Merge branch 'develop' into dopey_fermi

docs/Dev_ToDo.md

@@ -85,6 +85,7 @@
 - Should flick through other defect codes (see
  https://shakenbreak.readthedocs.io/en/latest/Code_Compatibility.html, also `AiiDA-defects`) and see if
  there's any useful functionality we want to add!
+- Add short example notebook showing how to generate a defect PES for carrier capture or NEB calculations (don't use `IBRION = 2` for NEB).
 
 ## SK To-Do for next update:
 - `doped` repo/docs cleanup `TODO`s above

docs/Tips.rst

@@ -461,6 +461,13 @@ etc.).
  defect supercell, directly from just the relaxed structures, regardless of whether these defects were
  generated/parsed with ``doped``.
 
+.. note::
+
+ Wyckoff letters for lattice sites can depend on the ordering of elements in the conventional standard
+ structure, for which doped uses the ``spglib`` convention (e.g. in the ``DefectsGenerator`` info
+ output).
+
+
 Serialization & Data Provenance (``JSON``/``csv``)
 --------------------------------------------------
 To aid calculation reproducibility, data provenance and easy sharing/comparison of pre- and post-processing

doped/analysis.py

@@ -119,7 +119,7 @@ def check_and_set_defect_entry_name(
 ) -> None:
  """
  Check that ``possible_defect_name`` is a recognised format by doped (i.e.
- in the format "{defect_name}_{optional_site_info}_{charge_state}").
+ in the format ``"{defect_name}_{optional_site_info}_{charge_state}"``).
 
  If the DefectEntry.name attribute is not defined or does not end with the
  charge state, then the entry will be renamed with the doped default name

doped/generation.py

@@ -1124,6 +1124,9 @@ def __init__(
  ``DefectEntry.charge_state_guessing_log`` attributes. See docs for examples of
  modifying the generated charge states.
 
+ Note that Wyckoff letters can depend on the ordering of elements in the conventional
+ standard structure, for which doped uses the ``spglib`` convention.
+
  Args:
  structure (Structure):
  Structure of the host material (as a pymatgen Structure object).
@@ -1836,8 +1839,6 @@ def _defect_generator_info(self):
  info_string += (
  "The number in the Wyckoff label is the site multiplicity/degeneracy of that defect in the "
  f"conventional ('conv.') unit cell, which comprises {fu} formula unit(s) of {formula}.\n"
- "Note that Wyckoff letters can depend on the ordering of elements in the conventional "
- "standard structure, for which doped uses the spglib convention."
  )
 
  return info_string
@@ -2172,6 +2173,10 @@ def __repr__(self):
  """
  Returns a string representation of the DefectsGenerator object, and
  prints the DefectsGenerator info.
+
+ Note that Wyckoff letters can depend on the ordering of elements in
+ the conventional standard structure, for which doped uses the ``spglib``
+ convention.
  """
  return (
  self.__str__()

doped/thermodynamics.py

@@ -217,7 +217,7 @@ def raw_energy_from_chempots(composition: Union[str, dict, Composition], chempot
  raw_energies_dict = dict(next(iter(chempots["limits"].values())))
 
  if any(el.symbol not in raw_energies_dict for el in composition.elements):
- raise ValueError(
+ warnings.warn(
  f"The chemical potentials dictionary (with elements {list(raw_energies_dict.keys())} does not "
  f"contain all the elements in the host composition "
  f"({[el.symbol for el in composition.elements]})!"

doped/utils/symmetry.py

@@ -398,9 +398,9 @@ def get_wyckoff(frac_coords, struct, symm_ops: Optional[list] = None, equiv_site
  symm_dataset, unique_sites = _get_symm_dataset_of_struc_with_all_equiv_sites(
  frac_coords, struct, symm_ops, symprec=symprec
  )
- conv_cell_factor = len(symm_dataset["std_positions"]) / len(symm_dataset["wyckoffs"])
+ conv_cell_factor = len(symm_dataset.std_positions) / len(symm_dataset.wyckoffs)
  multiplicity = int(conv_cell_factor * len(unique_sites))
- wyckoff_label = f"{multiplicity}{symm_dataset['wyckoffs'][-1]}"
+ wyckoff_label = f"{multiplicity}{symm_dataset.wyckoffs[-1]}"
 
  return (wyckoff_label, unique_sites) if equiv_sites else wyckoff_label
 
@@ -1126,7 +1126,7 @@ def point_symmetry_from_defect(defect, symm_ops=None, symprec=0.01):
  symm_dataset, _unique_sites = _get_symm_dataset_of_struc_with_all_equiv_sites(
  defect.site.frac_coords, defect.structure, symm_ops=symm_ops, symprec=symprec
  )
- spglib_point_group_symbol = schoenflies_from_hermann(symm_dataset["site_symmetry_symbols"][-1])
+ spglib_point_group_symbol = schoenflies_from_hermann(symm_dataset.site_symmetry_symbols[-1])
  if spglib_point_group_symbol is not None:
  return spglib_point_group_symbol
 
@@ -1240,7 +1240,7 @@ def point_symmetry_from_defect_entry(
  # then easy, can just be taken from symmetry dataset of defect structure
  symm_dataset = _get_sga(defect_entry.defect.structure, symprec=symprec).get_symmetry_dataset()
  return schoenflies_from_hermann(
- symm_dataset["site_symmetry_symbols"][defect_entry.defect.defect_site_index]
+ symm_dataset.site_symmetry_symbols[defect_entry.defect.defect_site_index]
  )
 
  supercell = _get_defect_supercell(defect_entry) if relaxed else _get_bulk_supercell(defect_entry)
@@ -1344,15 +1344,15 @@ def point_symmetry_from_defect_entry(
  # This issue is avoided for relaxed defect supercells as we take the symm_ops of our reduced
  # symmetry cell rather than that of the bulk (so no chance of spurious symmetry upgrade from
  # equivalent sites), and hence the max point symmetry is the point symmetry of the defect
- spglib_point_group_symbol = schoenflies_from_hermann(symm_dataset["site_symmetry_symbols"][-1])
+ spglib_point_group_symbol = schoenflies_from_hermann(symm_dataset.site_symmetry_symbols[-1])
 
  # Note that, if the supercell is non-periodicity-breaking, then the site symmetry can be simply
  # determined using the point group of the unrelaxed defect structure:
  # unrelaxed_defect_supercell = defect_entry.calculation_metadata.get(
  # "unrelaxed_defect_structure", defect_supercell
  # )
  # return schoenflies_from_hermann(
- # _get_sga(unrelaxed_defect_supercell, symprec).get_symmetry_dataset()["pointgroup"],
+ # _get_sga(unrelaxed_defect_supercell, symprec).get_symmetry_dataset().pointgroup,
  # )
  # But current approach works for all cases with unrelaxed defect structures
 
@@ -1361,15 +1361,15 @@ def point_symmetry_from_defect_entry(
  # the defect (e.g. for split-interstitials, split-vacancies, swapped vacancies etc),
  # so use 'pointgroup' output (in this case the reduced symmetry avoids the symmetry-upgrade
  # possibility with the equivalent sites, as when relaxed=False)
- spglib_point_group_symbol = schoenflies_from_hermann(symm_dataset["pointgroup"])
+ spglib_point_group_symbol = schoenflies_from_hermann(symm_dataset.pointgroup)
 
  # This also works (at least for non-periodicity-breaking supercells) for relaxed defects in
  # most cases, but is slightly less robust (more sensitive to ``symprec`` choice) than the
  # approach above:
  # schoenflies_from_hermann(
  # _get_sga(
  # defect_supercell, symprec=symprec
- # ).get_symmetry_dataset()["pointgroup"]
+ # ).get_symmetry_dataset().pointgroup
  # )
 
  if spglib_point_group_symbol is not None:
@@ -1416,7 +1416,7 @@ def _check_relaxed_defect_symmetry_determination(
 
  if unrelaxed_defect_structure is not None:
  unrelaxed_spglib_point_group_symbol = schoenflies_from_hermann(
- _get_sga(unrelaxed_defect_structure, symprec=symprec).get_symmetry_dataset()["pointgroup"],
+ _get_sga(unrelaxed_defect_structure, symprec=symprec).get_symmetry_dataset().pointgroup,
  )
 
  bulk_supercell = _get_bulk_supercell(defect_entry)
@@ -1428,9 +1428,7 @@ def _check_relaxed_defect_symmetry_determination(
  symprec=symprec,
  dist_tol=symprec,
  )
- bulk_spglib_point_group_symbol = schoenflies_from_hermann(
- symm_dataset["site_symmetry_symbols"][-1]
- )
+ bulk_spglib_point_group_symbol = schoenflies_from_hermann(symm_dataset.site_symmetry_symbols[-1])
 
  if bulk_spglib_point_group_symbol != unrelaxed_spglib_point_group_symbol:
  if verbose: