modeling and simulation of nano systems Lectures

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Installation:
in windows : Download LAMMPS and install. Link
in Linux :
1.In Terminal first add repository by :

sudo add-apt-repository ppa:gladky-anton/lammps
sudo apt-get update

2.then install by :

sudo apt-get install lammps-daily

Let’s start!

As a Start, we will run and modify some code from Example directory.

*Note : Please Let me know if I had any mistake.

Code 1 : Simulate friction of two surfaces with triangle cross section.

# 2d friction simulation
log AliBakhshi.log
dimension	2
boundary	p s p
atom_style	atomic
units lj

lattice		hex 0.9

region		box block 0 50 0 22 -0.25 0.25
create_box	4 box

mass		1 1.0
mass		2 1.0
mass		3 1.0
mass		4 1.0

#region		box block 0 50 0 22 -0.25 0.25
region          lo-fixed block INF INF INF 1.1 INF INF
region          lo-slab block INF INF INF 7 INF INF
region          above-lo block INF INF INF 7 INF INF side out
region          hi-fixed block INF INF 20.9 INF INF INF
region          hi-slab block INF INF 15 INF INF INF
region          below-hi block INF INF 15 INF INF INF side out

region		    lo-asperity1 cone y 5 0 5 0 8 12
region		    lo-asperity2 cone y 15 0 5 0 8 12
region			lo-asperity union 2 lo-asperity1 lo-asperity2
region		    hi-asperity1 cone y 34 0 0 5 9 15
region		    hi-asperity2 cone y 24 0 0 5 9 15 
region		    hi-asperity3 cone y 44 0 0 5 9 15
region			hi-asperity union 3 hi-asperity1 hi-asperity2 hi-asperity3

region asd sphere 0 0 0 0 side out
region		lo-half-sphere intersect 2 lo-asperity above-lo
region		hi-half-sphere intersect 2 hi-asperity below-hi
region lo-slab1 intersect 2 lo-slab asd

create_atoms	1 region lo-slab1
create_atoms	1 region hi-slab
create_atoms	2 region lo-half-sphere
create_atoms	3 region hi-half-sphere

pair_style	lj/cut 2.5
pair_coeff	* * 1.0 1.0

group	    lo region lo-slab
group		lo type 2
group		hi region hi-slab
group		hi type 3
group		lo-fixed region lo-fixed
group		hi-fixed region hi-fixed
group		boundary union lo-fixed hi-fixed
group		mobile subtract all boundary
group lhs region lo-half-sphere
group hhs region hi-half-sphere

set		group lo-fixed type 4
set		group hi-fixed type 4

compute         new mobile temp/partial 0 1 0
velocity	mobile create 0.1 482748 temp new
velocity	hi set 0.2 0.0 0.0 sum yes

fix		1 all nve
fix		2 boundary setforce 0.0 0.0 0.0
fix		3 mobile temp/rescale 200 0.1 0.1 0.02 1.0
fix_modify	3 temp new
fix             4 all enforce2d

timestep	0.025
thermo		100                 
thermo_modify	temp new
dump 10 all xyz 100 fric.xyz
dump		11 lhs custom 100 dump.fl id type x y z vx vy vz fx fy fz
dump		12 hhs custom 100 dump.fh id type x y z vx vy vz fx fy fz
run		20000                   
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