[DFTB-Plus-User] R: R: R: UV-Vis Calculations and in error (NrOfExcitations)
Thomas Niehaus
thomas.niehaus at univ-lyon1.fr
Mon Feb 20 10:41:05 CET 2023
Dear Daniele,
the input and output file you sent me are inconsistent. The input file has
Temperature [K] = 0.0
while your output file has
Electronic temperature: 0.950045E-03 H
I was able to (roughly) reproduce the output by setting this
temperature. But with temperature you have fractional filling. Setting
T=0 K does not converge for me.
Can you send a consistent set of input/output files that show the
integer occupations in band.out? We can start to find the origin of the
problem from there.
My current guess is that your structure is metallic. Can you converge
the SCF at the PBE/DFT level (with non-zero band gap)? If this is not
the case then also DFTB will have a hard time.
Best regards
Thomas
On 2/16/23 4:14 PM, daniele.veclani at isof.cnr.it wrote:
>
> Dear Thomas,
>
> “Can you please send the geometry and input file for this job?”
>
> Yes attached
>
> Sure, but why do you set 'Charge = -3' if the total charge is +3?
>
> Sorry, in the previous mail I ported the wrong charges. The correct
> one are
>
> Protein -2;
>
> ligand -1;
>
> tot -3
>
> As just set in the input file (attached protein_ligand).
>
> “I can not reproduce this. For me the
> recipes_DFTB+/linresp/macromolecule job runs smooth with dftb+ 22.2 (I
> don't expect dftb+21.2 to be any different).”
>
> I am also attaching (tutorial) files related to the error that I get
> when I ran the tutorial. Maybe some error during the installation of
> the software?
>
> Thanks for your help
>
> Best,
>
> Daniele.
>
> *Da:*DFTB-Plus-User <dftb-plus-user-bounces at mailman.zfn.uni-bremen.de>
> *Per conto di *Thomas Niehaus
> *Inviato:* giovedì 16 febbraio 2023 11:12
> *A:* dftb-plus-user at mailman.zfn.uni-bremen.de
> *Oggetto:* Re: [DFTB-Plus-User] R: R: UV-Vis Calculations and in error
> (NrOfExcitations)
>
> Dear Daniele,
>
> On 2/16/23 9:58 AM, daniele.veclani at isof.cnr.it
> <mailto:daniele.veclani at isof.cnr.it> wrote:
>
> Dear Thomas,
>
> “when you say the system was well optimized, did you check the
> state occupations at the final structure (-> band.out)?”
>
> Yes, I check the state occupations at the final structure
> (band.out) and no fractional occupations was observed.
>
> I report below a fragment of the band.out file corresponding to
> the HOMO-LUMO gap:
>
> “ 1884 -4.784 2.00000
>
> 1885 -4.677 2.00000
>
> 1886 -4.581 2.00000
>
> 1887 -4.314 2.00000
>
> 1888 -2.723 0.00000
>
> 1889 -2.124 0.00000
>
> 1890 -1.949 0.00000”
>
> Can you please send the geometry and input file for this job?
>
> Is your system zwitterionic, are the ligands maybe charged....
>
> Yes, protein have a charge of +4 while ligand have a -1 charge
> (total charge +3). I have to respect these charges because I have
> to study the system at a given pH.
>
> Sure, but why do you set 'Charge = -3' if the total charge is +3?
>
> Did you run the tutorial with the geometry and input file for that
> tutorial?
>
> Yes, I ran the geometry and input file found in
> recipes_DFTB+/linresp/macromolecule, however I obtain then same error.
>
> I use a 21.2 version of DFTB+ software.
>
> I can not reproduce this. For me the
> recipes_DFTB+/linresp/macromolecule job runs smooth with dftb+ 22.2 (I
> don't expect dftb+21.2 to be any different).
>
> Best Thomas
>
> Best,
>
> Daniele.
>
> *Da:*DFTB-Plus-User
> <dftb-plus-user-bounces at mailman.zfn.uni-bremen.de>
> <mailto:dftb-plus-user-bounces at mailman.zfn.uni-bremen.de> *Per
> conto di *Thomas Niehaus
> *Inviato:* mercoledì 15 febbraio 2023 17:27
> *A:* dftb-plus-user at mailman.zfn.uni-bremen.de
> <mailto:dftb-plus-user at mailman.zfn.uni-bremen.de>
> *Oggetto:* Re: [DFTB-Plus-User] R: UV-Vis Calculations and in
> error (NrOfExcitations)
>
> Dear Daniele,
>
> when you say the system was well optimized, did you check the
> state occupations at the final structure (-> band.out)? Is your
> system zwitterionic, are the ligands maybe charged....
>
> Did you run the tutorial with the geometry and input file for that
> tutorial? I don't understand what you mean with relative geometry.
>
> Best Thomas
>
> On 2/15/23 5:03 PM, daniele.veclani at isof.cnr.it
> <mailto:daniele.veclani at isof.cnr.it> wrote:
>
> Dear Thomas,
>
> first of all thanks for your reply, no my system is a protein
> fragment + ligand, and this system was well optimized before
> the UV-vis calculation.I don't understand where the metallic
> character can come from. However I get the same error even if
> I run the tutorial input (with relative geometry) found in the
> DTFB+ recipes (recipes_DFTB+/linresp/macromolecule).
>
> And I don't understand why also the tutorial calculation crashes.
>
> Do you have any suggestion?
>
> Best regards,
>
> Daniele.
>
> *Da:*DFTB-Plus-User
> <dftb-plus-user-bounces at mailman.zfn.uni-bremen.de>
> <mailto:dftb-plus-user-bounces at mailman.zfn.uni-bremen.de> *Per
> conto di *Thomas Niehaus
> *Inviato:* mercoledì 15 febbraio 2023 16:56
> *A:* dftb-plus-user at mailman.zfn.uni-bremen.de
> <mailto:dftb-plus-user at mailman.zfn.uni-bremen.de>
> *Oggetto:* Re: [DFTB-Plus-User] UV-Vis Calculations and in
> error (NrOfExcitations)
>
> Dear Daniele,
>
> it seems that your system is metallic. There are several
> fractional occupations. This means that the response matrix to
> diagonalize becomes gigantic and that there are clusters of
> near zero excitation energies which the iterative eigensolver
> can not separate.
>
> I would suggest to identify the origin of the metallic
> behaviour. Is the structure chemically sound?
>
> Best regards
>
> Thomas
>
>
>
>
>
>
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> --
>
> Prof. Dr. Thomas Niehaus
>
> Institut Lumière Matière
>
> UMR5306 CNRS
>
> Université Claude Bernard Lyon 1
>
> Domaine Scientifique de La Doua
>
> 10 rue Ada Byron
>
> 69622 Villeurbanne CEDEX, France
>
> --
>
> Office: Brillouin building, 4th floor, room 006
>
> Tel: +33 472 431 571
>
> Home page:http://ilm-perso.univ-lyon1.fr/~tniehaus
>
> Lab:http://ilm.univ-lyon1.fr
>
>
>
>
>
> _______________________________________________
>
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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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>
> --
> Prof. Dr. Thomas Niehaus
> Institut Lumière Matière
> UMR5306 CNRS
> Université Claude Bernard Lyon 1
> Domaine Scientifique de La Doua
> 10 rue Ada Byron
> 69622 Villeurbanne CEDEX, France
> --
> Office: Brillouin building, 4th floor, room 006
> Tel: +33 472 431 571
> Home page:http://ilm-perso.univ-lyon1.fr/~tniehaus
> Lab:http://ilm.univ-lyon1.fr
>
>
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--
Prof. Dr. Thomas Niehaus
Institut Lumière Matière
UMR5306 CNRS
Université Claude Bernard Lyon 1
Domaine Scientifique de La Doua
10 rue Ada Byron
69622 Villeurbanne CEDEX, France
--
Office: Brillouin building, 4th floor, room 006
Tel: +33 472 431 571
Home page: http://ilm-perso.univ-lyon1.fr/~tniehaus
Lab: http://ilm.univ-lyon1.fr
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