Converter between openPMD and GDF

About

This software provides conversion between files in openPMD schema and the GDF file format.

The software is written in python 3, python 2 is not supported. For the rest of the document by python we assume some python3 binary.

Installing

Clone this repository by running

git clone https://github.com/ComputationalRadiationPhysics/openPMD-converter-GDF.git

or download an archive from the github page and unpack it.

The primary dependency is openPMD-api, which can be installed e.g., by

python -m pip install -r requirements.txt

or for conda users via

conda install -c conda-forge openpmd-api matplotlib h5py

For further installation methods please see the full list of available installation methods.

Converting from GDF to openPMD

To convert a GDF file into an openPMD formatted file run the gdf_to_openPMD.py module as follows:

python gdf_to_openPMD -gdf_file gdf_file -openPMD_output file_in_openPMD_format

where

• gdf_file is the path to an input GDF file;
• file_in_openPMD_format is the path to an output openPMD-format file.

The format is selected according to the file extension: current supported: .h5 (HDF5), .bp (ADIOS1) or .json (JSON).

Example

To run the script for the provided examples, run the following from a project directory:

python3 gdf_to_openPMD.py -gdf examples/example_1.gdf -openPMD_output examples/example_1.h5
python3 gdf_to_hdf.py -gdf examples/example_1.gdf -gdf examples/example_1.bp

Converting from openPMD to GDF

To convert an openPMD-format file into a GDF file run the openPMD_to_gdf.py module as follows:

python3 openPMD_to_gdf.py -openPMD_input openPMD-format_file -gdf gdf_file -species (optional)

where parameters

• -openPMD_input is the path to an input openPMD format file;
• -gdf is the path to an output GDF file, by default openPMD_input path + .cgf
• -species chosen particle species.

The format is selected according to the file extension: current supported: .h5 (HDF5), .bp (ADIOS1) or .json (JSON).

Example

To run the script for the provided example, run the following from a project directory:

python3 openPMD_to_gdf.py -openPMD_input examples/example_3.h5 -gdf examples/result4.gdf

Limitations

Convertor does not work with datasets larger than 268435455, because of GDF standard limitations.