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Re: Error of Particle node not found

From: Jean-Noël Grad
Subject: Re: Error of Particle node not found
Date: Thu, 14 Nov 2019 13:39:18 +0100
User-agent: Mozilla/5.0 (X11; Linux i686; rv:60.0) Gecko/20100101 Thunderbird/60.9.0


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:

The issue is reproducible in 4.1. @Jonas is this behavior documented? The user guide section on constant pH doesn't mention it:


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!


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