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
- NAMD-LMI: https://github.com/Ionizing/NAMD-LMI (0.2.0 or upper)
- rsgrad: https://github.com/Ionizing/rsgrad (0.5.0 or upper)
- 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.
- Location:
0K/namd
This folder contains the NAMD-LMI input files to reproduce the NAMD result at 0 Kelvin.
- Reproduction steps:
-
Go to
0K/2x3/scf
and runrsgrad 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. -
Go to
0K/namd/single-electron
and runnamd_lmi hamil -c 02_hamil_config.toml
to generateHAMIL-0K-single-electron-efield.h5
. -
Go to
0K/namd/single-electron/excitation
and runnamd_lmi surfhop -c 03_surfhop_config.toml
to run the actual NAMD process. -
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.
For 50 K:
- Location:
50K/nve
and50K/static_ncl
These two folders contains the NVE trajectory at 50 Kelvin.
- Reproduction steps:
-
Run VASP at
50K/nve
to obtain XDATCAR. -
Run
genstatic.py
to generate therun/
folder and move it to50K/static_ncl
-
Submit a slurm job using
sub_vasp_namd
at50K/static_ncl
(you may need to modify it to adopt you job scheduling system) -
Run
mixWave.py
to perform linear unitary transform on degenerated states in WAVECARs.
The process for 100 K is same as 50 K.
For 50 K:
-
Go to
50K/namd
and runnamd_lmi nac -c 01_nac_config.toml
to calculate non-adiabatic coupling files, the couplings will be written toNAC-50K.h5
-
Run NAMD at
50K/namd/single-electron
and50K/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
.