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

[Christoph Junghans]

Hi Hanjo,

you are right, for spring and angle etc it works.
I had the problem with rigid bonds, sorry for the confusion.

Bye,

Christoph

Limbach,Hans Joerg,LAUSANNE,NRC-FS schrieb:
> 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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> > > address@hidden
> > > https://fias.uni-frankfurt.de/mailman/listinfo/espresso-devel
> > >
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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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>
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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