phono3py/example/NaCl-rd/README.md

Example of using random directional displacements

How to use symfc

This example utilizes an NaCl calculation result from A. Togo and A. Seko, J. Chem. Phys. 160, 211001 (2024). Supercells of 2x2x2 and 4x4x4 conventional unit cells are chosen for the third-order force constants (fc3) and second-order force constants (fc2), respectively. Displacement-force datasets consisting of 100 supercells for fc3 and 2 supercells for fc2 are extracted and stored in phono3py_params_NaCl.yaml.xz. Random directional displacements of a constant 0.03 Angstrom are used.

To calculate force constants, an external force constants calculator is necessary. Here, the symfc tool (available at https://github.com/symfc/symfc) is used, which can be easily installed via pip or conda.

The fc3.hdf5 and fc2.hdf5 are computed using the command:

% phono3py-load phono3py_params_NaCl.yaml.xz --symfc -v

Lattice thermal conductivity (LTC) is calculated with the following command:

% phono3py-load phono3py_params_NaCl.yaml.xz --br --ts 300 --mesh 50

By this, LTC is obtained around 8.3 W/m-k.

How to use pypolymlp

When supercell energies are included in phono3py_params.yaml like file, the polynomial machine learning potential (poly-MLP) by pypolymlp can be used to calculate fc3 by the following command:

% phono3py-load phono3py_params_NaCl.yaml.xz --pypolymlp --symfc --rd 400 -v

the procedure below is performed:

1. Poly-MLPs are computed from the displacement-force dataset for fc3. This is activated by --pypolymlp option.
2. 800=400+400 supercells for random directional displacements are generated, where 400+400 means 400 supercells with random displacements (u) and 400 supercells with opposite displacement vectors (-u). This is activated by --rd 400 option. The default displacement distance is 0.001 Angstrom in --pypolymlp mode. Since random displacements are generated --symfc has to be specified for fc3. In this example, random displacements are used for fc2, too, --symfc is applied to both of fc3 and fc2. Without --rd option, systematic displacements are generated, for which the option --fc-calc "symfc|" has to be specified instead of --symfc (equivalent to --fc-calc "symfc|symfc")).
3. Forces on atoms in these 800 supercells are calculated using poly-MLP.
4. Force constants are calculated.

The fc3.hdf5 and fc2.hdf5 are obtained. Using these force constants, LTC is calculated by

% phono3py-load phono3py_params_NaCl.yaml.xz --br --ts 300 --mesh 50

and the LTC value of around 8.2 W/m-k is obtained.

Generating phono3py_params.yaml from vasprun.xml's

phono3py_params.yaml is generated from

% phono3py phono3py_disp.yaml --cf3 NaCl-vasprun/vasprun-{00001..00100}.xml --cf2 NaCl-vasprun/vasprun-ph0000{1,2}.xml --sp

This command reads electronic energies of supercells from vasprun.xmls and writes them into phono3py_params.yaml, too. Here, phono3py_disp.yaml is not included in this example, but phono3py_params_NaCl.yaml.xz can be used to run this example since corresponding information of displacements is included in this file, too.