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add POSCAR.lobster support in featurizer #186

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merged 1 commit into from
Nov 21, 2023
Merged

add POSCAR.lobster support in featurizer #186

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129 changes: 94 additions & 35 deletions lobsterpy/featurize/batch.py
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Original file line number Diff line number Diff line change
Expand Up @@ -134,12 +134,23 @@ def _featurizecoxx(self, path_to_lobster_calc) -> pd.DataFrame:
"icoxxlist_path": "ICOHPLIST.lobster",
}
for file, default_value in req_files.items():
file_path = dir_name / default_value
req_files[file] = file_path # type: ignore
if not file_path.exists():
gz_file_path = Path(zpath(file_path))
if gz_file_path.exists():
req_files[file] = gz_file_path # type: ignore
# Check if "POSCAR" exists, and if not, check for "POSCAR.lobster"
if file == "structure_path":
for filename in [default_value, "POSCAR.lobster"]:
poscar_path = dir_name / filename
req_files[file] = poscar_path # type: ignore
if not poscar_path.exists():
gz_file_path = Path(zpath(poscar_path))
if gz_file_path.exists():
req_files[file] = gz_file_path # type: ignore
break
else:
file_path = dir_name / default_value
req_files[file] = file_path # type: ignore
if not file_path.exists():
gz_file_path = Path(zpath(file_path))
if gz_file_path.exists():
req_files[file] = gz_file_path # type: ignore

coxxcar_path = req_files.get("coxxcar_path")
structure_path = req_files.get("structure_path")
Expand Down Expand Up @@ -262,12 +273,22 @@ def _featurizecharges(self, path_to_lobster_calc) -> pd.DataFrame:
"structure_path": "POSCAR",
}
for file, default_value in req_files.items():
file_path = dir_name / default_value
req_files[file] = file_path # type: ignore
if not file_path.exists():
gz_file_path = Path(zpath(file_path))
if gz_file_path.exists():
req_files[file] = gz_file_path # type: ignore
if file == "structure_path":
for filename in [default_value, "POSCAR.lobster"]:
poscar_path = dir_name / filename
req_files[file] = poscar_path # type: ignore
if not poscar_path.exists():
gz_file_path = Path(zpath(poscar_path))
if gz_file_path.exists():
req_files[file] = gz_file_path # type: ignore
break
else:
file_path = dir_name / default_value
req_files[file] = file_path # type: ignore
if not file_path.exists():
gz_file_path = Path(zpath(file_path))
if gz_file_path.exists():
req_files[file] = gz_file_path # type: ignore

charge_path = req_files.get("charge_path")
structure_path = req_files.get("structure_path")
Expand Down Expand Up @@ -633,11 +654,19 @@ def _fingerprint_df(self, path_to_lobster_calc) -> pd.DataFrame:
are_cobis = False
are_coops = False

structure_path = dir_name / "POSCAR"
if not structure_path.exists():
gz_file_path = Path(zpath(structure_path))
if gz_file_path.exists():
structure_path = gz_file_path
for filename in ["POSCAR", "POSCAR.lobster"]:
structure_path = dir_name / filename
if not structure_path.exists():
gz_file_path = Path(zpath(structure_path))
if gz_file_path.exists():
structure_path = gz_file_path # type: ignore
break

# structure_path = dir_name / "POSCAR"
# if not structure_path.exists():
# gz_file_path = Path(zpath(structure_path))
# if gz_file_path.exists():
# structure_path = gz_file_path

coxx = FeaturizeCOXX(
path_to_coxxcar=str(coxxcar_path),
Expand Down Expand Up @@ -750,12 +779,22 @@ def _get_sg_df(self, path_to_lobster_calc) -> pd.DataFrame:
}

for file, default_value in req_files.items():
file_path = dir_name / default_value
req_files[file] = file_path # type: ignore
if not file_path.exists():
gz_file_path = Path(zpath(file_path))
if gz_file_path.exists():
req_files[file] = gz_file_path # type: ignore
if file == "structure_path":
for filename in [default_value, "POSCAR.lobster"]:
poscar_path = dir_name / filename
req_files[file] = poscar_path # type: ignore
if not poscar_path.exists():
gz_file_path = Path(zpath(poscar_path))
if gz_file_path.exists():
req_files[file] = gz_file_path # type: ignore
break
else:
file_path = dir_name / default_value
req_files[file] = file_path # type: ignore
if not file_path.exists():
gz_file_path = Path(zpath(file_path))
if gz_file_path.exists():
req_files[file] = gz_file_path # type: ignore

charge_path = str(req_files.get("charge_path"))
cohpcar_path = str(req_files.get("cohpcar_path"))
Expand Down Expand Up @@ -887,12 +926,22 @@ def _get_dos_moments_df(self, path_to_lobster_calc) -> pd.DataFrame:
"structure_path": "POSCAR",
}
for file, default_value in req_files.items():
file_path = dir_name / default_value
req_files[file] = file_path # type: ignore
if not file_path.exists():
gz_file_path = Path(zpath(file_path))
if gz_file_path.exists():
req_files[file] = gz_file_path # type: ignore
if file == "structure_path":
for filename in [default_value, "POSCAR.lobster"]:
poscar_path = dir_name / filename
req_files[file] = poscar_path # type: ignore
if not poscar_path.exists():
gz_file_path = Path(zpath(poscar_path))
if gz_file_path.exists():
req_files[file] = gz_file_path # type: ignore
break
else:
file_path = dir_name / default_value
req_files[file] = file_path # type: ignore
if not file_path.exists():
gz_file_path = Path(zpath(file_path))
if gz_file_path.exists():
req_files[file] = gz_file_path # type: ignore

doscar_path = req_files.get("doscar_path")
structure_path = req_files.get("structure_path")
Expand Down Expand Up @@ -928,12 +977,22 @@ def _get_dos_fingerprints_df(self, path_to_lobster_calc) -> pd.DataFrame:
"structure_path": "POSCAR",
}
for file, default_value in req_files.items():
file_path = dir_name / default_value
req_files[file] = file_path # type: ignore
if not file_path.exists():
gz_file_path = Path(zpath(file_path))
if gz_file_path.exists():
req_files[file] = gz_file_path # type: ignore
if file == "structure_path":
for filename in [default_value, "POSCAR.lobster"]:
poscar_path = dir_name / filename
req_files[file] = poscar_path # type: ignore
if not poscar_path.exists():
gz_file_path = Path(zpath(poscar_path))
if gz_file_path.exists():
req_files[file] = gz_file_path # type: ignore
break
else:
file_path = dir_name / default_value
req_files[file] = file_path # type: ignore
if not file_path.exists():
gz_file_path = Path(zpath(file_path))
if gz_file_path.exists():
req_files[file] = gz_file_path # type: ignore

doscar_path = req_files.get("doscar_path")
structure_path = req_files.get("structure_path")
Expand Down
34 changes: 22 additions & 12 deletions lobsterpy/featurize/core.py
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Original file line number Diff line number Diff line change
Expand Up @@ -384,18 +384,28 @@ def get_lobsterpy_cba_dict(
}

for file, default_value in req_files_lobsterpy.items():
file_path = dir_name / default_value
req_files_lobsterpy[file] = file_path # type: ignore
if not file_path.exists():
gz_file_path = Path(zpath(file_path))
if gz_file_path.exists():
req_files_lobsterpy[file] = gz_file_path # type: ignore
else:
raise Exception(
"Path provided for Lobster calc directory seems incorrect."
"It does not contain COHPCAR.lobster, ICOHPLIST.lobster, POSCAR and "
"CHARGE.lobster files needed for automatic analysis using LobsterPy"
)
if file == "structure_path":
for filename in [default_value, "POSCAR.lobster"]:
poscar_path = dir_name / filename
req_files_lobsterpy[file] = poscar_path # type: ignore
if not poscar_path.exists():
gz_file_path = Path(zpath(poscar_path))
if gz_file_path.exists():
req_files_lobsterpy[file] = gz_file_path # type: ignore
break
else:
file_path = dir_name / default_value
req_files_lobsterpy[file] = file_path # type: ignore
if not file_path.exists():
gz_file_path = Path(zpath(file_path))
if gz_file_path.exists():
req_files_lobsterpy[file] = gz_file_path # type: ignore
else:
raise Exception(
"Path provided for Lobster calc directory seems incorrect."
"It does not contain COHPCAR.lobster, ICOHPLIST.lobster, POSCAR and "
"CHARGE.lobster files needed for automatic analysis using LobsterPy"
)

cohpcar_path = req_files_lobsterpy.get("cohpcar_path")
charge_path = req_files_lobsterpy.get("charge_path")
Expand Down
0 ...test_data/Lobster_calcs/mp-2176/POSCAR.gz → ...a/Lobster_calcs/mp-2176/POSCAR.lobster.gz
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