Dear Antonio, Thanks very much for responding. To plot MSD(t) I just go through the standard? output file and collect all the calculated MSDs fo each atoms. The time is computed using each "nfi"(the first column of the output file). I will be gratefull if you indicate a postprocessing code. How to used an oscillating MDS to compute the diffusion coefficient as usually done?
Thanks once again **************************** Bertrand SITAMTZE YOUMBI Laboratory of Material Sciences Department of Physics University of Yaounde I-Cameroon ************************************ --- En date de?: Ven 30.4.10, Antonio Tilocca <uccaati at ucl.ac.uk> a ?crit?: De: Antonio Tilocca <uccaati at ucl.ac.uk> Objet: Re: [Pw_forum] About the mean square displacement in CP output ?: pw_forum at pwscf.org Date: Vendredi 30 avril 2010, 16h09 Dear Bertrand: I am not sure I understand how you are extracting the MSD(t) from the CP trajectory: are you just plotting the final values shown in the standard output file, or (as it would be recommended) calculating them by post-processing the trajectory file? In any event, a flat, oscillating MSD(t), after an initial increase, is exactly what you would expect for a solid. Antonio Tilocca UCL >From siyouber at yahoo.fr? Thu Apr 29 15:09:27 2010 >From: siyouber at yahoo.fr (Bertrand SITAMTZE) >Date: Thu, 29 Apr 2010 13:09:27 +0000 (GMT) >Subject: [Pw_forum] About the mean square displacement in CP output >I am running CP dynamic with fixed temperature for a given solid system, >using cp.x. The microcanonical calculation went very well with a >conserved energy.Now the energy is still conserved. But my emphasis is on > the mean >square displacement(MSD) of atoms. They are calculated and plotted as a >function of time. At the begining, the dependence seems to be linear at >after, the MSD seem to oscillate around certain values which can be taken >as a mean value after a sufficiently long time. My questions are: 1) >According to the litterature, the dependence at the beginning should be >quadratic and became linear after a long time. But for condensed system >as >a solid it is, the MSD should saturate after a very long time. What is >happening for my case? 2) The MSD computed with cp.x are tree >dimensionnal. Please, confirm it or not. 3) In which file should I see >how >those MSD are computed? _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100430/f76fc471/attachment.htm
