[DFTB-Plus-User] Fragment count and identification code

[Gabriele Penazzi]

Dear Debasis,

I'm not aware of any solution out of the box, but I had a similar problem.

I wrote down few hundred lines script in python using ase (
https://wiki.fysik.dtu.dk/ase/) for parsing the structure files and
building the bondmap. However this was done in post-processing and it's
slow, not a problem for me (I was evaluating a few snapshots), but you
can surely do it much more efficiently if you need to trace thousands of
snapshots.

Unluckily my script is not general purpose at all (I want to generalize
it, but this is not going to happen quickly), so it couldn't be used as
is, but if you (or someone for you) are willing to implement something
on your own and you need some hints, or you want to give a look at my
script (but ONLY to get some inspiration, you cannot use it as it is and
I strongly suggest you to write it from scratch), contact me.

Gabriele



On 09/13/2012 08:36 PM, Debasis Sengupta wrote:
> All,
> I am running a MD simulation where molecules react and produce
> fragments (other molecules).  Does anyone have a script/code to count
> the total number of fragments along the trajectory? Also, it will be
> best if this also identifies the types of fragments and their counts.
> For example, if a molecule C4H10 breaks into C2H2 and H2 (like 2 C2H2
> and 3 H2), the code should be able to count the number each fragment
> type (C4H0, C2H2 and H2) along the trajectory.  I would really
> appreciate if any one has one such code and willing to share.  Thanks
> Debasis Sengupta
>


-- 
Dr. Gabriele Penazzi
BCCMS - University of Bremen

http://www.bccms.uni-bremen.de/
http://sites.google.com/site/gabrielepenazzi/

phone: +49 (0) 421 218 62337
fax: +49 (0) 421 218 62770

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