My simulation contains two main stages. In the first stage, the system
experiences rapid change. In the second stage, I want the atoms to be
relaxed at a constant temperature and run it for a relatively long time
to reach the equilibrium state. I want to use ReaxFF potential for the
first stage since it can describe the interactions in this stage, and I
want to use REBO potential in the second stage.
Since these two potentials are using different units, my plan is that at
the end of the first simulation, the configuration of the final state is
written into a data file. After that, I need to convert the values of
the data file based on the units used by the two different potential.
And then load the modified data file into the second simulation and use
REBO potential. My question is that is this scheme feasible to be
implemented. And are there any fundamental drawbacks to divide a
simulation into this kinds of two stages?
I have not used either of these pair styles. However it is very
common to split a simulation into multiple stages.
I usually use the "write_data" command (or "write_restart" command)
to save the state of the system at the end of the first stage of the
simulation. If something goes wrong during the second stage, you can
use the "read_data" (or "read_restart") command to restore the
simulation from the end of stage 1, instead of starting the simulation
again from the beginning.
According to the documentation for REBO:
"You can use the AIREBO, AIREBO-M or REBO potential with any
LAMMPS units, but you would need to create your own AIREBO or AIREBO-M
potential file with coefficients listed in the appropriate units, if
your simulation does not use “metal” units."
According to the documentation for REAX:
"The potential files provided with LAMMPS in the potentials
directory are parameterized for real units. You can use the ReaxFF
potential with any LAMMPS units, but you would need to create your own
potential file with coefficients listed in the appropriate units if
your simulation does not use “real” units."
...So, choose which units you want to use for measuring energy
(Kcal/mole or eV), and convert the other file to those units.
(Fortunately, in both cases, distance is specified in units of
I suggest creating two different dump files. This way if you need to
re-run stage 2, you will not accidentally erase your first trajectory
dump dAll all custom 100000 traj_stage1.lammpstrj id type x y z ix iy iz
dump dAll all custom 100000 traj_stage2.lammpstrj id type x y z ix iy iz
Note: The following suggestion is probably not relevant to you. If
you are using "atom_style molecule" or "atom_style full", then I would
use these commands in instead:
dump dAll all custom 100000 traj_stage1.lammpstrj id mol type x y z ix iy iz
dump dAll all custom 100000 traj_stage2.lammpstrj id mol type x y z ix iy iz
This extra information ("mol", "ix", "iy", and "iz") makes it easier
to visualize the trajectory (dump file) containing molecules in VMD.
When running the stage 2 simulation, the "reset_timestep" command may be useful.
I don't know if this helped.