Dear Lammps users,
Hi, I am calculating thermal conductivity of Graphene on amorphous SiO2 substrate using both EMD (Green-Kubo) and NEMD (MP) methods. I created an initial structure set up with VMD topotools (nanotube & inorganic material builder), which is contained in a data file. I am using airebo for C, tersoff for Si and O, and vdW (lj/cut) for interactions between C-Si and C-O.
For both EMD and NEMD simulations, problems occurred during the structure relaxation. During NPT or NVT run, the graphene sheet on the amorphous SiO2 moved far away from the substrate, eventually reached the box top, and broke. I have set the boundary condition to be (p p f) where graphene is on xy plane. I first though it might have been the vdW repulsion-attraction phenomena and checked the parameters for lj/cut interactions, but they seemed to be correct (parameter values extracted from literature). I wonder if anyone has any clue on why this is happening.
One more question. It does not seem to be very meaningful to relax amorphous structure though, I just tried to relax both Graphene and SiO2. When I did that, I observed some atoms were lost (or moved out of the box). I set the simulation to ignore the lost atoms, so the simulation could run nonetheless though, is there anyway to prevent the atoms to move that much?
Please find the input script below.
Thank you in advance,
Chris
setup problem
units metal
boundary p p f
atom_style atomic
read_data …/data.mergedGrSiO2
lattice custom ${alat} a1 1 0 0 a2 0 1.73203 0 a3 0 0 10 basis 0 0 0 basis 0.5 0.16666666666666666 0 basis 0.5 0.5 0 basis 0 0.6666666666666666 0
group gr id <= 2304
group sub id > 2304
pair_style hybrid airebo 3.0 tersoff lj/cut 2.5
pair_coeff * * airebo /home/kpark39/programs/lammps-1Feb14/potentials/CH.airebo C NULL NULL
pair_coeff * * tersoff /home/kpark39/programs/lammps-1Feb14/potentials/SiO.tersoff NULL O Si
pair_coeff 1 2 lj/cut 0.006734 3.275
pair_coeff 1 3 lj/cut 0.008890 3.628
neighbor 2.0 bin
neigh_modify delay 10
timestep ${dt}
thermo_modify lost ignore
velocity all create $T 4928459 mom yes rot yes dist gaussian
dump 1 all cfg 10000 dump.config.*.cfg mass type xs ys zs vx vy vz x y z
1st equilibration run
#fix 1 all nvt temp $T $T 0.5
fix 1 all npt temp $T $T 0.5 x 0 0 0.5 y 0 0 0.5
thermo 1000
run 50000
velocity all scale $T
unfix 1
undump 1
thermal conductivity calculation
reset_timestep 0
compute myKE all ke/atom
compute myPE all pe/atom
compute myStress all stress/atom virial
compute flux all heat/flux myKE myPE myStress
variable Jx equal c_flux[1]/vol
variable Jy equal c_flux[2]/vol
variable Jz equal c_flux[3]/vol
dump 2 all cfg $d dump.config..cfg mass type xs ys zs vx vy vz x y z
fix 1 all nve
fix JJ all ave/correlate $s $p d &
c_flux[1] c_flux[2] c_flux[3] type auto &
file profile.heatflux ave running
variable V2 equal 80*80*60
variable scale equal {convert}/${kB}s*{dt}/$T/T/{V2}
variable k11 equal trap(f_JJ[3]){scale}
variable k22 equal trap(f_JJ[4])*{scale}
variable k33 equal trap(f_JJ[5])${scale}
thermo $d
thermo_style custom step temp v_Jx v_Jy v_Jz v_k11 v_k22 v_k33
run 2000000