Dear all,
I want to simulate a 2D liquid (square domain) with two copper solid walls
on the top and bottom of the domain and apply two different high and low
constant temperatures on the copper walls in order to calculate the
temperature distribution as a result of the temperature gradient. I would
really appreciate if somebody could answer my following questions:
1. How can I create my geometry? Should I define two different lattices
for liquid and copper walls or I need to use other softwares such as VMD or
Packmol to create the data file for geometry?
the lattice command has no impact whatsoever on the simulation. you can
change it as many times as you want. the only purpose for the lattice
command is to have a simple template (or pattern) that can be used to
conveniently specify region or box dimensions that are commensurate with
that lattice, which applies to all commands that support the "units
lattice" or "units box" keywords (e.g. region).
when you specify the lattice command multiple times, the current command
wipes out the previous lattice settings, but does not modify any
position/length information specified before. when building a periodic
system with multiple lattice commands, you have to make certain, that the
lattices are reasonably well compatible, since the simulation box can only
be defined once and thus with an incompatible later lattice command, you
may fill a region with atoms that overlap at the boundary.
for simplicity, it is recommended to define all regions with the same
lattice active when using "units lattice", i.e. the default, or always use
"units box" to have a consistent reference for lengths.
for your specific system, you have to first figure out how to build a
single thermostatted wall layer, as that will require multiple regions (an
immobile region, a strongly thermostatted region and a non-thermostatted
region), then add a second wall layer on the opposite side of your
non-periodic box dimension, and check whether the layers become properly
equilibrated and thermalized. only then would i fill the remaining void
with your liquid atoms. you will have to experiment at this stage, what
would be a suitable lattice constant for it to have a proper fully
equilibrated system.
of course, VMD scripting or packmol or moltemplate or writing some custom
script/program that all would lead to a data file are all suitable
alternatives. what works best depends a lot on your personal preferences
and skills. i myself would probably try using create_atoms in LAMMPS first.
2. Is it appropriate to use LJ potential for LJ liquid particles, "eam"
potential for copper particles and again LJ potential for the interaction
between LJ liquid and copper particles?
this is frequently done. whether that is appropriate depends on what kind
of system it is that you want to model and what level of accuracy you
expect. since the metal wall part doesn't seem to be very adding much to
the system outside of a "somewhat wiggly, slightly corrugated surface", it
may even be sufficient to use LJ interactions throughout (provided the
equilibrated and thermalized solid LJ lattice geometry would be close
enough than what you get with EAM).
overall, my recommendation is to first figure out step-by-step how you can
build the system in general without paying too much attention to the kind
of potential and then worry about improving your model later. switching
potential parameters or pair styles is very easy to do in LAMMPS and
independent from how to construct or input a system.
axel.