ExodusII 6.05
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1/*! \mainpage ExodusII API Documentation
2
3\section intro Introduction
4
5EXODUS is the successor of the widely used finite element (FE) data file format EXODUS
6(henceforth referred to as EXODUS I) developed by Mills-Curran and Flanagan. It
7continues the concept of a common database for multiple application codes (mesh generators,
8analysis codes, visualization software, etc.) rather than code-specific utilities, affording
9flexibility and robustness for both the application code developer and application code user.
10By using the EXODUS data model, a user inherits the flexibility of using a large array of
11application codes (including vendor-supplied codes) which access this common data file
12directly or via translators.
13
14The uses of the EXODUS data model include the following:
15 - Problem definition -- mesh generation, specification of locations of boundary conditions and load application, specification of material types.
16 - Simulation -- model input and results output.
17 - Visualization -- model verification, results postprocessing, data interrogation, and analysis tracking.
18
19\section avail License and Availability
20The EXODUS library is licensed under the BSD open source license.
21
22Copyright (c) 2005 Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000
23with Sandia Corporation, the U.S. Government retains certain rights in this software.
24
25Redistribution and use in source and binary forms, with or without modification, are permitted
26provided that the following conditions are met:
27 - Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
28 - Redistributions in binary form must reproduce the above copyright notice, this list
29of conditions and the following disclaimer in the documentation and/or other
30materials provided with the distribution.
31 -Neither the name of Sandia Corporation nor the names of its contributors may be
32used to endorse or promote products derived from this software without specific
33prior written permission.
34
35THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
36"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
37LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
38A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
39OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
40SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
41LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
42DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
43THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
44(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
45OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
46
47The ExodusII library source code is available on Sourceforge at
48http://sourceforge.net/projects/exodusii
49
50For bug reports, documentation errors, and enhancement suggestions, contact:
51- Gregory D. Sjaardema
52- PHONE: (505) 844-2701
53- EMAIL: gdsjaar@sandia.gov
54
55\section devel Development of EXODUS
56
57The evolution of the EXODUS data model has been steered by FE application code developers
58who desire the advantages of a common data format. The EXODUS model has been
59designed to overcome deficiencies in the EXODUS I file format and meet the following
60functional requirements as specified by these developers:
61 - Random read/write access.
62 - Application programming interface (API) -- provide routines callable from FORTRAN, C, and C++ application codes.
63 - Extensible -- allow new data objects to be added without modifying the application programs that use the file format.
64 - Machine independent -- data should be independent of the machine which generated it.
65 - Real-time access during analysis -- allow access to the data in a file while the file is
66being created.
67
68To address these requirements, the open source database library
69etCDF (http://www.unidata.ucar.edu/software/netcdf/) was selected to handle the low-level data storage. The EXODUS
70II library functions provide the mapping between FE data objects and
71netCDF dimensions, attributes, and variables. Thus, the code developer
72interacts with the data model using the vocabulary of an FE analyst
73(element connectivity, nodal coordinates, etc.) and is relieved of the
74details of the data access mechanism.
75
76Because an EXODUS file is a netCDF file, an application program can
77access data via the EXODUS API or the netCDF API directly. Although
78accessing the data directly via the netCDF API requires more in-depth
79understanding of netCDF, this capability is a powerful feature that
80allows the development of auxiliary libraries of special purpose
81functions not offered in the standard EXODUS library. For example,
82if an application required access to the coordinates of a single node
83(the standard library function returns the coordinates for all of the
84nodes in the model), a simple function could be written that calls
85netCDF routines directly to read the data of interest.
86
87\section descrip Description of Data Objects
88
89The data in EXODUS files can be divided into three primary
90categories: initialization data, model, and results.
91
92Initialization data includes sizing parameters (number of nodes,
93number of elements, etc.), optional quality assurance information
94(names of codes that have operated on the data), and optional
95informational text.
96
97The model is described by data which are static (do not change through
98time). These data include nodal coordinates, element connectivity
99(node lists for each element), element attributes, and node sets and
100side sets (used to aid in applying loading conditions and boundary
101constraints).
102
103The results are optional and include five types of variables -- nodal,
104element, nodeset, sideset, and global -- each of which is stored
105through time. Nodal results are output (at each time step) for all the
106nodes in the model. An example of a nodal variable is displacement in
107the X direction. Element, nodeset, and sideset results are output (at
108each time step) for all entities (elements, nodes, sides) in one or
109more entity block. For example, stress may be an element
110variable. Another use of element variables is to record element status
111(a binary flag indicating whether each element is "alive" or "dead")
112through time. Global results are output (at each time step) for a
113single element or node, or for a single property. Linear momentum of a
114structure and the acceleration at a particular point are both examples
115of global variables. Although these examples correspond to typical FE
116applications, the data format is flexible enough to accommodate a
117spectrum of uses.
118
119A few conventions and limitations must be cited:
120
121 - There are no restrictions on the frequency of results output except
122 that the time value associated with each successive time step must
123 increase monotonically.
124 - To output results at different frequencies (i.e., variable A at
125 every simulation time step, variable B at every other time step)
126 multiple EXODUS files must be used.
127 - There are no limits to the number of each type of results, but once
128 declared, the number cannot change.
129 - If the mesh geometry or topology changes in time (i.e., number of
130 nodes increases, connectivity changes), then the new geometrymust be
131 output to a new EXODUS file.
132
133\section int64 Integer Bulkdata Storage Details
134
135The EXODUS database can store integer bulk data, entity map data, and
136mesh entity (block/set) ids in either 32-bit or 64-bit integer format. The data
137considered "bulk data" are:
138
139 - element, face, and edge connectivity lists,
140 - element, face, edge, and node set entity lists,
141
142The entity map data is any data stored in one of the 'map' objects on
143the exodus file. This includes:
144 - id maps
145 - number maps
146 - order maps
147 - processor node maps
148 - processor element maps.
149
150A mesh entity id is the id of any block (element block, edge block,
151...); set (node set, face set, ...), coordinate frame, and
152communication map.
153
154When an EXODUS file is created via the ex_create() function, the
155'mode' argument provides the mechanism for specifying how integer data
156will be passed as arguments to the API functions and also how the
157integer data will be stored on the database. The ex_open() function
158also provides a mechanism for specifying how integer data will be
159passed as arguments.
160
161The method uses the 'mode' argument to the ex_open() and
162ex_create() functions. The mode is a 32-bit integer in which certain
163bits are turned on by or'ing certain predefined constants.
164
165exoid = ex_create( EX_TEST_FILENAME,
166 EX_CLOBBER|EX_MAPS_INT64_DB|EX_MAPS_INT64_API,
167 &appWordSize, &diskWordSize );
168
169The constants related to the integer size (32-bit or 64-bit)
170specification are:
171
172- EX_MAPS_INT64_DB -- entity map data
173- EX_IDS_INT64_DB -- mesh entity ids
174- EX_BULK_INT64_DB -- bulk data
175- EX_ALL_INT64_DB -- (the above 3 or'd together)
176- EX_MAPS_INT64_API -- entity map data
177- EX_IDS_INT64_API -- mesh entity ids
178- EX_BULK_INT64_API -- bulk data
179- EX_ALL_INT64_API -- (the above 3 or'd together)
180
181The constants that end with "_DB" specify that that particular integer
182data is stored on the database as 64-bit integers; the constants that
183end with "_API" specify that that particular integer data is passed
184to/from API functions as 64-bit integers.
185
186If the range of the data being transmitted is larger than the
187permitted integer range (for example, if the data is stored on the
188database as 64-bit ints and the application specifies passing data as
18932-bit ints), the api function will return an error.
190
191The three types of integer data whose storage can be specified are
192- maps (EX_MAPS_INT64_),
193- "bulk data" including connectivity lists and entity lists (EX_BULK_INT64_), and
194- entity ids which are the ids of element, face, edge, and node sets
195 and blocks; and map ids (EX_IDS_INT64_)
196
197The function ex_int64_status(exoid) is used to determine the integer
198storage types being used for the EXODUS database 'exoid'. It returns
199an integer which can be and'ed with the above flags to determine
200either the storage type or function parameter type.
201
202For example, if
203(EX_MAPS_INT64_DB \& ex_int64_status(exoid)) is true, then map data is
204being stored as 64-bit integers for that database.
205
206It is not possible to determine the integer data size on a database
207without opening the database via an ex_open() call. However, the
208integer size specification for API functions can be changed at any
209time via the ex_set_int64_status(exoid, mode) function. The mode is
210one or more of EX_MAPS_INT64_API, EX_IDS_INT64_API, or
211EX_BULK_INT64_API, or'd together. Any exodus function calls after
212that point will use the specified integer size. Note that a call to
213ex_set_int64_status(exoid, mode) overrides any previous setting for
214the integer sizes used in the API. The ex_create() function is the
215only way to specify the integer sizes specification for database
216integers.
217
218\subsection int64_fortran_api Fortran API
219The fortran api is uses the same mechanism as was described above for
220the C API. If using the "8-byte real and 8-byte int" fortran mode
221typically used by the SEACAS applications (the compiler automatically
222promotes all integers and reals to 8-byte quantities), then the
223fortran exodus library will automatically enable the *_API
224options; the client still needs to specify the *_DB options.
225
226\subsection int64_fortran_imp Fortran Implementation
227
228The new capability to pass 64-bit integer data through the fortran and
229C API functions simplifies the implementation of the "8-byte real
2308-byte int" usage of the exodus library. Previously, the wrapper
231routines in addrwrap.F were required to convert the 8-byte integer
232data on the client side to/from 4-byte integers on the library
233side. This required extra memory allocation and complications that are
234now handled at the lowest level in the netcdf library. The
235map-related functions in the fortran api have all been converted to
236pass 64-bit integers down to the C API which has removed some code and
237simplified those functions.
238
239
240\section Database Options (Compression, Name Length, File Type)
241
242The ex_set_option() function call is used to set various options on the
243database. Valid values for 'option' are:
244
245| Option Name | Option Values
246-------------------------|---------------
247| EX_OPT_MAX_NAME_LENGTH | Maximum length of names that will be returned/passed via api call.
248| EX_OPT_COMPRESSION_TYPE | Not currently used; default is gzip
249| EX_OPT_COMPRESSION_LEVEL | In the range [0..9]. A value of 0 indicates no compression
250| EX_OPT_COMPRESSION_SHUFFLE | 1 if enabled, 0 if disabled
251| EX_OPT_INTEGER_SIZE_API | 4 or 8 indicating byte size of integers used in api functions.
252| EX_OPT_INTEGER_SIZE_DB | Query only, returns 4 or 8 indicating byte size of integers stored on database.
253
254The compression-related options are only available on netcdf-4 files
255since the underlying hdf5 compression functionality is used for the
256implementation. The compression level indicates how much effort should
257be expended in the compression and the computational expense increases
258with higher levels; in many cases, a compression level of 1 is
259sufficient.
260
261\defgroup ResultsData Results Data
262@{
263 This section describes data file utility functions for creating /
264 opening a file, initializing a file with global parameters, reading /
265 writing information text, inquiring on parameters stored in the data
266 file, and error reporting.
267@}
268
269\defgroup Utilities Data File Utilities
270 @{
271This section describes data file utility functions for creating /
272opening a file, initializing a file with global parameters, reading /
273writing information text, inquiring on parameters stored in the data
274file, and error reporting.
275 @}
276
277\defgroup ModelDescription Model Description
278 @{
279The routines in this section read and write information which
280describe an exodus finite element model. This includes nodal
281coordinates, element order map, element connectivity arrays,
282element attributes, node sets, side sets, and object properties.
283 @}
284
285
286*/