Regarding the Graphene Thermal conductivity

Dear all LAMMPS users,

While I am running the lammps code for the evaluation of thermal conductivity of Graphene with 20000 atoms with dimension box 200 X 100 X 2 having 2D layer with Tersoff potential I am getting the error like “Non Numeric positions-Simulation Unstable” during the simulation. I would like to know the reason and How can fix the problem. Please refer the input scripts here below.

  1. Sample Graphene_tersoff

  2. For thermal conductivity

  3. Sample Graphene:

Input for energy minimization

#------------------------INITIALIZATION----------------------------
units metal
boundary p p p

atom_style atomic

#-----------------------ATOM DEFINITION----------------------------

Generating a graphene structure

lattice custom 2.425 a1 1 0 0 a2 0 1.73203 0 a3 0.0 0.0 4 &
basis 0 0 0 basis 0.5 0.16666666666666666 0 basis 0.5 0.5 0 basis 0 0.6666666666666666 0

C atoms region

region grap block 0 100 0 50 0.5 1.5

Simulation box size

region boundary block 0 100 0 50 0 2

Combine regions

region whole union 2 grap boundary

Create viewing box

create_box 1 boundary

Creating C atoms

create_atoms 1 region grap
mass 1 12
group sample region grap

#------------------------FORCE FIELDS------------------------------

Interaction potential for silicon atoms

pair_style tersoff
pair_coeff * * BNC.tersoff C

neighbor 1.0 bin
neigh_modify delay 0 every 1 check yes page 500000 one 50000

#-------------------------SIMULATION PROCESS---------------------------------

Initial velocities at a given temperature

velocity all create 300 458273253 dist gaussian

Timestep to make the integration of the motion equation

timestep 0.001

Parameters to print out on the screen and log.lammps file

thermo_style custom step temp etotal vol lx ly lz press pxx pyy pzz cpu
thermo 1000

Saving atomic coordinates

dump 1 all custom 1000 [email protected]…7498…*.lammpstrj id type x y z

Energy minimization parameters

min_style cg
minimize 1.0e-10 1.0e-12 100000 10000

#-----SIMULATION DONE-------
print "Simulation complete

  1. For the evaulation of thermal conductivity:

Sample LAMMPS input script for thermal conductivity of Graphene

units real
variable T equal 300
variable V equal vol
variable dt equal 2.0
variable p equal 200 # correlation length
variable s equal 10 # sample interval
variable d equal $p*$s # dump interval

convert from LAMMPS real units to SI

variable kB equal 1.3806504e-23 # [J/K] Boltzmann
variable kCal2J equal 4186.0/6.02214e23
variable A2m equal 1.0e-10
variable fs2s equal 1.0e-15
variable convert equal {kCal2J}*{kCal2J}/{fs2s}/{A2m}

setup problem

dimension 3
boundary p p p

atom_style atomic

read_data Sample_Graphene_Tersoff
mass 1 12.0

pair_style tersoff
pair_coeff * * BNC.tersoff C

timestep ${dt}
thermo $d

equilibration and thermalization

velocity all create 300 102486 mom yes rot yes dist gaussian
fix NVT all nvt temp $T $T 0.01 drag 0.2
run 8000

#thermal conductivity calculation, switch to NVE if desired

unfix NVT
fix NVE all nve

reset_timestep 0
compute myKE all ke/atom
compute myPE all pe/atom
compute myStress all stress/atom NULL 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
fix JJ all ave/correlate $s $p d & c_flux[1] c_flux[2] c_flux[3] type auto file J0Jt.dat ave running variable scale equal {convert}/${kB}/$T/$T/$V*s*{dt}
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_style custom step temp v_Jx v_Jy v_Jz v_k11 v_k22 v_k33
dump 7 all custom 2000 Graphene_thermal_deform*.lammpstrj id type x y z
run 100000
variable k equal (v_k11+v_k22+v_k33)/3.0
variable ndens equal count(all)/vol
print “average conductivity: $k[W/mK] @ T K, {ndens} /A^3”

This is one of the most common error messages:
lammps.sandia.gov/doc/Section_errors.html

and it indicates unstable dynamics.

One thing that stands out is using real units with the same Tersoff potential file:
http://lammps.sandia.gov/doc/pair_tersoff.html

Please review carefully your input configuration, and look for any other inconsistencies.

Giacomo