openpmd/openpmd-example-datasets

:gift: HDF5 Example Files

openPMD example datasets

This repository contains examples of openPMD datasets, in three different geometries:

• 2D Cartesian
• 3D Cartesian
• Cylindrical with azimuthal decomposition ("thetaMode")

The structure.h5 is an openPMD 1.1.0 compliant file contains the bare bones structure with no associated data.

In order to obtain these datasets:

• Clone this repository

git clone https://github.com/openPMD/openPMD-example-datasets.git

• Uncrompress the files

cd openPMD-example-datasets
tar -zxvf example-2d.tar.gz
tar -zxvf example-3d.tar.gz
tar -zxvf example-thetaMode.tar.gz
...

How were these files created?

Files created with the Particle-In-Cell code Warp

The files example-2d.tar.gz, example-3d.tar.gz and example-thetaMode.tar.gz were produced with the Particle-In-Cell code Warp. The resolution is intentionally very low, so as to produce data of manageable size.

The scripts that were used in order to produce these openPMD files from Warp can be found in the directory scripts/warp.

Examples created with the finite-element code FEMM

The files example-femm-3d.h5 and example-femm-thetaMode.h5 were produced using the finite-element code FEMM.

The scripts that were used in order to produce these openPMD files can be found in the directory scripts/femm.

Examples created with the Particle-In-Cell code PIConGPU

The files legacy_datasets.tar.gz were produced with the Particle-In-Cell code PIConGPU.

openpmd-example-datasets's Issues

Shape of Const Records (Warp)

@C0nsultant just realized the constant record component in Warp have a wrong shape (for particle records) right now.

The shape attribute in those files is 1 but should be the number of particles (N,).

Issue with `spack` installation instructions

When following these instructions with system=ubuntu; compute=openmp, I get the following error when doing spack install:

Package 'py-pil' not found.

This is quite confusing, since none of the packages are called py-pil. I checked that this does not come from the package py-pip (by removing it from the list of packages to install), so it seems that one of the other python packages is pulling this as a dependency.

Add ADIOS example Datasets

For reference purposes, it would be convenient to have (validated) sample files in formats other than HDF5.

This also should uncover possible incompatabilities and inconsistencies between file formats (e.g. HDF5 and ADIOS lack bool due to their C roots, see openPMD/openPMD-api#50).

ADIOS is a major backend in the community and thus should deserve some attention. As the author of openPMD/openPMD-api#126, it was difficult to verify file correctness without any ground thruth.

basePath is resolved in all examples

In all examples the attribute basePath is set to "/data/{}/" with {} being the iteration.
Following the standard, basePath should be /data/%T/ instead.

see openPMD/openPMD-validator/#11

Add the ParticlePatches

Once the format of the Particle Patches has been decided in the standard

No particles in 3D example

There are no particles in the 3D example data set.

Add README and a LICENSE

Anonymous Cloning (Git lfs)

@RemiLehe we actually found the problem we previously had with git lfs and the need to "enter your github credentials".

There is a specific syntax for anonymous, read-only access that is also useful for people not having a github account: git://github.com/openPMD/openPMD-example-datasets.git.

The https syntax (https://github.com/openPMD/openPMD-example-datasets.git) and the ssh syntax ([email protected]:openPMD/openPMD-example-datasets.git) are both for read and possible write-access remotes.