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Fix branch directory check in io.vasp.outputs.get_band_structure_from_vasp_multiple_branches #4061

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e651d90
docstring tweak and support Path
DanielYang59 Sep 11, 2024
e524dfd
isfile -> isdir fix
DanielYang59 Sep 11, 2024
0a03a91
raise error if vasprun.xml missing in any branch dir
DanielYang59 Sep 11, 2024
c134361
sort pymatgen core imports
DanielYang59 Sep 11, 2024
ad7fac3
add some unit test
DanielYang59 Sep 11, 2024
ea0e81e
Merge branch 'master' into fix-multi-branch-band-struct
DanielYang59 Sep 12, 2024
f8ab30e
raise error if no vasprun.xml file found at all
DanielYang59 Sep 12, 2024
6be5ba9
Merge branch 'master' into fix-multi-branch-band-struct
DanielYang59 Sep 14, 2024
5dfd2d3
deprecation warning for fall back branch
DanielYang59 Sep 14, 2024
3ac59ec
Merge branch 'fix-multi-branch-band-struct' of https://github.com/Dan…
DanielYang59 Sep 14, 2024
b011e2f
Merge branch 'master' into fix-multi-branch-band-struct
DanielYang59 Sep 18, 2024
fb74f61
remove unused ignore tag
DanielYang59 Sep 18, 2024
f332066
Merge branch 'master' into fix-multi-branch-band-struct
DanielYang59 Sep 26, 2024
4d97716
add a temporary solution
DanielYang59 Sep 26, 2024
86d0718
update inherit_incar docstring
DanielYang59 Sep 30, 2024
c2a6595
Merge branch 'master' into fix-multi-branch-band-struct
DanielYang59 Oct 15, 2024
0009728
Merge branch 'master' into fix-multi-branch-band-struct
DanielYang59 Oct 21, 2024
11c0f65
Merge branch 'master' into fix-multi-branch-band-struct
DanielYang59 Oct 22, 2024
e1dd508
Merge branch 'master' into fix-multi-branch-band-struct
DanielYang59 Nov 13, 2024
2f6c257
Merge branch 'master' into fix-multi-branch-band-struct
DanielYang59 Nov 14, 2024
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2 changes: 1 addition & 1 deletion docs/index.md

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2 changes: 1 addition & 1 deletion src/pymatgen/electronic_structure/bandstructure.py
Original file line number Diff line number Diff line change
Expand Up @@ -1076,7 +1076,7 @@ def get_projections_on_elements_and_orbitals(


@overload
def get_reconstructed_band_structure( # type: ignore[overload-overlap]
def get_reconstructed_band_structure(
list_bs: list[BandStructure],
efermi: float | None = None,
) -> BandStructure:
Expand Down
69 changes: 38 additions & 31 deletions src/pymatgen/io/vasp/outputs.py
Original file line number Diff line number Diff line change
Expand Up @@ -4404,55 +4404,62 @@ class VaspParseError(ParseError):


def get_band_structure_from_vasp_multiple_branches(
dir_name: str,
dir_name: PathLike,
efermi: float | None = None,
projections: bool = False,
) -> BandStructureSymmLine | BandStructure | None:
"""Get band structure info from a VASP directory.

It takes into account that a run can be divided in several branches named
"branch_x". If the run has not been divided in branches the method will
turn to parsing vasprun.xml directly.
It takes into account that a run can be divided in several branches,
each inside a directory named "branch_x". If the run has not been
divided in branches the function will turn to parse vasprun.xml
directly from the selected directory.

Args:
dir_name: Directory containing all bandstructure runs.
efermi: Efermi for bandstructure.
projections: True if you want to get the data on site projections if
any. Note that this is sometimes very large
dir_name (PathLike): Parent directory containing all bandstructure runs.
efermi (float): Fermi level for bandstructure.
projections (bool): True if you want to get the data on site
projections if any. Note that this is sometimes very large

Returns:
A BandStructure Object.
None is there's a parsing error.
A BandStructure/BandStructureSymmLine Object.
None if no vasprun.xml found in given directory and branch directory.
"""
# TODO: Add better error handling!!!
if os.path.isfile(f"{dir_name}/branch_0"):
# Get all branch dir names
if os.path.isdir(f"{dir_name}/branch_0"):
# Get and sort all branch directories
branch_dir_names = [os.path.abspath(d) for d in glob(f"{dir_name}/branch_*") if os.path.isdir(d)]

# Sort by the directory name (e.g, branch_10)
sorted_branch_dir_names = sorted(branch_dir_names, key=lambda x: int(x.split("_")[-1]))

# Populate branches with Bandstructure instances
branches = []
for dname in sorted_branch_dir_names:
xml_file = f"{dname}/vasprun.xml"
if os.path.isfile(xml_file):
run = Vasprun(xml_file, parse_projected_eigen=projections)
branches.append(run.get_band_structure(efermi=efermi))
else:
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# TODO: It might be better to throw an exception
warnings.warn(f"Skipping {dname}. Unable to find {xml_file}")
# Collect BandStructure from all branches
bs_branches: list[BandStructure | BandStructureSymmLine] = []
for directory in sorted_branch_dir_names:
vasprun_file = f"{directory}/vasprun.xml"
if not os.path.isfile(vasprun_file):
raise FileNotFoundError(f"cannot find vasprun.xml in {directory=}")

run = Vasprun(vasprun_file, parse_projected_eigen=projections)
bs_branches.append(run.get_band_structure(efermi=efermi))

return get_reconstructed_band_structure(branches, efermi)
return get_reconstructed_band_structure(bs_branches, efermi)

xml_file = f"{dir_name}/vasprun.xml"
# Better handling of Errors
if os.path.isfile(xml_file):
return Vasprun(xml_file, parse_projected_eigen=projections).get_band_structure(
# Read vasprun.xml directly if no branch head (branch_0) is found
# TODO: remove this branch and raise error directly after 2025-09-14
vasprun_file = f"{dir_name}/vasprun.xml"
if os.path.isfile(vasprun_file):
warnings.warn(
(
f"no branch dir found, reading directly from {dir_name=}\n"
"this fallback branch would be removed after 2025-09-14\n"
"please check your data dir or use Vasprun.get_band_structure directly"
),
DeprecationWarning,
stacklevel=2,
)
return Vasprun(vasprun_file, parse_projected_eigen=projections).get_band_structure(
kpoints_filename=None, efermi=efermi
)

return None
raise FileNotFoundError(f"failed to find any vasprun.xml in selected {dir_name=}")


class Xdatcar:
Expand Down
3 changes: 2 additions & 1 deletion src/pymatgen/io/vasp/sets.py
Original file line number Diff line number Diff line change
Expand Up @@ -179,10 +179,11 @@ class VaspInputSet(InputGenerator, abc.ABC):
Curtarolo) for monoclinic. Defaults True.
validate_magmom (bool): Ensure that the missing magmom values are filled in with
the VASP default value of 1.0.
inherit_incar (bool): Whether to inherit INCAR settings from previous
inherit_incar (bool | list[str]): Whether to inherit INCAR settings from previous
calculation. This might be useful to port Custodian fixes to child jobs but
can also be dangerous e.g. when switching from GGA to meta-GGA or relax to
static jobs. Defaults to True.
Can also be a list of strings to specify which parameters are inherited.
auto_kspacing (bool): If true, determines the value of KSPACING from the bandgap
of a previous calculation.
auto_ismear (bool): If true, the values for ISMEAR and SIGMA will be set
Expand Down
46 changes: 43 additions & 3 deletions tests/io/vasp/test_outputs.py
Original file line number Diff line number Diff line change
Expand Up @@ -12,13 +12,15 @@
import numpy as np
import pytest
from monty.io import zopen
from monty.shutil import decompress_file
from monty.tempfile import ScratchDir
from numpy.testing import assert_allclose
from pytest import approx

from pymatgen.core import Element
from pymatgen.core.lattice import Lattice
from pymatgen.core.structure import Structure
from pymatgen.electronic_structure.bandstructure import BandStructureSymmLine
from pymatgen.electronic_structure.bandstructure import BandStructure, BandStructureSymmLine
from pymatgen.electronic_structure.core import Magmom, Orbital, OrbitalType, Spin
from pymatgen.entries.compatibility import MaterialsProjectCompatibility
from pymatgen.io.vasp.inputs import Incar, Kpoints, Poscar, Potcar
Expand All @@ -39,6 +41,7 @@
Wavecar,
Waveder,
Xdatcar,
get_band_structure_from_vasp_multiple_branches,
)
from pymatgen.io.wannier90 import Unk
from pymatgen.util.testing import FAKE_POTCAR_DIR, TEST_FILES_DIR, VASP_IN_DIR, VASP_OUT_DIR, PymatgenTest
Expand Down Expand Up @@ -1484,13 +1487,50 @@ def test_init(self):
assert len(oszicar.electronic_steps) == len(oszicar.ionic_steps)
assert len(oszicar.all_energies) == 60
assert oszicar.final_energy == approx(-526.63928)
assert set(oszicar.ionic_steps[-1]) == set({"F", "E0", "dE", "mag"})
assert set(oszicar.ionic_steps[-1]) == {"F", "E0", "dE", "mag"}

def test_static(self):
fpath = f"{TEST_DIR}/fixtures/static_silicon/OSZICAR"
oszicar = Oszicar(fpath)
assert oszicar.final_energy == approx(-10.645278)
assert set(oszicar.ionic_steps[-1]) == set({"F", "E0", "dE", "mag"})
assert set(oszicar.ionic_steps[-1]) == {"F", "E0", "dE", "mag"}


class TestGetBandStructureFromVaspMultipleBranches:
def test_read_multi_branches(self):
"""TODO: use real multi-branch bandstructure calculation."""
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Contributor Author

@DanielYang59 DanielYang59 Sep 26, 2024

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I would mark this as ready for review but I have to leave this TODO tag here because I have no experience with multi-branch bandstructure calculation. This may not be a real world calculation as the vasprun.xml is the same for all branches.

with ScratchDir("."):
# Create branches
for idx in range(3): # simulate 3 branches
branch_name = f"branch_{idx}"
os.makedirs(branch_name)
copyfile(f"{VASP_OUT_DIR}/vasprun.force_hybrid_like_calc.xml.gz", f"./{branch_name}/vasprun.xml.gz")
decompress_file(f"./{branch_name}/vasprun.xml.gz")

get_band_structure_from_vasp_multiple_branches(".")

def test_missing_vasprun_in_branch_dir(self):
"""Test vasprun.xml missing from branch_*."""
with ScratchDir("."):
os.makedirs("no_vasp/branch_0", exist_ok=False)

with pytest.raises(FileNotFoundError, match="cannot find vasprun.xml in directory"):
get_band_structure_from_vasp_multiple_branches("no_vasp")

def test_no_branch_head(self):
"""Test branch_0 is missing and read dir_name/vasprun.xml directly."""
with ScratchDir("."):
copyfile(f"{VASP_OUT_DIR}/vasprun.force_hybrid_like_calc.xml.gz", "./vasprun.xml.gz")
decompress_file("./vasprun.xml.gz")

with pytest.warns(DeprecationWarning, match="no branch dir found, reading directly from"):
bs = get_band_structure_from_vasp_multiple_branches(".")
assert isinstance(bs, BandStructure)

def test_cannot_read_anything(self):
"""Test no branch_0/, no dir_name/vasprun.xml, no vasprun.xml at all."""
with pytest.raises(FileNotFoundError, match="failed to find any vasprun.xml in selected"), ScratchDir("."):
get_band_structure_from_vasp_multiple_branches(".")


class TestLocpot(PymatgenTest):
Expand Down