Re: Regarding particles moving outside the box

[Martin Kaiser]

Hey Chandra,

I assume that you use vmd for visualization. Try using the command "pbc wrap" (without the quotation marks) in the vmd console. Espresso stores the un-wrapped coordinates in the vtf file and this command tells vmd to fold them into the box.

Of course, check that pbc are activated in you system

Alternatively, you can change the behaviour of writevcf() in the file 

src/python/espressomd/io/writer/vtf.py

to print part.pos_folded instead of part.pos. This makes espresso print the folded coordinates directly into the vtf file.

Best,

Martin

On Jan 13, 2022 13:12, chandra shekhar maurya <chandra15294@gmail.com> wrote:

Hello everyone,

I am simulating tutorial "Ferrofluid - Part 3". Which is a 3D system. I am using a vtf file to visulise the particles within the box. But the particles move outside the box. Is it the problem of the system or vtf file?

How can I fix it?

#print("Equilibration...")
equil_rounds = 1000
equil_steps = 10
equil_cycle =1
from espressomd.io.writer import vtf
fp = open('trajectory_monomer2.vtf', mode='w+t')
vtf.writevsf(system, fp)
vtf.writevcf(system, fp)
for i in range(equil_rounds):
for j in range(equil_cycle):
        system.integrator.run(equil_steps)
vtf.writevcf(system, fp)
fp.close()

Thanks & Regards

Chandra Shekhar Maurya

Mechanical Eng. Dept.

Indian Institute of Technology Patna

Contact No:9793572837