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fix: optimize atom type mapping #5043

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Merged
njzjz merged 2 commits into from
Nov 11, 2025
Merged

fix: optimize atom type mapping #5043

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96da487
fix: optimize atom type mapping
OutisLi Nov 10, 2025
ff8aee9
vectorize
OutisLi Nov 10, 2025
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11 changes: 4 additions & 7 deletions deepmd/utils/data.py
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Original file line number Diff line number Diff line change
Expand Up @@ -103,13 +103,10 @@ def __init__(
f"Elements {missing_elements} are not present in the provided `type_map`."
)
if not self.mixed_type:
# Use vectorized operation for better performance with large atom counts
# Create a mapping array where old_type_idx -> new_type_idx
max_old_type = max(self.atom_type) + 1
type_mapping = np.zeros(max_old_type, dtype=np.int32)
for old_idx in range(len(self.type_map)):
type_mapping[old_idx] = type_map.index(self.type_map[old_idx])
self.atom_type = type_mapping[self.atom_type].astype(np.int32)
old_to_new_type_idx = np.array(
[type_map.index(name) for name in self.type_map], dtype=np.int32
)
self.atom_type = old_to_new_type_idx[self.atom_type].astype(np.int32)
else:
self.enforce_type_map = True
sorter = np.argsort(type_map)
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