[DFTB-Plus-User] Correctness of SCC convergence in DFT+NEGF

Tue Jul 1 11:03:45 CEST 2014

On 06/30/2014 02:59 PM, anz118466 at cse.iitd.ac.in wrote:
> Hi Gabriele,
>
> Thanks for the reply! The transmission is indeed wrong.
>
> After a few more simulations, I realised that the convergence success
> changes with the applied bias. The system converged at zero bias and the
> Transmission looks correct. Same for 1V. But, at bias of something like
> 0.6 V or 0.8 V, the noise creeps back in. Your thoughts?

I noticed that you use a semiconducting electrode region, and maybe you
don't put any virtual doping the Fermi level is in the gap.
If this is the case, you should be sure what you're trying to represent
here, as the code in principle allows for that, but I would say that
this is a situation where you need to be careful about the physics of
the system.

At equilibrium the picture is clearer, but if you then apply bias on a
system where you can not inject carriers, at least in some bias windows,
it gets more complicated.

Best,
Gabriele

>
> Best Regards,
> Anusha
>
>
>
>
>> On 06/27/2014 11:09 AM, anz118466 at cse.iitd.ac.in wrote:
>>> Hello,
>>>
>>> I am not sure if the peak in SCC error is a correct thing to have and if
>>> I
>>> should go ahead with this result. Any feedback/opinion would be much
>>> appreciated.
>> Hi Anusha,
>>
>> you should check the detailed.out, if the SCC cycle goes that crazy you
>> may have converged to the trivial zero solution, which is physically
>> wrong. In that case you'll have also a crazy transmission, basicaly
>> noise close to zero. If on the other hand the charges are similar to the
>> DFTB calculation then the solution should be reasonable.
>>
>> Best
>> Gabriele
>>
>>
>>
>>> Thanking you.
>>>
>>> Kind Regards,
>>> Anusha
>>>
>>>
>>>
>>>> Hi Gabriele,
>>>>
>>>> As suggested by you, I performed a periodic calculation for my system
>>>> as
>>>> per the steps outlined here
>>>> (http://www.dftb-plus.info/fileadmin/DFTB-Plus/public/recipes/html/basics/bandstruct.html).
>>>> The system converged in 89 steps for a 'SCCTolerance' of 1e-4.
>>>>
>>>> I then fed the charges.bin to the transport calculation and the system
>>>> converged after 430 steps. It does, however, again hit the peak
>>>> observed
>>>> in SCC error before. I am attaching the dftb_in.hsd and the trend of
>>>> the
>>>> 'SCC error' for your reference.
>>>>
>>>> Thanks & Regards,
>>>> Anusha
>>>>
>>>>> Hi Anusha,
>>>>>
>>>>> no, I mean a calculation without transport, Poisson solver and Green's
>>>>> function.
>>>>> Just a plain supercell DFTB calculation in the Gamma point solved by
>>>>> diagonalization.
>>>>>
>>>>> Best,
>>>>> Gabriele
>>>>>
>>>>>
>>>>> On 06/23/2014 08:44 PM, anz118466 at cse.iitd.ac.in wrote:
>>>>>> Hi Garbiele,
>>>>>>
>>>>>> I am trying to set the PBC along transport direction by using:
>>>>>>
>>>>>>  OverrideBulkBC = Periodic {
>>>>>>         Boundaries = y
>>>>>>     }
>>>>>>
>>>>>> I wanted to confirm if this is the right way of doing this.
>>>>>>
>>>>>> Kind Regards,
>>>>>> Anusha
>>>>>>
>>>>>>
>>>>>>
>>>>>>> On 06/23/2014 05:32 PM, anz118466 at cse.iitd.ac.in wrote:
>>>>>>>> Hi Gabriele,
>>>>>>>>
>>>>>>>> Thank you for the reply.
>>>>>>>>
>>>>>>>> I am not sure if I understand correctly on trying a regular
>>>>>>>> periodic
>>>>>>>> calculation...could you shed more light?
>>>>>>> Hi Anusha,
>>>>>>>
>>>>>>> I mean a DFTB calculation with periodic boundary conditions along
>>>>>>> transport direction instead of a transport calculation with open
>>>>>>> boundary conditions.
>>>>>>> If it doesn't converge with a periodic calculation, hardly it will
>>>>>>> converge with open boundaries. I'm saying to try it because
>>>>>>> physisorbed
>>>>>>> or weakly bounded systems are dangerous beasts in DFTB
>>>>>>>
>>>>>>>> I am attaching the zero-bias transmission for just the nanoribbon
>>>>>>>> for
>>>>>>>> your
>>>>>>>> reference.
>>>>>>> It's a semiconducting system, that's why increasing temperature to
>>>>>>> 300K
>>>>>>> doesn't help.
>>>>>>>> Kind Regards,
>>>>>>>> Anusha
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>> Hi Anusha,
>>>>>>>>>
>>>>>>>>> not an easy system, I'd say. Could you try a 'regular' DFTB
>>>>>>>>> periodic
>>>>>>>>> calculation? Weakly bounded systems can be tricky even without
>>>>>>>>> transport, you should check whether you get a reasonable
>>>>>>>>> energetics
>>>>>>>>> with
>>>>>>>>> a periodic calculation.
>>>>>>>>>
>>>>>>>>> The broyden is a bit fast, at most I would lower the value (0.05),
>>>>>>>>> but
>>>>>>>>> I
>>>>>>>>> don't think it will help. If you have a periodic result, you may
>>>>>>>>> try
>>>>>>>>> to
>>>>>>>>> set an initial charge value for every atom in the transport
>>>>>>>>> calculation.
>>>>>>>>>
>>>>>>>>> I think that the Poisson box is large enough. Is the nanoribbon
>>>>>>>>> metallic?
>>>>>>>>>
>>>>>>>>> Best,
>>>>>>>>> Gabriele
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> On 06/23/2014 04:42 PM, anz118466 at cse.iitd.ac.in wrote:
>>>>>>>>>> Hi Gabriele,
>>>>>>>>>>
>>>>>>>>>> For the second testcase, I had kept the poisson box as (30,30)
>>>>>>>>>> Angstroms
>>>>>>>>>> along the x and z directions. The transport direction is along
>>>>>>>>>> y-axis
>>>>>>>>>> and
>>>>>>>>>> the 'MinimalGrid' was 0.2. These settings gave the weird
>>>>>>>>>> convergence
>>>>>>>>>> trend
>>>>>>>>>> I had shared before.
>>>>>>>>>>
>>>>>>>>>> I repeated the simulation with a bigger poisson box (50,50)
>>>>>>>>>> Angstroms
>>>>>>>>>> along x and z axis, and a 'MinimalGrid' of 0.3. No convergence
>>>>>>>>>> was
>>>>>>>>>> achieved even after 700 iterations. In both the cases, the
>>>>>>>>>> broyden
>>>>>>>>>> 'MixingParameter' was kept as 0.3 and 'Temperature' as 300K. I am
>>>>>>>>>> at
>>>>>>>>>> a
>>>>>>>>>> loss on how to proceed now.
>>>>>>>>>>
>>>>>>>>>> I am attaching the .gen file for your reference and also, the
>>>>>>>>>> detailed.out
>>>>>>>>>> for the (30,30) poisson box simulation. Kindly have a look. Any
>>>>>>>>>> feedback
>>>>>>>>>> would be very helpful.
>>>>>>>>>>
>>>>>>>>>> Thanks and Regards,
>>>>>>>>>> Anusha
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>> Hi Anusha,
>>>>>>>>>>>
>>>>>>>>>>> the Poisson box may indeed play a very important role in the
>>>>>>>>>>> convergence
>>>>>>>>>> path.
>>>>>>>>>>> When everything is properly setup, equilibrium calculation are
>>>>>>>>>>> very
>>>>>>>>>> often similar to a periodic dftb+ calculation, an SCC cicle of 14
>>>>>>>>>> steps
>>>>>>>>>> is fine (a bit fast, even).
>>>>>>>>>>> Hundreds of steps is definitely long and I would be suspicious
>>>>>>>>>>> as
>>>>>>>>>>> well.
>>>>>>>>>> Also the SCC error gets very large.
>>>>>>>>>>> My experience is that a small Poisson box (along any direction)
>>>>>>>>>>> can
>>>>>>>>>>> be
>>>>>>>>>> responsible for it. The mixer is quite robust, therefore I
>>>>>>>>>> observed
>>>>>>>>>> that
>>>>>>>>>> with a small Poisson box you can still reach convergence to the
>>>>>>>>>> exact
>>>>>>>>>> solution but with very long and weird SCC steps. I suggest you to
>>>>>>>>>> check
>>>>>>>>>> that, in case of non-periodic calculation, you have enough vacuum
>>>>>>>>>> around
>>>>>>>>>> the device (if you can reach it computationally, a couple of nm
>>>>>>>>>> on
>>>>>>>>>> each
>>>>>>>>>> side for each direction). The minimal grid step default is
>>>>>>>>>> usually
>>>>>>>>>> fine,
>>>>>>>>>> at worst try to reduce it slightly (0.3).
>>>>>>>>>>> I rarely observed convergence to the trivial zero solution, i.e.
>>>>>>>>>>> all
>>>>>>>>>>> the
>>>>>>>>>> electrons are shot away. I suggest you to check the detailed.out
>>>>>>>>>> and
>>>>>>>>>> verify that the charge population is reasonable.
>>>>>>>>>>> Hope this helps
>>>>>>>>>>> Gabriele
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> On 06/20/2014 03:58 PM, anz118466 at cse.iitd.ac.in wrote:
>>>>>>>>>>>> Dear all,
>>>>>>>>>>>>
>>>>>>>>>>>> I have simulated two testcases on the DFTB+NEGF. Both consist
>>>>>>>>>>>> of
>>>>>>>>>>>> a
>>>>>>>>>> biomolecule on a GNR. I observed two very different trends in SCC
>>>>>>>>>> convergence while simulating for the transmission spectra, which
>>>>>>>>>> I
>>>>>>>>>> am
>>>>>>>>>> sharing here.
>>>>>>>>>>>> The first case consists of 1795 atoms in total and saw an
>>>>>>>>>>>> extremely
>>>>>>>>>> fast convergence in just 14 steps. The second one, however, had
>>>>>>>>>> 604
>>>>>>>>>> atoms and saw convergence in around 600+ steps. Also, the SCC
>>>>>>>>>> error
>>>>>>>>>> in
>>>>>>>>>> the second case increased gradually first and then decreased
>>>>>>>>>> rapidly.
>>>>>>>>>> For example, the SCC error reached a high of 0.21776430E+03 in
>>>>>>>>>> 402
>>>>>>>>>> steps. It then gradually decreased to 0.31423479E+02 in another
>>>>>>>>>> 200
>>>>>>>>>> steps, and fell sharply to 0.15680539E-05 in another 5 steps. The
>>>>>>>>>> value
>>>>>>>>>> of
>>>>>>>>>>>> 'SCCTolerance'
>>>>>>>>>>>> was kept 1e-4 in both the cases.
>>>>>>>>>>>>
>>>>>>>>>>>> Looking at these two trends, I am confused with the correctness
>>>>>>>>>>>> of
>>>>>>>>>>>> the
>>>>>>>>>> final output. How do I ensure that no numerical noise has crept
>>>>>>>>>> in
>>>>>>>>>> any
>>>>>>>>>> of
>>>>>>>>>>>> my two testcases? Also, I observe that the final output changes
>>>>>>>>>>>> by
>>>>>>>>>> modifying the poisson box dimensions. Is there any rule of thumb
>>>>>>>>>> regarding
>>>>>>>>>>>> the choice of the poisson box? Please let me know if you need
>>>>>>>>>>>> more
>>>>>>>>>>>> data
>>>>>>>>>> from me for further clarification.
>>>>>>>>>>>> Thanks & Regards,
>>>>>>>>>>>> Anusha Iyer
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>> DFTB-Plus-User mailing list
>>>>>>>>>>>> DFTB-Plus-User at dftb-plus.info
>>>>>>>>>>>> http://www.dftb-plus.info/mailman/listinfo/dftb-plus-user
>>>>>>>>>>>>
>>>>>>>>>>> --
>>>>>>>>>>> Dr. Gabriele Penazzi
>>>>>>>>>>> BCCMS - University of Bremen
>>>>>>>>>>>
>>>>>>>>>>> http://www.bccms.uni-bremen.de/
>>>>>>>>>>> http://sites.google.com/site/gabrielepenazzi/
>>>>>>>>>>>
>>>>>>>>>>> phone: +49 (0) 421 218 62337
>>>>>>>>>>> fax: +49 (0) 421 218 62770
>>>>>>>>>>>
>>>>>>>>>>> _______________________________________________
>>>>>>>>>>> DFTB-Plus-User mailing list
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>>>>>>>>>>>
>>>>>>>>>> _______________________________________________
>>>>>>>>>> DFTB-Plus-User mailing list
>>>>>>>>>> DFTB-Plus-User at dftb-plus.info
>>>>>>>>>> http://www.dftb-plus.info/mailman/listinfo/dftb-plus-user
>>>>>>>>> --
>>>>>>>>> Dr. Gabriele Penazzi
>>>>>>>>> BCCMS - University of Bremen
>>>>>>>>>
>>>>>>>>> http://www.bccms.uni-bremen.de/
>>>>>>>>> http://sites.google.com/site/gabrielepenazzi/
>>>>>>>>>
>>>>>>>>> phone: +49 (0) 421 218 62337
>>>>>>>>> fax: +49 (0) 421 218 62770
>>>>>>>>>
>>>>>>>>> _______________________________________________
>>>>>>>>> DFTB-Plus-User mailing list
>>>>>>>>> DFTB-Plus-User at dftb-plus.info
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>>>>>>>>>
>>>>>>>> _______________________________________________
>>>>>>>> DFTB-Plus-User mailing list
>>>>>>>> DFTB-Plus-User at dftb-plus.info
>>>>>>>> http://www.dftb-plus.info/mailman/listinfo/dftb-plus-user
>>>>>>> --
>>>>>>> Dr. Gabriele Penazzi
>>>>>>> BCCMS - University of Bremen
>>>>>>>
>>>>>>> http://www.bccms.uni-bremen.de/
>>>>>>> http://sites.google.com/site/gabrielepenazzi/
>>>>>>>
>>>>>>> phone: +49 (0) 421 218 62337
>>>>>>> fax: +49 (0) 421 218 62770
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> DFTB-Plus-User mailing list
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>>>>>>>
>>>>>> _______________________________________________
>>>>>> DFTB-Plus-User mailing list
>>>>>> DFTB-Plus-User at dftb-plus.info
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>>>>> --
>>>>> Dr. Gabriele Penazzi
>>>>> BCCMS - University of Bremen
>>>>>
>>>>> http://www.bccms.uni-bremen.de/
>>>>> http://sites.google.com/site/gabrielepenazzi/
>>>>>
>>>>> phone: +49 (0) 421 218 62337
>>>>> fax: +49 (0) 421 218 62770
>>>>>
>>>>> _______________________________________________
>>>>> DFTB-Plus-User mailing list
>>>>> DFTB-Plus-User at dftb-plus.info
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>>>>>
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>>
>> --
>> Dr. Gabriele Penazzi
>> BCCMS - University of Bremen
>>
>> http://www.bccms.uni-bremen.de/
>> http://sites.google.com/site/gabrielepenazzi/
>>
>> phone: +49 (0) 421 218 62337
>> fax: +49 (0) 421 218 62770
>>
>> _______________________________________________
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>> DFTB-Plus-User at dftb-plus.info
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>>
>
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-- 
Dr. Gabriele Penazzi
BCCMS - University of Bremen

http://www.bccms.uni-bremen.de/
http://sites.google.com/site/gabrielepenazzi/

phone: +49 (0) 421 218 62337
fax: +49 (0) 421 218 62770