Construction of graph_data.npz File

graph_data.npz is the core input format for HamGNN, containing material structure information and Hamiltonian matrix data. The following describes its construction method.

General Process

Regardless of which DFT software is used, the basic process for constructing graph_data.npz is as follows:

1. Structure File Conversion: Convert material structure files (such as POSCAR, CIF) to the corresponding DFT software input format

2. Non-self-consistent Hamiltonian Calculation: Use post-processing tools to generate files containing non-self-consistent Hamiltonian H0 (matrices that do not depend on self-consistent charge density, such as kinetic energy matrices)

3. DFT Calculation (Optional): Run complete DFT calculations to obtain real Hamiltonians (required for training set construction, can be skipped for pure prediction)

4. Data Packaging: Call the appropriate graph_data_gen script to package structure and Hamiltonian matrix data into graph_data.npz

OpenMX Process

1. Structure Conversion: Edit the poscar2openmx.yaml configuration file, setting appropriate paths and DFT parameters (for non-SOC data, set scf.SpinPolarization: Off and scf.SpinOrbit.Coupling: off; for SOC data, set scf.SpinPolarization: nc and scf.SpinOrbit.Coupling: on):

   system_name: 'Si'
   poscar_path: "/path/to/poscar/*.vasp" # Path to POSCAR or CIF files
   filepath: '/path/to/save/dat/file' # Directory to save OpenMX files
   basic_command: |+  # OpenMX calculation parameters
     #
     #      File Name
     #
     System.CurrrentDirectory         ./    # default=./
     System.Name                     Si
     DATA.PATH           /path/to/DFT_DATA   # default=../DFT_DATA19
     # ...other OpenMX parameters...
   

2. Non-self-consistent Hamiltonian Calculation: Run openmx_postprocess on the generated .dat files:

   mpirun -np ncpus ./openmx_postprocess openmx.dat
   

   This will generate an overlap.scfout file containing overlap matrices and non-self-consistent Hamiltonian information.

3. DFT Calculation (Optional, required for training set):

   mpirun -np ncpus openmx openmx.dat > openmx.std
   

   This will generate a .scfout file containing self-consistent Hamiltonians.

4. Data Packaging: Configure graph_data_gen.yaml:

   nao_max: 26  # Maximum number of atomic orbitals
   graph_data_save_path: '/path/to/save/graph_data'
   read_openmx_path: '/path/to/HamGNN/interfaces.openmx/read_openmx'
   max_SCF_skip: 200
   scfout_paths: '/path/to/scfout/files'  # Directory of .scfout files
   dat_file_name: 'openmx.dat'
   std_file_name: 'openmx.std'  # Set to null if no DFT calculation
   scfout_file_name: 'openmx.scfout'  # Use 'overlap.scfout' for prediction
   soc_switch: False  # Set to True for SOC data
   

   Then run:

   graph_data_gen --config graph_data_gen.yaml
   

SIESTA/HONPAS Process

1. Structure Conversion: Edit the poscar_path and filepath parameters in the poscar2siesta.py script, then run:

   python poscar2siesta.py
   

2. DFT Calculation: Use HONPAS to perform DFT calculations to obtain .HSX Hamiltonian matrix files.

3. Non-self-consistent Hamiltonian Calculation: Run the following command to generate non-self-consistent Hamiltonians and overlap matrices:

   mpirun -np Ncores honpas_1.2_H0 < input.fdf
   

   This will generate an overlap.HSX file.

4. Data Packaging: Modify the parameters in the graph_data_gen_siesta.py script, then run:

   python graph_data_gen_siesta.py
   

ABACUS Process

1. Structure Conversion: Use poscar2abacus.py to generate ABACUS input files.

2. DFT Calculation and Post-processing: Run ABACUS calculations and use abacus_postprocess to extract H0 matrices.

3. Data Packaging: Use the graph_data_gen_abacus.py script to integrate data and generate graph_data.npz.