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From: |
"Daksha, Chaitanya Mrityunjay" <daksha@...2437...> |

Date: |
Wed, 30 Aug 2017 20:26:10 +0000 |

Thank you for your response. If you don't mind, I have a few questions:

Would it be possible for you to provide any reference(s) for this subtraction? The sources I've looked through don't apply this subtraction, at least to the best of my knowledge. I have attached them for viewing purpose. But, please correct me if I am wrong.

Also, if I wanted to implement the subtraction, could you suggest ways it may be possible in my script? I do not think it is possible to implement the subtraction prior to the 'compute flux' command, since it requires arguments that are also computes. Therefore, I would be unable to create variables for the new potential and kinetic energies, post subtraction.

Thank you once again,

Chad Daksha

You should subtract the *average* of total energy from particle's total energy for the HCACF to decay to zero.

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On Tue, Aug 29, 2017 at 3:06 PM, Daksha, Chaitanya Mrityunjay
<daksha@...2437...> wrote:

Dear LAMMPS Users,

I am trying to calculate the thermal conductivity of a (10,10) CNT that is 5 nm in length using the Green-Kubo formalism. I modified the liquid Argon LAMMPS thermal conductivity example for CNT. First, I equilibrated the CNT structure at 300K, and then I ran the simulation to get the heat flux, heat current auto correlation function (HCACF) and thermal conductivity. To plot the HCACF, I averaged columns 4, 5, and 6 in the ‘J0Jt.dat’ file for every 1000 timesteps (which is my dump interval).

Currently I am having two problems -

- The HCACF does not decay to zero. I have tried running the simulation for up to 1200 ps, but the HCACF still did not decay to zero.
- The thermal conductivity value I attain differs based on the correlation length parameter I use in the ‘fix ave/correlate’ command. Should the conductivity be independent of correlation length? If not, then how should I determine the appropriate correlation length?

I checked the LAMMPS email archive, but I was not able to find anything specific to my issues. Attached is the LAMMPS script, as well as other input data files. There is also a graph of the HCACF over time attached.

I would appreciate any insights as to why the HCACF does not decay to zero.

Thank you,

Chad Daksha

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**Attachment:
Luke-JHT-2007-Thermal Conductivity of SWNT.pdf**

**Attachment:
Yao-2013-Thermal conduction of carbon nanotubes using molecular dynamics.pdf**

**Attachment:
Che-2000-Thermal Conductivity of CNTs.pdf**

# input script for SWNT simulation in LAMMPS #-------10--------20--------30--------40--------50--------60--------70--------80 # Variables variable input index coordi-cnt.txt # INITIALIZATION units metal boundary p p p atom_style atomic variable T equal 300.0 variable dt equal 0.0002 # ps variable p equal 100 # correlation length variable s equal 10 # sample interval variable d equal $p*$s # dump interval thermo 1000 timestep ${dt} # ps # ATOM DEFINITION read_data ${input} # FORCE FIELD pair_style airebo 3.0 1 1 pair_coeff * * CH.airebo C # SETTINGS neighbor 1.0 bin neigh_modify delay 1 # Calculating Volume variable diameter equal (sqrt(3)*1.42*sqrt(10^2+10*10+10^2))/PI #(10,10) armchair CNT; assuming C-C bond distance of 1.42 variable radius equal ${diameter}/2 variable height equal "lz" #Height is equal to z-dimension length variable V equal 2*PI*${radius}*3.4*${height} # Convert from metal units to SI variable kB equal 1.3806504e-23 # [J/K] Boltzmann variable eV2J equal 1.602176565e-19 variable A2m equal 1.0e-10 variable ps2s equal 1.0e-12 variable convert equal ${eV2J}*${eV2J}/${ps2s}/${A2m} group Carbon type 1 # ------------------------------------------------------------------------------ variable temp equal temp # output for VMD dump 1 all custom 10000 dump.uhmwpe-coord id type x y z dump 2 all xyz 10000 dump.uhmwpe-xyz-format dump_modify 2 element C ## --- Relaxation --- fix 51 all nvt temp $T $T 0.1 run 200000 ## --- Thermal Conductivity Calculation --- unfix 51 fix 51 all nve reset_timestep 0 compute myKE all ke/atom compute myPE all pe/atom compute myStress all stress/atom NULL virial compute flux all heat/flux myKE myPE myStress variable Jx equal c_flux[1]/$V variable Jy equal c_flux[2]/$V variable Jz equal c_flux[3]/$V 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 cpu v_Jx v_Jy v_Jz v_k11 v_k22 v_k33 run 2000000 variable k equal (v_k11+v_k22+v_k33)/3.0 print "average conductivity: $k[W/mK] @ $T K" unfix 51 print "Run is complete!"

**Follow-Ups**:**Re: [lammps-users] Issues with CNT Thermal Conductivity Calculations***From:*Santosh Mogurampelly <vedhava@...24...>

**References**:**[lammps-users] Issues with CNT Thermal Conductivity Calculations***From:*"Daksha, Chaitanya Mrityunjay" <daksha@...2437...>

**Re: [lammps-users] Issues with CNT Thermal Conductivity Calculations***From:*Santosh Mogurampelly <vedhava@...24...>

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