vesta_vectors.py

A Python 3 script to visualise the extent of atomic displacement - useful for ab-initio defect calculations. Uses the Vesta file format, which can be generated from a number of other structure data file formats using the Vesta software. The only dependancy outside of the Python standard Library is NumPy, which is included in standard scientific Python distributions.

Input

Two Vesta files: one for the initial structure (before relaxation), and one for the final structure (after relaxation).

Output

A Vesta file that contains vectors connecting the initial and final atomic positions.

Command line options

-f  --filenames  
      description: name of initial and final Vesta files
      type: string  
      default: initial.vesta final.vesta
      
-r  --radius   
      description: vector radius (in angstrom)
      type: float
      default: 0.5
      
-c  --colour
      description: vector colour (in RGB)
      type: list(int)
      default: [255,0,0]
      
-x  --cutoff
      description: vectors with a modulus below this value will not be displayed (in angstrom)
      type: float
      default: 0.1
      
-sf --scale_factor
      description: scale all vector moduli by this amount
      type: float
      default: 1.0
      
-ca --centre_atom
      description: the output Vesta structure is centred around an atom in the initial structure, specified by this index position (indexing from one)
      type: int
      default: None
      
-ar --atoms_removed
      description: index position of atoms in initial structure which have been removed in final structure (indexing from one)
      type: list(int)
      default: []
      
-ai --atoms_inserted
      description: index position of atoms which have been inserted into the final structure (indexing from one)
      type: list(int)
      default: []      

Example

Example input (initial.vesta, final.vesta) and output (vectors.vesta) data for a CdTe cell is contained in the ./data folder.

python3 vesta_vectors.py -f ./data/initial.vesta ./data/final.vesta -ar 512 -ca 512

This will generate the file vectors.vesta. The argument -ar is used because the final structure file has a Te vacancy defect; atom number 512 has been removed from the initial structure file. The argument -ca is used because we want the output structure to be centred around this defect.

When the output file vectors.vesta is opened in Vesta, you will see the following:

All the atoms and bonds are removed so that the vectors can be seen clearly. Any displacement vector with magnitude below 0.1 Angstrom is not displayed - this can be adjusted with the -x / --cutoff argument. It is easy to make further adjustments to the output structure via Vesta - for example, I can turn off lighting effects, increase the size of the atoms, and adjust the z-axis boundary to give:

Warnings!

• This script has not been extensively tested - use at your own risk and check that the final vectors make sense.
• The atoms must appear in the same order in the initial and final vesta files (it is possible to specify which atoms have been added or removed, if any)
• It is assumed that there has been no change in cell volume or shape.

Bugs

If vesta_vectors.py is not behaving as you expect, please raise an issue.