building external force based on position

[Louis PERRIN]

Hello,

I am currently using HOOMD-Blue for some basic molecular dynamics. In my last project, I wanted to add some external force based on y position of each particle over time : if y(t)>=0, F(t)=(1,0,0), else, F(t)=(-1,0,0). In order to do that, I want to create two groups containing respectively particles with y position above 0, and particles with y position under 0.

There are two questions that I couldn't answer when I tried to do that : firstly, how can I access position of each particle at every time-step to update the groups ? Secondly, Are the group structures built to contain the same particles tags over the whole simulation or can the tags be modified at each time step ?

Thank you for reading my message.

Louis Perrin

[Joshua Anderson]

Louis,

1) Use the local snapshot API to access particle positions efficiently: https://hoomd-blue.readthedocs.io/en/latest/package-hoomd.html#hoomd.State.cpu_local_snapshot

2) Define a custom filter to select your particles: https://hoomd-blue.readthedocs.io/en/latest/module-hoomd-filter.html

3) Selected particle tags are cached for performance. You can force an update of that cache when needed: https://hoomd-blue.readthedocs.io/en/latest/module-hoomd-update.html#hoomd.update.FilterUpdater

------
Joshua A. Anderson, Ph.D.
Research Area Specialist, Chemical Engineering, University of Michigan

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