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

anz118466 at cse.iitd.ac.in anz118466 at cse.iitd.ac.in
Fri Jun 27 11:09:32 CEST 2014


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.

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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>>>>>>>>
>>>>>>> _______________________________________________
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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
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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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>>>>
>>>
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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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