Dataset card

README.md

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+---
+license: cc-by-4.0
+pretty_name: QMOF
+tags:
+- chemistry
+- materials-science
+- metal-organic-frameworks
+---
+
+# QMOF
+
+The QMOF Database (Rosen et al., 2021 and 2022), version 18: metal-organic frameworks and
+coordination polymers relaxed with PBE-D3(BJ). It is the database of the
+[MOF Explorer](https://materialsproject.org/mofs) of the Materials Project.
+
+| | |
+|---|---|
+| Structures | 20,372 |
+| Atoms | 2,312,743, 17 to 500 per structure (114 on average, median 96) |
+| Elements | 79, from H to Pu |
+| With a band gap at HLE17 / HSE06* / HSE06 | 10,756 / 10,811 / 10,810 |
+
+## Labels
+
+| Field | Source | Unit |
+|---|---|---|
+| `total_energy` | `outputs.pbe.energy_total` | eV, of the cell |
+| `band_gap` | `outputs.pbe.bandgap` | eV |
+
+`formation_energy_per_atom` and `energy_above_hull` are `NaN`.
+
+| `properties[...]` | Source | Unit |
+|---|---|---|
+| `band_gap_hle17`, `band_gap_hse06_10hf`, `band_gap_hse06` | `outputs.<theory>.bandgap` | eV, `NaN` when not computed |
+| `energy_vdw` | `outputs.pbe.energy_vdw`, the D3(BJ) part of the energy | eV |
+| `net_magmom` | `outputs.pbe.net_magmom` | μB |
+| `pld`, `lcd` | pore-limiting and largest cavity diameters (Zeo++) | Å |
+| `density` | `info.density` | g/cm³ |
+| `synthesized` | 1 if the structure comes from an experimental database | 0 or 1 |
+
+## Things to know
+
+- **Not on the scale of the crystal datasets.** `total_energy` is a raw PBE-D3(BJ) energy with
+  the settings of QMOF. It cannot be compared with the energies of the Materials Project or of
+  LeMat-Bulk, and there is no convex hull.
+- **Large cells.** One structure in ten has more than 200 atoms. The radius graph lists the
+  pairs of atoms of each structure: use smaller batches than for MP-20.
+- **Experimental and hypothetical.** `synthesized` is 0 for the hypothetical structures (from
+  ToBaCCo, Boyd & Woo, and others).
+- **Identifiers** are not in the file. `all_index.parquet` gives for each row its `qmof_id`,
+  its name in the source database, its formula, its DOI and its MOFid.
+- The partial charges, bond orders and magnetic moments per atom of the source are not in
+  the file.
+- No structure with partial occupancy was found in the database.
+- **Licence**: CC BY 4.0. Cite the two papers of the database.
+
+## Format
+
+HDF5 files of flat concatenated arrays, the format of the other datasets of
+[materials-toolkits](https://huggingface.co/materials-toolkits):
+
+| Dataset | Shape | Type | Content |
+|---|---|---|---|
+| `lattice` | (n_struct, 3, 3) | float32 | lattice vectors as rows, in Å; the identity for a molecule |
+| `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; positions in Å for a molecule |
+| `z` | (n_atoms,) | int64 | atomic numbers |
+| `pbc` | (n_struct, 3) | bool | whether the structure is periodic along each lattice vector |
+| `total_energy`, `formation_energy_per_atom`, `energy_above_hull`, `band_gap` | (n_struct,) | float32 | labels, NaN when unknown |
+| `properties/<name>` | (n_struct,) | float32 | the properties listed above, NaN when unknown |
+
+The position of an atom in Å is `x @ lattice`. The lattice of a crystal is rebuilt from the
+lengths and the angles of its cell, in the standard orientation (first vector along x), and
+its fractional coordinates are wrapped into the cell. The `batch` array is an artefact of the
+writer and is not used when reading. Row *i* of an index file describes structure *i*.
+
+## Usage
+
+```python
+from torchms.data import HDF5Dataset
+
+dataset = HDF5Dataset.from_hub("materials-toolkits/qmof", "all.hdf5")
+structures = dataset[:32]            # batched Structures
+structures.properties                # the named properties, one value per structure
+```
+
+Built with [torchms](https://gitlab.univ-artois.fr/astrid.klipfel/torch-ms).
+
+## Source and checks
+
+- [QMOF Database](https://doi.org/10.6084/m9.figshare.13147324.v18), figshare, version 18:
+  `qmof.json` and `qmof_structure_data.json` of `qmof_database.zip`, checked with its MD5.
+- Built by `scripts/build_qmof.py`. Every structure was compared with the database, read by
+  pymatgen: number of atoms, elements, coordinates, lattice, total energy, the four band gaps
+  and the largest cavity diameter.
+- Repository: [materials-toolkits/qmof](https://huggingface.co/datasets/materials-toolkits/qmof),
+  file `all.hdf5`.