Author Topic: AL molecules not bonding  (Read 5388 times)

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Offline ams_nanolab

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AL molecules not bonding
« on: June 18, 2015, 12:22 »
The Al molecules in ATK Builder are not showing any bonds between them, kindly fix this.

Offline Jess Wellendorff

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Re: AL molecules not bonding
« Reply #1 on: June 18, 2015, 13:40 »
Could you please be a bit more specific? Which molecules do you mean? What version of VNL are you running? I just tried to add a molecule with an aluminum atom in it, and it looked fine...

Offline ams_nanolab

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Re: AL molecules not bonding
« Reply #2 on: June 18, 2015, 14:38 »
Just add Aluminum (only Al and not a compound) from the stash, repeat, there's no bonds. I'm on windows 7 x64 VNL 14.2.

Offline Umberto Martinez

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Offline ams_nanolab

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Re: AL molecules not bonding
« Reply #4 on: June 22, 2015, 12:46 »
Ya that's good. But having bonds gives a better perspective of the structure.  ;D Also funny that only for Al they are missing, would be easier to build contacts with Al if this could be resolved as I'm getting no idea if I'm creating the "correct" surface (as in papers) or not without the bonds.  :o

Offline Jess Wellendorff

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Re: AL molecules not bonding
« Reply #5 on: June 22, 2015, 14:29 »
I see your point :) Unfortunately, VNL 2014 does not support changing the "threshold" for bond visualization. However, I think this a great user request, so we have asked our developer team to implement such functionality for the upcoming 2015 release.

Thanks for pointing this out!

Offline Anders Blom

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Re: AL molecules not bonding
« Reply #6 on: June 23, 2015, 22:14 »
Just to cover all aspects, what the "correct" surface is cannot really be determined by just looking at ball-and-stick models. In the end, only a geometry optimization will tell you what the equilibrium ("ideal") structure is.

That said, I also think it's very useful to see bonds sometimes, so I made my own plugin which makes this possible. I will publish it under a different topic, to place it in the right category.

Offline Anders Blom

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Offline Anders Blom

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Re: AL molecules not bonding
« Reply #8 on: July 23, 2015, 08:33 »
Can you give an example? It's probably because the distances are NOT the same, by some small amount perhaps.

Offline Anders Blom

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Re: AL molecules not bonding
« Reply #9 on: July 23, 2015, 10:50 »
Yes but the bonds are not draw from Z-plane to Z-plane, but from atom to atom, so the X/Y coordinates matter too.