Question about equilibration npt

Hi all,

lately I am dealing with thermal conductivity of silicon, precisely it is 5x5x300nm system of crystal silicon.

Here is a part of my code to LAMMPS:

#npt equillibration
velocity all create 300 345941 dist gaussian
fix 1 all npt temp 300 300 .1 iso 1 1 8
run 2000

My question is: why during my calculations temperature decreasing roughly to 150K, where I can observe some oscillations of temperature, and after that (after 1000 steps) reaches 300K?
Maybe that is why my final value of thermal conductivity is twice bigger than it should be?

I am enclosing graph of my temperature of my sample in a function of time.

Thank you in advance for your answer.


That must be because of equipartition theorem.
You must be starting the simulation with all the atoms in their equilibrium position, i.e. zero initial potential energy. Then, the initial kinetic energy introduced in the system with the “velocity all create 300” will be distributed by half in KE and PE, so you get that decrese to 150K (half initial KE). You can monitor these things with the thermo output.

In the long run the thermostat is able to target your desired temperature by introducing more energy to the system.

that’s my guess.