Author Topic: How build an asymmetric molecular junction??  (Read 2207 times)

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Offline Sandra

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How build an asymmetric molecular junction??
« on: March 2, 2016, 14:25 »

The “mini-tutorial on how to build a 3x3 gold [111] system” shows how inserts a second gold surface by means of the “Coordinate Tools>Mirror”, and you get a junction configuration like:
[ABC]ABCA-Molecule-ACBA[CBA].

In my case, to avoid any stacking faults,  I would like to build a junction with an asymmetric configuration instead of a mirror one, like:
[ABC]ABC-Molecule-ABC[ABC]
Are there any easy way to build it like in the tutorial?, or I need to build the two electrodes independently, and then to use the  “Builders>Interface” tool to that.

Thanks

Offline Anders Blom

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Re: How build an asymmetric molecular junction??
« Reply #1 on: March 2, 2016, 15:16 »
I would build a long supercell ABC-ABC-ABC-ABC-ABC-ABC of gold.
Then make a cut in the middle, by selecting half of the atom (large z), and move them to the right
(use Bulk Tools>Stretch Cell while setting "Selected atoms are MOVED"), to make room for the molecule
Then drop the molecule in place, attach properly to left electrode (coordinated and placed as you want)
Then move back the right surface to attach to the molecule (same tool)

Offline Sandra

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Re: How build an asymmetric molecular junction??
« Reply #2 on: March 3, 2016, 09:54 »
Thanks a lot!
It is an easier way to do that!!