In QE, the position output file contains the positions of the atoms wrapped inside the unit cell. For calculating mean square displacement we need to remove those translation vectors. So, can you suggest me how to remove those vectors?
Hello
The simplest way (by hand) is to count number of specific atom's passage through box boundary and then add box size (in this direction) to the coordinate of your atom (or if particle goes back by opposite box boundary just subtract box size).
Or else try to look for automated postprocessing software/script.
Konrad
Try to build a projector matrix from the generators of the translational vectors:
projector with Dirac's bra-ket notation:
P=1-∑(i) |translation(i)>
Thanks for your reply... I have written a code to remove the artificial translation. But as you have mentioned can you just mention what are the postprocessing software/script. thanks in advance for your reply..
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