exodusII_io_helper.h

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// The libMesh Finite Element Library.
// Copyright (C) 2002-2019 Benjamin S. Kirk, John W. Peterson, Roy H. Stogner
 
// 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 along with this library; if not, write to the Free Software
// Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
 
#ifndef LIBMESH_EXODUSII_IO_HELPER_H
#define LIBMESH_EXODUSII_IO_HELPER_H
 
#include "libmesh/libmesh_config.h"
 
#ifdef LIBMESH_HAVE_EXODUS_API
 
// Local includes
#include "libmesh/parallel_object.h"
#include "libmesh/point.h"
#include "libmesh/boundary_info.h" // BoundaryInfo::BCTuple
#include "libmesh/enum_elem_type.h" // INVALID_ELEM
 
// C++ includes
#include <iostream>
#include <string>
#include <vector>
#include <map>
 
// Macros to simplify checking Exodus error codes
#define EX_CHECK_ERR(code, msg)                 \
  do {                                          \
    if ((code) < 0) {                           \
      libmesh_error_msg((msg));                 \
    } } while (0)
 
#define EX_EXCEPTIONLESS_CHECK_ERR(code, msg)   \
  do {                                          \
    if ((code) < 0) {                           \
      libMesh::err << (msg) << std::endl;       \
      libmesh_exceptionless_error();            \
    } } while (0)
 
// Before we include a header wrapped in a namespace, we'd better make
// sure none of its dependencies end up in that namespace
#include <errno.h>
#include <stddef.h>
#include <stdlib.h>
#include <stdint.h>
 
#include <libmesh/ignore_warnings.h>
namespace exII {
extern "C" {
#include "exodusII.h" // defines MAX_LINE_LENGTH, MAX_STR_LENGTH used later
}
}
#include <libmesh/restore_warnings.h>
 
namespace libMesh
{
 
// Forward declarations
class MeshBase;
 
class ExodusII_IO_Helper : public ParallelObject
{
public:
  ExodusII_IO_Helper(const ParallelObject & parent,
                     bool v=false,
                     bool run_only_on_proc0=true,
                     bool single_precision=false);
  ExodusII_IO_Helper (const ExodusII_IO_Helper &) = default;
  ExodusII_IO_Helper (ExodusII_IO_Helper &&) = default;
  ExodusII_IO_Helper & operator= (const ExodusII_IO_Helper &) = default;
  ExodusII_IO_Helper & operator= (ExodusII_IO_Helper &&) = default;
  virtual ~ExodusII_IO_Helper();
 
  const char * get_elem_type() const;
 
  void open(const char * filename, bool read_only);
 
  void read_header();
 
  void read_qa_records();
 
  void print_header();
 
  void read_nodes();
 
  void read_node_num_map();
 
  void print_nodes(std::ostream & out = libMesh::out);
 
  void read_block_info();
 
  int get_block_id(int index);
 
  std::string get_block_name(int index);
 
  int get_side_set_id(int index);
 
  std::string get_side_set_name(int index);
 
  int get_node_set_id(int index);
 
  std::string get_node_set_name(int index);
 
  void read_elem_in_block(int block);
 
  void read_edge_blocks(MeshBase & mesh);
 
  void read_elem_num_map();
 
  void read_sideset_info();
 
  void read_nodeset_info();
 
  void read_sideset(int id, int offset);
 
  void read_nodeset(int id);
 
  void read_all_nodesets();
 
  void close();
 
  int inquire(int req_info, std::string error_msg="");
 
  void read_time_steps();
 
  void read_num_time_steps();
 
  void read_nodal_var_values(std::string nodal_var_name, int time_step);
 
  void read_elemental_var_values(std::string elemental_var_name,
                                 int time_step,
                                 std::map<dof_id_type, Real> & elem_var_value_map);
 
  virtual void create(std::string filename);
 
  virtual void initialize(std::string title, const MeshBase & mesh, bool use_discontinuous=false);
 
  virtual void write_nodal_coordinates(const MeshBase & mesh, bool use_discontinuous=false);
 
  virtual void write_elements(const MeshBase & mesh, bool use_discontinuous=false);
 
  virtual void write_sidesets(const MeshBase & mesh);
 
  virtual void write_nodesets(const MeshBase & mesh);
 
  virtual void initialize_element_variables(std::vector<std::string> names,
                                            const std::vector<std::set<subdomain_id_type>> & vars_active_subdomains);
 
  void initialize_nodal_variables(std::vector<std::string> names);
 
  void initialize_global_variables(std::vector<std::string> names);
 
  void write_timestep(int timestep, Real time);
 
  void
  write_sideset_data (const MeshBase & mesh,
                      int timestep,
                      const std::vector<std::string> & var_names,
                      const std::vector<std::set<boundary_id_type>> & side_ids,
                      const std::vector<std::map<BoundaryInfo::BCTuple, Real>> & bc_vals);
 
  void
  read_sideset_data (const MeshBase & mesh,
                     int timestep,
                     std::vector<std::string> & var_names,
                     std::vector<std::set<boundary_id_type>> & side_ids,
                     std::vector<std::map<BoundaryInfo::BCTuple, Real>> & bc_vals);
 
  void write_element_values
  (const MeshBase & mesh,
   const std::vector<Real> & values,
   int timestep,
   const std::vector<std::set<subdomain_id_type>> & vars_active_subdomains);
 
  void write_element_values_element_major
  (const MeshBase & mesh,
   const std::vector<Real> & values,
   int timestep,
   const std::vector<std::set<subdomain_id_type>> & vars_active_subdomains,
   const std::vector<std::string> & derived_var_names,
   const std::map<subdomain_id_type, std::vector<std::string>> & subdomain_to_var_names);
 
  void write_nodal_values(int var_id, const std::vector<Real> & values, int timestep);
 
  void write_information_records(const std::vector<std::string> & records);
 
  void write_global_values(const std::vector<Real> & values, int timestep);
 
  void read_global_values(std::vector<Real> & values, int timestep);
 
  void use_mesh_dimension_instead_of_spatial_dimension(bool val);
 
  void write_as_dimension(unsigned dim);
 
  void set_coordinate_offset(Point p);
 
  std::vector<std::string> get_complex_names(const std::vector<std::string> & names) const;
 
  std::vector<std::set<subdomain_id_type>> get_complex_vars_active_subdomains(
    const std::vector<std::set<subdomain_id_type>> & vars_active_subdomains) const;
 
  std::map<subdomain_id_type, std::vector<std::string>>
  get_complex_subdomain_to_var_names(
    const std::map<subdomain_id_type, std::vector<std::string>> & subdomain_to_var_names) const;
 
  class Conversion;
 
  class NamesData;
 
  void message(const std::string & msg);
 
  void message(const std::string & msg, int i);
 
  // File identification flag
  int ex_id;
 
  // General error flag
  int ex_err;
 
  // Number of dimensions in the mesh
  int num_dim;
 
  // Number of global variables
  int num_global_vars;
 
  // Number of sideset variables
  int num_sideset_vars;
 
  // Total number of nodes in the mesh
  int num_nodes;
 
  // Total number of elements in the mesh
  int num_elem;
 
  // Total number of element blocks
  int num_elem_blk;
 
  // Total number of edges
  int num_edge;
 
  // Total number of edge blocks. The sum of the number of edges in
  // each block must equal num_edge.
  int num_edge_blk;
 
  // Total number of node sets
  int num_node_sets;
 
  // Total number of element sets
  int num_side_sets;
 
  // Number of elements in this block
  int num_elem_this_blk;
 
  // Number of nodes in each element
  int num_nodes_per_elem;
 
  // Number of attributes for a given block
  int num_attr;
 
  // Total number of elements in all side sets
  int num_elem_all_sidesets;
 
  // Vector of element block identification numbers
  std::vector<int> block_ids;
 
  // Vector of edge block identification numbers
  std::vector<int> edge_block_ids;
 
  // Vector of nodes in an element
  std::vector<int> connect;
 
  // Vector of the sideset IDs
  std::vector<int> ss_ids;
 
  // Vector of the nodeset IDs
  std::vector<int> nodeset_ids;
 
  // Number of sides (edges/faces) in current set
  std::vector<int> num_sides_per_set;
 
  // Number of nodes in current set
  std::vector<int> num_nodes_per_set;
 
  // Number of distribution factors per set
  std::vector<int> num_df_per_set;
 
  // Number of distribution factors per set
  std::vector<int> num_node_df_per_set;
 
  // Starting indices for each nodeset in the node_sets_node_list vector.
  // Used in the calls to ex_{put,get}_concat_node_sets().
  std::vector<int> node_sets_node_index;
 
  // Starting indices for each nodeset in the node_sets_dist_fact vector.
  // Used in the calls to ex_{put,get}_concat_node_sets().
  std::vector<int> node_sets_dist_index;
 
  // Node ids for all nodes in nodesets, concatenated together.
  // Used in the calls to ex_{put,get}_concat_node_sets().
  std::vector<int> node_sets_node_list;
 
  // Distribution factors for all nodes in all nodesets, concatenated together.
  // Used in the calls to ex_{put,get}_concat_node_sets().
  std::vector<Real> node_sets_dist_fact;
 
  // List of element numbers in all sidesets
  std::vector<int> elem_list;
 
  // Side (face/edge) number actually on the boundary
  std::vector<int> side_list;
 
  // Node number actually on the boundary
  std::vector<int> node_list;
 
  // Side (face/edge) id number
  std::vector<int> id_list;
 
  // Optional mapping from internal [0,num_nodes) to arbitrary indices
  std::vector<int> node_num_map;
 
  // Optional mapping from internal [0,num_elem) to arbitrary indices
  std::vector<int> elem_num_map;
 
  // x locations of node points
  std::vector<Real> x;
 
  // y locations of node points
  std::vector<Real> y;
 
  // z locations of node points
  std::vector<Real> z;
 
  //  Problem title (Use vector<char> to emulate a char *)
  std::vector<char> title;
 
  // Type of element in a given block
  std::vector<char> elem_type;
 
  // Maps libMesh element numbers to Exodus element numbers
  // gets filled in when write_elements gets called
  std::map<int, int> libmesh_elem_num_to_exodus;
  std::vector<int> exodus_elem_num_to_libmesh;
 
  // Map of all node numbers connected to local node numbers to their exodus numbering.
  // The exodus numbers are stored in here starting with 1
  std::map<int, int> libmesh_node_num_to_exodus;
  std::vector<int> exodus_node_num_to_libmesh;
 
  // The number of timesteps in the file, as returned by ex_inquire
  int num_time_steps;
 
  // The timesteps stored in the solution file, filled by read_time_steps()
  std::vector<Real> time_steps;
 
  // The number of nodal variables in the Exodus file
  int num_nodal_vars;
 
  // The names of the nodal variables stored in the Exodus file
  std::vector<std::string> nodal_var_names;
 
  // Holds the nodal variable values for a given variable, one value per node
  std::vector<Real> nodal_var_values;
 
  // The number of elemental variables in the Exodus file
  int num_elem_vars;
 
  // The names of the elemental variables stored in the Exodus file
  std::vector<std::string> elem_var_names;
 
  // Holds the elemental variable values for a given variable, one value per element
  std::vector<Real> elem_var_values;
 
  // The names of the global variables stored in the Exodus file
  std::vector<std::string> global_var_names;
 
  // The names of the sideset variables stored in the Exodus file
  std::vector<std::string> sideset_var_names;
 
  // Maps of Ids to named entities
  std::map<int, std::string> id_to_block_names;
  std::map<int, std::string> id_to_edge_block_names;
  std::map<int, std::string> id_to_ss_names;
  std::map<int, std::string> id_to_ns_names;
 
  // On/Off message flag
  bool verbose;
 
  // This flag gets set after the Exodus file has been successfully opened for writing.
  // Both the create() and open() (if called with EX_WRITE) functions may set this flag.
  bool opened_for_writing;
 
  // This flag gets set after the open() function has been successfully called.
  // We call open() to open an ExodusII file for reading.
  bool opened_for_reading;
 
  // When either create() or open() is called, the Helper stores the
  // name of the opened file as current_filename.  This way, the
  // ExodusII_IO object can check to see if, on subsequent writes, the
  // user is asking to write to a *different* filename from the one
  // that is currently open, and signal an error.  The current
  // ExodusII_IO implementation is designed to work with a single file
  // only, so if you want to write to multiple Exodus files, use a
  // different ExodusII_IO object for each one.
  std::string current_filename;
 
  enum ExodusVarType {NODAL=0, ELEMENTAL=1, GLOBAL=2, SIDESET=3};
  void read_var_names(ExodusVarType type);
 
  const ExodusII_IO_Helper::Conversion &
  get_conversion(const ElemType type) const;
 
  const ExodusII_IO_Helper::Conversion &
  get_conversion(std::string type_str) const;
 
protected:
  void check_existing_vars(ExodusVarType type, std::vector<std::string> & names, std::vector<std::string> & names_from_file);
 
  void write_var_names(ExodusVarType type, const std::vector<std::string> & names);
 
  // If true, whenever there is an I/O operation, only perform if if we are on processor 0.
  bool _run_only_on_proc0;
 
  // True once the elem vars are initialized
  bool _elem_vars_initialized;
 
  // True once the global vars are initialized
  bool _global_vars_initialized;
 
  // True once the nodal vars are initialized
  bool _nodal_vars_initialized;
 
  // If true, use the Mesh's dimension (as determined by the dimension
  // of the elements comprising the mesh) instead of the mesh's
  // spatial dimension, when writing.  By default this is false.
  bool _use_mesh_dimension_instead_of_spatial_dimension;
 
  // Use this for num_dim when writing the Exodus file.  If non-zero, supersedes
  // any value set in _use_mesh_dimension_instead_of_spatial_dimension.
  unsigned _write_as_dimension;
 
  // On output, shift every point by _coordinate_offset
  Point _coordinate_offset;
 
  // If true, forces single precision I/O
  bool _single_precision;
 
  struct MappedOutputVector
  {
    // If necessary, allocates space to store a version of vec_in in a
    // different precision than it was input with.
    MappedOutputVector(const std::vector<Real> & vec_in,
                       bool single_precision_in);
 
    ~MappedOutputVector() = default;
 
    // Returns void * pointer to either the mapped data or the
    // original data, as necessary.
    void * data();
 
  private:
    const std::vector<Real> & our_data;
    bool single_precision;
    std::vector<double> double_vec;
    std::vector<float> float_vec;
  };
 
  struct MappedInputVector
  {
    MappedInputVector(std::vector<Real> & vec_in,
                      bool single_precision_in);
    ~MappedInputVector();
 
    // Returns void * pointer to either the mapped data or the
    // original data, as necessary.
    void * data();
 
  private:
    std::vector<Real> & our_data;
    bool single_precision;
    std::vector<double> double_vec;
    std::vector<float> float_vec;
  };
 
 
private:
 
  void read_var_names_impl(const char * var_type,
                           int & count,
                           std::vector<std::string> & result);
 
  void write_var_names_impl(const char * var_type,
                            int & count,
                            const std::vector<std::string> & names);
 
  std::map<std::string, ElemType> element_equivalence_map;
  void init_element_equivalence_map();
 
  std::map<ElemType, ExodusII_IO_Helper::Conversion> conversion_map;
  void init_conversion_map();
};
 
 
 
 
 
 
 
 
class ExodusII_IO_Helper::Conversion
{
public:
 
  Conversion()
    : node_map(nullptr),
      inverse_node_map(nullptr),
      side_map(nullptr),
      inverse_side_map(nullptr),
      shellface_map(nullptr),
      inverse_shellface_map(nullptr),
      shellface_index_offset(0),
      libmesh_type(INVALID_ELEM),
      exodus_type("")
  {}
 
  int get_node_map(int i) const;
 
  int get_inverse_node_map(int i) const;
 
  int get_side_map(int i) const;
 
  int get_inverse_side_map(int i) const;
 
  int get_shellface_map(int i) const;
 
  int get_inverse_shellface_map(int i) const;
 
  ElemType libmesh_elem_type() const;
 
  std::string exodus_elem_type() const;
 
  std::size_t get_shellface_index_offset() const;
 
  static const int invalid_id;
 
  const std::vector<int> * node_map;
 
  const std::vector<int> * inverse_node_map;
 
  const std::vector<int> * side_map;
 
  const std::vector<int> * inverse_side_map;
 
  const std::vector<int> * shellface_map;
 
  const std::vector<int> * inverse_shellface_map;
 
  size_t shellface_index_offset;
 
  ElemType libmesh_type;
 
  std::string exodus_type;
};
 
 
 
class ExodusII_IO_Helper::NamesData
{
public:
  explicit
  NamesData(size_t n_strings, size_t string_length);
 
  void push_back_entry(const std::string & name);
 
  char ** get_char_star_star();
 
  char * get_char_star(int i);
 
private:
  // C++ data structures for managing string memory
  std::vector<std::vector<char>> data_table;
  std::vector<char *> data_table_pointers;
 
  size_t counter;
  size_t table_size;
};
 
 
} // namespace libMesh
 
#endif // LIBMESH_HAVE_EXODUS_API
 
#endif // LIBMESH_EXODUSII_IO_HELPER_H