Overall process

NAMD-LMI is divided into three parts: nac, hamil and surfhop, corresponding to the calculation of non-adiabatic coupling, Hamiltonian and surface hopping.

1. Run VASP like traditional Hefei-NAMD;
2. Run namd_lmi nac -c config to calculate non-adiabatic coupling. A visualization script nac_plot.py is also available via namd_lmi nac --generate pp.
3. Run namd_lmi hamil -c config to generate Hamiltonian plus external field. The external field is described in a rhai script, which can be generated via namd_lmi hamil --generate efield. A visualization script hamil_plot.py is also available via namd_lmi hamil --generate pp.
4. Run namd_lmi surfhop -c config to run surface hopping and get the real time evolution of the population. A visualization script surfhop_plot.py is also available via namd_lmi surfhop --generate pp.