README.md

metadata

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:

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

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.

Source and checks

• CoRE MOF 2019 Dataset, 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, files asr.hdf5 and fsr.hdf5.