run lammps

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