Dear Lammps users,

I’ve been trying to run equilibration for monolayer graphene over 8 layers copper using reaxff potential. I applied setforce 0 0 0 to the bottom 4 layers of copper and ran minimization. Following this, I ran the equilibration using NVE and a berdensen thermostat at 600 K (for the upper 4 layers of copper and graphene). Now I am a bit confused on how I should choose a temperature dampening factor. What parameters are we supposed to see?

I ran it at a tilmestep of 0.15fs(for units real is in fs) and I set the Tdamp value at 10.

fix 3 cu_upper temp/berendsen 600 600 5.0

when I did this, I see no vibrating atoms when I visualized on VMD.

Next, I tried with a Tdamp value of 0.003

fix 3 cu_upper temp/berendsen 600 600 0.003

This gave values of ‘nan’ for temp, pressure, energy and center of mass.

If somebody could please guide me and give a better picture of how we choose this dampening factor, I would really appreciate it.

Much thanks!

I am attaching my code here.

#Input file for Cu-Graphene

#INITIALISATION-----------------

units real

dimension 3

boundary p p p

atom_style charge

read_data input.dat

#SET POTENTIAL-----------------

pair_style reax

pair_coeff * * ffield.reax 10 1

#DEFINE GROUPS AND AND VARIABLES--------------

variable cubase_zhi equal 5.4225

variable cuupper_zlo equal 7.2300

variable cuupper_zhi equal 12.6525

variable grapheneheight equal 16.6525

region cubase block INF INF INF INF 0 {cubase_zhi} units box region cuupper block INF INF INF INF {cuupper_zlo} {cuupper_zhi} units box region graph block INF INF INF INF {grapheneheight} ${grapheneheight} units box

group cu_base region cubase

group cu_upper region cuupper

group graphene region graph

#PREMLIMNARY MINIMISATION--------

fix freeze cu_base setforce 0 0 0

dump min all atom 1 result_min.lammpstrj

minimize 1.0e-7 1.0e-9 10000 100000

undump min

reset_timestep 0

#EQUILIBRATION-------------------

timestep 0.15

fix 1 cu_upper nve

fix 2 graphene nve

fix 3 cu_upper temp/berendsen 600 600 0.003

fix 4 graphene temp/berendsen 600 600 0.003

thermo 200

compute cmass all com

thermo_style custom step temp etotal c_cmass[1] c_cmass[2] c_cmass[3]

thermo_modify lost ignore

dump equi all atom 1 result_equi.lammpstrj

run 2000

undump equi