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I am using VASP to calculate material properties. I want to know how to extract the lattice parameters from my cells automatically with a script. I know about the method with VESTA (described here How to extract lattice constants a and c from relaxed hexagonal structure using VASP?), but doing this manually for every composition takes way too much time.

Since I am familiar with bash from running my calculations I would like to use a bash-script that calculates a, b, c, α, β, and γ from the relaxed CONTCAR file that I can loop over my directories. Is this possible to do in bash or do I need to resort to python or something similar?

Edit:

as requested, an example would be this CONTCAR file. Since there are 64 individual atoms and the the relevant lines are 2-5 in all cases, I am omitting the lines at the bottom. This is a supercell, which means the lattice parameters are multiplied, but the script should not need to address that.

2x2x2 supercell ternary nitride         
1.00000000000000     
 8.3651760123584129    0.0104817210801190   -0.0093895223039569
 0.0104823789019837    8.3504089378499629   -0.0085602185310777
-0.0093916727121912   -0.0085617113679278    8.3470735253222390
Al   Ti   N 
16    16    32
Direct
0.0003223292397248  0.9972239351012413  0.0011915008883630
0.4991700057920037  0.9984995833496634  0.5000934141482651
...

A preferred output for this cell would then be

 8.36519 8.35042 8.34708 90.1176 90.1289 89.8562

for a, b, c, α, β, and γ. Separation by tabs, commas, or semicolons would also be acceptable.

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    $\begingroup$ +1. Welcome to our new community, and thank you for contributing your question here! We hope to see much more of you in the future !!! Can you please provide an example of one of your CONTCAR files in a code block, then in another code block show us the output you'd like the bash script to give? $\endgroup$ Feb 16 at 19:16
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I'd recommend ASE, a ready solution not to re-invent the wheel and ensure all the boundary cases are properly handled. Also this code will be easier to maintain in future:

#!/usr/bin/env python

import sys

from ase.io.vasp import read_vasp
from ase.geometry import cell_to_cellpar


try:
    ase_obj = read_vasp(sys.argv[1])
except IndexError:
    sys.exit('A CIF path must be given!')

print("%.5f %.5f %.5f %.4f %.4f %.4f" % tuple(
    cell_to_cellpar(ase_obj.cell)
))

If you want to extract rather the conventional cell, not primitive, try to apply spglib in between:

#!/usr/bin/env python

import sys

from ase.io.vasp import read_vasp
from ase import Atoms
from ase.geometry import cell_to_cellpar
import spglib


try:
    ase_obj = read_vasp(sys.argv[1])
except IndexError:
    sys.exit('A CIF path must be given!')

cell, scaled_pos, numbers = spglib.standardize_cell(ase_obj, to_primitive=False)

ase_obj = Atoms(
    scaled_positions=scaled_pos,
    numbers=numbers,
    cell=cell,
    pbc=True
)
print("%.5f %.5f %.5f %.4f %.4f %.4f" % tuple(
    cell_to_cellpar(ase_obj.cell)
))
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  • $\begingroup$ The other answer works out of the box if a file named "CONTCAR" is present in the directory. What do I need to do to with this code to use the CONTCAR file? I only get the error 'A CIF path must be given!' $\endgroup$
    – And
    Feb 18 at 8:54
  • 1
    $\begingroup$ $> ./this_script.py path/to/your/CONTCAR $\endgroup$ Feb 18 at 15:05
  • $\begingroup$ I am having some trouble with the output. The lengths of a, b, and c seem to work fine, but the angles are somehow completely different from the VESTA output. For example VESTA gives me for a somewhat hexagonal cell 91.1, 80.6, and 115.6, whereas this script gives me 80.6, 64.4, and 88.9. Is this somehow related to the primitive cell? $\endgroup$
    – And
    Feb 24 at 12:34
  • $\begingroup$ I don't know much about VESTA. There might be some additional cell transformations involved. The easiest option to make sure the structures are identical is to visualize them both, translate the cell in all the directions, and compare (e.g. measuring interatomic distances). $\endgroup$ Feb 24 at 15:42
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Of course, you can use python. For example:

  • CONTCAR template:

    GeTe
    1.00000000000000
    4.2642961037835692   -0.0182827012387123   -0.0127716218381237
    2.2215279123437899    3.6399683038796313   -0.0127716218406244
    2.2215279123442269    1.2405016904345516    3.4220882400997064
    Ge   Te
    1     1
    Direct
    -0.0008620876194062 -0.0008620876194055 -0.0008620876194060
     0.5218621726194035  0.5218621076194079  0.5218621136194089
    
     0.00000000E+00  0.00000000E+00  0.00000000E+00
     0.00000000E+00  0.00000000E+00  0.00000000E+00
    
  • Lattice parameters from VESTA:

    a =  4.26435 Å      α = 58.8490° 
    b =  4.26435 Å      β = 58.8490°
    c =  4.26435 Å      γ = 58.8490°
    
  • Python script:

    import numpy as np
    
    with open("CONTCAR","r") as f:
        lines=f.readlines()
    
    lat_mat=np.zeros((3,3))
    for i in range(3):
        lat_mat[i,:]=list(map(float,lines[2+i].strip().split()))
    
    a=np.sqrt(np.sum(lat_mat[0,:]**2))
    b=np.sqrt(np.sum(lat_mat[1,:]**2))
    c=np.sqrt(np.sum(lat_mat[2,:]**2))
    print(a,b,c)
    
    alpha = np.arccos(np.dot(lat_mat[1,:],lat_mat[2,:])/b/c)*360/2/np.pi
    beta  = np.arccos(np.dot(lat_mat[0,:],lat_mat[2,:])/a/c)*360/2/np.pi
    gamma = np.arccos(np.dot(lat_mat[0,:],lat_mat[1,:])/a/b)*360/2/np.pi
    print(alpha,beta,gamma)
    
  • Python output:

    4.26435442150775   4.264354421585447  4.264354421518477
    
    58.84900754415152  58.84900754404418  58.849007544603154
    

You may realize this with a bash script. Also, the atomic simulation environment (ASE) can do this.

Hope it helps.

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    $\begingroup$ +1 and with that, congrats on now reaching 8000 points Jack! One thing that might improve this answer is to put the python and VESTA output in code blocks so that it all looks neater, more consistent and more professional. To the OP, this Python script is probably a better solution than using a Bash script, since it involves all those arccos functions and sqrt functions. You can do trig functions in Bash, but it doesn't save you much compared to using Jack's Python script, see this for example: stackoverflow.com/q/23854380/1271772. $\endgroup$ Feb 17 at 5:29

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