komorebi566 / new-version-spectral-decomposition-python-tools

(NEW) Tools for computing spectral heat current distribution using LAMMPS NEMD simulations.

Spectral decomposition of thermal conductance tools

This is an improved project

Due to my previous stupidity, I limited the scope of the project. The previous project needed to ensure that the number of atoms on the left and right ends of the illusion interface was equal. But in principle it is not required.

Notes:

When use this method to calculation some material with very low thermal conductivity, maybe one can get some very strange results (the spectral heat flux will turn to negative or positive). I don't know why, but one can increase the temperature difference between the heat source and sink to address this problem. I would appreciate it if someone could email me the mechanism behind it.

If you use the code, the following citations are highly recommended.

1. K. Sääskilahti, J. Oksanen, J. Tulkki, and S. Volz, Phys. Rev. B 90, 134312 (2014)
2. K. Sääskilahti, J. Oksanen, S. Volz, and J. Tulkki, Phys. Rev. B 91, 115426 (2015)
3. Xu K, Deng S, Liang T, et al, Efficient mechanical modulation of the phonon thermal conductivity of Mo₆S₆ nanowires. Nanoscale, 2022
4. Yao Y, Ren G, Yu Y, et al., Thermal conduction mechanism of ferroelastic Zr‐Y‐Yb‐Ta‐Nb‐O high‐entropy oxides with glass‐like thermal conductivity. Journal of the American Ceramic Society, 2022

Files need to be modified

• relax_thermal.in (input file for lammps, and use to get the atoms velocity)
• forces.in (input file for force_calculate.py, in order to call the python interface of lammps)
• SHC_generate.py (Main program, useful for calculating spectral decomposition thermal conductance)

Usage

1. According to one specific needs, modify the potential format in the files (relax_thermal.in and forces.in)

• Modify in relax_thermal.in and forces.in file

# ************ Modify in relax_thermal.in and forces.in file ************
# *********************  Potential  function setting  *****************

pair_style                 tersoff
pair_coeff            *      *           BNC.tersoff        B        C       N

# ************ Modify in relax_thermal.in and forces.in file ************
#  *************************  For Y direction  **************************************

variable         y_max        equal           ly              # Depends on the direction of heat transport
variable         P            equal     ${y_max}/2-100
variable         P1           equal     ${y_max}/2+100

variable         tmp1         equal     ${P1}-${P}
variable         tmp          equal     ${tmp1}/40

variable         L1           equal     ${P}+3*${tmp}
variable         R1           equal     ${P1}-3*${tmp}

• Modify in relax_thermal.in file

variable        dmid         equal            6         ## Set to 6 (A) here, one can modify it
variable        middle       equal        ${y_max}/2 
variable        mid_left     equal     ${middle}-${dmid}
variable        mid_right    equal     ${middle}+${dmid}

• Modify in relax_thermal.in file (For dn parameter)

# **************************  Collect Velocities for the calculation of force constants *************************

variable      dn     equal    15            

dump          vels   interface   custom    ${dn}   vels.dat   id   type   vx   vy   vz
dump_modify   vels   format      line      "%d   %d   %0.8g   %0.8g   %0.8g"
dump_modify   vels   sort        id

2. Read the calling part at the end of the SHC_generate.py file and modify it according to needs.

    postprocessor = SHCPostProc(compact_velocities_file,
                                fileprefix,            # forces.in
                                dt_md = md_timestep,   # timestep
                                dn = dn,               # Dump interval
                                scaleFactor = unit_scaling_factor,
                                LAMMPSDumpFile = atomic_velocities_file, # velocity file
                                widthWin = frequency_window_width,
                                LAMMPSInFile = in_file,
                                in_plane = False,
                                out_of_plane = False,
                                reCalcVels = True,
                                reCalcFC = True)

3. Compile the compactify_vels.cpp file, and add the generated compactify_vels to the command path.

g++  compactify_vels.cpp  -o  compactify_vels

4. run

• lmp_mpi < relax_thermal.in

• python SHC_generate.py

  If one want to run lammps and python in parallel, one can use following command (need to set if_MPI = True in SHC_generate.py file):

  mpirun  -np  10  python  SHC_generate.py   # for generate the force constant in parallel

  ---

  Maybe one need to modify the input file according to the error report

  • tips: check the generate_force.log file is a good option

  If you are lucky, maybe you don’t need to modify anything

Output

1. Spectral thermal conductance

​ This picture is very similar to the reference (see below)

2. Accumulated conductance