sp3-passivation with H for bare Si nanorod

[nori]

Dear Everyone,

I made a script for passivating dangling bonds of bare Si nanorod with Hydrogen and share it with you.
(passivate_sp3.py)
The usage is as follows:
1. Open Custom Builder and drop "passivate_sp3.py" onto the Custom Builder window.
2. make a structure of bare Si nanorod like "sinr110_bare.py" using Builder, Database, and Custom Builder.
3. drop the script of bare Si nanorod onto "Drop unpassivated system here" in the Custom Builder window.

After step 3, you can obtain sp3-passivated Si nanorod like "sinr110_passivated.png".

This script is still prototype and any kinds of feedback is appreciated

[kstokbro]

Hi Nori,
I corrected a small error in your script for handling molecule configurations. It now works very nice for molecules.

I made a silicon cluster, using the following steps

1. Use wulf constructer in custom builder to make silicon cluster
2. transfer the structure to the builder and select silicon atoms with only one neighbour, remove these atoms
3. drop the passivate_sp3_rev.py on the custom builder
4. transfer the structure from the builder to the new custom builder

[nori]

Dear kstokbro,

Thank you for the correction and giving us the example of usage

[nori]

Dear everyone,

I've made another version of the script, which enables one to do sp3 passivation of Silicon nanowire.
"nanowire" in the above sentence means that the structure has periodicity along z direction.

The usage is as follows:
1. prepare bare Si nanowire like "bare_sinw110.py",
2. launch Custom Builder,
3. Drop "passivate_sp3_2.py" onto "Drop your builder..." in the Custom Builder window,
4. Drop "bare_sinw110.py" onto "Drop unpassivated system here".

[yogita]

hi nori,

I m very new in ATK n using 11.8.2,  want to passivate Cu2O molecules arrangements,
can you help me?

thanks

[kstokbro]

In the  builder of ATK 12.8 it is possible to passivate organic elements. Thus, import you configuration into the builder and press the passivation symbol, to passivate the O atoms.

[yogita]

thanks