble3 ray = n1 - n0;
    const double ray_length = norm_2(ray);
    ray /= ray_length;
 
    if (
 
        (dot < 0 && dist_max > std::numeric_limits<double>::epsilon()) ||
        (std::abs(dist_min) < std::numeric_limits<double>::epsilon() &&
         dist_max > std::numeric_limits<double>::epsilon())
 
    ) {
 
      // Edges is on two sides of the surface
      const double s = dist[0] / (dist[0] - dist[1]);
      const double dist = s * ray_length;
 
      auto add_edge = [&](auto dist) {
        edgesToCut[e].dIst = dist;
        edgesToCut[e].lEngth = ray_length;
        edgesToCut[e].unitRayDir = ray;
        edgesToCut[e].rayPoint = n0;
        cutEdges.insert(e);
 
        aveLength += norm_2(ray);
        maxLength = fmax(maxLength, norm_2(ray));
        ++nb_ave_length;
      };
 
      add_edge(dist);
    }
  }
  aveLength /= nb_ave_length;
 
  if (debug)
    CHKERR SaveData(m_field.get_moab())("cut_edges.vtk", cutEdges);
 
  if (debug)
    CHKERR SaveData(m_field.get_moab())("cut_edges_vol.vtk",
                                        get_adj(cutEdges, 3));
 
  MoFEMFunctionReturn(0);
}
 
MoFEMErrorCode CutMeshInterface::projectZeroDistanceEnts(
    Range *fixed_edges, Range *corner_nodes, const double geometry_tol,
    const double close_tol, const int verb, const bool debug) {
  CoreInterface &m_field = cOre;
  moab::Interface &moab = m_field.get_moab();
  Skinner skin(&moab);
  CutMeshFunctionBegin;
 
  auto get_ent_adj = [&moab](const EntityHandle v, const int dim) {
    Range a;
    if (dim)
      CHKERR moab.get_adjacencies(&v, 1, dim, true, a);
    return a;
  };
 
  auto get_adj = [&moab](const Range r, const int dim) {
    Range a;
    if (dim)
      CHKERR moab.get_adjacencies(r, dim, false, a, moab::Interface::UNION);
    else
      CHKERR moab.get_connectivity(r, a, true);
    return a;
  };
 
  auto get_skin = [&skin](const auto r) {
    Range s;
    CHKERR skin.find_skin(0, r, false, s);
    return s;
  };
 
 
  auto get_range = [](std::vector<EntityHandle> v) {
    Range r;
    r.insert_list(v.begin(), v.end());
    return r;
  };
 
  auto get_coords = [&](const auto v) {
    VectorDouble3 coords(3);
    CHKERR moab.get_coords(&v, 1, &coords[0]);
    return coords;
  };
 
  Tag th_normal_dist;
  CHKERR moab.tag_get_handle("DIST_SURFACE_NORMAL_VECTOR", th_normal_dist);
 
  auto get_normal_dits = [&](const EntityHandle v) {
    VectorDouble3 dist_vec(3);
    CHKERR moab.tag_get_data(th_normal_dist, &v, 1, &*dist_vec.begin());
    return dist_vec;
  };
 
  auto get_prj_point = [&](const EntityHandle v, const Range edges,
                           const double geometry_tol) {
    auto get_tuple = [](const EntityHandle e, const double dist,
                        const double l) { return std::make_tuple(e, dist, l); };
 
    std::tuple<EntityHandle, double, double> min_tuple{0, 0, 0};
 
    for (auto e : edges) {
      auto eit = edgesToCut.find(e);
      if (eit != edgesToCut.end()) {
 
        auto get_dist = [&](auto eit) {
          int num_nodes;
          const EntityHandle *conn;
          CHKERR moab.get_connectivity(eit->first, conn, num_nodes, true);
          if (conn[0] == v)
            return eit->second.dIst;
          else if (conn[1] == v)
            return (eit->second.lEngth - eit->second.dIst);
          else
            THROW_MESSAGE("Data inconsistency");
        };
 
        const auto d = get_dist(eit);
        if (std::get<0>(min_tuple) == 0) {
          min_tuple = get_tuple(e, d, eit->second.lEngth);
        } else if (std::get<1>(min_tuple) > d) {
          min_tuple = get_tuple(e, d, eit->second.lEngth);
        }
      }
    }
 
    const auto geom_dist_vec = get_normal_dits(v);
    const auto geom_tol = norm_2(geom_dist_vec);
    const auto l = std::get<2>(min_tuple);
 
    if (geom_tol < l * geometry_tol) {
      return std::make_pair(get_coords(v), l);
 
    } else {
      const auto &d = edgesToCut.at(std::get<0>(min_tuple));
      return std::make_pair(VectorDouble3(d.rayPoint + d.dIst * d.unitRayDir),
                            l);
    }
  };
 
  auto get_in_range = [](auto v, auto &r) { return (r.find(v) != r.end()); };
 
  auto project_nodes = [&](auto nodes_to_check) {
    if (debug)
      CHKERR SaveData(moab)("nodes_to_check.vtk", nodes_to_check);
 
    auto get_fix_e = [](auto fixed_edges) {
      if (fixed_edges)
        return *fixed_edges;
      else
        return Range();
    };
 
    const auto fix_e = get_fix_e(fixed_edges);
    const auto skin_e = get_adj(unite(get_skin(vOlume), constrainSurface), 1);
    const auto cut_fix = intersect(cutEdges, fix_e);
    const auto cut_skin = intersect(cutEdges, skin_e);
 
    Range corner_n;
    if (corner_nodes)
      corner_n = intersect(*corner_nodes, nodes_to_check);
    auto fixe_n = intersect(get_adj(fix_e, 0), nodes_to_check);
    auto skin_n = intersect(get_adj(skin_e, 0), nodes_to_check);
 
    std::vector<std::pair<EntityHandle, TreeData>> vertices_on_cut_edges;
    vertices_on_cut_edges.reserve(nodes_to_check.size());
 
    auto add_zero_vertex = [&](const EntityHandle v, auto &&new_pos) {
      auto coords = get_coords(v);
      auto ray = new_pos - coords;
      auto l = norm_2(ray);
      TreeData data;
      data.dIst = l;
      if (l > std::numeric_limits<double>::epsilon()) {
        data.unitRayDir = ray / l;
      } else {
        data.dIst = 0;
        data.unitRayDir = ray;
      }
      data.rayPoint = coords;
      return std::make_pair(v, data);
    };
 
    auto intersect_v = [&](const auto v, const auto r) {
      return intersect(r, get_ent_adj(v, 1));
    };
 
    for (auto v : nodes_to_check) {
 
      const auto e = intersect_v(v, cutEdges);
      if (!e.empty()) {
 
        if (get_in_range(v, corner_n)) {
          auto p = get_prj_point(v, e, 0);
          if (norm_2(get_coords(v) - p.first) < close_tol * p.second) {
            vertices_on_cut_edges.push_back(add_zero_vertex(v, get_coords(v)));
            continue;
          }
 
        } else if (get_in_range(v, fixe_n)) {
          const auto b = intersect_v(v, cut_fix);
          if (!b.empty()) {
            auto p = get_prj_point(v, b, geometry_tol);
            if (norm_2(get_coords(v) - p.first) < close_tol * p.second) {
              vertices_on_cut_edges.push_back(add_zero_vertex(v, p.first));
              continue;
            }
 
          } else if (get_in_range(v, skin_n)) {
            const auto b = intersect_v(v, cut_skin);
            if (!b.empty()) {
              auto p = get_prj_point(v, b, geometry_tol);
              if (norm_2(get_coords(v) - p.first) < close_tol * p.second) {
                vertices_on_cut_edges.push_back(add_zero_vertex(v, p.first));
                continue;
              }
            }
 
          }
        }
 
        auto p = get_prj_point(v, e, geometry_tol);
        if (norm_2(get_coords(v) - p.first) < close_tol * p.second) {
          if (get_in_range(v, fixe_n) || get_in_range(v, skin_n))
            vertices_on_cut_edges.push_back(add_zero_vertex(v, get_coords(v)));
          else
            vertices_on_cut_edges.push_back(add_zero_vertex(v, p.first));
          }
        }
        
    }
 
    auto get_distances = [&](auto &data) {
      std::map<EntityHandle, double> dist_map;
      if (!data.empty()) {
        Tag th;
        CHKERR moab.tag_get_handle("DIST_SURFACE_NORMAL_SIGNED", th);
 
        std::vector<EntityHandle> verts;
        verts.reserve(data.size());
        for (auto d : data)
          verts.emplace_back(d.first);
        std::vector<double> distances(verts.size());
        CHKERR moab.tag_get_data(th, &*verts.begin(), verts.size(),
                                 &*distances.begin());
        for (size_t i = 0; i != verts.size(); ++i)
          dist_map[verts[i]] = distances[i];
      }
      return dist_map;
    };
 
    auto dist_map = get_distances(vertices_on_cut_edges);
    if (!dist_map.empty()) {
      auto cmp = [&dist_map](const auto &a, const auto &b) {
        return dist_map[a.first] < dist_map[b.first];
      };
      std::sort(vertices_on_cut_edges.begin(), vertices_on_cut_edges.end(),
                cmp);
    }
 
    return vertices_on_cut_edges;
  };
 
  auto get_min_quality =
      [&](const Range &adj_tets,
          const map<EntityHandle, TreeData> &vertices_on_cut_edges,
          const std::pair<EntityHandle, TreeData> *test_data_ptr) {
        double min_q = 1;
        for (auto t : adj_tets) {
          int num_nodes;
          const EntityHandle *conn;
          CHKERR m_field.get_moab().get_connectivity(t, conn, num_nodes, true);
          VectorDouble12 coords(12);
          CHKERR moab.get_coords(conn, num_nodes, &coords[0]);
 
          auto set_new_coord = [](auto d) {
            return d.rayPoint + d.dIst * d.unitRayDir;
          };
 
          for (auto n : {0, 1, 2, 3}) {
            auto n_coords = getVectorAdaptor(&coords[3 * n], 3);
            if (test_data_ptr) {
              if (test_data_ptr->first == conn[n]) {
                noalias(n_coords) = set_new_coord(test_data_ptr->second);
              }
            }
            auto mit = vertices_on_cut_edges.find(conn[n]);
            if (mit != vertices_on_cut_edges.end()) {
              noalias(n_coords) = set_new_coord(mit->second);
            }
          }
          min_q = std::min(min_q, Tools::volumeLengthQuality(&coords[0]));
        }
        return min_q;
      };
 
  auto get_zero_distance_verts = [&](const auto &&vertices_on_cut_edges) {
    std::vector<EntityHandle> zero_dist_vec;
    zero_dist_vec.reserve(vertices_on_cut_edges.size());
    for (auto t : vertices_on_cut_edges) {
 
      auto adj_tet = intersect(vOlume, get_ent_adj(t.first, 3));
      const double q0 = get_min_quality(adj_tet, verticesOnCutEdges, nullptr);
      const double q = get_min_quality(adj_tet, verticesOnCutEdges, &t);
      if (std::isnormal(q) && (q / q0) > projectEntitiesQualityTrashold) {
        verticesOnCutEdges[t.first] = t.second;
        zero_dist_vec.push_back(t.first);
      }
    }
    return zero_dist_vec;
  };
 
  auto vol_cut_ents = intersect(vOlume, get_adj(cutEdges, 3));
 
  auto get_zero_distant_ents = [&](auto bridge_ents, const int dim,
                                   const int bridge_dim) {
    auto ents =
        intersect(get_adj(bridge_ents, dim), get_adj(vol_cut_ents, dim));
    auto ents_to_remove =
        get_adj(subtract(get_adj(ents, bridge_dim), bridge_ents), dim);
    return subtract(ents, ents_to_remove);
  };
 
  verticesOnCutEdges.clear();
  zeroDistanceVerts.clear();
  zeroDistanceVerts.merge(
      get_range(get_zero_distance_verts(project_nodes(get_adj(cutEdges, 0)))));
  zeroDistanceEnts = subtract(get_zero_distant_ents(zeroDistanceVerts, 2, 0),
                              get_skin(vOlume));
 
  if (debug)
    CHKERR SaveData(moab)("zero_distance_verts.vtk", zeroDistanceVerts);
  if (debug)
    CHKERR SaveData(moab)("zero_distance_ents.vtk", zeroDistanceEnts);
 
  for (auto f : zeroDistanceVerts) {
    auto adj_edges = get_ent_adj(f, 1);
    for (auto e : adj_edges) {
      cutEdges.erase(e);
      edgesToCut.erase(e);
    }
  }
 
  if (debug)
    CHKERR SaveData(moab)("cut_edges_to_cut.vtk", cutEdges);
 
  MoFEMFunctionReturn(0);
}
 
MoFEMErrorCode CutMeshInterface::cutEdgesInMiddle(const BitRefLevel bit,
                                                  Range &cut_vols,
                                                  Range &cut_surf,
                                                  Range &cut_verts,
                                                  const bool debug) {
  CoreInterface &m_field = cOre;
  moab::Interface &moab = m_field.get_moab();
  MeshRefinement *refiner;
  auto ref_ents_ptr = m_field.get_ref_ents();
  CutMeshFunctionBegin;
 
  if (cutEdges.size() != edgesToCut.size())
    SETERRQ(PETSC_COMM_SELF, MOFEM_DATA_INCONSISTENCY, "Data inconsistency");
 
  auto refine_mesh = [&]() {
    MoFEMFunctionBegin;
    CHKERR m_field.getInterface(refiner);
    CHKERR refiner->addVerticesInTheMiddleOfEdges(cutEdges, bit);
    CHKERR refiner->refineTets(vOlume, bit, QUIET, debug);
    MoFEMFunctionReturn(0);
  };
 
  CHKERR refine_mesh();
 
  if (debug)
    if (cutEdges.size() != edgesToCut.size())
      SETERRQ(PETSC_COMM_SELF, MOFEM_DATA_INCONSISTENCY, "Data inconsistency");
 
  cut_vols.clear();
  CHKERR m_field.getInterface<BitRefManager>()->getEntitiesByTypeAndRefLevel(
      bit, BitRefLevel().set(), MBTET, cut_vols);
  cut_surf.clear();
  CHKERR m_field.getInterface<BitRefManager>()->getEntitiesByTypeAndRefLevel(
      bit, bit, MBTRI, cut_surf);
 
  if (debug)
    CHKERR SaveData(moab)("cut_surf_from_bit.vtk", cut_surf);
 
  // Find new vertices on cut edges
  cut_verts.clear();
  cut_verts.merge(zeroDistanceVerts);
 
  for (auto &m : edgesToCut) {
    auto vit = ref_ents_ptr->get<Composite_ParentEnt_And_EntType_mi_tag>().find(
        boost::make_tuple(MBVERTEX, m.first));
    if (vit ==
        ref_ents_ptr->get<Composite_ParentEnt_And_EntType_mi_tag>().end()) {
      SETERRQ(PETSC_COMM_SELF, MOFEM_DATA_INCONSISTENCY,
              "No vertex on cut edges, that make no sense");
    }
    const boost::shared_ptr<RefEntity> &ref_ent = *vit;
    if ((ref_ent->getBitRefLevel() & bit).any()) {
      EntityHandle vert = ref_ent->getEnt();
      cut_verts.insert(vert);
      verticesOnCutEdges[vert] = m.second;
    } else {
      SETERRQ(
          PETSC_COMM_SELF, MOFEM_DATA_INCONSISTENCY,
          "Vertex has wrong bit ref level %s",
          boost::lexical_cast<std::string>(ref_ent->getBitRefLevel()).c_str());
    }
  }
 
  // Add zero distance entities faces
  Range tets_skin;
  Skinner skin(&moab);
  CHKERR skin.find_skin(0, cut_vols, false, tets_skin);
  tets_skin.merge(constrainSurface);
 
  // At that point cut_surf has all newly created faces, now take all
  // nodes on those faces and subtract nodes on cut edges. Faces adjacent to
  // nodes which left are not part of surface.
  cut_surf.merge(zeroDistanceEnts.subset_by_type(MBTRI));
  Range diff_verts;
  CHKERR moab.get_connectivity(cut_surf, diff_verts, true);
  diff_verts = subtract(diff_verts, cut_verts);
 
  Range subtract_faces;
  CHKERR moab.get_adjacencies(diff_verts, 2, false, subtract_faces,
                              moab::Interface::UNION);
  cut_surf = subtract(cut_surf, unite(subtract_faces, tets_skin));
 
  cut_verts.clear();
  CHKERR moab.get_connectivity(cut_surf, cut_verts, true);
 
  // Check non-mainfolds
  auto check_for_non_minfold = [&]() {
    MoFEMFunctionBegin;
    Range surf_edges;
    CHKERR moab.get_adjacencies(cut_surf, 1, false, surf_edges,
                                moab::Interface::UNION);
    for (auto e : surf_edges) {
 
      Range faces;
      CHKERR moab.get_adjacencies(&e, 1, 2, false, faces);
      faces = intersect(faces, cut_surf);
      if (faces.size() > 2) {
 
        bool resolved = false;
 
        // Check for haning node
        Range nodes;
        CHKERR moab.get_connectivity(faces, nodes, true);
        for (auto n : nodes) {
          Range adj_faces;
          CHKERR moab.get_adjacencies(&n, 1, 2, false, adj_faces);
          adj_faces = intersect(adj_faces, cut_surf);
          if (adj_faces.size() == 1) {
            cut_surf.erase(adj_faces[0]);
            resolved = true;
          }
        }
 
        // Check for two edges minfold
        Range adj_edges;
        CHKERR moab.get_adjacencies(faces, 1, false, adj_edges,
                                    moab::Interface::UNION);
        adj_edges = intersect(adj_edges, surf_edges);
        adj_edges.erase(e);
        for (auto other_e : adj_edges) {
          Range other_faces;
          CHKERR moab.get_adjacencies(&other_e, 1, 2, false, other_faces);
          other_faces = intersect(other_faces, cut_surf);
          if (other_faces.size() > 2) {
            other_faces = intersect(other_faces, faces);
            cut_surf = subtract(cut_surf, other_faces);
            resolved = true;
          }
        }
 
        if (!resolved && !debug)
          SETERRQ(PETSC_COMM_WORLD, MOFEM_DATA_INCONSISTENCY,
                  "Non-mainfold surface");
 
        cut_verts.clear();
        CHKERR moab.get_connectivity(cut_surf, cut_verts, true);
      }
    }
    MoFEMFunctionReturn(0);
  };
 
  CHKERR check_for_non_minfold();
 
  if (debug)
    CHKERR SaveData(moab)("cut_surf.vtk", cut_surf);
 
  MoFEMFunctionReturn(0);
}
 
MoFEMErrorCode CutMeshInterface::moveMidNodesOnCutEdges(Tag th) {
  CoreInterface &m_field = cOre;
  moab::Interface &moab = m_field.get_moab();
  CutMeshFunctionBegin;
 
  // Range out_side_vertices;
  for (auto m : verticesOnCutEdges) {
    double dist = m.second.dIst;
    VectorDouble3 new_coors = m.second.rayPoint + dist * m.second.unitRayDir;
    if (th)
      CHKERR moab.tag_set_data(th, &m.first, 1, &new_coors[0]);
    else
      CHKERR moab.set_coords(&m.first, 1, &new_coors[0]);
  }
 
  MoFEMFunctionReturn(0);
}
 
MoFEMErrorCode CutMeshInterface::moveMidNodesOnTrimmedEdges(Tag th) {
  CoreInterface &m_field = cOre;
  moab::Interface &moab = m_field.get_moab();
  CutMeshFunctionBegin;
  for (auto &v : verticesOnTrimEdges) {
    double dist = v.second.dIst;
    VectorDouble3 new_coors = v.second.rayPoint + dist * v.second.unitRayDir;
    if (th)
      CHKERR moab.tag_set_data(th, &v.first, 1, &new_coors[0]);
    else
      CHKERR moab.set_coords(&v.first, 1, &new_coors[0]);
  }
  MoFEMFunctionReturn(0);
}
 
MoFEMErrorCode CutMeshInterface::findEdgesToTrim(Range *fixed_edges,
                                                 Range *corner_nodes, Tag th,
                                                 const double tol_trim_close,
                                                 const bool debug) {
  CoreInterface &m_field = cOre;
  moab::Interface &moab = m_field.get_moab();
  CutMeshFunctionBegin;
 
  // takes body skin
  Skinner skin(&moab);
  Range tets_skin;
  CHKERR skin.find_skin(0, cutNewVolumes, false, tets_skin);
  tets_skin.merge(constrainSurface);
 
  // vertices on the skin
  Range tets_skin_verts;
  CHKERR moab.get_connectivity(tets_skin, tets_skin_verts, true);
  // edges on the skin
  Range tets_skin_edges;
  CHKERR moab.get_adjacencies(tets_skin, 1, false, tets_skin_edges,
                              moab::Interface::UNION);
 
  // get edges on new surface
  Range cut_surface_edges;
  CHKERR moab.get_adjacencies(cutNewSurfaces, 1, false, cut_surface_edges,
                              moab::Interface::UNION);
  Range cut_surface_verts;
  CHKERR moab.get_connectivity(cutNewSurfaces, cut_surface_verts, true);
 
  Range corners;
  if (corner_nodes)
    corners = *corner_nodes;
 
  Range fix_edges;
  if (fixed_edges)
    fix_edges = *fixed_edges;
 
  Range fixed_edges_verts;
  if (fixed_edges)
    CHKERR moab.get_connectivity(*fixed_edges, fixed_edges_verts, true);
 
  Range surface_skin;
  if (fRont.empty())
    CHKERR skin.find_skin(0, sUrface, false, surface_skin);
  else
    surface_skin = fRont;
 
  auto get_point_coords = [&](EntityHandle v) {
    VectorDouble3 point(3);
    if (th)
      CHKERR moab.tag_get_data(th, &v, 1, &point[0]);
    else
      CHKERR moab.get_coords(&v, 1, &point[0]);
    return point;
  };
 
  struct VertMap {
    const double d;
    const EntityHandle v;
    const EntityHandle e;
    VertMap(const double d, const EntityHandle v, const EntityHandle e)
        : d(d), v(v), e(e) {}
  };
 
  typedef multi_index_container<
      VertMap,
      indexed_by<
          ordered_non_unique<member<VertMap, const double, &VertMap::d>>,
          ordered_non_unique<member<VertMap, const EntityHandle, &VertMap::v>>,
          ordered_non_unique<member<VertMap, const EntityHandle, &VertMap::e>>
 
          >>
      VertMapMultiIndex;
 
  VertMapMultiIndex verts_map;
 
  auto add_vert = [&](const EntityHandle v, const EntityHandle e,
                      const double dist) {
    verts_map.insert(VertMap(dist, v, e));
  };
 
  // clear data ranges
  trimEdges.clear();
  edgesToTrim.clear();
  verticesOnTrimEdges.clear();
  trimNewVertices.clear();
 
  auto cut_this_edge = [&](const EntityHandle e, const double length, auto &ray,
                           auto &ray_point) {
    trimEdges.insert(e);
    edgesToTrim[e].dIst = 1;
    edgesToTrim[e].lEngth = length;
    edgesToTrim[e].unitRayDir.resize(3, false);
    edgesToTrim[e].rayPoint.resize(3, false);
    for (int ii = 0; ii != 3; ++ii)
      edgesToTrim[e].unitRayDir[ii] = ray(ii);
    for (int ii = 0; ii != 3; ++ii)
      edgesToTrim[e].rayPoint[ii] = ray_point(ii);
  };
 
  FTensor::Index<'i', 3> i;
  FTensor::Index<'j', 3> j;
  FTensor::Index<'k', 3> k;
 
  int num_nodes;
 
  auto get_tag_data = [&](auto th, auto conn) {
    FTensor::Tensor1<double, 3> t;
    CHKERR moab.tag_get_data(th, &conn, 1, &t(0));
    return t;
  };
 
  double max_edge_length = 0;
 
  /// Project front entities on on the cut surface plane
  if (!fRont.empty()) {
    // Calculate distances
    treeSurfPtr = boost::shared_ptr<OrientedBoxTreeTool>(
        new OrientedBoxTreeTool(&moab, "ROOTSETSURF", true));
    CHKERR treeSurfPtr->build(cutNewSurfaces, rootSetSurf);
 
    for (auto s : surface_skin) {
 
      auto project_on_surface = [&](auto &t) {
        FTensor::Tensor1<double, 3> t_p;
 
        EntityHandle facets_out;
        CHKERR treeSurfPtr->closest_to_location(&t(0), rootSetSurf, &t_p(0),
                                                facets_out);
 
        FTensor::Tensor1<double, 3> t_normal;
        CHKERR m_field.getInterface<Tools>()->getTriNormal(facets_out,
                                                           &t_normal(0));
        t_normal(i) /= sqrt(t_normal(i) * t_normal(i));
        const double dot = t_normal(i) * (t_p(i) - t(i));
        t_p(i) = t(i) + dot * t_normal(i);
 
        return t_p;
      };
 
      const EntityHandle *conn;
      CHKERR moab.get_connectivity(s, conn, num_nodes, true);
 
      VectorDouble6 coords_front(6);
      CHKERR moab.get_coords(conn, num_nodes, &coords_front[0]);
 
      FTensor::Tensor1<double *, 3> t_f0(&coords_front[0], &coords_front[1],
                                         &coords_front[2]);
      FTensor::Tensor1<double *, 3> t_f1(&coords_front[3], &coords_front[4],
                                         &coords_front[5]);
 
      auto t_p_f0 = project_on_surface(t_f0);
      auto t_p_f1 = project_on_surface(t_f1);
 
      CHKERR moab.set_coords(&conn[0], 1, &t_p_f0(0));
      CHKERR moab.set_coords(&conn[1], 1, &t_p_f1(0));
    }
  }
 
  if (debug)
    CHKERR SaveData(moab)("surface_skin_to_trim.vtk", surface_skin);
 
  CHKERR createFrontLevelSets(cutNewSurfaces, th, QUIET, debug);
  Tag th_dist_front_vec;
  CHKERR moab.tag_get_handle("DIST_FRONT_VECTOR", th_dist_front_vec);
 
  // iterate over edges on cut surface
  for (auto e : cut_surface_edges) {
 
    auto get_conn_edge = [&moab](auto e) {
      // Get edge connectivity and coords
      const EntityHandle *conn_edge;
      int num_nodes;
      CHKERR moab.get_connectivity(e, conn_edge, num_nodes, true);
      return conn_edge;
    };
 
    auto get_coords_edge = [&moab](auto conn_edge) {
      std::array<double, 6> coords_edge;
      CHKERR moab.get_coords(conn_edge, 2, coords_edge.data());
      return coords_edge;
    };
 
    auto get_ftensor_coords = [](const double *ptr) {
      return FTensor::Tensor1<double, 3>{ptr[0], ptr[1], ptr[2]};
    };
 
    auto conn_edge = get_conn_edge(e);
    auto coords_edge = get_coords_edge(conn_edge);
 
    auto t_dist0 = get_tag_data(th_dist_front_vec, conn_edge[0]);
    auto t_dist1 = get_tag_data(th_dist_front_vec, conn_edge[1]);
    auto t_e0 = get_ftensor_coords(&coords_edge[0]);
    auto t_e1 = get_ftensor_coords(&coords_edge[3]);
 
    FTensor::Tensor1<double, 3> t_edge_delta;
    t_edge_delta(i) = t_e1(i) - t_e0(i);
    const double edge_length2 = t_edge_delta(i) * t_edge_delta(i);
    const double edge_length = sqrt(edge_length2);
    if (edge_length == 0)
      SETERRQ(PETSC_COMM_SELF, MOFEM_DATA_INCONSISTENCY, "Zero edge length");
 
    auto add_edge = [&](auto t_cut) {
      FTensor::Tensor1<double, 3> t_ray;
      if (t_cut < 0.5) {
        t_ray(i) = t_cut * t_edge_delta(i);
        add_vert(conn_edge[0], e, fabs(t_cut));
        add_vert(conn_edge[1], e, fabs(t_cut - 1));
        cut_this_edge(e, edge_length, t_ray, t_e0);
      } else {
        FTensor::Tensor1<double, 3> t_edge_point;
        t_edge_point(i) = t_e0(i) + t_cut * t_edge_delta(i);
        t_ray(i) = t_edge_point(i) - t_e1(i);
        add_vert(conn_edge[0], e, fabs(t_cut));
        add_vert(conn_edge[1], e, fabs(t_cut - 1));
        cut_this_edge(e, edge_length, t_ray, t_e1);
      }
      max_edge_length = std::max(max_edge_length, edge_length);
    };
 
    auto trim_cross_edges = [&]() {
      if (std::min(t_dist0(i) * t_dist0(i), t_dist1(i) * t_dist1(i)) <
          edge_length2) {
 
        auto make_pair = [&](const double d, const double te) {
          return std::make_pair(d, te);
        };
 
        auto min_pair = make_pair(-1, -1);
 
        for (auto f : surface_skin) {
 
          auto conn_front = get_conn_edge(f);
          auto coords_front = get_coords_edge(conn_front);
          auto t_f0 = get_ftensor_coords(&coords_front[0]);
          auto t_f1 = get_ftensor_coords(&coords_front[3]);
 
          double te;
          double tf;
 
          auto res = Tools::minDistanceFromSegments(
              &t_e0(0), &t_e1(0), &t_f0(0), &t_f1(0), &te, &tf);
 
          if (res != Tools::NO_SOLUTION) {
 
            auto check = [](auto v) {
              return (v > -std::numeric_limits<double>::epsilon() &&
                      (v - 1) < std::numeric_limits<double>::epsilon());
            };
 
            if (check(te) && check(tf)) {
 
              FTensor::Tensor1<double, 3> t_delta, t_cross;
              t_delta(i) = (t_e0(i) + te * t_edge_delta(i)) -
                           (t_f0(0) + tf * (t_f1(i) - t_f0(i)));
 
              t_delta(i) /= edge_length;
 
              const double dot = t_delta(i) * t_delta(i);
 
              if (min_pair.first < 0 || min_pair.first > dot) {
 
                if (dot < tol_trim_close * tol_trim_close)
                  min_pair = make_pair(dot, te);
              }
            }
          }
        }
 
        if (min_pair.first > -std::numeric_limits<double>::epsilon()) {
          add_edge(min_pair.second);
          return true;
        }
      }
 
      return false;
    };
 
    if (!trim_cross_edges()) {
 
      const double dot = t_dist0(i) * t_dist1(i);
      const double dot_direction0 = t_dist0(i) * t_edge_delta(i);
      const double dot_direction1 = t_dist1(i) * t_edge_delta(i);
 
      if (dot < std::numeric_limits<double>::epsilon() &&
          dot_direction0 > -std::numeric_limits<double>::epsilon() &&
          dot_direction1 < std::numeric_limits<double>::epsilon()) {
 
        const double s0 = t_dist0(i) * t_edge_delta(i) / edge_length;
        const double s1 = t_dist1(i) * t_edge_delta(i) / edge_length;
        const double t_cut = s0 / (s0 - s1);
 
        add_edge(t_cut);
      }
    }
  }
 
  if (debug)
    CHKERR SaveData(moab)("edges_potentially_to_trim.vtk", cut_surface_edges);
 
  if (debug)
    CHKERR SaveData(moab)("edges_selected_to_trim.vtk", trimEdges);
 
  auto get_quality_change = [&](const Range &adj_tets, const EntityHandle &v,
                                const VectorDouble3 &new_pos) {
    double q0 = 1;
    CHKERR m_field.getInterface<Tools>()->minTetsQuality(adj_tets, q0, th);
 
    double min_q = 1;
    for (auto t : adj_tets) {
      int num_nodes;
      const EntityHandle *conn;
      CHKERR m_field.get_moab().get_connectivity(t, conn, num_nodes, true);
      VectorDouble12 coords(12);
      if (th)
        CHKERR moab.tag_get_data(th, conn, num_nodes, &coords[0]);
      else
        CHKERR moab.get_coords(conn, num_nodes, &coords[0]);
 
      for (int n = 0; n != 4; ++n) {
        auto n_coords = getVectorAdaptor(&coords[3 * n], 3);
        if (conn[n] == v) {
          noalias(n_coords) = new_pos;
        } else {
          auto m = verticesOnTrimEdges.find(conn[n]);
          if (m != verticesOnTrimEdges.end())
            noalias(n_coords) =
                m->second.rayPoint + m->second.dIst * m->second.unitRayDir;
        }
      }
 
      const double q = Tools::volumeLengthQuality(&coords[0]);
      if (!std::isnormal(q)) {
        min_q = -2;
        break;
      }
      min_q = std::min(min_q, q);
    }
    return min_q / q0;
  };
 
  Range checked_verts;
  auto add_trim_vert = [&](const EntityHandle v, const EntityHandle e) {
    if (!(trimNewVertices.find(v) != trimNewVertices.end())) {
      auto &r = edgesToTrim.at(e);
      VectorDouble3 ray_point = get_point_coords(v);
      VectorDouble3 new_pos = r.rayPoint + r.dIst * r.unitRayDir;
      VectorDouble3 unit_ray_dir = ray_point - new_pos;
      Range adj_tets;
      CHKERR moab.get_adjacencies(&v, 1, 3, false, adj_tets);
      adj_tets = intersect(adj_tets, cutNewVolumes);
      double q = get_quality_change(adj_tets, v, new_pos);
      if (q > projectEntitiesQualityTrashold) {
        VectorDouble3 ray_dir = new_pos - ray_point;
        double dist = norm_2(ray_dir);
        verticesOnTrimEdges[v].dIst = 1;
        verticesOnTrimEdges[v].lEngth = dist;
        verticesOnTrimEdges[v].unitRayDir = ray_dir;
        verticesOnTrimEdges[v].rayPoint = ray_point;
        trimNewVertices.insert(v);
      }
      checked_verts.insert(v);
    }
  };
 
  auto add_no_move_trim = [&](const EntityHandle v, const EntityHandle e) {
    if (!(trimNewVertices.find(v) != trimNewVertices.end())) {
      auto &m = edgesToTrim.at(e);
      verticesOnTrimEdges[v] = m;
      verticesOnTrimEdges[v].rayPoint = get_point_coords(v);
      verticesOnTrimEdges[v].lEngth = 0;
      verticesOnTrimEdges[v].dIst = 0;
      trimNewVertices.insert(v);
      checked_verts.insert(v);
    }
  };
 
  // Iterate over all vertives close to surface front and check if those can
  // be moved
 
  // filer nodes which distance is in given tolerance
  auto hi = verts_map.get<0>().upper_bound(tol_trim_close);
  verts_map.get<0>().erase(hi, verts_map.end());
 
  auto remove_verts = [&](Range nodes) {
    for (auto n : nodes) {
      auto r = verts_map.get<1>().equal_range(n);
      verts_map.get<1>().erase(r.first, r.second);
    }
  };
 
  auto trim_verts = [&](const Range verts, const bool move) {
    VertMapMultiIndex verts_map_tmp;
    for (auto p = corners.pair_begin(); p != corners.pair_end(); ++p) {
      auto lo = verts_map.get<1>().lower_bound(p->first);
      auto hi = verts_map.get<1>().upper_bound(p->second);
      verts_map_tmp.insert(lo, hi);
    }
    if (move) {
      for (auto &m : verts_map_tmp.get<0>())
        add_trim_vert(m.v, m.e);
    } else {
      for (auto &m : verts_map_tmp.get<0>())
        add_no_move_trim(m.v, m.e);
    }
  };
 
  auto trim_edges = [&](const Range ents, const bool move) {
    VertMapMultiIndex verts_map_tmp;
    for (auto p = ents.pair_begin(); p != ents.pair_end(); ++p) {
      auto lo = verts_map.get<2>().lower_bound(p->first);
      auto hi = verts_map.get<2>().upper_bound(p->second);
      verts_map_tmp.insert(lo, hi);
      verts_map.get<2>().erase(lo, hi);
    }
    if (move) {
      for (auto &m : verts_map_tmp.get<0>())
        add_trim_vert(m.v, m.e);
    } else {
      for (auto &m : verts_map_tmp.get<0>())
        add_no_move_trim(m.v, m.e);
    }
  };
 
  auto intersect_self = [&](Range &a, const Range b) { a = intersect(a, b); };
 
  map<std::string, Range> range_maps;
 
  // Edges on surface skin
  CHKERR skin.find_skin(0, cutNewSurfaces, false, range_maps["surface_skin"]);
  // Edges as trimmed
  intersect_self(range_maps["surface_skin"], trimEdges);
  // Edges are on fixed edges
  range_maps["fixed_edges_on_surface_skin"] =
      intersect(range_maps["surface_skin"], fix_edges);
 
  // Edges adjacent to fixed edges
  CHKERR moab.get_adjacencies(fixed_edges_verts, 1, false,
                              range_maps["fixed_edges_verts_edges"],
                              moab::Interface::UNION);
  intersect_self(range_maps["fixed_edges_verts_edges"], trimEdges);
 
  CHKERR moab.get_connectivity(
      range_maps["fixed_edges_verts_edges"],
      range_maps["fixed_edges_verts_edges_verts_on_the_skin"], false);
  intersect_self(range_maps["fixed_edges_verts_edges_verts_on_the_skin"],
                 tets_skin_verts);
 
  // Do not move nodes at the corners
  trim_verts(corners, false);
  remove_verts(corners);
 
  // Trim edges on the body skin move
  trim_edges(range_maps["fixed_edges_on_surface_skin"], true);
  remove_verts(range_maps["fixed_edges_on_surface_skin_verts"]);
 
  // Trim edges nodes on the skin but edge not on the skin do not
  trim_verts(range_maps["fixed_edges_verts_edges_verts_on_the_skin"], false);
  remove_verts(range_maps["fixed_edges_verts_edges_verts_on_the_skin"]);
 
  // Trim edges on the cut skin move
  trim_edges(range_maps["surface_skin"], true);
  trim_verts(tets_skin_verts, false);
  remove_verts(tets_skin_verts);
 
  for (auto &m : verts_map.get<0>())
    add_trim_vert(m.v, m.e);
 
  for (auto m : verticesOnTrimEdges) {
    EntityHandle v = m.first;
    Range adj;
    CHKERR moab.get_adjacencies(&v, 1, 1, false, adj);
    for (auto e : adj) {
      edgesToTrim.erase(e);
      trimEdges.erase(e);
    }
  }
 
  if (debug)
    if (!trimNewVertices.empty())
      CHKERR SaveData(moab)("trim_close_vertices.vtk", trimNewVertices);
 
  if (debug)
    if (!trimEdges.empty())
      CHKERR SaveData(moab)("trim_edges.vtk", trimEdges);
 
  MoFEMFunctionReturn(0);
}
 
MoFEMErrorCode CutMeshInterface::trimEdgesInTheMiddle(const BitRefLevel bit,
                                                      const bool debug) {
  CoreInterface &m_field = cOre;
  moab::Interface &moab = m_field.get_moab();
  MeshRefinement *refiner;
  auto ref_ents_ptr = m_field.get_ref_ents();
  CutMeshFunctionBegin;
 
  CHKERR m_field.getInterface(refiner);
  CHKERR refiner->addVerticesInTheMiddleOfEdges(trimEdges, bit);
  CHKERR refiner->refineTets(cutNewVolumes, bit, QUIET, debug);
 
  trimNewVolumes.clear();
  CHKERR m_field.getInterface<BitRefManager>()->getEntitiesByTypeAndRefLevel(
      bit, BitRefLevel().set(), MBTET, trimNewVolumes);
 
  for (map<EntityHandle, TreeData>::iterator mit = edgesToTrim.begin();
       mit != edgesToTrim.end(); mit++) {
    auto vit = ref_ents_ptr->get<Composite_ParentEnt_And_EntType_mi_tag>().find(
        boost::make_tuple(MBVERTEX, mit->first));
    if (vit ==
        ref_ents_ptr->get<Composite_ParentEnt_And_EntType_mi_tag>().end())
      SETERRQ(PETSC_COMM_SELF, MOFEM_DATA_INCONSISTENCY,
              "No vertex on trim edges, that make no sense");
 
    const boost::shared_ptr<RefEntity> &ref_ent = *vit;
    if ((ref_ent->getBitRefLevel() & bit).any()) {
      EntityHandle vert = ref_ent->getEnt();
      trimNewVertices.insert(vert);
      verticesOnTrimEdges[vert] = mit->second;
    }
  }
 
  // Get faces which are trimmed
  trimNewSurfaces.clear();
  CHKERR m_field.getInterface<BitRefManager>()->getEntitiesByTypeAndRefLevel(
      bit, bit, MBTRI, trimNewSurfaces);
 
  Range trim_new_surfaces_nodes;
  CHKERR moab.get_connectivity(trimNewSurfaces, trim_new_surfaces_nodes, true);
  trim_new_surfaces_nodes = subtract(trim_new_surfaces_nodes, trimNewVertices);
  trim_new_surfaces_nodes = subtract(trim_new_surfaces_nodes, cutNewVertices);
  Range faces_not_on_surface;
  CHKERR moab.get_adjacencies(trim_new_surfaces_nodes, 2, false,
                              faces_not_on_surface, moab::Interface::UNION);
  trimNewSurfaces = subtract(trimNewSurfaces, faces_not_on_surface);
 
  // Get surfaces which are not trimmed and add them to surface
  Range all_surfaces_on_bit_level;
  CHKERR m_field.getInterface<BitRefManager>()->getEntitiesByTypeAndRefLevel(
      bit, BitRefLevel().set(), MBTRI, all_surfaces_on_bit_level);
  all_surfaces_on_bit_level =
      intersect(all_surfaces_on_bit_level, cutNewSurfaces);
 
  trimNewSurfaces = unite(trimNewSurfaces, all_surfaces_on_bit_level);
 
  MoFEMFunctionReturn(0);
}
 
MoFEMErrorCode CutMeshInterface::trimSurface(Range *fixed_edges,
                                             Range *corner_nodes,
                                             const double tol, Tag th,
                                             const bool debug) {
  CoreInterface &m_field = cOre;
  moab::Interface &moab = m_field.get_moab();
  Skinner skin(&moab);
 
  auto get_adj = [&moab](const Range r, const int dim) {
    Range a;
    if (dim)
      CHKERR moab.get_adjacencies(r, dim, false, a, moab::Interface::UNION);
    else
      CHKERR moab.get_connectivity(r, a, true);
    return a;
  };
 
  auto get_skin = [&skin](const auto r) {
    Range s;
    CHKERR skin.find_skin(0, r, false, s);
    return s;
  };
 
  CutMeshFunctionBegin;
 
  auto trim_tets_skin = get_skin(trimNewVolumes);
  auto trim_tets_skin_edges = get_adj(trim_tets_skin, 1);
  auto trim_surface_edges = get_adj(trimNewSurfaces, 1);
 
  auto contarain_edges =
      intersect(trim_surface_edges, get_adj(constrainSurface, 1));
  if (fixed_edges)
    contarain_edges.merge(
        intersect(fixed_edges->subset_by_type(MBEDGE), trim_surface_edges));
 
  Range barrier_vertices(trimNewVertices);
  if (corner_nodes) {
    // Add nodes which re adjacent to corner nodes
    barrier_vertices.merge(get_adj(
        intersect(get_adj(intersect(*corner_nodes, barrier_vertices), 2),
                  trimNewSurfaces),
        0));
  }
 
  auto get_nodes_with_one_node_on_fixed_edge_other_not = [&]() {
    const auto fixed_edges_on_surface =
        intersect(*fixed_edges, trim_surface_edges);
    const auto skin_fixed_edges_on_surface = get_skin(fixed_edges_on_surface);
    const auto barrier_nodes = subtract(skin_fixed_edges_on_surface,
                                  get_adj(get_skin(trimNewSurfaces), 0));
    return barrier_nodes;
  };
 
  if (fixed_edges)
    barrier_vertices.merge(get_nodes_with_one_node_on_fixed_edge_other_not());
 
  auto add_close_surface_barrier = [&]() {
    MoFEMFunctionBegin;
 
    // Ten algorytm dedykuje destylarni Bowmore. Jeżeli coś pójdzie nie tak, coś
    // pęknie inaczej niż trzeba, to pełną odpowiedzialność ponosi Beam Suntory
    // UK Ltd.
 
    CHKERR buildTree();
 
    auto test_edges =
        subtract(trim_surface_edges, get_adj(constrainSurface, 1));
    if (fixed_edges)
      test_edges = subtract(test_edges, *fixed_edges);
    auto trim_surface_nodes = get_adj(test_edges, 0);
    trim_surface_nodes = subtract(trim_surface_nodes, barrier_vertices);
    if (fixed_edges)
      trim_surface_nodes =
          subtract(trim_surface_nodes, get_adj(*fixed_edges, 0));
 
    Range trim_skin;
    trim_skin.merge(contarain_edges);
    if (fRont.empty())
      trim_skin.merge(get_skin(sUrface));
    else
      trim_skin.merge(fRont);
    if (fixed_edges)
      trim_skin.merge(intersect(*fixed_edges, trim_surface_edges));
 
    if (debug && !trim_skin.empty())
      CHKERR SaveData(m_field.get_moab())("trim_skin.vtk", trim_skin);
 
    VectorDouble coords(3 * trim_surface_nodes.size());
    if (th)
      CHKERR moab.tag_get_data(th, trim_surface_nodes, &*coords.begin());
    else
      CHKERR moab.get_coords(trim_surface_nodes, &*coords.begin());
 
    if (!trim_skin.empty()) {
 
      std::vector<double> min_distances(trim_surface_nodes.size(), -1);
      CHKERR cOre.getInterface<Tools>()->findMinDistanceFromTheEdges(
          &*coords.begin(), trim_surface_nodes.size(), trim_skin,
          &*min_distances.begin());
 
      auto coords_ptr = &*coords.begin();
      auto min_dist = &*min_distances.begin();
 
      std::vector<EntityHandle> add_nodes;
      add_nodes.reserve(trim_surface_nodes.size());
 
      for (auto n : trim_surface_nodes) {
 
        if ((*min_dist) > std::numeric_limits<double>::epsilon()) {
          VectorDouble3 point_out(3);
 
          EntityHandle facets_out;
          CHKERR treeSurfPtr->closest_to_location(coords_ptr, rootSetSurf,
                                                  &point_out[0], facets_out);
 
          VectorDouble3 delta = point_out - getVectorAdaptor(coords_ptr, 3);
          VectorDouble3 normal(3);
          CHKERR m_field.getInterface<Tools>()->getTriNormal(facets_out,
                                                             &normal[0]);
 
          normal /= norm_2(normal);
          delta -= inner_prod(normal, delta) * normal;
 
          double dist = norm_2(delta);
          if (dist < tol * (*min_dist))
            add_nodes.emplace_back(n);
        }
 
        coords_ptr += 3;
        min_dist += 1;
      }
 
      barrier_vertices.insert_list(add_nodes.begin(), add_nodes.end());
    }
 
    MoFEMFunctionReturn(0);
  };
 
  auto remove_faces_on_skin = [&]() {
    MoFEMFunctionBegin;
    Range skin_faces = intersect(trimNewSurfaces, trim_tets_skin);
    if (!skin_faces.empty()) {
      barrier_vertices.merge(get_adj(skin_faces, 0));
      for (auto f : skin_faces)
        trimNewSurfaces.erase(f);
    }
    MoFEMFunctionReturn(0);
  };
 
  auto get_trim_free_edges = [&]() {
    // get current surface skin
    Range trim_surf_skin;
    CHKERR skin.find_skin(0, trimNewSurfaces, false, trim_surf_skin);
    trim_surf_skin = subtract(trim_surf_skin, trim_tets_skin_edges);
 
    Range trim_surf_skin_verts;
    CHKERR moab.get_connectivity(trim_surf_skin, trim_surf_skin_verts, true);
    for (auto e : barrier_vertices)
      trim_surf_skin_verts.erase(e);
 
    Range free_edges;
    CHKERR moab.get_adjacencies(trim_surf_skin_verts, 1, false, free_edges,
                                moab::Interface::UNION);
    free_edges =
        subtract(intersect(free_edges, trim_surf_skin), contarain_edges);
 
    return free_edges;
  };
 
  CHKERR remove_faces_on_skin();
  CHKERR add_close_surface_barrier();
 
  if (debug && !barrier_vertices.empty())
    CHKERR SaveData(m_field.get_moab())("barrier_vertices.vtk",
                                        barrier_vertices);
 
  int nn = 0;
  Range out_edges;
  while (!(out_edges = get_trim_free_edges()).empty()) {
 
    if (debug && !trimNewSurfaces.empty())
      CHKERR SaveData(m_field.get_moab())(
          "trimNewSurfaces_" + boost::lexical_cast<std::string>(nn) + ".vtk",
          trimNewSurfaces);
 
    if (debug && !out_edges.empty())
      CHKERR SaveData(m_field.get_moab())(
          "trimNewSurfacesOutsideVerts_" +
              boost::lexical_cast<std::string>(nn) + ".vtk",
          out_edges);
 
    Range outside_faces;
    CHKERR moab.get_adjacencies(out_edges, 2, false, outside_faces,
                                moab::Interface::UNION);
    trimNewSurfaces = subtract(trimNewSurfaces, outside_faces);
    ++nn;
  }
 
  if (debug && !trimNewSurfaces.empty())
    CHKERR SaveData(m_field.get_moab())(
        "trimNewSurfaces_" + boost::lexical_cast<std::string>(nn) + ".vtk",
        trimNewSurfaces);
 
  MoFEMFunctionReturn(0);
}
 
MoFEMErrorCode
CutMeshInterface::removePathologicalFrontTris(const BitRefLevel split_bit,
                                              Range &ents) {
  CoreInterface &m_field = cOre;
  moab::Interface &moab = m_field.get_moab();
  PrismInterface *interface;
  CutMeshFunctionBegin;
  CHKERR m_field.getInterface(interface);
  // Remove tris on surface front
  {
    Range front_tris;
    EntityHandle meshset;
    CHKERR moab.create_meshset(MESHSET_SET, meshset);
    CHKERR moab.add_entities(meshset, ents);
    CHKERR interface->findFacesWithThreeNodesOnInternalSurfaceSkin(
        meshset, split_bit, true, front_tris);
    CHKERR moab.delete_entities(&meshset, 1);
    ents = subtract(ents, front_tris);
  }
  // Remove entities on skin
  Range tets;
  CHKERR m_field.getInterface<BitRefManager>()->getEntitiesByTypeAndRefLevel(
      split_bit, BitRefLevel().set(), MBTET, tets);
  // Remove entities on skin
  Skinner skin(&moab);
  Range tets_skin;
  CHKERR skin.find_skin(0, tets, false, tets_skin);
  ents = subtract(ents, tets_skin);
 
  MoFEMFunctionReturn(0);
}
 
MoFEMErrorCode CutMeshInterface::splitSides(const BitRefLevel split_bit,
                                            const BitRefLevel bit,
                                            const Range &ents, Tag th) {
  CoreInterface &m_field = cOre;
  moab::Interface &moab = m_field.get_moab();
  PrismInterface *interface;
  CutMeshFunctionBegin;
  CHKERR m_field.getInterface(interface);
  EntityHandle meshset_volume;
  CHKERR moab.create_meshset(MESHSET_SET, meshset_volume);
  CHKERR m_field.getInterface<BitRefManager>()->getEntitiesByTypeAndRefLevel(
      split_bit, BitRefLevel().set(), MBTET, meshset_volume);
  EntityHandle meshset_surface;
  CHKERR moab.create_meshset(MESHSET_SET, meshset_surface);
  CHKERR moab.add_entities(meshset_surface, ents);
  CHKERR interface->getSides(meshset_surface, split_bit, true);
  CHKERR interface->splitSides(meshset_volume, bit, meshset_surface, true,
                               true);
  CHKERR moab.delete_entities(&meshset_volume, 1);
  CHKERR moab.delete_entities(&meshset_surface, 1);
  if (th) {
    Range prisms;
    ierr = m_field.getInterface<BitRefManager>()->getEntitiesByTypeAndRefLevel(
        bit, BitRefLevel().set(), MBPRISM, prisms);
    for (Range::iterator pit = prisms.begin(); pit != prisms.end(); pit++) {
      int num_nodes;
      const EntityHandle *conn;
      CHKERR moab.get_connectivity(*pit, conn, num_nodes, true);
      MatrixDouble data(3, 3);
      CHKERR moab.tag_get_data(th, conn, 3, &data(0, 0));
      CHKERR moab.tag_set_data(th, &conn[3], 3, &data(0, 0));
    }
  }
  MoFEMFunctionReturn(0);
}
 
MoFEMErrorCode CutMeshInterface::mergeBadEdges(
    const int fraction_level, const Range &tets, const Range &surface,
    const Range &fixed_edges, const Range &corner_nodes, Range &edges_to_merge,
    Range &out_tets, Range &new_surf, Tag th, const bool update_meshsets,
    const BitRefLevel *bit_ptr, const bool debug) {
  CoreInterface &m_field = cOre;
  moab::Interface &moab = m_field.get_moab();
  CutMeshFunctionBegin;
 
  /**
   * \brief Merge nodes
   */
  struct MergeNodes {
    CoreInterface &mField;
    const bool onlyIfImproveQuality;
    Tag tH;
    bool updateMehsets;
 
    MergeNodes(CoreInterface &m_field, const bool only_if_improve_quality,
               Tag th, bool update_mehsets)
        : mField(m_field), onlyIfImproveQuality(only_if_improve_quality),
          tH(th), updateMehsets(update_mehsets) {
      mField.getInterface(nodeMergerPtr);
    }
    NodeMergerInterface *nodeMergerPtr;
    MoFEMErrorCode mergeNodes(int line_search, EntityHandle father,
                              EntityHandle mother, Range &proc_tets,
                              bool add_child = true) {
      moab::Interface &moab = mField.get_moab();
      MoFEMFunctionBegin;
      const EntityHandle conn[] = {father, mother};
      Range vert_tets;
      CHKERR moab.get_adjacencies(conn, 2, 3, false, vert_tets,
                                  moab::Interface::UNION);
      vert_tets = intersect(vert_tets, proc_tets);
      Range out_tets;
      CHKERR nodeMergerPtr->mergeNodes(father, mother, out_tets, &vert_tets,
                                       onlyIfImproveQuality, 0, line_search,
                                       tH);
 
      if (add_child && nodeMergerPtr->getSuccessMerge()) {
 
        Range::iterator lo, hi = proc_tets.begin();
        for (auto pt = vert_tets.pair_begin(); pt != vert_tets.pair_end();
             ++pt) {
          lo = proc_tets.lower_bound(hi, proc_tets.end(), pt->first);
          if (lo != proc_tets.end()) {
            hi = proc_tets.upper_bound(lo, proc_tets.end(), pt->second);
            proc_tets.erase(lo, hi);
          } else
            break;
        }
        proc_tets.merge(out_tets);
 
        auto &parent_child_map = nodeMergerPtr->getParentChildMap();
 
        struct ChangeChild {
          EntityHandle child;
          ChangeChild(const EntityHandle child) : child(child) {}
          void operator()(NodeMergerInterface::ParentChild &p) {
            p.cHild = child;
          }
        };
 
        std::vector<decltype(parentsChildMap.get<0>().begin())> it_vec;
        it_vec.reserve(parentsChildMap.size());
 
        for (auto &p : parent_child_map) {
 
          it_vec.clear();
          for (auto it = parentsChildMap.get<0>().equal_range(p.pArent);
               it.first != it.second; ++it.first)
            it_vec.emplace_back(it.first);
 
          for (auto it = parentsChildMap.get<1>().equal_range(p.pArent);
               it.first != it.second; ++it.first)
            it_vec.emplace_back(parentsChildMap.project<0>(it.first));
 
          for (auto &it : it_vec)
            parentsChildMap.modify(it, ChangeChild(p.cHild));
        }
 
        parentsChildMap.insert(parent_child_map.begin(),
                               parent_child_map.end());
      }
      MoFEMFunctionReturn(0);
    }
 
    MoFEMErrorCode updateRangeByChilds(Range &new_surf, Range &edges_to_merge,
                                       Range &not_merged_edges,
                                       bool add_child) {
      moab::Interface &moab = mField.get_moab();
      CutMeshFunctionBegin;
      if (add_child) {
 
        std::vector<EntityHandle> parents_ents_vec(parentsChildMap.size());
        for (auto &it : parentsChildMap)
          parents_ents_vec.emplace_back(it.pArent);
        Range parent_ents;
        parent_ents.insert_list(parents_ents_vec.begin(),
                                parents_ents_vec.end());
 
        Range surf_parent_ents = intersect(new_surf, parent_ents);
        new_surf = subtract(new_surf, surf_parent_ents);
        Range child_surf_ents;
        CHKERR updateRangeByChilds(parentsChildMap, surf_parent_ents,
                                   child_surf_ents);
        new_surf.merge(child_surf_ents);
 
        Range edges_to_merge_parent_ents =
            intersect(edges_to_merge, parent_ents);
        edges_to_merge = subtract(edges_to_merge, edges_to_merge_parent_ents);
        Range merged_child_edge_ents;
        CHKERR updateRangeByChilds(parentsChildMap, edges_to_merge_parent_ents,
                                   merged_child_edge_ents);
 
        Range not_merged_edges_child_ents =
            intersect(not_merged_edges, parent_ents);
        not_merged_edges =
            subtract(not_merged_edges, not_merged_edges_child_ents);
        Range not_merged_child_edge_ents;
        CHKERR updateRangeByChilds(parentsChildMap, not_merged_edges_child_ents,
                                   not_merged_child_edge_ents);
 
        merged_child_edge_ents =
            subtract(merged_child_edge_ents, not_merged_child_edge_ents);
        edges_to_merge.merge(merged_child_edge_ents);
        not_merged_edges.merge(not_merged_child_edge_ents);
 
        if (updateMehsets) {
          for (_IT_CUBITMESHSETS_FOR_LOOP_(
                   (*mField.getInterface<MeshsetsManager>()), cubit_it)) {
            EntityHandle cubit_meshset = cubit_it->meshset;
            Range meshset_ents;
            CHKERR moab.get_entities_by_handle(cubit_meshset, meshset_ents,
                                               true);
            Range child_ents;
            CHKERR updateRangeByChilds(parentsChildMap, meshset_ents,
                                       child_ents);
            CHKERR moab.add_entities(cubit_meshset, child_ents);
          }
        }
      }
 
      MoFEMFunctionReturn(0);
    };
 
  private:
    NodeMergerInterface::ParentChildMap parentsChildMap;
    std::vector<EntityHandle> childsVec;
 
    inline MoFEMErrorCode updateRangeByChilds(
        const NodeMergerInterface::ParentChildMap &parent_child_map,
        const Range &parents, Range &childs) {
      MoFEMFunctionBeginHot;
      childsVec.clear();
      childsVec.reserve(parents.size());
      for (auto pit = parents.pair_begin(); pit != parents.pair_end(); pit++) {
        auto it = parent_child_map.lower_bound(pit->first);
        if (it != parent_child_map.end()) {
          for (auto hi_it = parent_child_map.upper_bound(pit->second);
               it != hi_it; ++it)
            childsVec.emplace_back(it->cHild);
        }
      }
      childs.insert_list(childsVec.begin(), childsVec.end());
      MoFEMFunctionReturnHot(0);
    }
  };
 
  /**
   * \brief Calculate edge length
   */
  struct LengthMap {
    Tag tH;
    CoreInterface &mField;
    moab::Interface &moab;
    const double maxLength;
    LengthMap(CoreInterface &m_field, Tag th, double max_length)
        : tH(th), mField(m_field), moab(m_field.get_moab()),
          maxLength(max_length) {
      gammaL = 1.;
      gammaQ = 3.;
      acceptedThrasholdMergeQuality = 0.5;
    }
 
    double
        gammaL; ///< Controls importance of length when ranking edges for merge
    double
        gammaQ; ///< Controls importance of quality when ranking edges for merge
    double acceptedThrasholdMergeQuality; ///< Do not merge quality if quality
                                          ///< above accepted thrashold
 
    MoFEMErrorCode operator()(const Range &tets, const Range &edges,
                              LengthMapData_multi_index &length_map,
                              double &ave) const {
      int num_nodes;
      const EntityHandle *conn;
      std::array<double, 12> coords;
      MoFEMFunctionBegin;
      VectorAdaptor s0(3, ublas::shallow_array_adaptor<double>(3, &coords[0]));
      VectorAdaptor s1(3, ublas::shallow_array_adaptor<double>(3, &coords[3]));
      VectorDouble3 delta(3);
 
      struct NodeQuality {
        EntityHandle node;
        double quality;
        NodeQuality(const EntityHandle node) : node(node), quality(1) {}
      };
 
      typedef multi_index_container<
          NodeQuality, indexed_by<
 
                           sequenced<>,
 
                           hashed_non_unique<tag<Ent_mi_tag>,
                                             member<NodeQuality, EntityHandle,
                                                    &NodeQuality::node>>
 
                           >>
          NodeQuality_sequence;
 
      NodeQuality_sequence node_quality_sequence;
 
      Range edges_nodes;
      CHKERR moab.get_connectivity(tets, edges_nodes, false);
      Range edges_tets;
      CHKERR moab.get_adjacencies(edges, 3, false, edges_tets,
                                  moab::Interface::UNION);
      edges_tets = intersect(edges_tets, tets);
 
      for (auto node : edges_nodes)
        node_quality_sequence.emplace_back(node);
 
      for (auto tet : edges_tets) {
 
        CHKERR moab.get_connectivity(tet, conn, num_nodes, true);
        if (tH)
          CHKERR moab.tag_get_data(tH, conn, num_nodes, coords.data());
        else
          CHKERR moab.get_coords(conn, num_nodes, coords.data());
 
        const double q = Tools::volumeLengthQuality(coords.data());
 
        for (auto n : {0, 1, 2, 3}) {
          auto it = node_quality_sequence.get<1>().find(conn[n]);
          if (it != node_quality_sequence.get<1>().end())
            const_cast<double &>(it->quality) = std::min(q, it->quality);
        }
      }
 
      for (auto edge : edges) {
 
        CHKERR moab.get_connectivity(edge, conn, num_nodes, true);
 
        if (tH)
          CHKERR moab.tag_get_data(tH, conn, num_nodes, coords.data());
        else
          CHKERR moab.get_coords(conn, num_nodes, coords.data());
 
        double q = 1;
        for (auto n : {0, 1}) {
          auto it = node_quality_sequence.get<1>().find(conn[n]);
          if (it != node_quality_sequence.get<1>().end())
            q = std::min(q, it->quality);
        }
 
        if (q < acceptedThrasholdMergeQuality) {
          noalias(delta) = (s0 - s1) / maxLength;
          double dot = inner_prod(delta, delta);
          double val = pow(q, gammaQ) * pow(dot, 0.5 * gammaL);
          length_map.insert(LengthMapData(val, q, edge));
        }
      }
 
      ave = 0;
      for (LengthMapData_multi_index::nth_index<0>::type::iterator mit =
               length_map.get<0>().begin();
           mit != length_map.get<0>().end(); mit++) {
        ave += mit->qUality;
      }
      ave /= length_map.size();
      MoFEMFunctionReturn(0);
    }
  };
 
  /**
   * \brief Topological relations
   */
  struct Toplogy {
 
    CoreInterface &mField;
    Tag tH;
    Toplogy(CoreInterface &m_field, Tag th) : mField(m_field), tH(th) {}
 
    enum TYPE {
      FREE = 0,
      SKIN = 1 << 0,
      SURFACE = 1 << 1,
      SURFACE_SKIN = 1 << 2,
      FRONT_ENDS = 1 << 3,
      FIX_EDGES = 1 << 4,
      FIX_CORNERS = 1 << 5
    };
 
    typedef map<int, Range> SetsMap;
 
    MoFEMErrorCode classifyVerts(const Range &surface, const Range &tets,
                                 const Range &fixed_edges,
                                 const Range &corner_nodes,
                                 const Range &constrain_surface,
                                 SetsMap &sets_map) const {
      moab::Interface &moab(mField.get_moab());
      Skinner skin(&moab);
      CutMeshFunctionBegin;
 
      sets_map[FIX_CORNERS].merge(corner_nodes);
      Range fixed_verts;
      CHKERR moab.get_connectivity(fixed_edges, fixed_verts, true);
      sets_map[FIX_EDGES].swap(fixed_verts);
 
      Range tets_skin;
      CHKERR skin.find_skin(0, tets, false, tets_skin);
      Range tets_skin_edges;
      CHKERR moab.get_adjacencies(tets_skin, 1, false, tets_skin_edges,
                                  moab::Interface::UNION);
 
      // constrain surface
      Range constrain_surface_verts;
      CHKERR moab.get_connectivity(constrain_surface, constrain_surface_verts,
                                   true);
      Range constrain_surface_edges;
      CHKERR moab.get_adjacencies(constrain_surface, 1, false,
                                  constrain_surface_edges,
                                  moab::Interface::UNION);
 
      // surface skin
      Range surface_skin;
      CHKERR skin.find_skin(0, surface, false, surface_skin);
      Range front_in_the_body;
      front_in_the_body = subtract(surface_skin, tets_skin_edges);
      Range front_in_the_body_verts;
      CHKERR moab.get_connectivity(front_in_the_body, front_in_the_body_verts,
                                   true);
      Range front_ends;
      CHKERR skin.find_skin(0, front_in_the_body, false, front_ends);
      front_ends.merge(
          intersect(front_in_the_body_verts, constrain_surface_verts));
      sets_map[FRONT_ENDS].swap(front_ends);
 
      Range surface_skin_verts;
      CHKERR moab.get_connectivity(surface_skin, surface_skin_verts, true);
      sets_map[SURFACE_SKIN].swap(surface_skin_verts);
 
      // surface
      Range surface_verts;
      CHKERR moab.get_connectivity(surface, surface_verts, true);
      sets_map[SURFACE_SKIN].merge(
          intersect(constrain_surface_verts, surface_verts));
      sets_map[SURFACE].swap(surface_verts);
 
      // skin
      Range tets_skin_verts;
      CHKERR moab.get_connectivity(tets_skin, tets_skin_verts, true);
      sets_map[SKIN].swap(tets_skin_verts);
      sets_map[SKIN].merge(constrain_surface_verts);
 
      Range tets_verts;
      CHKERR moab.get_connectivity(tets, tets_verts, true);
      sets_map[FREE].swap(tets_verts);
 
      MoFEMFunctionReturn(0);
    }
 
    MoFEMErrorCode getProcTets(const Range &tets, const Range &edges_to_merge,
                               Range &proc_tets) const {
      moab::Interface &moab(mField.get_moab());
      CutMeshFunctionBegin;
      Range edges_to_merge_verts;
      CHKERR moab.get_connectivity(edges_to_merge, edges_to_merge_verts, true);
      Range edges_to_merge_verts_tets;
      CHKERR moab.get_adjacencies(edges_to_merge_verts, 3, false,
                                  edges_to_merge_verts_tets,
                                  moab::Interface::UNION);
      edges_to_merge_verts_tets = intersect(edges_to_merge_verts_tets, tets);
      proc_tets.swap(edges_to_merge_verts_tets);
      MoFEMFunctionReturn(0);
    }
 
    MoFEMErrorCode removeBadEdges(const Range &surface, const Range &tets,
                                  const Range &fixed_edges,
                                  const Range &corner_nodes,
                                  const Range &constrain_surface,
                                  Range &edges_to_merge,
                                  Range &not_merged_edges) {
      moab::Interface &moab(mField.get_moab());
      CutMeshFunctionBegin;
 
      // find skin
      Skinner skin(&moab);
      Range tets_skin;
      CHKERR skin.find_skin(0, tets, false, tets_skin);
      Range surface_skin;
      CHKERR skin.find_skin(0, surface, false, surface_skin);
 
      // constrain surface
      Range constrain_surface_verts;
      CHKERR moab.get_connectivity(constrain_surface, constrain_surface_verts,
                                   true);
      Range constrain_surface_edges;
      CHKERR moab.get_adjacencies(constrain_surface, 1, false,
                                  constrain_surface_edges,
                                  moab::Interface::UNION);
 
      // end nodes
      Range tets_skin_edges;
      CHKERR moab.get_adjacencies(tets_skin, 1, false, tets_skin_edges,
                                  moab::Interface::UNION);
 
      Range surface_front;
      surface_front = subtract(surface_skin, tets_skin_edges);
      Range surface_front_nodes;
      CHKERR moab.get_connectivity(surface_front, surface_front_nodes, true);
 
      Range ends_nodes;
      CHKERR skin.find_skin(0, surface_front, false, ends_nodes);
      ends_nodes.merge(intersect(surface_front_nodes, constrain_surface_verts));
 
      // remove bad merges
      surface_skin.merge(constrain_surface);
      tets_skin_edges.merge(constrain_surface_edges);
 
      // get surface and body skin verts
      Range surface_edges;
      CHKERR moab.get_adjacencies(surface, 1, false, surface_edges,
                                  moab::Interface::UNION);
      // get nodes on the surface
      Range surface_edges_verts;
      CHKERR moab.get_connectivity(surface_edges, surface_edges_verts, true);
      // get vertices on the body skin
      Range tets_skin_edges_verts;
      CHKERR moab.get_connectivity(tets_skin_edges, tets_skin_edges_verts,
                                   true);
 
      Range edges_to_remove;
 
      // remove edges self connected to body skin
      {
        Range ents_nodes_and_edges;
        ents_nodes_and_edges.merge(tets_skin_edges_verts);
        ents_nodes_and_edges.merge(tets_skin_edges);
        CHKERR removeSelfConectingEdges(ents_nodes_and_edges, edges_to_remove,
                                        false);
      }
      edges_to_merge = subtract(edges_to_merge, edges_to_remove);
      not_merged_edges.merge(edges_to_remove);
 
      // remove edges self connected to surface
      {
        Range ents_nodes_and_edges;
        ents_nodes_and_edges.merge(surface_edges_verts);
        ents_nodes_and_edges.merge(surface_edges);
        ents_nodes_and_edges.merge(tets_skin_edges_verts);
        ents_nodes_and_edges.merge(tets_skin_edges);
        CHKERR removeSelfConectingEdges(ents_nodes_and_edges, edges_to_remove,
                                        false);
      }
      edges_to_merge = subtract(edges_to_merge, edges_to_remove);
      not_merged_edges.merge(edges_to_remove);
 
      // remove edges adjacent corner_nodes execpt those on fixed edges
      Range fixed_edges_nodes;
      CHKERR moab.get_connectivity(fixed_edges, fixed_edges_nodes, true);
      {
        Range ents_nodes_and_edges;
        ents_nodes_and_edges.merge(fixed_edges_nodes);
        ents_nodes_and_edges.merge(ends_nodes);
        ents_nodes_and_edges.merge(corner_nodes);
        ents_nodes_and_edges.merge(fixed_edges);
        CHKERR removeSelfConectingEdges(ents_nodes_and_edges, edges_to_remove,
                                        false);
      }
      edges_to_merge = subtract(edges_to_merge, edges_to_remove);
      not_merged_edges.merge(edges_to_remove);
 
      // remove edges self connected to surface
      CHKERR removeSelfConectingEdges(surface_edges, edges_to_remove, false);
      edges_to_merge = subtract(edges_to_merge, edges_to_remove);
      not_merged_edges.merge(edges_to_remove);
 
      // remove edges self contented on surface skin
      {
        Range ents_nodes_and_edges;
        ents_nodes_and_edges.merge(surface_skin);
        ents_nodes_and_edges.merge(fixed_edges_nodes);
        CHKERR removeSelfConectingEdges(ents_nodes_and_edges, edges_to_remove,
                                        false);
      }
      edges_to_merge = subtract(edges_to_merge, edges_to_remove);
      not_merged_edges.merge(edges_to_remove);
 
      // remove edges connecting crack front and fixed edges, except those short
      {
        Range ents_nodes_and_edges;
        ents_nodes_and_edges.merge(surface_skin.subset_by_type(MBEDGE));
        ents_nodes_and_edges.merge(fixed_edges.subset_by_type(MBEDGE));
        CHKERR removeSelfConectingEdges(ents_nodes_and_edges, edges_to_remove,
                                        false);
      }
      edges_to_merge = subtract(edges_to_merge, edges_to_remove);
      not_merged_edges.merge(edges_to_remove);
 
      // remove crack front nodes connected to the surface, except those short
      {
        Range ents_nodes_and_edges;
        ents_nodes_and_edges.merge(surface_front_nodes);
        ents_nodes_and_edges.merge(surface_front);
        ents_nodes_and_edges.merge(tets_skin_edges_verts);
        ents_nodes_and_edges.merge(tets_skin_edges);
        CHKERR removeSelfConectingEdges(ents_nodes_and_edges, edges_to_remove,
                                        false);
      }
      edges_to_merge = subtract(edges_to_merge, edges_to_remove);
      not_merged_edges.merge(edges_to_remove);
 
      MoFEMFunctionReturn(0);
    }
 
  private:
    MoFEMErrorCode removeSelfConectingEdges(const Range &ents,
                                            Range &edges_to_remove,
                                            bool debug) const {
      moab::Interface &moab(mField.get_moab());
      CutMeshFunctionBegin;
      // get nodes
      Range ents_nodes = ents.subset_by_type(MBVERTEX);
      if (ents_nodes.empty()) {
        CHKERR moab.get_connectivity(ents, ents_nodes, true);
      }
      // edges adj. to nodes
      Range ents_nodes_edges;
      CHKERR moab.get_adjacencies(ents_nodes, 1, false, ents_nodes_edges,
                                  moab::Interface::UNION);
      // nodes of adj. edges
      Range ents_nodes_edges_nodes;
      CHKERR moab.get_connectivity(ents_nodes_edges, ents_nodes_edges_nodes,
                                   true);
      // hanging nodes
      ents_nodes_edges_nodes = subtract(ents_nodes_edges_nodes, ents_nodes);
      Range ents_nodes_edges_nodes_edges;
      CHKERR moab.get_adjacencies(ents_nodes_edges_nodes, 1, false,
                                  ents_nodes_edges_nodes_edges,
                                  moab::Interface::UNION);
      // remove edges adj. to hanging edges
      ents_nodes_edges =
          subtract(ents_nodes_edges, ents_nodes_edges_nodes_edges);
      ents_nodes_edges =
          subtract(ents_nodes_edges, ents.subset_by_type(MBEDGE));
 
      edges_to_remove.swap(ents_nodes_edges);
      if (debug) {
        CHKERR SaveData(moab)("edges_to_remove.vtk", edges_to_remove);
      }
      MoFEMFunctionReturn(0);
    }
  };
 
  Range not_merged_edges;
  CHKERR Toplogy(m_field, th)
      .removeBadEdges(surface, tets, fixed_edges, corner_nodes,
                      constrainSurface, edges_to_merge, not_merged_edges);
  Toplogy::SetsMap sets_map;
  CHKERR Toplogy(m_field, th)
      .classifyVerts(surface, tets, fixed_edges, corner_nodes, constrainSurface,
                     sets_map);
  if (debug) {
    for (Toplogy::SetsMap::reverse_iterator sit = sets_map.rbegin();
         sit != sets_map.rend(); sit++) {
      std::string name = "classification_verts_" +
                         boost::lexical_cast<std::string>(sit->first) + ".vtk";
      if (!sit->second.empty())
        CHKERR SaveData(moab)(name, sit->second);
    }
  }
  Range proc_tets;
  CHKERR Toplogy(m_field, th).getProcTets(tets, edges_to_merge, proc_tets);
  out_tets = subtract(tets, proc_tets);
 
  if (bit_ptr) {
    Range all_out_ents = out_tets;
    for (int dd = 2; dd >= 0; dd--) {
      CHKERR moab.get_adjacencies(out_tets, dd, false, all_out_ents,
                                  moab::Interface::UNION);
    }
    CHKERR m_field.getInterface<BitRefManager>()->addBitRefLevel(all_out_ents,
                                                                 *bit_ptr);
  }
 
  int nb_nodes_merged = 0;
  LengthMapData_multi_index length_map;
  new_surf = surface;
 
  auto save_merge_step = [&](const int pp, const Range collapsed_edges) {
    MoFEMFunctionBegin;
    Range adj_faces;
    CHKERR moab.get_adjacencies(proc_tets, 2, false, adj_faces,
                                moab::Interface::UNION);
    std::string name;
    name = "node_merge_step_" + boost::lexical_cast<std::string>(pp) + ".vtk";
    CHKERR SaveData(moab)(
        name, unite(intersect(new_surf, adj_faces), collapsed_edges));
    name =
        "edges_to_merge_step_" + boost::lexical_cast<std::string>(pp) + ".vtk";
    CHKERR SaveData(moab)(
        name, unite(intersect(new_surf, adj_faces), edges_to_merge));
    MoFEMFunctionReturn(0);
  };
 
  if (debug)
    CHKERR save_merge_step(0, Range());
 
  double ave0 = 0, ave = 0, min = 0, min_p = 0, min_pp;
  for (int pp = 0; pp != nbMaxMergingCycles; ++pp) {
 
    int nb_nodes_merged_p = nb_nodes_merged;
    length_map.clear();
    min_pp = min_p;
    min_p = min;
    CHKERR LengthMap(m_field, th, aveLength)(proc_tets, edges_to_merge,
                                             length_map, ave);
 
    if(!length_map.empty())
      min = length_map.get<2>().begin()->qUality;
    if (pp == 0) {
      ave0 = ave;
    }
 
    int nn = 0;
    Range collapsed_edges;
    MergeNodes merge_nodes(m_field, true, th, update_meshsets);
 
    for (auto mit = length_map.get<0>().begin();
         mit != length_map.get<0>().end(); mit++, nn++) {
 
      if (!mit->skip) {
 
        auto get_father_and_mother =
            [&](EntityHandle &father, EntityHandle &mother, int &line_search) {
              MoFEMFunctionBegin;
              int num_nodes;
              const EntityHandle *conn;
              CHKERR moab.get_connectivity(mit->eDge, conn, num_nodes, true);
              std::array<int, 2> conn_type = {0, 0};
              for (int nn = 0; nn != 2; nn++) {
                for (Toplogy::SetsMap::reverse_iterator sit = sets_map.rbegin();
                     sit != sets_map.rend(); sit++) {
                  if (sit->second.find(conn[nn]) != sit->second.end()) {
                    conn_type[nn] |= sit->first;
                  }
                }
              }
              int type_father, type_mother;
              if (conn_type[0] > conn_type[1]) {
                father = conn[0];
                mother = conn[1];
                type_father = conn_type[0];
                type_mother = conn_type[1];
              } else {
                father = conn[1];
                mother = conn[0];
                type_father = conn_type[1];
                type_mother = conn_type[0];
              }
              if (type_father == type_mother) {
                line_search = lineSearchSteps;
              }
              MoFEMFunctionReturn(0);
            };
 
        int line_search = 0;
        EntityHandle father, mother;
        CHKERR get_father_and_mother(father, mother, line_search);
        CHKERR merge_nodes.mergeNodes(line_search, father, mother, proc_tets);
        if (m_field.getInterface<NodeMergerInterface>()->getSuccessMerge()) {
          const EntityHandle father_and_mother[] = {father, mother};
          Range adj_tets;
          CHKERR moab.get_adjacencies(father_and_mother, 1, 3, false, adj_tets);
          Range adj_tets_nodes;
          CHKERR moab.get_connectivity(adj_tets, adj_tets_nodes, true);
          Range adj_edges;
          CHKERR moab.get_adjacencies(adj_tets_nodes, 1, false, adj_edges,
                                      moab::Interface::UNION);
          for (auto ait : adj_edges) {
            auto miit = length_map.get<1>().find(ait);
            if (miit != length_map.get<1>().end())
              (const_cast<LengthMapData &>(*miit)).skip = true;
          }
          nb_nodes_merged++;
          collapsed_edges.insert(mit->eDge);
        }
 
        if (nn > static_cast<int>(length_map.size() / fraction_level))
          break;
        if (mit->qUality > ave)
          break;
      }
    }
 
    CHKERR merge_nodes.updateRangeByChilds(new_surf, edges_to_merge,
                                           not_merged_edges, true);
 
    MOFEM_LOG_C("WORLD", Sev::verbose,
                "(%d) Number of nodes merged %d ave q %3.4e min q %3.4e", pp,
                nb_nodes_merged, ave, min);
 
    if (debug)
      CHKERR save_merge_step(pp + 1, collapsed_edges);
 
    if (nb_nodes_merged == nb_nodes_merged_p)
      break;
    if (min > 1e-2 && min == min_pp)
      break;
    if (min > ave0)
      break;
 
    Range adj_edges;
    CHKERR moab.get_adjacencies(proc_tets, 1, false, adj_edges,
                                moab::Interface::UNION);
    edges_to_merge = intersect(edges_to_merge, adj_edges);
    CHKERR Toplogy(m_field, th)
        .removeBadEdges(new_surf, proc_tets, fixed_edges, corner_nodes,
                        constrainSurface, edges_to_merge, not_merged_edges);
  }
 
  auto reconstruct_refined_ents = [&]() {
    MoFEMFunctionBegin;
    CHKERR reconstructMultiIndex(*m_field.get_ref_ents());
    MoFEMFunctionReturn(0);
  };
 
  // Add function which reconstruct core multi-index. Node merging is messy
  // process and entity parent could be changed without notification to
  // multi-index. TODO Issue has to be tracked down better, however in principle
  // is better not to modify multi-index each time parent is changed, that makes
  // code slow. Is better to do it in the bulk as below.
  CHKERR reconstruct_refined_ents();
 
  if (bit_ptr)
    CHKERR m_field.getInterface<BitRefManager>()->setBitRefLevel(proc_tets,
                                                                 *bit_ptr);
 
  out_tets.merge(proc_tets);
  Range adj_faces;
  CHKERR moab.get_adjacencies(out_tets, 2, false, adj_faces,
                              moab::Interface::UNION);
  new_surf = intersect(new_surf, adj_faces);
 
  MoFEMFunctionReturn(0);
}
 
MoFEMErrorCode CutMeshInterface::mergeBadEdges(
    const int fraction_level, const BitRefLevel cut_bit,
    const BitRefLevel trim_bit, const BitRefLevel bit, const Range &surface,
    const Range &fixed_edges, const Range &corner_nodes, Tag th,
    const bool update_meshsets, const bool debug) {
  CoreInterface &m_field = cOre;
  CutMeshFunctionBegin;
  Range tets_level;
  CHKERR m_field.getInterface<BitRefManager>()->getEntitiesByTypeAndRefLevel(
      trim_bit, BitRefLevel().set(), MBTET, tets_level);
 
  Range edges_to_merge;
  CHKERR m_field.getInterface<BitRefManager>()->getEntitiesByRefLevel(
      trim_bit, cut_bit | trim_bit, edges_to_merge);
 
  // get all entities not in database
  Range all_ents_not_in_database_before;
  CHKERR cOre.getInterface<BitRefManager>()->getAllEntitiesNotInDatabase(
      all_ents_not_in_database_before);
 
  edges_to_merge = edges_to_merge.subset_by_type(MBEDGE);
  if (debug)
    CHKERR SaveData(m_field.get_moab())("edges_to_merge.vtk", edges_to_merge);
 
  Range out_new_tets, out_new_surf;
  CHKERR mergeBadEdges(fraction_level, tets_level, surface, fixed_edges,
                       corner_nodes, edges_to_merge, out_new_tets, out_new_surf,
                       th, update_meshsets, &bit, debug);
 
  // get all entities not in database after merge
  Range all_ents_not_in_database_after;
  CHKERR cOre.getInterface<BitRefManager>()->getAllEntitiesNotInDatabase(
      all_ents_not_in_database_after);
 
  // delete hanging entities
  all_ents_not_in_database_after =
      subtract(all_ents_not_in_database_after, all_ents_not_in_database_before);
  Range meshsets;
  CHKERR m_field.get_moab().get_entities_by_type(0, MBENTITYSET, meshsets,
                                                 false);
  for (auto m : meshsets)
    CHKERR m_field.get_moab().remove_entities(m,
                                              all_ents_not_in_database_after);
 
  m_field.get_moab().delete_entities(all_ents_not_in_database_after);
 
  mergedVolumes.swap(out_new_tets);
  mergedSurfaces.swap(out_new_surf);
 
  MoFEMFunctionReturn(0);
}
 
MoFEMErrorCode CutMeshInterface::setTagData(Tag th, const BitRefLevel bit) {
  CoreInterface &m_field = cOre;
  moab::Interface &moab = m_field.get_moab();
  CutMeshFunctionBegin;
  Range nodes;
  if (bit.none())
    CHKERR moab.get_entities_by_type(0, MBVERTEX, nodes);
  else
    CHKERR m_field.getInterface<BitRefManager>()->getEntitiesByTypeAndRefLevel(
        bit, BitRefLevel().set(), MBVERTEX, nodes);
  std::vector<double> coords(3 * nodes.size());
  CHKERR moab.get_coords(nodes, &coords[0]);
  CHKERR moab.tag_set_data(th, nodes, &coords[0]);
  MoFEMFunctionReturn(0);
}
 
MoFEMErrorCode CutMeshInterface::setCoords(Tag th, const BitRefLevel bit,
                                           const BitRefLevel mask) {
  CoreInterface &m_field = cOre;
  moab::Interface &moab = m_field.get_moab();
  CutMeshFunctionBegin;
  Range nodes;
  if (bit.none())
    CHKERR moab.get_entities_by_type(0, MBVERTEX, nodes);
  else
    CHKERR m_field.getInterface<BitRefManager>()->getEntitiesByTypeAndRefLevel(
        bit, mask, MBVERTEX, nodes);
  std::vector<double> coords(3 * nodes.size());
  CHKERR moab.tag_get_data(th, nodes, &coords[0]);
  CHKERR moab.set_coords(nodes, &coords[0]);
  MoFEMFunctionReturn(0);
}
 
MoFEMErrorCode CutMeshInterface::saveCutEdges(const std::string prefix) {
  CoreInterface &m_field = cOre;
  moab::Interface &moab = m_field.get_moab();
  MoFEMFunctionBegin;
  CHKERR SaveData(moab)(prefix + "out_vol.vtk", vOlume);
  CHKERR SaveData(moab)(prefix + "out_surface.vtk", sUrface);
  CHKERR SaveData(moab)(prefix + "out_cut_edges.vtk", cutEdges);
  CHKERR SaveData(moab)(prefix + "out_cut_new_volumes.vtk", cutNewVolumes);
  CHKERR SaveData(moab)(prefix + "out_cut_new_surfaces.vtk", cutNewSurfaces);
  CHKERR SaveData(moab)(prefix + "out_cut_zero_distance_ents.vtk",
                        zeroDistanceEnts);
  MoFEMFunctionReturn(0);
}
 
MoFEMErrorCode CutMeshInterface::saveTrimEdges() {
  moab::Interface &moab = cOre.getInterface<CoreInterface>()->get_moab();
  MoFEMFunctionBegin;
  CHKERR SaveData(moab)("out_trim_surface.vtk", sUrface);
  CHKERR SaveData(moab)("out_trim_new_volumes.vtk", trimNewVolumes);
  CHKERR SaveData(moab)("out_trim_new_surfaces.vtk", trimNewSurfaces);
  CHKERR SaveData(moab)("out_trim_edges.vtk", trimEdges);
  MoFEMFunctionReturn(0);
}
 
}