Preparing Input (PySCF)

Preparing Input (PySCF)

The first step of any simulations with Green is the preparation of the input data, which includes the calculation of the Coulomb and one-body integrals as well as a starting density matrix out of geometry, atom, k-point, and basis information. Green provides a convenient python package green-mbtools Currently we use an interface with PySCF to prepare input data. If your python installation does not have green-mbtools available (type python and, in the python prompt, import green_mbtools), you will need to follow the instructions at PyPI or execute pip install green-mbtools.

Initial Mean Field solution

To generate input data a user has to call the python/init_data_df.py script located either in the source directory or in the installation directory (for a simple example see next page). The following parameters are mandatory:

  • --a path to a file containing crystal geometry in xyz format
  • --atom path to a file containing unit cell description
  • --nk number of reciprocal space points in each direction
  • --basis Gaussian basis set, it can be specified as a single basis for every atom in the unit cell or for each atom individually

Pseudopotentials

Some basis sets require to use effective potential for core electron that are removed from the calculation. For that reason Green allows to specify psuedo potential using --pseudo keyword.

By default the script will init_data_df.py will generate the file input.h5. This file contains all necessary parameters and an initial mean-field solution of the system. In addition, the script will generate the df_int and df_hf_int directories which contain the Coloumb and one-body integrals of the system.

High-symmetry path

After the simulation is performed, results (such as band structures) could be displayed along a high-symmetry path. Before performing Green’s function calculations, it helps to prepare the overlap matrix and one-electron integrals along this path in the Brillouin zone. To obtain these quantities, we use init_data_df.py once again, but with the flag --job sym_path. In addition to this option, one needs to specify the high-symmetry points on the path and the total number of points along the path by providing the two parameters --high_symmetry_path and --high_symmetry_path_points. To see all available high-symmetry points for a chosen system, use theoption --print_high_symmetry_points.

Coulomb integrals generation

Finite size correction