[lammps-users] Orthogonal box to triclinic box

Dear all lammps users,
How can I transform the orthogonal box into the triclinic box? I want to add position 0.0 0.0 0.0 as cell origin in the attached file. I see this section but won’t find a way to solve this problem.
8.2.2. Triclinic (non-orthogonal) simulation boxes — LAMMPS documentation

7300meta.dat (350 KB)

Dear Kibria

you can use the change_box command (https://docs.lammps.org/change_box.html) using the keyword “triclinic”.
This way you do not need to edit the data file.

hope it helps
Evangelos Voyiatzis

Στις Πέμ, 25 Νοε 2021 στις 6:24 μ.μ., ο/η Kibria Imtiaz Shabbir <[email protected]> έγραψε:

When I make the crystalline structure of Cu50Zr50, it will be triclinic and cell origin is 0.0 0.0 0.0. But when I make it metallic glass (amorphous structure) via heating and rapid cooling in LAMMPS its cell origin has changed due to that I cant apply the tensile test on S P S or P S P or P S S condition. All atoms are not assigned to the simulation box.

While I make the amorphous structure, cell origin has changed. The problem occurs in this stage.

Please give any recommendations regarding this problem.

There are multiple issues with your e-mail(s).
a) your description in the second e-mail contradicting what you have been asking about in the original e-mail. How can you expect correct help when you do not describe the issue correctly? Why not tell what your problem is in more detail straight away?
b) your analysis is incorrect: in LAMMPS the cell origin does NOT move.
c) assuming that you are doing the melting/quenching with fully periodic boundary conditions, you can perform tensile tests using fix deform and then do not have to worry about dropped atoms due to being them being placed outside the box
d) switching from all periodic to partial periodic requires additional equilibration since you will generate a system with high tension where you change periodicity and effectively cut through a bulk system and now have unrelaxed atoms at the newly created surfaces
e) the error about not all atoms being assigned to the simulation box usually is a consequence of changing boundary conditions and box dimensions inconsistently and incorrectly. with periodic boundaries the atoms will be wrapped and image flags applied. you can (and should) in that case also set all image flags to zero and probably also insert a “run 0” command to trigger a reneighboring which will enforce that atoms are strictly contained in their subdomains.