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File Formats

This page provides an overview of parsing libraries interfaced from AtomsIO and an (incomplete) list of file formats they support. The parsing libraries are listed in order of preference, i.e. the order in which AtomsIO.load_system, AtomsIO.save_system, AtomsIO.load_trajectory and AtomsIO.save_trajectory will attempt the parsing libraries until one flags that it supports parsing/writing such a format. If a file format is thus listed in combination with multiple parsers, the above methods will only ever consult the first of the parser libraries. Note that one can always overwrite the automatic AtomsIO selection by providing the parser library explicitly as first argument.

AtomsIO also features an integration with a number of python libraries (such as ASE) to support parsing a wide range of atomic structure files. These python-based are not enabled by default to avoid introducing Python dependencies for down-stream code when this can be avoided. Python-dependent code paths can be activated by a simple using AtomsIOPython before calling load_system or save_system or similar. This should automatically install all required python dependencies.

Note

Unfortunately atomistic file formats are usually horribly underspecified and generally not all details are supported in all formats. Common examples are that some file formats are unable to store velocity information, others only work for non-periodic systems etc. Therefore even though we try to be careful in AtomsIO, it frequently happens that some information is lost when writing a system to disk. An additional caveat is that the way how particular atomistic properties are mapped to individual data fields of a file format is not standardised amongst parser libraries. To recover a system as closely as possible, it is thus advisable to choose the same parser library for writing and reading a file.

Tip

For the reasons mentioned above a good long-term storage format (in the eyes of the AtomsIO authors) is the extended XYZ format via the AtomsIO.ExtxyzParser. This format and parser has a well-documented specification and moreover leads to a human-readable plain-text file.

The following list all currently available parsers, in the order they are tried (top to bottom):