Reproduction data for the paper "Spin Valley Dynamics Entangled with Optical Fields, Phonons, and Spin-Orbit Coupling in Monolayer MoSe2"

Paper link: https://onlinelibrary.wiley.com/doi/10.1002/adom.202403069

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Tool requirements

• NAMD-LMI: https://github.com/Ionizing/NAMD-LMI (0.2.0 or upper)
• rsgrad: https://github.com/Ionizing/rsgrad (0.5.0 or upper)

Electronic structure at 0 K

• Location: 0K/

This folder contains the VASP input files to calculate the electronic structure of monolayer MoSe2 in primitive cell and supercell.

• Reproduction steps:

Just run VASP at each folder containing INCAR, remember to copy CHGCAR from corresponding scf folders when calculating band structures.

Photo-excitation process at 0 K

• Location: 0K/namd

This folder contains the NAMD-LMI input files to reproduce the NAMD result at 0 Kelvin.

• Reproduction steps:

1. Go to 0K/2x3/scf and run rsgrad model-nac --brange 213 220 to obtain "NAC-0K.h5". rsgrad can be downloaded from https://github.com/Ionizing/rsgrad/releases , 0.5.5 or higher versions are needed.

2. Go to 0K/namd/single-electron and run namd_lmi hamil -c 02_hamil_config.toml to generate HAMIL-0K-single-electron-efield.h5.

3. Go to 0K/namd/single-electron/excitation and run namd_lmi surfhop -c 03_surfhop_config.toml to run the actual NAMD process.

4. Head to 0K/namd/single-electron/excitation/result and run ../surfhop_plot.py to obtain figures.

There are also simulations for systems with multiple electrons at 0K/namd/multi-electron, and the reproduction process is similar to the steps shown in the above.

AIMD at 50 K and 100 K

For 50 K:

• Location: 50K/nve and 50K/static_ncl

These two folders contains the NVE trajectory at 50 Kelvin.

• Reproduction steps:

1. Run VASP at 50K/nve to obtain XDATCAR.

2. Run genstatic.py to generate the run/ folder and move it to 50K/static_ncl

3. Submit a slurm job using sub_vasp_namd at 50K/static_ncl (you may need to modify it to adopt you job scheduling system)

4. Run mixWave.py to perform linear unitary transform on degenerated states in WAVECARs.

The process for 100 K is same as 50 K.

NAMD at 50 K and 100 K

For 50 K:

1. Go to 50K/namd and run namd_lmi nac -c 01_nac_config.toml to calculate non-adiabatic coupling files, the couplings will be written to NAC-50K.h5

2. Run NAMD at 50K/namd/single-electron and 50K/namd/multi-electron with similar processes shown in step 2 to step 4 at 0 K.

The process for 100 K is same as 50 K.

You may need the following reference result files, which will be uploaded to https://github.com/Ionizing/adom.202403069/releases due to GitHub file size limit.

• 50K/namd/NAC-50K.h5

• 50K/namd/single-electron/HAMIL-50K-single-electron-efield.h5

• 50K/namd/single-electron/HAMIL-50K-single-electron-noefield.h5

• 50K/namd/multi-electron/HAMIL-50K-multi-electron-efield.h5

• 50K/namd/multi-electron/HAMIL-50K-multi-electron-noefield.h5

• 100K/namd/NAC-100K.h5

• 100K/namd/single-electron/HAMIL-100K-single-electron-efield.h5

• 100K/namd/single-electron/HAMIL-100K-single-electron-noefield.h5

• 100K/namd/multi-electron/HAMIL-100K-multi-electron-efield.h5

• 100K/namd/multi-electron/HAMIL-100K-multi-electron-noefield.h5

There are also hamil_plot.py to plot figures for HAMIL-xxx.h5, use it with ./hamil_plot.py HAMIL-xxx.h5.