[lammps-users] some help

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1

Hi,
I’m working on simulating a nanodiamond molecule using the AIREBO potential. My input file is given below -

units metal
atom_style molecular
dimension 3

pair_style airebo 3.0 1 1
read_data nanodiamonds.txt
pair_coeff * * …/potentials/CH.airebo C

fix 2 all nve
velocity all create 298.0 9999999989
fix 1 all temp/rescale 1 298.0 298.0 1 1

timestep 0.0001
thermo_style custom step temp press etotal pe epair
thermo 100

run 10000
unfix 1

timestep 0.0001
thermo_style custom step temp press etotal pe epair
thermo 100
dump 1 all custom 50 dump.nano id type x y z vx vy vz

run 10000

The data file ‘nanodiamonds.txt’ contains only the initial starting positions of the atoms in the nanodiamond molecule. The molecule does not properly equilibrate, that is the total energy does not reach a stable value. I was wondering if my input file was correct and if there is anything I can do other than increasing the timesteps for equilibration and changing the length of the timestep.
Thanks for the help.

-Ferdaus

2

How many atoms in your system. Does the temperature
equilibrate reasonably well to a stable value? Have you
visualized the system to insure it is doing something reasonable?

Steve

3

The system has 2052 atoms. I have visualized the system and it seems to be doing what it should be doing. The temperature rescales to 298 K so I guess the temperature is stabilizes pretty well, however the total energy of the system keeps decreasing. Based on the recent run, I have tried equilibrating for 500000 timesteps, the change in total energy with respect to time seems to be decreasing. Would increasing the number of timesteps be a reasonable idea?

-Ferdaus

4

If the temperature is stable and the overall energy is decreasing,
that can only mean that the system is decreasing its potential
energy, e.g. it is crystallizing. At some point that will stop
and you will fully equilibrate. Whether a crystallized geometry
is what you want for your problem is another question.

Steve