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support assigning 'type_map' for mixed_type #540

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Merged
wanghan-iapcm merged 2 commits into from
Sep 15, 2023
Merged

support assigning 'type_map' for mixed_type #540

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a1fc992
support assigning 'type_map' for mixed_type
iProzd Sep 13, 2023
8a160e9
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Sep 13, 2023
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18 changes: 17 additions & 1 deletion dpdata/deepmd/mixed.py
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Original file line number Diff line number Diff line change
Expand Up @@ -46,6 +46,17 @@ def _load_set(folder, nopbc: bool):
def to_system_data(folder, type_map=None, labels=True):
# data is empty
data = load_type(folder)
old_type_map = data["atom_names"].copy()
if type_map is not None:
assert isinstance(type_map, list)
missing_type = [i for i in old_type_map if i not in type_map]
assert (
not missing_type
), f"These types are missing in selected type_map: {missing_type} !"
index_map = np.array([type_map.index(i) for i in old_type_map])
data["atom_names"] = type_map.copy()
else:
index_map = None
data["orig"] = np.zeros([3])
if os.path.isfile(os.path.join(folder, "nopbc")):
data["nopbc"] = True
Expand All @@ -63,7 +74,12 @@ def to_system_data(folder, type_map=None, labels=True):
nframes = np.reshape(cells, [-1, 3, 3]).shape[0]
all_cells.append(np.reshape(cells, [nframes, 3, 3]))
all_coords.append(np.reshape(coords, [nframes, -1, 3]))
all_real_atom_types.append(np.reshape(real_atom_types, [nframes, -1]))
if index_map is None:
all_real_atom_types.append(np.reshape(real_atom_types, [nframes, -1]))
else:
all_real_atom_types.append(
np.reshape(index_map[real_atom_types], [nframes, -1])
)
if eners is not None:
eners = np.reshape(eners, [nframes])
if labels:
Expand Down