| --- |
| 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 |
| |
| ```python |
| 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). |
| |
