Do not add auxiliary cell to uploaded/generated gas phase structures

aiidalab_widgets_base/structures.py

@@ -375,9 +375,14 @@ class StructureUploadWidget(ipw.VBox):
     )
 
     def __init__(
-        self, title="", description="Upload Structure", allow_trajectories=False
+        self,
+        title="",
+        description="Upload Structure",
+        allow_trajectories=False,
+        add_auxiliary_cell=True,
     ):
         self.title = title
+        self.add_auxiliary_cell = add_auxiliary_cell
         self.file_upload = ipw.FileUpload(
             description=description, multiple=False, layout={"width": "initial"}
         )
@@ -403,11 +408,11 @@ def _validate_and_fix_ase_cell(self, ase_structure, vacuum_ang=10.0):
         if not ase_structure:
             return None
 
+        if not self.add_auxiliary_cell:
+            return ase_structure
+
         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
@@ -758,8 +763,9 @@ class SmilesWidget(ipw.VBox):
 
     SPINNER = """<i class="fa fa-spinner fa-pulse" style="color:red;" ></i>"""
 
-    def __init__(self, title=""):
+    def __init__(self, title="", add_auxiliary_cell=True):
         self.title = title
+        self.add_auxiliary_cell = add_auxiliary_cell
         try:
             from rdkit import Chem  # noqa: F401
             from rdkit.Chem import AllChem  # noqa: F401
@@ -790,12 +796,10 @@ def __init__(self, title=""):
     def _make_ase(self, species, positions, smiles):
         """Create ase Atoms object."""
         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):
@@ -831,7 +835,10 @@ def _rdkit_opt(self, smiles, steps):
         positions = mol.GetConformer().GetPositions()
         natoms = mol.GetNumAtoms()
         species = [mol.GetAtomWithIdx(j).GetSymbol() for j in range(natoms)]
-        return self._make_ase(species, positions, smiles)
+        ase_mol = self._make_ase(species, positions, smiles)
+        if self.add_auxiliary_cell:
+            ase_mol.cell = np.ptp(ase_mol.positions, axis=0) + 10
+        return ase_mol
 
     def _mol_from_smiles(self, smiles, steps=1000):
         """Convert SMILES to ASE structure using RDKit"""

tests/test_structures.py

@@ -199,10 +199,11 @@ def raise_not_existent(pk):
     )
 
 
+@pytest.mark.parametrize("add_auxiliary_cell", (False, True))
 @pytest.mark.usefixtures("aiida_profile_clean")
-def test_structure_upload_widget(file_upload_change):
+def test_structure_upload_widget(add_auxiliary_cell, file_upload_change):
     """Test the `StructureUploadWidget`."""
-    widget = awb.StructureUploadWidget()
+    widget = awb.StructureUploadWidget(add_auxiliary_cell=add_auxiliary_cell)
     assert widget.structure is None
 
     # Simulate the structure upload.
@@ -220,6 +221,16 @@ def test_structure_upload_widget(file_upload_change):
     assert widget.structure.get_chemical_formula() == "Si2"
     assert np.all(widget.structure[0].position == [0, 0, 0])
 
+    if add_auxiliary_cell:
+        cell = widget.structure.cell
+        assert all(np.greater(np.diag(cell), [10, 10, 10]))
+        assert np.array_equal(cell.angles(), [90.0, 90.0, 90.0])
+    else:
+        # There should be no cell, which ASE represents with a zero cell
+        assert not any(widget.structure.pbc)
+        assert not np.any(widget.structure.cell)
+        assert not widget.structure.cell.volume
+
 
 @pytest.mark.parametrize(
     ("fname", "fcontent", "errmsg"),
@@ -275,6 +286,12 @@ def test_smiles_widget():
     widget._on_button_pressed()
     assert isinstance(widget.structure, ase.Atoms)
     assert widget.structure.get_chemical_formula() == "CH4"
+    # By default, a rectangular cell is added (10 angstroms in each direction)
+    # but PBC is False
+    assert not any(widget.structure.pbc)
+    cell = widget.structure.cell
+    assert all(np.greater(np.diag(cell), [10, 10, 10]))
+    assert np.array_equal(cell.angles(), [90.0, 90.0, 90.0])
 
     # Regression test that we can generate 1-atom and 2-atom molecules
     widget.smiles.value = "[O]"
@@ -293,6 +310,23 @@ def test_smiles_widget():
     assert widget.structure is None
 
 
+@pytest.mark.usefixtures("aiida_profile_clean")
+def test_smiles_widget_without_cell():
+    """Test the `SmilesWidget`."""
+    widget = awb.SmilesWidget(add_auxiliary_cell=False)
+    assert widget.structure is None
+
+    # Simulate the structure generation.
+    widget.smiles.value = "C"
+    widget._on_button_pressed()
+    assert isinstance(widget.structure, ase.Atoms)
+    assert widget.structure.get_chemical_formula() == "CH4"
+    # There should be no cell, which ASE represents with a zero cell
+    assert not any(widget.structure.pbc)
+    assert not np.any(widget.structure.cell)
+    assert not widget.structure.cell.volume
+
+
 @pytest.mark.usefixtures("aiida_profile_clean")
 def test_smiles_canonicalization():
     """Test the SMILES canonicalization via RdKit."""