Source code for

# This Source Code Form is subject to the terms of the Mozilla Public
# License, v. 2.0. If a copy of the MPL was not distributed with this
# file, You can obtain one at
import numpy as np
from scipy.sparse import lil_matrix

# Import sile objects
from .sile import SileScaleUp
from ..sile import *

__all__ = ['rhamSileScaleUp']

[docs]class rhamSileScaleUp(SileScaleUp): """ rham file object for ScaleUp This file contains the real-space Hamiltonian for a ScaleUp simulation """
[docs] @sile_fh_open() def read_hamiltonian(self, geometry=None): """ Reads a Hamiltonian from the Sile """ from sisl import Hamiltonian # Create a copy as we may change the # internal atoms (due to wrong orbital values) g = geometry.copy() # First line is comment self.readline() # First read the entire file lines = self.readlines() def pl(line): l = line.split() s = int(l[0]) isc = list(map(int, l[1:4])) o1, o2 = map(int, l[4:6]) rH, iH = map(float, l[6:8]) return s, isc, o1-1, o2-1, rH, iH ns = 0 no = 0 m_sc = np.zeros([3], np.int32) # To save creating a new list for i, line in enumerate(lines): lines[i] = pl(line) ns = max(lines[i][0], ns) m_sc[0] = max(abs(lines[i][1][0]), m_sc[0]) m_sc[1] = max(abs(lines[i][1][1]), m_sc[1]) m_sc[2] = max(abs(lines[i][1][2]), m_sc[2]) no = max(lines[i][2], no) # Correct for C-index if no + 1 != # First try and read the orbocc file try: species = get_sile(str(self.file).replace(".rham", ".orbocc")).read_atom() for i, atom in enumerate(species.atom): g.atoms._atom[i] = atom except Exception: # Allowed pass due to pythonic reading pass # Check again, to be sure... if no + 1 != raise ValueError('The Geometry has a different number of ' 'orbitals, please correct by adding the orbocc file.') # Now, we know the size etc. of the Hamiltonian m_sc = m_sc * 2 + 1 if np.any(g.nsc != m_sc): # Correct the number of supercells g.set_nsc(m_sc) # List of Hamiltonians per spin Hs = [None] * ns # Get system size no = no_s = g.no_s old_s = 0 for s, isc, o1, o2, rH, iH in lines: if s != old_s: # We need to create a new Hamiltonian H = lil_matrix((no, no_s), dtype=np.float64) old_s = s Hs[s-1] = H i = g.sc_index(isc) H[o1, o2 + i * no] = rH # Currently we skip the imaginary part as it should be zero. H = Hamiltonian.fromsp(g, Hs) H.finalize() return H
add_sile('rham', rhamSileScaleUp, case=False, gzip=True)