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.Orbitals.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.HamiltonianSp(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.num_eigs), 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()[:, :h.num_eigs],
atol=1e-4)
def main():
# specify atomic coordinates in xyz format
path_to_xyz_file = """2
Bulk Si cell
Si1 0.000 0.000 0.000
Si2 1.375 1.375 1.375"""
# specify basis set
Orbitals.orbital_sets = {'Si': 'SiliconSP3D5S'}
# create a Hamiltonian object storing the Hamiltonian matrices
h = Hamiltonian(xyz=path_to_xyz_file)
h.initialize()
# set periodic boundary conditions
h.set_periodic_bc(primitive_cell)
# define wave vector coordinates
sym_points = ['L', 'GAMMA', 'X', 'W', 'K', 'L', 'W', 'X', 'K', 'GAMMA']
num_points = [15, 20, 15, 10, 15, 15, 15, 15, 20]
k_points = get_k_coords(sym_points, num_points, 'Si')
# compute band structure
band_structure = np.zeros((sum(num_points), h.h_matrix.shape[0]))
for jj, item in enumerate(k_points):
band_structure[jj, :], _ = h.diagonalize_periodic_bc(item)
# visualize
ax = plt.axes()
ax.set_title('Band structure of the bulk silicon')
ax.set_ylabel('Energy (eV)')
ax.plot(np.sort(np.real(band_structure))[:, :8], 'k')
ax.plot([0, band_structure.shape[0]], [0, 0],
'--',
color='k',
linewidth=0.5)
plt.xticks(np.insert(np.cumsum(num_points) - 1, 0, 0), labels=sym_points)
ax.xaxis.grid()
plt.show()
def preprocess_data(param_file, k_points_file, xyz, code_name):
"""
Parameters
----------
param_file :
k_points_file :
xyz :
code_name :
Returns
-------
"""
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, 'Si')
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
[a1, -a2, 0.0]])
# --------------------------- wave vectors -------------------------
lat_const_rec = 2 * np.pi / (3 * np.sqrt(3) * lat_const)
special_k_points = {
'GAMMA': [0, 0, 0],
'K': [lat_const_rec * np.sqrt(3), lat_const_rec, 0],
'K_prime': [lat_const_rec * np.sqrt(3), -lat_const_rec, 0],
'M': [lat_const_rec * np.sqrt(3), 0, 0]
}
sym_points = ['GAMMA', 'M', 'K', 'GAMMA']
num_points = [25, 25, 25]
k_points = get_k_coords(sym_points, num_points, special_k_points)
# ------------------------------------------------------------------
fig_counter = 1
def graphene_first_nearest_neighbour():
coords = """2
Graphene
C1 0.00 0.00 0.00
C2 {} 0.00 0.00
""".format(lat_const)
# --------------------------- Basis set --------------------------