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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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<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 style="margin-top: 0px; margin-bottom: 0px;" class="">Dear QE experts,</div>
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<div style="margin-top: 0px; margin-bottom: 0px;" class="">I am trying to evaluate MSD for my simulation.</div>
<div style="margin-top: 0px; margin-bottom: 0px;" class="">My problem is that when an atom exits the simulation cell. </div>
<div style="margin-top: 0px; margin-bottom: 0px;" class="">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 style="margin-top: 0px; margin-bottom: 0px;" class=""><span id="cid:eb89eef8-985a-4e94-b8fb-1e770ba0adec"><Screenshot from 2017-10-30 14-53-57.png></span><br class="">
Best Regards</div>
<div style="margin-top: 0px; margin-bottom: 0px;" class="">Nam Tran</div>
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