Getting nan errors.

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1

Hi,

I am getting nan errors for the LAMMPS input script attached. The time steps used and the neighbor distances seem right. Could somebody please advise what may be causing the problem. I am trying to understand the diffusion of a single extra atom atop a moving set of atoms constituting the “mobile” group from the script.

Regards,
Saketh.

Starting.in (1.47 KB)

StartingSi1Log.lammps (151 KB)

StartingSi1.xyz (11.1 KB)

2

Hi,

I am getting nan errors for the LAMMPS input script attached. The time steps
used and the neighbor distances seem right. Could somebody please advise
what may be causing the problem. I am trying to understand the diffusion of

you have to always validate _all_ your input data.
in this case, your simulation cell dimensions are
not consistent with your atom data. so you get
overlapping atoms and hence NaNs.
MD is strictly GI-GO.

check out the attached snapshot from VMD.

axel.

vmdscene.jpg