seacas-docs/ioss_html/Ioex__DatabaseIO_8h_source.html

// 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

Ioex_BaseDatabaseIO.h

Ioss_CodeTypes.h

IOSS_NODISCARD
#define IOSS_NODISCARD
Definition Ioss_CodeTypes.h:55

Ioss_MPI_Comm
int Ioss_MPI_Comm
Definition Ioss_CodeTypes.h:64

Ioss_DBUsage.h

Ioss_Field.h

Ioss_Map.h

Ioss_Utils.h

Ioex::BaseDatabaseIO
Definition Ioex_BaseDatabaseIO.h:78

Ioex::DatabaseIO
Definition Ioex_DatabaseIO.h:62

Ioex::DatabaseIO::read_elements
void read_elements(const Ioss::ElementBlock &block)

Ioex::DatabaseIO::get_field_internal
int64_t get_field_internal(const Ioss::StructuredBlock *, const Ioss::Field &, void *, size_t) const override
Definition Ioex_DatabaseIO.h:96

Ioex::DatabaseIO::get_side_field
int64_t get_side_field(const Ioss::SideBlock *sd_blk, const Ioss::Field &field, void *data, size_t data_size) const

Ioex::DatabaseIO::put_side_field
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.

Ioex::DatabaseIO::read_nodal_coordinates
int64_t read_nodal_coordinates()

Ioex::DatabaseIO::put_field_internal
int64_t put_field_internal(const Ioss::StructuredBlock *, const Ioss::Field &, void *, size_t) const override
Definition Ioex_DatabaseIO.h:147

Ioss::Assembly
A homogeneous collection of other GroupingEntities.
Definition Ioss_Assembly.h:31

Ioss::Blob
A homogeneous collection of other GroupingEntities.
Definition Ioss_Blob.h:31

Ioss::CommSet
Definition Ioss_CommSet.h:27

Ioss::EdgeBlock
A collection of element edges with the same topology.
Definition Ioss_EdgeBlock.h:29

Ioss::EdgeSet
A collection of element edges.
Definition Ioss_EdgeSet.h:30

Ioss::ElementBlock
A collection of elements having the same topology.
Definition Ioss_ElementBlock.h:29

Ioss::ElementSet
A collection of elements.
Definition Ioss_ElementSet.h:30

Ioss::EntitySet
Base class for all 'set'-type grouping entities, which means that members of the set are not necessar...
Definition Ioss_EntitySet.h:38

Ioss::FaceBlock
A collection of element faces with the same topology.
Definition Ioss_FaceBlock.h:29

Ioss::FaceSet
A collection of element faces.
Definition Ioss_FaceSet.h:30

Ioss::Field
Holds metadata for bulk data associated with a GroupingEntity.
Definition Ioss_Field.h:25

Ioss::GroupingEntity
Base class for all 'grouping' entities. The following derived classes are typical:
Definition Ioss_GroupingEntity.h:67

Ioss::Map
Definition Ioss_Map.h:46

Ioss::NodeBlock
A collection of all nodes in the region.
Definition Ioss_NodeBlock.h:33

Ioss::NodeSet
A collection of nodes.
Definition Ioss_NodeSet.h:29

Ioss::PropertyManager
A collection of Ioss::Property objects.
Definition Ioss_PropertyManager.h:36

Ioss::Region
A grouping entity that contains other grouping entities.
Definition Ioss_Region.h:93

Ioss::SideBlock
A collection of element sides having the same topology.
Definition Ioss_SideBlock.h:37

Ioss::SideSet
A collection of element sides.
Definition Ioss_SideSet.h:29

Ioss::StructuredBlock
A structured zone – i,j,k.
Definition Ioss_StructuredBlock.h:91

Ioex
A namespace for the exodus database format.
Definition Ioex_BaseDatabaseIO.C:209

Ioex::VariableNameMap
std::map< std::string, int, std::less<> > VariableNameMap
Definition Ioex_BaseDatabaseIO.h:61

Ioss
The main namespace for the Ioss library.
Definition Ioad_DatabaseIO.C:40

Ioss::DatabaseUsage
DatabaseUsage
Specifies how an Ioss::DatabaseIO object will be used.
Definition Ioss_DBUsage.h:13

Ioss::IfDatabaseExistsBehavior
IfDatabaseExistsBehavior
Definition Ioss_DBUsage.h:32

Ioex::CommunicationMetaData
Definition Ioex_Internals.h:264