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

Ant ant... at gmail.com
Wed Oct 23 19:52:29 UTC 2019


Thank you very much, Travis! 

1. 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

2. When you said that box size is only need to "unwrap everything 
correctly," does that mean that I could enter anything at the VMD GUI for 
the cell parameter and still get a correct RDF?  

3. Thanks a lot for your code.  So it reads my .xyz file, adds the data 
from my cell file, then gives me a file that I can read into VMD.  Sorry 
for the newbie question, but how would I read it in?  Thanks so much for 
taking the time for this.
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