Do not add auxiliary cell to uploaded/generated structures

aiidalab_widgets_base/structures.py

@@ -384,32 +384,6 @@ def __init__(
             children=[self.file_upload, supported_formats, self._status_message]
         )
 
-    def _validate_and_fix_ase_cell(self, ase_structure, vacuum_ang=10.0):
-        """
-        Checks if the ase Atoms object has a cell set,
-        otherwise sets it to bounding box plus specified "vacuum" space
-        """
-        if not ase_structure:
-            return None
-
-        cell = ase_structure.cell
-
-        # TODO: Since AiiDA 2.0, zero cell is possible if PBC=false
-        # so we should honor that here and do not put artificial cell
-        # around gas phase molecules.
-        if (
-            np.linalg.norm(cell[0]) < 0.1
-            or np.linalg.norm(cell[1]) < 0.1
-            or np.linalg.norm(cell[2]) < 0.1
-        ):
-            # if any of the cell vectors is too short, consider it faulty
-            # set cell as bounding box + vacuum_ang
-            bbox = np.ptp(ase_structure.positions, axis=0)
-            new_structure = ase_structure.copy()
-            new_structure.cell = bbox + vacuum_ang
-            return new_structure
-        return ase_structure
-
     def _on_file_upload(self, change=None):
         """When file upload button is pressed."""
         for fname, item in change["new"].items():
@@ -451,10 +425,7 @@ def _read_structure(self, fname, content):
                 if self.allow_trajectories:
                     return TrajectoryData(
                         structurelist=[
-                            StructureData(
-                                ase=self._validate_and_fix_ase_cell(ase_struct)
-                            )
-                            for ase_struct in structures
+                            StructureData(ase=ase_struct) for ase_struct in structures
                         ]
                     )
                 else:
@@ -463,7 +434,7 @@ def _read_structure(self, fname, content):
                         """
                     return None
 
-            return self._validate_and_fix_ase_cell(structures[0])
+            return structures[0]
 
 
 class StructureExamplesWidget(ipw.VBox):
@@ -683,7 +654,7 @@ def _on_select_structure(self, _=None):
 
 
 class SmilesWidget(ipw.VBox):
-    """Convert SMILES into 3D structure."""
+    """Convert SMILES into a 3D structure."""
 
     structure = tl.Instance(ase.Atoms, allow_none=True)
 
@@ -698,8 +669,9 @@ def __init__(self, title=""):
             super().__init__(
                 [
                     ipw.HTML(
-                        "The SmilesWidget requires the rdkit library, "
+                        "The SMILES widget requires the rdkit library, "
                         "but the library was not found."
+                        "You can install it with <code>pip install rdkit<code>"
                     )
                 ]
             )
@@ -726,12 +698,10 @@ def _make_ase(self, species, positions, smiles):
         if len(species) > 2:
             positions = PCA(n_components=3).fit_transform(positions)
         atoms = ase.Atoms(species, positions=positions, pbc=False)
-        atoms.cell = np.ptp(atoms.positions, axis=0) + 10
         atoms.center()
         # We're attaching this info so that it
         # can be later stored as an extra on AiiDA Structure node.
         atoms.info["smiles"] = smiles
-
         return atoms
 
     def _rdkit_opt(self, smiles, steps):