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Remove unnecessary conversions to numpy arrays (fixes gsd writer issue), remove self.atomistic from __repr__ method. #95

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Merged
merged 2 commits into from
Jun 23, 2025
Merged

Remove unnecessary conversions to numpy arrays (fixes gsd writer issue), remove self.atomistic from __repr__ method. #95

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590685a
remove self.atomistic from repr method
Jun 23, 2025
759a753
remove unnecessary np array conversions
Jun 23, 2025
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7 changes: 3 additions & 4 deletions grits/coarsegrain.py
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Original file line number Diff line number Diff line change
Expand Up @@ -139,7 +139,6 @@ def __repr__(self):
"""Format the CG_Compound representation."""
return (
f"<{self.name}: {self.n_particles} beads "
+ f"(from {self.atomistic.n_particles} atoms), "
+ "pos=({:.4f},{: .4f},{: .4f}), ".format(*self.pos)
+ f"{self.n_bonds:d} bonds>"
)
Expand Down Expand Up @@ -719,7 +718,7 @@ def save(self, cg_gsdfile, start=0, stop=None, stride=1):
)
if bond_pair not in bond_types:
bond_types.append(bond_pair)
_id = np.where(np.array(bond_types) == bond_pair)[0]
_id = bond_types.index(bond_pair)
bond_ids.append(_id)
else:
bond_types = None
Expand Down Expand Up @@ -777,9 +776,9 @@ def save(self, cg_gsdfile, start=0, stop=None, stride=1):
if N_bonds > 0:
new_snap.bonds.N = N_bonds
new_snap.bonds.group = self._bond_array
new_snap.bonds.typeid = np.array(bond_ids)
new_snap.bonds.typeid = bond_ids
if bond_types is not None:
new_snap.bonds.types = np.array(bond_types)
new_snap.bonds.types = bond_types
else:
new_snap.bonds.types = None
new_snap.bonds.type_shapes = bond_type_shapes
Expand Down
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