Problem with defining correct cubic simulation box

Dear LAMMPS users,

suppose that the lattice structure of your material is monoclinic such as SiC, SiN and etc. However, you have to do your simulation on a cubic simulation box. For the sake of thism I used the following code, define a cubic region and fill it with atoms as follow:

units metal
atom_style atomic
dimension 3
boundary p p p

#------------Define variable------------------------
variable n equal 10

variable a equal 7.5572

variable b equal 7.5572
variable c equal 2.8852
variable gamma equal “120.0030/180PI"
variable singamma equal “sin(v_gamma)”
variable cosgamma equal “cos(v_gamma)”
variable bx equal "v_b
v_cosgamma”
variable by equal “v_bv_singamma"
variable prismx equal "v_b
v_cosgamma/v_n”

#------------Define Si3N4 lattice------------------------
lattice custom 1 &
a1 a 0.0 0.0 & a2 {bx} ${by} 0.0 &
a3 0 0.0 $c &
basis 0.1742 0.7678 0.2500 &
basis 0.2322 0.4064 0.2500 &
basis 0.5936 0.8258 0.2500 &
basis 0.8258 0.2322 0.7500 &
basis 0.7678 0.5936 0.7500 &
basis 0.4064 0.1742 0.7500 &
basis 0.3333 0.6667 0.2500 &
basis 0.6667 0.3333 0.7500 &
basis 0.3302 0.0299 0.2500 &
basis 0.9701 0.3003 0.2500 &
basis 0.6997 0.6698 0.2500 &
basis 0.6698 0.9701 0.7500 &
basis 0.0299 0.6997 0.7500 &
basis 0.3003 0.3302 0.7500 &
orient x 1 0 0 orient y 0 1 0 orient z 0 0 1

#------------------Create SiC nanowire--------------

region zona1 block 0 75 0 75 0 15 units box

create_box 2 zona1
create_atoms 1 box &
basis 1 2 &
basis 2 2 &
basis 3 2 &
basis 4 2 &
basis 5 2 &
basis 6 2 &
basis 7 1 &
basis 8 1 &
basis 9 1 &
basis 10 1 &
basis 11 1 &
basis 12 1 &
basis 13 1 &
basis 14 1 &

write_data SiC.in

So, my problem is that the structure doesn’t look correct for the sake of periodicity. I attached an image of it and circle around the section of the boundary that as I switch on show periodic image in Ovito, it doesn’t look correct. I mean the structure doesn’t look uniform as we go from left of the boundary to the right of it.

Capture.PNG

Dear LAMMPS users,

suppose that the lattice structure of your material is monoclinic such as
SiC, SiN and etc. However, you have to do your simulation on a cubic
simulation box.

no, you don't. LAMMPS can handle orthogonal and triclinic box shapes.

For the sake of thism I used the following code, define a
cubic region and fill it with atoms as follow:

[...]

So, my problem is that the structure doesn't look correct for the sake of
periodicity. I attached an image of it and circle around the section of the
boundary that as I switch on show periodic image in Ovito, it doesn't look
correct. I mean the structure doesn't look uniform as we go from left of the
boundary to the right of it.

that is difficult to tell from that perspective. it is very likely,
that this is an optical illusion, caused by a tiny inconsistency in
the cell lengths and assigned lattice positions plus the lack of depth
perception.

i would run a minimization and record a trajectory. if there are
really issues with periodicity, you should see notable deformations at
those perceived to be incorrect periodic replication areas.

axel.