From 08b4a047e0c9c51e6697630eb3d4892913ae6b62 Mon Sep 17 00:00:00 2001
From: Jusong Yu <jusong.yeu@gmail.com>
Date: Tue, 3 Oct 2023 22:14:45 +0000
Subject: [PATCH] Not create cell for 0D

`_validate_and_fix_ase_cell` function is not needed anymore, since it add a
dummy cell to gas phase molecule. In the old AiiDA, there needed to be default
cell, otherwise StructureData would not work.
But that has been fixed so we should get rid of this login in AWB.

The fix in aiida-core was done here aiidateam/aiida-core#5341
and released in version 2.0 https://github.com/aiidateam/aiida-core/blob/main/CHANGELOG.md#v200---2022-04-27
---
 aiidalab_widgets_base/structures.py | 33 +++--------------------------
 1 file changed, 3 insertions(+), 30 deletions(-)

diff --git a/aiidalab_widgets_base/structures.py b/aiidalab_widgets_base/structures.py
index e5f5100b1..6f2fc32d4 100644
--- a/aiidalab_widgets_base/structures.py
+++ b/aiidalab_widgets_base/structures.py
@@ -376,32 +376,6 @@ 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():
@@ -444,9 +418,9 @@ def _read_structure(self, fname, content):
                     return TrajectoryData(
                         structurelist=[
                             StructureData(
-                                ase=self._validate_and_fix_ase_cell(ase_struct)
+                                ase=ase_structure,
                             )
-                            for ase_struct in structures
+                            for ase_structure in structures
                         ]
                     )
                 else:
@@ -455,7 +429,7 @@ def _read_structure(self, fname, content):
                         """
                     return None
 
-            return self._validate_and_fix_ase_cell(structures[0])
+            return structures[0]
 
 
 class StructureExamplesWidget(ipw.VBox):
@@ -720,7 +694,6 @@ 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.