Exercise: Thermal conductivity of CuI from BTE#
In this exercise, you will:
- Calculate thermal conductivity from BTE
- Compare phonon lifetime from aiGK and BTE
Setting up Phono3py calculations#
Prepare geometry#
The BTE calculation with Phono3py requires first principle calculations of displaced supercells.
To prepare the calculation, we need to prepare primitive cell geometry.in and a supercell matrix of the target system,
following the same procedure as introduced in the section of Setting up phonon calculations
in the previous phonon tutorial.
Prepare phono3py.in#
Apart from the settings for first principles calculation, [phono3py] settings
need specifying, including the supercell matrix that we require, and the working directory.
Here is a example of phono3py.in
Example of phono3py.in
[files]
geometry: geometry.in
[calculator]
name: aims
socketio: true
[calculator.parameters]
xc: pbesol
compute_forces: true
[calculator.kpoints]
density: 2
[calculator.basissets]
Cu: light
I: light
[phono3py]
supercell_matrix: [-3, 3, 3, 3, -3, 3, 3, 3, -3]
cutoff_pair_distance: 6.0
workdir: phono3py
The supercell_matrix should be carefully chosen as we discussed before in phonon calculations.
The third-order force decays fast for non-ionic crystals, so a cutoff_pair_distance can be
applied to reduce number of the displaced supercells. For CuI, the cutoff distance of \(6.0\) Å will
reduce the number of the displaced structures from \(716\) to \(102\).
In practice calculations, both the supercell size and cutoff distances should be carefully converged.
After preparing geometry.in and phono3py.in, we need to submit the calculation with a submission script
Example for the submission script on the webinar cluster submit.sh
#!/bin/bash -l
# Standard output and error:
#SBATCH -o ./slurm.stdout
#SBATCH -e ./slurm.stderr
# Initial working directory:
# Standard output and error:
#SBATCH -o ./slurm.stdout
#SBATCH -e ./slurm.stderr
# Initial working directory:
#SBATCH -D ./
# Job Name:
#SBATCH -J FHI-aims
# Number of nodes and MPI tasks per node:
#SBATCH --nodes=1
# HPC7a
#SBATCH --tasks-per-node=192
#
# Wall clock limit:
#SBATCH --time=10:00:00
module purge
module load fhi-aims vibes
vibes run phono3py
Output information
[vibes.run] run phono3py workflow with settings from phono3py.in
[calculator] Update aims k_grid with kpt density of 2 to [2, 2, 2]
[calculator] .. add `sc_accuracy_rho: 1e-06` to parameters (default)
[calculator] .. add `relativistic: atomic_zora scalar` to parameters (default)
[calculator] .. add `output_level: MD_light` to parameters (default)
[calculator] Add basisset `light` for atom `Cu` to basissets folder.
[calculator] Add basisset `light` for atom `I` to basissets folder.
[calculator] Calculator: aims
[calculator] settings:
[calculator] xc: pbesol
[calculator] compute_forces: True
[calculator] k_grid: [2, 2, 2]
[calculator] sc_accuracy_rho: 1e-06
[calculator] relativistic: atomic_zora scalar
[calculator] output_level: MD_light
[calculator] use_pimd_wrapper: ('localhost', 10011)
[calculator] aims_command: /talos/u/shuoz/bin/run_gpu_vibes.sh
[calculator] species_dir: /talos/u/shuoz/data/240919_aigk_tutorial/phono3py/phono3py/basissets
[vibes] Run phonopy workflow in working directory
/talos/u/shuoz/data/240919_aigk_tutorial/phono3py/phono3py
[trajectory] Start phonopy postprocess:
[trajectory] Parse `/talos/u/shuoz/data/240919_aigk_tutorial/phono3py/phono3py/trajectory.son`
[son] open file: /talos/u/shuoz/data/240919_aigk_tutorial/phono3py/phono3py/trajectory.son
[socketio] Use SocketIO with host localhost and port 10011
[backup] /talos/u/shuoz/data/240919_aigk_tutorial/phono3py/phono3py/calculations does not exist, nothing to back up.
[vibes] Compute structure 1 of 102: working
[vibes] Compute structure 1 of 102: finished.
[vibes] Compute structure 2 of 102: working
...
In the output information, you will find that 102 displaced supercells are generated for calculating the third order force constant.
Postprocess#
After the calculation is finished, we need to change directory to phono3py/output,
and run
The mesh setting --mesh 6 6 6 is the \(q\) mesh density where the phonon-phonon
scattering events is calculated. The thermal conductivity related properties will be
written into kappa-m666.hdf5.
Output of phono3py-load phono3py_params.yaml --mesh 6 6 6 --br
...
----------- Thermal conductivity (W/m-k) with tetrahedron method -----------
# T(K) xx yy zz yz xz xy
0.0 0.000 0.000 0.000 0.000 0.000 0.000
10.0 3712.697 3712.697 3712.697 -0.000 -0.000 -0.000
20.0 583.927 583.927 583.927 -0.000 -0.000 -0.000
30.0 160.918 160.918 160.918 -0.000 -0.000 -0.000
40.0 73.503 73.503 73.503 -0.000 -0.000 -0.000
50.0 44.940 44.940 44.940 -0.000 -0.000 -0.000
60.0 32.054 32.054 32.054 -0.000 -0.000 -0.000
70.0 24.949 24.949 24.949 -0.000 -0.000 -0.000
80.0 20.490 20.490 20.490 -0.000 -0.000 -0.000
90.0 17.435 17.435 17.435 -0.000 -0.000 -0.000
100.0 15.208 15.208 15.208 -0.000 -0.000 -0.000
110.0 13.509 13.509 13.509 -0.000 -0.000 -0.000
120.0 12.167 12.167 12.167 -0.000 -0.000 -0.000
130.0 11.079 11.079 11.079 -0.000 -0.000 -0.000
140.0 10.176 10.176 10.176 -0.000 -0.000 -0.000
150.0 9.415 9.415 9.415 -0.000 -0.000 -0.000
160.0 8.764 8.764 8.764 -0.000 -0.000 -0.000
170.0 8.200 8.200 8.200 -0.000 -0.000 -0.000
180.0 7.706 7.706 7.706 -0.000 -0.000 -0.000
190.0 7.270 7.270 7.270 -0.000 -0.000 -0.000
200.0 6.882 6.882 6.882 -0.000 -0.000 -0.000
210.0 6.534 6.534 6.534 -0.000 -0.000 -0.000
220.0 6.220 6.220 6.220 -0.000 -0.000 -0.000
230.0 5.936 5.936 5.936 -0.000 -0.000 -0.000
240.0 5.677 5.677 5.677 -0.000 -0.000 -0.000
250.0 5.440 5.440 5.440 -0.000 -0.000 -0.000
260.0 5.223 5.223 5.223 -0.000 -0.000 -0.000
270.0 5.022 5.022 5.022 -0.000 -0.000 -0.000
280.0 4.837 4.837 4.837 -0.000 -0.000 -0.000
290.0 4.665 4.665 4.665 -0.000 -0.000 -0.000
300.0 4.504 4.504 4.504 -0.000 -0.000 -0.000
310.0 4.355 4.355 4.355 -0.000 -0.000 -0.000
320.0 4.215 4.215 4.215 -0.000 -0.000 -0.000
330.0 4.085 4.085 4.085 -0.000 -0.000 -0.000
340.0 3.962 3.962 3.962 -0.000 -0.000 -0.000
350.0 3.846 3.846 3.846 -0.000 -0.000 -0.000
360.0 3.737 3.737 3.737 -0.000 -0.000 -0.000
370.0 3.634 3.634 3.634 -0.000 -0.000 -0.000
380.0 3.537 3.537 3.537 -0.000 -0.000 -0.000
390.0 3.444 3.444 3.444 -0.000 -0.000 -0.000
400.0 3.357 3.357 3.357 -0.000 -0.000 -0.000
410.0 3.274 3.274 3.274 -0.000 -0.000 -0.000
420.0 3.194 3.194 3.194 -0.000 -0.000 -0.000
430.0 3.119 3.119 3.119 -0.000 -0.000 -0.000
440.0 3.047 3.047 3.047 -0.000 -0.000 -0.000
450.0 2.979 2.979 2.979 -0.000 -0.000 -0.000
460.0 2.913 2.913 2.913 -0.000 -0.000 -0.000
470.0 2.850 2.850 2.850 -0.000 -0.000 -0.000
480.0 2.790 2.790 2.790 -0.000 -0.000 -0.000
490.0 2.733 2.733 2.733 -0.000 -0.000 -0.000
500.0 2.677 2.677 2.677 -0.000 -0.000 -0.000
510.0 2.624 2.624 2.624 -0.000 -0.000 -0.000
520.0 2.573 2.573 2.573 -0.000 -0.000 -0.000
530.0 2.524 2.524 2.524 -0.000 -0.000 -0.000
540.0 2.477 2.477 2.477 -0.000 -0.000 -0.000
550.0 2.432 2.432 2.432 -0.000 -0.000 -0.000
560.0 2.388 2.388 2.388 -0.000 -0.000 -0.000
570.0 2.346 2.346 2.346 -0.000 -0.000 -0.000
580.0 2.305 2.305 2.305 -0.000 -0.000 -0.000
590.0 2.266 2.266 2.266 -0.000 -0.000 -0.000
600.0 2.228 2.228 2.228 -0.000 -0.000 -0.000
610.0 2.191 2.191 2.191 -0.000 -0.000 -0.000
620.0 2.155 2.155 2.155 -0.000 -0.000 -0.000
630.0 2.121 2.121 2.121 -0.000 -0.000 -0.000
640.0 2.087 2.087 2.087 -0.000 -0.000 -0.000
650.0 2.055 2.055 2.055 -0.000 -0.000 -0.000
660.0 2.024 2.024 2.024 -0.000 -0.000 -0.000
670.0 1.993 1.993 1.993 -0.000 -0.000 -0.000
680.0 1.964 1.964 1.964 -0.000 -0.000 -0.000
690.0 1.935 1.935 1.935 -0.000 -0.000 -0.000
700.0 1.908 1.908 1.908 -0.000 -0.000 -0.000
710.0 1.881 1.881 1.881 -0.000 -0.000 -0.000
720.0 1.854 1.854 1.854 -0.000 -0.000 -0.000
730.0 1.829 1.829 1.829 -0.000 -0.000 -0.000
740.0 1.804 1.804 1.804 -0.000 -0.000 -0.000
750.0 1.780 1.780 1.780 -0.000 -0.000 -0.000
760.0 1.756 1.756 1.756 -0.000 -0.000 -0.000
770.0 1.733 1.733 1.733 -0.000 -0.000 -0.000
780.0 1.711 1.711 1.711 -0.000 -0.000 -0.000
790.0 1.689 1.689 1.689 -0.000 -0.000 -0.000
800.0 1.668 1.668 1.668 -0.000 -0.000 -0.000
810.0 1.647 1.647 1.647 -0.000 -0.000 -0.000
820.0 1.627 1.627 1.627 -0.000 -0.000 -0.000
830.0 1.608 1.608 1.608 -0.000 -0.000 -0.000
840.0 1.588 1.588 1.588 -0.000 -0.000 -0.000
850.0 1.570 1.570 1.570 -0.000 -0.000 -0.000
860.0 1.551 1.551 1.551 -0.000 -0.000 -0.000
870.0 1.533 1.533 1.533 -0.000 -0.000 -0.000
880.0 1.516 1.516 1.516 -0.000 -0.000 -0.000
890.0 1.499 1.499 1.499 -0.000 -0.000 -0.000
900.0 1.482 1.482 1.482 -0.000 -0.000 -0.000
910.0 1.466 1.466 1.466 -0.000 -0.000 -0.000
920.0 1.450 1.450 1.450 -0.000 -0.000 -0.000
930.0 1.434 1.434 1.434 -0.000 -0.000 -0.000
940.0 1.419 1.419 1.419 -0.000 -0.000 -0.000
950.0 1.404 1.404 1.404 -0.000 -0.000 -0.000
960.0 1.389 1.389 1.389 -0.000 -0.000 -0.000
970.0 1.375 1.375 1.375 -0.000 -0.000 -0.000
980.0 1.361 1.361 1.361 -0.000 -0.000 -0.000
990.0 1.347 1.347 1.347 -0.000 -0.000 -0.000
1000.0 1.333 1.333 1.333 -0.000 -0.000 -0.000
...
We find that the thermal conductivity at 300 K is 4.5 W/mK at this \(q\) mesh density. For production calculations, you should converge the mesh size. For example, with a \(20 \times 20 \times 20\) mesh, we get a converged, room-temperature thermal conductivity of 5.92 W/mK.
Important
In comparison to our result, the experimental thermal conductivity of CuI is reported to be much lower, around 1.68 W/mK 1. Our BTE calculation overestimates this value by more than 350%. We will discuss the reasons for this disagreement in the following section.
Solutions#
You find all the solution to all the above exercises by clicking on the button below.
Show solutions to the Perturbative method
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CRC Handbook of Chemistry and Physics, David R. Lide, Ed. 79th Edition, CRC Press, Boca Raton, FL, 1998. ↩