Dear LAMMPS users,

I got thermal conductivity in GNR with L=75 nm and width=15nm equal 2973.9881803332687[W/mK] @ 300 k .but when i apply defect , the thermal conductivity will increase instead of reduse .the defect is delete 456 atom carbon in cube region

i must change values of Nevery,Nrepeat, when i apply defect?. I don’t know what numbers are true for these?

units metal

variable T equal 300

variable V equal vol

variable p equal 2000 # correlation length

variable s equal 2 # sample interval

variable d equal $p*$s # dump interval

variable d equal 2000*$s

variable d equal 2000*2

variable dt equal 0.001

# convert from LAMMPS real units to SI

variable kB equal 1.3806504e-23 # [J/K] Boltzmann

variable ev2J equal 1.60217653e-19

variable A2m equal 1.0e-10

variable ps2s equal 1.0e-12

variable convert equal {ev2J}*{ev2J}/{ps2s}/{A2m}

variable convert equal 1.60217653e-019*{ev2J}/{ps2s}/{A2m}
variable convert equal 1.60217653e-019*1.60217653e-019/{ps2s}/{A2m}
variable convert equal 1.60217653e-019*1.60217653e-019/9.9999999999999998e-013/{A2m}

variable convert equal 1.60217653e-019*1.60217653e-019/9.9999999999999998e-013/1e-010

# setup problem

dimension 3

atom_style atomic

boundary p p p

read_data data.box

orthogonal box = (0 -100 0) to (50 100 50)

1 by 1 by 1 MPI processor grid

44064 atoms

region right block 5 25 60 65 0 2 units box

group right region right

456 atoms in group right

mass 1 12.000

pair_style tersoff

pair_coeff * * sic.tersoff C

timestep 0.001

thermo $d

thermo 4000

# equilibration and thermalization

velocity all create $T 1234 mom yes rot yes dist gaussian

velocity all create 300 1234 mom yes rot yes dist gaussian

delete_atoms region right

Deleted 456 atoms, new total = 43608

fix NVT all nvt temp $T $T 0.001 drag 0.02

fix NVT all nvt temp 300 $T 0.001 drag 0.02

fix NVT all nvt temp 300 300 0.001 drag 0.02

dump 1 all xyz 200 dump.xyz

run 4000

Memory usage per processor = 65.0334 Mbytes

Step Temp E_pair E_mol TotEng Press

0 300.16976 60020156 0 60021848 1.2682975e+008

4000 300.38051 -257973.14 0 -256280 175939.16

Loop time of 5376.78 on 1 procs for 4000 steps with 43608 atoms

Pair time () = 5348.28 (99.47)
Neigh time () = 15.5844 (0.289847)

Comm time () = 2.23081 (0.0414896)
Outpt time () = 2.4024 (0.0446811)

Other time (%) = 8.27801 (0.153958)

Nlocal: 43608 ave 43608 max 43608 min

Histogram: 1 0 0 0 0 0 0 0 0 0

Nghost: 27194 ave 27194 max 27194 min

Histogram: 1 0 0 0 0 0 0 0 0 0

Neighs: 0 ave 0 max 0 min

Histogram: 1 0 0 0 0 0 0 0 0 0

FullNghs: 2.0361e+006 ave 2.0361e+006 max 2.0361e+006 min

Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 2036102

Ave neighs/atom = 46.691

Neighbor list builds = 116

Dangerous builds = 2

# 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 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

fix JJ all ave/correlate 2 $p $d c_flux[1] c_flux[2] c_flux[3] type auto file J0Jt.dat ave running

fix JJ all ave/correlate 2 2000 $d c_flux[1] c_flux[2] c_flux[3] type auto file J0Jt.dat ave running

fix JJ all ave/correlate 2 2000 4000 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 scale equal 2.566969633282841e-016/${kB}/$T/$T/$V*s*{dt}

variable scale equal 2.566969633282841e-016/1.3806504000000001e-023/$T/$T/$V*s*{dt}

variable scale equal 2.566969633282841e-016/1.3806504000000001e-023/300/$T/$V*s*{dt}

variable scale equal 2.566969633282841e-016/1.3806504000000001e-023/300/300/$V*s*{dt}

variable scale equal 2.566969633282841e-016/1.3806504000000001e-023/300/300/500000*s*{dt}

variable scale equal 2.566969633282841e-016/1.3806504000000001e-023/300/300/500000*2*{dt}
variable scale equal 2.566969633282841e-016/1.3806504000000001e-023/300/300/500000*2*0.001
variable k11 equal trap(f_JJ[3])*{scale}

variable k11 equal trap(f_JJ[3])*8.2633184517250094e-007
variable k22 equal trap(f_JJ[4])*{scale}
variable k22 equal trap(f_JJ[4])*8.2633184517250094e-007
variable k33 equal trap(f_JJ[5])*{scale}

variable k33 equal trap(f_JJ[5])*8.2633184517250094e-007

thermo_style custom step temp v_Jx v_Jy v_Jz v_k11 v_k22 v_k33

run 8000

Memory usage per processor = 78.2298 Mbytes

Step Temp Jx Jy Jz k11 k22 k33

0 300.38051 0.009232223 0.002334846 -0.014331305 8.8039399 0.56309409 21.214654

4000 299.58903 -0.00084436811 -0.0014041688 -0.0084586756 99.231854 -1.7423237 1181.3462

8000 299.42427 0.0016410622 0.0047518503 -0.003760334 352.15429 181.80008 17456.413

Loop time of 4967.16 on 1 procs for 8000 steps with 43608 atoms

Pair time () = 4917.86 (99.0075)
Neigh time () = 11.4036 (0.22958)

Comm time () = 3.55681 (0.0716065)
Outpt time () = 4.82041 (0.0970456)

Other time (%) = 29.5196 (0.594296)

Nlocal: 43608 ave 43608 max 43608 min

Histogram: 1 0 0 0 0 0 0 0 0 0

Nghost: 21630 ave 21630 max 21630 min

Histogram: 1 0 0 0 0 0 0 0 0 0

Neighs: 0 ave 0 max 0 min

Histogram: 1 0 0 0 0 0 0 0 0 0

FullNghs: 1.95125e+006 ave 1.95125e+006 max 1.95125e+006 min

Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 1951252

Ave neighs/atom = 44.7453

Neighbor list builds = 93

Dangerous builds = 0

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”

average conductivity: 5996.7889867439699[W/mK] @ 300 k, 0.087216000000000002 /A^3