8 votes

What are the freely available crystal-structure visualization softwares?

nglview and nvc Recently I found it hard to make the pymatgen structure_vtk visualization method to work. I believe it might be deprecated in favour of ...
Maurits Houck's user avatar
6 votes
Accepted

How to convert MoO3 bulk structure to MoO3 (010) plane surface via VESTA software?

You can do that with VESTA for sure, but it is a tedious process and it is hard to explain it without adding so many figures for each step. I suggest you to use ASE and Python tools to do that. Here I ...
Jaafar Mehrez's user avatar
6 votes
Accepted

For a single unit cell calculation, is it necessary to add a vacuum?

In a single unit cell calculation, the inclusion of vacuum space depends on the specific requirements and characteristics of your system. Here are a few situations that you should consider about ...
Jaafar Mehrez's user avatar
5 votes
Accepted

Having difficulty creating the β-tellurene structure in VESTA

Creating a structure is not a trial-and-error process. Here are some tips you can use. From the Supplementary Data of the article you used, in section 2, Table S1, the authors gave the data for the ...
Camps's user avatar
  • 23.3k
5 votes
Accepted

How to make Pd(111) supercell (√3×√3)R30 via VESTA

This would be a pain to do in GUIs like VESTA and Avogadro. In ASE, this can be done just in one line by ase.build.fcc111_root: ...
Shaun Han's user avatar
  • 1,855
5 votes
Accepted

How can visualize a rectangular super cell of Graphene by VESTA

Yes, you can do that in VESTA. First you need a structure file. I use VASP so here's the POSCAR I used. ...
CW Tan's user avatar
  • 1,276
3 votes

Why I got more atoms than expected when generating POSCAR from VESTA

When you input the coordinates into VESTA, they should be the symmetrically distinct basis atoms. If you hit "Apply" after inputting only the first Cl atom, you can see that the other two Cl ...
rmza7's user avatar
  • 329
3 votes

VESTA using command line

In line with the comments, I'm not sure if you can achieve this in VESTA, but a simple ASE or Pymatgen based script can easily do it. This is the Pymatgen script I use. ...
CW Tan's user avatar
  • 1,276
3 votes

Hetrobilayer charge density by using quantume espresso

From ResearchGate: The CHGCAR files have different values of NGX, NGY, and NGZ. So, you are seeing the error. You need to have all the three values same, so you can specify them in the INCAR before ...
Abdul Muhaymin's user avatar
3 votes
Accepted

How to generate the remaining sites in a cubic lattice from a given POSCAR/cif in Python?

I sort of get what OP wants to achieve based on the comment section, but what a strange request! Nonetheless, this can be easily done by both pymatgen and the Atomic Simulation Environment (ASE). The ...
Shaun Han's user avatar
  • 1,855
2 votes
Accepted

How does VESTA render files with POSCAR format

Your unit cell has a lot of atoms outside. Here's the default rendering from Avogadro 1.98, showing the unit cell in white: Notice that the center of your tube straddles the lattice vector. Here's ...
Geoff Hutchison's user avatar

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