<table cellspacing="0" cellpadding="0" border="0" ><tr><td valign="top" style="font: inherit;">Dear Antonio and all users, <br><br>Thanks for responses you have given until now. But I am a bit confused.<br><br>Please could sombody tels me how to compute the <span style="font-weight: bold;">diffusion coefficient in a solid</span> using Ab-initio Molecular dynamics?<br><br><br>Best regards<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>--- En date de : <b>Lun 3.5.10, 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:
Lundi 3 mai 2010, 11h45<br><br><div class="plainMail"><br>Dear Bertrand,<br><br>the way you are obtaining the MSD(t) is not the best: in that way, every<br>time point is only averaged using a single time origin, whereas it is<br>advisable, for a better statistics, to perform an extended average over a large<br>number of non-correlated time origins, as described (with examples of<br>codes) in the Allen-Tildesley book, for instance. However, the trend that<br>you obtain with your approximate approach is qualitatively correct.<br><br>As for your other question, as Sandro has already pointed out, the zero<br>slope of your (constant) MSD(t) shows the absence of diffusion,<br>as expected for a solid, on your short observation time.<br><br>Antonio Tilocca<br>UCL<br><br><br>> Message: 2<br>> Date: Fri, 30 Apr 2010 15:15:36 +0000 (GMT)<br>> From: Bertrand SITAMTZE <<a ymailto="mailto:siyouber@yahoo.fr"
href="/mc/compose?to=siyouber@yahoo.fr">siyouber@yahoo.fr</a>><br>> Subject: Re: [Pw_forum] About the mean square displacement in CP<br>> output<br>> To: PWSCF Forum <<a ymailto="mailto:pw_forum@pwscf.org" href="/mc/compose?to=pw_forum@pwscf.org">pw_forum@pwscf.org</a>><br>> Message-ID: <<a ymailto="mailto:414847.4559.qm@web26504.mail.ukl.yahoo.com" href="/mc/compose?to=414847.4559.qm@web26504.mail.ukl.yahoo.com">414847.4559.qm@web26504.mail.ukl.yahoo.com</a>><br>> Content-Type: text/plain; charset="iso-8859-1"<br>><br>> Dear Antonio,<br>><br>> Thanks very much for responding. To plot MSD(t) I just go through the<br>> standard? output file and collect all the calculated MSDs fo each atoms.<br>> The time is computed using each "nfi"(the first column of the output<br>> file). I will be gratefull if you indicate a postprocessing code. How to<br>> used an oscillating MDS to compute the
diffusion coefficient as usually<br>> done?<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?: Ven 30.4.10, Antonio Tilocca <<a ymailto="mailto:uccaati@ucl.ac.uk" href="/mc/compose?to=uccaati@ucl.ac.uk">uccaati@ucl.ac.uk</a>> a ?crit?:<br>><br>> De: Antonio Tilocca <<a ymailto="mailto:uccaati@ucl.ac.uk" href="/mc/compose?to=uccaati@ucl.ac.uk">uccaati@ucl.ac.uk</a>><br>> Objet: Re: [Pw_forum] About the mean square displacement in CP output<br>> ?: <a ymailto="mailto:pw_forum@pwscf.org" href="/mc/compose?to=pw_forum@pwscf.org">pw_forum@pwscf.org</a><br>> Date: Vendredi 30 avril 2010, 16h09<br>><br>><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>_______________________________________________<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>