docs on complexes + periodic image

docs/source/content/defining-defects.ipynb

@@ -159,11 +159,17 @@
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-    "The `defect_structure` for each complex is shown blow.\n",
+    "The `defect_structure` for each complex is shown below.\n",
     "\n",
     "<img src=\"https://raw.githubusercontent.com/materialsproject/pymatgen-analysis-defects/main/docs/source/_static/img/defect_complex_equiv.png\" width=\"800\"/>\n",
     "\n",
-    "By inspection it is clear that `def_comp0` and `def_comp2` are symmetrically equivalent to each other and distinct from `def_comp1`, and our basic implementation of defect equivalence is able to verify this:\n"
+    "By inspection, `def_comp0` and `def_comp2` appear symmetrically equivalent to each other at first and distinct from `def_comp1`.\n",
+    "However, there are two distinct Mg_Ga+V_N complexes in the structure:\n",
+    "\n",
+    "- One where the two parts of the defect complex are nearest neighbors (`def_comp0`).\n",
+    "- One where the two defects are next-nearest neighbors (`def_comp2`).\n",
+    "\n",
+    "Since our defect complex definition accounts for an effective _Center of Mass_ site, we can properly account for periodic boundary conditions. the two defect complexes will be considered not equal."
    ]
   },
   {
@@ -172,21 +178,10 @@
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-    "assert def_comp0 == def_comp2\n",
+    "assert def_comp0 != def_comp2\n",
     "assert def_comp0 != def_comp1"
    ]
   },
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-   "source": [
-    "However some defect complexes might become nonequivalent based on the periodic image you consider for the combination of sites.\n",
-    "\n",
-    "<div class=\"alert alert-block alert-info\"><b>Note:</b> To deal with these edge cases, we might have to add a dummy \"DefectComplex\" species at the \"center\" of the defect complex which will fix the selection of periodic for the different sites.  This is easy to implement but should be done when there is a good test case.\n",
-    "</div>\n"
-   ]
-  },
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@@ -245,12 +240,7 @@
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