Hefei-NAMD

Hefei-NAMD Non-adiabatic molecular dynamics applies surface hopping to incorporate quantum mechanical effects into molecular dynamics simulations. Surface hopping partially incorporates the non-adiabatic effects by including excited adiabatic surfaces in the calculations, and allowing for ‘hops’ between these surfaces.

Detailed instructions on installing and running Hefei-NAMD can be found on its official website.

ABACUS provides results of molecular dynamics simulations for Hefei-NAMD to do non-adiabatic molecular dynamics simulations.

The steps are as follows :

1. Add output parameters in INPUT when running MD using ABACUS .

out_wfc_lcao    1
out_mat_hs      1  

Then we obtain output files of hamiltonian matrix, overlap matrix, and wavefunction to do NAMD simulation.

2. Clone Hefei-NAMD codes optimized for ABACUS from website.

3. Modify parameters in Args.py including directory of ABACUS output files and NAMD parameters. We can see detailed explanation for all parameters in Args.py.

4. Run NAC.py to prepare related files for NAMD simulations.

sbatch sub_nac

5. Run SurfHop.py to perform NAMD simulations.

sbatch sub_sh

And results are under directory namddir in Args.py.