Logging velocity for all particles over all time steps

[molecular dynamics]

Hello all,

I am a CPARC student working with HOOMD with the goal of obtaining the viscosity of a molecular system using Green-Kubo relations. To accomplish this, I'll be using the integration of the velocity auto-correlation function, which requires the velocity of all particles over all time steps. I've been able to get the (x,y,z) velocity for all the particles in a single frame by initializing the simulation at a certain frame and using "system.particles.velocity". However, when I try to loop over the frames in the simulation or even manually change the frame without restarting the system, I get the error:

"**ERROR**: Cannot initialize more than once"

Does anybody have a script for obtaining these velocities, or if there is another method I should be using? I am self-taught in Python, so any help would be appreciated.

Thank you,

Drake Ghaderi

[Joshua Anderson]

Drake,

If you need to perform analysis on the particle velocities on every time step, use a custom operation. Use local snapshots for performance. There is a complete tutorial here: https://hoomd-blue.readthedocs.io/en/v3.0.0/tutorial/04-Custom-Actions-In-Python/00-index.html

If you need the velocity less often, you can save it to a GSD file for offline analysis.
------
Joshua A. Anderson, Ph.D.
Research Area Specialist, Chemical Engineering, University of Michigan

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[molecular dynamics]

Thank you very much for your prompt reply, I will give it a try!