Supported File Formats

In the updated MDANSE version, there have been significant changes to the supported file formats for input and output. This section provides an overview of these changes and the file formats used by MDANSE.

HDF5 File Format and GUI Integration

In the new version of MDANSE, the primary file format for both trajectory storage and analysis results is Hierarchical Data Format (HDF5) . HDF5 is a versatile file format designed for efficiently organizing and managing large data sets. It employs a hierarchical structure, akin to a file system, and supports n-dimensional arrays with associated metadata attributes. HDF5 is widely adopted, and even NetCDF version 4 is built on top of HDF5. Using HDF5 ensures platform independence, efficient data storage, and comprehensive self-contained information within trajectory files.

This transition to HDF5 as the primary storage format enhances data compatibility and accessibility within MDANSE. Furthermore, the integration of a graphical user interface (GUI) provides an intuitive and user-friendly interface for performing analyses and managing file conversions. Users can interact with MDANSE through the GUI to directly convert trajectories from different formats to the required HDF5 format using the Trajectory Converter tool.

DAT File Format

An alternative output format of Analysis results is in the form of DAT files, which are text-based and easily readable. Each DAT file corresponds to a specific variable generated during the analysis. If the Text option is selected, a tarball is generated, which contains multiple files, including:

  • jobinfo.txt: A text file documenting the analysis options selected during the analysis.

  • Variable DAT files: Each file is named after the variable it contains and includes the following information:

    • Variable name

    • Type of plot (representing plot dimensions)

    • Variable’s placement on the x-axis (if plotted on the y-axis in the 2D/3D Plotter)

    • Units of data

    • Length of the trajectory (indicated as slice:[length])

    • A list of numbers representing the variable data

The DAT format simplifies data sharing and analysis, providing a clear and human-readable representation of analysis results.

MDANSE Scripts

MDANSE now includes Python scripts that capture the complete analysis setup, including all selected options. These scripts are designed to be run using the Python interpreter bundled with MDANSE. Running these scripts automates the execution of a specific analysis with predefined settings, simplifying repetitive tasks and ensuring consistency in analysis procedures.

This update streamlines the analysis process and facilitates the reproducibility of results within MDANSE.