# Regarding TDamp for NVE using units real

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

#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

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?

please search through the mailing list archives, there are *many*
discussions on how to properly equilibrate such slab configurations
and their parameters. there are also examples,
discussions/recommendations in different parts of the manual and
slides from LAMMPS tutorials.

axel.

You should also monitor the temperature with
the thermo output. If the system equilibrate
to 600K then you’re in good shape. If
you only tried damping factors of 5 and 0.003
try something in between. For real units 5 = 5psec
= 5000 timesteps (too big), 0.003 = 3 time steps
(far too small).

Steve