QuantumATK Forum

QuantumATK => General Questions and Answers => Topic started by: ams_nanolab on June 18, 2015, 12:22

Title: AL molecules not bonding
Post by: ams_nanolab on June 18, 2015, 12:22

The Al molecules in ATK Builder are not showing any bonds between them, kindly fix this.

Title: Re: AL molecules not bonding
Post by: Jess Wellendorff 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...

Title: Re: AL molecules not bonding
Post by: ams_nanolab 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.

Title: Re: AL molecules not bonding
Post by: Umberto Martinez on June 18, 2015, 15:23

Please check:
http://quantumwise.com/support/faq/item/846-bonds-between-some-atoms-are-missing

Title: Re: AL molecules not bonding
Post by: ams_nanolab 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

Title: Re: AL molecules not bonding
Post by: Jess Wellendorff 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!

Title: Re: AL molecules not bonding
Post by: Anders Blom 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.

Title: Re: AL molecules not bonding
Post by: Anders Blom on June 23, 2015, 22:30

http://quantumwise.com/forum/index.php?topic=3463

Title: Re: AL molecules not bonding
Post by: Anders Blom 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.

Title: Re: AL molecules not bonding
Post by: Anders Blom 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.