Question on Setting Up basis_pos Files for Twister

[Brynn Karst]

Hello, I am a beginner starting to use Twister. I encountered an issue when using the code with my own systems, bilayer WSe₂ and MoS₂. I extracted the coordinates of the three atoms from the optimized POSCAR of a single layer to create the basis_pos files. While the generated structure has the correct number of atoms, it looks incorrect in VESTA compared to the example structures, without the expected hexagonal arrangement (see attached image).

I noticed that in the provided basis_pos files, the x and y coordinates of S or Se atoms are the same, which seems to be different from the coordinates found in structures from the Materials Project, whether in the 3R or 2H phases, where the x and y coordinates differ. Could you please advise on this discrepancy?

[Indrajit Maity]

Hi Brynn,

It's difficult to suggest anything without the explicit directory details. 

However, I believe Materials Project would be right! If you are using relaxation with lammps with the initial structure as in Twister, it shouldn't matter what you start with. As LAMMPS will change the positions based on the forcefields. 

Hope this helps,

Indrajit 

On Tue, 3 Sep 2024, 17:41 Brynn Karst, <karst...@gmail.com> wrote:

Hello, I am a beginner starting to use Twister. I encountered an issue when using the code with my own systems, bilayer WSe₂ and MoS₂. I extracted the coordinates of the three atoms from the optimized POSCAR of a single layer to create the basis_pos files. While the generated structure has the correct number of atoms, it looks incorrect in VESTA compared to the example structures, without the expected hexagonal arrangement (see attached image).

I noticed that in the provided basis_pos files, the x and y coordinates of S or Se atoms are the same, which seems to be different from the coordinates found in structures from the Materials Project, whether in the 3R or 2H phases, where the x and y coordinates differ. Could you please advise on this discrepancy?

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[Indrajit Maity]

Another comment to add:

Please take a look at the lattice vectors a_i of materials project and Twister. I think in the Materials Project it's 120 degrees but in Twister it's 60 degrees. Therefore, the in-plane fractional coordinates of the atoms relative to the lattice vectors may change.

Best wishes,

Indrajit

On Tue, Sep 3, 2024 at 5:41 PM Brynn Karst <karst...@gmail.com> wrote:

Hello, I am a beginner starting to use Twister. I encountered an issue when using the code with my own systems, bilayer WSe₂ and MoS₂. I extracted the coordinates of the three atoms from the optimized POSCAR of a single layer to create the basis_pos files. While the generated structure has the correct number of atoms, it looks incorrect in VESTA compared to the example structures, without the expected hexagonal arrangement (see attached image).

I noticed that in the provided basis_pos files, the x and y coordinates of S or Se atoms are the same, which seems to be different from the coordinates found in structures from the Materials Project, whether in the 3R or 2H phases, where the x and y coordinates differ. Could you please advise on this discrepancy?

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