thermal conductive

dear all users

i wnat to calculate thermal conductivity of gold nano particle in two
conditions :

1- nanoparticle alone
2- nanoparticle based on graphene

in 1 calculated good
but in 2 the result is very far away of reality because in the script
heat flux divided to box volume and the box in 2 is larger than 1 but
nanoparticles have same volume in 2 as 1 so how can i calculated
thermal conductivity just of nano particles in 2 ?

i see mailing list and read so much of commends but i can not find a good guide

this is script that i use for 1372 atom gold as FCC cubic

script of thermal conductivity of nanoparticle alone by cubic box
dimension = 28 A

# settings

variable T equal 300
variable V equal vol
variable dt equal 0.001

variable kB equal 1.3806504e-23 # [J/K] Boltzmann
variable eV2J equal 1.602e-19
variable A2m equal 1.0e-10
variable ps2s equal 1.0e-12
variable convert equal \{eV2J\}\*{eV2J}/\{ps2s\}/{A2m}
variable alat equal 2.456

variable p equal 10000 # correlation length
variable s equal 10 # sample interval
variable d equal $p*$s # dump interval

# setup problem

units metal
boundary p p p
atom_style atomic

#lattice fcc 4.0800 orient x 1 0 0 orient y 0 1 0 orient z 0 0 1
#region box block 0 7 0 7 0 7 units lattice
#create_box 1 box
#create_atoms 1 region box
#replicate 1 1 1
#mass 1 196.97

read_data 1372.data

velocity all create $T 4928459 mom yes rot yes dist gaussian

pair_style eam
pair_coeff * * Au_u3.eam
neighbor 2.0 bin
neigh_modify delay 10
timestep ${dt}

dump 1 all cfg 100000 dump.config.*.cfg mass type xs ys zs
vx vy vz x y z
dump 20 all atom 100000 thermalconductive.lammpstrj

# 1st equilibration run

fix 1 all npt temp $T $T 0.5 iso 0.0 0.0 100.0 drag 1
thermo 100000
run 1000000

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 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

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 scale equal {convert}/${kB}*s\*{dt}/$T/T/vol 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

variable kappa equal (v_k11+v_k22+v_k33)/3.0
print "running average conductivity: ${kappa}"

2 - script of thermal coductivity of nanoparticle based on graghene by
box dimension ( x=49 y =49 z =72)

# settings

variable T equal 300
variable V equal vol
variable dt equal 0.001

variable kB equal 1.3806504e-23 # [J/K] Boltzmann
variable eV2J equal 1.602e-19
variable A2m equal 1.0e-10
variable ps2s equal 1.0e-12
variable convert equal \{eV2J\}\*{eV2J}/\{ps2s\}/{A2m}
variable alat equal 2.456

variable p equal 10000 # correlation length
variable s equal 10 # sample interval
variable d equal $p*$s # dump interval

# setup problem

units metal
boundary p p p
atom_style atomic

#lattice fcc 4.0800 orient x 1 0 0 orient y 0 1 0 orient z 0 0 1
#region box block 0 7 0 7 0 7 units lattice
#create_box 1 box
#create_atoms 1 region box
#replicate 1 1 1
#mass 1 196.97

read_data cut1372t.data

pair_style hybrid lj/cut 9.0 eam
pair_coeff 2 2 eam Au_u3.eam
pair_coeff 1 2 lj/cut 0.048427138 3.187
pair_coeff 1 1 lj/cut 0.0 0.0
neigh_modify delay 10
timestep ${dt}

group S type 1
group M type 2

velocity all create $T 4928459 mom yes rot yes dist gaussian

dump 1 all cfg 100000 dump.config.*.cfg mass type xs ys zs
vx vy vz x y z
dump 20 all atom 100000 thermalconductive.lammpstrj

# 1st equilibration run

fix 1 M npt temp $T $T 0.5 iso 0.0 0.0 100.0 drag 1
thermo 100000
run 1000000

velocity M scale $T

unfix 1
undump 1
# thermal conductivity calculation

reset_timestep 0

compute myKE M ke/atom
compute myPE M pe/atom
compute myStress M 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

dump 2 all cfg $d dump.config.*.cfg mass type xs ys zs vx vy vz x y z
fix 1 M nve
fix JJ M ave/correlate $s $p d &                 c\_flux\[1\] c\_flux\[2\] c\_flux\[3\] type auto &                 file profile\.heatflux ave running variable scale equal {convert}/${kB}*s\*{dt}/$T/T/vol 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

variable kappa equal (v_k11+v_k22+v_k33)/3.0
print "running average conductivity: ${kappa}"

The Green-Kubo method realized by the "compute heat/flux" and "fix ave/correlate" commands is only applicable to homogeneous systems. For systems like yours, you should use the NEMD methods.

Ray