<table cellspacing="0" cellpadding="0" border="0" ><tr><td valign="top" style="font: inherit;">Dear Antonio,<br><br>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.<br>How to used an oscillating MDS to compute the diffusion coefficient as usually done?<br><br>Thanks once again<br><br><br>****************************<br>Bertrand SITAMTZE YOUMBI<br>Laboratory of Material Sciences<br>Department of Physics<br>University of Yaounde I-Cameroon<br>************************************<br><br><br><br>--- En date de : <b>Ven 30.4.10, Antonio Tilocca <i><uccaati@ucl.ac.uk></i></b> a écrit :<br><blockquote style="border-left: 2px solid rgb(16, 16, 255); margin-left: 5px; padding-left: 5px;"><br>De: Antonio Tilocca
<uccaati@ucl.ac.uk><br>Objet: Re: [Pw_forum] About the mean square displacement in CP output<br>À: pw_forum@pwscf.org<br>Date: Vendredi 30 avril 2010, 16h09<br><br><div class="plainMail"><br>Dear Bertrand:<br><br>I am not sure I understand how you are extracting the MSD(t) from the CP<br>trajectory: are you just plotting the final values shown in the standard<br>output file, or (as it would be recommended) calculating them by<br>post-processing the trajectory file? In any event, a flat, oscillating<br>MSD(t), after an initial increase, is exactly what you would<br>expect for a solid.<br><br>Antonio Tilocca<br>UCL<br><br><br><br>>From siyouber at yahoo.fr Thu Apr 29 15:09:27 2010<br>>From: siyouber at yahoo.fr (Bertrand SITAMTZE)<br>>Date: Thu, 29 Apr 2010 13:09:27 +0000 (GMT)<br>>Subject: [Pw_forum] About the mean square displacement in CP output<br><br>>I am running CP dynamic with fixed temperature for a given solid
system,<br>>using cp.x. The microcanonical calculation went very well with a<br>>conserved energy.Now the energy is still conserved. But my emphasis is on<br>> the mean<br>>square displacement(MSD) of atoms. They are calculated and plotted as a<br>>function of time. At the begining, the dependence seems to be linear at<br>>after, the MSD seem to oscillate around certain values which can be taken<br>>as a mean value after a sufficiently long time. My questions are: 1)<br>>According to the litterature, the dependence at the beginning should be<br>>quadratic and became linear after a long time. But for condensed system<br>>as<br>>a solid it is, the MSD should saturate after a very long time. What is<br>>happening for my case? 2) The MSD computed with cp.x are tree<br>>dimensionnal. Please, confirm it or not. 3) In which file should I see<br>>how<br>>those MSD are
computed?<br><br>_______________________________________________<br>Pw_forum mailing list<br><a ymailto="mailto:Pw_forum@pwscf.org" href="/mc/compose?to=Pw_forum@pwscf.org">Pw_forum@pwscf.org</a><br><a href="http://www.democritos.it/mailman/listinfo/pw_forum" target="_blank">http://www.democritos.it/mailman/listinfo/pw_forum</a><br></div></blockquote></td></tr></table><br>