Question of Rigid rods Tutorial

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s Kalan

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Jun 8, 2023, 2:57:10 PM6/8/23
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Hello,

The central rigid body is indicating by R and constituent particles are shown by A in tutorial of MD-rigid rods. If we consider the Lj interaction between R and R, A and A, R and A, we can write it in a line as: 

lj.pair_coeff.set(['R', 'R'],['A', 'A'], ['R', 'A'], epsilon=1.0, sigma=1.0)

However, the command for particles LJ interaction is 

lj.pair_coeff.set(['R', 'A'], ['R', 'A'], epsilon=1.0, sigma=1.0) 

For me it is like there is LJ interaction between R and A. I don't know why is the  ['R', 'A'] pair is repeated for a second time.  How to interpret this command? Is it meaning that there is only Lj interaction between Rtype and A type? There are not Lj interaction between R types, meaning [R, R]. How about interaction between A types particles [A, A]. 

Thanks for any help,
Somaiyeh





Joshua Anderson

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Jun 12, 2023, 11:40:55 AM6/12/23
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Somaiyeh,

HOOMD-blue, v2.9.x is unsupported. Here is the relevant documentation for v4.0.0: https://hoomd-blue.readthedocs.io/en/v4.0.0/module-hoomd-data.html#hoomd.data.typeparam.TypeParameter
------
Joshua A. Anderson, Ph.D.
Research Area Specialist, Chemical Engineering, University of Michigan

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s Kalan

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Jun 13, 2023, 10:52:12 AM6/13/23
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Hi Joshua,

Thanks, I got it.

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