grad_mat_prep for siesta

[Youhaojen]

Dear Yang Zhong,

In the example, I found that the Ham_type for calculating mobility is set to Siesta, but grad_mat_prep only supports OpenMX. Are there any plans to update the Siesta support soon?

Best regards,
Hao-Jen You

[QuantumLab-ZY]

Dear @Youhaojen,

The scripts for preprocessing the Hamiltonian of Siesta/Honpas to obtain the input of HamEPC are available in a compressed package attached to this response. Other scripts used for packaging the Siesta/Honpas Hamiltonian into graph_data.npz as input for HamGNN are available at https://github.com/QuantumLab-ZY/HamGNN/tree/main/utils_siesta. The preprocessing involves a series of scripts executed in a specific order to generate the required input for HamEPC. The general process is: perturb_supercell.py -> HamGNN -> gather_HS.py -> dS_dH_cal.py -> dSon_cal.py -> grad_mat_cal.py. Each script serves a distinct purpose:

1. perturb_supercell.py: Generates perturbed supercell configurations.
2. HamGNN: Computes the Hamiltonian matrix using the generated supercells.
3. gather_HS.py: Aggregates Hamiltonian (H) and overlap (S) matrices from the calculations.
4. dS_dH_cal.py: Calculates derivatives of H and S with respect to atomic displacements.
5. dSon_cal.py: Computes the correction for the gradient of the overlap matrix.
6. grad_mat_cal.py: Finalizes gradient matrices required for HamEPC input.

Best regards,
Yang Zhong

grad_mat_prepare_honpas.zip

[Youhaojen]

Dear Yang Zhong,

Thanks for your friendly reply. I will try it.

[cl25796]

Dear Prof. Zhong @QuantumLab-ZY,

I used HONPAS and successfully followed the workflow: perturb_supercell.py → HamGNN → gather_HS.py → dS_dH_cal.py.

However, I was unable to run dSon_cal.py, as it requires the files HS_Ga.json and dSon_Ga.npy, which were not included in the zip file you provided or generated in the previous steps. Could you please also send these two files? Thank you very much!

Input of dSon_cal.py:
########### input Parameters begin ###############
work_dir = '/data/home/yzhong/EPC_test/GaAs3/PBE/dSon'
HS_path = f'{work_dir}/HS_Ga.json'
dSon_path = f'{work_dir}/dSon_Ga.npy'
delta_r = 0.001 # the unit is angstrom
########### input Parameters end ##################

Best regards,
Chen