Merge pull request #76 from SMTG-Bham/develop

Develop

CHANGELOG.rst

@@ -1,6 +1,12 @@
 Change Log
 ==========
 
+v.2.4.4
+----------
+- Make oxidation state guessing more efficient, semi-significant speed up in generation/parsing for tough cases.
+- Add `bulk_site_concentration` property to `DefectEntry`, giving the concentration of the corresponding lattice site of that defect in the pristine bulk.
+- Minor updates to ensure compatibility with recent ``pymatgen`` and ``ASE`` releases.
+
 v.2.4.3
 ----------
 - Remove ``spglib<=2.0.2`` dependency (set to avoid unnecessary warnings), and update installation instructions accordingly.

docs/Dev_ToDo.md

@@ -87,7 +87,6 @@
  there's any useful functionality we want to add!
 
 ## SK To-Do for next update:
-- Remove `typing-extensions` requirement from `pyproject.toml`, once new `pymatgen-analysis-defects` released.
 - `doped` repo/docs cleanup `TODO`s above
 - Quick-start tutorial suggested by Alex G
 - Add chempot grid plotting tool, shown in `JOSS_plots` using Alex's chemical potential grid, and test (and remove TODO from JOSS plots notebook).

docs/Troubleshooting.rst

@@ -14,7 +14,7 @@ message about the origin of the problem, it is likely to be an issue with your v
 
 .. code:: bash
 
- pip install pymatgen pymatgen-analysis-defects --upgrade
+ pip install pymatgen pymatgen-analysis-defects monty --upgrade
  pip install doped --upgrade
 
 If this does not solve your issue, please check the specific cases noted below. If your issue still isn't

doped/analysis.py

@@ -10,7 +10,7 @@
 import contextlib
 import os
 import warnings
-from multiprocessing import Pool, Queue, cpu_count
+from multiprocessing import Pool, cpu_count
 from typing import TYPE_CHECKING, Optional, Union
 
 import numpy as np
@@ -26,7 +26,7 @@
 from tqdm import tqdm
 
 from doped import _doped_obj_properties_methods, _ignore_pmg_warnings
-from doped.core import DefectEntry, _guess_and_set_oxi_states_with_timeout, _rough_oxi_state_cost_from_comp
+from doped.core import DefectEntry, guess_and_set_oxi_states_with_timeout
 from doped.generation import get_defect_name_from_defect, get_defect_name_from_entry, name_defect_entries
 from doped.thermodynamics import DefectThermodynamics
 from doped.utils.parsing import (
@@ -706,18 +706,14 @@ def __init__(
 
  # try parsing the bulk oxidation states first, for later assigning defect "oxi_state"s (i.e.
  # fully ionised charge states):
- if _rough_oxi_state_cost_from_comp(self.bulk_vr.final_structure.composition) > 1e6:
- self._bulk_oxi_states: Union[dict, bool] = False # will take very long to guess oxi_state
- else:
- queue: Queue = Queue()
- self._bulk_oxi_states = _guess_and_set_oxi_states_with_timeout(
- self.bulk_vr.final_structure, queue=queue
- )
- if self._bulk_oxi_states:
- self.bulk_vr.final_structure = queue.get() # oxi-state decorated structure
- self._bulk_oxi_states = {
- el.symbol: el.oxi_state for el in self.bulk_vr.final_structure.composition.elements
- }
+ self._bulk_oxi_states: Union[dict, bool] = False
+ if bulk_struct_w_oxi := guess_and_set_oxi_states_with_timeout(
+ self.bulk_vr.final_structure, break_early_if_expensive=True
+ ):
+ self.bulk_vr.final_structure = bulk_struct_w_oxi
+ self._bulk_oxi_states = {
+ el.symbol: el.oxi_state for el in self.bulk_vr.final_structure.composition.elements # type: ignore
+ }
 
  self.defect_dict = {}
  self.bulk_corrections_data = { # so we only load and parse bulk data once