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Do not add auxiliary cell to uploaded/generated structures #592

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Do not add auxiliary cell to uploaded/generated structures #592

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40 changes: 5 additions & 35 deletions aiidalab_widgets_base/structures.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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():
Expand Down Expand Up @@ -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:
Expand All @@ -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):
Expand Down Expand Up @@ -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)

Expand All @@ -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>"
)
]
)
Expand All @@ -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):
Expand Down
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