pyTEMlib 0.2023.8.0__py2.py3-none-any.whl → 0.2024.2.0__py2.py3-none-any.whl

pyTEMlib/config_dir.py

@@ -7,7 +7,6 @@
 config_dir: setup of directory ~/.pyTEMlib for custom sources and database
 """
 import os
-import numpy as np
 
 # import wget
 if os.name == 'posix':

pyTEMlib/crystal_tools.py

@@ -27,6 +27,7 @@ import ase.data.colors
 
 import matplotlib.pylab as plt  # basic plotting
 from scipy.spatial import cKDTree
+import scipy
 _spglib_present = True
 try:
     import spglib
@@ -137,26 +138,26 @@ def get_projection(crystal, layers=1):
     for pro in projected:
         atomic_numbers.append(projected_crystal.get_atomic_numbers()[pro].sum())
         
-    projected_crystal.rotate(np.degrees(angle)%360, 'z', rotate_cell=True)
+    projected_crystal.rotate(np.degrees(angle) % 360, 'z', rotate_cell=True)
     
-    near_base = np.array([projected_crystal.cell[0,:2], -projected_crystal.cell[0,:2],
-                          projected_crystal.cell[1,:2], -projected_crystal.cell[1,:2],
-                          projected_crystal.cell[0,:2] + projected_crystal.cell[1,:2],
-                          -(projected_crystal.cell[0,:2] + projected_crystal.cell[1,:2])])
-    lines = np.array( [[[0, near_base[0,0]],[0, near_base[0,1]]],
-                       [[0, near_base[2,0]],[0, near_base[2,1]]],
-                       [[near_base[0,0], near_base[4,0]],[near_base[0,1], near_base[4,1]]],
-                       [[near_base[2,0], near_base[4,0]],[near_base[2,1], near_base[4,1]]]])
+    near_base = np.array([projected_crystal.cell[0, :2], -projected_crystal.cell[0, :2],
+                          projected_crystal.cell[1, :2], -projected_crystal.cell[1, :2],
+                          projected_crystal.cell[0, :2] + projected_crystal.cell[1, :2],
+                          -(projected_crystal.cell[0, :2] + projected_crystal.cell[1, :2])])
+    lines = np.array([[[0, near_base[0, 0]], [0, near_base[0, 1]]],
+                      [[0, near_base[2, 0]], [0, near_base[2, 1]]],
+                      [[near_base[0, 0], near_base[4, 0]], [near_base[0, 1], near_base[4, 1]]],
+                      [[near_base[2, 0], near_base[4, 0]], [near_base[2, 1], near_base[4, 1]]]])
     projected_atoms = []
     for index in projected:
-       projected_atoms.append(index[0])
+        projected_atoms.append(index[0])
     
-    projected_crystal.info['projection']={'indices': projected, 
-                                          'projected': projected_atoms,
-                                          'projected_Z': atomic_numbers, 
-                                          'angle': np.degrees(angle)+180%360,
-                                          'near_base': near_base,
-                                          'lines': lines}    
+    projected_crystal.info['projection'] = {'indices': projected,
+                                            'projected': projected_atoms,
+                                            'projected_Z': atomic_numbers,
+                                            'angle': np.degrees(angle)+180 % 360,
+                                            'near_base': near_base,
+                                            'lines': lines}
     return projected_crystal
 
 
@@ -283,13 +284,8 @@ def ball_and_stick(atoms, extend=1, max_bond_length=0.):
     neighbor_list.update(super_cell)
     bond_matrix = neighbor_list.get_connectivity_matrix()
 
-    del_double = []
-    for (k, s) in bond_matrix.keys():
-        if k > s:
-            del_double.append((k, s))
-    for key in del_double:
-        bond_matrix.pop(key)
-
+    bond_matrix = np.triu(bond_matrix.toarray())
+    bond_matrix = scipy.sparse.dok_array(bond_matrix)
     if super_cell.info is None:
         super_cell.info = {}
     super_cell.info['plot_cell'] = {'bond_matrix': bond_matrix, 'corner_vectors': corner_vectors,
@@ -298,7 +294,7 @@ def ball_and_stick(atoms, extend=1, max_bond_length=0.):
     return super_cell
 
 
-def plot_unit_cell(atoms, extend=1, max_bond_length=1.0, ax = None):
+def plot_unit_cell(atoms, extend=1, max_bond_length=1.0, ax=None):
     """
     Simple plot of unit cell
     """
@@ -309,8 +305,8 @@ def plot_unit_cell(atoms, extend=1, max_bond_length=1.0, ax = None):
     positions = super_cell.positions - super_cell.cell.lengths()/2
 
     if ax is None:
-       fig = plt.figure()
-       ax = fig.add_subplot(111, projection='3d')
+        fig = plt.figure()
+        ax = fig.add_subplot(111, projection='3d')
     # draw unit_cell
 
     for line in super_cell.info['plot_cell']['corner_matrix'].keys():