1. Introduction

The molecular dynamics software LAMMPS can be used to handle soft matter problems. In particular, it is relatively easy to create impressive movies by simulating and visualizing the formation of structures such as membranes. Let’s take the example of micelle in the LAMMPS package and visualize it with the visualization software ovito. The operating environment is MateriApps LIVE! version 3.3.

2. Preparation

First, create a working directory in your home directory and move to the working directory.

cd $HOME
mkdir lammps
cd lammps

Then copy the LAMMPS examples/micelle directory and move to it.

cp -r /usr/share/lammps/examples/micelle ./
cd micelle

3. Editing an input file

You will find the input file in.micelle in the micelle directory. Edit this file to visualize the state during the calculation.

emacs in.micelle

Any editing software will do. Emacs is used here, but MateriApps LIVE! includes other editors such as vim, nano, and Mousepad, so choose your favorite editor. The contents of the file are as follows:

# 2d micelle simulation

dimension	2

neighbor	0.3 bin
neigh_modify	delay 5

atom_style	bond

# Soft potential push-off

read_data	data.micelle
special_bonds	fene

...

thermo		50

#dump		1 all atom 2000 dump.micelle

...

reset_timestep	0
run		1000

In the beginning, dimension 2 specifies a two-dimensional calculation. At the last part of the file, on the line starting with “#dump 1 …”, omit the first “#” and change this line as

dump		1 all atom 2000 dump.micelle

In addition, the last line of the input file “run 1000” is modified as

run		100000

After finishing the edit of the input file, save the file and exit the editor. (In Emacs, save with ctrl-x ctrl-s and exit with ctrl-x ctrl-c.)

4. Performing Calculations with LAMMPS

Run LAMMPS using the edited input file in.micelle.

lammps < in.micelle

If there is no error message and “Total wall time” is displayed at the end, the execution has completed successfully. The file dump.micelle is now generated in the same directory. (You can check it with the ls command.)

5. Visualization by ovito

Open the generated file with ovito.

ovito dump.micelle

You should see the following screenshot (This screeenshot is after pressing the play button, but there should be a screen where micelles are not formed yet). Press the button at the bottom right to play the video. You can see the particles gathering to form a micellar structure.

6. Summary

This is an easy visualization for relatively small molecular dynamics calculations. For visualization of systems containing many particles, the visualization becomes heavy in the environment of MateriApps LIVE!. Therefore, it is more efficient to install visualization software (such as VMD) directly on your desktop and visualize it after transferring the dump data to your machine.