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<div class="">Dear Nam,</div>
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<div class="">My understanding is that the trajectory as printed in VASP’s XDATCAR is folded or wrapped. As you can see in msd.f90,:</div>
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<div class="">write(6,*) 'Name of unwrapped xyz file’</div>
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<div class="">So the input file should be unwrapped. In other words, you have to first unwrap the coordinates in XDATCAR. Then you can use msd.f90.</div>
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<div class="">To unwrap the coordinates, there are other codes on that website such as unwrap_PBC.f90.</div>
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<div class="">Cheers,</div>
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</div>
<div class="">Vahid</div>
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<div><br class="">
<blockquote type="cite" class="">
<div class="">On Oct 30, 2017, at 9:25 PM, Nam Tran <<a href="mailto:vnt981@uowmail.edu.au" class="">vnt981@uowmail.edu.au</a>> wrote:</div>
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<div style="margin-top: 0px; margin-bottom: 0px;" class="">Dear Vahid</div>
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<div style="margin-top: 0px; margin-bottom: 0px;" class="">I don't know whether VASP folds back atoms in their output or not. If they do then the msd.f90 you recommended is not accurate. Because the code simply calculate the distance between two position</div>
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<div style="margin-top: 0px; margin-bottom: 0px;" class=""><span class="">dRx = Rx(j) - Rx0(j) </span></div>
<div style="margin-top: 0px; margin-bottom: 0px;" class=""><span class="">dRy = Ry(j) - Ry0(j) </span></div>
<div style="margin-top: 0px; margin-bottom: 0px;" class=""><span class="">dRz = Rz(j) - Rz0(j) </span></div>
<div style="margin-top: 0px; margin-bottom: 0px;" class=""><span class="">sum_msd = sum_msd + (dRx**2 + dRy**2 + dRz**2)</span><br class="">
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<div style="margin-top: 0px; margin-bottom: 0px;" class="">One thing is that I tried to create a .axsf file using cppx. And the atoms seem to be not folded back. Can someone confirm me that?</div>
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<div style="margin-top: 0px; margin-bottom: 0px;" class="">Best Regards,</div>
<div style="margin-top: 0px; margin-bottom: 0px;" class="">Nam Tran</div>
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<font face="Calibri, sans-serif" style="font-size: 11pt;" class=""><b class="">From:</b><span class="Apple-converted-space"> </span><a href="mailto:pw_forum-bounces@pwscf.org" class="">pw_forum-bounces@pwscf.org</a> <<a href="mailto:pw_forum-bounces@pwscf.org" class="">pw_forum-bounces@pwscf.org</a>>
on behalf of Vahid Askarpour <<a href="mailto:vh261281@dal.ca" class="">vh261281@dal.ca</a>><br class="">
<b class="">Sent:</b><span class="Apple-converted-space"> </span>Monday, October 30, 2017 11:00:01 PM<br class="">
<b class="">To:</b><span class="Apple-converted-space"> </span>PWSCF Forum<br class="">
<b class="">Subject:</b><span class="Apple-converted-space"> </span>Re: [Pw_forum] How to calculate Mean Square Displacement (MSD)</font>
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There is a collection of fortran codes (for VASP mainly but can easily be adapted) for processing simulation output including MSD calculation and the treatment of periodic images. They can be found at <a href="https://github.com/boates" class="">https://github.com/boates</a> under
the Physics repository (see msd.f90).
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<div class="">Cheers,</div>
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<div class="">Vahid</div>
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<div class="">Vahid Askarpour<br class="">
Department of Physics and Atmospheric Science<br class="">
Dalhousie University,<br class="">
Halifax, NS, Canada<br class="">
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<blockquote type="cite" class="">
<div class="">On Oct 30, 2017, at 4:29 AM, Nam Tran <<a href="mailto:vnt981@uowmail.edu.au" class="">vnt981@uowmail.edu.au</a>> wrote:</div>
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<div class="" style="margin-top: 0px; margin-bottom: 0px;">Dear QE experts,</div>
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<div class="" style="margin-top: 0px; margin-bottom: 0px;">I am trying to evaluate MSD for my simulation.</div>
<div class="" style="margin-top: 0px; margin-bottom: 0px;">My problem is that when an atom exits the simulation cell. </div>
<div class="" style="margin-top: 0px; margin-bottom: 0px;">I do not know whether I should consider the distance with atom that goes about outside the box (a) or its image (b). Please check the image below (Blue is the original position t=0, red is the position
at time t)</div>
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<div class="" style="margin-top: 0px; margin-bottom: 0px;"><span id="cid:eb89eef8-985a-4e94-b8fb-1e770ba0adec" class=""><Screenshot from 2017-10-30 14-53-57.png></span><br class="">
Best Regards</div>
<div class="" style="margin-top: 0px; margin-bottom: 0px;">Nam Tran</div>
</div>
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