HDF5

HDF5 Files - Hierarchical Data Format

HDF5 is the dominant format for scientific computing data, providing efficient storage for large, complex datasets.

Documentation: hdfgroup.org | Python API: docs.h5py.org

Available Datasets

openPMD_2d_sample.h5

• Size: 286 KB
• Type: Plasma simulation (2D)
• Standard: openPMD (Open Standard for Particle-Mesh Data)
• Description: 2D electromagnetic field data from plasma physics simulation

openPMD_3d_sample.h5

• Size: 286 KB
• Type: Plasma simulation (3D)
• Standard: openPMD
• Description: 3D particle and field data from plasma simulation

md_adk_protein.h5

• Size: 287 KB
• Type: Molecular dynamics trajectory
• Source: MDAnalysis test dataset
• Description: Adenylate kinase protein trajectory with atomic coordinates

protein_1CRN.pdb

• Size: 49 KB
• Type: Protein structure
• Resolution: 0.945 Å
• Description: Crambin protein from Protein Data Bank

lysozyme_2LYZ.pdb

• Size: 131 KB
• Type: Protein structure
• Description: Chicken lysozyme crystal structure

Where to Find More Data

• OpenPMD Examples: github.com/openPMD/openPMD-example-datasets
• Protein Data Bank: rcsb.org - 200,000+ protein structures
• MDAnalysis Datasets: mdanalysis.org/MDAnalysisData
• HDF Group Resources: portal.hdfgroup.org/display/HDF5/Examples

Shadow Datasets

For TB-scale HDF5 datasets, see:

• Shadow-Datasets/Molecular-Dynamics.md
• Shadow-Datasets/Astrophysics-Cosmology.md