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

Thu Jun 26 12:27:21 CEST 2014

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
>>> 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
>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: dftb_in.hsd
Type: application/octet-stream
Size: 1445 bytes
Desc: not available
URL: <http://www.dftb-plus.info/pipermail/dftb-plus-user/attachments/20140626/198ec413/attachment.obj>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: trend.dat
Type: chemical/x-mopac-input
Size: 8062 bytes
Desc: not available
URL: <http://www.dftb-plus.info/pipermail/dftb-plus-user/attachments/20140626/198ec413/attachment.mop>