To whom it may concern,
I am doing shear simulations with a Lennard-Jones potential using a Langevin thermostat. Here is the part of the code I’m using:
fix th_lang all langevin 0.1 0.1 100 12305 zero yes
fix th_verlet all nve
fix s_box all deform 1 xy erate 0.1 remap v flip yes units box
compute s_temp all temp/deform
fix_modify th_lang temp s_temp
The positions are saved using periodic conditions with the format “x y z”. When I control the distance between the positions of the saved particles in the dump file, I find particles with a distance much less than 10e-2, even when the deformation is not yet applied, that means.: xy=xz=yz=0. This is impossible because the potential energy and the stress tensor show reasonable results. Why is this happening? I calculate the distance between particles considering the box matrix, so I consider the deformation of the box over time.
Thank you for your help.