Freezing of atoms during minimization in crystals

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1

Dear All,
I have a conceptual doubt regarding freezing of the atoms in the crystal during minimization in order to mimic the semi-infinite crystal surface. The following procedure has been used in order to create the semi-infinite crystal surface of Aluminium.

  1. Calculate lattice constant at the desired temperature
  2. Use the lattice constant calculated to create atoms in the region to make a slab
  3. Freeze (by using setforce command) lower half portion of the slab and minimize the system
  4. Unfreeze (Unfix the setforce) lower half portion and equilibrate at the desired temperature

I am freezing the lower half of the slab to get bulk like characteristics below the free surface to mimic the semi-infinite surface. My question is when we unfreeze and equilibrate the system doesn’t the previously frozen atoms will minimize eventually with time? I visually compared two sets (with and without freezing) of simulation and I can see that at the end of the equilibration both the simulations give the same parametric value (Potential Energy).

Thank you

2

Your procedure sounds fine, it you unfreeze some atoms and equilibrate
you either need to assign thermal velocities to the unfrozen atoms
or wait for the system to re-quilibrate with the thermostat.

Steve

3

Thank you Steve for your response. But after proper equilibration, the resultant slab, would it be having bulk like characteristics at the bottom layers (atoms at lower layers have been unfrozen before equilibration)?

Prasanna

4

I would guess yes. But you are asking how to interpret MD output, rather
than a LAMMPS Q. The former depends on how you setup and run
your simulation. You are better off discussing that with colleagures or
your advisor.

Steve