[lammps-users] compute tc command


I add “compute tc command” into lammps, the usage for it is like this:

compute tc command
Syntax:
compute ID group-ID tc c_temp-ID c_flux-ID v_factor_ac v_factor_tc direction portion M tc_ntimestep_start tc_ntimestep_freq


- ID, group-ID are documented in compute command
- tc = style name of this compute command
- temp-ID = ID of a compute that calculates temperature
- flux-ID = ID of a compute that calculates heat flux vector
- factor_ac = ID of a variable( Now it makes no sense, because I’ve modified the codes to obtain the normalized HCACF, so you can just keep it as 1.0 )
- factor_tc = ID of a variable whose value is used to transform the thermal conductivity unit defined in “units command” to the units desired
- direction = x or y or z or iso, direction for thermal conductivity computation
- portion = first(total heat flux: jc + jv) or second(just conductive portion: jc only) for heat flux contribution
- M = M value in discrete Green Kubo thermal conductivity expression
- tc_ntimestep_start = starting timestep for “ac.dat” and “tc.dat” output(timestep units, not time units)
- tc_ntimestep_freq = output frequency for “ac.dat” and “tc.dat” (timestep units, not time units)

The command can output two files “ac.dat”(Normalized HCACF) and “tc.dat”(thermal conductivity), every “tc_ntimestep_freq” timesteps, and start at “tc_ntimestep” timestep.
And the value returned from this command is thermal conductivity value at each timestep, so you can obtain a file like “tc_time.dat” using fix ave/time command, then you can get a curve, whose vertical value is thermal conductivity, and horizontal value is timesteps.
You just keep “factor_ac” as 1.0, “v_factor_ac” can be used to transform dimensionless units defined by “units command” in lammps to SI units or other units you desire.

Citing: Discrete GK expression is cited from PK Schelling’s article "Comparison of atomic-level simulation methods for computing thermal conductivity " (2002), Eqs. 9, as attached.

Note: Because thermal conductivity computation is accumulated as timestep increases, so you can only cite the compute tc command once, for example, if you cite it in “thermo_style”, then you can’t cite it in a “fix ave/time”.

Usage:

for example:

compute myKE all ke/atom
compute myPE all pe/atom
compute myStress all stress/atom virial
variable factor_ac equal 1.0
variable factor_tc equal 1.3806504e-23*sqrt(1.67e-21/6.633e-26)/3.405e-10^2
compute jflux all heat/flux myKE myPE myStress
compute tc all tc c_thermo_temp c_jflux v_factor_ac v_factor_tc iso first 10000 900000 100000
fix tc_out all ave/time 1 1 1 c_tc file tc_time.dat


Xiaoliang
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compute_tc.cpp (12.9 KB)

compute_tc.h (1.23 KB)

Schellingetal-2002.pdf (147 KB)

Isn’t it more efficient to write the heat flux data to some date file after the data is collected and then use FFT to compute the autocorrelation than to use a double loop in LAMMPS?

Zhun-Yong

Yes, it’s another way of computing autocorrelation, and maybe it’s more efficient, but I didn’t try it.

Xiaoliang

10年6月19日,周六, Zhun-Yong ONG <zhunyong@…24…> 写道: