[DFTB-Plus-User] Mismatch in repulsive potential for Ga-C and C-Ga in hyb set

Hofer, Thomas T.Hofer at uibk.ac.at
Wed May 4 10:46:39 CEST 2022 

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/>
>
>     _______________________________________________
>     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>
>
>
> _______________________________________________
> 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


--
Dr. Bálint Aradi
Bremen Center for Computational Materials Science, University of Bremen
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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.zfn.uni-bremen.de/pipermail/dftb-plus-user/attachments/20220504/54947db9/attachment.htm>

More information about the DFTB-Plus-User mailing list