def test_bulk_silicon():
a_si = 5.50
PRIMITIVE_CELL = [[0, 0.5 * a_si, 0.5 * a_si], [0.5 * a_si, 0, 0.5 * a_si],
[0.5 * a_si, 0.5 * a_si, 0]]
tb.Atom.orbital_sets = {'Si': 'SiliconSP3D5S'}
xyz_file = """2
Si2 cell
Si1 0.0000000000 0.0000000000 0.0000000000
Si2 1.3750000000 1.3750000000 1.3750000000
"""
h = tb.Hamiltonian(xyz=xyz_file, nn_distance=2.5)
h.initialize()
h.set_periodic_bc(PRIMITIVE_CELL)
sym_points = ['L', 'GAMMA', 'X']
num_points = [10, 25]
k = tb.get_k_coords(sym_points, num_points, 'Si')
band_sructure = []
vals = np.zeros((sum(num_points), h.h_matrix.shape[0]), dtype=np.complex)
for jj, item in enumerate(k):
vals[jj, :], _ = h.diagonalize_periodic_bc(item)
band_structure = np.real(np.array(vals))
np.testing.assert_allclose(band_structure,
expected_bulk_silicon_band_structure(),
atol=1e-4)
def main4():
from tb.aux_functions import get_k_coords
path_to_xyz_file = """2
Bilayer Bismuth
Bi 0.000000 2.499364 0.868720
Bi 2.164513 1.249682 -0.868720
"""
# path_to_pdf_file = '../band_structure_of_bulk_bismuth.pdf'
species = 'Bi'
basis_set = 'Bismuth'
sym_points = ['M', 'GAMMA', 'K']
# sym_points = ['GAMMA', 'GAMMA']
num_points = [40, 40]
# num_points = [1]
indices_of_bands = range( 0, 16 )
primitive_cell = data_bi_bulk.cell
Atom.orbital_sets = { species: basis_set }
h = Hamiltonian(xyz=path_to_xyz_file, nn_distance=4.7, so_coupling=0.9)
h.initialize(radial_dep)
h.set_periodic_bc(primitive_cell)
plot_atom_positions(h.atom_list, h.ct.virtual_and_interfacial_atoms, radial_dep)
k_points = get_k_coords( sym_points, num_points, species )
list_of_spin_orbit_couplings = [0.27]
# list_of_spin_orbit_couplings = np.linspace(0, 0.333333, 40)
band_structure = []
for ii, item in enumerate(list_of_spin_orbit_couplings):
for jj, item in enumerate(k_points):
# h = Hamiltonian(xyz=path_to_xyz_file, nn_distance=5.6)
# h.initialize(radial_dep)
# h.set_periodic_bc(primitive_cell, radial_dep)data_bi_bulk.py
data_bi_bulk.LAMBDA = list_of_spin_orbit_couplings[ii]
[eigenvalues, _] = h.diagonalize_periodic_bc(k_points[jj])
band_structure.append(eigenvalues)
band_structure = np.array(band_structure)
ax = plt.axes()
ax.plot(band_structure[ :, indices_of_bands ])
ax.set_xlabel( "" )
ax.set_ylabel( "Energy (eV)" )
ax.set_title( "" )
plt.tight_layout()
plt.ylim((-2, 2))
plt.show()
def main2():
from tb.aux_functions import get_k_coords
path_to_xyz_file = 'input_samples/bulk_bismuth.xyz'
# path_to_pdf_file = '../band_structure_of_bulk_bismuth.pdf'
species = 'Bi'
basis_set = 'Bismuth'
sym_points = ['K', 'GAMMA', 'T', 'W', 'L', 'LAMBDA']
# sym_points = ['K', 'X', 'GAMMA', 'L', 'U', 'T']
# sym_points = ['GAMMA', 'GAMMA']
# sym_points = ['K', 'GAMMA', 'T']
num_points = [20, 20, 20, 20, 20]
# num_points = [1]
# num_points = [20, 20]
indices_of_bands = range(0, 16)
cell_a = examples.data_bi_bulk.a_bi * np.array([[(-1.0 / 2.0), (-np.sqrt(3.0) / 6.0), 0.0],
[ ( 1.0 / 2.0 ), ( -np.sqrt(3.0) / 6.0 ), 0.0 ],
[ 0.0, ( np.sqrt(3.0) / 3.0 ), 0.0 ]])
cell_c = examples.data_bi_bulk.c_bi * np.array([[0.0, 0.0, (1.0 / 3.0)],
[ 0.0, 0.0, ( 1.0 / 3.0 ) ],
[ 0.0, 0.0, ( 1.0 / 3.0 ) ]])
primitive_cell = cell_a + cell_c
Atom.orbital_sets = { species: basis_set }
h = Hamiltonian( xyz = path_to_xyz_file, nn_distance = 4.6, so_coupling=1.2)
h.initialize( radial_dep )
h.set_periodic_bc(primitive_cell.tolist())
k_points = get_k_coords( sym_points, num_points, species )
band_structure = []
for jj, item in enumerate( k_points ):
[ eigenvalues, _ ] = h.diagonalize_periodic_bc( k_points[ jj ] )
band_structure.append( eigenvalues )
band_structure = np.array( band_structure )
print(h.is_hermitian())
ax = plt.axes()
ax.plot( band_structure[ :, indices_of_bands ] )
ax.set_xlabel( "" )
ax.set_ylabel( "Energy (eV)" )
ax.set_title( "" )
plt.tight_layout()
plt.show()
def main1():
from tb import get_k_coords
path_to_xyz_file = 'input_samples/bulk_silicon.xyz'
species = 'Si'
basis_set = 'SiliconSP3D5S'
sym_points = [ 'L', 'GAMMA', 'X' ]
num_points = [ 20, 20 ]
indices_of_bands = range( 0, 8 )
primitive_cell = examples.data_bi_bulk.a_si * np.array([[0.0, 0.5, 0.5],
[0.5, 0.0, 0.5],
[0.5, 0.5, 0.0]])
Atom.orbital_sets = { species: basis_set }
h = Hamiltonian( xyz = path_to_xyz_file)
h.initialize()
h.set_periodic_bc( primitive_cell )
k_points = get_k_coords( sym_points, num_points, species )
band_structure = []
for jj, item in enumerate( k_points ):
[ eigenvalues, _ ] = h.diagonalize_periodic_bc( k_points[ jj ] )
band_structure.append( eigenvalues )
band_structure = np.array( band_structure )
ax = plt.axes()
ax.plot( band_structure[ :, indices_of_bands ] )
ax.set_xlabel( "" )
ax.set_ylabel( "Energy (eV)" )
ax.set_title( "" )
plt.tight_layout()
plt.show()
def preprocess_data(param_file, k_points_file, xyz, code_name):
params = tb.yaml_parser(param_file) # parse parameter file
if k_points_file is None: # default k-points
if len(params['primitive_cell']) == 3:
sym_points = [
'L', 'GAMMA', 'X', 'W', 'K', 'L', 'W', 'X', 'K', 'GAMMA'
]
num_points = [15, 20, 15, 10, 15, 15, 15, 15, 20]
wave_vector = tb.get_k_coords(sym_points, num_points)
else:
wave_vector = [[0.0, 0.0, 0.0]]
else: # read k-points file if its path is provided from the command line arguments
wave_vector = np.loadtxt(k_points_file)
# read xyz file if its path is provided from the command line arguments
if isinstance(xyz, str):
with open(xyz, 'r') as myfile:
params['xyz'] = myfile.read()
if not isinstance(code_name, str):
code_name = 'band_structure'
return params, wave_vector, code_name