QuantumATK Forum

QuantumATK => General Questions and Answers => Topic started by: Yueyang on July 2, 2016, 17:04

Title: VibrationalMode
Post by: Yueyang on July 2, 2016, 17:04

When I look at the vibration of a structure through the VibrationalMode, I want to obtain the coordinates of the structure at a certain time point,
How can I make it? The Vibration Visualizer provide only the option to export images!

Title: Re: VibrationalMode
Post by: Ulrik G. Vej-Hansen on July 12, 2016, 09:13

If you use the python interface you can get a trajectory file for a certain vibrational mode by using the "movie" method, as described here: http://www.quantumwise.com/documents/manuals/latest/ReferenceManual/index.html/ref.vibrationalmode.html

Is that what you need?

Title: Re: VibrationalMode
Post by: Yueyang on July 17, 2016, 08:43

Hi,
Actually, I want to get the coordinates of the vibrating model, like a car file or a cif file, instead of a picture.

I have tried your method.
I first read the nc file:    a=nlread('myncfile.nc')[4]
And then tried to obtain the information of a mode with the command "a. mode(1, 300*Kelvin)"
but something goes wrong (The mode ... is not available).

Can you give me some further advices?
Thank you!

Title: Re: VibrationalMode
Post by: Anders Blom on July 17, 2016, 13:03

That probably just because you didn't include 1 in mode_indices when you computed the VibrationalMode object.

Title: Re: VibrationalMode
Post by: Yueyang on July 20, 2016, 07:12

Just as you said, the problem is solved.

Thank you very much!