[DFTB-Plus-User] Dispersion correction in DFTB+NEGF

Thu Jun 12 10:12:03 CEST 2014

Hi Gabriele,

Yes, I used the 'ulimit -s unlimited' option and also did some
partitioning. It gave the error in all these cases. Memory is indeed not
sufficient for my system. Thanks for the help! :)

Best Regards,
Anusha

> On 06/10/2014 12:19 PM, anz118466 at cse.iitd.ac.in wrote:
>> Hi Gabriele,
>>
>> As suggested, I tried to simulate with a smaller system in the 32-bit
>> system. It produced no error (with and without dispersion correction). I
>> believe it must be due to the larger system that the allocation error
>> occurred. Any way to circumvent this?
>
> Dear Anusha,
>
> did you remove stack memory limitation? (see troubleshooting section of
> the manual)
> If you already did, then your system is just too big and doesn't fit in
> memory.
>
> Are you defining a partitioning (correct definition of FirstLayerAtoms
> field, see also the online cookbook)? An efficient partitioning may
> limit the memory consumption a lot and you can go far beyond 1500 atoms,
> but this works good for quasi-1d systems. If the system is very bulky
> and no partitioning is possible, you have no other chance than moving to
> a machine with more memory or reduce (if you can) the system size.
>
> Best
> Gabriele
>
>
>
>
>>
>> Thanks & Regards,
>> Anusha Iyer
>>
>>
>>
>>> On 06/10/2014 07:52 AM, anz118466 at cse.iitd.ac.in wrote:
>>>> Hi Gabriele,
>>>>
>>>> I tried to simulate a testcase I have been running on another machine
>>>> (64-bit). The 64-bit machine gives no such error, but the current
>>>> machine
>>>> exits with the error.
>>>>
>>>> I believe that the simulation works in 64-bit, but the current machine
>>>> is
>>>> a 32-bit one (i686). I had compiled the i686 DFTB+ from the source few
>>>> days back. When I run the transport simulations, the dftb+ gives no
>>>> error
>>>> for the source/drain calculations. However, when I try to run the
>>>> device
>>>> input file, it exits with the 'ALLOCATION ERROR'. This 32-bit machine
>>>> has
>>>> 8 cores and 24GB RAM.
>>>>
>>>> In addition to above, I had a more general query. In the course of
>>>> performing DFTB+ calculations, I have realised that the SCC
>>>> convergence
>>>> highly depends on the input geometry. For small geometries, it would
>>>> make
>>>> sense to optimise in DFTB+ first. But, I am handling a 1500+ atom
>>>> system.
>>>> Kindly share how an optimised geometry can be generated in such a case
>>>> to
>>>> achieve convergence.
>>> Dear Anusha,
>>>
>>> I don't see how this is related to the dispersion correction. You
>>> should
>>> try a SMALL test case, to see if you can reproduce the bug with the
>>> minimum amount of information possible. Moreover, I can not estimate if
>>> your memory is enough or not without details on your system, an
>>> allocation error may be due as well to insufficient memory. The
>>> source/drain calculation is typically much less memory demanding.
>>>
>>> Unluckily there is no brute force way to relax a large structure,
>>> however you could be able to relax a 1500 atoms structure with the
>>> parallel version of DFTB+. Otherwise you'll have to rely on cheaper
>>> methods for the relaxation, like a classical force field.
>>>
>>> Best
>>> Gabriele
>>>
>>>
>>>> Thanks and Regards,
>>>> Anusha
>>>>
>>>>
>>>>
>>>>> On 06/08/2014 03:25 PM, anz118466 at cse.iitd.ac.in wrote:
>>>>>> Dear all,
>>>>>>
>>>>>> I had a small query regarding the DFTB+NEGF package. Is dispersion
>>>>>> correction supported for the same? The DFTB+NEGF manual mentions
>>>>>> about
>>>>>> the
>>>>>> use of SlaterKirkwood model. Can I include this in my transport
>>>>>> calculations for considering van der waals forces?
>>>>> Dear Anusha,
>>>>>
>>>>> we are generally trying to keep all the usual DFTB+ features in the
>>>>> transport trunk, therefore we did not specifically remove anything
>>>>> for
>>>>> dispersion correction but neither we tested a case like you mention.
>>>>>
>>>>> The reason is that van der Waals forces are long electrostatic forces
>>>>> and they do not enter directly the electronic Hamiltonian, therefore
>>>>> they do not affect charge transport. One case I could imagine would
>>>>> be
>>>>> if you want to calculate forces out of equilibrium and include also
>>>>> dispersion correction, but such a feature is not supported yet.
>>>>>
>>>>> Going back to the allocation error, which should not be there in any
>>>>> case, can you give us some more information?
>>>>> How large is the system? Did you try a small test case? Does the
>>>>> normal
>>>>> transport calculation without SlaterKirkwood correction work
>>>>> properly?
>>>>>
>>>>> Best,
>>>>> Gabriele
>>>>>
>>>>>
>>>>>> Also, when I incorporated the dispersion block in my dftb+negf
>>>>>> simulation,
>>>>>> I encountered the following error:
>>>>>>
>>>>>> ALLOCATION ERROR
>>>>>>
>>>>>> Is this due to some memory shortage?
>>>>>>
>>>>>> 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
>>>>>
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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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