Wrapped / unwrapped coordinates

dynasor
1

Hello,

I have (again) a basic question regarding the calculation of the incoherent intermediate scattering function. From my understanding, unwrapped coordinates (i.e., continuous trajectory) are typically needed for this computation, similar to the calculation of the mean squared displacement.

Could you please clarify if this is correct?

If unwrapped coordinates are indeed required, how is this handled in Dynasor? I looked through the code and examples, but it seems that the convention is to use wrapped trajectories.

Thank you for your help!

2

That is correct.

Dynasor works with Fourier transformed quantities which solves this issue in this particular case as long as commensurate k-points are used.

In general in MD many quantities are also calculated using relative positions between pairs of atoms and wrapped using the minimum image convention.