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Chargemol fixes for VASP POTCAR 64 #4545

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Chargemol fixes for VASP POTCAR 64 #4545

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32 changes: 26 additions & 6 deletions src/pymatgen/command_line/chargemol_caller.py
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Original file line number Diff line number Diff line change
Expand Up @@ -49,6 +49,7 @@
import warnings
from glob import glob
from shutil import which
from tempfile import TemporaryFile
from typing import TYPE_CHECKING

import numpy as np
Expand Down Expand Up @@ -116,6 +117,7 @@ def __init__(
self._potcar_path = self._get_filepath(path, "POTCAR")
self._aeccar0_path = self._get_filepath(path, "AECCAR0")
self._aeccar2_path = self._get_filepath(path, "AECCAR2")
self._temp_potcar_file = None

if run_chargemol and not (
self._chgcar_path and self._potcar_path and self._aeccar0_path and self._aeccar2_path
Expand All @@ -132,7 +134,24 @@ def __init__(
warnings.warn("No CHGCAR found. Some properties may be unavailable.", stacklevel=2)

if self._potcar_path:
self.potcar = Potcar.from_file(self._potcar_path)
potcar = Potcar.from_file(self._potcar_path)
self.nelect = [p.nelectrons for p in potcar]

# chargemol can't process version 64 POTCARs current because of the SHA and COPY fields
CHGMOL_BAD_POTCAR_KEYS = ("SHA", "COPYR")
if any(k in p.data for p in potcar for k in CHGMOL_BAD_POTCAR_KEYS):
self._temp_potcar_file = TemporaryFile() # noqa: SIM115
with open(self._temp_potcar_file.name, "w") as f:
f.write(
"\n".join(
line
for p in potcar
for line in p.data.splitlines()
if not any(k in line for k in CHGMOL_BAD_POTCAR_KEYS)
)
)
f.seek(0)
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@shyuep shyuep Nov 15, 2025

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Not sure what this seek is intended to do?

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@esoteric-ephemera esoteric-ephemera Nov 17, 2025

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The seek is needed upon reopening the temp file or the cursor might stay at the tail of the file rather than the head

self._potcar_path = self._temp_potcar_file.name
else:
warnings.warn("No POTCAR found. Some properties may be unavailable.", stacklevel=2)

Expand All @@ -144,6 +163,9 @@ def __init__(
else:
self._from_data_dir(chargemol_output_path=path)

if self._temp_potcar_file:
self._temp_potcar_file.close()

@staticmethod
def _get_filepath(path, filename, suffix=""):
"""Get the full path to the filename in the path. Works even if the file has
Expand Down Expand Up @@ -304,12 +326,10 @@ def get_charge(self, atom_index, nelect=None, charge_type: Literal["ddec", "cm5"
"""
if nelect:
charge = nelect + self.get_charge_transfer(atom_index, charge_type=charge_type)
elif self.potcar and self.natoms:
elif self.nelect and self.natoms:
charge = None
potcar_indices = []
for idx, val in enumerate(self.natoms):
potcar_indices += [idx] * val
nelect = self.potcar[potcar_indices[atom_index]].nelectrons
potcar_indices = [idx for idx, val in enumerate(self.natoms) for _ in range(val)]
nelect = self.nelect[potcar_indices[atom_index]]
charge = nelect + self.get_charge_transfer(atom_index, charge_type=charge_type)
else:
charge = None
Expand Down
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