[DFTB-Plus-User] Failure in diagonalisation routine ZHEEVR for Li-S systems
Wu, Qisheng
qisheng_wu at brown.edu
Wed Nov 16 20:33:22 CET 2022
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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> > > 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>>
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> DFTB-Plus-User at mailman.zfn.uni-bremen.de <mailto:
> DFTB-Plus-User at mailman.zfn.uni-bremen.de>>>
> > > >
> > >
> >
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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/
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