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Messages - AsifShah

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Dear Admin/Others,
When doing device from bulk, it chooses minimal electrode length as one atom. However, I want to keep 2 or 3 atoms as my electrode I tried changing +/-  as shown in attachment, also tried changing left & right values below (see attachment) & electrode extension length but it does not help change the electrode length & keeps it fixed as one atom. How to rectify it? I found that changing left & right values below had no effect on the electrode size. Kindly help.
Check the attachments below.

(The reason why I want to change it to 2 or 3 atoms is because in electrode validator it says large matrix elements error & asks to increase electrode size)

General Questions and Answers / Bandstructures
« on: Yesterday at 11:28 »
Dear Admin/Anyone,
Could you kindly explain why any multiple of 3 chosen for a supercell (in this case for moS2) produces a different bandstructure than other sizes. It can be seen below that for a supercell of 3x3 & 9x9 we have VBM & CBM along G point whereas for other sizes such as 4x4,5x5 it is along KM points?
 Is it something with software or I am missing something here?
See the attachment below

General Questions and Answers / Re: convergence problem
« on: June 21, 2022, 14:17 »
You need to increase it thats the only way. I faced same issue some time ago but got results.
Try 300 maybe

General Questions and Answers / Re: convergence problem
« on: June 21, 2022, 14:11 »
If you are using Semiempirical calculator, then in that go to iteration control & if you have unticked no scf iteration then below it there will be maximum steps written as 100, change it to 400 & recompute. I am not sure but there is a way I guess to recompute only not converged points instead of rerunning whole calculations.

General Questions and Answers / Re: convergence problem
« on: June 20, 2022, 14:39 »
I see you are using Gold (as electrode I guess). From my experience with Gold adsorption calculations they taken long to optimize (converge). I normally run from command line & not from user interface & I see two files apart from .py during run. One is log file & another is name something like optimizationxxxxxx.log . Most infiormation of optimization were found in this optimizationxxx.log file.

General Questions and Answers / Re: convergence problem
« on: June 18, 2022, 12:00 »
Sometimes it doesn't converge because K points are not enough. 1x1x1 could be one problem. Check log file and save it then run with higher k points for same time & compare two log files to see if K point convergence is the issue

General Questions and Answers / Re: convergence problem
« on: June 18, 2022, 09:28 »
Depending on number of k points & size of device, transport calculations usually take long time.

I am calculating the dissociation energy of Hydrogen molecule.
The formula used is E(disso)=E(H2)-2E(H)
where E(H2) is the total energy calculated using two methods as:
1. Spin unpolarised/polarized using B3LYP functionals giving energies - 32, -32 respectively.
2. Spin unpolarised/polarised using PBE functionals giving energies - 31.651, -27.181 respectively.
Since H2 is spin unpolarised molecule & when choosing unpolarised/polarised using B3LYP both give same energy -32 which makes sense but why does PBE give different results for spin polarised & spin unpolarised?

It is okay. I suggest to read some literature on Mulliken charge as it is not reliable in some cases & some people report other methods. For intro look into "Chemlibre Mulliken Charge" in Google.

I would suggest use 'atkpython filename' from terminal instead.(Quotes Ignored)

Firstly, I doubt the charge on C & O after adsorption because oxygen is more electronegative than carbon so charge should be flowing to oxygen from carbon but maybe I am missing something here. Recheck it else NVM.
Secondly, If CO charge charge has reduced it means AGNR has taken some charge from CO, (Here I suggest to see electron density 1D plot & see the minimum electron density in bonding region which should give u idea of how much CO is interacting with AGNR. It looks the charge transfer is not much happening here.

Dear mariosimoni,
Yes, I if you want to just calculate energies then it should be possible to do it. NEGF would be more comprehensive & detailed though time expensive I guess.

You will need to compare it with pristine case. Eg in normal conditions carbon has ideal charge of 4 & hydrogen has 1 & oxygen has 6 so on.. Now u can check which atoms in ur current file have changed their charge & compare it with the ideal charge.

From the Mulliken Charge file I see there is no difference from ideal values. Probably your source file .py has something wrong. If possible you can share your .py file.

Once you are done with bringing potential from say sentaurus? What simulation you would carry out on QATK? Will you be using NEGF? If so then I guess you want to use U (potential) into the NEGF equations which I think is not a good method because normally you require self consistent solution of NEGF with poison equation to arrive at final solution. So you will require to extract charge from NEGF into sentuarus & back potential from sentuarus into NEGF until convergence is achieved which I think is not possible to do or is challenging to do unless both devices on sentaurus & QATK resemble to one another.

PS: THis is just a hypothesis , do let me know if there is a way around.

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