mesh.h

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/*!
 *
 * Copyright (C) 2015 Technical University of Liberec.  All rights reserved.
 * 
 * This program is free software; you can redistribute it and/or modify it under
 * the terms of the GNU General Public License version 3 as published by the
 * Free Software Foundation. (http://www.gnu.org/licenses/gpl-3.0.en.html)
 * 
 * This program is distributed in the hope that it will be useful, but WITHOUT
 * ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
 * FOR A PARTICULAR PURPOSE.  See the GNU General Public License for more details.
 *
 * 
 * @file    mesh.h
 * @brief   
 */

#ifndef MAKE_MESH_H
#define MAKE_MESH_H

#include <vector>
#include <mpi.h>

#include "mesh/mesh_types.hh"

#include "mesh/nodes.hh"
//#include "mesh/elements.h"
//#include "mesh/sides.h"
#include "mesh/edges.h"
#include "mesh/neighbours.h"
#include "mesh/boundaries.h"
#include "mesh/intersection.hh"
#include "mesh/partitioning.hh"
#include "mesh/region_set.hh"


#include "input/input_type_forward.hh"
#include "input/accessors_forward.hh"
#include "system/exceptions.hh"




#define ELM  0
#define BC  1
#define NODE  2

/**
 *  This parameter limits volume of elements from below.
 */
#define MESH_CRITICAL_VOLUME 1.0E-12

/**
 * Provides for statement to iterate over the Nodes of the Mesh.
 * The parameter is FullIter local variable of the cycle, so it need not be declared before.
 * Macro assume that variable Mesh *mesh; is declared and points to a valid Mesh structure.
 */
#define FOR_NODES(_mesh_, i) \
    for( NodeFullIter i( (_mesh_)->node_vector.begin() ); \
        i != (_mesh_)->node_vector.end(); \
        ++i)

/**
 * Macro for conversion form Iter to FullIter for nodes.
 */
#define NODE_FULL_ITER(_mesh_,i) \
    (_mesh_)->node_vector.full_iter(i)

/**
 * Macro to get "NULL" ElementFullIter.
 */
#define NODE_FULL_ITER_NULL(_mesh_) \
    NodeFullIter((_mesh_)->node_vector)

/**
 * Macro for conversion form Iter to FullIter for elements.
 */
#define ELEM_FULL_ITER(_mesh_,i) \
    (_mesh_)->element.full_iter(i)


#define FOR_NODE_ELEMENTS(i,j)   for((j)=0;(j)<(i)->n_elements();(j)++)
#define FOR_NODE_SIDES(i,j)      for((j)=0;(j)<(i)->n_sides;(j)++)


class BoundarySegment {
public:
    static Input::Type::Record input_type;
};

//=============================================================================
// STRUCTURE OF THE MESH
//=============================================================================

class Mesh {
public:
    TYPEDEF_ERR_INFO( EI_ElemLast, int);
    TYPEDEF_ERR_INFO( EI_ElemNew, int);
    TYPEDEF_ERR_INFO( EI_RegLast, std::string);
    TYPEDEF_ERR_INFO( EI_RegNew, std::string);
    DECLARE_EXCEPTION(ExcDuplicateBoundary,
            << "Duplicate boundary elements! \n"
            << "Element id: " << EI_ElemLast::val << " on region name: " << EI_RegLast::val << "\n"
            << "Element id: " << EI_ElemNew::val << " on region name: " << EI_RegNew::val << "\n");



    static const unsigned int undef_idx=-1;
    static const Input::Type::Record & get_input_type();



    /** Labels for coordinate indexes in arma::vec3 representing vectors and points.*/
    enum {x_coord=0, y_coord=1, z_coord=2};

    /**
     * Constructor from an input record.
     * Do not process input record. That is done in init_from_input.
     */
    Mesh(Input::Record in_record, MPI_Comm com = MPI_COMM_WORLD);
    /**
     * Common part of both previous constructors and way how to reinitialize a mesh from the  given input record.
     */
    void reinit(Input::Record in_record);

    /// Destructor.
    ~Mesh();

    inline unsigned int n_nodes() const {
        return node_vector.size();
    }

    inline unsigned int n_elements() const {
        return element.size();
    }

    inline unsigned int n_boundaries() const {
        return boundary_.size();
    }

    inline unsigned int n_edges() const {
        return edges.size();
    }

    unsigned int n_corners();

    inline const RegionDB &region_db() const {
        return region_db_;
    }

    /**
     * Returns pointer to partitioning object. Partitioning is created during setup_topology.
     */
    Partitioning *get_part();

    Distribution *get_el_ds() const
    { return el_ds; }

    int *get_row_4_el() const
    { return row_4_el; }

    int *get_el_4_loc() const
    { return el_4_loc; }

    /**
     * Returns MPI communicator of the mesh.
     */
    inline MPI_Comm get_comm() const { return comm_; }


    void make_intersec_elements();

    unsigned int n_sides();

    inline unsigned int n_vb_neighbours() const {
        return vb_neighbours_.size();
    }

    /**
     * Returns maximal number of sides of one edge, which connects elements of dimension @p dim.
     * @param dim Dimension of elements sharing the edge.
     */
    unsigned int max_edge_sides(unsigned int dim) const { return max_edge_sides_[dim-1]; }

    /**
     * Reads mesh from stream.
     *
     * Method is especially used in unit tests.
     */
    void read_gmsh_from_stream(istream &in);
    /**
     * Reads input record, creates regions, read the mesh, setup topology. creates region sets.
     */
    void init_from_input();


    /**
     * Returns vector of ID numbers of elements, either bulk or bc elemnts.
     */
    vector<int> const & elements_id_maps( bool boundary_domain) const;


    ElementAccessor<3> element_accessor(unsigned int idx, bool boundary=false);

    /**
     * Reads elements and their affiliation to regions and region sets defined by user in input file
     * Format of input record is defined in method RegionSetBase::get_input_type()
     *
     * @param region_list Array input AbstractRecords which define regions, region sets and elements
     */
    void read_regions_from_input(Input::Array region_list);

    /// Vector of nodes of the mesh.
    NodeVector node_vector;
    /// Vector of elements of the mesh.
    ElementVector element;

    /// Vector of boundary sides where is prescribed boundary condition.
    /// TODO: apply all boundary conditions in the main assembling cycle over elements and remove this Vector.
    vector<Boundary> boundary_;
    /// vector of boundary elements - should replace 'boundary'
    /// TODO: put both bulk and bc elements (on zero level) to the same vector or make better map id->element for field inputs that use element IDs
    /// the avoid usage of ElementVector etc.
    ElementVector bc_elements;

    /// Vector of MH edges, this should not be part of the geometrical mesh
    std::vector<Edge> edges;

    //flow::VectorId<int> bcd_group_id; // gives a index of group for an id

    /**
     * Vector of individual intersections of two elements.
     * This is enough for local mortar.
     */
    vector<Intersection>  intersections;

    /**
     * For every element El we have vector of indices into @var intersections array for every intersection in which El is master element.
     * This is necessary for true mortar.
     */
    vector<vector<unsigned int> >  master_elements;

    /**
     * Vector of compatible neighbourings.
     */
    vector<Neighbour> vb_neighbours_;

    int n_insides; // # of internal sides
    int n_exsides; // # of external sides
    int n_sides_; // total number of sides (should be easy to count when we have separated dimensions

    int n_lines; // Number of line elements
    int n_triangles; // Number of triangle elements
    int n_tetrahedras; // Number of tetrahedra elements

    // Temporary solution for numbering of nodes on sides.
    // The data are defined in RefElement<dim>::side_nodes,
    // Mesh::side_nodes can be removed as soon as Element
    // is templated by dimension.
    //
    // for every side dimension D = 0 .. 2
    // for every element side 0 .. D+1
    // for every side node 0 .. D
    // index into element node array
    vector< vector< vector<unsigned int> > > side_nodes;

    /**
     * Check usage of regions, set regions to elements defined by user, close RegionDB
     */
    void check_and_finish();
    
    const BIHTree &get_bih_tree();

    // For each node the vector contains a list of elements that use this node
    vector<vector<unsigned int> > node_elements;


protected:

    /**
     *  This replaces read_neighbours() in order to avoid using NGH preprocessor.
     *
     *  TODO:
     *  - Avoid maps:
     *
     *    4) replace EdgeVector by std::vector<Edge> (need not to know the size)
     *
     *    5) need not to have temporary array for Edges, only postpone setting pointers in elements and set them
     *       after edges are found; we can temporary save Edge index instead of pointer in Neigbours and elements
     *
     *    6) Try replace Edge * by indexes in Neigbours and elements (anyway we have mesh pointer in elements so it is accessible also from Neigbours)
     *
     */
    void make_neighbours_and_edges();

    /**
     * On edges sharing sides of many elements it may happen that each side has its nodes ordered in a different way.
     * This method finds the permutation for each side so as to obtain the ordering of side 0.
     */
    void make_edge_permutations();
    /**
     * Create element lists for nodes in Mesh::nodes_elements.
     */
    void create_node_element_lists();
    /**
     * Find intersection of element lists given by Mesh::node_elements for elements givne by @p nodes_list parameter.
     * The result is placed into vector @p intersection_element_list. If the @p node_list is empty, and empty intersection is
     * returned.
     */
    void intersect_element_lists(vector<unsigned int> const &nodes_list, vector<unsigned int> &intersection_element_list);
    /**
     * Remove elements with dimension not equal to @p dim from @p element_list. Index of the first element of dimension @p dim-1,
     * is returned in @p element_idx. If no such element is found the method returns false, if one such element is found the method returns true,
     * if more elements are found we report an user input error.
     */
    bool find_lower_dim_element(ElementVector&elements, vector<unsigned int> &element_list, unsigned int dim, unsigned int &element_idx);

    /**
     * Returns true if side @p si has same nodes as in the list @p side_nodes.
     */
    bool same_sides(const SideIter &si, vector<unsigned int> &side_nodes);

    /**
     * Initialize all mesh structures from raw information about nodes and elements (including boundary elements).
     * Namely: create remaining boundary elements and Boundary objects, find edges and compatible neighborings.
     */
    void setup_topology();


    void element_to_neigh_vb();

    void count_element_types();
    void count_side_types();

    /**
     * Possibly modify region id of elements sets by user in "regions" part of input file.
     *
     * TODO: This method needs check in issue 'Review mesh setting'.
     * Changes have been done during generalized region key and may be causing problems
     * during the further development.
     */
    void modify_element_ids(const RegionDB::MapElementIDToRegionID &map);

    unsigned int n_bb_neigh, n_vb_neigh;

    /// Vector of both bulk and boundary IDs. Bulk elements come first, then boundary elements, but only the portion that appears
    /// in input mesh file and has ID assigned.
    ///
    /// TODO: Rather should be part of GMSH reader, but in such case we need store pointer to it in the mesh (good idea, but need more general interface for readers)
    mutable vector<int> bulk_elements_id_, boundary_elements_id_;
    /// Number of elements read from input.
    unsigned int n_all_input_elements_;

    /// Maximal number of sides per one edge in the actual mesh (set in make_neighbours_and_edges()).
    unsigned int max_edge_sides_[3];

    /**
     * Database of regions (both bulk and boundary) of the mesh. Regions are logical parts of the
     * domain that allows setting of different data and boundary conditions on them.
     */
    RegionDB region_db_;
    /**
     * Mesh partitioning. Created in setup_topology.
     */
    std::shared_ptr<Partitioning> part_;

    /**
     * BIH Tree for intersection and observe points lookup.
     */
    std::shared_ptr<BIHTree> bih_tree_;
    /**
     * Accessor to the input record for the mesh.
     */
    Input::Record in_record_;

    /**
     * MPI communicator used for partitioning and ...
     */
    MPI_Comm comm_;

    friend class GmshMeshReader;
    friend class RegionSetBase;


private:

    /// Index set assigning to global element index the local index used in parallel vectors.
    int *row_4_el;
    /// Index set assigning to local element index its global index.
    int *el_4_loc;
    /// Parallel distribution of elements.
    Distribution *el_ds;
};


#include "mesh/side_impl.hh"
#include "mesh/element_impls.hh"
#include "mesh/neighbours_impl.hh"

/**
 * Provides for statement to iterate over the Elements of the Mesh.
 * The parameter is FullIter local variable of the cycle, so it need not be declared before.
 * Macro assume that variable Mesh *mesh; is declared and points to a valid Mesh structure.
 */
#define FOR_ELEMENTS(_mesh_,__i) \
    for( ElementFullIter __i( (_mesh_)->element.begin() ); \
        __i != (_mesh_)->element.end(); \
        ++__i)

/**
 * Macro for conversion form Iter to FullIter for elements.
 */
#define ELEMENT_FULL_ITER(_mesh_,i) \
    (_mesh_)->element.full_iter(i)

/**
 * Macro to get "NULL" ElementFullIter.
 */
#define ELEMENT_FULL_ITER_NULL(_mesh_) \
    ElementFullIter((_mesh_)->element)


#define FOR_BOUNDARIES(_mesh_,i) \
for( std::vector<Boundary>::iterator i= (_mesh_)->boundary_.begin(); \
    i != (_mesh_)->boundary_.end(); \
    ++i)

/**
 * Macro for conversion form Iter to FullIter for boundaries.
 */
#define BOUNDARY_FULL_ITER(_mesh_,i) \
    (_mesh_)->boundary.full_iter(i)

/**
 * Macro to get "NULL" BoundaryFullIter.
 */
#define BOUNDARY_NULL(_mesh_) \
    BoundaryFullIter((_mesh_)->boundary)


/**
 * Provides for statement to iterate over the Edges of the Mesh. see FOR_ELEMENTS
 */
#define FOR_EDGES(_mesh_,__i) \
    for( vector<Edge>::iterator __i = (_mesh_)->edges.begin(); \
        __i !=(_mesh_)->edges.end(); \
        ++__i)

#define FOR_SIDES(_mesh_, it) \
    FOR_ELEMENTS((_mesh_), ele)  \
        for(SideIter it = ele->side(0); it->el_idx() < ele->n_sides(); ++it)

#define FOR_SIDE_NODES(i,j) for((j)=0;(j)<(i)->n_nodes;(j)++)


#define FOR_NEIGHBOURS(_mesh_, it) \
    for( std::vector<Neighbour>::iterator it = (_mesh_)->vb_neighbours_.begin(); \
         (it)!= (_mesh_)->vb_neighbours_.end(); ++it)

#define FOR_NEIGH_ELEMENTS(i,j) for((j)=0;(j)<(i)->n_elements;(j)++)
#define FOR_NEIGH_SIDES(i,j)    for((j)=0;(j)<(i)->n_sides;(j)++)


#endif
//-----------------------------------------------------------------------------
// vim: set cindent: