iOpenShell » Q-Chem specific questions » how to plot electronic structure along the aimd trajectory?

how to plot electronic structure along the aimd trajectory?

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Author Post
Member
Registered: Sep 2016
Posts: 3
What is the best way to plot the electronic structure (total density, homo, lumo, etc) along the aimd trajectory (as an animation)?

I generated FChk file with the option

aimd_steps 50
time_step 20
aimd_print 2
GUI 2
Member
Registered: Sep 2007
Posts: 58
Hi, dcho,

What visualization tools are you using?
Member
Registered: Sep 2016
Posts: 3
Hi Wesley,

primarily iQmol, but any visualization tools are okay.
Member
Registered: Sep 2007
Posts: 58
Hi dcho,

Sorry for late reply. Although Fchk contains all information needed, IQmol does not support MO/density animation along a trajectory yet. We are going to add this feature soon.

Q-Chem AIMD can export MOs in Molden format. Using Jmol visualization software with a customized script is able to view MOs/densities as an animation. Here is a example:

This link contains MOs in Molden formated extracted from a water AIMD calculation:
https://github.com/ZQyou/jmol-tools/tree/master/test

In the following links, the first file is the config file containing the name and the number of Molden files, and the second file is the plot script.
https://github.com/ZQyou/jmol-tools/blob/master/params.spt
https://github.com/ZQyou/jmol-tools/blob/master/plot.spt

How to demo:
1. Download the test files and scripts, and make sure they are stored in the same folder.
2. Run Jmol and load the first Molden file.
3. Open the console in Jmol and type load "plot.spt"

Wesley
Member
Registered: Sep 2016
Posts: 3
Hi Wesley,

It perfectly works! Thanks Wesley!

However, I made a small change in the scripts to use for my case.

"var" was removed from three lines of in the scripts "params.spt" and "plot.spt" as follows.

var numMoldens = 10;
var inputName = "test.out.mld";
for (var n=1 ; n <= numMoldens ; n++) {

Thanks again and I will be waiting for the update in the next IQmol release.

Daeheum
Member
Registered: Oct 2016
Posts: 2
Hi dcho,

would you mind giving me a input example for generate the aimd trajectory file, thank you very much

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iOpenShell » Q-Chem specific questions » how to plot electronic structure along the aimd trajectory?