VMD-L Mailing List

From: Francesca Lønstad Bleken (FrancescaL.Bleken_at_sintef.no)
Date: Thu Sep 24 2015 - 01:37:00 CDT

Thank you for this suggestion.
However this command just redefines the definition of the unit cell. What I want to do is to draw the unit cell repeated, but not the whole unit cell (as can be done in the representations dialogue), so as to repeat atoms close to the edges.

Best,
Francesca

From: Morgan, Brittany [mailto:Brittany.Morgan_at_umassmed.edu]
Sent: 23. september 2015 15:36
To: Francesca Lønstad Bleken; vmd-l_at_ks.uiuc.edu
Subject: RE: visualising unit cell "plus a little more"

You could try redefining the size of the periodic cell to be a little bit bigger using "pbc set {X Y Z} -all".

http://www.ks.uiuc.edu/Research/vmd/plugins/pbctools/

________________________________
From: owner-vmd-l_at_ks.uiuc.edu<mailto:owner-vmd-l_at_ks.uiuc.edu> [owner-vmd-l_at_ks.uiuc.edu] on behalf of Francesca Lønstad Bleken [FrancescaL.Bleken_at_sintef.no]
Sent: Wednesday, September 23, 2015 5:34 AM
To: vmd-l_at_ks.uiuc.edu<mailto:vmd-l_at_ks.uiuc.edu>
Subject: vmd-l: visualising unit cell "plus a little more"
Hi,

I would like to visualize the unit cell "plus a little more" in each direction in order to see all the atoms at the cell edges. I have found that you can extend the unit cell by multiple images in the graphical representations box under periodic, but is there a way to do this in non-integers? I imagine it should be possible in the console, but have not found it.

What I want is to show all atoms within -0.1 and 1.1 of the unit cell in all directions.

I think I can do this by making a 3x3x3 periodic structure and manually choose which atoms to be shown and not, but it would be great if there was a less cumbersome method to do this.

Best regards,
Francesca

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Francesca L. Bleken
Research Scientist, Ph.D.
Department for Nano and Hybrid Materials
SINTEF Materials and Chemistry
Mobile: +47 95 20 79 71
www.sintef.no<http://www.sintef.no/>
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