say the executable file is lammps, the input script is in.lj
to run the code
./lammps < in.lj
to run parallel version of the code
mpirun -np 4 lmp_linux < in.lj
In the input file in.lj, there are thousands of types of commands you can put.
To output snapshots
dump 1 all xyz 100 movie.xyz # .xyz format every 100 timestep
# (the first column of the .xyz file will be atomic number Z)
dump_modify 1 element Zr Cu # by default, LAMMPS output atom name as numbers Z; this command make letter output
dump 2 all dcd 100 movie.dcd # .dcd format every 100 timestep
dump_modify 2 unwrap yes
To increase/decrease the temperature with certain rate
fix 1 all npt temp 2000 0.01 0.1 iso 0 0 0.2 # cool from T = 2000 to 0.01; constant 0 pressure;Tdamp=0.1;Pdamp=0.2
run 10000 # the rate is set by time steps = (2000-0.01)/10000
http://lammps.sandia.gov/threads/msg08390.html