[lammps-users] Limits of molecular domain: Maybe a bug?

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1

Dear Steve,

Perhaps this is a bug.

When using the lattice command with the non-periodic boundary conditions (e.g. boundary p p s) the reported limits of the molecular domains remains as if the domain were periodic. For instance, if:

boundary p p s
variable xx equal 2
lattice diamond 5.43
region box block 0 {xx} 0 {xx} 0 20

The reported value for zhi is 205.43 instead of 19.755.43.

Although this won’t affect the force calculation since their is no periodicity in z, it will affect other methods that use the limits of the boundaries. BTW, if I do NVE steps and print zhi, its value does not change significantly, However, there are atoms that move beyond the printed zlo or zhi.

Are the limits of the domain updated with minumum and maximum positions of the atoms for this type of boundary?

Regards, Javier

2

If you use boundary "s", then the box size (in z) should
always be slightly larger/smaller than the atoms, whether
on timestep 0 or later. The box size printed out after
the create box command may well be what you tell it,
e.g. 20*5.43 in this case. But you haven't created
any atoms yet. If you dump atoms at timestep 0,
is the box size corrected, i.e. what I said above?

Steve