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OVITO

  • Openness:3 ★★★
  • Document quality:3 ★★★

An open-source application for visualization of atoms and molecules developed for molecular dynamics. This application supports a number of input file formats for molecular configration, and can perform visualization of three-dimensional atom configration as well as creation of a animation. The main feature of this application is that various useful analysis tools can be used by intuitive control of a graphical user interface (GUI).

Visualization of LAMMPS results using OVITO in MateriApps LIVE!
Last Update:2024/12/12
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Note: Unfortunately, OVITO has not been installed on the Docker version of MateriApps LIVE!. If you use the docker version, output LAMMPS results to a shared folder between MateriApps LIVE! and the host machine, and then visualize them using OVITO installed on the host side.

  • Run nemd in LAMMPS examples on MateriApps LIVE!.
    Copy /usr/share/lammps/examples/nemd to your home directory.
$ cp -r /usr/share/lammps/examples/nemd ~/
  • Go to nemd directory.
$ cd ~/nemd
  • Modify in.nemd in nemd directory using an editor.
    Execute the following command to launch the mousepad editor.
$ mousepad in.nemd

The modification to in.nemd is as follows:

Before：#dump 1 all custom 5000 dump.nemd id type x y z
After：dump 1 all custom 5000 dump.nemd id type x y z

After editing the input, select “Save” from the File menu in the upper left corner to overwrite and save the file. After saving, close mousepad by clicking the cross in the upper right corner of the window.

  • Execute LAMMPS
$ mpirun -np 2 lmp < in.nemd

After LAMMPS has been successfully executed, check whether dump.nemd is generated.

$ ls

dump.nemd     in.nemd    log.lammps
  • Launch OVITO
$ ovito dump.nemd

A screen like this is displayed.

  • Display the radial distribution function (RDF).
    Select “coordination analysis” under “add modification” in the red square in the following figures to display the radial distribution function (RDF).

  • Watch video.

Click “▶️ ” in the red square in the following figure to watch video of the LAMPPS result.

 

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