Running NVT with CP2K, atoms running out of the box with periodic boundary conditions

[陈东]

When I was using xTB to run NVT with Xe atoms in graphite crystals, I found that it was a periodic boundary condition, but the Xe atoms that crossed the boundary did not reach the other side of the box, but instead ran out of the box. What happened?

[Krack Matthias]

That is the expected behavior, because CP2K prints the (continuous) coordinates to the trajectory file without applying PBC in order to keep the information about the atomic diffusion. You have to wrap back the atoms yourself to visualize the evolution of the system.

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