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

[Giovanni La Penna]

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