PYATB

PYATB#

Introduction#

PYATB (Python ab initio tight binding simulation package) is an open-source software package designed for computing electronic structures and related properties based on the ab initio tight binding Hamiltonian. The Hamiltonian can be directly obtained after conducting self-consistent calculations with ABACUS using numerical atomic orbital (NAO) bases. The package comprises three modules - Bands, Geometric, and Optical, each providing a comprehensive set of tools for analyzing different aspects of a material’s electronic structure.

Installation#

git clone https://github.com/pyatb/pyatb.git
cd pyatb
python setup.py install --record log

To customize the setup.py file, you must make changes to the CXX and LAPACK_DIR variables in line with your environment. CXX denotes the C++ compiler you intend to use, for instance, icpc (note that it should not be the mpi version). Furthermore, LAPACK_DIR is used to specify the Intel MKL path.

After completing the installation process, you can access the pyatb executable and corresponding module, which can be imported using the import pyatb command.

How to use#

We take Bi\(_2\)Se\(_3\) as an example to illustrate how to use ABACUS to generate the tight binding Hamiltonian required for PYATB, and then perform calculations related to PYATB functions.

  1. Perform ABACUS self consistent calculation:

INPUT_PARAMETERS

# System variables
suffix                Bi2Se3
ntype                 2
calculation           scf
esolver_type          ksdft
symmetry              1
init_chg              atomic

# Plane wave related variables
ecutwfc               100

# Electronic structure
basis_type            lcao
ks_solver             genelpa
nspin                 4
smearing_method       gauss
smearing_sigma        0.02
mixing_type           broyden
mixing_beta           0.7
scf_nmax              200
scf_thr               1e-8
lspinorb              1
noncolin              0

# Variables related to output information
out_chg               1
out_mat_hs2           1
out_mat_r             1

After the key parameters out_mat_hs2 and out_mat_r are turned on, ABACUS will generate files containing the Hamiltonian matrix \(H(R)\), overlap matrix \(S(R)\), and dipole matrix \(r(R)\) after completing the self-consistent calculation. These parameters can be found in the ABACUS INPUT file.

  1. Copy the HR, SR, and rR files output by ABACUS’s self-consistent calculation, which are located in the OUT* directory and named data-HR-sparse_SPIN0.csr, data-SR-sparse_SPIN0.csr, and data-rR-sparse.csr, respectively. Copy these files to the working directory and write the Input file for PYATB:

INPUT_PARAMETERS
{
    nspin                          4
    package                        ABACUS
    fermi_energy                   9.557219691497478
    fermi_energy_unit              eV
    HR_route                       data-HR-sparse_SPIN0.csr
    SR_route                       data-SR-sparse_SPIN0.csr
    rR_route                       data-rR-sparse.csr
    HR_unit                        Ry
    rR_unit                        Bohr
    max_kpoint_num                 8000
}

LATTICE
{
    lattice_constant               1.8897162
    lattice_constant_unit          Bohr
    lattice_vector
    -2.069  -3.583614  0.000000
     2.069  -3.583614  0.000000
     0.000   2.389075  9.546667
}

BAND_STRUCTURE
{
    wf_collect                     0
    kpoint_mode                    line
    kpoint_num                     5
    high_symmetry_kpoint
    0.00000 0.00000 0.0000 100  # G
    0.00000 0.00000 0.5000 100  # Z
    0.50000 0.50000 0.0000 100  # F
    0.00000 0.00000 0.0000 100  # G
    0.50000 0.00000 0.0000 1    # L
}

For specific input file writing, please refer to PYATB’s quick start.

  1. Perform PYATB calculation:

export OMP_NUM_THREADS=2
mpirun -np 6 pyatb

After the calculation is completed, the band structure data and figures of Bi\(_2\)Se\(_3\) can be found in the Out/Band_Structure folder.