very useful, thanks
--- On Sun, 5/3/09, Marcos Verissimo Alves <marcos.veriss...@uclouvain.be>
wrote:
> From: Marcos Verissimo Alves <marcos.veriss...@uclouvain.be>
> Subject: Re: [SIESTA-L] single input to perform several tasks
> To: SIESTA-L@listserv.uam.es
> Date: Sunday, May 3, 2009, 3:36 PM
> Not really, but you can make a bash script to do this (find
> an example
> attached after he end of the explanation). What this script
> does is:
>
> 1) Creates three files to be included for the three
> different siesta runs,
> with the appropriate parameters for each calculation.
>
> 2) Creates three fdf files that will be changed fro run to
> run only in the
> include file to be read.
>
> 3) Runs siesta three times with appropriate names for each
> run, reading
> the output from the previous calculation. To make sure,
> copies the
> STRUCT_OUT and XV files to new ones with the name of the
> corresponding
> run. This is because I am not sure if a phonon calculation
> will output a
> struct/xv file for each displacement.
>
> Of course, you should replace whatever X appears in the
> script with the
> appropriate parameters...
>
> Cheers,
>
> Marcos
>
> #!/bin/bash
>
> cat > task.relax << EOF
>
> MeshCutoff XXX Ry
> MD.TypeOfRun CG
> MD.NumCGSteps 500
> #... all other parameters related to relaxation here ...
>
> %block kgrid_Monkhorst_Pack
> xx xx xx x.x
> xx xx xx x.x
> xx xx xx x.x
> %endblock kgrid_Monkhorst_Pack
>
> EOF
>
> cat > task.phonon << EOF
>
> MeshCutoff XXX Ry
> MD.TypeOfRun FC
> #... all other parameters related to phonon calculations
> here ...
>
> %block kgrid_Monkhorst_Pack
> xx xx xx x.x
> xx xx xx x.x
> xx xx xx x.x
> %endblock kgrid_Monkhorst_Pack
>
> EOF
>
> cat > task.pdos_ldos << EOF
>
> MeshCutoff XXX Ry
> MD.TypeOfRun CG
> MD.NumCGSteps 000
>
> %block ProjectedDensityOfStates
> xxx xxx xxx xxx eV
> %endblock ProjectedDensityOfStates
>
> %block LocalDensityOfStates
> xxx xxx eV
> %endblock LocalDensityOfStates
>
> %block kgrid_Monkhorst_Pack
> xx xx xx x.x
> xx xx xx x.x
> xx xx xx x.x
> %endblock kgrid_Monkhorst_Pack
>
> EOF
>
>
> for run in relax pdos_ldos phonon
> do
>
> #In the first run, the blah.relax.STRUCT_OUT file will not
> exist.
> #It doesn't matter, all that will happen is an error
> that will not stop
> #the rest of the script from being executed - I'm not
> caring much about
> #programming elegance here :)
>
> cp blah.relax.STRUCT_OUT blah.STRUCT_IN
>
> cat > blah.$run.fdf << EOF
>
> SystemName blah
> SystemLabel blah
>
> %include task.$run
>
> MD.UseStructFile .true.
>
> AtomicCoordinatesFormat Fractional
> %block AtomicCoordinatesAndAtomicSpecies
> ... Place the atomic coordinates in fractional format here.
> ... They will be overridden by the pdos and phonon run,
> which
> ... will read the coordinates from file from the STRUCT_IN
> file
> %endblock AtomicCoordinatesAndAtomicSpecies
>
> #rest of fdf file flags that will not change
> #from one run to the other come here
>
> EOF
>
> mpirun -np X siesta < blah.$run.fdf > blah.$run.out
> cp blah.STRUCT_OUT blah.$run.STRUCT_OUT
>
> done
>
>
>
> Vous avez écrit / You have written / Lei ha scritto /
> Você escreveu...
> Jonas Baltrusaitis
> > Hi,
> >
> > I was just wondering if there is a way to setup a
> single input to perform
> > several consecutive tasks, e.g. geometry optimization
> followed by
> > frequency calculation followed by DOS and PDOS
> calculations? Similar to
> > Gaussian or NWChem where one input can be used for
> numerous tasks
> >
> > thanks
> >
> > Jonas Baltrusaitis
> > University of Iowa
> >
> >
> >
> >
>
>
> --
> Dr. Marcos Verissimo Alves
> Post-Doctoral Fellow
> Unité de Physico-Chimie et de Physique des Matériaux
> (PCPM)
> Université Catholique de Louvain
> 1 Place Croix du Sud, B-1348
> Louvain-la-Neuve
> Belgique
>
> ------
>
> Gort, Klaatu barada nikto. Klaatu barada nikto. Klaatu
> barada nikto.
>
> Free translation:
>
> Gort, Google is your friend. Google is your friend. Google
> is your friend.
