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49 lines
2.2 KiB
ReStructuredText
49 lines
2.2 KiB
ReStructuredText
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.. _hdf5_base:
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.. module:: pytriqs.archive
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HDF5 interface
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###################################
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In TRIQS, the main data storage format is `HDF5 <http://www.hdfgroup.org/HDF5/>`_ (Hierarchical Data Format v5).
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The best picture of a hdf5 file is that of a **tree**, where :
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* **Leaves** of the tree are basic types : scalars (int, long, double, string) and rectangular arrays of these scalars (any dimension : 1,2,3,4...).
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* Subtrees (branches) are called **groups**
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* Groups and leaves have a name, so an element of the tree has naturally a **path** :
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e.g. /group1/subgroup2/leave1 and so on.
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* Any path (groups, leaves) can be optionally tagged with an **attribute**, in addition to their name,
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typically a string (or any scalar)
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`Any data with a tree structure with arrays or scalar leaves can be naturally stored in hdf5 files`.
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To be more precise, we call hereafter a data **hdf-compliant** `iif` it can be reversibly transformed into
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* a tree structure with scalar/arrays leaves.
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* or a dictionary `keys -> values`, where `keys` are strings (field names) and `values` are scalars, arrays or any other hdf-compliant data.
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Due to the recursive nature of trees, the two definitions are equivalent.
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An hdf-compliant data can be naturally saved in a subgroup of an HDF5 file by adding (cf example below) new leaves for all scalar and arrays
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and new subgroup for other hdf-compliant data.
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Using HDF5 format has several advantages :
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* Most basic objects of TRIQS, like Green function, are hdf-compliant.
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* TRIQS provides a **simple and intuitive interface HDFArchive** to manipulate them.
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* HDF5 is **standard**, well maintained and widely used.
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* HDF5 is **portable** from various machines (32-bits, 64-bits, various OS, etc...)
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* HDF5 can be read and written in **many langages** (python, C/C++, F90, etc...), beyond TRIQS. One is not tied to a particular program.
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* Simple operations to explore and manipulate the tree are provided by simple unix shell commands (e.g. h5ls, h5diff).
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* It is a binary format, hence it is compact and has compression options.
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* It is to a large extent **auto-documented** : the structure of the data speaks for itself.
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.. toctree::
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:maxdepth: 5
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tutorial
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ref
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