[DFTB-Plus-User] Optimizing polyyne chain in DFTB+ for low BLA range: Need guidance

Wed Jun 14 20:27:28 CEST 2023

Hello, ben
Thank you for your prompt response and valuable insights regarding the
optimization of BLA in polyenes using DFTB+. I appreciate your guidance and
the information you provided.

Regarding the specific details of my calculations, I am pleased to attach
the input file dftb_in.hsd with you. for the Electronic temperature, I find
this value in the output file :              0.950520E-03 H
 0.258650E-01 eV

The numerical difference, often referred to as the error or deviation, can
be calculated using the formula:  Error = |Calculated BLA - Reference BLA|

Thank you again for your assistance and expertise in this matter. Your
insights have been invaluable in guiding my research, and I appreciate your
continued support.

Best regards,

Khadidja

On Wed, Jun 14, 2023, 17:41 Benjamin Hourahine <
benjamin.hourahine at strath.ac.uk> wrote:

> Hello Khadidja,
>
> In the case of polyenes (i.e. the alternating double-single kind), LDA/GGA
> and DFTB substantially underestimate BLA, but the hybrids or +U approach
> increase this into the experimental ranges.
>
> For polyyenes (tripple-single), I haven't tested them. But a test for a
> pure C chain in a periodic geometry with DFTB2 mio, and starting from a
> symmetry broken geometry, gives bond ratios of 0.48:0.52. This is at low
> temperatures and has a narrow band gap. Starting from the symmetric BA, I
> get a slightly higher energy structure (10 meV / C atom) with a BLA of 0.
>
> Which geometry optimizer, electronic temperature and parameter sets are
> you using, and numerically how does the BLA compare to the reference values?
>
> Regards
>
> Ben
>
> ------------------------------
> *From:* DFTB-Plus-User <dftb-plus-user-bounces at mailman.zfn.uni-bremen.de>
> on behalf of Khadidja Chaib Edderraa <k.chaibedderraa at univ-chlef.dz>
> *Sent:* 13 June 2023 17:46
> *To:* User list for DFTB+ related questions <
> dftb-plus-user at mailman.zfn.uni-bremen.de>
> *Subject:* Re: [DFTB-Plus-User] Optimizing polyyne chain in DFTB+ for low
> BLA range: Need guidance
>
> Hello,
>  Regarding the use of corrections (dftb+U and hybrid functional ) to dftb+
> in order to obtain results closer to the experimental or previous dft
> calculations, I used the two corrections that you provided me as a
> solution, but the obtained results always show an increase in BLA, which is
> already considered greater than what it should be compared to the results
> obtained using dft. I want to know if dftb+ gives large values to the BLA
> ?, or are there other controls that should be added to control giving
> smaller values to the BLA (0.01 Å- 0.04 Å) ?
> Can I use external slater koster files that are compatible with the
> polyyne chains I'm studying? I hope you can help me with this because I
> could not proceed with this research especially when I tried to compare my
> results with previous dft results.
> Thank you for your time.
>
> Regard,
>
> On Mon, Jun 5, 2023, 14:27 Benjamin Hourahine <
> benjamin.hourahine at strath.ac.uk> wrote:
>
> Hello Khadidja,
>
> There are some examples in the test set, as well as a description in the
> manual.
>
> The current release (22.2) supports hybrid functionals for molecular
> systems, and requires the ob2 parameter set. You will need to add to the
> hamiltonian block:
>
> Hamiltonian = DFTB {
>   SCC = Yes
>   RangeSeparated = LC {
>     Screening = MatrixBased {}
>   }
> .
> .
> .
> }
>
> The alternative of the +U methods do not require a specific parameter set
> and is available for periodic and molecular systems. The value of U is
> somewhat empirical, there is an argument that it should be a fraction of
> the atomic Hubbard U values depending on which functional is being used (
> https://doi.org/10.1021/JP070173B)
>
> Hamiltonian = DFTB {
>   SCC = Yes
> OrbitalPotential = {
>    Functional = {FLL}
>    C = {
>      Shells = {1 2} # sp block on the C
>      UJ = 0.18235
>    }
>    #Functional = {pSIC}
>    #C = {
>    #  Shells = {1 2} # sp block on the C
>    #  UJ = 0.1
>    #}
>   }
> .
> .
> .
> }
>
> For polyacetylene, the above values gave reasonable BLA.
>
> Regards
>
> Ben
>
> Dr. B. Hourahine
> Senior Lecturer and Director of Student Support
> Department of Physics, SUPA
> University of Strathclyde, John Anderson Building,
> 107 Rottenrow, Glasgow G4 0NG, UK.
> +44 141 548 2325, benjamin.hourahine at strath.ac.uk
>
> [image: University of Strathclyde]
>
> *THE QUEEN’S ANNIVERSARY PRIZES*
> *2019 & 2021*
> For Higher and Further Education
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> The Times & The Sunday Times
>
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> Scotland, number SC015263.
> Please consider the environment before printing this e-mail.
> ------------------------------
> *From:* DFTB-Plus-User <dftb-plus-user-bounces at mailman.zfn.uni-bremen.de>
> on behalf of Hafid KHALFOUN <h.khalfoun at univ-chlef.dz>
> *Sent:* 02 June 2023 23:27
> *To:* User list for DFTB+ related questions <
> dftb-plus-user at mailman.zfn.uni-bremen.de>
> *Subject:* Re: [DFTB-Plus-User] Optimizing polyyne chain in DFTB+ for low
> BLA range: Need guidance
>
> Dear Benjamin, thank you for your response .
> How do we include these corrections ?  On the skf files ? on the
> dftb_in.hsd file by adding a new block ?
> How do we build this hybrid functional ?
> Can you be more explicit , please ? Can I find some issues on this topic ?
> thanks
>
>
>
>
> Le ven. 2 juin 2023 à 16:01, Benjamin Hourahine <
> benjamin.hourahine at strath.ac.uk> a écrit :
>
> Hello Khadidja,
>
> BLA is fairly sensitive to functional in DFT, with mean-field functionals
> (LDA/GGA) often getting this incorrect. DFTB2 or 3 has the same issues, so
> as with DFT, either hybrid functionals or +U corrections may be needed.
>
> The BLA for polyacetylene is definitely closer to the experimental values
> with these corrections. Hybrids should be used with ob2, while +U can be
> applied on top of the mio set.
>
> Regards
>
> Ben
>
> Dr. B. Hourahin
> Senior Lecturer and Director of Student Support
> Department of Physics, SUPA
> University of Strathclyde, John Anderson Building,
> 107 Rottenrow, Glasgow G4 0NG, UK.
> +44 141 548 2325, benjamin.hourahine at strath.ac.uk
>
> [image: University of Strathclyde]
>
> *THE QUEEN’S ANNIVERSARY PRIZES*
> *2019 & 2021*
> For Higher and Further Education
>
> *UNIVERSITY OF THE YEAR*
> *2012 & 2019*
> Times Higher Education
>
> *SCOTTISH UNIVERSITY OF THE YEAR*
> *2020*
> The Times & The Sunday Times
>
> The University of Strathclyde is a charitable body, registered in
> Scotland, number SC015263.
> Please consider the environment before printing this e-mail.
> ------------------------------
> *From:* DFTB-Plus-User <dftb-plus-user-bounces at mailman.zfn.uni-bremen.de>
> on behalf of Khadidja Chaib Edderraa <k.chaibedderraa at univ-chlef.dz>
> *Sent:* 02 June 2023 13:29
> *To:* dftb-plus-user at mailman.zfn.uni-bremen.de <
> dftb-plus-user at mailman.zfn.uni-bremen.de>
> *Subject:* Re: [DFTB-Plus-User] Optimizing polyyne chain in DFTB+ for low
> BLA range: Need guidance
>
> CAUTION: This email originated outside the University. Check before
> clicking links or attachments.
> Hello,
> I am writing to you to provide further details regarding the structure I
> used before optimization for the chain. The structural parameters I
> employed were d1=1.51 Å and d2=1.22 Å. However, after performing the
> relaxation, I obtained a BLA value of approximately 0.11 Å, which is
> significantly larger than the range predicted by DFT (0.01-0.05 Å).
>
> On Fri, Jun 2, 2023, 12:10 Khadidja Chaib Edderraa <
> k.chaibedderraa at univ-chlef.dz> wrote:
>
> Dear ,
>
> I hope this email finds you well. I am currently working on optimizing a
> polyyne chain using DFTB+ and aiming to achieve a low range of bond length
> alternation (BLA) in my system. After exploring the available resources, I
> believe your expertise in DFTB+ could provide valuable insights and
> guidance for my research.
>
> To provide some context, my research focuses on  ensuring that the
> molecular structure represents the most stable configuration and optimizing
> the polyyne chain is crucial for achieving BLA values  that align closely
> with experimental and other simulation data.
>
> The specific details of the polyyne chain I'm studying are as follows:
> - Number of carbon atoms: 2 carbon
> - Parameterisation data (Slater-Koster files)  used to perform
> calculations : 3ob, mio, ob2, matsi
> - Geometry optimization:  using  conjugate gradient algorithm but have not
> obtained the desired results.
>
> My main questions are as follows:
> 1. What are the recommended optimization settings or parameters for a
> polyyne chain in DFTB+ to achieve a low BLA range?
> 2. Are there any specific convergence criteria that I should consider
> during the optimization process?
> 3. Are there any DFTB+ features or functionalities that could be
> particularly useful for optimizing polyyne chains and reducing the BLA
> range?
>
> Thank you very much, and I look forward to your response.
>
> Sincerely,
> Khadidja
> k.chaibedderraa at univ-chlef.dz
>
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