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Re: [ESPResSo-devel] Book-keeping of bonded partners

From: Christoph Junghans
Subject: Re: [ESPResSo-devel] Book-keeping of bonded partners
Date: Thu, 03 Apr 2008 09:12:15 +0200
User-agent: Thunderbird (X11/20080213)

Hi Tristan,

some time ago I had the same problem. My solution is the following:
-set up the real interaction between particle i and i+1.
-set up a virtual bond between particle i+1 and i.

Normally Espresso will crash, if you set up bonded interaction in both direction, but the virtual bond does nothing else than been in the bond list. No contribution to energy, pressure etc. You can imagine it as a spring with k=0, but without calculating the zero contributions.

Is this what you need?



Tristan Bereau schrieb:
Dear all,

I am implementing a new non-bonded interaction that requires knowledge
about bonded partners.
At the C level of Espresso, is there an easy way to determine all the
bonded partners of a particle ?

Say I have particles only connected by bond length potentials (just an
example). If I take one particle (let's call it 'i'), I can get its
bonded partner 'i+1' from the bond length, but not particle 'i-1'
(that's because it is particle 'i-1' that stores particle 'i' as a
bonded partner).

Right now I'm cheating by using the information given by bond angles
between neighboring partners. Particle 'i' has a bond angle with 'i-1'
and 'i+1'. This method works only if I use that potential... Is there
any way I can do something more elegant ?

As a side note, I get information about bonded partners by using the
properties of particle i :
p_i+1 = local_particles[p_i->bl.e[...]];
I hope this is what I should be doing.

Many thanks,


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Dipl.-Phys. Christoph Junghans
Max Planck Institute for Polymer Research
Theory Group
POBox 3148
D 55021 Mainz, Germany

Phone: +49 6131 379 335

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