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Trajectories in XYZ format
#38133 12/17/20 04:02 PM
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Hi,

when writing XYZ formated trajectories, only the first characters of the element names are stored in the XYZ file, e.g. all the chlorides (Cl) are stored as carbons (C).
Is this a bug or am I missing something here? This is my Dynamics command:

Code
dyna leap cpt restart -
  timestep 0.001 nstep 10000 nprint 1000 -
  iunrea 50 iuncrd 30 nsavc 100 -
  iunxyz 60 nsavx 100 mxyz 1 -
  hoover reft 310.0 tmass @tmass -
  pcons pref 1.0 pmass @pmass pgamma 0.0 pint -
  ihtfrq 0 ieqfrq 0 ichecw 0 iasors 1 iasvel 1 iscvel 0 -
  ntrfrq 500 echeck 100.0

Re: Trajectories in XYZ format
cosmoshy #38134 12/17/20 07:44 PM
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rmv Online Content
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I checked the code, and it seems to deliberately write just the first character of the atom names for XYZ output. It would be easy enough to fix, just a few lines in one source file. I could post the correction in the "Bug Reports and Fixes" forum if you'd like.

I should note that WRITE COOR XYZ does write the full atom names, but only does a single coordinate set at a time. You can create a standard DCD trajectory and post-process it via a loop over frames, but it would still be single files.


Rick Venable
computational chemist

Re: Trajectories in XYZ format
cosmoshy #38135 12/17/20 08:33 PM
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Thanks for the quick reply, I appreciate it if you could also post the correction in the "Bug Reports and Fixes" forum.

Re: Trajectories in XYZ format
cosmoshy #38137 12/17/20 09:30 PM
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rmv Online Content
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I've posted the fix here


Rick Venable
computational chemist


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