Mean Squared Displacement

[James Graft]

I am a new hoomd user and am part of a MD project with the purpose of obtaining viscosities. Typically, to find viscosities, I find the mean squared displacement (from positional data) of the simulation, divide it by 6 (To calculate the Diffusion constant). Then, we apply the Stokes-Einstein relation for spherical particles moving through a liquid: 

Is there any inbuilt routine for calculating the mean squared displacement? I did come across deprecated.analyze, but the issue is that it is deprecated… Does anyone know an alternative way to calculate the mean squared displacement, or perhaps a more direct way to calculate viscosity in hoomd?

Thank you!

[Jens Glaser]

Hi James,

It’s true that the in-build analyze.msd() is deprecated, which doesn’t mean you can’t use it.

However, the attached python code uses some freud to unwrap trajectories and a fast MSD routine somewhere from stackoverflow to compute the MSD fast from a .gsd. Freud is obtained from here:

https://bitbucket.org/glotzer/freud

To use it on a .gsd file, you need to dump the gsd with the option dynamic=[‘property’,’momentum’].

- Jens

[Sheelan Sengupta Chowdhury]

I am also trying to find out MSD, either hy HOOMD or using freud. deprecated in not available in the HOOMD version I am using.

But found a MSD analyzer in github though didn't understood how or whether to use it (or not).

https://github.com/joaander/hoomd-blue/blob/master/hoomd/deprecated/MSDAnalyzer.h

The attached code is also showing error in my comp. Any lead related to this topic will be very helpful for me. Please reply.

Regards,

Sheelan.