IOSS  2.0
Iofx_DatabaseIO.h
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33 // -*- Mode: c++ -*-
34 #ifndef IOSS_Iofx_DatabaseIO_h
35 #define IOSS_Iofx_DatabaseIO_h
36 
37 #include <Ioss_DBUsage.h>
38 #include <Ioss_Field.h>
39 #include <Ioss_Map.h>
40 #include <Ioss_Utils.h>
41 #include <exodus/Ioex_DatabaseIO.h>
42 
43 #include <exodusII.h>
44 
45 #include <algorithm>
46 #include <cstdint>
47 #include <ctime>
48 #include <map>
49 #include <set>
50 #include <sstream>
51 #include <string>
52 #include <vector>
53 
54 namespace Ioss {
55  class GroupingEntity;
56  class Region;
57  class EntityBlock;
58  class NodeBlock;
59  class EdgeBlock;
60  class FaceBlock;
61  class ElementBlock;
62  class EntitySet;
63  class NodeSet;
64  class EdgeSet;
65  class FaceSet;
66  class ElementSet;
67  class SideBlock;
68  class SideSet;
69  class StructuredBlock;
70  class CommSet;
71  class ElementTopology;
72 } // namespace Ioss
73 
74 namespace Ioex {
75  struct CommunicationMetaData;
76 } // namespace Ioex
77 
78 /** \brief A namespace for the file-per-process version of the
79  * parallel exodus database format.
80  */
81 namespace Iofx {
82  class DatabaseIO : public Ioex::DatabaseIO
83  {
84  public:
85  DatabaseIO(Ioss::Region *region, const std::string &filename, Ioss::DatabaseUsage db_usage,
86  MPI_Comm communicator, const Ioss::PropertyManager &props);
87  DatabaseIO(const DatabaseIO &from) = delete;
88  DatabaseIO &operator=(const DatabaseIO &from) = delete;
89  ~DatabaseIO() override{};
90 
91  private:
92  // Check to see if database state is ok...
93  // If 'write_message' true, then output a warning message indicating the problem.
94  // If 'error_message' non-null, then put the warning message into the string and return it.
95  // If 'bad_count' non-null, it counts the number of processors where the file does not exist.
96  // if ok returns false, but *bad_count==0, then the routine does not support this argument.
97  bool ok__(bool write_message = false, std::string *error_msg = nullptr,
98  int *bad_count = nullptr) const override;
99 
100  void get_step_times__() override;
101 
102  bool open_input_file(bool write_message, std::string *error_msg, int *bad_count,
103  bool abort_if_error) const;
104  bool handle_output_file(bool write_message, std::string *error_msg, int *bad_count,
105  bool overwrite, bool abort_if_error) const;
106  bool check_valid_file_ptr(bool write_message, std::string *error_msg, int *bad_count,
107  bool abort_if_error) const;
108 
109  int64_t get_field_internal(const Ioss::Region *reg, const Ioss::Field &field, void *data,
110  size_t data_size) const override;
111  int64_t get_field_internal(const Ioss::NodeBlock *nb, const Ioss::Field &field, void *data,
112  size_t data_size) const override;
113  int64_t get_field_internal(const Ioss::EdgeBlock *eb, const Ioss::Field &field, void *data,
114  size_t data_size) const override;
115  int64_t get_field_internal(const Ioss::FaceBlock *eb, const Ioss::Field &field, void *data,
116  size_t data_size) const override;
117  int64_t get_field_internal(const Ioss::ElementBlock *eb, const Ioss::Field &field, void *data,
118  size_t data_size) const override;
119  int64_t get_field_internal(const Ioss::StructuredBlock *sb, const Ioss::Field &field,
120  void *data, size_t data_size) const override
121  {
122  return -1;
123  }
124 
125  int64_t get_field_internal(const Ioss::SideBlock *fb, const Ioss::Field &field, void *data,
126  size_t data_size) const override;
127  int64_t get_field_internal(const Ioss::NodeSet *ns, const Ioss::Field &field, void *data,
128  size_t data_size) const override;
129  int64_t get_field_internal(const Ioss::EdgeSet *ns, const Ioss::Field &field, void *data,
130  size_t data_size) const override;
131  int64_t get_field_internal(const Ioss::FaceSet *ns, const Ioss::Field &field, void *data,
132  size_t data_size) const override;
133  int64_t get_field_internal(const Ioss::ElementSet *ns, const Ioss::Field &field, void *data,
134  size_t data_size) const override;
135  int64_t get_field_internal(const Ioss::SideSet *fs, const Ioss::Field &field, void *data,
136  size_t data_size) const override;
137  int64_t get_field_internal(const Ioss::CommSet *cs, const Ioss::Field &field, void *data,
138  size_t data_size) const override;
139 
140  int64_t put_field_internal(const Ioss::Region *reg, const Ioss::Field &field, void *data,
141  size_t data_size) const override;
142  int64_t put_field_internal(const Ioss::NodeBlock *nb, const Ioss::Field &field, void *data,
143  size_t data_size) const override;
144  int64_t put_field_internal(const Ioss::EdgeBlock *eb, const Ioss::Field &field, void *data,
145  size_t data_size) const override;
146  int64_t put_field_internal(const Ioss::FaceBlock *eb, const Ioss::Field &field, void *data,
147  size_t data_size) const override;
148  int64_t put_field_internal(const Ioss::ElementBlock *eb, const Ioss::Field &field, void *data,
149  size_t data_size) const override;
150  int64_t put_field_internal(const Ioss::SideBlock *fb, const Ioss::Field &field, void *data,
151  size_t data_size) const override;
152  int64_t put_field_internal(const Ioss::NodeSet *ns, const Ioss::Field &field, void *data,
153  size_t data_size) const override;
154  int64_t put_field_internal(const Ioss::EdgeSet *ns, const Ioss::Field &field, void *data,
155  size_t data_size) const override;
156  int64_t put_field_internal(const Ioss::FaceSet *ns, const Ioss::Field &field, void *data,
157  size_t data_size) const override;
158  int64_t put_field_internal(const Ioss::ElementSet *ns, const Ioss::Field &field, void *data,
159  size_t data_size) const override;
160  int64_t put_field_internal(const Ioss::SideSet *fs, const Ioss::Field &field, void *data,
161  size_t data_size) const override;
162  int64_t put_field_internal(const Ioss::CommSet *cs, const Ioss::Field &field, void *data,
163  size_t data_size) const override;
164 
165  int64_t put_field_internal(const Ioss::StructuredBlock *sb, const Ioss::Field &field,
166  void *data, size_t data_size) const override
167  {
168  return -1;
169  }
170  int64_t put_Xset_field_internal(ex_entity_type type, const Ioss::EntitySet *ns,
171  const Ioss::Field &field, void *data, size_t data_size) const;
172  int64_t get_Xset_field_internal(ex_entity_type type, const Ioss::EntitySet *ns,
173  const Ioss::Field &field, void *data, size_t data_size) const;
174 
175  public:
176  // Temporarily made public for use during Salinas transition
177  // to using Ioss
178  int get_file_pointer() const override; // Open file and set exodusFilePtr.
179  private:
180  int64_t read_nodal_coordinates();
181  void read_elements(const Ioss::ElementBlock &block);
182 
183  void compute_node_status() const;
184 
185  // Metadata-related functions.
186  void read_meta_data__() override;
187  void read_communication_metadata();
188 
189  int64_t read_transient_field(ex_entity_type type, const Ioex::VariableNameMap &variables,
190  const Ioss::Field &field, const Ioss::GroupingEntity *ge,
191  void *data) const;
192 
193  int64_t read_attribute_field(ex_entity_type type, const Ioss::Field &field,
194  const Ioss::GroupingEntity *ge, void *data) const;
195 
196  int64_t write_attribute_field(ex_entity_type type, const Ioss::Field &field,
197  const Ioss::GroupingEntity *ge, void *data) const;
198 
199  // Handles subsetting of side blocks.
200  int64_t read_ss_transient_field(const Ioss::Field &field, int64_t id, void *variables,
201  std::vector<int> &is_valid_side) const;
202 
203  // Should be made more generic again so can rejoin with write_element_transient field
204  void write_nodal_transient_field(ex_entity_type type, const Ioss::Field &field,
205  const Ioss::NodeBlock *ge, int64_t count,
206  void *variables) const;
207  // Should be made more generic again so can rejoin with write_nodal_transient field
208  void write_entity_transient_field(ex_entity_type type, const Ioss::Field &field,
209  const Ioss::GroupingEntity *ge, int64_t count,
210  void *variables) const;
211  void write_meta_data() override;
212  void gather_communication_metadata(Ioex::CommunicationMetaData *meta);
213 
214  // Read related metadata and store it in the region...
215  void read_region();
216  void get_edgeblocks();
217  void get_faceblocks();
218  void get_elemblocks();
219  void get_blocks(ex_entity_type entity_type, int rank_offset, const std::string &basename);
220 
221  void get_sidesets();
222 
223  template <typename T>
224  void get_sets(ex_entity_type type, int64_t count, const std::string &base,
225  const T * /*unused*/);
226  void get_nodesets();
227  void get_edgesets();
228  void get_facesets();
229  void get_elemsets();
230 
231  void get_commsets();
232 
233  // ID Mapping functions.
234  const Ioss::Map &get_map(ex_entity_type type) const;
235  const Ioss::Map &get_map(Ioss::Map &entity_map, int64_t entityCount, ex_entity_type entity_type,
236  ex_inquiry inquiry_type) const;
237 
238  // Internal data handling
239  int64_t handle_node_ids(void *ids, int64_t num_to_get) const;
240  int64_t handle_element_ids(const Ioss::ElementBlock *eb, void *ids, size_t num_to_get) const;
241  int64_t handle_face_ids(const Ioss::FaceBlock *eb, void *ids, size_t num_to_get) const;
242  int64_t handle_edge_ids(const Ioss::EdgeBlock *eb, void *ids, size_t num_to_get) const;
243 
244  int64_t get_side_connectivity(const Ioss::SideBlock *fb, int64_t id, int64_t my_side_count,
245  void *fconnect, bool map_ids) const;
246  template <typename INT>
247  int64_t get_side_connectivity_internal(const Ioss::SideBlock *fb, int64_t id,
248  int64_t side_count, INT *fconnect, bool map_ids) const;
249  int64_t get_side_distributions(const Ioss::SideBlock *fb, int64_t id, int64_t my_side_count,
250  double *dist_fact, size_t data_size) const;
251 
252  int64_t get_side_field(const Ioss::SideBlock *ef_blk, const Ioss::Field &field, void *data,
253  size_t data_size) const;
254  int64_t put_side_field(const Ioss::SideBlock *fb, const Ioss::Field &field, void *data,
255  size_t data_size) const;
256 
257  mutable bool isSerialParallel{
258  false}; //!< true if application code is controlling the processor id.
259  };
260 } // namespace Iofx
261 #endif
Ioss
The main namespace for the Ioss library.
Definition: Iocgns_DatabaseIO.h:50
Ioss_DBUsage.h
Ioss::EntitySet
Base class for all &#39;set&#39;-type grouping entities, which means that members of the set are not necessar...
Definition: Ioss_EntitySet.h:61
Ioss::NodeSet
A collection of nodes.
Definition: Ioss_NodeSet.h:53
Ioss::FaceBlock
A collection of element faces with the same topology.
Definition: Ioss_FaceBlock.h:53
Ioss::FaceSet
A collection of element faces.
Definition: Ioss_FaceSet.h:54
Ioss::GroupingEntity
Base class for all &#39;grouping&#39; entities. The following derived classes are typical: ...
Definition: Ioss_GroupingEntity.h:93
Ioss::EdgeSet
A collection of element edges.
Definition: Ioss_EdgeSet.h:54
Ioss_Map.h
Iofx::DatabaseIO::put_field_internal
int64_t put_field_internal(const Ioss::StructuredBlock *sb, const Ioss::Field &field, void *data, size_t data_size) const override
Definition: Iofx_DatabaseIO.h:165
Ioss::SideBlock
A collection of element sides having the same topology.
Definition: Ioss_SideBlock.h:61
Ioss::ElementBlock
A collection of elements having the same topology.
Definition: Ioss_ElementBlock.h:48
Ioex::VariableNameMap
std::map< std::string, int, std::less< std::string > > VariableNameMap
Definition: Ioex_DatabaseIO.h:80
Ioss::StructuredBlock
A structured zone – i,j,k.
Definition: Ioss_StructuredBlock.h:98
Ioss::ElementSet
A collection of elements.
Definition: Ioss_ElementSet.h:54
Iofx::DatabaseIO::get_field_internal
int64_t get_field_internal(const Ioss::StructuredBlock *sb, const Ioss::Field &field, void *data, size_t data_size) const override
Definition: Iofx_DatabaseIO.h:119
Ioss::DatabaseUsage
DatabaseUsage
Specifies how an Ioss::DatabaseIO object will be used.
Definition: Ioss_DBUsage.h:40
Ioss_Utils.h
Ioex
A namespace for the exodus database format.
Definition: Ioex_IOFactory.C:61
Ioss::NodeBlock
A collection of all nodes in the region.
Definition: Ioss_NodeBlock.h:53
INT
int INT
Definition: Ioss_StructuredBlock.h:53
Ioss::Map
Definition: Ioss_Map.h:52
Ioss::CommSet
Definition: Ioss_CommSet.h:51
Ioex_DatabaseIO.h
Ioss_Field.h
anonymous_namespace{Iodw_DatabaseIO.C}::get_file_pointer
int get_file_pointer()
Definition: Iodw_DatabaseIO.C:64
Ioss::Region
A grouping entity that contains other grouping entities.
Definition: Ioss_Region.h:98
Ioex::CommunicationMetaData
Definition: Ioex_Internals.h:370
Ioss::SideSet
A collection of element sides.
Definition: Ioss_SideSet.h:59
Ioss::Field
Holds metadata for bulk data associated with a GroupingEntity.
Definition: Ioss_Field.h:47
MPI_Comm
int MPI_Comm
Definition: Ioss_CodeTypes.h:79
Iofx::DatabaseIO
Definition: Iofx_DatabaseIO.h:82
Ioex::DatabaseIO
Definition: Ioex_DatabaseIO.h:96
Ioss::PropertyManager
A collection of Ioss::Property objects.
Definition: Ioss_PropertyManager.h:49
Iofx::DatabaseIO::~DatabaseIO
~DatabaseIO() override
Definition: Iofx_DatabaseIO.h:89
anonymous_namespace{Iovs_DatabaseIO.C}::entity_type
entity_type
Definition: Iovs_DatabaseIO.C:81
anonymous_namespace{Ioss_Utils.C}::data
std::vector< char > data
Definition: Ioss_Utils.C:78
Ioss::EdgeBlock
A collection of element edges with the same topology.
Definition: Ioss_EdgeBlock.h:53
Iofx
A namespace for the file-per-process version of the parallel exodus database format.
Definition: Iofx_DatabaseIO.C:157