[QE-users] Post processing for cp.x code in quantum espresso

[Jayraj Anadani]

thank you so much

regard
jayraj anadani

On Wed, Sep 14, 2022 at 5:39 PM Giovanni La Penna <giovanni.lapenna at cnr.it>
wrote:

> Dear Jayraj Anadani,
>
> One easy way is to read the animated x-crysden format with VMD,
> then write coordinates into CHARMM DCD format, finally use
> Gromacs analysis tools or LAMMPS compute commands
> (rerun with molfile package). Or VMD itself.
> Check results to correctly handle periodic boundary conditions.
> If the system is large, conversion must be done in segments
> of trjactories, because VMD keeps the whole trajectory
> in memory.
> Below a simple VMD script, to run with "vmd -dispdev text -e file.vmd":
>
> #!/usr/local/bin/vmd
> # VMD script written by save_state : 1.47 $
> # VMD version: 1.9.2
> set path "./"
> set path1 "./"
> set inputname "md50K"
>
> mol new $path/$inputname.axsf type xsf first 0 last -1 step 1 filebonds 1
> autobonds 1 waitfor all
> #eventual trajectory to load into topology previously read:
> #mol addfile $path1/$inputname1.axsf type xsf first 0 last -1 step 1
> filebonds 1 autobonds 1 waitfor all
> set sel [atomselect top {all}]
> animate write dcd $path1/$inputname.dcd sel $sel beg 1 end -1
> exit
>
>
> Best,
>       Giovanni La Penna
>
> National research council of Italy
> Institute of chemistry of organometallic compounds
> via Madonna del Piano 10, 50019 Sesto Fiorentino (FI), Italy
> http://sites.google.com/view/wwwgiovannilapennait
>
> On Tue, Sep 13, 2022 at 12:25:32PM +0530, Jayraj Anadani wrote:
> > Hello QE Community Support Team,
> >
> > There very less number of resources available on post processing and
> actual
> > method on specially cp.x code using quantum espresso.
> > My question is
> > How we can visualise cp.x output file? There is cppp.x in which we can
> > convert .pos,.cell, and .for file into xsf or axsf format but how to
> > analyse different properties like Radial distribution function (RDF)
> means
> > squre displacement (MSD) etc.?
> > Also, most of tools like ovito,xcrysden,VESTA,VMD support lammps and
> castep
> > md file directly but cp.x generate completely different file format so
> > which is the best way or any tool to analyse output of cp.x code. i also
> > used code "cp2xsf.f90" but it is only convert cp pos,for and cell file
> into
> > axsf trajectory how to find RDF and MSD from that ?
> >
> > Thank you
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