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improve speedup of large lattice #1198

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Sep 13, 2024
Merged

improve speedup of large lattice #1198

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7 changes: 4 additions & 3 deletions mbuild/lattice.py
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Original file line number Diff line number Diff line change
Expand Up @@ -625,6 +625,7 @@ def populate(self, compound_dict=None, x=1, y=1, z=1):
ret_lattice = mb.Compound()

# Create (clone) a mb.Compound for the newly generate positions
compoundsList = [] # particles to add at the end
elementsSet = set()
if compound_dict is None:
for key_id, all_pos in cell.items():
Expand All @@ -641,15 +642,15 @@ def populate(self, compound_dict=None, x=1, y=1, z=1):
for pos in all_pos:
particle_to_add = mb.clone(particle)
particle_to_add.translate_to(list(pos))
ret_lattice.add(particle_to_add)
compoundsList.append(particle_to_add)
else:
for key_id, all_pos in cell.items():
if isinstance(compound_dict[key_id], mb.Compound):
compound_to_move = compound_dict[key_id]
for pos in all_pos:
tmp_comp = mb.clone(compound_to_move)
tmp_comp.translate_to(list(pos))
ret_lattice.add(tmp_comp)
compoundsList.append(tmp_comp)
else:
err_type = type(compound_dict.get(key_id))
raise TypeError(
Expand All @@ -661,7 +662,7 @@ def populate(self, compound_dict=None, x=1, y=1, z=1):
warnings.warn(
f"Element assumed from cif file to be {element}.", UserWarning
)

ret_lattice.add(compoundsList)
# Create mbuild.box
ret_lattice.box = mb.Box(
lengths=[a * x, b * y, c * z], angles=self.angles
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