Re: Error of Particle node not found

[Jean-Noël Grad]

Hi,

I'm not too familiar with the constant pH method, maybe Jonas can help 
here. From what I understand, the constant pH method will create and 
delete particles, yet the list of particle ids doesn't shrink upon 
particle deletion (maybe due to particle recycling?).

The line `system.part[k].pos` will fail because the particle was 
deleted. However `system.part[:].pos[k]` will work just fine, because 
the ParticleSlice has a bitmask to skip deleted particles; when printing 
debug messages in the core, I get a jump around values of k that refer 
to deleted particles:
...
get_particle_node(237)
get_particle_node(238)
get_particle_node(240)
get_particle_node(241)
...

The issue is reproducible in 4.1. @Jonas is this behavior documented? 
The user guide section on constant pH doesn't mention it:
http://espressomd.org/html/doc/advanced_methods.html#constant-ph-simulation-using-the-reaction-ensemble

Best,
JN

On 11/7/19 8:49 AM, Jiaxing Yuan wrote:
> Dear all,
>
> I am simulating a system of electrolytes where charge regulation occurs 
> so the total particle number is changing during the simulation. However, 
> in the production run process of my script, an error of "Particle node 
> not found" is observed.  I confirm if I remove the lines below, the 
> script works well:
>
> for k in range(number_of_particles):
>          print(system.part[k].type, file=f_config)
>      print("position", file=f_config)
>      for k in range(number_of_particles):
>          print(system.part[k].pos, file=f_config)
>
> So I am confused about why these lines lead to an error. What is the 
> correct way to output the configuration so that one can analyze the 
> configuration? My script is attached below, thank you!
>
> Best,
> Jiaxing