How to visualize lammps trajectory with dynamic number of atoms?


I am running simulations in lammps with fix evaporate command. I dump the trajectories using the dump command, but when I try to read the trajectories in vmd, it only opens the first time-step. I believe this is due to the unfixed number of atoms in the system. Does anyone know what is the right command to use here? Or should I post-process the .trj file using another App?


Please note that this is really more a question about VMD than about LAMMPS and you are more likely to get more competent answers on the VMD-l mailing list instead.

That said, VMD basically assumes that the number of atoms does not change. It does not happen for the typical applications that VMD was written for. There are some hacks in the VMD molfile plugin for LAMMPS to work around some limits (e.g. the LAMMPSMAXATOMS environment variable), but this is really something to be used in a pinch but not on a regular basis.

For possible alternatives, there is a list here: Visualization Tools for use with LAMMPS
Long ago, it used to be that AtomEye was the visualization software most commonly used with LAMMPS, but more recently I think that OVITO has become the most popular visualization software (the OVITO folks most certainly are very responsive and supportive and many are LAMMPS users as well).

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Hi @m.adibi,

To provide support to @akohlmey’s remark, I also do simulations with varying number of atoms and OVITO can read the dump files out of the box.

That said, it is very different from VMD, but the user manual is well written and there is a dedicated OVITO section on this forum on which the developers are also active.

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