crystal tool now compatible

pycroscopy · Jan 27, 2024 · 6cdc048 · 6cdc048
1 parent 33e6cd3
commit 6cdc048
Show file tree

Hide file tree

Showing 3 changed files with 6 additions and 14 deletions.
diff --git a/notebooks/0_pyTEMlib.ipynb b/notebooks/0_pyTEMlib.ipynb
@@ -36,10 +36,11 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
    "outputs": [],
-   "source": []
+   "source": [],
+   "metadata": {
+    "collapsed": false
+   }
   }
  ],
  "metadata": {

diff --git a/pyTEMlib/crystal_tools.py b/pyTEMlib/crystal_tools.py
@@ -283,16 +283,7 @@ 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))
-    del_double.sort(reverse=False)
-    for key in del_double:
-        # Todo: why is ther a key error
-        # bond_matrix.pop(key)
-        pass
-
+    bond_matrix = np.triu(bond_matrix.toarray())
     if super_cell.info is None:
         super_cell.info = {}
     super_cell.info['plot_cell'] = {'bond_matrix': bond_matrix, 'corner_vectors': corner_vectors,

diff --git a/tests/test_crystal_tools.py b/tests/test_crystal_tools.py
@@ -43,7 +43,7 @@ def test_ball_and_stick(self):
                          [0, 0, 0, 0, 0, 0, 0, 0, 1],
                          [0, 0, 0, 0, 0, 0, 0, 0, 1],
                          [0, 0, 0, 0, 0, 0, 0, 0, 0]]
-        # np.testing.assert_allclose(cell_2_plot.info['plot_cell']['bond_matrix'].toarray(), bonds_desired)
+        np.testing.assert_allclose(cell_2_plot.info['plot_cell']['bond_matrix'], bonds_desired)
 
     def test_from_dictionary(self):
         tags = {'unit_cell': np.array([[4.05, 0, 0], [0, 4.05, 0], [0, 0, 4.05]]),