This document describes the structure of CGNS, its software, and its documentation. The Overview, which was written primarily for new and prospective users of CGNS,
introduces terminology,
identifies the elements of the system and their relationships,
describes the various documents that elaborate the details.
Reading the material on the purpose and general description of CGNS should help users determine whether CGNS will meet their needs. Those wanting a bit more detail should read the section describing the various elements of CGNS. For those interested only in understanding the scope and capabilities of CGNS, or for the end user unconcerned with the internal workings of the system, the Overview may prove sufficient documentation by itself.
The Overview also includes certain information that is current as of the document date but which may change with time. All information on CGNS compatible “applications” software (i.e., external programs such as grid generators, flow codes, or postprocessors) is of this type. Also subject to change is the information on the acquisition of the software and documentation, and the current status of CGNS.
The general purpose of CGNS is to provide a standard for recording and recovering computer data associated with the numerical solution of the equations of fluid dynamics.
CGNS consists of a collection of conventions, and software implementing those conventions, for the storage and retrieval of CFD (Computational Fluid Dynamics) data. The system consists of two parts: (1) a standard format for recording the data, and (2) software that reads, writes, and modifies data in that format. The format is a conceptual entity established by the documentation, and is intended to be general, portable, expandable, and durable. The software is a physical product supplied to enable developers to access and produce data recorded in that format. All CGNS software is completely free and open to anyone.
The CGNS standard, applied through the use of the supplied software, is intended to:
facilitate the exchange of CFD data between sites between applications codes across computing platforms stabilize the archiving of CFD data The principal target of CGNS is data normally associated with compressible viscous flow (i.e., the Navier-Stokes equations), but the standard is also applicable to subclasses such as Euler and potential flows. The CGNS standard addresses the following types of data.
Structured, unstructured, and hybrid grids Flow solution data, which may be nodal, cell-centered, face-centered, or edge-centered Multizone interface connectivity, both abutting and overset Boundary conditions Flow equation descriptions, including the equation of state, viscosity and thermal conductivity models, turbulence models, and multi-species chemistry models Time-dependent flow, including moving and deforming grids Dimensional units and nondimensionalization information Reference states Convergence history Association to CAD geometry definitions Much of the standard and the software is applicable to computational field physics in general. Disciplines other than fluid dynamics would need to augment the data definitions and storage conventions, but the fundamental database software, which provides platform independence, is not specific to fluid dynamics.
A CGNS database describes the current state of one or more entire CFD (Computational Fluid Dynamics) problems, including the following:
grid flowfield boundary conditions topological connection information auxiliary data (e.g., nondimensionalization parameters, reference states) Not all of these data need to be present at any particular time. The overall view is that of a shared database that can be accessed by the various software tools common to CFD, such as solvers, grid generators, field visualizers, and postprocessors. Each of these “applications” serves as an editor of the data, adding to, modifying, or interpreting it according to that application’s specific role.
CGNS conventions and software provide for the recording of a complete and flexible problem description. The exact meaning of a subsonic inflow boundary condition, for example, can be described in complete detail if desired. User comments can be included nearly anywhere, affording the opportunity, for instance, for date stamping or history information to be included. Dimension and sizing information is carefully defined. Any number of flow variables may be recorded, with or without standard names, and it is also possible to add user-defined or site-specific data. These features afford the opportunity for applications to perform extensive error checking if desired.
Because of this generality, CGNS provides for the recording of much more descriptive information than current applications normally use. However, the provisions for this data are layered so that much of it is optional. It should be practical to convert most current applications to CGNS with little or no conceptual change, retaining the option to take advantage of more detailed descriptions as that becomes desirable.
CGNS specifications currently cover the bulk of CFD data that one might wish to exchange among sites or applications; for instance, nearly any type of field data can be recorded, and, based on its name, found and understood by any code that needs it. Global data (e.g., freestream Mach number, Reynolds number, angle of attack) and physical modeling instructions (e.g., thin layer assumptions, turbulence model) may be specified. Nevertheless, there are items specific to individual applications for which there is currently no specification within CGNS. Most commonly, these are operational instructions, such as number of sweeps, solution method, multigrid directives, and so on. Owing to the miscellaneous nature of this data, there has been no attempt to codify it within a global standard. It is therefore expected that many applications will continue to require small user-generated input files, presumably in ASCII format.
CGNS itself does not initiate action or undertake any function normally handled by the operating system. The user still performs CFD tasks according to existing processes. This includes selecting the computing platform, maintaining the files, and launching the applications.
However, the ease of communication between applications that CGNS provides should motivate the development of new batch and interactive mechanisms for the convenient application of CFD tools.
Introduction Structure of a CGNS Database Standard Interface Data Structures (SIDS) SIDS File Mapping Database Manager Mid-Level Library, or API Documentation Introduction CGNS concerns itself with the recording and retrieval of data associated with the computation of fluid flows. Included are such structures as grids, flowfields, boundary conditions, and zone connectivity information. CGNS “understands” this data in the sense that it contains conventions for recording it based on its structure and its role in CFD.
The underlying design of CGNS is that of a common database that is accessed (read, written, or modified) by a collection of “applications” programs such as solvers, grid generators, and postprocessors.
CGNS itself does not synthesize, modify, or interpret the data it stores. The applications create, edit, or display the data; CGNS is limited to recording and retrieving it. Each application’s program accesses the data directly using CGNS function calls installed in the application by its developer. The applications are not regarded as part of CGNS itself.
CGNS is passive. It does not initiate action and cannot “push” information into the applications codes or “pull” information out. Rather, the codes must request the information they seek and store the information they produce. The applications must be launched by a user who organizes the location and content of the database. The process and sequence of events remain under user control. Thus CGNS facilitates, but does not incorporate, the development of batch or interactive environments designed to control the CFD process.
The elements of CGNS address all activities associated with the storage of the data on external media and its movement to and from the applications programs. These elements include the following:
The Standard Interface Data Structures (SIDS), which specify the intellectual content of CFD data and the conventions that govern naming and terminology. The SIDS File Mapping, which specifies the exact location where the CFD data defined by the SIDS is to be stored within a database file. The Database Manager, which consists of both a file format specification and its I/O software, which handles the actual reading and writing of data from and to external storage media. The following sections discuss in more detail the roles of the CGNS elements and introduce their documentation.
Structure of a CGNS Database In this section, the conceptual structure of a CGNS database, and the nodes from which it is built, are discussed. This describes the way in which the CGNS software “sees” the database, not necessarily the way in which it is implemented. The details of the implementation are left to the underlying database manager.
A CGNS database consists of a collection of elements called nodes. These nodes are arranged in a tree structure that is logically similar to a UNIX file system. The nodes are said to be connected in a “child-parent” relationship according to the following simple rules:
Each node may have any number of child nodes. Except for one node, called the root, each node is the child of exactly one other node, called its parent. The root node has no parent. Structure of a Node Each node has exactly the same internal structure. The entities associated with each node are the following: Node Identifier (ID) Name Label Data Type Dimension Dimension Values Data Child Table Node Identifier. The Node ID is a floating point number assigned by the system when the database is opened or created. Applications may record the ID and use it to return directly to the corresponding node when required. The Node ID is valid only while the database is open; subsequent openings of the same database may be expected to yield different IDs.
Name. The Name field holds a character string chosen by the user or specified by the SIDS to identify the particular instance of the data being recorded.
Label. The Label, also a character string, is specified by the CGNS mapping conventions and identifies the kind of data being recorded. For example, a node with label Zone_t may record (at and below it) information on the zone with Name “UnderWing.” No node may have more than one child with the same name, but the CGNS mapping conventions commonly specify many children with the same label. For some nodes, the mapping conventions specify that the name field has significance for the meaning of the data (e.g., EnthalpyStagnation). Although the user may specify another name, these “paper” conventions serve the transfer of data between users and between applications. These names and their meanings are established by the SIDS.
Data Type, Dimension, Dimension Values, Data. Nodes may or may not contain data. For those that do, CGNS specifies a single array whose type (integer, etc.), dimension, and size are recorded in the Data Type, Dimension, and Dimension Value fields, respectively. The mapping conventions specify some nodes that serve to establish the tree structure and point to further data below but contain no data themselves. For these nodes, the Data Type is MT, and the other fields are empty. A link to another node within the current or an external CGNS database is indicated by a Data Type of LK
Child Table. The Child Table contains a list of the node’s children. It is maintained by the database manager as children are created and deleted.
High-Level Organization of the CGNS Database For a full specification of the location of CFD data in the CGNS database, the user should see the SIDS File Mapping document. For convenience, we summarize the high-level structure below. A CGNS database consists of a tree of nodes implemented as all or part of one or more database files. All information is identified by and accessed through a single node in one of these files.
By definition, the root node of a CGNS database has the Label CGNSBase_t. The name of the CGNS database can be specified by the user and is stored in the “Name” field of the CGNSBase_t node. Current CGNS conventions require that the CGNSBase_t node be located directly below a “root node” in the database file identified by the name “/”.
A database file may contain multiple CGNS databases, and thus multiple CGNSBase_t nodes. However, each node labeled CGNSBase_t in a single file must have a unique name. The user or application must know the name of the file containing the entry-level node and, if there is more than one node labeled CGNSBase_t in that file, the name of the database as well.
Below the CGNSBase_t node, the mapping conventions specify a subnode for each zone. This node has label Zone_t. Its Name refers to the particular zone whose characteristics are recorded at and below the node, such as “UnderWing.” In general, names can be specified by the user, but defaults are specified for nodes that the user does not choose to name. For the Zone_t nodes, the defaults are Zone1, Zone2, and so forth, in order of creation. A similar convention for default names applies elsewhere. It is impossible to create a node without a name (or with a name of zero length). The CGNS Mid-Level Library conforms to the default convention.
Below each zone node will be found nodes for the grid, flowfield, boundary conditions, and connectivity information; these, in turn, are parents of nodes specifying extent, spatial location, and so on.
The file mapping specifies that one or more “Descriptor” nodes may be inserted anywhere in the file. Descriptor nodes are used to record textual information regarding the file contents. The size of Descriptor nodes is unlimited, so entire documents could be named and stored within the data field if desired. Descriptors are intended to store human-readable text, and they are not processed by any supplied CGNS software (except, of course, that the text may be stored and retrieved).
It is possible, by using the linking capability of CGNS, for a child of any node to be a node in another database file, or elsewhere within the same file. This mechanism enables one database to share a grid, for example, with another database without duplicating the information.
Standard Interface Data Structures (SIDS) The establishment of a standard for storing CFD-related information requires a detailed specification of the content and meaning of the data to be stored. For example, it is necessary to state the meaning of the words “boundary condition” in a form sufficiently concrete to be recorded precisely, and yet sufficiently flexible to embrace current and future practice. The Standard Interface Data Structures (SIDS) document describes this “intellectual content” of CFD-related data in detail.
An exact description of the intellectual content is required not only to define the precise form of the data but also to guarantee that the meaning of the data is consistently interpreted by practitioners. Thus the SIDS include a collection of naming conventions that specify the precise meaning of nomenclature (e.g., the strings DensityStatic and BCWallViscous).
The SIDS are written in a self-contained C-like descriptive language. SIDS data structures are defined in a hierarchical manner in which more complex entities are built from simpler ones. These structures are closely reflected in CGNS-compliant files: simple entities are often stored in single nodes, while more complex structures are stored in entire subtrees.
SIDS File Mapping Because of the generality of the tree structure, there are many conceivable means of encoding CFD data. But for any application to access, say, the boundary conditions for zone “UnderWing”, requires a single convention with regard to where in the file that data has been stored. The SIDS File Mapping document, sometimes referred to as the “File Mapping,” establishes the precise node, and properties of that node, where each piece of CGNS data should be recorded. The CGNS Mid-Level Library relies on the File Mapping to locate CFD-related data within the file. The mapping provides locations for an extensive set of CFD data. Most applications will make use of only a small subset of this data. Further, inasmuch as applications are viewed as editors that are in the process of building the database, most of them are intended for use on incomplete data sets. Therefore, it is not required that all the data elements specified by the CGNS conventions be complete in order for a database to be CGNS compliant. The user must ensure that the current state of the database will support whatever application he may launch. Of course, the application should gracefully handle any absence or deficiency of data.
CGNS conventions do not specify the following:
the use the applications programs may make of the data the means by which the applications programs modify the data the form in which the data is stored internal to an application The validity, accuracy and completeness of the data are determined entirely by the applications software. The tree structure also makes it possible for applications to ignore data for which they have no use. (In fact, they cannot even discover the data’s existence without a specific inquiry.) Therefore, it is permissible for an file containing a CGNS database to contain additional nodes not specified by the mapping. Such nodes will be disregarded by software not prepared to use them. However, if data essential to the CFD process is stored in a manner not consistent with CGNS conventions, that data becomes invisible and therefore useless to other applications.
Note that the SIDS serve not only to facilitate the mapping of data onto the file structure but also to standardize the meaning of the recorded data. Thus there are two kinds of conventions operative within CGNS. Adherence to the File Mapping conventions guarantees that the software will be able to find and read the data. Adherence to the SIDS guarantees uniformity of meaning among users and between applications. The SIDS File Mapping document establishes the context of CGNS for a database manager; the SIDS define the nomenclature, content, and meaning of the stored data.
The File Mapping generally avoids the storage of redundant data. Sometimes an application may require an alternate (but intellectually equivalent) form of the data; in such cases it is recommended that the alternate form be prepared at the time of use and kept separate from the CGNS data. This avoids habitual reliance on the alternate form, which would invalidate the standard.
Database Manager A database manager contains the I/O software, which handles the actual reading and writing of data from and to external storage media. It must conform, at least in context, to that specified by the SIDS File Mapping document, and provide a minimal number of data access routines (referred to as core routines). In principle, it is possible to install CGNS I/O into an application using only these core routines. However, such an approach would require the installer to access the data at a very fundamental level and would result in lengthy sequences of core function calls. Therefore, the CGNS system also includes a Mid-Level Library, an API (Application Programming Interface) that contains additional routines intended to facilitate higher-level access to the data. These are CFD-knowledgeable routines suitable for direct installation into applications codes. The CGNS software was originally developed around ADF (Advanced Data Format) as it’s database manager, thus much of the concepts and structures of CGNS originated from there.
In version 2.4 of the CGNS software, HDF5 (Hierarchical Data Format was introduced as an alternative database manager. At that time, either ADF or HDF5 (but not both) was selectable at build time.
It should be noted that because of HDF5’s parallel and compression capability as well as its support, the CGNS Steering Committee has made the decision to slowly transition (beginning in 2005) to HDF5 as the official data storage mechanism. However, ADF will continue to be available for use, with the CGNS mid-level library capable of (1) using either format and (2) translating back and forth between the two.
Beginning with CGNS version 3.0, both ADF and HDF5 are supported concurrently and transparently by CGNS. To facilitate this, a new set of core routines, described in the CGIO User’s Guide, have been developed as a replacement to the individual ADF and HDF5 core routines. These allow general access to the low-level I/O, irrespective of the underlying database manager.
Mid-Level Library, or API The CGNS Mid-Level Library, or Applications Programming Interface (API), is one of the most directly visible parts of CGNS, and it is of particular interest to applications code developers. It consists of a set of routines that are designed to allow applications to access CGNS data according to the role of the data in CFD. Unlike the ADF (or HDF5) Core, routines in the CGNS Mid-Level Library “understand” the SIDS-defined CFD data structures and the File Mapping. This enables applications developers to insert CGNS I/O into their applications without having detailed knowledge of the File Mapping. For instance, an application might use CGNS mid-level calls to retrieve all boundary conditions for a given zone.
The CGNS Mid-Level Library document contains complete descriptions and usage instructions for all mid-level routines. All calls are provided in both C and Fortran.
Documentation The CGNS elements described above are documented individually, and are available as follows:
Standard Interface Data Structures SIDS File Mapping Manual Mid-Level Library CGIO User’s Guide ADF Implementation HDF5 Implementation In addition, the following documentation is also recommended:
CGNS Overview and Entry-Level Document (this document) A User’s Guide to CGNS “The CGNS System”, AIAA Paper 98-3007 [PDF (496K, 16 pages)] “Advances in the CGNS Database Standard for Aerodynamics and CFD”, AIAA Paper 2000-0681 [PDF (106K, 11 pages)] “CFD General Notation System (CGNS): Status and Future Directions”, AIAA Paper 2002-0752, [PDF (289K, 13 pages)] The specific documents of interest vary with the level of intended use of CGNS. Prospective Users Prospective users are presumably unfamiliar with CGNS. They will probably wish to begin with the current Overview document, or, if they require more detailed information, the AIAA papers listed above. Beyond that, most will find a quick read of the SIDS File Mapping Manual (or enlightening as to the logical form of the contents of CGNS files. Browsing the figures in the File Mapping Manual, as well as the SIDS itself, will provide some feel for the scope of the system. The User’s Guide to CGNS, and the CGNS Mid-Level Library document, should give an indication of what might be required to implement CGNS in a given application. Prospective users should probably not concern themselves with the details of ADF or HDF5.
End Users The end user is the practitioner of CFD who generates the grids, runs the flow codes and/or analyzes the results. For this user, a scan of this Overview document will sufficiently explain the overall workings of the system. This includes end user responsibilities for matters not governed by CGNS, such as the maintenance of files and directories. The end user will also find useful the User’s Guide to CGNS, as well as those portions of the SIDS which deal with standard data names. The AIAA papers listed above may also be useful if more details about the capabilities of CGNS are desired.
Applications Code Developers The applications code developer builds or maintains code to support the various sub-processes encountered in CFD, e.g., grid generation, flow solution, post-processing, or flow visualization. The code developer must be able to install CGNS compliant I/O. The most convenient method for doing so is to utilize the CGNS Mid-Level Library. The User’s Guide to CGNS is the starting point for learning to use the Mid-Level Library to create and use CGNS files. The CGNS Mid-Level Library document itself should also be considered essential. This library of routines will perform the most common I/O operations in a CGNS-compliant manner. However, even when the Mid-Level Library suffices to implement all necessary I/O, an understanding of the file mapping and SIDS will be useful. It will likely be necessary to consult the SIDS to determine the precise meaning of the nomenclature.
Applications code developers wishing to read or write data that isn’t supported by the Mid-Level Library, will need to use the CGIO low-level routines to access the underlying database manager directly. The CGIO User’s Guide documents these routines in detail.
CGNS System Developers CGNS System development can be kept somewhat compartmentalized. Developers responsible for the maintenance or building of supplements to the ADF Core, need not concern themselves with documentation other than the ADF User Guide. (Development and maintenance of HDF5 is under the purview of NCSA, so has no relevance here.) System developers wishing to add to the CGNS Mid-Level Library will need all the documents. Theoretical developments, such as extensions to the SIDS, may possibly be undertaken with a knowledge of the SIDS alone, but such contributions must also be added to the SIDS File Mapping before they can be implemented.
The development of CGNS-compliant applications, e.g., grid generators, postprocessors, and the like, has not been a direct undertaking of the CGNS team. Rather, it has been the intent to make the attractiveness of interoperable CFD applications, together with general acceptance of the CGNS standard by Boeing, NASA, and others, sufficient to induce applications developers to incorporate CGNS I/O into their offerings.
Several CGNS-compatible applications have indeed been developed, and more continue to appear, this web site has a page with an informational list of the known applications compliant with CGNS.
The CGNS software is available free of charge, under the terms of the CGNS License. Also available there are the cgnstools utilities, the source code examples from A User’s Guide to CGNS, and additional Fortran source code examples.
The CGNS Library contains source code for the Mid-Level Library, the CGIO core, and the ADF and HDF5 implementations, plus CMake and configure scripts for building the library for a variety of platforms.
The CGNS documentation may be accessed via the CGNS Documentation home page. In addition to current version, documentation may also be available for the previous and beta versions of CGNS. All the CGNS documentation is available in HTML form (PDF is no longer being supported except for the SIDS).
In addition to the CGNS documentation itself, several conference papers and slide presentations are available, as well as minutes from the CGNS meetings and telecons.