ComputationalRadiationPhysics / openPMD-converter-GDF

converter between openPMD and GDF

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.