[DFTB-Plus-User] Re: Failure in diagonalisation routine ZHEEVR for Li-S systems
Wu, Qisheng
qisheng_wu at brown.edu
Mon Nov 14 17:34:52 CET 2022
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) 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
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), 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> wrote:
> -----------------------------
>
> Message: 2
> Date: Fri, 11 Nov 2022 10:04:42 +0000
> From: PERSSON Martin <Martin.PERSSON at 3ds.com>
> To: User list for DFTB+ related questions
> <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>
> 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>> 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<mailto:
> dftb-plus-user-request at mailman.zfn.uni-bremen.de>
> > <mailto:dftb-plus-user-request at mailman.zfn.uni-bremen.de<mailto:
> dftb-plus-user-request at mailman.zfn.uni-bremen.de>>> wrote:
> >
> > Send DFTB-Plus-User mailing list submissions 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>>
> >
> > To subscribe or unsubscribe via the World Wide Web, visit
> >
> 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
> >
> >
> > or, via email, send a message with subject or body 'help' to
> > dftb-plus-user-request at mailman.zfn.uni-bremen.de<mailto:
> dftb-plus-user-request at mailman.zfn.uni-bremen.de>
> > <mailto:dftb-plus-user-request at mailman.zfn.uni-bremen.de<mailto:
> dftb-plus-user-request at mailman.zfn.uni-bremen.de>>
> >
> > You can reach the person managing the list at
> > dftb-plus-user-owner at mailman.zfn.uni-bremen.de<mailto:
> dftb-plus-user-owner at mailman.zfn.uni-bremen.de>
> > <mailto:dftb-plus-user-owner at mailman.zfn.uni-bremen.de<mailto:
> dftb-plus-user-owner at mailman.zfn.uni-bremen.de>>
> >
> > When replying, please edit your Subject line so it is more specific
> > than "Re: Contents of DFTB-Plus-User digest..."
> >
> >
> > 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>>>
> > 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>>
> > 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>>>
> > 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
> >>
> > >
> > > 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>>
> > >
> >
> 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/>
> >
> >
> > -------------- 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/20221107/2202d405/attachment-0001.sig
> <
> http://mailman.zfn.uni-bremen.de/pipermail/dftb-plus-user/attachments/20221107/2202d405/attachment-0001.sig
> >>
> >
> > ------------------------------
> >
> > Subject: Digest Footer
> >
> > _______________________________________________
> > 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
> >
> >
> >
> > ------------------------------
> >
> > End of DFTB-Plus-User Digest, Vol 99, Issue 6
> > *********************************************
> >
> >
> > _______________________________________________
> > 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/
>
>
> This email and any attachments are intended solely for the use of the
> individual or entity to whom it is addressed and may be confidential and/or
> privileged.
>
> If you are not one of the named recipients or have received this email in
> error,
>
> (i) you should not read, disclose, or copy it,
>
> (ii) please notify sender of your receipt by reply email and delete this
> email and all attachments,
>
> (iii) Dassault Systèmes does not accept or assume any liability or
> responsibility for any use of or reliance on this email.
>
>
> Please be informed that your personal data are processed according to our
> data privacy policy as described on our website. Should you have any
> questions related to personal data protection, please contact 3DS Data
> Protection Officer https://www.3ds.com/privacy-policy/contact/
>
> -------------- next part --------------
> An HTML attachment was scrubbed...
> URL: <
> http://mailman.zfn.uni-bremen.de/pipermail/dftb-plus-user/attachments/20221111/606dfc0e/attachment.htm
> >
>
> ------------------------------
>
> Subject: Digest Footer
>
> _______________________________________________
> 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
>
>
> ------------------------------
>
> End of DFTB-Plus-User Digest, Vol 99, Issue 11
> **********************************************
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.zfn.uni-bremen.de/pipermail/dftb-plus-user/attachments/20221114/5ae20d33/attachment.htm>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: band_structures_comparison.jpg
Type: image/jpeg
Size: 94283 bytes
Desc: not available
URL: <http://mailman.zfn.uni-bremen.de/pipermail/dftb-plus-user/attachments/20221114/5ae20d33/attachment.jpg>
More information about the DFTB-Plus-User
mailing list