Transformation of triclinic 2D structures to orthogonal box and setting periodic boundary conditions

LAMMPS
,
1

hello,

  1. Can we really convert a triclinic box of a 2D system into an orthogonal simulation box?

atom_style atomic
read_data mos2.dat
comm_modify cutoff 10.0
replicate 1 2 1
change_box all xy final 0.0
change_box all ortho
set group all image 0 0 0
write_data o-mos2.data

It works definitely, but I am a bit skeptical about it, because I see that the generated output alters the cell parameters slightly to make it orthogonal.

  1. Regarding the periodic boundary condition that I am supposed to input is ‘p p f’, because I need it to be periodic along the x- & y-directions and not in the z-direction. But, every time I apply the same it shows atoms are getting lost. So, I thought may be extending the box dimension along the z-axis, keeping the 2D- sheet right in between the box, is a good idea. But, I noticed the atoms in the sheet just disintegrates in all directions.
    Am I doing everything wrong?

Regards
Bishwajit

2

It is up to you to determine whether the operations that you are asking LAMMPS to do result in the desired outcome. If you use the “change_box” command the way you do, atom coordinates will be transformed along the box transformation with an affine transformation. Whether that is what you want, is up to you to decide. LAMMPS has no way to check whether a transformation is meaningful or not; it just blindly does what you ask for.

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