error with drag molecule configuration into costum/ molecular junction

[spin]

Dear all
I have a problem with drag-and-drop the molecule configuration into costum. I want to have a two electrode system with a molecule in central region but it has not any reaction and the only thing in it is the default molecule in VNL!!!!

tnx

[kstokbro]

can you post the molecule that you are trying to drag, such that we can use it for testing

[spin]

can you post the molecule that you are trying to drag, such that we can use it for testing

the molecule is Adamantane (C10H16).

[kstokbro]

Try the following:
import the file adamantane.xyz into the builder,
next drag the molecule from the builder into the molecular junction custom builder
set repeat to 4x4
and atoms to 19 and 31,
this works for me, see attached

[spin]

Thank you very much
But the shape that is desired is different,  please take a look on it.

[Anders Blom]

Your problem is quite possibly related not to the molecule itself, but the way you are trying to use it with VNL. So please be careful to specify all details, it's not enough to know which molecule, but the problem might lie in the file you are importing, for example. If it's a PDB file, VNL will not know how to handle it. Etc. The devil is in the details

[spin]

I made the Adamantane molecule in VNL and I got the coordinates of all atoms in VNL by myself and the shape of molecule has the specific format adjusted with VNL, is there any way to make the molecular junction without using costum?

[Anders Blom]

Fine, but as the post above by kstokbro shows, provided the molecule is in the correct format, there is no problem to set up the system. I suggest you use his approach.

[spin]

Try the following:
import the file adamantane.xyz into the builder,
next drag the molecule from the builder into the molecular junction custom builder
set repeat to 4x4
and atoms to 19 and 31,
this works for me, see attached

t

should I depict the molecule in 2 dimension? whether VNL can not calculate the 3 dimension molecules?

[Anders Blom]

Of course ATK can handle 3D molecules I didn't note the actual molecule was a bit different in your case, however at any rate, as I have said many times, what seems to be the matter is what precisely you are dropping on the "molecule dropzone". Is it a file, and if so which file format, or do you drag from another Builder, or an Editor? If you try the approach described in kstokbro's post, then just adapt the file to represent your molecule instead of his, let's see where that gets you. Or post your molecule (coordinates, the file, not a picture from Wikipedia) so we can try to help with the actual problem, instead of this kind of abstract discussion which I think doesn't really lead anywhere.

[spin]

The Adamantane configuration made by VNL and also picture of the 2 electrode system  are attached. 

[spin]

and I tested the xyz file sent by kstokbro, it doesn't work for me. I think the custom molecular junction works only for the default molecule.

[Anders Blom]

All works fine. I took your Python file, dropped it into the Molecule Device Builder, set atoms to 14 and 25, and right absorption height to 2.5 Å (just for something), and all looks ok.

You will need to adjust the exact distances, of course, and perhaps also set the repetitions to 4x4.

[spin]

Thank you very much
It is nice now and there are no problem with it.

for havin the linear electrode ( only a chain) the configuration of adamantane is changed, do you have any proposal for having a linear electrode?

[Anders Blom]

Why changed?

The electrodes should generally speaking be chosen to reflect the problem you are trying to simulate. The 1D density of states and band structure of an atomic chain is usually quite different from an electrode made of e.g. a gold 111 surface, so the results will be different. Which you prefer, again, depends on what you are trying to achieve.