Start LAMMPS in 5 min. on Mac

It’s very easy to start molecular dynamics (MD) on Mac.

Molecular Dynamics

Molecular dynamics (MD) is a computer simulation method for studying the physical movements of atoms and molecules.

Wikipedia

We can simulate the energy or motion of atoms by molecular dynamics (MD). An atom is too small to see it directly. However, we can observe an atom, its motion, reaction and so on, via MD. Recently, we can use MD very easily.

LAMMPS

LAMMPS is a molecular dynamics software and is free. We can use Lammps.

Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) is a molecular dynamics program from Sandia National Laboratories. LAMMPS makes use of Message Passing Interface (MPI) for parallel communication and is free and open-source software, distributed under the terms of the GNU General Public License.

Wikipedia

Install LAMMPS on Mac

For Mac, installation of LAMMPS is very easy.

(If you have not installed Homebrew, install Homebrew first.

Install Homebrew

Homebrew is a free and open-source software package management system.

Paste the following code in a macOS Terminal prompt.

/usr/bin/ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"

Now Homebrew is installed. Very easy!

Install LAMMPS

Lammps can be installed using homebrew with the following code.

brew install lammps

Now LAMMPS is installed in you computer.

Start LAMMPS

You can find the examples in “/usr/local/opt/lammps/share/lammps/examples/”. Here, we try to run “crack”. Go to “crack” directory.

cd /usr/local/opt/lammps/share/lammps/examples/crack

Modify “in.crack” file as follwing. (Delete “#” on line 69 to 71)

# 2d LJ crack simulation

dimension	2
boundary	s s p

atom_style	atomic
neighbor	0.3 bin
neigh_modify	delay 5

# create geometry

lattice		hex 0.93
region		box block 0 100 0 40 -0.25 0.25
create_box	5 box
create_atoms	1 box

mass		1 1.0
mass		2 1.0
mass		3 1.0
mass		4 1.0
mass		5 1.0

# LJ potentials

pair_style	lj/cut 2.5
pair_coeff	* * 1.0 1.0 2.5

# define groups

region	        1 block INF INF INF 1.25 INF INF
group		lower region 1
region		2 block INF INF 38.75 INF INF INF
group		upper region 2
group		boundary union lower upper
group		mobile subtract all boundary

region		leftupper block INF 20 20 INF INF INF
region		leftlower block INF 20 INF 20 INF INF
group		leftupper region leftupper
group		leftlower region leftlower

set		group leftupper type 2
set		group leftlower type 3
set		group lower type 4
set		group upper type 5

# initial velocities

compute	  	new mobile temp
velocity	mobile create 0.01 887723 temp new
velocity	upper set 0.0 0.3 0.0
velocity	mobile ramp vy 0.0 0.3 y 1.25 38.75 sum yes

# fixes

fix		1 all nve
fix		2 boundary setforce NULL 0.0 0.0

# run

timestep	0.003
thermo		200
thermo_modify	temp new

neigh_modify	exclude type 2 3

#dump		1 all atom 500 dump.crack

dump		2 all image 250 image.*.jpg type type &
		zoom 1.6 adiam 1.5
dump_modify	2 pad 4

#dump		3 all movie 250 movie.mpg type type &
#		zoom 1.6 adiam 1.5
#dump_modify	3 pad 4

run		5000

After modification, run lammps with the following code.

lmp_serial -in in.crack

After the short calculation, you can find the jpeg files.

open image.*

Congratulations! You can success to run MD with LAMMPS.

Leave a Comment

Your email address will not be published. Required fields are marked *