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| DatabaseIO (Ioss::Region *region, const std::string &filename, Ioss::DatabaseUsage db_usage, Ioss_MPI_Comm communicator, const Ioss::PropertyManager &props) |
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IOSS_NODISCARD int | get_file_pointer () const override |
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| BaseDatabaseIO (Ioss::Region *region, const std::string &filename, Ioss::DatabaseUsage db_usage, Ioss_MPI_Comm communicator, const Ioss::PropertyManager &props) |
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IOSS_NODISCARD std::string | get_format () const override |
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IOSS_NODISCARD unsigned | entity_field_support () const override |
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| DatabaseIO ()=delete |
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| DatabaseIO (const DatabaseIO &)=delete |
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| DatabaseIO (DatabaseIO &&)=delete |
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DatabaseIO & | operator= (const DatabaseIO &)=delete |
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DatabaseIO & | operator= (DatabaseIO &&)=delete |
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virtual | ~DatabaseIO () |
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IOSS_NODISCARD bool | ok (bool write_message=false, std::string *error_message=nullptr, int *bad_count=nullptr) const |
| Check to see if database state is OK.
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IOSS_NODISCARD bool | using_parallel_io () const |
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IOSS_NODISCARD int64_t | node_global_to_local (int64_t global, bool must_exist) const |
| Get the local (process-specific) node number corresponding to a global node number.
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IOSS_NODISCARD int64_t | element_global_to_local (int64_t global) const |
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virtual IOSS_NODISCARD bool | node_major () const |
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void | release_memory () |
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virtual void | finalize_database () const |
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void | set_pfs_name (const std::string &name) const |
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IOSS_NODISCARD std::string | get_pfs_name () const |
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void | set_dw_name (const std::string &name) const |
| this will be the name in BB namespace
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IOSS_NODISCARD std::string | get_dw_name () const |
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IOSS_NODISCARD std::string | get_dw_path () const |
| We call this ONLY after we assure that using_dw() is TRUE.
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void | check_set_dw () const |
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IOSS_NODISCARD bool | using_dw () const |
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IOSS_NODISCARD std::string | get_filename () const |
| Get the file name associated with the database.
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IOSS_NODISCARD const std::string & | decoded_filename () const |
| Get a file-per-processor filename associated with the database.
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IOSS_NODISCARD bool | is_input () const |
| Determine whether the database is an input database.
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IOSS_NODISCARD Ioss::DatabaseUsage | usage () const |
| Get the Ioss::DatabaseUsage type of the database.
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virtual IOSS_NODISCARD bool | needs_shared_node_information () const |
| Determine whether the database needs information about process ownership of nodes.
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IOSS_NODISCARD Ioss::IfDatabaseExistsBehavior | open_create_behavior () const |
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void | set_region (Region *region) |
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void | open_dw (const std::string &filename) const |
| If we are planning to use BB(aka Burst Buffer) service, we will call simple C API provided by Cray DataWarp module.
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void | close_dw () const |
| Function which invokes stageout from BB to Disk, prior to completion of final close.
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void | openDatabase () const |
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void | closeDatabase () const |
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void | flush_database () const |
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bool | open_group (const std::string &group_name) |
| If a database type supports groups and if the database contains groups, open the specified group.
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bool | create_subgroup (const std::string &group_name) |
| If a database type supports groups, create the specified group as a child of the current group.
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bool | begin (Ioss::State state) |
| Set the database to the given State.
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bool | end (Ioss::State state) |
| Return the database to STATE_CLOSED.
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bool | begin_state (int state, double time) |
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bool | end_state (int state, double time) |
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void | read_meta_data () |
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void | get_step_times () |
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virtual IOSS_NODISCARD bool | internal_edges_available () const |
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virtual IOSS_NODISCARD bool | internal_faces_available () const |
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IOSS_NODISCARD const std::vector< std::string > & | get_information_records () const |
| Get all information records (informative strings) for the database.
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void | add_information_records (const std::vector< std::string > &info) |
| Add multiple information records (informative strings) to the database.
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void | add_information_record (const std::string &info) |
| Add an information record (an informative string) to the database.
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IOSS_NODISCARD const std::vector< std::string > & | get_qa_records () const |
| Get all QA records, each of which consists of 4 strings, from the database.
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void | add_qa_record (const std::string &code, const std::string &code_qa, const std::string &date, const std::string &time) |
| Add a QA record, which consists of 4 strings, to the database.
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IOSS_NODISCARD bool | get_logging () const |
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void | set_logging (bool on_off) |
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IOSS_NODISCARD bool | get_nan_detection () const |
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void | set_nan_detection (bool on_off) |
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template<typename T > |
int64_t | get_field (const T *reg, const Field &field, void *data, size_t data_size) const |
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template<typename T > |
int64_t | put_field (const T *reg, const Field &field, void *data, size_t data_size) const |
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template<typename T > |
int64_t | get_zc_field (const T *reg, const Field &field, void **data, size_t *data_size) const |
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IOSS_NODISCARD bool | is_parallel_consistent () const |
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void | set_parallel_consistency (bool on_off) |
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IOSS_NODISCARD bool | get_use_generic_canonical_name () const |
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void | set_use_generic_canonical_name (bool yes_no) |
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IOSS_NODISCARD bool | ignore_database_names () const |
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void | ignore_database_names (bool yes_no) |
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IOSS_NODISCARD bool | get_ignore_realn_fields () const |
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void | set_ignore_realn_fields (bool yes_no) |
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IOSS_NODISCARD std::string | get_component_name (const Ioss::Field &field, Ioss::Field::InOut in_out, int component) const |
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IOSS_NODISCARD char | get_field_separator () const |
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IOSS_NODISCARD bool | get_field_recognition () const |
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IOSS_NODISCARD bool | get_field_strip_trailing_ () const |
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void | set_field_separator (char separator) |
| Set the character used to separate a field suffix from the field basename when recognizing vector, tensor fields.
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void | set_field_recognition (bool yes_no) |
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void | set_field_strip_trailing_ (bool yes_no) |
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IOSS_NODISCARD DuplicateFieldBehavior | get_duplicate_field_behavior () const |
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void | set_lower_case_variable_names (bool true_false) const |
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void | set_surface_split_type (Ioss::SurfaceSplitType split_type) |
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IOSS_NODISCARD Ioss::SurfaceSplitType | get_surface_split_type () const |
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void | set_block_omissions (const std::vector< std::string > &omissions, const std::vector< std::string > &inclusions={}) |
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void | set_assembly_omissions (const std::vector< std::string > &omissions, const std::vector< std::string > &inclusions={}) |
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void | get_block_adjacencies (const Ioss::ElementBlock *eb, std::vector< std::string > &block_adjacency) const |
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void | compute_block_membership (Ioss::SideBlock *efblock, std::vector< std::string > &block_membership) const |
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IOSS_NODISCARD AxisAlignedBoundingBox | get_bounding_box (const Ioss::NodeBlock *nb) const |
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IOSS_NODISCARD AxisAlignedBoundingBox | get_bounding_box (const Ioss::ElementBlock *eb) const |
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IOSS_NODISCARD AxisAlignedBoundingBox | get_bounding_box (const Ioss::StructuredBlock *sb) const |
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IOSS_NODISCARD int | int_byte_size_api () const |
| Returns 4 or 8.
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IOSS_NODISCARD Region * | get_region () const |
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void | set_cycle_count (int count) const |
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IOSS_NODISCARD int | get_cycle_count () const |
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void | set_overlay_count (int count) const |
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IOSS_NODISCARD int | get_overlay_count () const |
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void | set_file_per_state (bool yes_no) const |
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IOSS_NODISCARD bool | get_file_per_state () const |
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void | set_time_scale_factor (double factor) |
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IOSS_NODISCARD const Ioss::ParallelUtils & | util () const |
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IOSS_NODISCARD const Ioss::PropertyManager & | get_property_manager () const |
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IOSS_NODISCARD int | parallel_rank () const |
| Get the processor that this mesh database is on.
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IOSS_NODISCARD int | parallel_size () const |
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IOSS_NODISCARD bool | is_parallel () const |
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void | progress (const std::string &output) const |
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virtual std::vector< size_t > | get_entity_field_data (const std::string &field_name, const std::vector< Ioss::ElementBlock * > &elem_blocks, void *data, size_t data_size) const |
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template<> |
void | create_group (EntityType type, const std::string &, const std::vector< std::string > &group_spec, const SideSet *) |
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void | get_step_times_nl () override |
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bool | handle_output_file (bool write_message, std::string *error_msg, int *bad_count, bool overwrite, bool abort_if_error) const override |
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bool | check_valid_file_ptr (bool write_message, std::string *error_msg, int *bad_count, bool abort_if_error) const |
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int64_t | put_field_internal (const Ioss::Region *reg, const Ioss::Field &field, void *data, size_t data_size) const override |
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int64_t | put_field_internal (const Ioss::Blob *blob, const Ioss::Field &field, void *data, size_t data_size) const override |
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int64_t | put_field_internal (const Ioss::Assembly *assem, const Ioss::Field &field, void *data, size_t data_size) const override |
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int64_t | put_field_internal (const Ioss::NodeBlock *nb, const Ioss::Field &field, void *data, size_t data_size) const override |
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int64_t | put_field_internal (const Ioss::EdgeBlock *eb, const Ioss::Field &field, void *data, size_t data_size) const override |
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int64_t | put_field_internal (const Ioss::FaceBlock *eb, const Ioss::Field &field, void *data, size_t data_size) const override |
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int64_t | put_field_internal (const Ioss::ElementBlock *eb, const Ioss::Field &field, void *data, size_t data_size) const override |
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int64_t | put_field_internal (const Ioss::SideBlock *fb, const Ioss::Field &field, void *data, size_t data_size) const override |
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int64_t | put_field_internal (const Ioss::NodeSet *ns, const Ioss::Field &field, void *data, size_t data_size) const override |
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int64_t | put_field_internal (const Ioss::EdgeSet *ns, const Ioss::Field &field, void *data, size_t data_size) const override |
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int64_t | put_field_internal (const Ioss::FaceSet *ns, const Ioss::Field &field, void *data, size_t data_size) const override |
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int64_t | put_field_internal (const Ioss::ElementSet *ns, const Ioss::Field &field, void *data, size_t data_size) const override |
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int64_t | put_field_internal (const Ioss::SideSet *ss, const Ioss::Field &field, void *data, size_t data_size) const override |
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int64_t | put_field_internal (const Ioss::CommSet *cs, const Ioss::Field &field, void *data, size_t data_size) const override |
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int64_t | put_field_internal (const Ioss::StructuredBlock *, const Ioss::Field &, void *, size_t) const override |
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int64_t | put_Xset_field_internal (const Ioss::EntitySet *ns, const Ioss::Field &field, void *data, size_t data_size) const |
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int64_t | get_Xset_field_internal (const Ioss::EntitySet *ns, const Ioss::Field &field, void *data, size_t data_size) const |
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int64_t | read_nodal_coordinates () |
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void | read_elements (const Ioss::ElementBlock &block) |
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void | compute_node_status () const |
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void | read_meta_data_nl () override |
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void | read_communication_metadata () |
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int64_t | read_transient_field (const Ioexnl::VariableNameMap &variables, const Ioss::Field &field, const Ioss::GroupingEntity *ge, void *data) const |
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int64_t | read_attribute_field (const Ioss::Field &field, const Ioss::GroupingEntity *ge, void *data) const |
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int64_t | write_attribute_field (const Ioss::Field &field, const Ioss::GroupingEntity *ge, void *data) const |
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int64_t | read_ss_transient_field (const Ioss::Field &field, int64_t id, void *variables, std::vector< int > &is_valid_side) const |
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void | write_nodal_transient_field (const Ioss::Field &field, const Ioss::NodeBlock *ge, int64_t count, void *variables) const |
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void | write_entity_transient_field (const Ioss::Field &field, const Ioss::GroupingEntity *ge, int64_t count, void *variables) const |
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void | write_meta_data (Ioss::IfDatabaseExistsBehavior behavior) override |
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void | gather_communication_metadata (Ioexnl::CommunicationMetaData *meta) |
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void | read_region () |
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void | get_edgeblocks () |
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void | get_faceblocks () |
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void | get_elemblocks () |
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void | get_blocks (ex_entity_type entity_type, int rank_offset, const std::string &basename) |
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void | get_sidesets () |
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template<typename T > |
void | get_sets (ex_entity_type type, int64_t count, const std::string &base, const T *) |
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void | get_nodesets () |
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void | get_edgesets () |
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void | get_facesets () |
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void | get_elemsets () |
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void | get_commsets () |
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IOSS_NODISCARD const Ioss::Map & | get_map (ex_entity_type type) const |
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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 |
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int64_t | handle_node_ids (void *ids, int64_t num_to_get) const |
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int64_t | handle_element_ids (const Ioss::ElementBlock *eb, void *ids, size_t num_to_get) const |
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int64_t | handle_face_ids (const Ioss::FaceBlock *eb, void *ids, size_t num_to_get) const |
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int64_t | handle_edge_ids (const Ioss::EdgeBlock *eb, void *ids, size_t num_to_get) const |
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int64_t | get_side_connectivity (const Ioss::SideBlock *sd_blk, int64_t id, int64_t my_side_count, void *fconnect, bool map_ids) const |
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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 |
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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 |
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int64_t | get_side_field (const Ioss::SideBlock *sd_blk, const Ioss::Field &field, void *data, size_t data_size) const |
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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.
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IOSS_NODISCARD bool | ok_nl (bool write_message=false, std::string *error_message=nullptr, int *bad_count=nullptr) const override |
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IOSS_NODISCARD bool | begin_nl (Ioss::State state) override |
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IOSS_NODISCARD bool | end_nl (Ioss::State state) override |
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void | open_state_file (int state) |
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bool | begin_state_nl (int state, double time) override |
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bool | end_state_nl (int state, double time) override |
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IOSS_NODISCARD int | maximum_symbol_length () const override |
| Get the length of the longest name in the database file.
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void | set_maximum_symbol_length (int requested_symbol_size) override |
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size_t | handle_block_ids (const Ioss::EntityBlock *eb, ex_entity_type map_type, Ioss::Map &entity_map, void *ids, size_t num_to_get, size_t offset) const |
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void | compute_block_membership_nl (Ioss::SideBlock *efblock, std::vector< std::string > &block_membership) const override |
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IOSS_NODISCARD int | int_byte_size_db () const override |
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void | set_int_byte_size_api (Ioss::DataSize size) const override |
| Returns 4 or 8.
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void | write_results_metadata (bool gather_data, Ioss::IfDatabaseExistsBehavior behavior) |
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void | openDatabase_nl () const override |
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void | closeDatabase_nl () const override |
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virtual int | free_file_pointer () const |
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IOSS_NODISCARD int | get_current_state () const |
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void | put_qa () |
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void | put_info () |
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template<typename T > |
void | internal_gather_results_metadata (ex_entity_type type, std::vector< T * > entities) |
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void | generate_sideset_truth_table () |
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void | output_results_names (ex_entity_type type, VariableNameMap &variables, bool reduction) const |
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int | gather_names (VariableNameMap &variables, const Ioss::GroupingEntity *ge, int index, bool reduction) |
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void | get_nodeblocks () |
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void | get_assemblies () |
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void | get_blobs () |
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void | update_block_omissions_from_assemblies () |
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void | add_attribute_fields (Ioss::GroupingEntity *block, int attribute_count, const std::string &type) |
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void | common_write_meta_data (Ioss::IfDatabaseExistsBehavior behavior) |
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void | output_other_meta_data () |
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int64_t | internal_add_results_fields (ex_entity_type type, Ioss::GroupingEntity *entity, int64_t position, int64_t block_count, Ioss::IntVector &truth_table, Ioexnl::VariableNameMap &variables) |
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int64_t | add_results_fields (Ioss::GroupingEntity *entity, int64_t position=0) |
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int64_t | add_reduction_results_fields (Ioss::GroupingEntity *entity) |
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void | add_mesh_reduction_fields (int64_t id, Ioss::GroupingEntity *entity) |
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void | add_region_fields () |
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void | store_reduction_field (const Ioss::Field &field, const Ioss::GroupingEntity *ge, void *variables) const |
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void | get_reduction_field (const Ioss::Field &field, const Ioss::GroupingEntity *ge, void *variables) const |
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void | write_reduction_fields () const |
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void | read_reduction_fields () const |
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IOSS_NODISCARD int | get_database_step (int global_step) const |
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void | flush_database_nl () const override |
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void | finalize_write (int state, double sim_time) |
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| DatabaseIO (Region *region, std::string filename, Ioss::DatabaseUsage db_usage, Ioss_MPI_Comm communicator, const Ioss::PropertyManager &props) |
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void | set_common_side_topology () const |
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template<typename T > |
void | create_groups (const std::string &property_name, EntityType type, const std::string &type_name, const T *set_type) |
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template<typename T > |
void | create_group (EntityType type, const std::string &type_name, const std::vector< std::string > &group_spec, const T *set_type) |
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void | handle_groups () |
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void | check_side_topology () const |
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int | m_exodusFilePtr {-1} |
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int | m_exodusBasePtr {-1} |
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std::string | m_groupName |
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EntityIdSet | ids_ |
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int | exodusMode {EX_CLOBBER} |
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int | dbRealWordSize {8} |
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int | maximumNameLength {32} |
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int | spatialDimension {0} |
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int64_t | edgeCount {0} |
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int64_t | faceCount {0} |
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std::map< ex_entity_type, int > | m_groupCount |
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Ioss::Int64Vector | nodeCmapIds |
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Ioss::Int64Vector | nodeCmapNodeCnts |
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Ioss::Int64Vector | elemCmapIds |
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Ioss::Int64Vector | elemCmapElemCnts |
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int64_t | commsetNodeCount {0} |
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int64_t | commsetElemCount {0} |
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std::map< ex_entity_type, Ioss::IntVector > | m_truthTable |
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std::map< ex_entity_type, VariableNameMap > | m_variables |
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std::map< ex_entity_type, VariableNameMap > | m_reductionVariables |
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std::map< ex_entity_type, std::map< int64_t, ValueContainer > > | m_reductionValues |
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std::vector< unsigned char > | nodeConnectivityStatus |
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std::map< std::string, Ioss::Int64Vector > | activeNodeSetNodesIndex |
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time_t | timeLastFlush {0} |
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int | flushInterval {-1} |
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bool | fileExists {false} |
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bool | minimizeOpenFiles {false} |
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bool | blockAdjacenciesCalculated {false} |
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bool | nodeConnectivityStatusCalculated |
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Ioss::PropertyManager | properties |
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ElementTopology * | commonSideTopology {nullptr} |
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std::string | originalDBFilename {} |
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std::string | DBFilename {} |
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std::string | decodedFilename {} |
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std::string | bbName {} |
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std::string | pfsName {} |
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std::string | dwPath {} |
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Ioss::State | dbState {STATE_INVALID} |
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int | myProcessor {0} |
| number of processor this database is for
|
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int64_t | nodeCount {0} |
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int64_t | elementCount {0} |
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TopoContainer | sideTopology {} |
| Used to speed up faceblock/edgeblock calculations.
|
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int | cycleCount {0} |
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int | overlayCount {0} |
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double | timeScaleFactor {1.0} |
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Ioss::SurfaceSplitType | splitType {SPLIT_BY_TOPOLOGIES} |
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Ioss::DatabaseUsage | dbUsage {} |
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Ioss::DataSize | dbIntSizeAPI {USE_INT32_API} |
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bool | filePerState {false} |
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bool | usingDataWarp {false} |
|
bool | isParallel {false} |
| true if running in parallel
|
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bool | lowerCaseVariableNames {true} |
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bool | usingParallelIO {false} |
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std::vector< std::string > | blockOmissions {} |
|
std::vector< std::string > | blockInclusions {} |
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std::vector< std::string > | assemblyOmissions {} |
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std::vector< std::string > | assemblyInclusions {} |
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std::vector< std::string > | informationRecords {} |
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std::vector< std::string > | qaRecords {} |
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Ioss::Map | nodeMap {"node", DBFilename, myProcessor} |
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Ioss::Map | edgeMap {"edge", DBFilename, myProcessor} |
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Ioss::Map | faceMap {"face", DBFilename, myProcessor} |
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Ioss::Map | elemMap {"element", DBFilename, myProcessor} |
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std::vector< std::vector< bool > > | blockAdjacency |
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int64_t Ioexnl::DatabaseIO::handle_node_ids |
( |
void * | ids, |
|
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int64_t | num_to_get ) const |
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private |
There are two modes we need to support in this routine:
- Initial definition of node map (local->global) and nodeMap.reverse (global->local).
- Redefinition of node map via 'reordering' of the original map when the nodes on this processor are the same, but their order is changed (or count because of ghosting)
So, there will be two maps the 'nodeMap.map' map is a 'direct lookup' map which maps current local position to global id and the 'nodeMap.reverse' is an associative lookup which maps the global id to 'original local'. There is also a 'nodeMap.reorder' which is direct lookup and maps current local position to original local.
The ids coming in are the global ids; their position is the "local id-1" (That is, data[0] contains the global id of local node 1 in this node block).
int local_position = nodeMap.reverse[NodeMap[i+1]] (the nodeMap.map and nodeMap.reverse are 1-based)
To determine which map to update on a call to this function, we use the following heuristics: – If the database state is 'STATE_MODEL:', then update the 'nodeMap.reverse' and 'nodeMap.map'
– If the database state is not STATE_MODEL, then leave the 'nodeMap.reverse' and 'nodeMap.map' alone since they correspond to the information already written to the database. [May want to add a STATE_REDEFINE_MODEL]
– In both cases, update the nodeMap.reorder
NOTE: The mapping is done on TRANSIENT fields only; MODEL fields should be in the original order...