fixed error detected by pylint

.travis.yml

@@ -30,7 +30,7 @@ install:
 # command to run tests
 script:
     - nosetests --with-coverage
-    - pylint --errors-only nanonet
+    - pylint --errors-only --generated-members=coolwarm,accumulate --ignored-modules=numpy,scipy --ignored-classes=numpy,spipy --extension-pkg-whitelist=numpy,scipy  nanonet/
 branches:
     only:
         - master

nanonet/negf/continued_fraction_representation.py

@@ -1,6 +1,6 @@
 import numpy as np
 from scipy.linalg import eig
-from negf.hamiltonian_chain import fd
+from nanonet.negf.hamiltonian_chain import fd
 
 
 def t_order_frac(x):

nanonet/negf/invdisttree.py

@@ -1,7 +1,6 @@
 from __future__ import division
 import numpy as np
 from scipy.spatial import cKDTree as KDTree
-    # http://docs.scipy.org/doc/scipy/reference/spatial.html
 
 __date__ = "2010-11-09 Nov"  # weights, doc
 

nanonet/negf/surf_greens_function.py

@@ -296,14 +296,14 @@ def main():
     sys.path.insert(0, '/home/mk/TB_project/tb')
     import nanonet.tb as tb
 
-    a = tb.Atom('A')
+    a = tb.Orbitals('A')
     a.add_orbital('s', -0.7)
-    b = tb.Atom('B')
+    b = tb.Orbitals('B')
     b.add_orbital('s', -0.5)
-    c = tb.Atom('C')
+    c = tb.Orbitals('C')
     c.add_orbital('s', -0.3)
 
-    tb.Atom.orbital_sets = {'A': a, 'B': b, 'C': c}
+    tb.Orbitals.orbital_sets = {'A': a, 'B': b, 'C': c}
 
     tb.set_tb_params(PARAMS_A_A={'ss_sigma': -0.5},
                      PARAMS_B_B={'ss_sigma': -0.5},
@@ -338,7 +338,7 @@ def main():
 
     for E in energy:
         print("============Eigenval decompositions============")
-        L, R, _, _, _ = surface_greens_function(E, h_l, h_0, h_r)
+        L, R = surface_greens_function(E, h_l, h_0, h_r)
         print("==============Schur decomposition==============")
         L1, R1 = surface_greens_function_poles_Shur(E, h_l, h_0, h_r)
         sgf_l.append(L)
@@ -373,7 +373,7 @@ def main1():
     sys.path.insert(0, '/home/mk/TB_project/tb')
     import nanonet.tb as tb
 
-    tb.Atom.orbital_sets = {'Si': 'SiliconSP3D5S', 'H': 'HydrogenS'}
+    tb.Orbitals.orbital_sets = {'Si': 'SiliconSP3D5S', 'H': 'HydrogenS'}
     h = tb.Hamiltonian(xyz='/home/mk/NEGF_project/SiNW.xyz', nn_distance=2.4)
     h.initialize()
     h.set_periodic_bc([[0, 0, 5.50]])
@@ -397,7 +397,7 @@ def main1():
 
     for j, E in enumerate(energy):
         # L, R = surface_greens_function_poles_Shur(j, E, h_l, h_0, h_r)
-        L, R, _, _, _ = surface_greens_function(E, h_l, h_0, h_r)
+        L, R = surface_greens_function(E, h_l, h_0, h_r)
 
         test_gf = E * np.identity(num_sites) - h_0 - L - R
 
@@ -505,7 +505,7 @@ def inverse_bs_problem():
     # h.initialize()
     # h.set_periodic_bc([[0, 0, 3.0]])
 
-    tb.Atom.orbital_sets = {'Si': 'SiliconSP3D5S', 'H': 'HydrogenS'}
+    tb.Orbitals.orbital_sets = {'Si': 'SiliconSP3D5S', 'H': 'HydrogenS'}
     h = tb.Hamiltonian(xyz='/home/mk/TB_project/input_samples/SiNW.xyz', nn_distance=2.4)
     h.initialize()
     h.set_periodic_bc([[0, 0, 5.50]])
@@ -551,10 +551,10 @@ def main2():
     sys.path.insert(0, '/home/mk/TB_project/tb')
     import nanonet.tb as tb
 
-    a = tb.Atom('A')
+    a = tb.Orbitals('A')
     a.add_orbital('s', -0.7)
 
-    tb.Atom.orbital_sets = {'A': a}
+    tb.Orbitals.orbital_sets = {'A': a}
 
     tb.set_tb_params(PARAMS_A_A={'ss_sigma': -0.5},
                      PARAMS_B_B={'ss_sigma': -0.5},
@@ -578,7 +578,7 @@ def main2():
     sgf_r = []
 
     for E in energy:
-        L, R, _, _, _ = surface_greens_function(E, h_l, h_0, h_r)
+        L, R = surface_greens_function(E, h_l, h_0, h_r)
         # L, R = surface_greens_function_poles_Shur(E, h_l, h_0, h_r)
         sgf_l.append(L)
         sgf_r.append(R)
@@ -607,10 +607,10 @@ def main3():
     sys.path.insert(0, '/home/mk/TB_project/tb')
     import nanonet.tb as tb
 
-    a = tb.Atom('A')
+    a = tb.Orbitals('A')
     a.add_orbital('s', -0.7)
 
-    tb.Atom.orbital_sets = {'A': a}
+    tb.Orbitals.orbital_sets = {'A': a}
 
     tb.set_tb_params(PARAMS_A_A={'ss_sigma': -0.5},
                      PARAMS_B_B={'ss_sigma': -0.5},
@@ -634,7 +634,7 @@ def main3():
     sgf_r = []
 
     for E in energy:
-        L, R, _, _, _ = surface_greens_function(E, h_l, h_0, h_r)
+        L, R = surface_greens_function(E, h_l, h_0, h_r)
         # L, R = surface_greens_function_poles_Shur(E, h_l, h_0, h_r)
         sgf_l.append(L)
         sgf_r.append(R)

nanonet/tb/aux_functions.py

@@ -310,90 +310,90 @@ def print_dict(dictionary):
     return out
 
 
-def split_into_subblocks(h_0, h_l, h_r):
-    """
-    Split Hamiltonian matrix and coupling matrices into subblocks
-
-    :param h_0:                     Hamiltonian matrix
-    :param h_l:                     left inter-cell coupling matrices
-    :param h_r:                     right inter-cell coupling matrices
-    :return h_0_s, h_l_s, h_r_s:    lists of subblocks
-    """
-
-    def find_nonzero_lines(mat, order):
-
-        if order == 'top':
-            line = mat.shape[0]
-            while line > 0:
-                if np.count_nonzero(mat[line - 1, :]) == 0:
-                    line -= 1
-                else:
-                    break
-        elif order == 'bottom':
-            line = -1
-            while line < mat.shape[0] - 1:
-                if np.count_nonzero(mat[line + 1, :]) == 0:
-                    line += 1
-                else:
-                    line = mat.shape[0] - (line + 1)
-                    break
-        elif order == 'left':
-            line = mat.shape[1]
-            while line > 0:
-                if np.count_nonzero(mat[:, line - 1]) == 0:
-                    line -= 1
-                else:
-                    break
-        elif order == 'right':
-            line = -1
-            while line < mat.shape[1] - 1:
-                if np.count_nonzero(mat[:, line + 1]) == 0:
-                    line += 1
-                else:
-                    line = mat.shape[1] - (line + 1)
-                    break
-        else:
-            raise ValueError('Wrong value of the parameter order')
-
-        return line
-
-    h_0_s = []
-    h_l_s = []
-    h_r_s = []
-
-    if isinstance(h_l, np.ndarray) and isinstance(h_r, np.ndarray):
-        h_r_h = find_nonzero_lines(h_r, 'bottom')
-        h_r_v = find_nonzero_lines(h_r[-h_r_h:, :], 'left')
-        h_l_h = find_nonzero_lines(h_l, 'top')
-        h_l_v = find_nonzero_lines(h_l[:h_l_h, :], 'right')
-
-    if isinstance(h_l, int) and isinstance(h_r, int):
-        h_l_h = h_l
-        h_r_v = h_l
-        h_r_h = h_r
-        h_l_v = h_r
-
-    edge, edge1 = compute_edge(h_0)
-
-    left_block = max(h_l_h, h_r_v)
-    right_block = max(h_r_h, h_l_v)
-
-    from nanonet.tb.sorting_algorithms import split_matrix_0, cut_in_blocks, split_matrix
-
-    blocks = split_matrix_0(h_0, left=left_block, right=right_block)
-    h_0_s, h_l_s, h_r_s = cut_in_blocks(h_0, blocks)
-
-    # blocks = compute_blocks(left_block, right_block, edge, edge1)
-    # j1 = 0
-    #
-    # for j, block in enumerate(blocks):
-    #     h_0_s.append(h_0[j1:block + j1, j1:block + j1])
-    #     if j < len(blocks) - 1:
-    #         h_l_s.append(h_0[block + j1:block + j1 + blocks[j + 1], j1:block + j1])
-    #         h_r_s.append(h_0[j1:block + j1, j1 + block:j1 + block + blocks[j + 1]])
-    #     j1 += block
-
-    return h_0_s, h_l_s, h_r_s, blocks
+# def split_into_subblocks(h_0, h_l, h_r):
+#     """
+#     Split Hamiltonian matrix and coupling matrices into subblocks
+#
+#     :param h_0:                     Hamiltonian matrix
+#     :param h_l:                     left inter-cell coupling matrices
+#     :param h_r:                     right inter-cell coupling matrices
+#     :return h_0_s, h_l_s, h_r_s:    lists of subblocks
+#     """
+#
+#     def find_nonzero_lines(mat, order):
+#
+#         if order == 'top':
+#             line = mat.shape[0]
+#             while line > 0:
+#                 if np.count_nonzero(mat[line - 1, :]) == 0:
+#                     line -= 1
+#                 else:
+#                     break
+#         elif order == 'bottom':
+#             line = -1
+#             while line < mat.shape[0] - 1:
+#                 if np.count_nonzero(mat[line + 1, :]) == 0:
+#                     line += 1
+#                 else:
+#                     line = mat.shape[0] - (line + 1)
+#                     break
+#         elif order == 'left':
+#             line = mat.shape[1]
+#             while line > 0:
+#                 if np.count_nonzero(mat[:, line - 1]) == 0:
+#                     line -= 1
+#                 else:
+#                     break
+#         elif order == 'right':
+#             line = -1
+#             while line < mat.shape[1] - 1:
+#                 if np.count_nonzero(mat[:, line + 1]) == 0:
+#                     line += 1
+#                 else:
+#                     line = mat.shape[1] - (line + 1)
+#                     break
+#         else:
+#             raise ValueError('Wrong value of the parameter order')
+#
+#         return line
+#
+#     h_0_s = []
+#     h_l_s = []
+#     h_r_s = []
+#
+#     if isinstance(h_l, np.ndarray) and isinstance(h_r, np.ndarray):
+#         h_r_h = find_nonzero_lines(h_r, 'bottom')
+#         h_r_v = find_nonzero_lines(h_r[-h_r_h:, :], 'left')
+#         h_l_h = find_nonzero_lines(h_l, 'top')
+#         h_l_v = find_nonzero_lines(h_l[:h_l_h, :], 'right')
+#
+#     if isinstance(h_l, int) and isinstance(h_r, int):
+#         h_l_h = h_l
+#         h_r_v = h_l
+#         h_r_h = h_r
+#         h_l_v = h_r
+#
+#     edge, edge1 = compute_edge(h_0)
+#
+#     left_block = max(h_l_h, h_r_v)
+#     right_block = max(h_r_h, h_l_v)
+#
+#     from nanonet.tb.sorting_algorithms import split_matrix_0, cut_in_blocks, split_matrix
+#
+#     blocks = split_matrix_0(h_0, left=left_block, right=right_block)
+#     h_0_s, h_l_s, h_r_s = cut_in_blocks(h_0, blocks)
+#
+#     # blocks = compute_blocks(left_block, right_block, edge, edge1)
+#     # j1 = 0
+#     #
+#     # for j, block in enumerate(blocks):
+#     #     h_0_s.append(h_0[j1:block + j1, j1:block + j1])
+#     #     if j < len(blocks) - 1:
+#     #         h_l_s.append(h_0[block + j1:block + j1 + blocks[j + 1], j1:block + j1])
+#     #         h_r_s.append(h_0[j1:block + j1, j1 + block:j1 + block + blocks[j + 1]])
+#     #     j1 += block
+#
+#     return h_0_s, h_l_s, h_r_s, blocks
 
 
 def compute_edge(mat):