Subtract drift/center of mass during MSD calculation

bjmorgan / kinisi

A Python package for estimating diffusion properties from molecular dynamics simulations.

https://kinisi.readthedocs.io

MIT License

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Subtract drift/center of mass during MSD calculation #57

Closed dembart closed 6 months ago

dembart commented 6 months ago

Hello,

What do you think, is subtracting the drift of the entire system a necessary feature when calculating MSD? Seems to be an important step for the non-periodic systems, but not sure about 3D periodicity. It was somehow implemented in pymatgen's analyzer (using center of the geometry of a non-mobile framework ions) and maybe you can add similar feature in your package

arm61 commented 6 months ago

We already perform a drift correction. @jd15489 can comment better but I believe that the drift of everything that isn't the identified specie is corrected for.

dembart commented 6 months ago

Yeah, you are right. Was not expecting the feature is hidden in parser.py. Sorry for disturbing!