[DFTB-Plus-User] DFTB-Plus-User Digest, Vol 67, Issue 7

Thu Mar 12 17:43:17 CET 2020

Hi Bálint!
Thanks for the clarification; along the same lines, I assume
that too-few-lines then lead to zero-padded integrals in DFTB+.
/Maxime

Op do 12 mrt. 2020 om 12:00 schreef <
dftb-plus-user-request at mailman.zfn.uni-bremen.de>:

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> Today's Topics:
>
>    1. Re: Size of Slater-Koster tables (Maxime Van den Bossche)
>    2. Re: Size of Slater-Koster tables (Bálint Aradi)
>    3. DFTB+ 19.1 memory leakage (Schwarz Dr., Paul (FTI))
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 11 Mar 2020 13:36:06 +0100
> From: Maxime Van den Bossche <maxime.cp.vandenbossche at gmail.com>
> To: dftb-plus-user at mailman.zfn.uni-bremen.de
> Subject: Re: [DFTB-Plus-User] Size of Slater-Koster tables
> Message-ID:
>         <CAFKLxHAAePM3K1AB94u2-vbZ+F5Xg+ue0EovCR=P-yj=
> du7Nug at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Hello again -- just a quick bump of the question below;
> it would be great if someone could clarify what's the
> precise behaviour of DFTB+ with regards to nGridPoints.
> There's no bug or problem, I just want to understand :).
> /Maxime
>
>
> Op wo 26 feb. 2020 om 21:45 schreef Maxime Van den Bossche <
> maxime.cp.vandenbossche at gmail.com>:
>
> > Hello,
> >
> > When going through some of the Slater-Koster files from dftb.org, I
> > noticed something that looked a little bit odd:
> >
> > The 'nGridPoints' value on the first line is supposed to represent the
> > number of points in the SK tables, but there seem to be quite a few files
> > that don't obey this, having either additional grid points or missing one
> > or two grid points, as e.g. in
> >
> > matsci-0-3/Si-Si.skf
> > pbc-0-3/Fe-Fe.skf
> > mio-1-1/C-C.skf
> >
> > Now, DFTB+ seems to deal with this just fine -- I suppose surplus lines
> > are simply skipped? And with the last integrals set to 0 in case a line
> is
> > missing?
> >
> > Best regards,
> > Maxime
> >
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> ------------------------------
>
> Message: 2
> Date: Wed, 11 Mar 2020 18:10:02 +0100
> From: Bálint Aradi <aradi at uni-bremen.de>
> To: dftb-plus-user at mailman.zfn.uni-bremen.de
> Subject: Re: [DFTB-Plus-User] Size of Slater-Koster tables
> Message-ID: <1e550e08-eaad-4ce7-3f7c-213d322fa6ee at uni-bremen.de>
> Content-Type: text/plain; charset="utf-8"
>
> Dear Maxime,
>
> On 3/11/20 1:36 PM, Maxime Van den Bossche via DFTB-Plus-User wrote:
> > Hello again -- just a quick bump of the question below;
> > it would be great if someone could clarify what's the
> > precise behaviour of DFTB+ with regards to nGridPoints.
> > There's no bug or problem, I just want to understand :).
>
> As documented in
>
> http://www.dftb.org/fileadmin/DFTB/public/misc/slakoformat.pdf
>
> DFTB+ reads the SK-integral values from lines (both bounds inclusive):
>
> 4 -> nGridPoints + 3 (homo-nuclear, simple format)
> 5 -> nGridPoints + 4 (homo-nuclear, extended format)
> 3 -> nGridPoints + 2 (hetero-nuclear, simple format)
> 4 -> nGridPoints + 3 (hetero-nuclear, extended format)
>
> The first line of each interval corresponds to the distance gridDist,
> every further line is gridDist farther apart.
>
> Some tables are longer due to historical reasons (people generating
> SK-files manually not understanding the details of the horrible
> SK-format...). Those extra lines are ignored by DFTB+.
>
>   Best regards,
>
>   Bálint
>
>
> --
> Dr. Bálint Aradi
> Bremen Center for Computational Materials Science, University of Bremen
> http://www.bccms.uni-bremen.de/cms/people/b-aradi/
>
>
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> ------------------------------
>
> Message: 3
> Date: Thu, 12 Mar 2020 09:12:31 +0000
> From: "Schwarz Dr., Paul (FTI)" <Paul.Schwarz at freudenberg.com>
> To: "dftb-plus-user at mailman.zfn.uni-bremen.de"
>         <dftb-plus-user at mailman.zfn.uni-bremen.de>
> Subject: [DFTB-Plus-User] DFTB+ 19.1 memory leakage
> Message-ID: <e073f60a00c64743b9790dc7c64e14b1 at freudenberg.com>
> Content-Type: text/plain; charset="utf-8"
>
> Dear DFTB+ users,
>
> I am experiencing memory leakage when doing molecular dynamics runs with
> DFTB+ on my machine.
> My system configuration is:
>
>   *   Ubuntu 18.04 LTS
>   *   Intel Xeon CPU
>   *   256 GB RAM
>
> I compiled DFTB+ with the ELSI library and have this issue with the ELPA
> solver. However, I also experience the memory leakage when using the QR
> solver.
> The system I'm simulating consists of 114 C atoms and 10 H atoms (nothing
> too wild here, no spin polarization).
>
> After setting up my starting structure I do a NVE simulation (see attached
> input file), starting with 'mpiexec -np 24 dftb+'. I set OMP_NUM_THREADS=1
> for the ELPA solver.
> I have logged my memory and it shows an exponential growth of memory
> usage, until after ~ 77.000 MD steps my complete 256 GB RAM are full and
> the simulation crashes with an MPI error
>
>
> ===================================================================================
> =   BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
> =   RANK 0 PID 19101 RUNNING AT xxxxxxxx
> =   KILLED BY SIGNAL: 9 (Killed)
>
> ===================================================================================
>
> Has anyone experienced the same problems or could help me resolve this
> issue?
> Thanks in advance
>
>
> Best regards,
> Paul Schwarz
>
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> End of DFTB-Plus-User Digest, Vol 67, Issue 7
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