Ioex_DatabaseIO.h

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// Copyright(C) 1999-2024 National Technology & Engineering Solutions
// of Sandia, LLC (NTESS).  Under the terms of Contract DE-NA0003525 with
// NTESS, the U.S. Government retains certain rights in this software.
//
// See packages/seacas/LICENSE for details
 
// -*- Mode: c++ -*-
#pragma once
 
#include "Ioss_DBUsage.h"
#include "Ioss_Field.h"
#include "Ioss_Map.h"
#include "Ioss_Utils.h"
#include "exodus/Ioex_BaseDatabaseIO.h"
#include <algorithm>
#include <cstdint>
#include <ctime>
#include <exodusII.h>
#include <map>
#include <set>
#include <sstream>
#include <string>
#include <vector>
 
#include "Ioss_CodeTypes.h"
#include "ioex_export.h"
 
namespace Ioss {
  class GroupingEntity;
  class Region;
  class EntityBlock;
  class NodeBlock;
  class EdgeBlock;
  class FaceBlock;
  class ElementBlock;
  class EntitySet;
  class NodeSet;
  class EdgeSet;
  class FaceSet;
  class ElementSet;
  class SideBlock;
  class SideSet;
  class StructuredBlock;
  class CommSet;
  class ElementTopology;
  class Assembly;
  class Blob;
  class Field;
  class Map;
  class PropertyManager;
} // namespace Ioss
 
namespace Ioex {
  struct CommunicationMetaData;
} // namespace Ioex
 
/** \brief A namespace for the file-per-process version of the
 *  parallel exodus database format.
 */
namespace Ioex {
  class IOEX_EXPORT DatabaseIO : public Ioex::BaseDatabaseIO
  {
  public:
    DatabaseIO(Ioss::Region *region, const std::string &filename, Ioss::DatabaseUsage db_usage,
               Ioss_MPI_Comm communicator, const Ioss::PropertyManager &props);
 
    // Kluge -- a few applications need access so can directly access exodus API
    IOSS_NODISCARD int get_file_pointer() const override; // Open file and set exodusFilePtr.
 
  private:
    void                get_step_times_nl() override;
    std::vector<double> get_db_step_times_nl() override;
    std::vector<double> internal_get_step_times_nl(bool setRegionTimeSteps);
 
    bool open_input_file(bool write_message, std::string *error_msg, int *bad_count,
                         bool abort_if_error) const override;
    bool handle_output_file(bool write_message, std::string *error_msg, int *bad_count,
                            bool overwrite, bool abort_if_error) const override;
    IOSS_NODISCARD bool check_valid_file_ptr(bool write_message, std::string *error_msg,
                                             int *bad_count, bool abort_if_error) const;
 
    int64_t get_field_internal(const Ioss::Region *reg, const Ioss::Field &field, void *data,
                               size_t data_size) const override;
    int64_t get_field_internal(const Ioss::Blob *blob, const Ioss::Field &field, void *data,
                               size_t data_size) const override;
    int64_t get_field_internal(const Ioss::Assembly *assem, const Ioss::Field &field, void *data,
                               size_t data_size) const override;
    int64_t get_field_internal(const Ioss::NodeBlock *nb, const Ioss::Field &field, void *data,
                               size_t data_size) const override;
    int64_t get_field_internal(const Ioss::EdgeBlock *eb, const Ioss::Field &field, void *data,
                               size_t data_size) const override;
    int64_t get_field_internal(const Ioss::FaceBlock *eb, const Ioss::Field &field, void *data,
                               size_t data_size) const override;
    int64_t get_field_internal(const Ioss::ElementBlock *eb, const Ioss::Field &field, void *data,
                               size_t data_size) const override;
    int64_t get_field_internal(const Ioss::StructuredBlock * /* sb */,
                               const Ioss::Field & /* field */, void * /* data */,
                               size_t /* data_size */) const override
    {
      return -1;
    }
 
    int64_t get_field_internal(const Ioss::SideBlock *fb, const Ioss::Field &field, void *data,
                               size_t data_size) const override;
    int64_t get_field_internal(const Ioss::NodeSet *ns, const Ioss::Field &field, void *data,
                               size_t data_size) const override;
    int64_t get_field_internal(const Ioss::EdgeSet *ns, const Ioss::Field &field, void *data,
                               size_t data_size) const override;
    int64_t get_field_internal(const Ioss::FaceSet *ns, const Ioss::Field &field, void *data,
                               size_t data_size) const override;
    int64_t get_field_internal(const Ioss::ElementSet *ns, const Ioss::Field &field, void *data,
                               size_t data_size) const override;
    int64_t get_field_internal(const Ioss::SideSet *ss, const Ioss::Field &field, void *data,
                               size_t data_size) const override;
    int64_t get_field_internal(const Ioss::CommSet *cs, const Ioss::Field &field, void *data,
                               size_t data_size) const override;
 
    int64_t put_field_internal(const Ioss::Region *reg, const Ioss::Field &field, void *data,
                               size_t data_size) const override;
    int64_t put_field_internal(const Ioss::Blob *blob, const Ioss::Field &field, void *data,
                               size_t data_size) const override;
    int64_t put_field_internal(const Ioss::Assembly *assem, const Ioss::Field &field, void *data,
                               size_t data_size) const override;
    int64_t put_field_internal(const Ioss::NodeBlock *nb, const Ioss::Field &field, void *data,
                               size_t data_size) const override;
    int64_t put_field_internal(const Ioss::EdgeBlock *eb, const Ioss::Field &field, void *data,
                               size_t data_size) const override;
    int64_t put_field_internal(const Ioss::FaceBlock *eb, const Ioss::Field &field, void *data,
                               size_t data_size) const override;
    int64_t put_field_internal(const Ioss::ElementBlock *eb, const Ioss::Field &field, void *data,
                               size_t data_size) const override;
    int64_t put_field_internal(const Ioss::SideBlock *fb, const Ioss::Field &field, void *data,
                               size_t data_size) const override;
    int64_t put_field_internal(const Ioss::NodeSet *ns, const Ioss::Field &field, void *data,
                               size_t data_size) const override;
    int64_t put_field_internal(const Ioss::EdgeSet *ns, const Ioss::Field &field, void *data,
                               size_t data_size) const override;
    int64_t put_field_internal(const Ioss::FaceSet *ns, const Ioss::Field &field, void *data,
                               size_t data_size) const override;
    int64_t put_field_internal(const Ioss::ElementSet *ns, const Ioss::Field &field, void *data,
                               size_t data_size) const override;
    int64_t put_field_internal(const Ioss::SideSet *ss, const Ioss::Field &field, void *data,
                               size_t data_size) const override;
    int64_t put_field_internal(const Ioss::CommSet *cs, const Ioss::Field &field, void *data,
                               size_t data_size) const override;
 
    int64_t put_field_internal(const Ioss::StructuredBlock * /* sb */,
                               const Ioss::Field & /* field */, void * /* data */,
                               size_t /* data_size */) const override
    {
      return -1;
    }
    int64_t put_Xset_field_internal(const Ioss::EntitySet *ns, const Ioss::Field &field, void *data,
                                    size_t data_size) const;
    int64_t get_Xset_field_internal(const Ioss::EntitySet *ns, const Ioss::Field &field, void *data,
                                    size_t data_size) const;
 
  private:
    int64_t read_nodal_coordinates();
    void    read_elements(const Ioss::ElementBlock &block);
 
    void compute_node_status() const;
 
    // Metadata-related functions.
    void read_meta_data_nl() override;
    void read_communication_metadata();
 
    int64_t read_transient_field(const Ioex::VariableNameMap &variables, const Ioss::Field &field,
                                 const Ioss::GroupingEntity *ge, void *data) const;
 
    int64_t read_attribute_field(const Ioss::Field &field, const Ioss::GroupingEntity *ge,
                                 void *data) const;
 
    int64_t write_attribute_field(const Ioss::Field &field, const Ioss::GroupingEntity *ge,
                                  void *data) const;
 
    // Handles subsetting of side blocks.
    int64_t read_ss_transient_field(const Ioss::Field &field, int64_t id, void *variables,
                                    std::vector<int> &is_valid_side) const;
 
    // Should be made more generic again so can rejoin with write_element_transient field
    void write_nodal_transient_field(const Ioss::Field &field, const Ioss::NodeBlock *ge,
                                     int64_t count, void *variables) const;
    // Should be made more generic again so can rejoin with write_nodal_transient field
    void write_entity_transient_field(const Ioss::Field &field, const Ioss::GroupingEntity *ge,
                                      int64_t count, void *variables) const;
    void write_meta_data(Ioss::IfDatabaseExistsBehavior behavior) override;
    void gather_communication_metadata(Ioex::CommunicationMetaData *meta);
 
    // Read related metadata and store it in the region...
    void read_region();
    void get_edgeblocks();
    void get_faceblocks();
    void get_elemblocks();
    void get_blocks(ex_entity_type entity_type, int rank_offset, const std::string &basename);
 
    void get_sidesets();
 
    template <typename T>
    void get_sets(ex_entity_type type, int64_t count, const std::string &base,
                  const T * /*unused*/);
    void get_nodesets();
    void get_edgesets();
    void get_facesets();
    void get_elemsets();
 
    void get_commsets();
 
    // ID Mapping functions.
    IOSS_NODISCARD const Ioss::Map &get_map(ex_entity_type type) const;
    IOSS_NODISCARD const Ioss::Map &get_map(Ioss::Map &entity_map, int64_t entity_count,
                                            ex_entity_type entity_type,
                                            ex_inquiry     inquiry_type) const;
 
    // Internal data handling
    int64_t handle_node_ids(void *ids, int64_t num_to_get) const;
    int64_t handle_element_ids(const Ioss::ElementBlock *eb, void *ids, size_t num_to_get) const;
    int64_t handle_face_ids(const Ioss::FaceBlock *eb, void *ids, size_t num_to_get) const;
    int64_t handle_edge_ids(const Ioss::EdgeBlock *eb, void *ids, size_t num_to_get) const;
 
    int64_t get_side_connectivity(const Ioss::SideBlock *sd_blk, int64_t id, int64_t my_side_count,
                                  void *fconnect, bool map_ids) const;
    template <typename INT>
    int64_t get_side_connectivity_internal(const Ioss::SideBlock *sd_blk, int64_t id,
                                           int64_t side_count, INT *fconnect, bool map_ids) const;
    int64_t get_side_distributions(const Ioss::SideBlock *sd_blk, int64_t id, int64_t my_side_count,
                                   double *dist_fact, size_t data_size) const;
 
    int64_t get_side_field(const Ioss::SideBlock *sd_blk, const Ioss::Field &field, void *data,
                           size_t data_size) const;
    int64_t put_side_field(const Ioss::SideBlock *sd_blk, const Ioss::Field &field, void *data,
                           size_t data_size) const;
 
    //!< true if application code is controlling the processor id.
    mutable bool isSerialParallel{false};
  };
} // namespace Ioex