"""
``doped`` is a python package for managing solid-state defect calculations,
with functionality to generate defect structures and relevant competing phases
(for chemical potentials), interface with ShakeNBreak
(https://shakenbreak.readthedocs.io) for defect structure-searching (see
https://www.nature.com/articles/s41524-023-00973-1), write VASP input files for
defect supercell calculations, and automatically parse and analyse the results.
"""
import contextlib
import inspect
import logging
import multiprocessing
import warnings
from importlib.metadata import PackageNotFoundError, version
from packaging.version import parse
from pymatgen.io.vasp.inputs import UnknownPotcarWarning
from pymatgen.io.vasp.sets import BadInputSetWarning
try:
import vise.util.logger
vise.util.logger.get_logger = logging.getLogger # to avoid repeated vise INFO messages with Parallel code
except ImportError:
warnings.warn(
"pydefect is required for performing the eFNV correction and eigenvalue/orbital analysis, and can "
"be installed with `pip install pydefect`."
)
def _check_pmg_compatibility():
try:
v_pmg_def = version("pymatgen-analysis-defects")
except PackageNotFoundError:
v_pmg_def = False
try:
v_pmg = version("pymatgen")
except Exception:
v_pmg = False
if not v_pmg_def:
raise TypeError(
"You do not have the `pymatgen-analysis-defects` package installed, which is required by "
"`doped`. Please install `pymatgen-analysis-defects` (with `pip install "
"pymatgen-analysis-defects`) and restart the kernel."
)
if parse(v_pmg) < parse("2022.7.25"):
raise TypeError(
f"You have the version {v_pmg} of `pymatgen` installed, which is incompatible with `doped`. "
f"Please update (with `pip install --upgrade pymatgen`) and restart the kernel."
)
_check_pmg_compatibility()
def _ignore_pmg_warnings():
# globally ignore these POTCAR warnings; `message` only needs to match start of message
warnings.filterwarnings("ignore", category=UnknownPotcarWarning)
warnings.filterwarnings("ignore", category=BadInputSetWarning)
warnings.filterwarnings("ignore", message="No POTCAR file with matching TITEL fields")
warnings.filterwarnings("ignore", message="Ignoring unknown variable type")
# Ignore because comment after 'ALGO = Normal' causes this unnecessary warning:
warnings.filterwarnings("ignore", message="Hybrid functionals only support")
warnings.filterwarnings("ignore", message="Use get_magnetic_symmetry()")
warnings.filterwarnings("ignore", message="Use of properties is now deprecated")
# avoid warning about selective_dynamics properties (can happen if user explicitly set "T T T" (or
# otherwise) for the bulk):
warnings.filterwarnings("ignore", message="Not all sites have property")
# ignore warning about structure charge that appears when getting Vasprun.as_dict():
warnings.filterwarnings("ignore", message="Structure charge")
_ignore_pmg_warnings()
def _doped_obj_properties_methods(obj):
"""
Return a tuple of the attributes & properties and methods of a given
object.
Used in the ``__repr__()`` methods of ``doped`` objects.
"""
attrs = {k for k in vars(obj) if not k.startswith("_")}
methods = set()
for k in dir(obj):
with contextlib.suppress(Exception):
if callable(getattr(obj, k)) and not k.startswith("_"):
methods.add(k)
properties = {name for name, value in inspect.getmembers(type(obj)) if isinstance(value, property)}
return attrs | properties, methods
[docs]
def get_mp_context():
"""
Get a multiprocessing context that is compatible with the current OS.
"""
try:
return multiprocessing.get_context("forkserver")
except ValueError: # forkserver not available on Windows OS
return multiprocessing.get_context("spawn")
[docs]
@contextlib.contextmanager
def pool_manager(processes: int | None = None):
r"""
Context manager for ``multiprocessing`` ``Pool``, to throw a clearer error
message when ``RuntimeError``\s are raised ``multiprocessing`` within
``doped`` is used in a python script.
See
https://doped.readthedocs.io/en/latest/Troubleshooting.html#errors-with-python-scripts
Args:
processes (int | None):
Number of processes to use with ``Pool``. If ``None``,
will use ``mp.cpu_count() - 1`` (i.e. one less than the
number of available CPUs).
Yields:
Pool:
A ``Pool`` object with the specified number of processes.
"""
pool = None
try:
mp = get_mp_context() # https://github.com/python/cpython/pull/100229
pool = mp.Pool(processes or max(1, mp.cpu_count() - 1))
yield pool
except RuntimeError as orig_exc:
if "freeze_support()" in str(orig_exc):
raise RuntimeError(
"When using doped in python scripts with multiprocessing (recommended), you must use the "
"`if __name__ == '__main__':` syntax, see "
"https://doped.readthedocs.io/en/latest/Troubleshooting.html#errors-with-python-scripts "
"-- alternatively you can set processes=1 (but this will be slower)"
) from orig_exc
raise orig_exc
finally:
if pool is not None:
pool.close()
pool.join()