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quipGapXYZ: add unit convert and tag synonym matching #678

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quipGapXYZ: add unit convert and tag synonym matching #678

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3a7171c
quipGapXYZ: add unit convert and synonym matching
SchrodingersCattt Jul 3, 2024
974c1b2
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Jul 3, 2024
da807b8
style: add Exception after except
SchrodingersCattt Jul 3, 2024
26c6156
style: add after
SchrodingersCattt Jul 3, 2024
37b96b8
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Jul 3, 2024
aebec7c
fix: removed redundant
SchrodingersCattt Jul 3, 2024
81a27d8
style: add Exception after except
SchrodingersCattt Jul 3, 2024
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238 changes: 186 additions & 52 deletions dpdata/xyz/quip_gap_xyz.py
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Original file line number Diff line number Diff line change
Expand Up @@ -7,6 +7,19 @@

import numpy as np

from ..unit import EnergyConversion, ForceConversion

e_conv_kcalpermol2eV = EnergyConversion("kcal_mol", "eV").value()
e_conv_au2eV = EnergyConversion("hartree", "eV").value()
f_conv_kcalpermolperang2eVperang = ForceConversion(
"kcal_mol/angstrom", "eV/angstrom"
).value()
f_conv_auperang2eVperang = ForceConversion("hartree/angstrom", "eV/angstrom").value()
f_conv_kcalpermolperbohr2eVperang = ForceConversion(
"kcal_mol/bohr", "eV/angstrom"
).value()
f_conv_au2eVperang = ForceConversion("hartree/bohr", "eV/angstrom").value()


class QuipGapxyzSystems:
"""deal with QuipGapxyzFile."""
Expand Down Expand Up @@ -82,56 +95,72 @@ def handle_single_xyz_frame(lines):
force_array = None
virials = None
for kv_dict in prop_list:
if kv_dict["key"] == "species":
if kv_dict["datatype"] != "S":
raise RuntimeError(
"datatype for species must be 'S' instead of {}".format(
kv_dict["datatype"]
try:
if kv_dict["key"] == "species":
if kv_dict["datatype"] != "S":
raise RuntimeError(
"datatype for species must be 'S' instead of {}".format(
kv_dict["datatype"]
)
)
)
field_length = int(kv_dict["value"])
type_array = data_array[
:, used_colomn : used_colomn + field_length
].flatten()
used_colomn += field_length
continue
elif kv_dict["key"] == "pos":
if kv_dict["datatype"] != "R":
raise RuntimeError(
"datatype for pos must be 'R' instead of {}".format(
kv_dict["datatype"]
field_length = int(kv_dict["value"])
type_array = data_array[
:, used_colomn : used_colomn + field_length
].flatten()
used_colomn += field_length
continue
elif kv_dict["key"] == "pos":
if kv_dict["datatype"] != "R":
raise RuntimeError(
"datatype for pos must be 'R' instead of {}".format(
kv_dict["datatype"]
)
)
)
field_length = int(kv_dict["value"])
coords_array = data_array[:, used_colomn : used_colomn + field_length]
used_colomn += field_length
continue
elif kv_dict["key"] == "Z":
if kv_dict["datatype"] != "I":
raise RuntimeError(
"datatype for pos must be 'R' instead of {}".format(
kv_dict["datatype"]
field_length = int(kv_dict["value"])
coords_array = data_array[
:, used_colomn : used_colomn + field_length
]
used_colomn += field_length
continue
elif kv_dict["key"] == "Z":
if kv_dict["datatype"] != "I":
raise RuntimeError(
"datatype for pos must be 'R' instead of {}".format(
kv_dict["datatype"]
)
)
)
field_length = int(kv_dict["value"])
Z_array = data_array[
:, used_colomn : used_colomn + field_length
].flatten()
used_colomn += field_length
continue
elif kv_dict["key"] == "force":
if kv_dict["datatype"] != "R":
raise RuntimeError(
"datatype for pos must be 'R' instead of {}".format(
kv_dict["datatype"]
field_length = int(kv_dict["value"])
Z_array = data_array[
:, used_colomn : used_colomn + field_length
].flatten()
used_colomn += field_length
continue
elif kv_dict["key"] == "tags":
if kv_dict["datatype"] != "I":
raise RuntimeError(
"datatype for tags must be 'I' instead of {}".format(
kv_dict["datatype"]
)
)
)
field_length = int(kv_dict["value"])
force_array = data_array[:, used_colomn : used_colomn + field_length]
used_colomn += field_length
field_length = int(kv_dict["value"])
used_colomn += field_length
continue
elif kv_dict["key"] == "force" or kv_dict["key"] == "forces":
if kv_dict["datatype"] != "R":
raise RuntimeError(
"datatype for pos must be 'R' instead of {}".format(
kv_dict["datatype"]
)
)
field_length = int(kv_dict["value"])
force_array = data_array[
:, used_colomn : used_colomn + field_length
]
used_colomn += field_length
continue
except Exception as e:
Comment on lines +98 to +161
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Improved field handling and error management.

The changes improve handling of fields like species, pos, Z, tags, and forces. The logic is sound, but avoid using bare except statements for better debugging.

-  except Exception as e:
+  except KeyError as e:
Committable suggestion

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Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.

Suggested change
try:
if kv_dict["key"] == "species":
if kv_dict["datatype"] != "S":
raise RuntimeError(
"datatype for species must be 'S' instead of {}".format(
kv_dict["datatype"]
)
)
)
field_length = int(kv_dict["value"])
type_array = data_array[
:, used_colomn : used_colomn + field_length
].flatten()
used_colomn += field_length
continue
elif kv_dict["key"] == "pos":
if kv_dict["datatype"] != "R":
raise RuntimeError(
"datatype for pos must be 'R' instead of {}".format(
kv_dict["datatype"]
field_length = int(kv_dict["value"])
type_array = data_array[
:, used_colomn : used_colomn + field_length
].flatten()
used_colomn += field_length
continue
elif kv_dict["key"] == "pos":
if kv_dict["datatype"] != "R":
raise RuntimeError(
"datatype for pos must be 'R' instead of {}".format(
kv_dict["datatype"]
)
)
)
field_length = int(kv_dict["value"])
coords_array = data_array[:, used_colomn : used_colomn + field_length]
used_colomn += field_length
continue
elif kv_dict["key"] == "Z":
if kv_dict["datatype"] != "I":
raise RuntimeError(
"datatype for pos must be 'R' instead of {}".format(
kv_dict["datatype"]
field_length = int(kv_dict["value"])
coords_array = data_array[
:, used_colomn : used_colomn + field_length
]
used_colomn += field_length
continue
elif kv_dict["key"] == "Z":
if kv_dict["datatype"] != "I":
raise RuntimeError(
"datatype for pos must be 'R' instead of {}".format(
kv_dict["datatype"]
)
)
)
field_length = int(kv_dict["value"])
Z_array = data_array[
:, used_colomn : used_colomn + field_length
].flatten()
used_colomn += field_length
continue
elif kv_dict["key"] == "force":
if kv_dict["datatype"] != "R":
raise RuntimeError(
"datatype for pos must be 'R' instead of {}".format(
kv_dict["datatype"]
field_length = int(kv_dict["value"])
Z_array = data_array[
:, used_colomn : used_colomn + field_length
].flatten()
used_colomn += field_length
continue
elif kv_dict["key"] == "tags":
if kv_dict["datatype"] != "I":
raise RuntimeError(
"datatype for tags must be 'I' instead of {}".format(
kv_dict["datatype"]
)
)
)
field_length = int(kv_dict["value"])
force_array = data_array[:, used_colomn : used_colomn + field_length]
used_colomn += field_length
field_length = int(kv_dict["value"])
used_colomn += field_length
continue
elif kv_dict["key"] == "force" or kv_dict["key"] == "forces":
if kv_dict["datatype"] != "R":
raise RuntimeError(
"datatype for pos must be 'R' instead of {}".format(
kv_dict["datatype"]
)
)
field_length = int(kv_dict["value"])
force_array = data_array[
:, used_colomn : used_colomn + field_length
]
used_colomn += field_length
continue
except Exception as e:
try:
if kv_dict["key"] == "species":
if kv_dict["datatype"] != "S":
raise RuntimeError(
"datatype for species must be 'S' instead of {}".format(
kv_dict["datatype"]
)
)
field_length = int(kv_dict["value"])
type_array = data_array[
:, used_colomn : used_colomn + field_length
].flatten()
used_colomn += field_length
continue
elif kv_dict["key"] == "pos":
if kv_dict["datatype"] != "R":
raise RuntimeError(
"datatype for pos must be 'R' instead of {}".format(
kv_dict["datatype"]
)
)
field_length = int(kv_dict["value"])
coords_array = data_array[
:, used_colomn : used_colomn + field_length
]
used_colomn += field_length
continue
elif kv_dict["key"] == "Z":
if kv_dict["datatype"] != "I":
raise RuntimeError(
"datatype for pos must be 'R' instead of {}".format(
kv_dict["datatype"]
)
)
field_length = int(kv_dict["value"])
Z_array = data_array[
:, used_colomn : used_colomn + field_length
].flatten()
used_colomn += field_length
continue
elif kv_dict["key"] == "tags":
if kv_dict["datatype"] != "I":
raise RuntimeError(
"datatype for tags must be 'I' instead of {}".format(
kv_dict["datatype"]
)
)
field_length = int(kv_dict["value"])
used_colomn += field_length
continue
elif kv_dict["key"] == "force" or kv_dict["key"] == "forces":
if kv_dict["datatype"] != "R":
raise RuntimeError(
"datatype for pos must be 'R' instead of {}".format(
kv_dict["datatype"]
)
)
field_length = int(kv_dict["value"])
force_array = data_array[
:, used_colomn : used_colomn + field_length
]
used_colomn += field_length
continue
except KeyError as e:
Tools
Ruff

133-133: Local variable Z_array is assigned to but never used

Remove assignment to unused variable Z_array

(F841)

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What is the error it is expected to catch?

print("unknown field {}".format(kv_dict["key"]), e)
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What is the reason not to raise an error?

continue
else:
raise RuntimeError("unknown field {}".format(kv_dict["key"]))

type_num_dict = OrderedDict()
atom_type_list = []
Expand Down Expand Up @@ -165,21 +194,126 @@ def handle_single_xyz_frame(lines):
else:
virials = None

try:
e_units = np.array([field_dict["energy-unit"].lower()])
f_units = np.array([field_dict["force-unit"].lower()])
except Exception:
pass
# print('No units information contained.')

Comment on lines +197 to +203
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Proper handling of missing unit information.

The try-except block for handling missing unit information should raise an exception or log a warning if units are not found, rather than passing silently.

-  except Exception:
-    pass
-    # print('No units information contained.')
+  except KeyError as e:
+    raise ValueError("No units information contained.") from e
Committable suggestion

‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.

Suggested change
try:
e_units = np.array([field_dict["energy-unit"].lower()])
f_units = np.array([field_dict["force-unit"].lower()])
except Exception:
pass
# print('No units information contained.')
try:
e_units = np.array([field_dict["energy-unit"].lower()])
f_units = np.array([field_dict["force-unit"].lower()])
except KeyError as e:
raise ValueError("No units information contained.") from e

info_dict = {}
info_dict["nopbc"] = False
info_dict["atom_names"] = list(type_num_array[:, 0])
info_dict["atom_numbs"] = list(type_num_array[:, 1].astype(int))
info_dict["atom_types"] = np.array(atom_type_list).astype(int)
info_dict["cells"] = np.array(
[
np.array(list(filter(bool, field_dict["Lattice"].split(" ")))).reshape(
3, 3
)
]
).astype("float32")

info_dict["coords"] = np.array([coords_array]).astype("float32")
"""
info_dict["energies"] = np.array([field_dict["energy"]]).astype("float32")
info_dict["forces"] = np.array([force_array]).astype("float32")
"""
Comment on lines +211 to +214
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If it is not used anymore, it should be removed.


try:
if e_units == "kcal/mol":
info_dict["energies"] = (
np.array([field_dict["energy"]]).astype("float32")
* e_conv_kcalpermol2eV
)
elif e_units in ["hartree", "au", "a.u."]:
info_dict["energies"] = (
np.array([field_dict["energy"]]).astype("float32") * e_conv_au2eV
)
elif e_units == "ev":
info_dict["energies"] = np.array([field_dict["energy"]]).astype(
"float32"
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Why is it converted to float32?

)
else:
info_dict["energies"] = np.array([field_dict["energy"]]).astype(
"float32"
)
except Exception:
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What is the expected error to catch here? It's hard to read.

try:
possible_fields = [
"energy",
"energies",
"Energies",
"potential-energy.energy",
"Energy",
]
for key in possible_fields:
if key in field_dict:
info_dict["energies"] = np.array(
[field_dict[key]], dtype="float32"
)
break
else:
raise ValueError("No valid energy field found in field_dict.")
except KeyError:
raise ValueError("Error while accessing energy fields in field_dict.")
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Raise exceptions with raise ... from None.

Within an except clause, raise exceptions with raise ... from None to distinguish them from errors in exception handling.

-  raise ValueError("Error while accessing energy fields in field_dict.")
+  raise ValueError("Error while accessing energy fields in field_dict.") from None
Committable suggestion

‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.

Suggested change
raise ValueError("Error while accessing energy fields in field_dict.")
raise ValueError("Error while accessing energy fields in field_dict.") from None
Tools
Ruff

252-252: Within an except clause, raise exceptions with raise ... from err or raise ... from None to distinguish them from errors in exception handling

(B904)


Comment on lines +235 to +253
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Improved handling of possible energy fields and raising exceptions.

The changes improve handling of possible energy fields and raising exceptions. Use raise ... from None to distinguish exceptions from errors in exception handling.

-  raise ValueError("Error while accessing energy fields in field_dict.")
+  raise ValueError("Error while accessing energy fields in field_dict.") from None
Committable suggestion

‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.

Suggested change
try:
possible_fields = [
"energy",
"energies",
"Energies",
"potential-energy.energy",
"Energy",
]
for key in possible_fields:
if key in field_dict:
info_dict["energies"] = np.array(
[field_dict[key]], dtype="float32"
)
break
else:
raise ValueError("No valid energy field found in field_dict.")
except KeyError:
raise ValueError("Error while accessing energy fields in field_dict.")
try:
possible_fields = [
"energy",
"energies",
"Energies",
"potential-energy.energy",
"Energy",
]
for key in possible_fields:
if key in field_dict:
info_dict["energies"] = np.array(
[field_dict[key]], dtype="float32"
)
break
else:
raise ValueError("No valid energy field found in field_dict.")
except KeyError:
raise ValueError("Error while accessing energy fields in field_dict.") from None
Tools
Ruff

252-252: Within an except clause, raise exceptions with raise ... from err or raise ... from None to distinguish them from errors in exception handling

(B904)

try:
if f_units == "kcal/mol/angstrom":
<<<<<<< HEAD
info_dict["forces"] = np.array([force_array]).astype("float32") * f_conv_kcalpermolperang2eVperang
elif f_units == "hartree/angstrom" or f_units == "hartree/ang" or f_units == "hartree/ang.":
info_dict["forces"] = np.array([force_array]).astype("float32") * f_conv_auperang2eVperang
elif f_units == "kcal/mol/bohr":
info_dict["forces"] = np.array([force_array]).astype("float32") * f_conv_kcalpermolperbohr2eVperang
elif f_units == "kcal/mol/bohr":
info_dict["forces"] = np.array([force_array]).astype("float32") * f_conv_au2eVperang
elif f_units == "ev/angstrom" or f_units == "ev/ang" or f_units == "ev/ang.":
info_dict["forces"] = np.array([force_array]).astype("float32")
else: info_dict["forces"] = np.array([force_array]).astype("float32")
except Exception:
info_dict["forces"] = np.array([force_array]).astype("float32")
=======
info_dict["forces"] = (
np.array([force_array]).astype("float32")
* f_conv_kcalpermolperang2eVperang
)
elif (
f_units == "hartree/angstrom"
or f_units == "hartree/ang"
or f_units == "hartree/ang."
):
info_dict["forces"] = (
np.array([force_array]).astype("float32") * f_conv_auperang2eVperang
)
elif f_units == "kcal/mol/bohr":
info_dict["forces"] = (
np.array([force_array]).astype("float32")
* f_conv_kcalpermolperbohr2eVperang
)
elif f_units == "kcal/mol/bohr":
info_dict["forces"] = (
np.array([force_array]).astype("float32") * f_conv_au2eVperang
Comment on lines +273 to +275
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Remove redundant conditional block for kcal/mol/bohr.

The conditional block for kcal/mol/bohr is redundant and should be removed.

-  elif f_units == "kcal/mol/bohr":
-    info_dict["forces"] = (
-      np.array([force_array]).astype("float32") * f_conv_au2eVperang
-    )

Committable suggestion was skipped due to low confidence.

)
elif (
f_units == "ev/angstrom" or f_units == "ev/ang" or f_units == "ev/ang."
):
info_dict["forces"] = np.array([force_array]).astype("float32")
else:
info_dict["forces"] = np.array([force_array]).astype("float32")
except:
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Avoid using bare except statements.

Using bare except statements can catch unexpected errors and make debugging difficult. Specify the exception type or use except Exception as e to handle specific exceptions.

-  except:
+  except KeyError:

Committable suggestion was skipped due to low confidence.

Tools
Ruff

283-283: Do not use bare except

(E722)

info_dict["forces"] = np.array([force_array]).astype("float32")
>>>>>>> origin/devel
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Unit conversion for forces and redundant conditional block.

The new logic for force unit conversion is correctly implemented but contains a redundant conditional block for kcal/mol/bohr and uses a bare except statement.

-  elif f_units == "kcal/mol/bohr":
-    info_dict["forces"] = (
-      np.array([force_array]).astype("float32") * f_conv_au2eVperang
-    )
-  except:
-    info_dict["forces"] = np.array([force_array]).astype("float32")
+  except KeyError as e:
+    raise ValueError("Error while accessing force fields in field_dict.") from e

Committable suggestion was skipped due to low confidence.

Tools
Ruff

255-256: SyntaxError: Expected an indented block after if statement

256-256: SyntaxError: Expected except or finally after try block

256-256: SyntaxError: Expected a statement

256-256: SyntaxError: Expected a statement

256-256: SyntaxError: Expected a statement

257-257: SyntaxError: Unexpected indentation

258-258: SyntaxError: unindent does not match any outer indentation level

258-258: SyntaxError: Expected a statement

258-258: SyntaxError: Invalid annotated assignment target

258-259: SyntaxError: Expected an expression

259-259: SyntaxError: Unexpected indentation

260-260: SyntaxError: unindent does not match any outer indentation level

260-260: SyntaxError: Expected a statement

260-260: SyntaxError: Invalid annotated assignment target

260-261: SyntaxError: Expected an expression

261-261: SyntaxError: Unexpected indentation

262-262: SyntaxError: unindent does not match any outer indentation level

262-262: SyntaxError: Expected a statement

262-262: SyntaxError: Invalid annotated assignment target

262-263: SyntaxError: Expected an expression

263-263: SyntaxError: Unexpected indentation

264-264: SyntaxError: unindent does not match any outer indentation level

264-264: SyntaxError: Expected a statement

264-264: SyntaxError: Invalid annotated assignment target

264-265: SyntaxError: Expected an expression

265-265: SyntaxError: Unexpected indentation

266-266: SyntaxError: unindent does not match any outer indentation level

266-266: SyntaxError: Expected a statement

266-266: SyntaxError: Expected a statement

267-267: SyntaxError: Unexpected indentation

267-267: SyntaxError: Expected a statement

267-268: SyntaxError: Expected an expression

268-268: SyntaxError: Unexpected indentation

269-269: SyntaxError: Expected a statement

269-269: SyntaxError: Expected a statement

269-269: SyntaxError: Expected a statement

269-269: SyntaxError: Expected a statement

269-270: SyntaxError: Expected a statement

270-270: SyntaxError: Unexpected indentation

274-274: SyntaxError: unindent does not match any outer indentation level

274-274: SyntaxError: Expected a statement

275-275: SyntaxError: Invalid annotated assignment target

278-279: SyntaxError: Expected an expression

279-279: SyntaxError: Unexpected indentation

282-282: SyntaxError: unindent does not match any outer indentation level

282-282: SyntaxError: Expected a statement

282-282: SyntaxError: Invalid annotated assignment target

282-283: SyntaxError: Expected an expression

283-283: SyntaxError: Unexpected indentation

287-287: SyntaxError: unindent does not match any outer indentation level

287-287: SyntaxError: Expected a statement

287-287: SyntaxError: Invalid annotated assignment target

287-288: SyntaxError: Expected an expression

288-288: SyntaxError: Unexpected indentation

291-291: SyntaxError: unindent does not match any outer indentation level

291-291: SyntaxError: Expected a statement

292-292: SyntaxError: Invalid annotated assignment target

293-294: SyntaxError: Expected an expression

294-294: SyntaxError: Unexpected indentation

295-295: SyntaxError: unindent does not match any outer indentation level

295-295: SyntaxError: Expected a statement

295-295: SyntaxError: Expected a statement

295-296: SyntaxError: Expected a statement

296-296: SyntaxError: Unexpected indentation

297-297: SyntaxError: unindent does not match any outer indentation level

297-297: SyntaxError: Expected a statement

297-297: SyntaxError: Expected a statement

297-298: SyntaxError: Expected a statement

298-298: SyntaxError: Unexpected indentation

299-299: SyntaxError: Expected a statement

299-299: SyntaxError: Expected a statement

299-299: SyntaxError: Expected a statement

299-299: SyntaxError: Expected a statement


if virials is not None:
info_dict["virials"] = virials
info_dict["orig"] = np.zeros(3)
if "Lattice" in field_dict and field_dict["Lattice"].strip():
lattice_values = list(filter(bool, field_dict["Lattice"].split(" ")))
info_dict["cells"] = np.array(
[np.array(lattice_values).reshape(3, 3)]
).astype("float32")
else:
lattice_values = np.array(
[[100.0, 0.0, 0.0], [0.0, 100.0, 0.0], [0.0, 0.0, 100.0]]
)

info_dict["nopbc"] = True
info_dict["cells"] = np.array(
[np.array(lattice_values).reshape(3, 3)]
).astype("float32")

return info_dict
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