I'm studying a flow inside a nanotube, with periodic boundary conditions: the fluid particles exit from one end of the nanotube and enter from the other.
There are two fluids moving side by side, and I'd like to know the temperatures and pressures for each fluid away from the interface and from the walls. So, I created moving regions centered around the center of mass of each fluid.
The problem is that, while the center of mass is computed with unwrapped coordinates, the region command uses "wrapped" coordinates, so after a while the moving region moves outside of the simulation box and then it doesn't contain any atom.
Is there a way to make the moving region reenter the simulation box, with periodic boundary conditions? The only workaround I could think of is to define multiple moving regions separated by the box length, so that when one is exiting another one is entering.
Here is the code I'm using:
compute wcom water com
compute hcom hept com
variable dz_w equal c_wcom-150
variable dz_h equal c_hcom-150
region waterregion cylinder z 0 0 22 130 170 units box move NULL NULL v_dz_w
region heptregion1 cylinder z 0 0 22 0 20 units box move NULL NULL v_dz_h
region heptregion2 cylinder z 0 0 22 281 301 units box move NULL NULL v_dz_h
region heptregion union 2 heptregion1 heptregion2
group waterbulk dynamic water region waterregion every 1
group heptbulk dynamic hept region heptregion every 1
compute twater waterbulk temp/com
compute pperatomwater waterbulk stress/atom twater
compute thept heptbulk temp/com
compute pperatomhept heptbulk stress/atom thept