Reference manual ############################## The :class:`HDFArchive` class offers a convenient interface between the python objects and the HDF5 files, similar to a dictionary (or a shelve). The module contains two classes : * :class:`HDFArchiveGroup` : operates on a subtree of the HDF5 file * :class:`HDFArchive` : an :class:`HDFArchiveGroup` at the root path, with a simple constructor. * :class:`HDFArchiveInert` : Typically, one constructs an :class:`HDFArchive` explicitely, the :class:`HDFArchiveGroup` is created during operations, e.g.:: h = HDFArchive( "myfile.h5", 'r') g = h['subgroup1'] # g is a HDFArchiveGroup. Apart from the root path and the constructor, the classes are the same (in fact :class:`HDFArchive` `is a` :class:`HDFArchiveGroup`). Let us first document :class:`HDFArchive`. .. warning:: :class:`HDFArchive` and :class:`HDFArchiveGroup` do **NOT** handle parallelism. Check however the :class:`HDFArchiveInert` below. HDFArchive ======================================= .. autoclass:: pytriqs.archive.HDFArchive HDFArchiveGroup ======================================= .. class:: HDFArchiveGroup There is no explicit constructor for the user of the class. The :class:`HDFArchiveGroup` support most of the operations supported by dictionaries. In the following, *H* is a :class:`HDFArchiveGroup`. .. describe:: len(H) Return the number of items in the :class:`HDFArchiveGroup` *H*. .. describe:: H[key] Return the item of *H* with key *key*, retrieved from the file. Raises a :exc:`KeyError` if *key* is not in the :class:`HDFArchiveGroup`. .. method:: get_raw (key) Returns the subgroup key, **without any reconstruction**, ignoring the HDF5_data_scheme. .. describe:: H[key] = value Set ``H[key]`` to *value*. .. describe:: del H[key] Remove ``H[key]`` from *H*. Raises a :exc:`KeyError` if *key* is not in the :class:`HDFArchiveGroup`. .. describe:: key in H Return ``True`` if *H* has a key *key*, else ``False``. .. describe:: key not in H Equivalent to ``not key in H``. .. describe:: iter(H) Return an iterator over the keys of the dictionary. This is a shortcut for :meth:`iterkeys`. .. method:: items() Generator returning couples (key, values) in the group. .. warning:: Note that in all these iterators, the objects will only be retrieved from the file and loaded into memory one by one. .. method:: keys() Generator returning the keys of the group. .. method:: update(d) Add into the archive the content of any mapping *d* : keys->values, with hfd-compliant values. .. method:: values() Generator returning the values in the group .. method:: create_group(K) Creates a new subgroup named `K` to the root path of the group. Raises exception if the subgroup already exists. .. method:: is_group(K) Return True iif K is a subgroup. .. method:: is_data(K) Return True iif K is a leaf. .. method:: read_attr(AttributeName) Return the attribute `AttributeName` of the root path of the group. If there is no attribute, return None. .. method:: root_path() Return the root path of the group .. method:: apply_on_leaves (f) For each named leaf (name,value) of the tree, it calls `f(name,value)`. f should return : - `None` : no action is taken - an `empty tuple` () : the leaf is removed from the tree - an hdf-compliant value : the leaf is replaced by the value HDFArchiveInert ======================================= .. class:: HDFArchiveInert :class:`HDFArchive` and :class:`HDFArchiveGroup` do **NOT** handle parallelism. In general, it is good practive to write/read only on the master node. Reading from all nodes on a cluster may lead to communication problems. To simplify the writing of code, the simple HDFArchiveInert class may be useful. It is basically inert but does not fail. .. describe:: H[key] Return H and never raise exception. E.g. H['a']['b'] never raises an exception. .. describe:: H[key] = value Does nothing. Usage in a mpi code, e.g. :: R = HDFArchive("Results.h5",'w') if mpi.is_master_node() else HDFArchiveInert() a= mpi.bcast(R['a']) # properly broadcast the R['a'] from the master to the nodes. R['b'] = X # sets R['b'] in the file on the master only, does nothing on the nodes. .. highlight:: python .. _HDF_Protocol: Hdf-compliant objects ======================================= By definition, hdf-compliant objects are those which can be stored/retrieved in an :class:`HDFArchive`. In order to be hdf-compliant, a class must : * have a `HDF5_data_scheme` tag properly registered. * implement one of the two protocols described below. .. _HDF_Protocol_data_scheme: HDF5 data scheme ----------------------- To each hdf-compliant object, we associate a `data scheme` which describes how the data is stored in the hdf5 tree, i.e. the tree structure with the name of the nodes and their contents. This `data scheme` is added in the attribute `HDF5_data_scheme` at the node corresponding to the object in the file. For a given class `Cls`, the `HDF5_data_scheme` is `Cls._hdf5_data_scheme_` if it exists or the name of the class `Cls.__name__`. The `HDF5_data_scheme` of a class must be registered in order for :class:`HDFArchive` to properly reconstruct the object when rereading. The class is registered using the module `hdf_archive_schemes` :: class myclass : pass #.... from pytriqs.archive.hdf_archive_schemes import register_class register_class (myclass) The function is .. py:function:: register_class (cls [, doc = None] ) :param cls: the class to be registered. :param doc: a doc directory Register the class for :class:`HDFArchive` use. The name of `data scheme` will be `myclass._hdf5_data_scheme_` if it is defined, or the name of the class otherwise. .. _HDF_Protocol_details: How does a class become hdf-compliant ? --------------------------------------- There are two ways in which a class can become hdf-compliant: .. toctree:: :maxdepth: 1 protocol1 protocol2