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Re: [lammps-users] How to build Silicon nitride monoclinic lattice structure in LAMMPS

# Re: [lammps-users] How to build Silicon nitride monoclinic lattice structure in LAMMPS

 From: Axel Kohlmeyer Date: Mon, 6 Nov 2017 13:52:31 -0500

On Mon, Nov 6, 2017 at 12:37 PM, Khourshaei Shar, Ali wrote:

Dear LAMMPS users,

Hi,

Currently I intend to build an initial lattice structure of Silicon nitride. The atomistic details based on an experiment is attached and I used the input commands as below. however, when I run this job it doesn't result a correct structure ( It gives something but It isn't correct ). So, I wonder if you could please help me out.  By the way, I studied "http://lammps.sandia.gov/doc/Section_howto.html#howto-12" so please don't reference me into that webpage.

i won't do that, but i will tell you, that ​the problem is no​t even a LAMMPS problem. the table in your picture provides positions with respect to a *space group*.
that is not what you input to LAMMPS. first you have expand the symmetry operations according to that space group to get all positions within your unit cell.
LAMMPS just computes what you tell it to do. if you feed it garbage, don't be surprised it will spit out garbage.

thus please grab a crystallography text book and look up what this all means and then look up the space group the in the wyckoff book or find a software that does generate a complete based on the provided space group and the information in the table.

axel.

Sincerely,

Ali

 6.1. Restarting a simulation. There are 3 ways to continue a long LAMMPS simulation. Multiple run commands can be used in the same input script.

# ---------- Initialize Simulation ---------------------
units metal
atom_style atomic
dimension 3
boundary p p p

#------------Define variable------------------------
variable a equal 7.5572
variable b equal 7.5572
variable c equal 2.8852
variable gamma equal "120.003/180*PI"
variable singamma equal "sin(v_gamma)"
variable cosgamma equal "cos(v_gamma)"
variable bx equal "v_b*v_cosgamma"
variable by equal "v_b*v_singamma"

#------------Define Si3N4 lattice------------------------
lattice custom 1.0 &
a1 \$a 0.0 0.0 &
a2 \${bx} \${by} 0.0 &
a3 0 0.0 \$c &
basis 0.3333 0.6667 0.2500 &
basis 0.3302 0.0299 0.2500 &
basis 0.1742 0.7678 0.2500 &
orient x 1 0 0 orient y 0 1 0 orient z 0 0 1

#------------------Create Si3N4 nanowire--------------

region        zona1 prism 0 1 0 1 0 1 -0.37 0 0
box tilt large
create_box    2 zona1
create_atoms    2 box &
basis 1 1 &
basis 2 1 &
basis 3 2 &

# Atom 1 = N and Atom 2 = Si
mass 1 14.01
mass 2 28.085
write_data Ali.in

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