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Replace POSCAR with CONTCAR in lobster.py #1389

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Merged
esoteric-ephemera merged 1 commit into from
Feb 6, 2026
Merged

Replace POSCAR with CONTCAR in lobster.py #1389

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44 changes: 22 additions & 22 deletions emmet-core/emmet/core/lobster.py
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Original file line number Diff line number Diff line change
Expand Up @@ -56,7 +56,7 @@ def aggregate_paths(
paths[p.name.split(".lobster")[0]] = p
for file_name in (
"POTCAR",
"POSCAR",
"CONTCAR",
"vasprun.xml",
"lobsterin",
"lobsterout",
Expand Down Expand Up @@ -336,14 +336,14 @@ def from_directory(
"orbital_resolved": False,
"start": None,
"summed_spins": False, # we will always use spin polarization here
"type_charge": None,
"type_charge": "Mulliken",
**lobsterpy_kwargs,
}

try:
start = time.time()
analyse = Analysis(
path_to_poscar=file_paths["POSCAR"],
path_to_poscar=file_paths["CONTCAR"],
path_to_icohplist=file_paths["ICOHPLIST"],
path_to_cohpcar=file_paths["COHPCAR"],
path_to_charge=file_paths["CHARGE"],
Expand Down Expand Up @@ -576,7 +576,7 @@ def from_directory(
**calc_quality_kwargs,
}
cal_quality_dict = Analysis.get_lobster_calc_quality_summary(
path_to_poscar=file_paths["POSCAR"],
path_to_poscar=file_paths["CONTCAR"],
path_to_vasprun=file_paths["vasprun.xml"],
path_to_charge=file_paths["CHARGE"],
path_to_potcar=file_paths.get("POTCAR"),
Expand Down Expand Up @@ -764,20 +764,20 @@ def from_directory(

# Read in lobsterout and lobsterin
file_paths = aggregate_paths(dir_name)
lobsterout_doc = Lobsterout(file_paths["lobsterout"]).get_doc()
lobsterout_doc = Lobsterout(file_paths["lobsterout"].as_posix()).get_doc()
lobster_out = LobsteroutModel(**lobsterout_doc)

lobster_in_dict = Lobsterin.from_file(file_paths["lobsterin"])
lobster_in_dict = Lobsterin.from_file(file_paths["lobsterin"].as_posix())
# convert keys to snake case
lobster_in = LobsterinModel(
**{ # type: ignore[arg-type]
k: lobster_in_dict.get(k.strip("_"))
k: lobster_in_dict.get(k.replace("_", ""))
for k in LobsterinModel.model_fields
}
)

# Do automatic bonding analysis with LobsterPy
struct = Structure.from_file(file_paths["POSCAR"])
struct = Structure.from_file(file_paths["CONTCAR"].as_posix())

# will perform two condensed bonding analysis computations
condensed_bonding_analysis = None
Expand Down Expand Up @@ -828,8 +828,8 @@ def from_directory(
"cohp_data": (
CompleteCohp.from_file(
fmt="LOBSTER",
structure_file=file_paths["POSCAR"],
filename=file_paths["COHPCAR"],
structure_file=file_paths["CONTCAR"].as_posix(),
filename=file_paths["COHPCAR"].as_posix(),
are_coops=False,
are_cobis=False,
)
Expand All @@ -839,8 +839,8 @@ def from_directory(
"coop_data": (
CompleteCohp.from_file(
fmt="LOBSTER",
structure_file=file_paths["POSCAR"],
filename=file_paths["COOPCAR"],
structure_file=file_paths["CONTCAR"].as_posix(),
filename=file_paths["COOPCAR"].as_posix(),
are_coops=True,
are_cobis=False,
)
Expand All @@ -850,8 +850,8 @@ def from_directory(
"cobi_data": (
CompleteCohp.from_file(
fmt="LOBSTER",
structure_file=file_paths["POSCAR"],
filename=file_paths["COBICAR"],
structure_file=file_paths["CONTCAR"].as_posix(),
filename=file_paths["COBICAR"].as_posix(),
are_coops=False,
are_cobis=True,
)
Expand Down Expand Up @@ -881,48 +881,48 @@ def from_directory(
),
dos=(
Doscar(
doscar=file_paths["DOSCAR"], structure_file=file_paths["POSCAR"]
doscar=file_paths["DOSCAR"].as_posix(), structure_file=file_paths["CONTCAR"].as_posix()
).completedos
if file_paths.get("DOSCAR")
else None
),
lso_dos=(
Doscar(
doscar=file_paths["DOSCAR.LSO"], structure_file=file_paths["POSCAR"]
doscar=file_paths["DOSCAR.LSO"].as_posix(), structure_file=file_paths["CONTCAR"].as_posix()
).completedos
if (store_lso_dos and file_paths.get("DOSCAR.LSO"))
else None
),
charges=(
Charge(filename=file_paths["CHARGE"])
Charge(filename=file_paths["CHARGE"].as_posix())
if file_paths.get("CHARGE")
else None
),
madelung_energies=(
MadelungEnergies(filename=file_paths["MadelungEnergies"])
MadelungEnergies(filename=file_paths["MadelungEnergies"].as_posix())
if file_paths.get("MadelungEnergies")
else None
),
site_potentials=(
SitePotential(filename=file_paths["SitePotentials"])
SitePotential(filename=file_paths["SitePotentials"].as_posix())
if file_paths.get("SitePotentials")
else None
),
gross_populations=(
Grosspop(filename=file_paths["GROSSPOP"])
Grosspop(filename=file_paths["GROSSPOP"].as_posix())
if file_paths.get("GROSSPOP")
else None
),
band_overlaps=(
Bandoverlaps(filename=file_paths["bandOverlaps"])
Bandoverlaps(filename=file_paths["bandOverlaps"].as_posix())
if file_paths.get("bandOverlaps")
else None
),
# include additional fields for all bonds
**(cohp_data if add_coxxcar_to_task_document else {}),
**{
k: Icohplist(
filename=file_paths[v],
filename=file_paths[v].as_posix(),
are_coops=(v == "ICOOPLIST"),
are_cobis=(v == "ICOBILIST"),
)
Expand Down