| --- |
| license: cc-by-4.0 |
| pretty_name: CoRE MOF 2019 |
| tags: |
| - chemistry |
| - materials-science |
| - metal-organic-frameworks |
| --- |
| |
| # CoRE MOF 2019 |
|
|
| The public structures of the Computation-Ready Experimental MOF database (Chung et al., 2019), |
| version 1.1.4: metal-organic frameworks **determined by experiment**, cleaned to be used in |
| simulations. Their solvent is removed in two ways, which make the two splits: |
|
|
| | Split | Structures | Atoms | Atoms per structure | |
| |---|---|---|---| |
| | `asr`, all solvent removed | 12,020 | 3,926,702 | 10 to 10,560, median 192 | |
| | `fsr`, free solvent removed | 7,061 | 2,388,025 | 10 to 10,560, median 204 | |
|
|
| In `fsr` the solvent bound to the metals is kept. Most structures of `fsr` are also in `asr`, |
| with the same name up to its suffix. |
|
|
| ## Labels |
|
|
| Structures come from experiment: the four labels (`total_energy`, `band_gap`, ...) are `NaN`. |
| The properties are the geometric ones of the table of the source, computed with Zeo++: |
|
|
| | `properties[...]` | Source column | Unit | |
| |---|---|---| |
| | `lcd`, `pld`, `lfpd` | largest cavity, pore limiting and largest free path diameters | Å | |
| | `density` | `cm3_g`, which holds the density | g/cm³ | |
| | `asa_m2_cm3`, `asa_m2_g` | accessible surface area | m²/cm³, m²/g | |
| | `nasa_m2_cm3`, `nasa_m2_g` | non accessible surface area | m²/cm³, m²/g | |
| | `void_fraction` | `AV_VF` | 0 to 1 | |
| | `av_cm3_g`, `nav_cm3_g` | accessible and non accessible volume | cm³/g | |
| | `has_oms` | 1 if the structure has an open metal site | 0 or 1 | |
| | `disorder` | 1 if the source put the structure in its `disorder` folder | 0 or 1 | |
|
|
| ## Things to know |
|
|
| - **Very large cells.** One structure in ten has more than 690 atoms, 559 of `asr` have more |
| than 1,000, and the largest has 10,560. The radius graph lists the pairs of atoms of a |
| structure: at 5 Å a cell of 2,000 atoms takes 0.5 GB on a GPU, one of 5,000 atoms 3.3 GB. |
| Filter by `num_atoms` or use batches of a few structures. |
| - **Nothing is filtered.** The 1,877 structures of `asr` and the 1,053 of `fsr` that the |
| source set apart as disordered are kept, with `disorder` set to 1. |
| `properties["disorder"] == 0` selects the others. |
| - **Experimental structures are not relaxed**, and hydrogens can be missing. |
| - **Atoms are in the order of the files.** 8 files of `asr` and 7 of `fsr` are not in P1: |
| their symmetry operations were applied by pymatgen. |
| - **Names** are not in the file. `asr_index.parquet` and `fsr_index.parquet` give for each |
| row the name of the structure in the source (a CSD refcode or the name of a file of |
| supporting information, with a suffix), its metals and its DOI. |
| - No structure with partial occupancy was found. |
| - **Licence**: CC BY 4.0. |
|
|
| ## 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/core-mof", "asr.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 |
|
|
| - [CoRE MOF 2019 Dataset](https://doi.org/10.5281/zenodo.7691378), Zenodo, version 1.1.4: |
| `2019-11-01-ASR-public_12020` and `2019-11-01-FSR-public_7061`, archives and tables, checked |
| with their MD5. |
| - Built by `scripts/build_core_mof.py`. The atoms are read as they are listed in each file. |
| Every structure was then compared with the reading of its file by pymatgen: cell, number of |
| atoms, and each atom at the position of one atom of the same element. Three properties were |
| compared with the table. |
| - Repository: [materials-toolkits/core-mof](https://huggingface.co/datasets/materials-toolkits/core-mof), |
| files `asr.hdf5` and `fsr.hdf5`. |
|
|
