Port UG chapter 1 and some cleanup (#1924)

25 files changed, 560 insertions, 4 deletions

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diff --git a/src/H5Fmodule.h b/src/H5Fmodule.h
index 4da58a4..0aba5cd 100644
--- a/src/H5Fmodule.h
+++ b/src/H5Fmodule.h
@@ -866,7 +866,7 @@
  * systems, environments, and applications. The drivers are listed in the table below.
  *
  * <table>
- * <caption>Supported file drivers</caption>
+ * <caption id="table_file_drivers">Supported file drivers</caption>
  * <tr>
  * <th>Driver Name</th>
  * <th>Driver Identifier</th>
diff --git a/src/H5Pmodule.h b/src/H5Pmodule.h
index 0439a3f..7885782 100644
--- a/src/H5Pmodule.h
+++ b/src/H5Pmodule.h
@@ -128,7 +128,7 @@
  * a property lists class for each of the following situations.
  *
  * <table>
- *     <caption align=top>Property list classes in HDF5</caption>
+ * <caption align=top id="table_plist">Property list classes in HDF5</caption>
  * <tr><th>Property List Class</th><th></th><th>For further discussion</th></tr>
  * <tr valign="top">
  *   <td>
@@ -323,7 +323,7 @@
  * property list classes, in gray above, are not user-accessible. The red empty set symbol indicates
  * that the \ref FMPL (FMPL) is an empty class; that is, it has no set table
  * properties. For more information, see \ref FileMountProps "File Mount Properties". Abbreviations
- * used in this figure are defined in the preceding table, “Property list classes in HDF5”.
+ * used in this figure are defined in the preceding table, \ref table_plist "Property list classes in HDF5".
  *
  * \subsubsection subsubsec_plist_lists Property Lists
  *
@@ -601,7 +601,7 @@
  * The new dataset creation property list’s identifier is returned in dcplA_id and the property list is
  * initialized with default dataset creation property values.
  *
- * A list of valid classes appears in the table "Property list classes in HDF5".
+ * A list of valid classes appears in the table \ref table_plist "Property list classes in HDF5".
  *
  * \code
  *     dcplB_id = H5Pcopy (dcplA_id);
diff --git a/src/H5module.h b/src/H5module.h
index 30f708b..6fadec8 100644
--- a/src/H5module.h
+++ b/src/H5module.h
@@ -30,22 +30,578 @@
  *
  * \section sec_data_model The HDF5 Data Model and File Structure
  * \subsection subsec_data_model_intro Introduction
+ * The Hierarchical Data Format (HDF) implements a model for managing and storing data. The
+ * model includes an abstract data model and an abstract storage model (the data format), and
+ * libraries to implement the abstract model and to map the storage model to different storage
+ * mechanisms. The HDF5 library provides a programming interface to a concrete implementation
+ * of the abstract models. The library also implements a model of data transfer, an efficient
+ * movement of data from one stored representation to another stored representation. The figure
+ * below illustrates the relationships between the models and implementations. This chapter
+ * explains these models in detail.
+ *
+ * <table>
+ * <tr>
+ * <td>
+ * \image html Dmodel_fig1.gif "HDF5 models and implementations"
+ * </td>
+ * </tr>
+ * </table>
+ *
+ * The <em>Abstract Data Model</em> is a conceptual model of data, data types, and data organization. The
+ * abstract data model is independent of storage medium or programming environment. The
+ * <em>Storage Model</em> is a standard representation for the objects of the abstract data model. The
+ * <a href="https://docs.hdfgroup.org/hdf5/develop/_s_p_e_c.html">HDF5 File Format Specification</a>
+ * defines the storage model.
+ *
+ * The <em>Programming Model</em> is a model of the computing environment and includes platforms from
+ * small single systems to large multiprocessors and clusters. The programming model manipulates
+ * (instantiates, populates, and retrieves) objects from the abstract data model.
+ *
+ * The <em>Library</em> is the concrete implementation of the programming model. The library exports the
+ * HDF5 APIs as its interface. In addition to implementing the objects of the abstract data model,
+ * the library manages data transfers from one stored form to another. Data transfer examples
+ * include reading from disk to memory and writing from memory to disk.
+ *
+ * <em>Stored Data</em> is the concrete implementation of the storage model. The <em>Storage Model</em>
+ * is mapped to several storage mechanisms including single disk files, multiple files (family of files),
+ * and memory representations.
+ *
+ * The HDF5 library is a C module that implements the programming model and abstract data
+ * model. The HDF5 library calls the operating system or other storage management software (for
+ * example, the MPI/IO Library) to store and retrieve persistent data. The HDF5 library may also
+ * link to other software such as filters for compression. The HDF5 library is linked to an
+ * application program which may be written in C, C++, Fortran, or Java. The application program
+ * implements problem specific algorithms and data structures and calls the HDF5 library to store
+ * and retrieve data. The figure below shows the dependencies of these modules.
+ *
+ * <table>
+ * <tr>
+ * <td>
+ * \image html Dmodel_fig2.gif "The library, the application program, and other modules"
+ * </td>
+ * </tr>
+ * </table>
+ *
+ * It is important to realize that each of the software components manages data using models and
+ * data structures that are appropriate to the component. When data is passed between layers
+ * (during storage or retrieval), it is transformed from one representation to another. The figure
+ * below suggests some of the kinds of data structures used in the different layers.
+ *
+ * The <em>Application Program</em> uses data structures that represent the problem and algorithms
+ * including variables, tables, arrays, and meshes among other data structures. Depending on its
+ * design and function, an application may have quite a few different kinds of data structures and
+ * different numbers and sizes of objects.
+ *
+ * The <em>HDF5 Library</em> implements the objects of the HDF5 abstract data model. Some of these
+ * objects include groups, datasets, and attributes. The application program maps the application
+ * data structures to a hierarchy of HDF5 objects. Each application will create a mapping best
+ * suited to its purposes.
+ *
+ * The objects of the HDF5 abstract data model are mapped to the objects of the HDF5 storage
+ * model, and stored in a storage medium. The stored objects include header blocks, free lists, data
+ * blocks, B-trees, and other objects. Each group or dataset is stored as one or more header and data
+ * blocks.
+ * @see <a href="https://docs.hdfgroup.org/hdf5/develop/_s_p_e_c.html">HDF5 File Format Specification</a>
+ * for more information on how these objects are organized. The HDF5 library can also use other
+ * libraries and modules such as compression.
+ *
+ * <table>
+ * <caption>Data structures in different layers</caption>
+ * <tr>
+ * <td>
+ * \image html Dmodel_fig3_a.gif
+ * </td>
+ * <td>
+ * \image html Dmodel_fig2.gif
+ * </td>
+ * <td>
+ * \image html Dmodel_fig3_c.gif
+ * </td>
+ * </tr>
+ * </table>
+ *
+ * The important point to note is that there is not necessarily any simple correspondence between
+ * the objects of the application program, the abstract data model, and those of the Format
+ * Specification. The organization of the data of application program, and how it is mapped to the
+ * HDF5 abstract data model is up to the application developer. The application program only
+ * needs to deal with the library and the abstract data model. Most applications need not consider
+ * any details of the
+ * <a href="https://docs.hdfgroup.org/hdf5/develop/_s_p_e_c.html">HDF5 File Format Specification</a>
+ * or the details of how objects of abstract data model are translated to and from storage.
+ *
  * \subsection subsec_data_model_abstract The Abstract Data Model
+ * The abstract data model (ADM) defines concepts for defining and describing complex data
+ * stored in files. The ADM is a very general model which is designed to conceptually cover many
+ * specific models. Many different kinds of data can be mapped to objects of the ADM, and
+ * therefore stored and retrieved using HDF5. The ADM is not, however, a model of any particular
+ * problem or application domain. Users need to map their data to the concepts of the ADM.
+ *
+ * The key concepts include:
+ * <ul><li>@ref subsubsec_data_model_abstract_file - a contiguous string of bytes in a computer
+ * store (memory, disk, etc.), and the bytes represent zero or more objects of the model</li>
+ * <li>@ref subsubsec_data_model_abstract_group - a collection of objects (including groups)</li>
+ * <li>@ref subsubsec_data_model_abstract_dataset - a multidimensional array of data elements with
+ * attributes and other metadata</li>
+ * <li>@ref subsubsec_data_model_abstract_space - a description of the dimensions of a multidimensional
+ * array</li>
+ * <li>@ref subsubsec_data_model_abstract_type - a description of a specific class of data element
+ * including its storage layout as a pattern of bits</li>
+ * <li>@ref subsubsec_data_model_abstract_attr - a named data value associated with a group,
+ * dataset, or named datatype</li>
+ * <li>@ref subsubsec_data_model_abstract_plist - a collection of parameters (some permanent and
+ * some transient) controlling options in the library</li>
+ * <li>@ref subsubsec_data_model_abstract_link - the way objects are connected</li></ul>
+ *
+ * These key concepts are described in more detail below.
+ *
  * \subsubsection subsubsec_data_model_abstract_file File
+ * Abstractly, an HDF5 file is a container for an organized collection of objects. The objects are
+ * groups, datasets, and other objects as defined below. The objects are organized as a rooted,
+ * directed graph. Every HDF5 file has at least one object, the root group. See the figure below. All
+ * objects are members of the root group or descendants of the root group.
+ *
+ * <table>
+ * <caption>The HDF5 file</caption>
+ * <tr>
+ * <td>
+ * \image html Dmodel_fig4_b.gif
+ * </td>
+ * </tr>
+ * <tr>
+ * <td>
+ * \image html Dmodel_fig4_a.gif
+ * </td>
+ * </tr>
+ * </table>
+ *
+ * HDF5 objects have a unique identity within a single HDF5 file and can be accessed only by their
+ * names within the hierarchy of the file. HDF5 objects in different files do not necessarily have
+ * unique identities, and it is not possible to access a permanent HDF5 object except through a file.
+ * For more information, see \ref subsec_data_model_structure.
+ *
+ * When the file is created, the file creation properties specify settings for the file. The file creation
+ * properties include version information and parameters of global data structures. When the file is
+ * opened, the file access properties specify settings for the current access to the file. File access
+ * properties include parameters for storage drivers and parameters for caching and garbage
+ * collection. The file creation properties are set permanently for the life of the file, and the file
+ * access properties can be changed by closing and reopening the file.
+ *
+ * An HDF5 file can be “mounted” as part of another HDF5 file. This is analogous to Unix file
+ * system mounts. The root of the mounted file is attached to a group in the mounting file, and all
+ * the contents can be accessed as if the mounted file were part of the mounting file.
+ *
+ * @see @ref sec_file.
+ *
  * \subsubsection subsubsec_data_model_abstract_group Group
+ * An HDF5 group is analogous to a file system directory. Abstractly, a group contains zero or
+ * more objects, and every object must be a member of at least one group. The root group is a
+ * special case; it may not be a member of any group.
+ *
+ * Group membership is actually implemented via link objects. See the figure below. A link object
+ * is owned by a group and points to a named object. Each link has a name, and each link points to
+ * exactly one object. Each named object has at least one and possibly many links to it.
+ *
+ * <table>
+ * <tr>
+ * <td>
+ * \image html Dmodel_fig5.gif "Group membership via link objects"
+ * </td>
+ * </tr>
+ * </table>
+ *
+ * There are three classes of named objects: group, dataset, and committed (named) datatype. See
+ * the figure below. Each of these objects is the member of at least one group, and this means there
+ * is at least one link to it.
+ *
+ * <table>
+ * <tr>
+ * <td>
+ * \image html Dmodel_fig6.gif "Classes of named objects"
+ * </td>
+ * </tr>
+ * </table>
+ *
+ * @see @ref sec_group.
+ *
  * \subsubsection subsubsec_data_model_abstract_dataset Dataset
+ * An HDF5 dataset is a multidimensional (rectangular) array of data elements. See the figure
+ * below. The shape of the array (number of dimensions, size of each dimension) is described by
+ * the dataspace object (described in the next section below).
+ *
+ * A data element is a single unit of data which may be a number, a character, an array of numbers
+ * or characters, or a record of heterogeneous data elements. A data element is a set of bits. The
+ * layout of the bits is described by the datatype (see below).
+ *
+ * The dataspace and datatype are set when the dataset is created, and they cannot be changed for
+ * the life of the dataset. The dataset creation properties are set when the dataset is created. The
+ * dataset creation properties include the fill value and storage properties such as chunking and
+ * compression. These properties cannot be changed after the dataset is created.
+ *
+ * The dataset object manages the storage and access to the data. While the data is conceptually a
+ * contiguous rectangular array, it is physically stored and transferred in different ways depending
+ * on the storage properties and the storage mechanism used. The actual storage may be a set of
+ * compressed chunks, and the access may be through different storage mechanisms and caches.
+ * The dataset maps between the conceptual array of elements and the actual stored data.
+ *
+ * <table>
+ * <tr>
+ * <td>
+ * \image html Dmodel_fig7_b.gif "The dataset"
+ * </td>
+ * </tr>
+ * </table>
+ *
+ * @see @ref sec_dataset.
+ *
  * \subsubsection subsubsec_data_model_abstract_space Dataspace
+ * The HDF5 dataspace describes the layout of the elements of a multidimensional array.
+ * Conceptually, the array is a hyper-rectangle with one to 32 dimensions. HDF5 dataspaces can be
+ * extendable. Therefore, each dimension has a current size and a maximum size, and the maximum
+ * may be unlimited. The dataspace describes this hyper-rectangle: it is a list of dimensions with
+ * the current and maximum (or unlimited) sizes. See the figure below.
+ *
+ * <table>
+ * <tr>
+ * <td>
+ * \image html Dmodel_fig8.gif "The dataspace"
+ * </td>
+ * </tr>
+ * </table>
+ *
+ * Dataspace objects are also used to describe hyperslab selections from a dataset. Any subset of the
+ * elements of a dataset can be selected for read or write by specifying a set of hyperslabs. A
+ * non-rectangular region can be selected by the union of several (rectangular) dataspaces.
+ *
+ * @see @ref sec_dataspace.
+ *
  * \subsubsection subsubsec_data_model_abstract_type Datatype
+ * The HDF5 datatype object describes the layout of a single data element. A data element is a
+ * single element of the array; it may be a single number, a character, an array of numbers or
+ * carriers, or other data. The datatype object describes the storage layout of this data.
+ *
+ * Data types are categorized into 11 classes of datatype. Each class is interpreted according to a set
+ * of rules and has a specific set of properties to describe its storage. For instance, floating point
+ * numbers have exponent position and sizes which are interpreted according to appropriate
+ * standards for number representation. Thus, the datatype class tells what the element means, and
+ * the datatype describes how it is stored.
+ *
+ * The figure below shows the classification of datatypes. Atomic datatypes are indivisible. Each
+ * may be a single object such as a number or a string. Composite datatypes are composed of
+ * multiple elements of atomic datatypes. In addition to the standard types, users can define
+ * additional datatypes such as a 24-bit integer or a 16-bit float.
+ * A dataset or attribute has a single datatype object associated with it. See Figure 7 above. The
+ * datatype object may be used in the definition of several objects, but by default, a copy of the
+ * datatype object will be private to the dataset.
+ *
+ * Optionally, a datatype object can be stored in the HDF5 file. The datatype is linked into a group,
+ * and therefore given a name. A committed datatype (formerly called a named datatype) can be
+ * opened and used in any way that a datatype object can be used.
+ *
+ * <table>
+ * <tr>
+ * <td>
+ * \image html Dmodel_fig9.gif "Datatype classifications"
+ * </td>
+ * </tr>
+ * </table>
+ *
+ * @see @ref sec_datatype.
+ *
  * \subsubsection subsubsec_data_model_abstract_attr Attribute
+ * Any HDF5 named data object (group, dataset, or named datatype) may have zero or more user
+ * defined attributes. Attributes are used to document the object. The attributes of an object are
+ * stored with the object.
+ *
+ * An HDF5 attribute has a name and data. The data portion is similar in structure to a dataset: a
+ * dataspace defines the layout of an array of data elements, and a datatype defines the storage
+ * layout and interpretation of the elements See the figure below.
+ *
+ * <table>
+ * <tr>
+ * <td>
+ * \image html Dmodel_fig10.gif "Attribute data elements"
+ * </td>
+ * </tr>
+ * </table>
+ *
+ * In fact, an attribute is very similar to a dataset with the following limitations:
+ * <ul><li>An attribute can only be accessed via the object</li>
+ * <li>Attribute names are significant only within the object</li>
+ * <li>An attribute should be a small object</li>
+ * <li>The data of an attribute must be read or written in a single access (partial reading or
+ * writing is not allowed)</li>
+ * <li>Attributes do not have attributes</li></ul>
+ *
+ * Note that the value of an attribute can be an object reference. A shared attribute or an attribute
+ * that is a large array can be implemented as a reference to a dataset.
+ *
+ * The name, dataspace, and datatype of an attribute are specified when it is created and cannot be
+ * changed over the life of the attribute. An attribute can be opened by name, by index, or by
+ * iterating through all the attributes of the object.
+ *
+ * @see @ref sec_attribute.
+ *
  * \subsubsection subsubsec_data_model_abstract_plist Property List
+ * HDF5 has a generic property list object. Each list is a collection of name-value pairs. Each class
+ * of property list has a specific set of properties. Each property has an implicit name, a datatype,
+ * and a value. See the figure below. A property list object is created and used in ways similar to
+ * the other objects of the HDF5 library.
+ *
+ * Property Lists are attached to the object in the library, and they can be used by any part of the
+ * library. Some properties are permanent (for example, the chunking strategy for a dataset), others
+ * are transient (for example, buffer sizes for data transfer). A common use of a Property List is to
+ * pass parameters from the calling program to a VFL driver or a module of the pipeline.
+ *
+ * Property lists are conceptually similar to attributes. Property lists are information relevant to the
+ * behavior of the library while attributes are relevant to the user’s data and application.
+ *
+ * <table>
+ * <tr>
+ * <td>
+ * \image html Dmodel_fig11_b.gif "The property list"
+ * </td>
+ * </tr>
+ * </table>
+ *
+ * Property lists are used to control optional behavior for file creation, file access, dataset creation,
+ * dataset transfer (read, write), and file mounting. Some property list classes are shown in the table
+ * below. Details of the different property lists are explained in the relevant sections of this
+ * document.
+ *
+ * <table>
+ * <caption>Property list classes and their usage</caption>
+ * <tr>
+ * <th>Property List Class</th>
+ * <th>Used</th>
+ * <th>Examples</th>
+ * </tr>
+ * <tr>
+ * <td>#H5P_FILE_CREATE</td>
+ * <td>Properties for file creation.</td>
+ * <td>Set size of user block.</td>
+ * </tr>
+ * <tr>
+ * <td>#H5P_FILE_ACCESS</td>
+ * <td>Properties for file access.</td>
+ * <td>Set parameters for VFL driver. An example is MPI I/O. </td>
+ * </tr>
+ * <tr>
+ * <td>#H5P_DATASET_CREATE</td>
+ * <td>Properties for dataset creation.</td>
+ * <td>Set chunking, compression, or fill value.</td>
+ * </tr>
+ * <tr>
+ * <td>#H5P_DATASET_XFER</td>
+ * <td>Properties for raw data transfer (read and write).</td>
+ * <td>Tune buffer sizes or memory management.</td>
+ * </tr>
+ * <tr>
+ * <td>#H5P_FILE_MOUNT</td>
+ * <td>Properties for file mounting.</td>
+ * <td></td>
+ * </tr>
+ * </table>
+ *
+ * @see @ref sec_plist.
+ *
  * \subsubsection subsubsec_data_model_abstract_link Link
+ * This section is under construction.
+ *
  * \subsection subsec_data_model_storage The HDF5 Storage Model
  * \subsubsection subsubsec_data_model_storage_spec The Abstract Storage Model: the HDF5 Format Specification
+ * The <a href="https://docs.hdfgroup.org/hdf5/develop/_s_p_e_c.html">HDF5 File Format Specification</a>
+ * defines how HDF5 objects and data are mapped to a linear
+ * address space. The address space is assumed to be a contiguous array of bytes stored on some
+ * random access medium. The format defines the standard for how the objects of the abstract data
+ * model are mapped to linear addresses. The stored representation is self-describing in the sense
+ * that the format defines all the information necessary to read and reconstruct the original objects
+ * of the abstract data model.
+ *
+ * The HDF5 File Format Specification is organized in three parts:
+ * <ul><li>Level 0: File signature and super block</li>
+ * <li>Level 1: File infrastructure</li>
+ * <ul><li>Level 1A: B-link trees and B-tree nodes</li>
+ * <li>Level 1B: Group</li>
+ * <li>Level 1C: Group entry</li>
+ * <li>Level 1D: Local heaps</li>
+ * <li>Level 1E: Global heap</li>
+ * <li>Level 1F: Free-space index</li></ul>
+ * <li>Level 2: Data object</li>
+ * <ul><li>Level 2A: Data object headers</li>
+ * <li>Level 2B: Shared data object headers</li>
+ * <li>Level 2C: Data object data storage</li></ul></ul>
+ *
+ * The Level 0 specification defines the header block for the file. Header block elements include a
+ * signature, version information, key parameters of the file layout (such as which VFL file drivers
+ * are needed), and pointers to the rest of the file. Level 1 defines the data structures used
+ * throughout the file: the B-trees, heaps, and groups. Level 2 defines the data structure for storing
+ * the data objects and data. In all cases, the data structures are completely specified so that every
+ * bit in the file can be faithfully interpreted.
+ *
+ * It is important to realize that the structures defined in the HDF5 file format are not the same as
+ * the abstract data model: the object headers, heaps, and B-trees of the file specification are not
+ * represented in the abstract data model. The format defines a number of objects for managing the
+ * storage including header blocks, B-trees, and heaps. The HDF5 File Format Specification defines
+ * how the abstract objects (for example, groups and datasets) are represented as headers, B-tree
+ * blocks, and other elements.
+ *
+ * The HDF5 library implements operations to write HDF5 objects to the linear format and to read
+ * from the linear format to create HDF5 objects. It is important to realize that a single HDF5
+ * abstract object is usually stored as several objects. A dataset, for example, might be stored in a
+ * header and in one or more data blocks, and these objects might not be contiguous on the hard
+ * disk.
+ *
  * \subsubsection subsubsec_data_model_storage_imple Concrete Storage Model
+ * The HDF5 file format defines an abstract linear address space. This can be implemented in
+ * different storage media such as a single file or multiple files on disk or in memory. The HDF5
+ * Library defines an open interface called the Virtual File Layer (VFL). The VFL allows different
+ * concrete storage models to be selected.
+ *
+ * The VFL defines an abstract model, an API for random access storage, and an API to plug in
+ * alternative VFL driver modules. The model defines the operations that the VFL driver must and
+ * may support, and the plug-in API enables the HDF5 library to recognize the driver and pass it
+ * control and data.
+ *
+ * A number of VFL drivers have been defined in the HDF5 library. Some work with a single file,
+ * and some work with multiple files split in various ways. Some work in serial computing
+ * environments, and some work in parallel computing environments. Most work with disk copies
+ * of HDF5 files, but one works with a memory copy. These drivers are listed in the
+ * \ref table_file_drivers "Supported file drivers" table.
+ *
+ * @see @ref subsec_file_alternate_drivers.
+ *
+ * Each driver isolates the details of reading and writing storage so that the rest of the HDF5 library
+ * and user program can be almost the same for different storage methods. The exception to this
+ * rule is that some VFL drivers need information from the calling application. This information is
+ * passed using property lists. For example, the Parallel driver requires certain control information
+ * that must be provided by the application.
+ *
  * \subsection subsec_data_model_structure The Structure of an HDF5 File
  * \subsubsection subsubsec_data_model_structure_file Overall File Structure
+ * An HDF5 file is organized as a rooted, directed graph. Named data objects are the nodes of the
+ * graph, and links are the directed arcs. Each arc of the graph has a name, and the root group has
+ * the name “/”. Objects are created and then inserted into the graph with the link operation which
+ * creates a named link from a group to the object. For example, the figure below illustrates the
+ * structure of an HDF5 file when one dataset is created. An object can be the target of more than
+ * one link. The names on the links must be unique within each group, but there may be many links
+ * with the same name in different groups. Link names are unambiguous: some ancestor will have a
+ * different name, or they are the same object. The graph is navigated with path names similar to
+ * Unix file systems. An object can be opened with a full path starting at the root group or with a
+ * relative path and a starting node (group). Note that all paths are relative to a single HDF5 file. In
+ * this sense, an HDF5 file is analogous to a single Unix file system.
+ *
+ * <table>
+ * <caption>An HDF5 file with one dataset</caption>
+ * <tr>
+ * <td>
+ * \image html Dmodel_fig12_a.gif
+ * </td>
+ * <td>
+ * \image html Dmodel_fig12_b.gif
+ * </td>
+ * </tr>
+ * </table>
+ *
+ * Note: In the figure above are two figures. The top figure represents a newly created file with one
+ * group, /. In the bottom figure, a dataset called /dset1 has been created.
+ *
+ * It is important to note that, just like the Unix file system, HDF5 objects do not have names. The
+ * names are associated with paths. An object has a unique (within the file) object identifier, but a
+ * single object may have many names because there may be many paths to the same object. An
+ * object can be renamed (moved to another group) by adding and deleting links. In this case, the
+ * object itself never moves. For that matter, membership in a group has no implication for the
+ * physical location of the stored object.
+ *
+ * Deleting a link to an object does not necessarily delete the object. The object remains available
+ * as long as there is at least one link to it. After all the links to an object are deleted, it can no
+ * longer be opened although the storage may or may not be reclaimed.
+ *
+ * It is important to realize that the linking mechanism can be used to construct very complex
+ * graphs of objects. For example, it is possible for an object to be shared between several groups
+ * and even to have more than one name in the same group. It is also possible for a group to be a
+ * member of itself or to be in a “cycle” in the graph. An example of a cycle is where a child is the
+ * parent of one of its own ancestors.
+ *
  * \subsubsection subsubsec_data_model_structure_path HDF5 Path Names and Navigation
+ * The structure of the file constitutes the name space for the objects in the file. A path name is a
+ * string of components separated by ‘/’. Each component is the name of a link or the special
+ * character “.” for the current group. Link names (components) can be any string of ASCII
+ * characters not containing ‘/’ (except the string “.” which is reserved). However, users are advised
+ * to avoid the use of punctuation and non-printing characters because they may create problems for
+ * other software. The figure below gives a BNF grammar for HDF5 path names.
+ *
+ * <em>A BNF grammar for path names</em>
+ * \code
+ *   PathName ::= AbsolutePathName | RelativePathName
+ *   Separator ::= "/" ["/"]*
+ *   AbsolutePathName ::= Separator [ RelativePathName ]
+ *   RelativePathName ::= Component [ Separator RelativePathName ]*
+ *   Component ::= "." | Name
+ *   Name ::= Character+ - {"."}
+ *   Character ::= {c: c in {{ legal ASCII characters } - {'/'}}
+ * \endcode
+ *
+ * An object can always be addressed by a full or absolute path which would start at the root group.
+ * As already noted, a given object can have more than one full path name. An object can also be
+ * addressed by a relative path which would start at a group and include the path to the object.
+ *
+ * The structure of an HDF5 file is “self-describing.” This means that it is possible to navigate the
+ * file to discover all the objects in the file. Basically, the structure is traversed as a graph starting at
+ * one node and recursively visiting the nodes of the graph.
+ *
  * \subsubsection subsubsec_data_model_structure_example Examples of HDF5 File Structures
+ * The figures below show some possible HDF5 file structures with groups and datasets. The first
+ * figure shows the structure of a file with three groups. The second shows a dataset created in
+ * “/group1”. The third figure shows the structure after a dataset called dset2 has been added to the
+ * root group. The fourth figure shows the structure after another group and dataset have been
+ * added.
+ *
+ * <table>
+ * <tr>
+ * <td>
+ * \image html Dmodel_fig14_a.gif "An HDF5 file structure with groups"
+ * </td>
+ * </tr>
+ * </table>
+ *
+ * Note: The figure above shows three groups; /group1 and /group2 are members of the root group.
+ *
+ * <table>
+ * <tr>
+ * <td>
+ * \image html Dmodel_fig14_b.gif "An HDF5 file structure with groups and a dataset"
+ * </td>
+ * </tr>
+ * </table>
+ *
+ * Note: The figure above shows that a dataset has been created in /group1: /group1/dset1.
+ *
+ * <table>
+ * <tr>
+ * <td>
+ * \image html Dmodel_fig14_c.gif " An HDF5 file structure with groups and datasets"
+ * </td>
+ * </tr>
+ * </table>
+ *
+ * Note: In the figure above, another dataset has been added as a member of the root group: /dset2.
+ *
+ * <table>
+ * <tr>
+ * <td>
+ * \image html Dmodel_fig14_c.gif " Another HDF5 file structure with groups and datasets"
+ * </td>
+ * </tr>
+ * </table>
+ *
+ * Note: In the figure above, another group and dataset have been added reusing object names:
+ * <em>/group2/group2/dset2</em>.
+ * <ol><li>HDF5 requires random access to the linear address space. For this reason it is not
+ * well suited for some data media such as streams.</li>
+ * <li>It could be said that HDF5 extends the organizing concepts of a file system to the internal
+ * structure of a single file.</li>
+ * <li>As of HDF5-1.4, the storage used for an object is reclaimed, even if all links are
+ * deleted.</li></ol>
  *
  * Next Chapter \ref sec_program
  *