Overlap Matrix

The overlap matrix is a defining component of a DFT data point in the atomic orbital basis, and is a requisite for DeepH inference:

\[ S_{i\alpha, j\beta}(\boldsymbol{R}_j-\boldsymbol{R}_i) = \int d^3 \boldsymbol{r} \phi^{*}_{i\alpha}(\boldsymbol{r}-\boldsymbol{R}_i-\mathcal{R}_i) \phi_{j\beta}(\boldsymbol{r}-\boldsymbol{R}_j-\mathcal{R}_j) \]

Here \(i,j\) label atoms, \(\alpha,\beta\) label orbitals on those atoms, \(\boldsymbol{R}_i,\boldsymbol{R}_j\) are lattice translation vectors to the unit cells containing atoms \(i,j\), and \(\mathcal{R}_i,\mathcal{R}_j\) are their positions within the unit cell. When SOC is present, \(\alpha\) and \(\beta\) have an additional spin degree of freedom.

In DeepH-dock, overlaps are computed using the efficient grid-based interpolation scheme used in the HPRO package, which was originally proposed by Sankey and Niklewski.

Terminal Tool

The user can use the terminal tool to compute overlap matrices given the basis files.

Current support:

1. siesta (.ion files)

For the case where spin-orbit coupling (SOC) is present, run

dock compute overlap path_to_poscar path_to_basis_files dft_code_name -s

For the spinless case, run

dock compute overlap path_to_poscar path_to_basis_files dft_code_name