I am conducting a LAMMPS simulation work to get thermal conductivity, using rNEMD method. To get a good grasp of this method, I tried to first understand the example available in Github, provided in this link “https://github.com/lammps/lammps-testing/blob/30d890b7a9608165f372dee7c1ba7823129b4269/tests/examples/KAPPA/in.mp”
However, I have difficulty understanding some parts of this method. I ran this code in my own system and I got the log file and temperature profile. Having said that, I am not sure how can I get use of the output information to calculate thermal conductivity.
According to the LAMMPS documentation, using “fix ave/chunk”, we can get a temperature gradient (dT/dz), outputted in the tmp.profile file. Therefore, I am supposing that in order to get the real temperature of each region, I have to do the following calculations:
T(final)= [(temperature gradient)*dz]+T(initial)
where T(initial) would be the total temperature of the system (e.g. 300 K). This part especially gets so confusing to me, as in the “Read me” section of Github (https://github.com/lammps/lammps-testing/blob/30d890b7a9608165f372dee7c1ba7823129b4269/tests/examples/KAPPA/README), it mentions the average temperature difference should be 1.16, which is not identical to my calculations. Also, reporting this method in lj units has added to the confusion. Thus, I would really appreciate any clarifications on this method.
Thank you very much for your time and consideration.