[DFTB-Plus-User] Re: Failure in diagonalisation routine ZHEEVR for Li-S systems
Bálint Aradi
aradi at uni-bremen.de
Wed Nov 16 08:32:58 CET 2022
Dear Qisheng Wu,
Probably your system is very much on the edge of diagonalizability (if
such a word exists...), and the two different DFTB+ versions use
different LAPACK implementation with slightly different diagonalizer /
Cholesky-decomposer numerics, leading to different results. When putting
very "big" and very "small" elements in a tightly packed solid, basis
dependence can become an issue. Usually, decreasing/increasing the basis
function extend of the big/small element can help to resolve the issue.
Best regards,
Bálint
On 14.11.22 17:34, Wu, Qisheng wrote:
> Dear Martin,
>
> Thanks a lot for the comments. Here are my replies:
>
> I checked the skf.aux file, it shows "NotOrbitalResolved".
>
> I believe the geometry optimizations in both standalone DFTB+ code and
> MS are working properly. The error actually occurred at the very initial
> step, so it has nothing to do with geometry optimizations. The error
> also occurred when doing single-point energy calculations.
>
> For the fitting, I followed the procedure reported in a previous work
> (https://doi.org/10.1021/acs.jpcc.8b01839
> <https://doi.org/10.1021/acs.jpcc.8b01839>) conducted in our group (Yue
> Qi group @ Brown Univ.), in which the parameters were fitted as an
> extension of the mio set with the MS parameterization tools. In that
> work, systematic validations were presented for the Li-containing
> systems, including Li metal, Li-containing inorganic crystals (LiH,
> Li2O, and Li2CO3), molecular species (LiOH, LiCH3, et al.), and some
> surface and interface systems. Those fitted parameters (both the
> electronic parameters of Li and the repulsive potentials) worked
> very well. At that time, there was no LIB 2019 yet. I do not want to
> make too many changes while trying to extend the parameterization set to
> include S and maybe also other elements.
>
> For band structure validations of li metal and Li2S bulk, please see the
> figure attached or through the following link:
> https://drive.google.com/file/d/1LSmYELMtIBQBlOlXgZjnACHUv208EnxU/view?usp=share_link <https://drive.google.com/file/d/1LSmYELMtIBQBlOlXgZjnACHUv208EnxU/view?usp=share_link>
>
> In my new fitting, the electronic parameters are slightly revised
> compared to what was reported in our previous work
> (https://doi.org/10.1021/acs.jpcc.8b01839
> <https://doi.org/10.1021/acs.jpcc.8b01839>), but you can see that the
> band structures near the Fermi level of Li metal are still well
> reproduced. The band structures of the valence bands of Li2S calculated
> with DFTB agree with Dmol3 calculations as well.
>
> I did not use dispersion correction while calculating the band
> structures with DFTB and Dmol3 in MS. I tested on dispersion correction
> (LJ, UFF parameters) while doing geometry optimizations with the
> standalone DFTB+ code, and found that it makes little difference.
>
> Thanks again for your time.
>
> Best regards,
> Qisheng Wu
>
>
> On Fri, Nov 11, 2022 at 5:05 AM
> <dftb-plus-user-request at mailman.zfn.uni-bremen.de
> <mailto:dftb-plus-user-request at mailman.zfn.uni-bremen.de>> wrote:
>
> -----------------------------
>
> Message: 2
> Date: Fri, 11 Nov 2022 10:04:42 +0000
> From: PERSSON Martin <Martin.PERSSON at 3ds.com
> <mailto:Martin.PERSSON at 3ds.com>>
> To: User list for DFTB+ related questions
> <dftb-plus-user at mailman.zfn.uni-bremen.de
> <mailto:dftb-plus-user at mailman.zfn.uni-bremen.de>>
> Subject: Re: [DFTB-Plus-User] Failure in diagonalisation routine
> ZHEEVR for Li-S systems
> Message-ID: <1c5596207e8348d49f887df843c9c81a at 3ds.com
> <mailto:1c5596207e8348d49f887df843c9c81a at 3ds.com>>
> Content-Type: text/plain; charset="utf-8"
>
> Dear Qisheng Wu,
>
> If you extended the MIO library “OrbitalResolvedScc” should be set
> to “No”. The MS DFTB+ parameterization tools ensure that these type
> of settings are consistent when you extend parameters. You can what
> settings should be used in the skf.aux file in the library.
>
> MS has its own drivers for Geometry optimization, Dynamics etc. so
> the optimizer likely takes a different path to the optimized geometry.
> Even though the MS 2020 version of DFTB+ is older it uses the same
> eigenvalue solvers. The only difference I noticed when updating was
> that we got slightly different geometries and dynamics results since
> the force evaluation has been updated, but those differences was
> very small.
>
> When you did the optimization did you fit the electronic settings
> for Li to the Li band structure using the scripted tools in MS?
> Have you checked the band structure for the Li2S and did you run
> with or without dispersion correction?
>
> Finally why did you extend the mio library? I think the “LIB 2019”
> library, containing Li-C-H-N-O-P-F, is available in MS 2020. It was
> mainly fitted and validated against small molecules so I can’t make
> promises about how it will perform for solids. But then so was mio.
>
> Best Regards,
> Martin PERSSON
> BIOVIA Scientific R&D Development Manager
>
> Dear Dr. Aradi,
>
> Thanks for your comment, but adding ShellResolvedScc = Yes does not
> solve the problem (DFTB+ 22.1).
>
> Adding OrbitalResolvedScc = Yes to simulation with DFTB+ 17.1 does
> not solve the problem as well.
>
> In terms of the version of DFTB+ in Materials Studio 2020, here is
> the reply from people who work for Dassault Systemes:
>
> "It is a modified version of the r4729 version of the DFTB+ code.
> It's from 2015. There is a few years gap in the updates of DFTB+
> since their rewrite of the code did not support all the features
> that were exposed in the MS version. The current release of MS has
> an up to date version of DFTB+."
>
> I will also ask them to see if they can help solve this problem.
> Thanks again.
>
> Best regards,
> Qisheng Wu
>
>
> On Wed, Nov 9, 2022 at 4:52 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:
> The only difference I can see, is that you commented out
> OrbitalResolvedScc in your input (which was changed to ShellResolvedScc
> at some point). That would be important to add to get similar results as
> with MS.
>
> As for periodic versus non-periodic: The overlap of the basis functions
> is in the periodic case bigger, so if your system is on the edge of
> having a linearly dependent basis set, chances are bigger, that you get
> a problem in the periodic case.
>
> Cheers,
>
> Bálint
>
>
> On 08.11.22 15:37, Wu, Qisheng wrote:
> > Dear Dr. Bálint Aradi,
> >
> > Many thanks for the quick reply. You are right that the S is
> supposed to
> > be with "d" as the maximal angular shell in the mio-set. I made the
> > change and re-run the geometry optimizations. Unfortunately, this
> does
> > not solve the problem. For the Li2S molecule, It turns out that
> it makes
> > very little difference in terms of Li-S bond length (2.005
> angstroms vs
> > 2.002 angstroms). But of course, "d" still should be used anyway.
> >
> > I have also looked at the input file generated within MS and
> attached it
> > to this email (Li2S_tetra.hsd). The version of DFTB+ in MS 2020
> might be
> > different (I do not know what version it is), and there are some
> > keywords that I did not previously use in my input. The Driver
> section
> > is also empty, whose possible reason is that MS uses its own
> driver to
> > conduct geometry optimizations (it's just my guess). After
> tailoring my
> > own inputs based on what I found in the input from MS (dftb_in.hsd as
> > attached), I was still not able to solve the problem.
> >
> > What I do not understand is that the calculation works for the Li2S
> > molecule but not for the Li2S bulk. It's really puzzling. I hope this
> > issue could be fixed in the end.
> >
> > By the way, I have tested using different versions of DFTB+ (e.g.,
> > 17.1), and the same error showed up for geometry optimization of the
> > Li2S bulk, but not for the Li2S molecule.
> >
> > Thanks again.
> >
> > Best regards,
> > Qisheng Wu
> >
> >
> > On Tue, Nov 8, 2022 at 6:00 AM
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> > Today's Topics:
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> > 1. Re: Failure in diagonalisation routine ZHEEVR for Li-S
> > systems (Bálint Aradi)
> >
> >
> >
> ----------------------------------------------------------------------
> >
> > Message: 1
> > Date: Mon, 7 Nov 2022 16:12:28 +0100
> > From: 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>> <mailto:aradi at uni-bremen.de
> <mailto:aradi at uni-bremen.de><mailto:aradi at uni-bremen.de
> <mailto:aradi at uni-bremen.de>>>>
> > To: 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>>
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> > Subject: Re: [DFTB-Plus-User] Failure in diagonalisation routine
> > ZHEEVR for Li-S systems
> > Message-ID:
> <8d8e2f4f-6368-a719-f281-d263b107c054 at uni-bremen.de
> <mailto:8d8e2f4f-6368-a719-f281-d263b107c054 at uni-bremen.de><mailto:8d8e2f4f-6368-a719-f281-d263b107c054 at uni-bremen.de <mailto:8d8e2f4f-6368-a719-f281-d263b107c054 at uni-bremen.de>>
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> > Content-Type: text/plain; charset="utf-8"; Format="flowed"
> >
> > Dear Qisheng Wu,
> >
> > The DFTB+ in MS is identical to the open source version,
> therefore,
> > I am
> > a little bit puzzled, why you get different behavior for the bulk
> > calculation.
> >
> > Check, whether the dftb+ input file generated by MS is
> equivalent to
> > yours. My guess would be the maximal angular momenta.
> Actually, in the
> > mio-set the S is supposed to be with "d" as maximal angular
> shell (and
> > you use "p" instead). Also probably MS uses only "s" for the
> Li and not
> > "p" as in your input?
> >
> > Best regards,
> >
> > Bálint
> >
> >
> > On 07.11.22 15:47, Wu, Qisheng wrote:
> > > Dear DFTB+ developers,
> > >
> > > I am currently working on a Li-S system and fitted Li-Li
> and L-S
> > > parameters as an extension of the /mio/ set using the DFTB+
> > module and
> > > parameterization tools as implemented in the Materials Studio
> > software.
> > > S-S is directly taken from the /mio/ set. To verify the
> > parameters, I
> > > first conducted geometry optimizations of Li2S bulk and Li2S
> > molecule,
> > > which ran very well through the DFTB+ module in the
> Materials Studio
> > > software.
> > >
> > > Then I switched to DFTB+ 22.1 code (precompiled executable for
> > x86_64),
> > > which I will need to use for large-scale simulations. The
> geometry
> > > optimization of the Li2S molecule worked very well, but
> that of
> > the L2S
> > > bulk failed, with the error information:
> > >
> > > "-> Failure in diagonalisation routine ZHEEVR, unable to
> complete
> > > Cholesky factorization of B 85"
> > >
> > > I checked some previous messages in this email list, and
> am aware
> > that
> > > this could be due to unphysical geometry. But I do not
> think this
> > is the
> > > case for my simulation since it worked well at least for
> the Li2S
> > molecule.
> > >
> > > I appreciate it if anyone can help address this issue,
> which will be
> > > very helpful for me to continue my research project. I
> have put
> > all the
> > > inputs (dftb_in.hsd), outputs (out), and parameter files
> (*skf)
> > in my
> > > google drive. Feel free to download that using the link below:
> > >
> > >
> >
> https://drive.google.com/file/d/1LL8GHzfI8pH4Nlr2ZJ8IN4q3xTVpQmy1/view?usp=share_link <https://drive.google.com/file/d/1LL8GHzfI8pH4Nlr2ZJ8IN4q3xTVpQmy1/view?usp=share_link> <https://drive.google.com/file/d/1LL8GHzfI8pH4Nlr2ZJ8IN4q3xTVpQmy1/view?usp=share_link <https://drive.google.com/file/d/1LL8GHzfI8pH4Nlr2ZJ8IN4q3xTVpQmy1/view?usp=share_link>> <https://drive.google.com/file/d/1LL8GHzfI8pH4Nlr2ZJ8IN4q3xTVpQmy1/view?usp=share_link <https://drive.google.com/file/d/1LL8GHzfI8pH4Nlr2ZJ8IN4q3xTVpQmy1/view?usp=share_link> <https://drive.google.com/file/d/1LL8GHzfI8pH4Nlr2ZJ8IN4q3xTVpQmy1/view?usp=share_link <https://drive.google.com/file/d/1LL8GHzfI8pH4Nlr2ZJ8IN4q3xTVpQmy1/view?usp=share_link>>>
> > >
> > > Best regards,
> > > Qisheng Wu
> > >
> > > _______________________________________________
> > > 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>>
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> > >
> >
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> >
> > --
> > 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/>>
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> --
> 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/>
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--
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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