mimic the behavior of nglview and transforms the "displayed_structure…

…" into the standard form (#576)

This PR transforms the "displayed_structure" into the standard form, where the a-axis aligns along the x-axis, prior to rendering in nglview. This ensures that nglview's internal handling does not further modify the structure unexpectedly. This ensures the atom positions and custom bonds calculated are matched.

aiidalab_widgets_base/viewers.py

@@ -1136,7 +1136,18 @@ def _observe_supercell(self, _=None):
             self.set_trait(
                 "displayed_structure", None
             )  # To make sure the structure is always updated.
-            self.set_trait("displayed_structure", self.structure.repeat(self.supercell))
+            # nglview displays structures by first saving them to a temporary "pdb" file, which necessitates
+            # converting the unit cell and atomic positions into a standard form where the a-axis aligns along the x-axis.
+            # This transformation can cause discrepancies between the atom positions and custom bonds calculated from the original structure.
+            # To mitigate this, we transform the "displayed_structure" into the standard form prior to rendering in nglview.
+            # This ensures that nglview's internal handling does not further modify the structure unexpectedly.
+            standard_structure = self.structure.copy()
+            standard_structure.set_cell(
+                self.structure.cell.standard_form()[0], scale_atoms=True
+            )
+            self.set_trait(
+                "displayed_structure", standard_structure.repeat(self.supercell)
+            )
 
     @tl.validate("structure")
     def _valid_structure(self, change):

miscellaneous/structures/Si.xyz

@@ -0,0 +1,4 @@
+2
+Lattice="3.81196 0.0 0.0 1.9059800000000005 3.3012541982101284 0.0 1.9059800000000005 1.100418066070043 3.112452306633254" Properties=species:S:1:pos:R:3 spacegroup="P 1" unit_cell=conventional pbc="T T T"
+Si       0.00000000       0.00000000       0.00000000
+Si       1.90598000       1.10041807       0.77811308

notebooks/structures.ipynb

@@ -56,7 +56,8 @@
     "        awb.StructureExamplesWidget(\n",
     "            title=\"From Examples\",\n",
     "            examples=[\n",
-    "                (\"Silicon oxide\", \"../miscellaneous/structures/SiO2.xyz\")\n",
+    "                (\"Silicon oxide\", \"../miscellaneous/structures/SiO2.xyz\"),\n",
+    "                (\"Silicon\", \"../miscellaneous/structures/Si.xyz\")\n",
     "            ]),\n",
     "    ],\n",
     "    editors = [\n",