Absurd Results while setting the temperature of the graphene Sheet

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1

Hi,

My objective is to bring the temperature of graphene sheet to 300K. The graphene sheets were build using the examples provided in moltemplate.

------input script-----

----------------------------- Initialization Section --------------------

include system.in.init

----------------------------- Atom Definition Section -------------------

read_data system.data

----------------------------- Settings Section --------------------------

include system.in.settings

----------------------------- Run Section -------------------------------

– simulation protocol –

dump 1 all custom 100 traj_nvt_surface.lammpstrj id mol type x y z ix iy iz
timestep 0.01
thermo_style custom step temp pe etotal press vol epair #ebond eangle edihed
thermo 500 # time interval for printing out “thermo” data

fix sheet Cgraphene rigid single langevin 300.0 300.0 5.0 428984
fix sheet1 Cgraphene nve

run 10000

unfix sheet
unfix sheet1

fix nvt Cgraphene nvt temp 300.0 300.0 10.0

timestep 0.05
run 5000

write_data system_after_surface_nvt.data

-------output after nvt-----------

Step Temp PotEng TotEng Press Volume E_pair
10000 1968756.5 8.5135257e+08 8.8068915e+08 33914408 6929000 8.5135257e+08
10500 130.45269 88079881 88081825 3497537.6 6929000 88079881
11000 149.42008 9177794.4 9180021 367510.81 6929000 9177794.4
11500 25.414477 4129011.1 4129389.8 166552.02 6929000 4129011.1
12000 9.0349136 2926053.4 2926188.1 118539.05 6929000 2926053.4
12500 4.4390259 2431755.9 2431822 98763.241 6929000 2431755.9
13000 2.6072496 2169827.9 2169866.8 88261.933 6929000 2169827.9
13500 1.7119558 2009258.5 2009284 81812.164 6929000 2009258.5
14000 1.212646 1901139.4 1901157.4 77461.804 6929000 1901139.4
14500 0.90731935 1823420.8 1823434.3 74329.792 6929000 1823420.8
15000 0.7075112 1764804.4 1764814.9 71964.219 6929000 1764804.4

can u explain why Im getting absurd results ??

PS- i tried by removing -rigid single- and the temperature seems to be stable around 300K but the sheet will be totally deformed.

2

You should generally read the documentation for the keywords you use:

https://lammps.sandia.gov/doc/fix_rigid.html

Note

You should not update the atoms in rigid bodies via other time-integration fixes (e.g. fix nve, fix nvt, fix npt, fix move), or you will have conflicting updates to positions and velocities resulting in unphysical behavior in most cases. When performing a hybrid simulation with some atoms in rigid bodies, and some not, a separate time integration fix like fix nve or fix nvt should be used for the non-rigid particles.

3

Thanks Giacomo!

Yes. The moltemplate graphene / nanotube example does not currently simulate the motion of the carbon atoms. They are held rigid. Only the water in that example is allowed to move. (If you try to apply a thermostat to immobile atoms, expect funny things to happen.)

Andrew

P.S. My apologies. That example was intended to demonstrate how to build a wall out of atoms to confine a liquid (water). I was too lazy to figure out what force field to use to actually allow the carbon atoms to move. I also worried that this a simulation might explode because the initial carbon atom configuration have not been relaxed beforehand. There is a discussion on this problem here:
http://www.moltemplate.org/examples/nanotube+water/README_realistic_junctions.txt

I confess this isn’t my area. I run simulations of coarse grained DNA. If anybody has suggestions how to improve the graphene / nanotube example, please send them to me and I will gladly update the example.