Defining a new potential

[PaulH]

Hi,

I have two questions:

1. Could define a new potential that depends on distance in one axis

For instance, We have V = k (z-z0)^2, so that force F = -k z \hat{z}

2. Once we define a new potential how do we use this new potential?

Normally I'd do:

harmonic = md.bond.harmonic()

harmonic.bond_coeff.set('A', k=100, r0=1.0)
    

Thanks,

 

def harmonic(r, rmin, rmax, kappa, r0): V = 0.5 * kappa * (r-r0)**2; F = -kappa*(r-r0); return (V, F) btable = bond.table(width=1000) btable.bond_coeff.set('bond1', func=harmonic, rmin=0.2, rmax=5.0, coeff=dict(kappa=330, r0=0.84)) btable.bond_coeff.set('bond2', func=harmonic, rmin=0.2, rmax=5.0, coeff=dict(kappa=30, r0=1.0))                   

[Joshua Anderson]

Paul,

`V = k (z-z0)^2` would be an external potential. You can implement new external potentials in C++ and add a Python class to interface with it. You would use this new potential using the Python class you write.
------
Joshua A. Anderson, Ph.D.
Research Area Specialist, Chemical Engineering, University of Michigan

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[Michael Howard]

Hi Paul,

I have a plugin that will harmonically restrain particles to a plane. It is in this package that you can install alongside hoomd:

https://github.com/mphowardlab/azplugins

Specifically, here is the class you need:

https://github.com/mphowardlab/azplugins/blob/d54fe88808d1d65fdcd4764e84c0310b6b4e8ca7/azplugins/restrain.py#L128-L221

To restrain all particles to a plane containing the point (0,0,z0) and normal in the +z direction (0,0,1) you would add:

azplugins.restrain.plane(group=hoomd.group.all(), point=(0,0,z0), normal=(0,0,1), k=10.0)

Note this potential uses the standard harmonic form u(d) = k/2 d^2, so you need to double the spring constant to get your potential. Also, there are a couple caveats about unwrapped vs. wrapped particle position, which are documented in the plugin.

Regards,

Mike

[Paul Hanakata]

Thanks for the explanation. Is there a short documentation detailing this?

How do I recompile HOOMD after adding a new potential to the source code?

Do I need to reinstall HOOMD?

Many thanks!

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[Paul Hanakata]

Hi Mike,

Thanks for sharing this plugin. I will give a try and email you if I have further questions.

[antoni...@googlemail.com]

Dear Paul,

You can compile the plugin two different ways, as external or internal plugin, see detailed instructions here. If you choose the internal plugin method you will have to recompile hoomd, if you compile it as external plugin you would not.  Documentation for the feature Mike mentioned is here.  Let us know if you have any further questions or issues. 

Best,

Antonia