[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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