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Fix LNONCOLLINEAR match in Outcar parser #4034

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merged 8 commits into from
Sep 4, 2024
Merged

Fix LNONCOLLINEAR match in Outcar parser #4034

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aed1b24
revert LNONCOLLINEAR match condition
DanielYang59 Sep 3, 2024
92b79f6
avoid hard coding number of spaces
DanielYang59 Sep 3, 2024
52d6751
NEED CONFIRM: turn on terminate_on_match for boolean tags
DanielYang59 Sep 3, 2024
345050a
put True/False in different branches
DanielYang59 Sep 3, 2024
1b6eaa5
add unit test for ncl True
DanielYang59 Sep 3, 2024
05ce389
reuse existing test file
DanielYang59 Sep 4, 2024
26d1c5e
revert using `terminate_on_match` as True
DanielYang59 Sep 4, 2024
0ec2fe4
Merge branch 'master' into fix-outcar-parse
DanielYang59 Sep 4, 2024
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36 changes: 19 additions & 17 deletions src/pymatgen/io/vasp/outputs.py
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Original file line number Diff line number Diff line change
Expand Up @@ -2106,19 +2106,14 @@ def __init__(self, filename: PathLike) -> None:
self.drift = self.data.get("drift", [])

# Check if calculation is spin polarized
self.spin = False
self.read_pattern({"spin": "ISPIN = 2"})
if self.data.get("spin", []):
self.spin = True
self.read_pattern({"spin": r"ISPIN\s*=\s*2"}, terminate_on_match=True)
self.spin = bool(self.data.get("spin", []))

# Check if calculation is non-collinear
self.noncollinear = False
self.read_pattern({"noncollinear": "LNONCOLLINEAR = T"})
if self.data.get("noncollinear", []):
self.noncollinear = False
self.read_pattern({"noncollinear": r"LNONCOLLINEAR\s*=\s*T"}, terminate_on_match=True)
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@janosh janosh Sep 4, 2024 •
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these lines suggest that the matches dict can contain less keys if terminate_on_match=True and so you might get a different self.data after self.data.update(matches). but given all tests pass, this may not happen in practice

pymatgen/src/pymatgen/io/pwscf.py

Lines 623 to 630 in edcd465

matches = regrep(
self.filename,
patterns,
reverse=reverse,
terminate_on_match=terminate_on_match,
postprocess=postprocess,
)
self.data.update(matches)

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any concerns @mkhorton?

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@DanielYang59 DanielYang59 Sep 4, 2024 •
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I think it might be safer for me to revert those changes in terminate_on_match until I'm 100% percent it wouldn't cause any breakage.

Currently there must have been some part of Outcar not covered by unit test, because the reverse reading in #4033 seems completely broken in Windows, but tests are still passing.

I would keep this into my TODO list, and have a closer look later.

self.noncollinear = bool(self.data.get("noncollinear", []))

# Check if the calculation type is DFPT
self.dfpt = False
self.read_pattern(
{"ibrion": r"IBRION =\s+([\-\d]+)"},
terminate_on_match=True,
Expand All @@ -2127,24 +2122,28 @@ def __init__(self, filename: PathLike) -> None:
if self.data.get("ibrion", [[0]])[0][0] > 6:
self.dfpt = True
self.read_internal_strain_tensor()
else:
self.dfpt = False

# Check if LEPSILON is True and read piezo data if so
self.lepsilon = False
self.read_pattern({"epsilon": "LEPSILON= T"})
self.read_pattern({"epsilon": r"LEPSILON\s*=\s*T"}, terminate_on_match=True)
if self.data.get("epsilon", []):
self.lepsilon = True
self.read_lepsilon()
# Only read ionic contribution if DFPT is turned on
if self.dfpt:
self.read_lepsilon_ionic()
else:
self.lepsilon = False

# Check if LCALCPOL is True and read polarization data if so
self.lcalcpol = False
self.read_pattern({"calcpol": "LCALCPOL = T"})
self.read_pattern({"calcpol": r"LCALCPOL\s*=\s*T"}, terminate_on_match=True)
if self.data.get("calcpol", []):
self.lcalcpol = True
self.read_lcalcpol()
self.read_pseudo_zval()
else:
self.lcalcpol = False

# Read electrostatic potential
self.electrostatic_potential: list[float] | None = None
Expand All @@ -2154,30 +2153,33 @@ def __init__(self, filename: PathLike) -> None:
if self.data.get("electrostatic", []):
self.read_electrostatic_potential()

self.nmr_cs = False
self.read_pattern({"nmr_cs": r"LCHIMAG = (T)"})
self.read_pattern({"nmr_cs": r"LCHIMAG\s*=\s*(T)"}, terminate_on_match=True)
if self.data.get("nmr_cs"):
self.nmr_cs = True
self.read_chemical_shielding()
self.read_cs_g0_contribution()
self.read_cs_core_contribution()
self.read_cs_raw_symmetrized_tensors()
else:
self.nmr_cs = False

self.nmr_efg = False
self.read_pattern({"nmr_efg": r"NMR quadrupolar parameters"})
if self.data.get("nmr_efg"):
self.nmr_efg = True
self.read_nmr_efg()
self.read_nmr_efg_tensor()
else:
self.nmr_efg = False

self.has_onsite_density_matrices = False
self.read_pattern(
{"has_onsite_density_matrices": r"onsite density matrix"},
terminate_on_match=True,
)
if "has_onsite_density_matrices" in self.data:
self.has_onsite_density_matrices = True
self.read_onsite_density_matrices()
else:
self.has_onsite_density_matrices = False

# Store the individual contributions to the final total energy
final_energy_contribs = {}
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Binary file added tests/files/io/vasp/outputs/OUTCAR.noncollinear.gz
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4 changes: 4 additions & 0 deletions tests/io/vasp/test_outputs.py
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Expand Up @@ -944,6 +944,10 @@ def test_polarization(self):
assert outcar.p_ion == approx([0.0, 0.0, -5.56684])
assert outcar.p_elec == approx([0.00024, 0.00019, 3.61674])

def test_noncollinear(self):
outcar_ncl = Outcar(f"{VASP_OUT_DIR}/OUTCAR.noncollinear.gz")
assert outcar_ncl.noncollinear is True

def test_pseudo_zval(self):
filepath = f"{VASP_OUT_DIR}/OUTCAR.BaTiO3.polar"
outcar = Outcar(filepath)
Expand Down