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deepmd/hdf5: handle empty systems and files #469

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Merged
wanghan-iapcm merged 1 commit into from
May 15, 2023
Merged

deepmd/hdf5: handle empty systems and files #469

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6 changes: 6 additions & 0 deletions dpdata/deepmd/hdf5.py
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Original file line number Diff line number Diff line change
Expand Up @@ -30,6 +30,9 @@ def to_system_data(
g = f[folder] if folder else f

data = {}
# ignore empty files or groups
if "type.raw" not in g.keys():
return data
data["atom_types"] = g["type.raw"][:]
ntypes = np.max(data["atom_types"]) + 1
natoms = data["atom_types"].size
Expand Down Expand Up @@ -140,6 +143,9 @@ def dump(
g = f.create_group(folder)
else:
g = f
# ignore empty systems
if not len(data["coords"]):
return
# dump raw (array in fact)
g.create_dataset("type.raw", data=data["atom_types"])
g.create_dataset("type_map.raw", data=np.array(data["atom_names"], dtype="S"))
Expand Down