[CP2K-user] How to plot RDFs for NPT simulations?

[Travis]

Hi,

Just some minor modifications then,
for ((i=0; i<310; i++)); do a=`echo "30 + $RANDOM/30" | bc`; b=`echo "30 + 
$RANDOM/30" | bc`; c=`echo "30 + $RANDOM/30" | bc`; vol=`echo "$a*$b*$c" | 
bc`; echo "$i $i $a 0 0 0 $b 0 0 0 $c $vol"; done > foo-1.cell

Just swap out the cell specification by angles with the 9 component one,

#!/usr/bin/env python3

'''
usage: python3 xyzcell2gro.py

Reads XMOL format file, adds lattice parameters, dumps Gromos file that can
be read by VMD.
'''

import glob
import os
import sys
import numpy as np

import ase
from ase.io import read, write

dir = os.getcwd()

# trajectory is XMOL format
# cell       is step time ax ay az bx by bz cx cy cz vol
for file in glob.glob('%s/*-pos-*.xyz' % dir):
   filename, fileext = os.path.splitext(file)
   fileroot, filescrap = filename.split('-pos')
   trj = read('%s%s' % (filename, fileext) , format='xyz', index=':')
   cel = np.loadtxt('%s-1.cell' % (fileroot), usecols=range(2,11), 
dtype=np.double)
   nframes = len(trj)
   for frame in range(nframes):
      trj[frame].set_cell([(cel[frame][0], cel[frame][1], cel[frame][2]),
                           (cel[frame][3], cel[frame][4], cel[frame][5]),
                           (cel[frame][6], cel[frame][7], cel[frame][8])])
      trj[frame].set_pbc([True, True, True])
      write('%s.g96' % (fileroot), trj[frame], format='gromos', append=True)

-T


On Wednesday, October 23, 2019 at 4:52:29 PM UTC-3, Ant wrote:
>
> Thank you very much, Travis! 
>
> Here are the first few lines of a .cell file directly from CP2K (below).  
> My cells are all cubic (90 degree angles, equal dimensions), so I can 
> change these to three columns; e.g., Ax, By, Cz.
>
> Step   Time [fs]       Ax [Angstrom]       Ay [Angstrom]       Az 
> [Angstrom]       Bx [Angstrom]       By [Angstrom]       Bz [Angstrom]     
>   Cx [Angstrom]       Cy [Angstrom]       Cz [Angstrom]      Volume 
> [Angstrom^3]
>
>        0       0.000       13.6105000000        0.0000000000        
> 0.0000000000        0.0000000000       13.6105000000        0.0000000000    
>     0.0000000000        0.0000000000       13.6105000000          
> 2521.2867393576
>
>        1       0.500       13.6102685896        0.0000000000        
> 0.0000000000        0.0000000000       13.6102685896        0.0000000000    
>     0.0000000000        0.0000000000       13.6102685896          
> 2521.1581382194
>
>        2       1.000       13.6101388560        0.0000000000        
> 0.0000000000        0.0000000000       13.6101388560        0.0000000000    
>     0.0000000000        0.0000000000       13.6101388560          
> 2521.0860435793
>
>        3       1.500       13.6101072636        0.0000000000        
> 0.0000000000        0.0000000000       13.6101072636        0.0000000000    
>     0.0000000000        0.0000000000       13.6101072636          
> 2521.0684874332
>
> This is finally making sense.  Now I understand why I have a problem.  My 
> simple XYZ trajectories don't contain my cell dimensions.  Your code adds 
> the cell dimensions and then I can read that new file right into the GUI 
> where I would usually read in my simple XYZ file.  It's great to finally 
> understand what is going on.  Thank you very much.
>
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