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