Crystal Structure and Databases¶
Structure Format¶
There are many file formats that can be used for presenting a crystal structure. Including:
| Structure Format | File Extension | Data | Comments |
|---|---|---|---|
| Crystallographic Information File | .cif |
Species, lattice, coordinates, symmetry, and atomic displacement parameters (ADPs) | Standard file for crystal structure databases such as ICSD. Can store symmetrized structure. |
| VASP Input Structure | POSCAR or CONTCAR or .vasp |
Species, lattice, coordinates, (possibly includes velocities) | VASP input and output |
| XYZ format | .xyz |
Species, coordinates | Only for non periodic system, e.g. molecule. Can hold multiple structures (snapshots), and it is widely used for small organic molecules. |
| Extended XYZ | .extxyz |
Species, coordinates, lattice, and properties (force, energy, stress, and any other properties). | Work for both periodic and non-periodic systems, and can hold multiple structures (snapshots). Widely used in emerging fields such as machine learning potentials. |
You can use ase.io.read and ase.io.write to read and write between different format. We will use extxyz for our structure database in MACE.
from ase.io import read, write
atoms = read('Al_empty.cif')
write(filename='Al_empty.extxyz', images=atoms, format='extxyz')
write(filename='Al_empty.vasp', images=atoms, format='vasp',direct=True)
Obtain structure¶
Experimentally, structures are mostly obtained by solving the diffraction patterns, including X-ray diffraction (XRD) and neutron diffraction (ND). The structure can then be solved and refined by changing the structure information (coordiantes, lattice, and thermal parameters) until the computed pattern matches the experimental diffraction pattern.
| X-ray diffraction | Neutron diffraction |
|---|---|
| Neighbours and isotopes cannot be discriminated | Neighbours and isotopes can be discriminated |
| Interact with electron clouds. Light elements are noise with the presence of heavy elements | Interact with nuclei. Suitable for light elements such as H (need to replace H by D) |
| No magnetic structure | Magnetic structure can be investigated |
| Strong adsorption | Lower adsorption (suitable for alloy) |
Structure Databases¶
You can find experimental structuers from some expeimental crystal structure databases:
- Inorganic Crystal Structure Database (ICSD): NUS has paid.
- The Cambridge Structural Database (CSD), free only with access code (CCDC number).
- Crystallography Open Database (COD), free but lower quality.
There are also some computed structure databases: