Mimicking decomposition of Silicon on 6H-SiC(000-1)

[adkins.99]

Edit: Sorry about all the misspellings and incoherent sentences on here previously. I may not have been awake when I started this topic; I was sleep typing. 

I was looking at this paper,

"Ogasawara N, Norimatsu W, Irle S, Kusunoki M. Growth mechanisms and selectivity for graphene or carbon nanotube formation on SiC (0001¯): A density-functional tight-binding molecular dynamics study. Chemical Physics Letters [serial online]. March 18, 2014;595-596:266-271. Available from: ScienceDirect, Ipswich, MA. Accessed September 12, 2015.

The author describes how the sublimation process for silicon on the 6H-SiC(000-1) surface was mimicked:

To mimic the decomposition process, we removed Si atoms one by one at intervals of 1.0 picoseconds (ps)...The removal order is also depicted in Figure 1 by way of circled numbers...

They don't go into any detail as to how they programmed it. I'm not sure how to pull that off without just doing simulation after simulation on each output successively after removing atoms one-by-one. Is there a straight forward way to do this that isn't as tedious? 
 

[Julian Schneider]

Not a really straightforward way, but you can do it all in a python script. I have attached an example script that uses a classical potential.
Please consider it only an example, and review and adapt the parameters (configuration, calculator, thermostat, equilibration time, evaporated atoms, etc.) as needed.

The script employs an equilibration simulation, and then a loop over all atoms that should be removed. In each cycle, the respective atom is removed, a new configuration is generated, the indices are updated, and an MD simulation is run.

[adkins.99]

Thanks, I was trying to program a loop in py that could do this but it was using up a lot of time, I'm not familiar with all the functions and arguments.

Another question I have about the 6H-faces, the (0001) face is said to be the Si-face, and (000-1) is the C-face. The unit cell has the outer most atoms the other way around...?

[Julian Schneider]

Yes, in this case it (0001) and (000-1) distinguish between a C-terminated surface and a Si-terminated surface. So, in simple words, whether you use the top or the bottom surface of the slab.