fixed examples

examples/si_nw_band_structure.py

@@ -1,103 +1,47 @@
+"""
+This example demonstrates calculation of the band structure
+for the silicon nanowire using a direct matrix diagonalization method.
+"""
 import numpy as np
 from nanonet.tb import HamiltonianSp
 from nanonet.tb import Orbitals
 from nanonet.tb.plotting import plot_bs_split, plot_atom_positions
 
 
-def radial_dep(coords):
-    norm_of_coords = np.linalg.norm(coords)
-    print(norm_of_coords)
-    if norm_of_coords < 3.3:
-        return 1
-    elif 3.7 > norm_of_coords > 3.3:
-        return 2
-    elif 5.0 > norm_of_coords > 3.7:
-        return 3
-    else:
-        return 100
-
-
-
 def main():
-    """
-    This function computes the band gap / band structure for Silicon Nanowire
-    :param path: directory path to where xyz input files are stored
-    :param flag: boolean statements
-    :return: band gap / band structure
-    """
-    # define orbitals sets
+    # use a predefined basis sets
     Orbitals.orbital_sets = {'Si': 'SiliconSP3D5S', 'H': 'HydrogenS'}
-    band_gaps = []
-    band_structures = []
 
+    # specify atomic coordinates file in xyz format
     path = "input_samples/SiNW2.xyz"
-    # path = "tb/third_party/si_slab.xyz"
-
-    # hamiltonian = Hamiltonian(xyz=path, nn_distance=1.1, lead_l=[[0, 0, 1]], lead_r=[[0, 4, 3]], so_coupling=0.06)
-
-    right_lead = [0, 33, 35, 17, 16, 51, 25,  9, 53, 68,  1,  8, 24]
-    left_lead = [40, 66, 58, 47, 48, 71, 72, 73, 74, 65]
 
-    def sorting(coords, **kwargs):
-        return np.argsort(coords[:, 2])
-
-    from nanonet.tb.sorting_algorithms import sort_projection as sorting
-
-    hamiltonian = HamiltonianSp(xyz=path, nn_distance=2.4,
-                              sort_func=sorting, left_lead=left_lead, right_lead=right_lead)
+    # define Hamiltonian object in the sparse format
+    hamiltonian = HamiltonianSp(xyz=path, nn_distance=2.4,)
     hamiltonian.initialize()
 
-    # if True:
-    #     plt.axis('off')
-    #     plt.imshow(np.log(np.abs(hamiltonian.h_matrix)))
-    #     plt.savefig('hamiltonian.pdf')
-    #     plt.show()
-
-    # from tb.aux_functions import split_into_subblocks
-    # a, b = blocksandborders(hamiltonian.h_matrix)
-
-    # bandwidth(hamiltonian.h_matrix)
-
-    # import scipy.spatial
-    # from scipy import sparse
-    # h_matrix_sparse = sparse.csr_matrix(hamiltonian.h_matrix)
-    # a = scipy.sparse.csgraph.reverse_cuthill_mckee(h_matrix_sparse, symmetric_mode=True)
-    # h_matrix1 = hamiltonian.h_matrix[:, a]
-    # h_matrix1 = h_matrix1[a, :]
-    #
-    # bandwidth(h_matrix1)
-
+    # set periodic boundary conditions
     a_si = 5.50
     PRIMITIVE_CELL = [[0, 0, a_si]]
     hamiltonian.set_periodic_bc(PRIMITIVE_CELL)
 
-    hl, h0, hr = hamiltonian.get_hamiltonians()
-    hl, h0, hr, _ = hamiltonian.get_hamiltonians_block_tridiagonal()
-
+    # define wave vector coordinates
     num_points = 20
     kk = np.linspace(0, 0.57, num_points, endpoint=True)
 
+    # compute band structure
     band_structure = []
-
     for jj in range(num_points):
-        print(jj)
+        print("{}. Processing wave vector {}".format(jj, [0, 0, kk[jj]]))
         vals, _ = hamiltonian.diagonalize_periodic_bc([0, 0, kk[jj]])
         band_structure.append(vals)
 
+    # visualize
     band_structure = np.array(band_structure)
-    band_structures.append(band_structure)
-
     cba = band_structure.copy()
     vba = band_structure.copy()
-
-    cba[cba < 0] = 1000
-    vba[vba > 0] = -1000
-
-    band_gap = np.min(cba) - np.max(vba)
-    band_gaps.append(band_gap)
-
-    if True:
-        plot_bs_split(kk, vba, cba)
+    cba[cba < 0] = np.inf
+    vba[vba > 0] = -np.inf
+    plot_bs_split(kk, vba, cba)
 
 
 if __name__ == '__main__':

examples/si_nw_transmission.py

@@ -5,7 +5,7 @@
 import matplotlib.pyplot as plt
 from nanonet.tb import Hamiltonian, HamiltonianSp
 from nanonet.tb import Orbitals
-from nanonet.tb.plotting import plot_bs_split, plot_atom_positions
+from nanonet.tb.sorting_algorithms import sort_projection
 
 
 def radial_dep(coords):
@@ -22,27 +22,14 @@ def radial_dep(coords):
 
 
 def main():
-    """
-    This function computes the band gap / band structure for Silicon Nanowire
-    :param path: directory path to where xyz input files are stored
-    :param flag: boolean statements
-    :return: band gap / band structure
-    """
     # define orbitals sets
     Orbitals.orbital_sets = {'Si': 'SiliconSP3D5S', 'H': 'HydrogenS'}
 
     path = "input_samples/SiNW2.xyz"
 
-    # hamiltonian = Hamiltonian(xyz=path, nn_distance=1.1, lead_l=[[0, 0, 1]], lead_r=[[0, 4, 3]], so_coupling=0.06)
-
     right_lead = [0, 33, 35, 17, 16, 51, 25,  9, 53, 68,  1,  8, 24]
     left_lead = [40, 66, 58, 47, 48, 71, 72, 73, 74, 65]
 
-    def sorting(coords, **kwargs):
-        return np.argsort(coords[:, 2])
-
-    from nanonet.tb.sorting_algorithms import sort_projection
-
     start = time.time()
     hamiltonian = Hamiltonian(xyz=path, nn_distance=2.4, sort_func=sort_projection, left_lead=left_lead, right_lead=right_lead)
     hamiltonian.initialize()