[CP2K-user] [CP2K:12408] Re: How to plot RDFs for NPT simulations?

[Travis]

Hi,

The file I generated looks like this,
TITLE
Gromos96 structure file written by ASE 
END
POSITION
    1 DUM   O          1   -0.466435441    0.134996386   -0.513981110
    1 DUM   H          2   -0.456093036    0.106021788   -0.419837619
    1 DUM   H          3   -0.420027567    0.062658494   -0.564346835
    1 DUM   O          4    0.115815785    0.219921049    0.557675443
    1 DUM   H          5    0.141607659    0.194800907    0.467369599
    1 DUM   H          6    0.041911702    0.157741781    0.572592000
    1 DUM   O          7    0.260380086    0.630856816   -0.541834739
    1 DUM   H          8    0.357742539    0.651611259   -0.535899313
    1 DUM   H          9    0.271335808    0.537091104   -0.513030977
END
BOX
   91.500000000   25.800000000   19.100000000    0.000000000    0.000000000 
   0.000000000    0.000000000    0.000000000    0.000000000
END

The atoms are colored by the name in column 3 and can be selected by 'name 
O' and so on. DUM is probably a molecule or force field tag.

As to your second point - did you output cell parameters at the same 
frequency as coordinates? If not, you would need to adjust the script to 
ignore the frames without parameters (index=':' is the only thing you would 
need to change). There's nothing in the Python code that limits the number 
of frames. It just assumes that the number of frames and the number of 
entries in .cell are equal.

-T


On Friday, October 25, 2019 at 1:03:22 PM UTC-3, Ant wrote:
>
> Travis, I used your code with my .cell file and trajectory (.xyz) 
> files--thank you.  Would you happen to have time for a couple of follow-up 
> questions on this?
>
> 1. It generated an output file like the one at the end of this message. 
> When I read it into VMD, it seemed to show all atoms as identical (i.e., 
> the atom types are not distinguished).  I'm guessing this has something to 
> do with the first and second columns.  I can't find an example online of 
> what they should be.  
>
> 2. Another problem is that the output file only contains about 300 time 
> steps.  This may not be something you can help with, but I thought I would 
> mention it just in case.  Thank you again very much.
>
> TITLE
> Gromos96 structure file written by ASE 
> END
> POSITION
>     1 DUM   Ar         1    0.271226802    1.105695742    0.687656962
>     1 DUM   Ar         2    0.171226802    0.705695742    0.287656962
>     1 DUM   Cl         3    0.987788274    0.553369424    0.340889882
>     1 DUM   Cl         4    1.017388949    1.095946397    1.012254758
>     1 DUM   O         5    0.171226802    1.056957424    0.287656962
>     1 DUM   O         6    0.087788274   -0.053369424    0.040889882
>     1 DUM   H         7    0.017388949    0.695946397   -0.212254758
>     1 DUM   H         8   -0.809217934    0.646737810    0.262515118
>    ...
>    ...
> END
> BOX
>     1.361050000    1.361050000    1.361050000    0.000000000   
>  0.000000000    0.000000000    0.000000000    0.000000000    0.000000000
> END
>
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