[DFTB-Plus-User] ​Re: Failure in diagonalisation routine ZHEEVR for Li-S systems

Wu, Qisheng qisheng_wu at brown.edu
Wed Nov 16 21:30:51 CET 2022


Dear Martin and Balint,

An error also occurred when I tried to conduct the same calculations using
the standalone DFTB+ code available in MS (r4729). I used the script
*RunDFTB.sh* provided by MS to run the calculation. But that worked when I
did the calculation directly within the MS user interface. It's strange.
Below is the error information:

-----------------
Operation failed!
ppotrf in scalafx_ppotrf_dcomplex
Info: 60
Operation failed!
ppotrf in scalafx_ppotrf_dcomplex
Info: 60
Operation failed!
ppotrf in scalafx_ppotrf_dcomplex
Info: 60
Operation failed!
ppotrf in scalafx_ppotrf_dcomplex
Info: 60
-------------------

Attached please see again the input (dftb_in.hsd) and output file
(dftb_in.dftb).


Best regards,
Qisheng Wu



> Dear Balint,
>
> Many thanks. But what do you mean by "decreasing/increasing the basis
> function extend of the big/small element"? Sorry, I do not understand this
> part. What exactly should I do about this?
>
> Best regards,
> Qisheng Wu
>
>
>
> > Message: 1
> > Date: Wed, 16 Nov 2022 08:32:58 +0100
> > From: Bálint Aradi <aradi at uni-bremen.de>
> > To: dftb-plus-user at mailman.zfn.uni-bremen.de
> > Subject: Re: [DFTB-Plus-User]  Re: Failure in diagonalisation
> >         routine ZHEEVR for Li-S systems
> > Message-ID: <93b0eabb-b13f-ad86-f006-14cc51038777 at uni-bremen.de>
> > Content-Type: text/plain; charset="utf-8"; Format="flowed"
> >
> > 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
> > >      > <dftb-plus-user-request at mailman.zfn.uni-bremen.de
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> > dftb-plus-user-request at mailman.zfn.uni-bremen.de <mailto:
> > dftb-plus-user-request at mailman.zfn.uni-bremen.de>>>> wrote:
> > >      >
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> > >      >
> > >      >     Today's Topics:
> > >      >
> > >      >         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>>
> > >      >     <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 <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:
> > >     <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>>
> > >      >     <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 <mailto:
> > 8d8e2f4f-6368-a719-f281-d263b107c054 at uni-bremen.de>>>>
> > >      >     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
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> > 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><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>
> > <
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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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> > >      >     End of DFTB-Plus-User Digest, Vol 99, Issue 6
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> > >      >
> > >      > _______________________________________________
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> > <
> 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/>
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> > >     ------------------------------
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> > >     End of DFTB-Plus-User Digest, Vol 99, Issue 11
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> > > _______________________________________________
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> https://mailman.zfn.uni-bremen.de/cgi-bin/mailman/listinfo/dftb-plus-user
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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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