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In a typical deposition problem the substrate (or the 'host') is at a given temperature (and surrounded by a thermal bath), while the deposited species usually have a different temperature, which, a while after deposition, equilibrates to the substrate temperature.

Why then in this LAMMPS example file an NVE ensemble is used for a deposition problem? The number of atoms in the simulation box increases over time, which means total energy is not fixed. Wouldn't NVT make more sense for a deposition problem?

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It is, in fact an NVT ensemble. The topmost layer of atoms of the substrate are coupled to a Langevin thermostat via

fix     2 mobile langevin 1.0 1.0 0.1 587283
fix     3 mobile nve

All other particles are not coupled to a thermostat, but this is will still simulate an NVT ensemble.

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  • $\begingroup$ 1) the deposited atoms have fix 1 addatoms nve - why? 2) why after defining a langevin for the mobile atoms, an nve is defined for the same group? $\endgroup$ – Sparkler Jan 5 '17 at 14:06
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    $\begingroup$ 1) The deposition takes place in vacuum. Thus, the deposited atoms are not coupled to a thermostat. In the experiment only the substrate is connected to a temperature control. In the simulation, only the substrate atoms are connected to the thermostat. 2) fix langevin adds a random force to the particles, but does not perform time integration. This is done with the fix nve command. See the documenataion for fix langevin $\endgroup$ – Julian Helfferich Jan 5 '17 at 14:20

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