[Pw_forum] Mean Square Displacement (MSD) of atoms

[Bertrand SITAMTZE]

Dear Giovanni

Thanks for your reply.

How to remove the artificial
translation when processing the coordinates?

Thanks once again.



--- En date de : Mar 18.1.11, Giovanni La Penna <glapenna at iccom.cnr.it> a écrit :

De: Giovanni La Penna <glapenna at iccom.cnr.it>
Objet: Re: [Pw_forum] Mean Square Displacement (MSD) of atoms
À: "PWSCF Forum" <pw_forum at pwscf.org>
Date: Mardi 18 janvier 2011, 11h01


Just a warning when adapting a code for msqd calculation.
Maybe it is well known, but repetita iuvant.

The *.pos trajectory files can be processed directly
because the atoms are free to exit the cell. In the
case of animated xsf files (those produced by cppp and
visible for graphical manipulations with Vmd or Xcrysden)
atoms that exit the cell are inserted from the opposite side.
In the jargon, they are wrapped in the cell.
So, in this latter case, do not forget to remove the artificial
translation when processing the coordinates.

               Giovanni

============================================================
Giovanni La Penna - National research council (Cnr)
Institute for chemistry of organo-metallic compounds (Iccom)
via Madonna del Piano 10,
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skype: giovannilapenna
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