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Merge remote-tracking branch 'origin/develop' into develop
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@kavanase
kavanase committed Sep 19, 2024
2 parents 119f8b2 + cb7df36 commit 38b8ab9
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Showing 12 changed files with 48,978 additions and 499 deletions.
18 changes: 11 additions & 7 deletions doped/core.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -1313,16 +1313,19 @@ def sc_entry_energy(self):

def plot_site_displacements(
self,
separated_by_direction: Optional[bool] = False,
relative_to_defect: Optional[bool] = False,
separated_by_direction: bool = False,
relative_to_defect: bool = False,
vector_to_project_on: Optional[list] = None,
use_plotly: Optional[bool] = False,
mpl_style_file: Optional[PathLike] = "",
use_plotly: bool = False,
style_file: Optional[PathLike] = "",
):
"""
Plot the site displacements as a function of distance from the defect
site.
Set ``use_plotly = True`` to get an interactive ``plotly`` plot, useful
for analysis!
Args:
separated_by_direction (bool):
Whether to plot the site displacements separated by the
Expand All @@ -1337,8 +1340,9 @@ def plot_site_displacements(
(e.g. [0, 0, 1]). Defaults to None (e.g. the displacements are calculated
in the cartesian basis x, y, z).
use_plotly (bool):
Whether to use plotly (True) or matplotlib (False).
mpl_style_file (PathLike):
Whether to use ``plotly`` (``True``) or ``matplotlib`` (``False``).
Defaults to ``False``. Set to ``True`` to get an interactive plot.
style_file (PathLike):
Path to a matplotlib style file to use for the plot. If None,
uses the default doped style file.
"""
Expand All @@ -1350,7 +1354,7 @@ def plot_site_displacements(
relative_to_defect=relative_to_defect,
vector_to_project_on=vector_to_project_on,
use_plotly=use_plotly,
style_file=mpl_style_file,
style_file=style_file,
)


Expand Down
108 changes: 59 additions & 49 deletions doped/generation.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -220,14 +220,7 @@ def closest_site_info(
)

if element_list is None:
element_list = [el.symbol for el in defect.structure.composition.elements] # host elements
element_list += sorted(
[ # extrinsic elements, sorted alphabetically for deterministic ordering in output:
el.symbol
for el in defect.defect_structure.composition.elements
if el.symbol not in element_list
]
)
element_list = _get_element_list(defect)

site_distances = sorted(
[
Expand Down Expand Up @@ -1453,18 +1446,22 @@ class (such as ``clustering_tol``, ``stol``, ``min_dist`` etc), or to
extrinsic_elements = list(set(extrinsic_elements)) # get only unique elements
else:
extrinsic_elements = []

host_element_list = [el.symbol for el in self.primitive_structure.composition.elements]
# if any "extrinsic" elements are actually host elements, remove them from the list and warn
# user:
# if any "extrinsic" elements are actually host elements, remove them and warn user:
if any(el in host_element_list for el in extrinsic_elements):
warnings.warn(
f"\nSpecified 'extrinsic' elements "
f"{[el for el in extrinsic_elements if el in host_element_list]} are present in "
f"the host structure, so do not need to be specified as 'extrinsic' in "
f"DefectsGenerator(). These will be ignored."
)
# sort extrinsic elements alphabetically for deterministic ordering in output:
extrinsic_elements = sorted([el for el in extrinsic_elements if el not in host_element_list])

# sort extrinsic elements by periodic group and atomic number for deterministic ordering:
extrinsic_elements = sorted(
[el for el in extrinsic_elements if el not in host_element_list],
key=_element_sort_func,
)

substitution_generator_obj = SubstitutionGenerator()
if isinstance(self.extrinsic, (str, list)): # substitute all host elements:
Expand Down Expand Up @@ -2227,6 +2224,52 @@ def __repr__(self):
)


def _get_element_list(defect: Union[Defect, DefectEntry, dict, list]) -> list[str]:
"""
Given an input ``Defect`` or ``DefectEntry``, or dictionary/list of these,
return a (non-duplicated) list of elements present in the defect
structures.
"""

def _get_single_defect_element_list(single_defect):
element_list = [el.symbol for el in single_defect.structure.composition.elements]
element_list += sorted(
[ # extrinsic elements, sorted by periodic group and atomic number for deterministic ordering
el.symbol
for el in single_defect.defect_structure.composition.elements
if el.symbol not in element_list
],
key=_element_sort_func,
)
return element_list

if isinstance(defect, (Defect, DefectEntry)):
return _get_single_defect_element_list(defect if isinstance(defect, Defect) else defect.defect)

# else is dict/list
defect_list = defect if isinstance(defect, list) else list(defect.values())
defect_list = [
entry_or_defect.defect if isinstance(entry_or_defect, DefectEntry) else entry_or_defect
for entry_or_defect in defect_list
]
host_element_list = [el.symbol for el in next(iter(defect_list)).structure.composition.elements]
extrinsic_element_list: list[str] = []
for single_defect in defect_list:
extrinsic_element_list.extend(
[
el.symbol
for el in single_defect.defect_structure.composition.elements
if el.symbol not in host_element_list
]
)
# sort extrinsic elements by periodic group and atomic number for deterministic ordering:
extrinsic_element_list = sorted(
set(extrinsic_element_list),
key=_element_sort_func,
)
return host_element_list + extrinsic_element_list


def _first_and_second_element(defect_name: str) -> tuple[str, str]:
"""
Return a tuple of the first and second element in the defect name.
Expand Down Expand Up @@ -2292,27 +2335,7 @@ def _sort_defect_entries(
state (from positive to negative).
"""
if element_list is None:
host_element_list = [
el.symbol
for el in next(iter(defect_entries_dict.values())).defect.structure.composition.elements
]
extrinsic_element_list: list[str] = []
for defect_entry in defect_entries_dict.values():
extrinsic_element_list.extend(
el.symbol
for el in [
*defect_entry.defect.structure.composition.elements,
*defect_entry.defect.site.species.elements,
]
if el.symbol not in host_element_list
)

# sort extrinsic elements by periodic group and atomic number for deterministic ordering in output:
extrinsic_element_list = sorted(
[el for el in extrinsic_element_list if el not in host_element_list],
key=_element_sort_func,
)
element_list = host_element_list + extrinsic_element_list
element_list = _get_element_list(defect_entries_dict)

try:
return dict(
Expand Down Expand Up @@ -2373,24 +2396,11 @@ def _sort_defects(defects_dict: dict, element_list: Optional[list[str]] = None):
Sorts defects by defect type (vacancies, substitutions, interstitials),
then by order of appearance of elements in the composition, then
alphabetically, then according to symmetry._frac_coords_sort_func.
by periodic group (main groups 1, 2, 13-18 first, then TMs), then by
atomic number, then according to ``symmetry._frac_coords_sort_func``.
"""
if element_list is None:
all_elements: list[str] = []
host_element_list = [
el.symbol for el in next(iter(defects_dict.values())).structure.composition.elements
]

for _defect_type, defect_list in defects_dict.items():
for defect in defect_list:
all_elements.extend(el.symbol for el in defect.defect_structure.composition.elements)
extrinsic_element_list = list(set(all_elements) - set(host_element_list))

# sort extrinsic elements alphabetically for deterministic ordering in output:
extrinsic_element_list = sorted(
[el for el in extrinsic_element_list if el not in host_element_list]
)
element_list = host_element_list + extrinsic_element_list
element_list = _get_element_list(defects_dict)

return {
defect_type: sorted(
Expand Down
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