I have the following POSCAR file of a tubular structure that was created using python

NT (n,m)=(5,0). T(x,y)=(1,2)
3.969568047197358 0.0 0.0
0.0 3.969568047197358 0.0
0.0 0.0 4.32
1.984784023598679 0.0 2.88
1.6057240055491107 1.1666267776525108 0.72
1.984784023598679 0.0 1.44
0.6133319934558785 1.8876417790820375 2.88
1.6057240049613253 1.1666267784615278 3.6
-0.6133319929803498 1.887641779236546 0.72
0.6133319934558785 1.8876417790820375 1.44
-1.6057240052552177 1.1666267780570196 2.88
-0.6133319939314065 1.887641778927529 3.6
-1.984784023598679 5.000005037854325e-10 0.72
-1.6057240052552177 1.1666267780570196 1.44
-1.605724005255218 -1.1666267780570192 2.88
-1.984784023598679 -5.000000176535521e-10 3.6
-0.6133319939314074 -1.8876417789275288 0.72
-1.605724005255218 -1.1666267780570192 1.44
0.6133319934558781 -1.8876417790820377 2.88
-0.6133319929803502 -1.8876417792365459 3.6
1.6057240049613248 -1.1666267784615285 0.72
0.6133319934558781 -1.8876417790820377 1.44
1.6057240055491104 -1.166626777652511 3.6 

When I try to render this file with VESTA, the atoms would overlap onto each other as shown in the Figure (a). However, while using other softwares such as ASE, OVITO, or AVOGADRO, I am able to see the correct strcture as in Figure (b).

I would like to know how does VESTA render the format of POSCAR or .vasp files. Moreover, how would vasp treat this POSCAR file, in other words can I use this structure as an input for electronic calculations using VASP?

enter image description here

  • $\begingroup$ I think something is wrong with your unit cell. I think you should enhance your cell parameters (in order to have the structure that you want) and everything should be fine no matter the software you use to visualize your structure. $\endgroup$
    – Laura
    Dec 12, 2023 at 14:00

1 Answer 1


Your unit cell has a lot of atoms outside. Here's the default rendering from Avogadro 1.98, showing the unit cell in white:

default positions

Notice that the center of your tube straddles the lattice vector.

Here's what happens if I "wrap" all the atoms into the unit cell using Avogadro 1.98 (i.e., converting to fractional, making sure they fall between 0 and 1, then converting back to Cartesian).

atoms wrapped into unit cell

The second one looks like the image you have from VESTA. It probably wraps the atoms into the unit cell by default.

Your second question is how it will be handled by VASP. While one rendering may be more pleasant to view, the two are equivalent to an electronic structure program. You can note that many atoms are nearly but not exactly equivalent in the "wrapped" view, and thus will probably cause problems with your calculation.

You will want to provide a unit cell / lattice with all non-equivalent atoms.

My suggestion would be to have your Python script do a final procedure to convert atoms into the wrapped coordinates to check for near-duplicates.

  • $\begingroup$ Thanks for your explanation, I will take wrapping the atoms into consideration. $\endgroup$ Dec 13, 2023 at 0:43

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