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MESQUITE -- The Mesh Quality Improvement Toolkit
Copyright 2004 Sandia Corporation and Argonne National
Laboratory. Under the terms of Contract DE-AC04-94AL85000
with Sandia Corporation, the U.S. Government retains certain
rights in 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
diachin2@llnl.gov, djmelan@sandia.gov, mbrewer@sandia.gov,
pknupp@sandia.gov, tleurent@mcs.anl.gov, tmunson@mcs.anl.gov ,
kraftche@cae.wisc.edu
***************************************************************** */
/*!
\file MeshImpl.hpp
\brief
\author Darryl Melander
\author Thomas Leurent
\author Jason Kraftcheck
\date 2003-04-17
*/
#ifndef MESQUITE_MESH_IMPL_HPP
#define MESQUITE_MESH_IMPL_HPP
#include "MeshInterface.hpp"
#include <map>
#include <iosfwd>
namespace MESQUITE_NS
{
class FileTokenizer;
class MeshImplData;
class MeshImplTags;
struct TagDescription;
/*! \class MeshImpl
\brief MeshImpl is a Mesquite implementation of the Mesh interface.
Applications can also provide their own implementation of the interface.
MeshImpl can read in mesh files in VTK format and ExodusII format.
*/
class MESQUITE_EXPORT MeshImpl : public Mesquite::Mesh
{
public:
//********* Functions that are NOT inherited ************
MeshImpl();
virtual ~MeshImpl();
MeshImpl(int num_vertex, int num_elem,
EntityTopology entity_topology,
const bool *fixed, const double **coords, const int **conn);
MeshImpl(int num_vertex, int num_elem,
const EntityTopology *element_topologies,
const bool *fixed, const double **coords, const int **conn);
void read_vtk(const char* in_filename, Mesquite::MsqError &err);
void write_vtk(const char* out_filename, Mesquite::MsqError &err);
void read_exodus(const char* in_filename, Mesquite::MsqError &err);
void write_exodus(const char* out_filename, Mesquite::MsqError &err);
void mark_skin_fixed( MsqError& err, bool clear_existing = true );
//********* Functions that ARE inherited ************
// Returns whether this mesh lies in a 2D or 3D coordinate system.
virtual int get_geometric_dimension(MsqError &err) ;
/** \brief Get all elements in mesh
*
* Get the handles of every element in the active mesh.
*/
virtual void get_all_elements( std::vector<ElementHandle>& handles,
MsqError& err );
/** \brief Get all vertices in mesh
*
* Get the handles of every vertex in the active mesh
*/
virtual void get_all_vertices( std::vector<VertexHandle>& vertices,
MsqError& err );
// Returns a pointer to an iterator that iterates over the
// set of all vertices in this mesh. The calling code should
// delete the returned iterator when it is finished with it.
// If vertices are added or removed from the Mesh after obtaining
// an iterator, the behavior of that iterator is undefined.
virtual VertexIterator* vertex_iterator(MsqError &err);
// Returns a pointer to an iterator that iterates over the
// set of all top-level elements in this mesh. The calling code should
// delete the returned iterator when it is finished with it.
// If elements are added or removed from the Mesh after obtaining
// an iterator, the behavior of that iterator is undefined.
virtual ElementIterator* element_iterator(MsqError &err);
//************ Vertex Properties ********************
//! Returns true or false, indicating whether the vertex
//! is allowed to be repositioned. True indicates that the vertex
//! is fixed and cannot be moved. Note that this is a read-only
//! property; this flag can't be modified by users of the
//! Mesquite::Mesh interface.
virtual void vertices_get_fixed_flag( const VertexHandle vert_array[],
bool fixed_flag_array[],
size_t num_vtx,
MsqError &err);
void vertices_set_fixed_flag( const VertexHandle vert_array[],
const bool fixed_flag_array[],
size_t num_vtx,
MsqError &err);
virtual void vertices_get_slaved_flag( const VertexHandle vert_array[],
bool slaved_flag_array[],
size_t num_vtx,
MsqError &err );
// Get/set location of a vertex
virtual void vertices_get_coordinates(const Mesh::VertexHandle vert_array[],
Mesquite::MsqVertex* coordinates,
size_t num_vtx,
MsqError &err);
virtual void vertex_set_coordinates(VertexHandle vertex,
const Vector3D &coordinates,
MsqError &err);
// Each vertex has a byte-sized flag that can be used to store
// flags. This byte's value is neither set nor used by the mesh
// implementation. It is intended to be used by Mesquite algorithms.
// Until a vertex's byte has been explicitly set, its value is 0.
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);
// Retrieve the byte value for the specified vertex or vertices.
// The byte value is 0 if it has not yet been set via one of the
// *_set_byte() functions.
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);
//**************** Vertex Topology *****************
/** \brief get elements adjacent to vertices
*
* Get adjacency data for vertices
*
*\param vertex_array Array of vertex handles specifying the
* list of vertices to retrieve adjacency
* data for.
*\param num_vertex Number of vertex handles in #vertex_array
*\param elements The array in which to place the handles of
* elements adjacent to the input vertices.
*\param offsets For each vertex in #vertex_array, the
* value in the corresponding position in this
* array is the index into #elem_array at
* which the adjacency list begins for that
* vertex.
*/
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 );
//*************** Element Topology *************
/** \brief Get element connectivity
*
* Get the connectivity (ordered list of vertex handles) for
* each element in the input array.
*
*\param elem_handles The array of element handles for which to
* retrieve the connectivity list.
*\param num_elems The length of #elem_handles
*\param vert_handles Array in which to place the vertex handles
* in each elements connectivity.
*\param offsets For each element in #elem_handles, the
* value in the same position in this array
* is the index into #vert_handles at which
* the connectivity list for that element begins.
*/
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);
// Returns the topologies of the given entities. The "entity_topologies"
// array must be at least "num_elements" in size.
virtual void elements_get_topologies(const ElementHandle *element_handle_array,
EntityTopology *element_topologies,
size_t num_elements,
MsqError &err);
//*************** Tags ***********
/** \brief Create a tag
*
* Create a user-defined data type that can be attached
* to any element or vertex in the mesh. For an opaque or
* undefined type, use type=BYTE and length=sizeof(..).
*
* \param tag_name A unique name for the data object
* \param type The type of the data
* \param length Number of values per entity (1->scalar, >1 ->vector)
* \param default_value Default value to assign to all entities - may be NULL
* \return - Handle for tag definition
*/
virtual TagHandle tag_create( const std::string& tag_name,
TagType type, unsigned length,
const void* default_value,
MsqError &err);
/** \brief Remove a tag and all corresponding data
*
* Delete a tag.
*/
virtual void tag_delete( TagHandle handle, MsqError& err );
/** \brief Get handle for existing tag, by name. */
virtual TagHandle tag_get( const std::string& name,
MsqError& err );
/** \brief Get properites of tag
*
* Get data type and number of values per entity for tag.
* \param handle Tag to get properties of.
* \param name_out Passed back tag name.
* \param type_out Passed back tag type.
* \param length_out Passed back number of values per entity.
*/
virtual void tag_properties( TagHandle handle,
std::string& name_out,
TagType& type_out,
unsigned& length_out,
MsqError& err );
/** \brief Set tag values on elements
*
* Set the value of a tag for a list of mesh elements.
* \param handle The tag
* \param num_elems Length of elem_array
* \param elem_array Array of elements for which to set the tag value.
* \param tag_data Tag data for each element, contiguous in memory.
* This data is expected to be
* num_elems*tag_length*sizeof(tag_type) bytes.
*/
virtual void tag_set_element_data( TagHandle handle,
size_t num_elems,
const ElementHandle* elem_array,
const void* tag_data,
MsqError& err );
/** \brief Set tag values on vertices
*
* Set the value of a tag for a list of mesh vertices.
* \param handle The tag
* \param num_elems Length of node_array
* \param node_array Array of vertices for which to set the tag value.
* \param tag_data Tag data for each element, contiguous in memory.
* This data is expected to be
* num_elems*tag_length*sizeof(tag_type) bytes.
*/
virtual void tag_set_vertex_data ( TagHandle handle,
size_t num_elems,
const VertexHandle* node_array,
const void* tag_data,
MsqError& err );
/** \brief Get tag values on elements
*
* Get the value of a tag for a list of mesh elements.
* \param handle The tag
* \param num_elems Length of elem_array
* \param elem_array Array of elements for which to get the tag value.
* \param tag_data Return buffer in which to copy tag data, contiguous
* in memory. This data is expected to be
* num_elems*tag_length*sizeof(tag_type) bytes.
*/
virtual void tag_get_element_data( TagHandle handle,
size_t num_elems,
const ElementHandle* elem_array,
void* tag_data,
MsqError& err );
/** \brief Get tag values on vertices.
*
* Get the value of a tag for a list of mesh vertices.
* \param handle The tag
* \param num_elems Length of elem_array
* \param elem_array Array of vertices for which to get the tag value.
* \param tag_data Return buffer in which to copy tag data, contiguous
* in memory. This data is expected to be
* num_elems*tag_length*sizeof(tag_type) bytes.
*/
virtual void tag_get_vertex_data ( TagHandle handle,
size_t num_elems,
const VertexHandle* node_array,
void* tag_data,
MsqError& err );
//**************** Memory Management ****************
// Tells the mesh that the client is finished with a given
// entity handle.
virtual void release_entity_handles( const EntityHandle *handle_array,
size_t num_handles,
MsqError &err );
// Instead of deleting a Mesh when you think you are done,
// call release(). In simple cases, the implementation could
// just call the destructor. More sophisticated implementations
// may want to keep the Mesh object to live longer than Mesquite
// is using it.
virtual void release();
// Remove all data
void clear();
protected:
/** Coordinate values per vertex */
int numCoords;
MeshImplData* myMesh;
MeshImplTags* myTags;
private:
//**************** VTK Parsing ****************
/** Read a data block from the file */
void vtk_read_dataset( FileTokenizer& file, MsqError& err );
/** Read structured point mesh */
void vtk_read_structured_points( FileTokenizer& file, MsqError& err );
/** Read structured grid mesh */
void vtk_read_structured_grid ( FileTokenizer& file, MsqError& err );
/** Read rectilinear grid structured mesh */
void vtk_read_rectilinear_grid ( FileTokenizer& file, MsqError& err );
/** Read polydata mesh */
void vtk_read_polydata ( FileTokenizer& file, MsqError& err );
/** Read unstructured mesh */
void vtk_read_unstructured_grid( FileTokenizer& file, MsqError& err );
/** Read file-level field data */
void vtk_read_field ( FileTokenizer& file, MsqError& err );
/** Helper function for vtk_read_polydata() - reads polygon subsection */
void vtk_read_polygons( FileTokenizer& file, MsqError& err );
/** Helper function for readers of structured mesh - create elements */
void vtk_create_structured_elems( const long* dims, MsqError& err );
/** Read attribute data for vertices */
void vtk_read_point_data( FileTokenizer& file, MsqError& err );
/** Read attribute data for elements */
void vtk_read_cell_data ( FileTokenizer& file, MsqError& err );
/** Store data read in vtk_read_point_data into mesh tags */
void vtk_store_point_data( const void* data, TagDescription& desc, MsqError& );
/** Store data read in vtk_read_cell_data into mesh tags */
void vtk_store_cell_data( const void* data, TagDescription& desc, MsqError& );
/** Read actual data for both vtk_read_point_data() and vtk_read_cell_data()
* Initializes all fields of passed TagDescription
*\return NULL if field data, otherwise pointer to malloc'd data.
*/
void* vtk_read_attrib_data( FileTokenizer& file,
long num_data_to_read,
TagDescription& tag_out,
MsqError& err );
/** Read a 2-D array of data of the specified type from the file
* Initializes size and type fields of passed TagDescroption */
void* vtk_read_typed_data( FileTokenizer& file, int type,
size_t per_elem, size_t num_elem,
TagDescription& tag_out,
MsqError& err );
/** Read field data
*\param count expected number of tuples, or zero if not known
*/
void* vtk_read_field_data( FileTokenizer& file, size_t count,
size_t field_count,
const std::string& field_name,
TagDescription& tag,
MsqError& err );
/** Read scalar attribute data
* Initializes size and type fields of passed TagDescroption */
void* vtk_read_scalar_attrib ( FileTokenizer& file, long count,
TagDescription& tag_out, MsqError& err );
/** Read color attribute data
* Initializes size and type fields of passed TagDescroption */
void* vtk_read_color_attrib ( FileTokenizer& file, long count,
TagDescription& tag_out, MsqError& err );
/** Read vector or normal attribute data
* Initializes size and type fields of passed TagDescroption */
void* vtk_read_vector_attrib ( FileTokenizer& file, long count,
TagDescription& tag_out, MsqError& err );
/** Read texture attribute data
* Initializes size and type fields of passed TagDescroption */
void* vtk_read_texture_attrib( FileTokenizer& file, long count,
TagDescription& tag_out, MsqError& err );
/** Read tensor (3x3 matrix) data
* Initializes size and type fields of passed TagDescroption */
void* vtk_read_tensor_attrib ( FileTokenizer& file, long count,
TagDescription& tag_out, MsqError& err );
/** Write tag data to VTK attributes */
void vtk_write_attrib_data( std::ostream& file,
const TagDescription& desc,
const void* data, size_t count,
MsqError& err ) const;
/** Convert tag data stored on vertices to boolean values.
* Deletes tag data.
* Passes back empty result vector if no tag.
*/
void tag_to_bool( const char* tag_name,
std::vector<bool>& vertex_vals,
MsqError& err );
//**************** End VTK Parsing ****************
};
}
#endif
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