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

Thu Jul 3 10:16:51 CEST 2014

Hi Gabriele,

Yes, it might indeed be the case. Thank you for your help!

Kind regards,
Anusha

> 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
>>>>>>>>>>>> DFTB-Plus-User at dftb-plus.info
>>>>>>>>>>>> http://www.dftb-plus.info/mailman/listinfo/dftb-plus-user
>>>>>>>>>>>>
>>>>>>>>>>> _______________________________________________
>>>>>>>>>>> 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
>>>>>>>>>> http://www.dftb-plus.info/mailman/listinfo/dftb-plus-user
>>>>>>>>>>
>>>>>>>>> _______________________________________________
>>>>>>>>> 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
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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
>>> http://www.dftb-plus.info/mailman/listinfo/dftb-plus-user
>>>
>>
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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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