16
$\begingroup$

Which software package(s) can be used to visualize the trajectory of VASP MD simulation?

VMD claims that there is a plugin to read the VASP output, while in the last version for Linux, I did not find it (it is there in Windows version of VMD), so I cannot check my results with my eyes directly, unless I download it from server or change the format to the format VMD accepted.

VESTA can read the format, but can only visualize the trajectory frame by frame, while I prefer to watch the movie.

Some related, but not duplicate, questions are

But my point here is to know the easiest way to check the MD simulation trajectory like watching the movie on Linux servers.

Improve this question
$\endgroup$
2
  • $\begingroup$ I'm not familiar with viesta. But How is frame by frame different than a movie? Viesta doesn't play all the frames without stopping? $\endgroup$
    – Cody Aldaz
    Oct 23, 2020 at 13:24
  • 2
    $\begingroup$ to more clarify, VESTA just can't move from the first frame to the next, I guess the soft read the first frame then drop the rest of trajectory, take it as one simple xdatcar format structure. $\endgroup$
    – jtyang
    Oct 23, 2020 at 13:51

4 Answers 4

Reset to default
8
$\begingroup$

VMD

I had to dig up the VMD script that I used for this. VMD doesn't detect the file type automatically, so you have to tell it to use VASP_XDATCAR5.

In the VMD Tk Console, you can load the XDATCAR file from VASP with the following command:

mol new XDATCAR type VASP_XDATCAR5

Or, if GUIs are your thing, you can open File -> New Molecule..., select the XDATCAR file, and select VASP_XDATCAR5 under "Determine file type".

Opening a VASP XDATCAR file in VMD.

Improve this answer
$\endgroup$
1
  • $\begingroup$ I accept this answer because I have install VMD. By the way I find out why I cannot use VMD properly: the pull down menu of selecting file types is too long, and it is broken because of some X window setting... I will use the CLI and try to fix the X window. $\endgroup$
    – Y. Zhai
    Oct 24, 2020 at 2:20
11
$\begingroup$

ASE

You can use ASE environment to visualize, it has different options as well. e.g., you can use this command: ase gui vasprun.xml

Improve this answer
$\endgroup$
3
  • 1
    $\begingroup$ I would also add that ASE can do a lot of post-processing via its scripting interface for more complicated visualization. $\endgroup$
    – Tristan Maxson
    Oct 23, 2020 at 16:39
  • $\begingroup$ +1. Just make sure to take a look at the edit I made so that you know the ideal formatting for next time. :) $\endgroup$
    – Nike Dattani
    Oct 23, 2020 at 22:07
  • $\begingroup$ I know more than visualization from these answer, thank you very much. I did not know ASE, but now I decide to learn it. We had some new ideas of analysis but wrote it in Fortran. Now we are thinking about implement it in Python and apparently ASE can be of great use. $\endgroup$
    – Y. Zhai
    Oct 24, 2020 at 2:25
6
$\begingroup$

JMol

To give you another option you can try Jmol which runs on Java and should be fairly straight forward to compile on a Linux machine. Although to be honest I personally do not use it, just figured I would add to the list here.

Improve this answer
$\endgroup$
2
  • $\begingroup$ +1. But the user said that they were not able to use VMD for this. Can you clarify? This would also help make your answer better quality (i.e. more of an "answer" than just a "comment"). $\endgroup$
    – Nike Dattani
    Oct 23, 2020 at 17:25
  • $\begingroup$ Sorry, I will try to clarify it. I am suggesting Jmol not VMD, but mentioning that I'm not very well versed in Jmol since I personally use VMD. $\endgroup$
    – Cavenfish
    Oct 23, 2020 at 17:37
5
$\begingroup$

OVITO

Another option is the Open VIsualistion TOol (OVITO) which has a user friendly interface, usable on multiple platform, and has some post processing and analysis tools readily available (plus a python interface to implement your own). According to the documentation it supports the following file formats : POSCAR / XDATCAR / CHGCAR

Improve this answer
$\endgroup$
1
  • $\begingroup$ +1. Welcome tot he site and thank you for contributing content here!! We hope to see much more of you here in the future !!!!! $\endgroup$
    – Nike Dattani
    Oct 24, 2020 at 19:54

You must log in to answer this question.

Not the answer you're looking for? Browse other questions tagged .