[DFTB-Plus-User] DFTB-Plus-User Digest, Vol 78, Issue 1

Wed Feb 3 15:19:24 CET 2021

Dear Prof.  Cristián G. Sánchez

Thank you for your email. The code worked very fine and thanks for your
suggestion regarding the usage of ASE. I will explore it.

Thank you very much.

Sincerely
Raghav

On Tue, Feb 2, 2021 at 2:15 PM <
dftb-plus-user-request at mailman.zfn.uni-bremen.de> wrote:

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> Today's Topics:
>
>    1. Re: Bond length plot in Ehrenfest dynamics (Cristian Sanchez)
>    2. Re: Command not found : setupgeom (Bálint Aradi)
>    3. issues on waveplot (toufik esssakhri)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Mon, 1 Feb 2021 13:00:51 -0300
> From: Cristian Sanchez <cristian.g.sanchez at gmail.com>
> To: User list for DFTB+ related questions
>         <dftb-plus-user at mailman.zfn.uni-bremen.de>
> Subject: Re: [DFTB-Plus-User] Bond length plot in Ehrenfest dynamics
> Message-ID: <E7921BEB-EE24-4AD2-815A-1097CF81CC82 at gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Dear Raghavendra,
>
> When preparing the recipe I used quite an ugly old school UNIX hack:
>
> grep MD tdcoords.xyz |awk '{print $5}' > time
> grep -A 6 MD tdcoords.xyz| awk '/MD/{if (NR!=1)print "";next}{printf
> $0}END{print "";}'  | awk '{ print sqrt(($9 -$2 )^2+($10-$3 )^2+($11-$4
> )^2) }' > C1.dat
> grep -A 6 MD tdcoords.xyz| awk '/MD/{if (NR!=1)print "";next}{printf
> $0}END{print "";}'  | awk '{ print sqrt(($16-$9
> )^2+($17-$10)^2+($18-$11)^2) }' > C2.dat
> grep -A 6 MD tdcoords.xyz| awk '/MD/{if (NR!=1)print "";next}{printf
> $0}END{print "";}'  | awk '{ print
> sqrt(($23-$16)^2+($24-$17)^2+($25-$18)^2) }' > C3.dat
> grep -A 6 MD tdcoords.xyz| awk '/MD/{if (NR!=1)print "";next}{printf
> $0}END{print "";}'  | awk '{ print
> sqrt(($30-$23)^2+($31-$24)^2+($32-$25)^2) }' > C4.dat
> grep -A 6 MD tdcoords.xyz| awk '/MD/{if (NR!=1)print "";next}{printf
> $0}END{print "";}'  | awk '{ print
> sqrt(($37-$30)^2+($38-$31)^2+($39-$32)^2) }' > C5.dat
> grep -A 6 MD tdcoords.xyz| awk '/MD/{if (NR!=1)print "";next}{printf
> $0}END{print "";}'  | awk '{ print sqrt(($2-$37)^2+($3-$38)^2+($4-$39)^2)
> }' > C6.dat
> pr -m -t  time C1.dat > C1b.dat
> pr -m -t  time C2.dat > C2b.dat
> pr -m -t  time C3.dat > C3b.dat
> pr -m -t  time C4.dat > C4b.dat
> pr -m -t  time C5.dat > C5b.dat
> pr -m -t  time C6.dat > C6b.dat
>
> It should produce the data files I used for the plot but is clearly not
> scalable. I understand that if you use the ASE modules in python you can
> read XYZ files and the processing should only require some a few lines.
>
> Best,
>
> Cristián
>
>
>
> Dr. Cristián G. Sánchez
>
> Investigador Principal
> Instituto Interdisciplinario de Ciencias Básicas (ICB)
> Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET)
>
> Profesor Asociado
> Facultad de Ciencias Exactas Físicas y Naturales (FCEN)
> Universidad Nacional de Cuyo (UNCuyo)
>
> Padre Jorge Contreras 1300, Parque General San Martín
> M5502JMA, Mendoza, Argentina
>
> http://www.cgsanchez.net/
> cristian.g.sanchez at gmail.com
> csanchez at mendoza-conicet.gob.ar
> --
>
> > On 28 Jan 2021, at 06:14, Raghavendra V <raghav011986 at gmail.com> wrote:
> >
> > Dear Friends,
> >
> > I am new to DFTB+ and I have been trying to repeat calculations given in
> the DFTB+ recipes. I tried to do the Ehrenfest Dynamics (
> https://dftbplus-recipes.readthedocs.io/en/latest/electronicdynamics/ehrenfest.html
> <
> https://dftbplus-recipes.readthedocs.io/en/latest/electronicdynamics/ehrenfest.html
> >)
> > and the calculation ran successfully. I would like to plot the graph
> given in the same page where the C-C bonds in benzene are plotted against
> time.
> >
> > I see that the "tdcoords.xyz <http://tdcoords.xyz/>" contain the
> molecular geoemtry at different times of the simulation. I'm not really
> sure how to extract the geometry for each time step and get the bond length
> of bond angle etc.
> >
> > I will be very thankful if someone could help me do this task.
> >
> > Kindly let me know if I am not clear.
> > Sincerely,
> >
> >  V. Raghavendra
> > Research Scholar
> > C/O Dr. V. Subramanian
> > Inorganic and Physical Chemistry Division
> > Central Leather Research Institute (CSIR-CLRI)
> > Adyar, Chennai - 600 020
> > Tamil Nadu, India
> >  http://clri.res.in/subramanian/index.html <
> http://clri.res.in/subramanian/group.html>
> >  Mobile - +91 9962 559 388
> > _______________________________________________
> > 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
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>
> ------------------------------
>
> Message: 2
> Date: Mon, 1 Feb 2021 22:39:28 +0100
> From: Bálint Aradi <aradi at uni-bremen.de>
> To: dftb-plus-user at mailman.zfn.uni-bremen.de
> Subject: Re: [DFTB-Plus-User] Command not found : setupgeom
> Message-ID: <41f0de0d-3ffe-fce5-a493-b12e130e7a21 at uni-bremen.de>
> Content-Type: text/plain; charset="utf-8"
>
> Dear Giverne Théo,
>
> As libNEGF only recently became available on Conda-forge, the last
> stable version of DFTB+ could not use it and consequently was built
> without transport and without the setupgeom tool. The conda version of
> the next stable release will very likely contain also the transport
> tools. Till then, as a workaround, please use the provided binaries or
> build the code from source, if MPI is needed.
>
> Best regards,
>
> Bálint
>
>
> On 29.01.21 12:31, Théo Giverne wrote:
> > ~~ edit ~~
> >
> > I have downloaded the executable form DFTB+ website
> > (https://dftbplus.org/download/dftb-stable) and I have found that under
> > prog/transporttools/ all the necessary files are here. But I have
> > install DFTB+ with Anaconda, and I checked the files in my dftb
> > environnement and it turns out anaconda doesn’t compile the transport
> > tools, actuallythe scripts are not even here…
> > Anyone has a solution ?
> >
> > thank you
> >
> > ~~ edit ~~
> >
> >> Le 29 janv. 2021 à 11:40, Théo Giverne <theo.giverne at etu.u-bordeaux.fr
> >> <mailto:theo.giverne at etu.u-bordeaux.fr>> a écrit :
> >>
> >> Dear users,
> >>
> >> I would like to simulate some transport and so I would like to use the
> >> setup geometry utility. I’m currently following the recipes about this
> >> subject, but when i want to run the exemple with the command
> >> /setupgeom/ i have a return « /command not found : setupgeom/ ».
> >> I use v20.2.1 and I have /dftbplus-tools/ installed.
> >>
> >> Please anyone know where /setupgeom/ tool is ?
> >>
> >> Sincerely,
> >>
> >> Giverne Théo
> >>
> >> +33 6 31 15 67 21
> >> theo.giverne at gmail.com <mailto:theo.giverne at gmail.com>
> >> theo.giverne at etu.u-bordeaux.fr <mailto:theo.giverne at etu.u-bordeaux.fr>
> >> 33000, Bordeaux, France
> >>
> >> Bordeaux University Institute of Technology — Materials Science and
> >> Engineering web page <https://www.iut.u-bordeaux.fr/sgm/>
> >>
> >
> >
> > _______________________________________________
> > 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
> >
>
>
> --
> 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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> ------------------------------
>
> Message: 3
> Date: Tue, 2 Feb 2021 08:45:28 +0000
> From: toufik esssakhri <tousak at hotmail.fr>
> To: "dftb-plus-user at mailman.zfn.uni-bremen.de"
>         <dftb-plus-user at mailman.zfn.uni-bremen.de>
> Subject: [DFTB-Plus-User] issues on waveplot
> Message-ID:
>         <
> AM4PR0302MB281976F5F77C466CFA551AF1ADB59 at AM4PR0302MB2819.eurprd03.prod.outlook.com
> >
>
> Content-Type: text/plain; charset="windows-1252"
>
>
> Dear all,
>
>
> I wanted to produce the spin density using waveplot, I got a Warning and I
> can’t get the cube file.
>
> ____________________
>
> WARNING!
>
> -> The following 7 node(s) have been ignored by the parser:
>
> (1)
>
> Path: waveplot/Basis/B
>
> Line: 63-103 (File: wfc.matsci-0-3.hsd)
>
> (2)
>
> Path: waveplot/Basis/N
>
> Line: 105-145 (File: wfc.matsci-0-3.hsd)
>
> (3)
>
> Path: waveplot/Basis/Na
>
> Line: 189-229 (File: wfc.matsci-0-3.hsd)
>
> (4)
>
> Path: waveplot/Basis/Al
>
> Line: 231-290 (File: wfc.matsci-0-3.hsd)
>
> (5)
>
> Path: waveplot/Basis/Si
>
> Line: 292-351 (File: wfc.matsci-0-3.hsd)
>
> (6)
>
> Path: waveplot/Basis/P
>
> Line: 353-412 (File: wfc.matsci-0-3.hsd)
>
> (7)
>
> Path: waveplot/Basis/Cu
>
> Line: 484-552 (File: wfc.matsci-0-3.hsd)
>
> ____________________
>
>
> I am using matsci dataset:
>
>
> # Definition of the basis
>
> Basis {
>
> Resolution = 0.01
>
> <<+ "wfc.matsci-0-3.hsd"
>
> }
>
>
> Best regards,
>
> Toufik
>
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> ------------------------------
>
> End of DFTB-Plus-User Digest, Vol 78, Issue 1
> *********************************************
>
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