[DFTB-Plus-User] Failure in diagonalisation routine ZHEEVR for Li-S systems
Bálint Aradi
aradi at uni-bremen.de
Thu Nov 17 08:51:10 CET 2022
Dear Qisheng Wu,
what I meant is, that if you generate the parametrization yourself, you
have control over the extent of the atomic orbitals via the wave
function compression radius. Setting it to a low value, will compress
the atomic orbitals and decrease their extent, while a high value
results in more delocalized atomic orbitals. Setting the wave function
compression radius for Li higher (compressing it less) may make the
diagonalization of closely packed LiS structures more robust.
Best regards,
Bálint
On 16.11.22 20:33, Wu, Qisheng wrote:
> 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 <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>
> 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
> <mailto: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>
> > <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> <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>
> > <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>
> > <mailto: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>
> > <mailto: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>
> > <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: <1c5596207e8348d49f887df843c9c81a at 3ds.com
> <mailto:1c5596207e8348d49f887df843c9c81a at 3ds.com>
> > <mailto: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>><mailto: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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> > >
> > > 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>><mailto:aradi at uni-bremen.de
> <mailto:aradi at uni-bremen.de>
> > <mailto:aradi at uni-bremen.de <mailto:aradi at uni-bremen.de>>>
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> > <mailto:aradi at uni-bremen.de <mailto:aradi at uni-bremen.de>>>>>
> > > To: 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>
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> > >
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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>>> <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>><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
> <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> <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>> <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> <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/>
> > <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/>
> > <http://www.bccms.uni-bremen.de/cms/people/b-aradi/
> <http://www.bccms.uni-bremen.de/cms/people/b-aradi/>>>
> > >
> > >
> > > -------------- next part --------------
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> > >
> > > ------------------------------
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> > > Subject: Digest Footer
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> > > DFTB-Plus-User mailing list
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> <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>
> > <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>>>>
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> > >
> > >
> > > ------------------------------
> > >
> > > End of DFTB-Plus-User Digest, Vol 99, Issue 6
> > > *********************************************
> > >
> > >
> > > _______________________________________________
> > > DFTB-Plus-User mailing list
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> <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>>>
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> >
> 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> <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/>
> > <http://www.bccms.uni-bremen.de/cms/people/b-aradi/
> <http://www.bccms.uni-bremen.de/cms/people/b-aradi/>>
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> > Subject: Digest Footer
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> > End of DFTB-Plus-User Digest, Vol 99, Issue 11
> > **********************************************
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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/>
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> ------------------------------
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> End of DFTB-Plus-User Digest, Vol 99, Issue 15
> **********************************************
>
--
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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