CutMeshInterface.hpp

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/** \file CutMeshInterface.hpp
 * \brief Cut mesh interface
 *
 * \ingroup mesh_cut
 */
 
#ifndef __CUTMESHINTERFACE_HPP__
#define __CUTMESHINTERFACE_HPP__
 
#include "UnknownInterface.hpp"
 
namespace MoFEM {
 
/**
 *  \brief Interface to cut meshes
 *
 * \ingroup mesh_cut
 */
struct CutMeshInterface : public UnknownInterface {
 
  MoFEMErrorCode query_interface(boost::typeindex::type_index type_index, UnknownInterface **iface) const;
 
  MoFEM::Core &cOre;
  CutMeshInterface(const MoFEM::Core &core);
  ~CutMeshInterface() {}
 
  int lineSearchSteps;
  int nbMaxMergingCycles;
  double projectEntitiesQualityTrashold;
 
  MoFEMErrorCode getSubInterfaceOptions() { return getOptions(); }
 
  /**
   * \brief Get options from command line
   * @return error code
   */
  MoFEMErrorCode getOptions() {
    MoFEMFunctionBegin;
    CHKERR PetscOptionsBegin(PETSC_COMM_WORLD, "cut_", "MOFEM Cut mesh options",
                             "none");
 
    CHKERR PetscOptionsInt("-linesearch_steps",
                           "number of bisection steps which line search do to "
                           "find optimal merged nodes position",
                           "", lineSearchSteps, &lineSearchSteps, PETSC_NULL);
 
    CHKERR PetscOptionsInt("-max_merging_cycles",
                           "number of maximal merging cycles", "",
                           nbMaxMergingCycles, &nbMaxMergingCycles, PETSC_NULL);
 
    CHKERR PetscOptionsScalar("-project_entities_quality_trashold",
                              "project entities quality trashold", "",
                              projectEntitiesQualityTrashold,
                              &projectEntitiesQualityTrashold, PETSC_NULL);
 
    ierr = PetscOptionsEnd();
    CHKERRG(ierr);
    MoFEMFunctionReturn(0);
  }
 
  MoFEMErrorCode setFront(const Range surface);
 
  /**
   * \brief set surface entities
   * @param  surface entities which going to be added
   * @return         error code
   */
  MoFEMErrorCode setSurface(const Range surface);
 
  /**
   * \brief copy surface entities
   * @param  surface entities which going to be added
   * @return         error code
   */
  MoFEMErrorCode copySurface(const Range surface, Tag th = NULL,
                             double *shift = NULL, double *origin = NULL,
                             double *transform = NULL,
                             const std::string save_mesh = "");
 
  /**
   * \brief set volume entities
   * @param  volume entities which going to be added
   * @return         error code
   */
  MoFEMErrorCode setVolume(const Range volume);
 
 
  /** 
   * @brief Set the constrain surface object
   * 
   * Add surfaces which are restricted by mesh cut. Example of surface which
   * needs to be respected is an interface, the boundary between two materials,
   * or crack surface.
   *  
   * @param surf 
   * @return MoFEMErrorCode 
   */
  MoFEMErrorCode setConstrainSurface(const Range surf);
 
  /**
   * \brief merge surface entities
   * @param  surface entities which going to be added
   * @return         error code
   */
  MoFEMErrorCode mergeSurface(const Range surface);
 
  /**
   * \brief merge volume entities
   * @param  volume entities which going to be added
   * @return         error code
   */
  MoFEMErrorCode mergeVolumes(const Range volume);
 
  MoFEMErrorCode snapSurfaceSkinToEdges(const Range fixed_edges,
                                        const double rel_tol,
                                        const double abs_tol, Tag th = nullptr,
                                        const bool debug = false);
 
  MoFEMErrorCode snapSurfaceToEdges(const Range surface_edges,
                                    const Range fixed_edges,
                                    const double rel_tol, const double abs_tol,
                                    Tag th = nullptr, const bool debug = false);
 
  /**
   * \brief build tree
   * @return error code
   */
  MoFEMErrorCode buildTree();
 
  /**
   * @brief Cut mesh only
   *
   * @param vol
   * @param cut_bit
   * @param th
   * @param tol_geometry
   * @param tol_cut_close
   * @param fixed_edges
   * @param corner_nodes
   * @param update_meshsets
   * @param debug
   * @return MoFEMErrorCode
   */
  MoFEMErrorCode cutOnly(Range vol, const BitRefLevel cut_bit, Tag th,
                         const double tol_geometry, const double tol_cut_close,
                         Range *fixed_edges = NULL, Range *corner_nodes = NULL,
                         const bool update_meshsets = false,
                         const bool debug = false);
 
  /**
   * @brief Trim mesh only
   *
   * @param trim_bit
   * @param th
   * @param tol_cut_close
   * @param fixed_edges
   * @param corner_nodes
   * @param update_meshsets
   * @param debug
   * @return MoFEMErrorCode
   */
  MoFEMErrorCode trimOnly(const BitRefLevel trim_bit, Tag th,
                          const double tol_trim_close,
                          Range *fixed_edges = NULL, Range *corner_nodes = NULL,
                          const bool update_meshsets = false,
                          const bool debug = false);
 
  /**
   * @brief Cut and trim
   *
   * @param first_bit
   * @param th
   * @param tol_geometry
   * @param tol_cut_close
   * @param tol_trim_close
   * @param fixed_edges
   * @param corner_nodes
   * @param update_meshsets
   * @param debug
   * @return MoFEMErrorCode
   */
  MoFEMErrorCode
  cutAndTrim(int &first_bit, Tag th, const double tol_geometry,
             const double tol_cut_close, const double tol_trim_close,
             Range *fixed_edges = NULL, Range *corner_nodes = NULL,
             const bool update_meshsets = false, const bool debug = false);
 
  /**
   * @brief Cut, trim and merge
   *
   * @param first_bit first bit of bit revel, subsequent set bits are for trim
   * and merge
   * @param fraction_level fraction of edges merged at each merge step
   * @param th tag storring mesh node positions
   * @param tol_geometry tolerance how mesh node should be close to cut surface (mesh
   * node is moved), should be small
   * @param tol_cut_close how crack node should be close to mesh (cut surface
   * node is moved), can be big
   * @param tol_trim_close how front node should be close to mesh, can be big
   * @param fixed_edges edges on which nodes can not be moved
   * @param corner_nodes nodes which can not be moved
   * @param update_meshsets update meshsets by parents
   * @param debug swich on debugging
   * @return MoFEMErrorCode
   */
  MoFEMErrorCode 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 = false,
                                 const bool debug = false);
 
  /**
   * @brief Create front from the surface
   *
   * @param debug
   * @return MoFEMErrorCode
   */
  MoFEMErrorCode makeFront(const bool debug = false);
 
  /**
   * @brief Calculate distance from mesh nodes to cut surface
   *
   * @param intersect_vol
   * @param verb
   * @param debug
   * @return MoFEMErrorCode
   */
  MoFEMErrorCode createSurfaceLevelSets(int verb = QUIET,
                                        const bool debug = false);
 
  /**
   * @brief Calculate distance from mesh nodes to surface front
   *
   * @param vol
   * @param th if not null take coordinates from tag
   * @param verb
   * @param debug
   * @return MoFEMErrorCode
   */
  MoFEMErrorCode createFrontLevelSets(Range vol, Tag th = nullptr,
                                      int verb = QUIET,
                                      const bool debug = false);
 
  /**
   * @brief Find level set volumes
   *
   * @param th
   * @param vol_edges
   * @param remove_adj_prims_edges
   * @param verb
   * @param debug
   * @param edges_file_name
   * @return MoFEMErrorCode
   */
  MoFEMErrorCode findLevelSetVolumes(Tag th, Range &vol_edges,
                                 const bool remove_adj_prims_edges,
                                 int verb = QUIET, const bool debug = false,
                                 const std::string edges_file_name = string());
 
  /**
   * @brief Find level set volumes
   *
   * @param update_front
   * @param verb
   * @param debug
   * @return MoFEMErrorCode
   */
  MoFEMErrorCode findLevelSetVolumes(int verb = QUIET,
                                     const bool debug = false);
 
  /**
   * @brief Refine and set level sets
   *
   * \note Should be run befor cutting
   *
   * @param refine_front refine nodes at front
   * @param update_front update level set at front
   * @param init_bit_level inital bit ref level to store refined meshes
   * @param surf_levels number of mesh surface refinement
   * @param front_levels
   * @param fixed_edges
   * @param verb
   * @param debug
   * @return MoFEMErrorCode
   */
  MoFEMErrorCode refineMesh(const int init_bit_level, const int surf_levels,
                            const int front_levels,
                            Range *fixed_edges = nullptr, int verb = QUIET,
                            const bool debug = false);
 
  /**
   * @brief find edges to cut
   *
   * @param vol is tetrahedrons search to cut
   * @param verb verbosity level
   * @param debug debugging
   * @return MoFEMErrorCode
   */
  MoFEMErrorCode findEdgesToCut(Range vol, int verb = QUIET,
                                const bool debug = false);
 
  /**
   * @brief Find entities on cut surface which can be projected
   *
   * @param fixed_edges pointer to fix edges
   * @param corner_nodes pointer to corner nodes
   * @param close tolerance is tolerance how close entities has to be
   * @param verb verbosity level
   * @param debug true for debuging purposes
   *
   */
  MoFEMErrorCode projectZeroDistanceEnts(Range *fixed_edges,
                                         Range *corner_nodes,
                                         const double geometry_tol = 0,
                                         const double close_tol = 0,
                                         const int verb = QUIET,
                                         const bool debug = false);
 
  /**
   * \brief cut edges
   *
   * For edges to cut (calculated by findEdgesToCut), edges are split in the
   * middle and then using MoFEM::MeshRefinement interface, tetrahedra mesh
   * are cut.
   *
   * @param  bit BitRefLevel of new mesh created by cutting edges
   * @return     error code
   */
  MoFEMErrorCode cutEdgesInMiddle(const BitRefLevel bit, Range &cut_vols,
                                  Range &cut_surf, Range &cut_verts,
                                  const bool debug = false);
 
  /**
   * \brief projecting of mid edge nodes on new mesh on surface
   * @return error code
   */
  MoFEMErrorCode moveMidNodesOnCutEdges(Tag th = NULL);
 
  /**
   * \brief Find edges to trimEdges
 
   * To make this work, you need to find edges to cut (findEdgesToCut), then
   * cut edges in the middle (cutEdgesInMiddle) and finally project edges on
   * the surface (moveMidNodesOnCutEdges)
 
   * @param  verb verbosity level
   * @return      error code
   */
  MoFEMErrorCode findEdgesToTrim(Range *fixed_edges, Range *corner_nodes,
                                 Tag th = NULL,
                                 const double tol = 1e-4,
                                 const bool debug = false);
 
  /**
   * \brief trim edges
   * @param  bit bit level of the trimmed mesh
   * @return     error code
   */
  MoFEMErrorCode trimEdgesInTheMiddle(const BitRefLevel bit,
                                      const bool debug = false);
 
  /**
   * \brief move trimmed edges mid nodes
   * @return error code
   */
  MoFEMErrorCode moveMidNodesOnTrimmedEdges(Tag th = NULL);
 
  /**
   * @brief Trim surface from faces beyond front
   *
   * @param fixed_edge
   * @param corner_nodes
   * @param debug
   * @return MoFEMErrorCode
   */
  MoFEMErrorCode trimSurface(Range *fixed_edge, Range *corner_nodes,
                             const double tol = 1e-4, Tag th = NULL,
                             const bool debug = false);
 
  /**
   * \brief Remove pathological elements on surface internal front
   *
   * Internal surface skin is a set of edges in iterior of the body on boundary
   * of surface. This set of edges is called surface front. If surface face has
   * three nodes on surface front, non of the face nodes is split and should be
   * removed from surface if it is going to be split.
   *
   * @param  split_bit split bit level
   * @param  bit       bit level of split mesh
   * @param  ents      ents on the surface which is going to be split
   * @return           error code
   */
  MoFEMErrorCode removePathologicalFrontTris(const BitRefLevel split_bit,
                                             Range &ents);
 
  /**
   * \brief split sides
   * @param  split_bit split bit level
   * @param  bit       bit level of split mesh
   * @param  ents      ents on the surface which is going to be split
   * @return           error code
   */
  MoFEMErrorCode splitSides(const BitRefLevel split_bit, const BitRefLevel bit,
                            const Range &ents, Tag th = NULL);
 
  /**
   * @brief Merge edges
   *
   * Sort all edges, where sorting is by quality calculated as edge length times
   * quality of tets adjacent to the edge. Edge is merged if quality if the mesh
   * is improved.
   *
   * @param fraction_level Fraction of edges attemt to be merged at iteration
   * @param tets Tets of the mesh which edges are merged
   * @param surface Surface created by edge spliting
   * @param fixed_edges edges which are geometrical corners of the body
   * @param corner_nodes vertices on the corners
   * @param merged_nodes  merged nodes
   * @param out_tets  returned test after merge
   * @param new_surf  new surface without merged edges
   * @param th  tag with nodal positons
   * @param bit_ptr set bit ref level to mesh without merged edges
   * @param debug
   * @return MoFEMErrorCode
   */
  MoFEMErrorCode mergeBadEdges(const int fraction_level, const Range &tets,
                               const Range &surface, const Range &fixed_edges,
                               const Range &corner_nodes, Range &merged_nodes,
                               Range &out_tets, Range &new_surf, Tag th,
                               const bool update_meshsets = false,
                               const BitRefLevel *bit_ptr = NULL,
                               const bool debug = false);
 
  /**
   * @brief Merge edges
   *
   * Sort all edges, where sorting is by quality calculated as edge length times
   * quality of tets adjacent to the edge. Edge is merged if quality if the mesh
   * is improved.
   */
  MoFEMErrorCode
  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 = NULL,
                const bool update_meshsets = false, const bool debug = false);
 
  /**
   * \brief set coords to tag
   * @param  th tag handle
   * @return    error code
   */
  MoFEMErrorCode setTagData(Tag th, const BitRefLevel bit = BitRefLevel());
 
  /**
   * \brief set coords from tag
   * @param  th tag handle
   * @return    error code
   */
  MoFEMErrorCode setCoords(Tag th, const BitRefLevel bit = BitRefLevel(),
                           const BitRefLevel mask = BitRefLevel().set());
 
  inline const Range &getVolume() const { return vOlume; }
  inline const Range &getSurface() const { return sUrface; }
  inline const Range &getFront() const { return fRont; }
 
  inline const Range &getCutEdges() const { return cutEdges; }
  inline const Range &getNewCutVolumes() const { return cutNewVolumes; }
  inline const Range &getNewCutSurfaces() const { return cutNewSurfaces; }
  inline const Range &getNewCutVertices() const { return cutNewVertices; }
  inline const Range &projectZeroDistanceEnts() const {
    return zeroDistanceEnts;
  }
 
  inline const Range &getTrimEdges() const { return trimEdges; }
  inline const Range &getNewTrimVolumes() const { return trimNewVolumes; }
  inline const Range &getNewTrimSurfaces() const { return trimNewSurfaces; }
  inline const Range &getNewTrimVertices() const { return trimNewVertices; }
 
  inline const Range &getMergedVolumes() const { return mergedVolumes; }
  inline const Range &getMergedSurfaces() const { return mergedSurfaces; }
 
  inline const Range &getCutSurfaceVolumes() const { return cutSurfaceVolumes; }
  inline const Range &getCutFrontVolumes() const { return cutFrontVolumes; }
 
  MoFEMErrorCode saveCutEdges(const std::string prefix = "");
 
  MoFEMErrorCode saveTrimEdges();
 
  inline boost::shared_ptr<OrientedBoxTreeTool> &getTreeSurfPtr() {
    return treeSurfPtr;
  }
 
  MoFEMErrorCode clearMap();
 
  struct SaveData {
    moab::Interface &moab;
    SaveData(moab::Interface &moab) : moab(moab) {}
    MoFEMErrorCode operator()(const std::string name, const Range &ents) {
      MoFEMFunctionBegin;
      EntityHandle meshset;
      CHKERR moab.create_meshset(MESHSET_SET, meshset);
      CHKERR moab.add_entities(meshset, ents);
      CHKERR moab.write_file(name.c_str(), "VTK", "", &meshset, 1);
      CHKERR moab.delete_entities(&meshset, 1);
      MoFEMFunctionReturn(0);
    }
  };
 
  struct LengthMapData {
    double lEngth;
    double qUality;
    EntityHandle eDge;
    bool skip;
    LengthMapData(const double l, double q, const EntityHandle e)
        : lEngth(l), qUality(q), eDge(e), skip(false) {}
  };
 
  typedef multi_index_container<
      LengthMapData,
      indexed_by<
 
          ordered_non_unique<
              member<LengthMapData, double, &LengthMapData::lEngth>>,
 
          hashed_unique<
              member<LengthMapData, EntityHandle, &LengthMapData::eDge>>,
 
          ordered_non_unique<
              member<LengthMapData, double, &LengthMapData::qUality>>
 
          >>
      LengthMapData_multi_index;
 
private:
  Range fRont;
  Range sUrface;
  Range vOlume;
 
  boost::shared_ptr<OrientedBoxTreeTool> treeSurfPtr;
  EntityHandle rootSetSurf;
 
  Range cutEdges;
  Range cutNewVolumes;
  Range cutNewSurfaces;
  Range zeroDistanceEnts;
  Range zeroDistanceVerts;
  Range cutNewVertices;
 
  Range trimNewVolumes;
  Range trimNewVertices;
  Range trimNewSurfaces;
  Range trimEdges;
 
  Range mergedVolumes;
  Range mergedSurfaces;
 
  struct TreeData {
    double dIst;
    double lEngth;
    VectorDouble3 unitRayDir;
    VectorDouble3 rayPoint;
  };
 
  map<EntityHandle, TreeData> edgesToCut;
  map<EntityHandle, TreeData> verticesOnCutEdges;
  map<EntityHandle, TreeData> edgesToTrim;
  map<EntityHandle, TreeData> verticesOnTrimEdges;
 
  double aveLength; ///< Average edge length
  double maxLength; ///< Maximal edge length
 
  Range cutSurfaceVolumes;
  Range cutFrontVolumes;
  Range constrainSurface;
};
} // namespace MoFEM
 
#endif //__CUTMESHINTERFACE_HPP__
 
/**
 * \defgroup mesh_cut CutMeshInterface
 * \brief Interface to mesh cut mesh
 *
 * \ingroup mofem
 */