Re: "Exception: The bonded interaction has not yet been added to the list of active bonds in Espresso."

[Jean-Noël Grad]

Hi,

To add a bond between particles, you need to first register the bond 
parameters in the espresso system:

import espressomd.interactions
hb = interactions.HarmonicBond(k=80, r_0=0.3, r_cut=1.5)
system.bonded_inter.add(hb)
for id in range(1, len(system.part)):
    system.part[id].add_bond((hb, id - 1))

Best regards,
JN

On 2019-11-02 22:56, Thiago Puccinelli wrote:
> Hello all,
>
> I have just installed the newest version of espresso... Since, I work
> with dimers and polymers, I was looking forward to simulate dimers
> with Harmonic interactions between its monomers... And it is here
> where lies my problem...
>
> For instance, when I set this interaction by using the command, as
> follows:
> "hb = interactions.HarmonicBond(k=80, r_0=0.3, r_cut=1.5)"
>
> After executing the script, I get something like this:
> File "poly.py", line 88, in <module> system.part[id].add_bond((hb, id
> - 1)) File "particle_data.pyx", line 1487, in
> espressomd.particle_data.ParticleHandle.add_bond File
> "particle_data.pyx", line 1420, in
> espressomd.particle_data.ParticleHandle.check_bond_or_throw_exception
> Exception: The bonded interaction has not yet been added to the list
> of active bonds in Espresso.
>
> Should I install any feature to use this kind of bonded interaction in
> my simulations?
>
> Best
> Thiago
>
> --
>
> Thiago Puccinelli Orlandi Nogueira
> Soft Matter Physics
> C.V. http://lattes.cnpq.br/5068320085993516
> tel. (+55) 92 99534-0404