ArrayMesh.hpp

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/* *****************************************************************
    MESQUITE -- The Mesh Quality Improvement Toolkit

    Copyright 2007 Sandia National Laboratories.  Developed at the
    University of Wisconsin--Madison under SNL contract number
    624796.  The U.S. Government and the University of Wisconsin
    retain certain rights to this software.

    This library is free software; you can redistribute it and/or
    modify it under the terms of the GNU Lesser General Public
    License as published by the Free Software Foundation; either
    version 2.1 of the License, or (at your option) any later version.

    This library 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
    Lesser General Public License for more details.

    You should have received a copy of the GNU Lesser General Public License
    (lgpl.txt) along with this library; if not, write to the Free Software
    Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA

    (2007) kraftche@cae.wisc.edu

  ***************************************************************** */

/** \file ArrayMesh.hpp
 *  \brief Access mesh stored in arrays
 *  \author Jason Kraftcheck
 */

#ifndef MSQ_ARRAY_MESH_HPP
#define MSQ_ARRAY_MESH_HPP

#include "Mesquite.hpp"
#include "MeshInterface.hpp"

namespace MBMesquite
{

class ArrayMesh : public Mesh
{
  public:
    /** Create a MBMesquite::Mesh instance that wraps application-provided
     *  arrays.
     *
     * Note:  An instance of this class will reference the passed in
     *        arrays.  It will not copy them.
     *
     *\param coords_per_vertex Dimension of the mesh (2 or 3)
     *\param num_vertices      Number of vertices in the mesh
     *\param interleaved_vertex_coords Vertex coordinates.  Ordered as
     *                         [x1, y1, z1, x2, y2, z2, ...]
     *\param vertex_fixed_flags One value per vertex.  Zero if vertex is
     *                         free, one if the position is fixed.
     *\param num_elements      Number of elements in the mesh
     *\param element_type      The type of the elements
     *\param element_connectivity_array Element connectivity, specified
     *                         as vertex indices such that the location
     *                         of the vertex coordinates in vertex_coords
     *                         is at 3 times the value in this array.
     *\param one_based_conn_indices Use one-based (Fortran) array indexing.
     *\param nodes_per_element Number of nodes in each element.  If not
     *                         specified, number of nodes in a linear
     *                         element with the type 'element_type' is
     *                         assumed.
     *\param vertex_slaved_flags One value per vertex.  Zero if vertex is
     *                         free, one if the vertex is slaved to the
     *                         logical position of the element mapping/shape
     *                         function..
     */
    ArrayMesh( int coords_per_vertex, unsigned long num_vertices, double* interleaved_vertex_coords,
               const int* vertex_fixed_flags, unsigned long num_elements, EntityTopology element_type,
               const unsigned long* element_connectivity_array, bool one_based_conn_indices = false,
               unsigned nodes_per_element = 0, const int* vertex_slaved_flags = 0 );

    /** Create a MBMesquite::Mesh instance that wraps application-provided
     *  arrays.
     *
     * Note:  An instance of this class will reference the passed in
     *        arrays.  It will not copy them.
     *
     *\param coords_per_vertex Dimension of the mesh (2 or 3)
     *\param num_vertices      Number of vertices in the mesh
     *\param interleaved_vertex_coords Vertex coordinates.  Ordered as
     *                         [x1, y1, z1, x2, y2, z2, ...]
     *\param vertex_fixed_flags One value per vertex.  Zero if vertex is
     *                         free, one if the poistion is fixed.
     *\param num_elements      Number of elements in the mesh
     *\param element_types     The topological type for each element.
     *\param element_connectivity_array Element connectivity, specified
     *                         as vertex indices such that the location
     *                         of the vertex coordinates in vertex_coords
     *                         is at 3 times the value in this array.
     *\param element_connectivity_offsets An optional array of length one greater
     *                         than num_elements.  Each entry other than
     *                         the last should contain the value of the
     *                         index into element_connectivity_array at
     *                         which the connectivity data for the
     *                         corresponding element begins.  The last
     *                         entry in the array must be the next-to-last
     *                         entry plus the length of the connectivity
     *                         data for the last element, such that the
     *                         length of the connectivity data for any
     *                         element 'e' can be calculated with:
     *                           n = element_connectivity_offsets[e+1] -
     *element_connectivity_offsets[e]
     *
     *                         If this array is not specified, then it
     *                         will be assumed that the length of the
     *                         connectivity data for each element is the
     *                         number of corners necessary to represent
     *                         its topological type (that it has no higher-order
     *                         nodes.)
     *\param one_based_conn_indices Use one-based (Fortran) array indexing.
     *\param vertex_slaved_flags One value per vertex.  Zero if vertex is
     *                         free, one if the vertex is slaved to the
     *                         logical position of the element mapping/shape
     *                         function..
     */
    ArrayMesh( int coords_per_vertex, unsigned long num_vertices, double* interleaved_vertex_coords,
               const int* vertex_fixed_flags, unsigned long num_elements, const EntityTopology* element_types,
               const unsigned long* element_connectivity_array,
               const unsigned long* element_connectivity_offsets = NULL, bool one_based_conn_indices = false,
               const int* vertex_slaved_flags = 0 );

    ArrayMesh();

    ~ArrayMesh();

    void clear_mesh();
    void set_mesh( int coords_per_vertex, unsigned long num_vertices, double* interleaved_vertex_coords,
                   const int* vertex_fixed_flags, unsigned long num_elements, EntityTopology element_type,
                   const unsigned long* element_connectivity_array, bool one_based_conn_indices = false,
                   unsigned nodes_per_element = 0, const int* vertex_slaved_flags = 0 );

    /**\brief Give mesquite access to per-entity application data via a tag
     *
     * Allow mesquite to access application-owned per-element and/or per-vertex
     * data by assigning a tag name to said data.  Mesquite will be allowed
     * to read application-owned data.  Any attempt by Mesquite to modify
     * the data will result in an internal error condition.
     *
     *\param tag_name  Tag name through which Mesquite can access the data
     *\param data_type The type of the data
     *\param vals_per_entity Number of values of type \c data_type that each entity has
     *                       Data is assumed to be interleaved such that all values
     *                       associated with a a single entity are adjacent in memory
     *\param vertex_data     A pointer to the region of memory in which per-vertex
     *                       values are stored.  May be NULL if per-vertex data is
     *                       not available.  Values are assumed to be in the same
     *                       order as the vertex coordinates passed to the constructor
     *                       or \c set_mesh.
     *\param vertex_data     A pointer to the region of memory in which per-element
     *                       values are stored.  May be NULL if per-element data is
     *                       not available.  Values are assumed to be in the same
     *                       order as the element connetivity passed to the constructor
     *                       or \c set_mesh.
     *\param default_value   Value to return for all vertices and/or all elements
     *                       if the cooresponding data array is null.  May be
     *                       NULL if no default value.
     */
    TagHandle add_read_only_tag_data( const char* tag_name, TagType data_type, int vals_per_entity,
                                      const void* vertex_data, const void* element_data, const void* default_value,
                                      MsqError& err );

    /**\brief Give mesquite access to per-entity application data via a tag
     *
     * Allow mesquite to access and/or set application-owned per-element
     * and/or per-vertex data by assigning a tag name to said data.
     *
     *\param tag_name  Tag name through which Mesquite can access the data
     *\param data_type The type of the data
     *\param vals_per_entity Number of values of type \c data_type that each entity has
     *                       Data is assumed to be interleaved such that all values
     *                       associated with a a single entity are adjacent in memory
     *\param vertex_data     A pointer to the region of memory in which per-vertex
     *                       values are stored.  May be NULL if per-vertex data is
     *                       not available.  Values are assumed to be in the same
     *                       order as the vertex coordinates passed to the constructor
     *                       or \c set_mesh.
     *\param vertex_data     A pointer to the region of memory in which per-element
     *                       values are stored.  May be NULL if per-element data is
     *                       not available.  Values are assumed to be in the same
     *                       order as the element connetivity passed to the constructor
     *                       or \c set_mesh.
     *\param default_value   Value to return for all vertices and/or all elements
     *                       if the cooresponding data array is null.  May be
     *                       NULL if no default value.
     */
    TagHandle add_writable_tag_data( const char* tag_name, TagType tag_data_type, int vals_per_entity,
                                     void* vertex_data, void* element_data, const void* default_value, MsqError& err );

    virtual int get_geometric_dimension( MsqError& err );

    virtual void get_all_elements( std::vector< ElementHandle >& elements, MsqError& err );
    virtual void get_all_vertices( std::vector< VertexHandle >& vertices, MsqError& err );

    virtual VertexIterator* vertex_iterator( MsqError& err );
    virtual ElementIterator* element_iterator( MsqError& err );

    virtual void vertices_get_fixed_flag( const VertexHandle vert_array[], std::vector< bool >& fixed_flag_array,
                                          size_t num_vtx, MsqError& err );
    virtual void vertices_get_slaved_flag( const VertexHandle vert_array[], std::vector< bool >& slaved_flag_array,
                                           size_t num_vtx, MsqError& err );
    virtual void vertices_get_coordinates( const VertexHandle vert_array[], MsqVertex* coordinates, size_t num_vtx,
                                           MsqError& err );
    virtual void vertex_set_coordinates( VertexHandle vertex, const Vector3D& coordinates, MsqError& err );

    virtual void vertex_set_byte( VertexHandle vertex, unsigned char byte, MsqError& err );
    virtual void vertices_set_byte( const VertexHandle* vert_array, const unsigned char* byte_array, size_t array_size,
                                    MsqError& err );

    virtual void vertex_get_byte( const VertexHandle vertex, unsigned char* byte, MsqError& err );
    virtual void vertices_get_byte( const VertexHandle* vertex, unsigned char* byte_array, size_t array_size,
                                    MsqError& err );

    virtual void vertices_get_attached_elements( const VertexHandle* vertex_array, size_t num_vertex,
                                                 std::vector< ElementHandle >& elements, std::vector< size_t >& offsets,
                                                 MsqError& err );

    virtual void elements_get_attached_vertices( const ElementHandle* elem_handles, size_t num_elems,
                                                 std::vector< VertexHandle >& vert_handles,
                                                 std::vector< size_t >& offsets, MsqError& err );

    virtual void elements_get_topologies( const ElementHandle* element_handle_array, EntityTopology* element_topologies,
                                          size_t num_elements, MsqError& err );

    virtual TagHandle tag_create( const std::string& tag_name, TagType type, unsigned length, const void* default_value,
                                  MsqError& err );

    virtual void tag_delete( TagHandle handle, MsqError& err );

    virtual TagHandle tag_get( const std::string& name, MsqError& err );

    virtual void tag_properties( TagHandle handle, std::string& name_out, TagType& type_out, unsigned& length_out,
                                 MsqError& err );

    virtual void tag_set_element_data( TagHandle handle, size_t num_elems, const ElementHandle* elem_array,
                                       const void* tag_data, MsqError& err );

    virtual void tag_set_vertex_data( TagHandle handle, size_t num_elems, const VertexHandle* node_array,
                                      const void* tag_data, MsqError& err );

    virtual void tag_get_element_data( TagHandle handle, size_t num_elems, const ElementHandle* elem_array,
                                       void* tag_data, MsqError& err );

    virtual void tag_get_vertex_data( TagHandle handle, size_t num_elems, const VertexHandle* node_array,
                                      void* tag_data, MsqError& err );

    virtual void release_entity_handles( const EntityHandle* handle_array, size_t num_handles, MsqError& err );

    virtual void release();

  private:
    inline const unsigned long* elem_verts( size_t elem_index, int& num_vertex ) const;

    void build_vertex_adjacency_list();

    int mDimension;                  //!< Coordinates per vertex
    unsigned long vertexCount;       //!< Number of vertices
    double* coordArray;              //!< Interleaved vertex coordinates
    const int* fixedFlags;           //!< Vertex fixed flags
    const int* slavedFlags;          //!< Vertex slaved flags
    unsigned char* vertexByteArray;  //!< Vertex bytes

    unsigned long elementCount;          //!< Number of elements
    const unsigned long* connArray;      //!< Element connectivity
    const unsigned long* connOffsets;    //!< Offsets into connectivity array
                                         //!< for each element.  If NULL, then
                                         //!< all elements are of the same type
                                         //!< and have the same number of vertices.
    unsigned long* allocConnOffsets;     //!< Same as connOffsets if allocated
                                         //!< by constructor.  NULL if connOffsets
                                         //!< is either NULL or application-provided
                                         //!< data.
    EntityTopology elementType;          //!< Type for all elements if connOffsets is NULL
    const EntityTopology* elementTypes;  //!< Type for each element type if connOffsets is not NULL
    unsigned nodesPerElement;            //!< Nodes per element if connOffsets is NULL
    bool oneBasedArrays;                 //!< FORTRAN-style array indexing

    unsigned long* vertexAdjacencyList;
    unsigned long* vertexAdjacencyOffsets;

    static unsigned bytes( TagType type );

    static void fill( unsigned char* buffer, const unsigned char* value, size_t size, size_t count );

    struct Tag
    {
        char* name;                       //!< Tag name (null-terminated string)
        TagType type;                     //!< tag data type
        unsigned size;                    //!< number of *bytes* per entity
        bool owned;                       //!< true if memory for tag storage is owned by this class
        unsigned char* vtxWritePtr;       //!< pointer to writable tag data (NULL if read-only)
        const unsigned char* vtxReadPtr;  //!< pointer to tag data
        unsigned char* eleWritePtr;       //!< pointer to writable tag data (NULL if read-only)
        const unsigned char* eleReadPtr;  //!< pointer to tag data
        unsigned char* defaultValue;      //!< Default value
        Tag* next;                        //!< Linked-list next pointer
    };

    Tag* allocate_tag( const char* name, bool owned, TagType type, unsigned size, const void* vertex_ro_data,
                       void* vertex_rw_data, const void* element_ro_data, void* element_rw_data,
                       const void* default_value, MsqError& err );

    Tag* tagList;

    bool valid() const;
};

}  // namespace MBMesquite

#endif