Author Topic: building a graphene nanoribbon and optimizing its geometry using atk-dft  (Read 4944 times)

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Offline rupen_86

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I have tried building zigzag-silicene nanoribbon in this way:
add->nanoriboon->replaced carbon atomsby silicon and changed bond length to 2.25 from default 1.4086 for carbon.and then selected 8 atoms wide->and repeated it 3 times-> then sent it to script generator and optimized its geometry using atk-dft but calculation did not converge at all ...algo i tried c-chain doping in it but i can't see some newly formed c-si and c-c bonds in the structure. plz let me know if i am doing it the right way or missing something.

thanks

Offline Jess Wellendorff

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We need to see the scripts you have prepared in order to help you. Log files would also be helpful. Please attach to this post.

Offline rupen_86

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this is the script which i have prepared. also i introduced buckling by pressing rattle tool few times.kindly suggest me if i am wrong somewhere as the main problem which i am facing is in geometry optimization using DFT. I followed the same procedure mentioned above  for building bulk  pristine Z-SINR before trying optimization of C-chain doped Z-SINR(Bulk)but same problem came in its optimization. Currently I am concentrating on bulk ribbon's properties. Then i would go for device level transport properties. plz suggest me the right way. while running the forces are not converging and this convergence is showing oscillating behavior thanks
« Last Edit: September 14, 2016, 16:01 by rupen_86 »

Offline Ulrik G. Vej-Hansen

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First off, you can get away with much fewer k-points in the C-direction when doing geometry optimization. I would guess that 5 is enough, but you should of course check that. If I run your script with 3 k-points (probably too low, but faster) the DFT calculation converges nicely for at least the first couple of optimization steps. Were you having problems in the first step?


Offline rupen_86

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is it possible to use too few k-points in c-direction for my work as in all the related papers in the literature people went for 50 to 100 k-pts in order to get accurate results. do we go for different k-pts for geometry optimization vs analysis.
with that sent script my forces were going like 4.12ev/angstrom->2.27ev/angstrom->2.25ev/angstrom and goes on and on with oscillatory character taking too much time. Is is good enough if i would go for fewer k-pts for optimization.
with so many k-pts analysis is not taking too much time without doing geometry optimization. main problem is with optimization only.plz help me out.

kindly check my log file as well.

thanks for frequent replies
« Last Edit: September 14, 2016, 16:44 by rupen_86 »

Offline Anders Blom

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You should not expect an optimization like this to converge in 4-5 steps. There is no oscillatory behavior seen in the log file, just 4 steps with large forces, but that's just the beginning of the optimization. It may take 15 or 30 iterations, hard to predict.

What I would change, to speed it up a bit hopefully, is to reduce the Si-C bond lengths from the beginning; the atoms have to move a long distance because those bonds are clearly too long, and that takes time. 9 to 15 k-points or something like that in the C direction should be fine., this is not a device where you  need 100 or 200 (for very specific reasons). That would speed up your calculation quite a bit, and actually I would first use SingleZetaPolarized at least to get a roughly ok structure, then you can refine it using DoubleZetaPolarized.

You can first disable stress optimization and just get the forces down to small amounts, because of the Si-C bond lengths in particular, and then optimize forces + stress as a subsequent step. Or, if the suggestions above make it run faster, then keep it as it is, then you don't have to run twice... But keep in mind that 0.1 GPa is a quite low stress threshold, it may take quite some time to get there. So at least for the SingleZetaPolarized run you can use a bit relaxed accuracy, like 0.04 eV/Ang for forces and 1 GPa for stress.

Seems you changed "interaction_max_range"; don't do that, it's not a useful parameter, set it back to default.

Finally, I can't help noticing that you run the calculation in serial. Not knowing what license you have, that may be your only choice, but you could speed it up 2-3 times by running in parallel over 4 processes if you have a quadcore machine, even on your desktop/laptop.

Good luck!

Offline rupen_86

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thanks for your valuable suggestions sir.

 plz let me know how can i change Si-C bond lengths in the builder, which you suggested,  from beginning as i started with building Z-SiNRs with Si-Si bond length 2.25 and then replaced Si atoms in one zig-zag chain by carbon atoms.
also i can not see any option in optimizer window to disable stress tolerance.how would i disable it then? i have licenced atk 13.8.0 on my desktop and atk 2016.0 release on 15 day trial on my laptop.
« Last Edit: September 15, 2016, 08:51 by rupen_86 »

Offline Anders Blom

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You can use the move tool, or Coordinate Tools>Translate. Or why not try the Quick Optimizer with a SiC potential.
Upgrading to 2016 will bring you a lot of benefits ;)

Offline rupen_86

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thankyou so much for your help... :) infact now i tried bringing forces down as per your advice and i got the results...now will do the same for doublezeta polarized basis set...but it took 34 steps converging in 1 hr 45 minutes ...