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Add bader_exe_path keyword to BaderAnalysis and run bader tests…
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… in CI (#3191)

* allow passing explicit file path to class BaderAnalysis via bader_exe_path

* better implementation

* add test_missing_file_bader_exe_path

* try installing bader exe in linux CI

* fix wget url

* google-style doc str

* fix FileNotFoundError: [Errno 2] No such file or directory: '/tmp/tmpad1zkrcz/CHGCAR'

in     def test_automatic_runner(self):
        test_dir = os.path.join(PymatgenTest.TEST_FILES_DIR, "bader")

>       summary = bader_analysis_from_path(test_dir)

* bader_analysis_from_objects chdir backto original dir

* fix two remaining failing tests

* del print statements
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@janosh
janosh committed Jul 28, 2023
1 parent 5637764 commit 0b7607a
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7 changes: 7 additions & 0 deletions .github/workflows/test.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -78,6 +78,13 @@ jobs:
for pkg in cmd_line/*;
do echo "$(pwd)/cmd_line/$pkg/Linux_64bit" >> "$GITHUB_PATH";
done
- name: Install Bader
if: runner.os == 'Linux'
run: |
wget http://theory.cm.utexas.edu/henkelman/code/bader/download/bader_lnx_64.tar.gz
tar xvzf bader_lnx_64.tar.gz
sudo mv bader /usr/local/bin/
continue-on-error: true
- name: Install dependencies
run: |
python -m pip install --upgrade pip wheel
Expand Down
213 changes: 91 additions & 122 deletions pymatgen/command_line/bader_caller.py
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Original file line number Diff line number Diff line change
Expand Up @@ -23,7 +23,6 @@
from tempfile import TemporaryDirectory

import numpy as np
from monty.dev import requires
from monty.io import zopen

from pymatgen.io.common import VolumetricData
Expand All @@ -37,73 +36,36 @@
__status__ = "Beta"
__date__ = "4/5/13"


BADEREXE = which("bader") or which("bader.exe")


class BaderAnalysis:
"""
Bader analysis for Cube files and VASP outputs.
.. attribute: data
Atomic data parsed from bader analysis. Essentially a list of dicts
of the form::
[
{
"atomic_vol": 8.769,
"min_dist": 0.8753,
"charge": 7.4168,
"y": 1.1598,
"x": 0.0079,
"z": 0.8348
},
...
]
.. attribute: vacuum_volume
Vacuum volume of the Bader analysis.
.. attribute: vacuum_charge
Vacuum charge of the Bader analysis.
.. attribute: nelectrons
Number of electrons of the Bader analysis.
.. attribute: chgcar
Chgcar object associated with input CHGCAR file.
.. attribute: atomic_densities
list of charge densities for each atom centered on the atom
excess 0's are removed from the array to reduce the size of the array
the charge densities are dicts with the charge density map,
the shift vector applied to move the data to the center, and the original dimension of the charge density map
charge:
{
"data": charge density array
"shift": shift used to center the atomic charge density
"dim": dimension of the original charge density map
}
Performs Bader analysis for Cube files and VASP outputs.
Attributes:
data (list[dict]): Atomic data parsed from bader analysis. Each dictionary in the list has the keys:
"atomic_vol", "min_dist", "charge", "x", "y", "z".
vacuum_volume (float): Vacuum volume of the Bader analysis.
vacuum_charge (float): Vacuum charge of the Bader analysis.
nelectrons (int): Number of electrons of the Bader analysis.
chgcar (Chgcar): Chgcar object associated with input CHGCAR file.
atomic_densities (list[dict]): List of charge densities for each atom centered on the atom.
Excess 0's are removed from the array to reduce its size. Each dictionary has the keys:
"data", "shift", "dim", where "data" is the charge density array,
"shift" is the shift used to center the atomic charge density, and
"dim" is the dimension of the original charge density map.
"""

@requires(
which("bader") or which("bader.exe"),
"BaderAnalysis requires the executable bader to be in the path."
" Please download the library at http://theory.cm.utexas"
".edu/vasp/bader/ and compile the executable.",
)
def __init__(
self,
chgcar_filename=None,
potcar_filename=None,
chgref_filename=None,
parse_atomic_densities=False,
cube_filename=None,
bader_exe_path: str | None = BADEREXE,
):
"""
Initializes the Bader caller.
Expand All @@ -112,16 +74,18 @@ def __init__(
chgcar_filename (str): The filename of the CHGCAR.
potcar_filename (str): The filename of the POTCAR.
chgref_filename (str): The filename of the reference charge density.
parse_atomic_densities (bool): Optional. turns on atomic partition of the charge density
parse_atomic_densities (bool, optional): turns on atomic partition of the charge density
charge densities are atom centered
cube_filename (str): Optional. The filename of the cube file.
cube_filename (str, optional): The filename of the cube file.
bader_exe_path (str, optional): The path to the bader executable.
"""
if not BADEREXE:
if not BADEREXE and not os.path.isfile(bader_exe_path or ""):
raise RuntimeError(
"BaderAnalysis requires the executable bader to be in the path."
" Please download the library at http://theory.cm.utexas"
".edu/vasp/bader/ and compile the executable."
"BaderAnalysis requires the executable bader be in the PATH or the full path "
f"to the binary to be specified via {bader_exe_path=}. Download the binary at "
"https://theory.cm.utexas.edu/henkelman/code/bader."
)
assert isinstance(BADEREXE, str) # mypy type narrowing

if not (cube_filename or chgcar_filename):
raise ValueError("You must provide either a cube file or a CHGCAR")
Expand All @@ -136,7 +100,7 @@ def __init__(
self.structure = self.chgcar.structure
self.potcar = Potcar.from_file(potcar_filename) if potcar_filename is not None else None
self.natoms = self.chgcar.poscar.natoms
chgrefpath = os.path.abspath(chgref_filename) if chgref_filename else None
chgref_path = os.path.abspath(chgref_filename) if chgref_filename else None
self.reference_used = bool(chgref_filename)

# List of nelects for each atom from potcar
Expand All @@ -152,16 +116,16 @@ def __init__(
self.is_vasp = False
self.cube = VolumetricData.from_cube(fpath)
self.structure = self.cube.structure
self.nelects = None
chgrefpath = os.path.abspath(chgref_filename) if chgref_filename else None
self.nelects = None # type: ignore
chgref_path = os.path.abspath(chgref_filename) if chgref_filename else None
self.reference_used = bool(chgref_filename)

tmpfile = "CHGCAR" if chgcar_filename else "CUBE"
with zopen(fpath, "rt") as f_in, open(tmpfile, "w") as f_out:
shutil.copyfileobj(f_in, f_out)
args = [BADEREXE, tmpfile]
args: list[str] = [BADEREXE, tmpfile]
if chgref_filename:
with zopen(chgrefpath, "rt") as f_in, open("CHGCAR_ref", "w") as f_out:
with zopen(chgref_path, "rt") as f_in, open("CHGCAR_ref", "w") as f_out:
shutil.copyfileobj(f_in, f_out)
args += ["-ref", "CHGCAR_ref"]
if parse_atomic_densities:
Expand Down Expand Up @@ -224,35 +188,35 @@ def __init__(
shift = (np.divide(chg.dim, 2) - index).astype(int)

# Shift the data so that the atomic charge density to the center for easier manipulation
shifted_data = np.roll(data, shift, axis=(0, 1, 2))
shifted_data = np.roll(data, shift, axis=(0, 1, 2)) # type: ignore

# Slices a central window from the data array
def slice_from_center(data, xwidth, ywidth, zwidth):
def slice_from_center(data, x_width, y_width, z_width):
x, y, z = data.shape
startx = x // 2 - (xwidth // 2)
starty = y // 2 - (ywidth // 2)
startz = z // 2 - (zwidth // 2)
start_x = x // 2 - (x_width // 2)
start_y = y // 2 - (y_width // 2)
start_z = z // 2 - (z_width // 2)
return data[
startx : startx + xwidth,
starty : starty + ywidth,
startz : startz + zwidth,
start_x : start_x + x_width,
start_y : start_y + y_width,
start_z : start_z + z_width,
]

# Finds the central encompassing volume which holds all the data within a precision
def find_encompassing_vol(data):
total = np.sum(data)
for i in range(np.max(data.shape)):
sliced_data = slice_from_center(data, i, i, i)
for idx in range(np.max(data.shape)):
sliced_data = slice_from_center(data, idx, idx, idx)
if total - np.sum(sliced_data) < 0.1:
return sliced_data
return None

d = {
dct = {
"data": find_encompassing_vol(shifted_data),
"shift": shift,
"dim": self.chgcar.dim,
}
atomic_densities.append(d)
atomic_densities.append(dct)
self.atomic_densities = atomic_densities

def get_charge(self, atom_index):
Expand Down Expand Up @@ -519,56 +483,61 @@ def bader_analysis_from_objects(chgcar, potcar=None, aeccar0=None, aeccar2=None)
:param aeccar2: (optional) Chgcar object from aeccar2 file
:return: summary dict
"""
with TemporaryDirectory() as tmp_dir:
if aeccar0 and aeccar2:
# construct reference file
chgref = aeccar0.linear_add(aeccar2)
chgref_path = os.path.join(tmp_dir, "CHGCAR_ref")
chgref.write_file(chgref_path)
else:
chgref_path = None

chgcar.write_file("CHGCAR")
chgcar_path = os.path.join(tmp_dir, "CHGCAR")

if potcar:
potcar.write_file("POTCAR")
potcar_path = os.path.join(tmp_dir, "POTCAR")
else:
potcar_path = None

ba = BaderAnalysis(
chgcar_filename=chgcar_path,
potcar_filename=potcar_path,
chgref_filename=chgref_path,
)

summary = {
"min_dist": [d["min_dist"] for d in ba.data],
"charge": [d["charge"] for d in ba.data],
"atomic_volume": [d["atomic_vol"] for d in ba.data],
"vacuum_charge": ba.vacuum_charge,
"vacuum_volume": ba.vacuum_volume,
"reference_used": bool(chgref_path),
"bader_version": ba.version,
}
orig_dir = os.getcwd()
try:
with TemporaryDirectory() as tmp_dir:
os.chdir(tmp_dir)
if aeccar0 and aeccar2:
# construct reference file
chgref = aeccar0.linear_add(aeccar2)
chgref_path = os.path.join(tmp_dir, "CHGCAR_ref")
chgref.write_file(chgref_path)
else:
chgref_path = None

if potcar:
charge_transfer = [ba.get_charge_transfer(i) for i in range(len(ba.data))]
summary["charge_transfer"] = charge_transfer
chgcar.write_file("CHGCAR")
chgcar_path = os.path.join(tmp_dir, "CHGCAR")

if chgcar.is_spin_polarized:
# write a CHGCAR containing magnetization density only
chgcar.data["total"] = chgcar.data["diff"]
chgcar.is_spin_polarized = False
chgcar.write_file("CHGCAR_mag")
if potcar:
potcar.write_file("POTCAR")
potcar_path = os.path.join(tmp_dir, "POTCAR")
else:
potcar_path = None

chgcar_mag_path = os.path.join(tmp_dir, "CHGCAR_mag")
ba = BaderAnalysis(
chgcar_filename=chgcar_mag_path,
chgcar_filename=chgcar_path,
potcar_filename=potcar_path,
chgref_filename=chgref_path,
)
summary["magmom"] = [d["charge"] for d in ba.data]

return summary
summary = {
"min_dist": [d["min_dist"] for d in ba.data],
"charge": [d["charge"] for d in ba.data],
"atomic_volume": [d["atomic_vol"] for d in ba.data],
"vacuum_charge": ba.vacuum_charge,
"vacuum_volume": ba.vacuum_volume,
"reference_used": bool(chgref_path),
"bader_version": ba.version,
}

if potcar:
charge_transfer = [ba.get_charge_transfer(i) for i in range(len(ba.data))]
summary["charge_transfer"] = charge_transfer

if chgcar.is_spin_polarized:
# write a CHGCAR containing magnetization density only
chgcar.data["total"] = chgcar.data["diff"]
chgcar.is_spin_polarized = False
chgcar.write_file("CHGCAR_mag")

chgcar_mag_path = os.path.join(tmp_dir, "CHGCAR_mag")
ba = BaderAnalysis(
chgcar_filename=chgcar_mag_path,
potcar_filename=potcar_path,
chgref_filename=chgref_path,
)
summary["magmom"] = [d["charge"] for d in ba.data]
finally:
os.chdir(orig_dir)

return summary
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