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From: |
Santosh Mogurampelly <vedhava@...24...> |

Date: |
Thu, 31 Aug 2017 02:05:52 -0400 |

On Wed, Aug 30, 2017 at 4:26 PM, Daksha, Chaitanya Mrityunjay <daksha@...43...437...> wrote:

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.

Subtracting average quantity while calculating time correlation functions is a general requirement, not specific to HCACF, but may not make any difference in many cases. Specific to HCACF, you may want to see the definitions in Eq. 2 and 3 of https://journals.aps.org/prb/pdf/10.1103/PhysRevB.43.6573 . However, when I tested on a different system using my code, I found no difference with and without subtracting the average energy. So lammps code must give you the same answer without the need of subtracting the average energy.

My suggestion in the previous reply was in fact based on an apparently wrong data you provided, in which the HCACF fluctuates around non-zero value even at long time. I suspect you wrongly interpreted J0Jt.dat output.

With sufficiently long enough correlation length of few picoseconds (attached input), I got the following HCACF with your input file.

Regarding your other questions, (1) your HCACF was not decaying to zero because you possibly used a short correlation length of 0.0002*100*10 = 0.2 ps (despite generating a nanosecond long trj); (2) you can see that the attached HCACF decays to zero in about 2 ps and as a general rule of thumb, you must need at least 10 such correlations long trj to get a decent estimate of thermal conductivity.

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

From:Santosh Mogurampelly <vedhava@...24...>

Sent:Tuesday, August 29, 2017 4:39:08 PM

To:Daksha, Chaitanya Mrityunjay

Cc:lammps-users@...655....net

Subject:Re: [lammps-users] Issues with CNT Thermal Conductivity CalculationsYou should subtract theaverageof total energy from particle's total energy for the HCACF to decay to zero.

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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Institute for Computational Molecular ScienceTemple University1925 N. 12th StPhiladelphia, PA 19122, USAhttps://scholar.google.com/citations?user=UkqEItoAAAAJ&hl=en ******************************

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********************************************************************************************************

Be Cool Be Happy

Post Doctoral Fellow; Office: SERC, 701C; +1-215-204-4221

Prof. Michael L. Klein group

Institute for Computational Molecular Science

Be Cool Be Happy

Post Doctoral Fellow; Office: SERC, 701C; +1-215-204-4221

Prof. Michael L. Klein group

Institute for Computational Molecular Science

Temple University

1925 N. 12th St

Philadelphia, PA 19122, USA

https://scholar.google.com/citations?user=UkqEItoAAAAJ&hl=en

*******************************************************************************************************

# 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 40000 # correlation length variable s equal 5 # sample interval variable d equal $p*$s # dump interval thermo ${d} 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!"

**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...>

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

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