using bond.fene potential

[John Beta]

Hello all,

I try to simulate a mixture of two types of particles.
The interaction potentials should be:
A-A: LJ
A-B: LJ
B-B: FENE+LJ

Unfortunately the FENE potential is only implemented as bond potential.
Is there an easy way to use it as pair potential.

If not, is there an easy way to set up the bonds between the particles of type B from the python script?
My first impression was that I'll have to loop over all the particles of type B and create a bond for each particle pair, but I think I didn't get it right.

Thanks a lot!

[Carolyn Phillips]

Hi John.

Off hand my first reaction is why would you want to do that?  Can you describe your use case?

 As you can see from

http://codeblue.umich.edu/hoomd-blue/doc/classhoomd__script_1_1bond_1_1fene.html

the FENE bond potential becomes very stiff as r approaches r0 and then becomes undefined.  This is why it is a bond.  In a well setup simulation, two particles that interact via the FENE potential will always be in close proximity.   And if two particles will always be neighbors, then the most efficient data structure describing their interaction is a bond.   Also... does this mean all your B particles will be bonded together?  If you have more than five or six such particles, the simulation will surely blow up as it simply cannot geometrically fit that many particles into the same space.

If you are trying to describe a system that can make and break bonds, that is a wholly different and far more tricky matter.

-Carolyn

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[John Beta]

Hi Carolyn,

I thought about some kind of cutoff radius. So the neighbours of each particle would be selected automatically.

But of course this was a stupid idea because it is not efficient at all and could evantually cause numeric instability.

I'll stick to the bond data structure.

Thanks again!