[lammps-users] isolated equilibration and then in common simulation box

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1

Hi, Dear all

I try to equilibrate two isolated atom clusters (e.g. silicon) separately and then put them together in a common simulation box, give them a go to see how they interact with each other.
The reason why not to equilibrate two cluster together in single simulation box is to avoid any interaction between them during equilibration.

What I can conceive is that run two separated equilibration for two clusters, dump the system information (coordinates, velocities, etc) after equilibrium then take the dump files as input data for mutual simulation.

Here are my questions:
1) How possible I ensure equilibrium of two cluster system instantly in mutual simulation stage rather than just another initialization? Maybe fix NVE upon the two clusters for a while?
2) How could I read velocity data from a dump file, though this may be unnecessary for this particular case.
3) Can 'restart' and its related commands do a bit of contribution?

Any suggestion on my hasty questions will be greatly appreciated.

Regards,

Peng. X. Song

2

If you slap two systems together, I think you'll have to
re-equilibrate. I'd write a script which puts your
new data file together. Pizza.py (see WWW page for
that tool) has some tools that would help massage dump
and data files if you know Python. If you dump restart
files (binary), the tools/restart2data tool will turn them
into data files (text).

Steve