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

[Limbach, Hans Joerg, LAUSANNE, NRC-FS]

Hi Christoph,

Espresso does not "normally" crash setting up bonded interactions in
both direction! There is no reason for this behaviour.

Reagrds,
Hanjo 

> -----Original Message-----
> From: address@hidden 
> [mailto:address@hidden On 
> Behalf Of Christoph Junghans
> Sent: jeudi, 3. avril 2008 09:12
> To: Tristan Bereau
> Cc: address@hidden
> Subject: Re: [ESPResSo-devel] Book-keeping of bonded partners
> 
> 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?
> 
> Bye,
> 
> Christoph
> 
> 
> 
> 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,
> > 
> > Tristan
> > 
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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
> Web: http://www.mpip-mainz.mpg.de/~junghans
> 
> 
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