[DFTB-Plus-User] Mismatch in repulsive potential for Ga-C and C-Ga in hyb set
Bálint Aradi
aradi at uni-bremen.de
Sat Jun 4 17:38:42 CEST 2022
Dear Thomas Hofer,
sorry for the very long response time. I had a look, and even in the
oldest version of these SK-files I could find (from 2005-07-23), the
repulsives are incorrect.
Unfortunately, I fear there is not much hope, that we can decide, which
one is the correct one, unless someone tries both and finds one
significantly better as the other. (At that time, an ancient code was
used for the DFTB calculations, which unfortunately had no sanity checks
on the file format...)
Best regards,
Bálint
On 04.05.22 10:46, Hofer, Thomas wrote:
> Dear developers, Dear DFTB users
>
>
> Recently, I have been experimenting with the hyb extension to the mio
> set, in particular the Ga - S - O - C - H interactions.
>
>
> When executing some test calculations including Ga and C, dftbplus
> raises an error highlighting a mismatch in the Ga-C and C-Ga repulsive
> interactions. When checking the repulsive entries in the skf-files they
> are indeed different.
>
>
> Next, we overlaid the two different functions for visualization, but
> they are entirely different, especially in the exponential range, but
> also in the regime of the spline functions. Based on the entries in the
> skf-files it is difficult to figure out, whether the Ga-C or C-Ga entry
> is the correct one. Inside the skf-file some contact information from
> 2007 is given, but it appears the respective person is not active
> anymore at this particular institution (and a web-search cannot
> determine the current affiliation. I am not sure this person is still
> active in academia...).
>
>
> My hope is that someone receiving this mailing list has been involved in
> the parametrization of the Ga-C / C-Ga interactions, or at least knows
> someone who can can help to resolve this point.
>
>
> Many thanks and best wishes,
>
> Thomas Hofer
>
>
> Sidenotes: i) It is mentioned in both skf-files that the "CGa_4H_8" test
> system is well reproduced by the DFTB parametrization. I already tried
> to re-create this test, however, I don't even know the exact structure
> of this molecule... Is the carbon tetrahedrally occupied by four -GaH_2
> residues, or is the Ga also forming some strange H-linked motif as for
> instance seen in B2H6? I run some DFT reference calculations to figure
> out the correct structure, but B3LYP bond distances don't fit to the
> DFTB reported in the skf-files and PBE is producing pure garbage, i.e.
> in this case these strange H-linked Ga...Ga interactions appear.
>
> ii) I already tried to generate two different "hyb" sets by employing
> either the one or the other repulsive potential in both the Ga-C and
> C-Ga files, but also this did not help to discrminate, which repulsive
> entry is the correct one.
>
>
> /---------------------------------------------------------------------------------------------------------/
> assoc. Prof. Dr. Thomas Hofer
> Department for Theoretical Chemistry
> Institute of General, Inorganic and Theoretical Chemistry
> Innrain 80-82
> University of Innsbruck
> 6020 Innsbruck
> Austria
> Phone: +43-512-507-57111
> Email: t.hofer at uibk.ac.at
> /---------------------------------------------------------------------------------------------------------/
>
>
>
>
>
> ------------------------------------------------------------------------
> *Von:* DFTB-Plus-User <dftb-plus-user-bounces at mailman.zfn.uni-bremen.de>
> im Auftrag von Ankur Gupta <ankur at lbl.gov>
> *Gesendet:* Dienstag, 3. Mai 2022 04:00
> *An:* User list for DFTB+ related questions
> *Betreff:* Re: [DFTB-Plus-User] Correct Way to Run MPI-enabled DFTB+
> (Conda Installation)
> Dear Dr. Aradi,
>
> Yes, I am also not able to understand what the source of this noise is.
> I am playing around with various options for the FIRE optimizer, but so
> far, I haven't succeeded in optimizing the structure within a reasonable
> number of steps.
>
> I have attached a sample input file with the email. I would be highly
> grateful if you could provide any further insight into the given
> structure's optimization.
>
> Best,
> Ankur
>
> On Mon, May 2, 2022 at 7:32 AM Bálint Aradi <aradi at uni-bremen.de
> <mailto:aradi at uni-bremen.de>> wrote:
>
> Dear Ankur,
>
> For sure, the xTB parameters were created without considering periodic
> structures. But even with a suboptimal parametrization, I'd not expect
> problems with the lattice optimization convergence. This looks to me
> more like some noise, which makes optimization with tight tolerances
> problematic. But currently, I am somewhat puzzled, where this noise
> should come from...
>
> Best regards,
>
> Bálint
>
>
> On 29.04.22 21:03, Ankur Gupta wrote:
> > Dear Dr. Aradi,
> >
> > I am already using the new geometry optimizers. I have tried all
> three
> > optimizers available (Rational, LBFGS, FIRE). It seems like the
> > optimization starts wandering when the max. gradient reaches around
> > 1.00E-03. So, we probably need to decrease the step size when the
> > maximum gradient is around that value. I am currently working with
> > simple periodic organic molecules, with only two molecules in a unit
> > cell, so I expect the optimization to converge within 150 steps.
> >
> > I have used GFN2-xTB (in the xTB code) for molecular
> optimizations of
> > large molecules and found it to be quite robust for a wide
> variety of
> > cases. However, since the xTB methods have not been
> parameterized for
> > periodic systems, I was wondering if that's the reason for their
> poor
> > performance in optimizing periodic systems.
> >
> > Best,
> > Ankur
> >
> > On Fri, Apr 29, 2022 at 2:36 AM Bálint Aradi <aradi at uni-bremen.de
> <mailto:aradi at uni-bremen.de>
> > <mailto:aradi at uni-bremen.de <mailto:aradi at uni-bremen.de>>> wrote:
> >
> > Dear Ankur,
> >
> > > I have another question related to the usage of DFTB+. I am
> > currently
> > > trying to optimize periodic organic systems (containing around
> > 60-110
> > > atoms) using the GFN2-xTB method; however, it seems like the
> > geometry
> > > optimization is extremely slow in terms of gradient
> convergence. For
> > > example, in around 300 geometry optimization steps, the
> gradient
> > norm
> > > dropped from 0.72 H/a0 to only 0.0005499 H/a0. Is there a
> way to
> > speed
> > > up the gradient convergence so that the geometry optimization
> > finishes
> > > in fewer steps?
> >
> > Use the new geometry optimizers (Driver =
> GeometryOptimization {}).
> > Depending on the system, if the potential surface is very
> flat, it can
> > be difficult to obtain the minimum.
> >
> > 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/
> <http://www.bccms.uni-bremen.de/cms/people/b-aradi/>
> > <http://www.bccms.uni-bremen.de/cms/people/b-aradi/
> <http://www.bccms.uni-bremen.de/cms/people/b-aradi/>>
> >
> > _______________________________________________
> > DFTB-Plus-User mailing list
> > DFTB-Plus-User at mailman.zfn.uni-bremen.de
> <mailto:DFTB-Plus-User at mailman.zfn.uni-bremen.de>
> > <mailto:DFTB-Plus-User at mailman.zfn.uni-bremen.de
> <mailto:DFTB-Plus-User at mailman.zfn.uni-bremen.de>>
> >
> https://mailman.zfn.uni-bremen.de/cgi-bin/mailman/listinfo/dftb-plus-user
> <https://mailman.zfn.uni-bremen.de/cgi-bin/mailman/listinfo/dftb-plus-user>
> >
> <https://mailman.zfn.uni-bremen.de/cgi-bin/mailman/listinfo/dftb-plus-user <https://mailman.zfn.uni-bremen.de/cgi-bin/mailman/listinfo/dftb-plus-user>>
> >
> >
> > _______________________________________________
> > DFTB-Plus-User mailing list
> > DFTB-Plus-User at mailman.zfn.uni-bremen.de
> <mailto:DFTB-Plus-User at mailman.zfn.uni-bremen.de>
> >
> https://mailman.zfn.uni-bremen.de/cgi-bin/mailman/listinfo/dftb-plus-user
> <https://mailman.zfn.uni-bremen.de/cgi-bin/mailman/listinfo/dftb-plus-user>
>
>
> --
> Dr. Bálint Aradi
> Bremen Center for Computational Materials Science, University of Bremen
> http://www.bccms.uni-bremen.de/cms/people/b-aradi/
> <http://www.bccms.uni-bremen.de/cms/people/b-aradi/>
>
> _______________________________________________
> DFTB-Plus-User mailing list
> DFTB-Plus-User at mailman.zfn.uni-bremen.de
> <mailto:DFTB-Plus-User at mailman.zfn.uni-bremen.de>
> https://mailman.zfn.uni-bremen.de/cgi-bin/mailman/listinfo/dftb-plus-user
> <https://mailman.zfn.uni-bremen.de/cgi-bin/mailman/listinfo/dftb-plus-user>
>
>
> _______________________________________________
> DFTB-Plus-User mailing list
> DFTB-Plus-User at mailman.zfn.uni-bremen.de
> https://mailman.zfn.uni-bremen.de/cgi-bin/mailman/listinfo/dftb-plus-user
--
Dr. Bálint Aradi
Bremen Center for Computational Materials Science, University of Bremen
http://www.bccms.uni-bremen.de/cms/people/b-aradi/
-------------- next part --------------
A non-text attachment was scrubbed...
Name: OpenPGP_signature
Type: application/pgp-signature
Size: 840 bytes
Desc: OpenPGP digital signature
URL: <http://mailman.zfn.uni-bremen.de/pipermail/dftb-plus-user/attachments/20220604/2b438f94/attachment.sig>
More information about the DFTB-Plus-User
mailing list