pretty_name: MP-20
tags:
- chemistry
- crystal
- material
size_categories:
- 10K<n<100K
MP-20
MP-20 contains 45,229 structures from the Materials Project with 1 to 20 atoms per unit cell, as released with CDVAE. The CDVAE paper reports 45,231 structures; the released files hold 45,229.
This repository holds the complete, unfiltered dataset (45,229 structures) preprocessed to HDF5 with pycrystalgen, one file per split of the original release.
Files
| File | Structures | Atoms per structure |
|---|---|---|
train.hdf5 |
27,136 | 1–20 |
val.hdf5 |
9,047 | 1–20 |
test.hdf5 |
9,046 | 1–20 |
Labels
| Field | Source column | Meaning |
|---|---|---|
formation_energy_per_atom |
formation_energy_per_atom |
formation energy in eV/atom |
energy_above_hull |
e_above_hull |
energy above the convex hull in eV/atom |
band_gap |
band_gap |
band gap in eV |
Fields with no source in this dataset are filled with NaN: total_energy.
Source columns that are not stored: spacegroup.number, pretty_formula, elements, material_id. Row i of a split file is row i of the
corresponding source CSV.
Format
Each file stores flat concatenated arrays:
| Dataset | Shape | Type | Content |
|---|---|---|---|
lattice |
(n_struct, 3, 3) | float32 | lattice vectors as rows, in angstrom |
num_atoms |
(n_struct,) | int64 | number of atoms of each structure |
ptr |
(n_struct,) | int64 | index of the first atom of each structure in x and z |
x |
(n_atoms, 3) | float32 | fractional coordinates in [0, 1) |
z |
(n_atoms,) | int64 | atomic numbers |
total_energy, formation_energy_per_atom, energy_above_hull, band_gap |
(n_struct,) | float32 | labels, NaN when unknown |
The lattice is rebuilt from the cell lengths and angles of the source CIF, so it is in the
standard orientation (first vector along x). The batch array is an artefact of the writer
and is not used when reading.
Usage
from pycrystalgen.data import HDF5Dataset
dataset = HDF5Dataset.from_hub("materials-toolkits/mp-20", "train.hdf5")
structures = dataset[:32] # batched Structures
Source and processing
- Source files:
https://github.com/txie-93/cdvae/tree/main/data/mp_20(train.csv,val.csv,test.csv). - Built with pycrystalgen commit
8e39dbb,scripts/build_cdvae.py: CSV to CIF, then CIF to HDF5, with no filter. - Checked against the source: same number of rows, every stored label equal to its source column row by row, and a sample of 300 structures per split compared with pymatgen's parsing of the same CIF (elements, fractional coordinates, lattice).
The data is redistributed from the sources below; refer to them for licence and terms of use.
References
- T. Xie et al., Crystal Diffusion Variational Autoencoder for Periodic Material Generation, ICLR 2022.
- A. Jain et al., Commentary: The Materials Project: A materials genome approach to accelerating materials innovation, APL Materials 1, 011002 (2013).