From 53e1f41564342032f4e35cd173e23f9dc49d92e5 Mon Sep 17 00:00:00 2001
From: Sean Kavanagh <s.kavanagh19@imperial.ac.uk>
Date: Wed, 29 Jan 2025 23:41:31 -0500
Subject: [PATCH] More docstring formatting
---
shakenbreak/analysis.py | 40 ++++----
shakenbreak/cli.py | 10 +-
shakenbreak/distortions.py | 10 +-
shakenbreak/energy_lowering_distortions.py | 24 ++---
shakenbreak/input.py | 103 +++++++++++----------
shakenbreak/io.py | 4 +-
shakenbreak/plotting.py | 38 ++++----
tests/test_input.py | 2 +-
8 files changed, 116 insertions(+), 115 deletions(-)
diff --git a/shakenbreak/analysis.py b/shakenbreak/analysis.py
index c4eb7e53..1cbc6f98 100644
--- a/shakenbreak/analysis.py
+++ b/shakenbreak/analysis.py
@@ -63,7 +63,7 @@ def _read_distortion_metadata(output_path: str) -> dict:
Args:
output_path (:obj:`str`):
- Path to directory containing ``distortion_metadata.json`
+ Path to directory containing ``distortion_metadata.json``
(Default: '.', current directory)
Returns:
@@ -155,14 +155,14 @@ def get_gs_distortion(defect_energies_dict: dict) -> tuple:
"""
Calculate energy difference between ``Unperturbed`` structure and
lowest energy distortion. Returns the energy (in eV) and bond
- distortion of the ground-state relative to ``Unperturbed`. If
+ distortion of the ground-state relative to ``Unperturbed``. If
``Unperturbed`` not present, returns (None, ground-state bond
distortion).
Args:
defect_energies_dict (:obj:`dict`):
Dictionary matching distortion to final energy, as
- produced by ``get_energies()`` or ``_sort_data`.
+ produced by ``get_energies()`` or ``_sort_data``.
Returns:
:obj:`tuple`:
@@ -211,7 +211,7 @@ def _sort_data(energies_file: str, verbose: bool = True, min_e_diff: float = 0.0
energies_file (:obj:`str`):
Path to ``yaml`` file with bond distortions and final energies
(in eV), obtained using the CLI command ``snb-parse`` or the
- function ``parse_energies()`.
+ function ``parse_energies()``.
verbose (:obj:`bool`):
Whether to print information about energy lowering
distortions, if found.
@@ -225,7 +225,7 @@ def _sort_data(energies_file: str, verbose: bool = True, min_e_diff: float = 0.0
Returns:
defect_energies_dict (:obj:`dict`):
Dictionary matching distortion to final energy, as
- produced by ``_organize_data()`
+ produced by ``_organize_data()``
energy_diff (:obj:`float`):
Energy difference between minimum energy structure and
``Unperturbed`` (in eV).
@@ -271,7 +271,7 @@ def analyse_defect_site(
site_num: Optional[int] = None,
vac_site: Optional[list] = None,
) -> tuple:
- """
+ r"""
Analyse coordination environment and bond distances to nearest
neighbours of defect site.
@@ -290,7 +290,7 @@ def analyse_defect_site(
Returns:
:obj:`tuple`:
- Tuple of coordination analysis and bond length DataFrames,
+ Tuple of coordination analysis and bond length ``DataFrame``\s,
respectively.
"""
# get defect site
@@ -338,11 +338,11 @@ def analyse_structure(
structure: Structure,
output_path: str = ".",
) -> tuple:
- """
+ r"""
Analyse the local distortion of the input defect structure. Requires
access to the ``distortion_metadata.json`` file generated with
ShakeNBreak to read info about defect site. If lacking this,
- can alternatively use ``analyse_defect_site()`.
+ can alternatively use ``analyse_defect_site()``.
Args:
defect_species (:obj:`str`):
@@ -350,12 +350,12 @@ def analyse_structure(
structure (:obj:`~pymatgen.core.structure.Structure`):
Defect structure to analyse
output_path (:obj:`str`):
- Path to directory containing ``distortion_metadata.json`
+ Path to directory containing ``distortion_metadata.json``
(Default: '.', current directory)
Returns:
:obj:`tuple`:
- Tuple of coordination analysis and bond length DataFrames,
+ Tuple of coordination analysis and bond length ``DataFrame``\s,
respectively.
"""
defect_name_without_charge = defect_species.rsplit("_", 1)[0]
@@ -391,14 +391,14 @@ def get_structures(
store them in a dictionary matching the bond distortion to the final
structure. By default, will read the structures from the distortion
subdirectories present in each defect folder. If only certain
- distortions should be parsed, use the argument ``bond_distortions`
+ distortions should be parsed, use the argument ``bond_distortions``
to specify them.
Args:
defect_species (:obj:`str`):
Defect name including charge (e.g. 'vac_1_Cd_0')
output_path (:obj:`str`):
- Path to top-level directory containing ``defect_species`
+ Path to top-level directory containing ``defect_species``
subdirectories.
(Default: current directory.
bond_distortions (:obj:`list`, optional):
@@ -489,7 +489,7 @@ def get_energies(
defect_species (:obj:`str`):
Defect name including charge (e.g. 'vac_1_Cd_0')
output_path (:obj:`str`):
- Path to top-level directory containing ``defect_species`
+ Path to top-level directory containing ``defect_species``
subdirectories.
(Default: current directory)
distortion_increment (:obj:`float`):
@@ -581,8 +581,8 @@ def calculate_struct_comparison(
"""
Calculate either the summed atomic displacement, with metric = "disp",
or the maximum distance between matched atoms, with metric = "max_dist",
- (default) between each distorted structure in ``defect_struct_dict`,
- and either 'Unperturbed' or a specified structure (`ref_structure`).
+ (default) between each distorted structure in ``defect_struct_dict``,
+ and either 'Unperturbed' or a specified structure (``ref_structure``).
For metric = "disp", atomic displacements below ``min_dist`` (in Å,
default 0.1 Å) are considered noise and omitted from the sum,
to reduce supercell size dependence.
@@ -704,7 +704,7 @@ def compare_structures(
) -> Union[None, pd.DataFrame]:
"""
Compare final bond-distorted structures with either 'Unperturbed' or
- a specified structure (`ref_structure`), and calculate the summed
+ a specified structure (``ref_structure``), and calculate the summed
atomic displacement (in Å), and maximum distance between matched
atomic sites (in Å).
@@ -713,7 +713,7 @@ def compare_structures(
Dictionary mapping bond distortion to (relaxed) structure
defect_energies_dict (:obj:`dict`):
Dictionary matching distortion to final energy (eV), as
- produced by ``_organize_data()`.
+ produced by ``_organize_data()``.
ref_structure (:obj:`str`` or :obj:`float`` or :obj:`Structure`):
Structure to use as a reference for comparison (to compute
atomic displacements). Either as a key from
@@ -723,7 +723,7 @@ def compare_structures(
(Default: "Unperturbed")
units (:obj:`str`):
Energy units label for outputs (either 'eV' or 'meV').
- Should be the same as the units in ``defect_energies_dict`,
+ Should be the same as the units in ``defect_energies_dict``,
as this does not modify the supplied values.
(Default: "eV")
min_dist (:obj:`float`):
@@ -1005,7 +1005,7 @@ def get_site_magnetizations(
List of distortions to analyse (e.g. ['Unperturbed', 0.1,
-0.2])
output_path (:obj:`str`):
- Path to top-level directory containing ``defect_species`
+ Path to top-level directory containing ``defect_species``
subdirectories.
(Default: current directory)
threshold (:obj:`float`, optional):
diff --git a/shakenbreak/cli.py b/shakenbreak/cli.py
index 0b238ae8..b5782e8c 100644
--- a/shakenbreak/cli.py
+++ b/shakenbreak/cli.py
@@ -242,7 +242,7 @@ def generate(
defect_struct = Structure.from_file(defect)
bulk_struct = Structure.from_file(bulk)
- # Note that here the Defect.defect_structure is the defect ``supercell`
+ # Note that here the Defect.defect_structure is the defect ``supercell``
# structure, not the defect ``primitive`` structure.
defect_object = input.identify_defect(
defect_structure=defect_struct,
@@ -926,7 +926,7 @@ def parse(defect, path, code, verbose):
def analyse(defect, path, code, ref_struct, verbose):
"""
Generate ``csv`` file mapping each distortion to its final energy (in eV) and its
- mean displacement (in Angstrom and relative to ``ref_struct`).
+ mean displacement (in Angstrom and relative to ``ref_struct``).
Can be run within a single defect folder, or in the top-level directory (either
specifying ``defect`` or looping through all defect folders).
@@ -1406,10 +1406,10 @@ def groundstate(
):
"""
Generate folders with the identified ground state structures. A folder (named
- ``directory`) is created with the ground state structure (named
- ``groundstate_filename`) for each defect present in the specified path (if ``path`` is
+ ``directory``) is created with the ground state structure (named
+ ``groundstate_filename``) for each defect present in the specified path (if ``path`` is
the top-level directory) or for the current defect if run within a defect folder.
- If the name of the structure/output files is not specified, the code assumes ``CONTCAR`
+ If the name of the structure/output files is not specified, the code assumes ``CONTCAR``
(e.g. geometry optimisations performed with VASP). If using a different code,
please specify the name of the structure/output files.
"""
diff --git a/shakenbreak/distortions.py b/shakenbreak/distortions.py
index 0fcb9aae..51522569 100644
--- a/shakenbreak/distortions.py
+++ b/shakenbreak/distortions.py
@@ -406,7 +406,7 @@ def rattle(
"""
Given a pymatgen Structure object, apply random displacements to all atomic
positions, with the displacement distances randomly drawn from a Gaussian
- distribution of standard deviation ``stdev`.
+ distribution of standard deviation ``stdev``.
Args:
structure (:obj:`~pymatgen.core.structure.Structure`):
@@ -587,7 +587,7 @@ def _local_mc_rattle_displacements(
Returns:
:obj:`numpy.ndarray`:
- atomic displacements (`Nx3`)
+ atomic displacements (Nx3)
"""
def scale_stdev(disp, r_min, r):
@@ -685,7 +685,7 @@ def _generate_local_mc_rattled_structures(
This process is repeated for each atom a number of times meaning
the magnitude of the final displacements is not *directly*
- connected to ``rattle_std`.
+ connected to ``rattle_std``.
This function has been adapted from https://gitlab.com/materials-modeling/hiphive
@@ -721,7 +721,7 @@ def _generate_local_mc_rattled_structures(
n_iter (:obj:`int`):
Number of Monte Carlo cycles
**kwargs:
- Additional keyword arguments to be passed to ``mc_rattle`
+ Additional keyword arguments to be passed to ``mc_rattle``
Returns:
:obj:`list`:
@@ -758,7 +758,7 @@ def local_mc_rattle(
"""
Given a pymatgen Structure object, apply random displacements to all atomic
positions, with the displacement distances randomly drawn from a Gaussian
- distribution of standard deviation ``stdev`. The random displacements
+ distribution of standard deviation ``stdev``. The random displacements
tail off as we move away from the defect site.
Args:
diff --git a/shakenbreak/energy_lowering_distortions.py b/shakenbreak/energy_lowering_distortions.py
index d9e40deb..64d4a0c4 100644
--- a/shakenbreak/energy_lowering_distortions.py
+++ b/shakenbreak/energy_lowering_distortions.py
@@ -104,9 +104,9 @@ def _compare_distortion(
**sm_kwargs,
) -> dict:
"""
- Compare the ground state distortion (`gs_distortion`) to the other
- favourable distortions stored in ``low_energy_defects`. If different,
- add distortion as separate entry to ``low_energy_defects`.
+ Compare the ground state distortion (``gs_distortion``) to the other
+ favourable distortions stored in ``low_energy_defects``. If different,
+ add distortion as separate entry to ``low_energy_defects``.
If same, store together with the other similar distortions.
Args:
@@ -645,7 +645,7 @@ def compare_struct_to_distortions(
) -> tuple:
"""
Compares the ground-state structure found for a certain defect charge
- state with all relaxed bond-distorted structures for ``defect_species`,
+ state with all relaxed bond-distorted structures for ``defect_species``,
to avoid redundant work (testing this distorted structure for other
charge states when it has already been found for them).
@@ -683,7 +683,7 @@ def compare_struct_to_distortions(
matching structure compared to its unperturbed reference, bond
distortion of the matching structure). True if a match is found
between the input structure and the relaxed bond-distorted
- structures for ``defect_species`, False if no match, None if no
+ structures for ``defect_species``, False if no match, None if no
converged structures found for defect_species.
"""
try:
@@ -693,7 +693,7 @@ def compare_struct_to_distortions(
code=code,
structure_filename=structure_filename,
)
- except FileNotFoundError: # catch exception raised by ``analysis.get_structures()`
+ except FileNotFoundError: # catch exception raised by ``analysis.get_structures()``
return None, None, None, None
defect_energies_dict = analysis.get_energies(
defect_species=defect_species, output_path=output_path, verbose=False
@@ -811,14 +811,14 @@ def write_retest_inputs(
"""
Create folders with relaxation input files for testing the low-energy
distorted defect structures found for other charge states of that
- defect, as identified with ``get_energy_lowering_distortions()`.
+ defect, as identified with ``get_energy_lowering_distortions()``.
Args:
low_energy_defects (:obj:`dict`):
Dictionary of defects for which bond distortion found an
energy-lowering distortion which is missed with normal
unperturbed relaxation), generated by
- ``get_energy_lowering_distortions()`. Has the form
+ ``get_energy_lowering_distortions()``. Has the form
{defect: [list of distortion dictionaries (with
corresponding charge states, energy lowering, distortion
factors, structures and charge states for which these
@@ -833,7 +833,7 @@ def write_retest_inputs(
(case-insensitive).
(Default: "vasp")
input_filename (:obj:`str`):
- Name of the code input file if different from ``ShakeNBreak`
+ Name of the code input file if different from ``ShakeNBreak``
default. Only applies to CP2K, Quantum Espresso, CASTEP and
FHI-aims. If not specified, ``ShakeNBreak`` default name is
assumed, that is: for Quantum Espresso: "espresso.pwi",
@@ -1195,19 +1195,19 @@ def write_groundstate_structure(
verbose: bool = False,
) -> None:
"""
- Writes the groundstate structure of each defect (if ``all=True`, default)
+ Writes the groundstate structure of each defect (if ``all=True``, default)
to the corresponding defect folder, with an optional name
(default "groundstate_POSCAR"), to then run continuation calculations.
Args:
all (:obj:`bool`):
Write groundstate structures for all defect folders in the
- (top-level) directory, specified by ``output_path`. If False,
+ (top-level) directory, specified by ``output_path``. If False,
``output_path`` should be a single defect folder, for which the
groundstate structure will be written.
output_path (:obj:`str`):
Path to top-level directory with your distorted defect
- calculation folders (if ``all=True`, else path to single defect
+ calculation folders (if ``all=True``, else path to single defect
folder)(need CONTCAR files for structure matching) and
distortion_metadata.json.
(Default: current directory = "./")
diff --git a/shakenbreak/input.py b/shakenbreak/input.py
index 4262afe1..4488953a 100644
--- a/shakenbreak/input.py
+++ b/shakenbreak/input.py
@@ -1,7 +1,7 @@
"""
Module containing functions to generate rattled and bond-distorted structures,
-as well as input files to run Gamma point relaxations with ``VASP`, ``CP2K`,
-`Quantum-Espresso`, ``FHI-aims`` and ``CASTEP`.
+as well as input files to run Gamma point relaxations with ``VASP``, ``CP2K``,
+``Quantum-Espresso``, ``FHI-aims`` and ``CASTEP``.
"""
import contextlib
@@ -50,8 +50,8 @@
def _warning_on_one_line(message, category, filename, lineno, file=None, line=None) -> str:
"""Output warning messages on one line."""
- # To set this as warnings.formatwarning, we need to be able to take in ``file`
- # and ``line`, but don't want to print them, so unused arguments here
+ # To set this as warnings.formatwarning, we need to be able to take in ``file``
+ # and ``line``, but don't want to print them, so unused arguments here
return f"{os.path.split(filename)[-1]}:{lineno}: {category.__name__}: {message}\n"
@@ -287,7 +287,7 @@ def _create_vasp_input(
output_path: str = ".",
**kwargs,
) -> str:
- """
+ r"""
Creates folders for storing VASP ShakeNBreak files.
Args:
@@ -304,16 +304,16 @@ def _create_vasp_input(
user_potcar_settings (:obj:`dict`):
Dictionary of user VASP POTCAR settings, to overwrite/update
the ``doped`` defaults (e.g. {'Fe': 'Fe_pv', 'O': 'O'}}). Highly
- recommended to look at output ``POTCAR`s, or ``shakenbreak`
- ``shakenbreak/SnB_input_files/default_POTCARs.yaml`, to see what the default
- ``POTCAR`` settings are. (Default: None)
+ recommended to look at output ``POTCAR``\s, or
+ ``shakenbreak/SnB_input_files/default_POTCARs.yaml``, to see what
+ the default ``POTCAR`` settings are. (Default: None)
output_path (:obj:`str`):
Path to directory in which to write distorted defect structures and
calculation inputs.
(Default is current directory = "./")
**kwargs:
Keyword arguments to pass to ``DefectDictSet.write_input()`` (e.g.
- ``potcar_spec`).
+ ``potcar_spec``).
Returns:
:obj:`str`:
@@ -559,7 +559,7 @@ def _get_defect_entry_from_defect(
charge_state: int = 0,
):
"""
- Generate a DefectEntry from a Defect object, whose defect structure
+ Generate a ``DefectEntry`` from a ``Defect`` object, whose defect structure
corresponds to the defect supercell (rather than unit cell). This is the case
when initialising Distortions() from an old doped/pycdt defect dict or from
structures specified by the user.
@@ -628,7 +628,7 @@ def _calc_number_electrons(
) -> int:
"""
Calculates the number of extra/missing electrons of the neutral
- defect species (in ``defect_object`) based on ``oxidation_states`.
+ defect species (in ``defect_object``) based on ``oxidation_states``.
Args:
defect_entry (:obj:`DefectEntry`):
@@ -1207,11 +1207,11 @@ def _find_sc_defect_coords(defect_entry):
"""
Find defect fractional coordinates in defect supercell.
- Targets cases where user generated DefectEntry manually and
+ Targets cases where user generated ``DefectEntry`` manually and
didn't set the ``sc_defect_frac_coords`` attribute.
Args:
- defect_entry (DefectEntry): DefectEntry object
+ defect_entry (DefectEntry): ``DefectEntry`` object
Returns:
frac_coords (list): Fractional coordinates of defect in defect supercell
@@ -1431,7 +1431,7 @@ def apply_snb_distortions(
) -> dict:
"""
Applies rattle and bond distortions to ``num_nearest_neighbours`` of the
- unperturbed defect structure of ``defect_entry`.
+ unperturbed defect structure of ``defect_entry``.
Args:
defect_entry (:obj:`DefectEntry`):
@@ -1644,8 +1644,8 @@ def apply_snb_distortions(
class Distortions:
"""
- Class to apply rattle and bond distortion to all defects in ``defect_entries`
- (each defect as a ``doped`` or ``pymatgen`` DefectEntry object).
+ Class to apply rattle and bond distortion to all defects in ``defect_entries``
+ (each defect as a ``doped`` or ``pymatgen`` ``DefectEntry`` object).
"""
def __init__(
@@ -1660,28 +1660,28 @@ def __init__(
distorted_atoms: Optional[list] = None,
**mc_rattle_kwargs,
):
- """
+ r"""
Args:
defect_entries (Union[DefectsGenerator, list, dict, DefectEntry]):
- Either a ``DefectsGenerator`` object from ``doped`, or a list/dictionary
- of, or single, DefectEntry object(s).
- E.g.: [DefectEntry(), DefectEntry(), ...], or single DefectEntry.
+ Either a ``DefectsGenerator`` object from ``doped``, or a list/dictionary
+ of, or single, ``DefectEntry`` object(s).
+ E.g.: ``[DefectEntry(), DefectEntry(), ...]``, or single ``DefectEntry``.
If a ``DefectsGenerator`` object or a dictionary (->
- {defect_species: DefectEntry}), the defect folder names will be
+ ``{defect_species: DefectEntry}``), the defect folder names will be
set equal to ``defect_species`` (with charge states included). If
a list or single ``DefectEntry`` object is provided, the defect
- folder names will be set equal to ``DefectEntry.name`` if the ``name`
- attribute is set for all input ``DefectEntry`s, otherwise generated
+ folder names will be set equal to ``DefectEntry.name`` if the ``name``
+ attribute is set for all input ``DefectEntry``\s, otherwise generated
according to the ``doped`` convention
(see: https://doped.readthedocs.io/en/latest/generation_tutorial.html).
Defect charge states (from which bond distortions are determined) are
taken from the ``DefectEntry.charge_state`` property.
- Alternatively, a defects dict generated by ``ChargedDefectStructures`
- from ``PyCDT`/`doped<2.0`` can also be used as input, and the defect names
+ Alternatively, a defects dict generated by ``ChargedDefectStructures``
+ from ``PyCDT``/``doped<2.0`` can also be used as input, and the defect names
and charge states generated by these codes will be used
- E.g.: {"bulk": {..}, "vacancies": [{...}, {...},], ...}
+ E.g.: ``{"bulk": {..}, "vacancies": [{...}, {...},], ...}``
oxidation_states (:obj:`dict`):
Dictionary of oxidation states for species in your material,
used to determine the number of defect neighbours to distort
@@ -1697,7 +1697,7 @@ def __init__(
(Default: None)
distortion_increment (:obj:`float`):
Bond distortion increment. Distortion factors will range from
- 0 to +/-0.6, in increments of ``distortion_increment`.
+ 0 to +/-0.6, in increments of ``distortion_increment``.
Recommended values: 0.1-0.3
(Default: 0.1)
bond_distortions (:obj:`list`):
@@ -2036,8 +2036,8 @@ def _parse_number_electrons(
where charge_change is the negative of the number of
extra/missing electrons.
defect_entry (:obj:`DefectEntry`):
- DefectEntry in dictionary of defect_entries. Must be a
- ``doped`` or ``pymatgen`` DefectEntry object.
+ ``DefectEntry`` in dictionary of defect_entries. Must be a
+ ``doped`` or ``pymatgen`` ``DefectEntry`` object.
verbose (:obj:`bool`):
Whether to print the number of extra/missing electrons for
the defect.
@@ -2171,15 +2171,15 @@ def _setup_distorted_defect_dict(
) -> dict:
"""
Setup ``distorted_defect_dict`` with info for ``defect`` in
- ``DefectEntry`.
+ ``DefectEntry``.
Args:
defect_entry (:obj:`doped.core.DefectEntry`):
- DefectEntry object to generate ``distorted_defect_dict`` from.
+ ``DefectEntry`` object to generate ``distorted_defect_dict`` from.
Returns:
:obj:`dict`
- Dictionary with information for ``defect`.
+ Dictionary with information for ``defect``.
"""
defect = defect_entry.defect
defect_type = defect.defect_type.name.lower()
@@ -2272,10 +2272,10 @@ def apply_distortions(
verbose: Optional[bool] = None,
) -> tuple[dict, dict]:
"""
- Applies rattle and bond distortion to all defects in ``defect_entries`.
+ Applies rattle and bond distortion to all defects in ``defect_entries``.
Returns a dictionary with the distorted (and undistorted) structures
for each charge state of each defect.
- If file generation is desired, instead use the methods ``write_<code>_files()`.
+ If file generation is desired, instead use the methods ``write_<code>_files()``.
Args:
verbose (:obj:`bool`):
@@ -2464,7 +2464,7 @@ def write_vasp_files(
verbose: Optional[bool] = None,
**kwargs,
) -> tuple[dict, dict]:
- """
+ r"""
Generates the input files for ``vasp_gam`` relaxations of all output
structures.
@@ -2472,20 +2472,20 @@ def write_vasp_files(
user_incar_settings (:obj:`dict`):
Dictionary of user VASP INCAR settings (e.g.
{"ENCUT": 300, ...}), to overwrite the ``ShakenBreak`` defaults
- for those tags. Highly recommended to look at output ``INCAR`s,
- or ``shakenbreak/SnB_input_files/incar.yaml`` to see what the default ``INCAR`
- settings are. Note that any flags that aren't numbers or
+ for those tags. Highly recommended to look at output ``INCAR``\s,
+ or ``shakenbreak/SnB_input_files/incar.yaml`` to see what the default
+ ``INCAR`` settings are. Note that any flags that aren't numbers or
True/False need to be input as strings with quotation marks
- (e.g. ``{"ALGO": "All"}`). (Default: None)
+ (e.g. ``{"ALGO": "All"}``). (Default: None)
user_potcar_functional (str):
POTCAR functional to use. Default is "PBE" and if this fails,
tries "PBE_52", then "PBE_54".
user_potcar_settings (:obj:`dict`):
Dictionary of user VASP POTCAR settings, to overwrite/update
the ``doped`` defaults (e.g. {'Fe': 'Fe_pv', 'O': 'O'}}). Highly
- recommended to look at output ``POTCAR`s, or ``shakenbreak`
- ``shakenbreak/SnB_input_files/default_POTCARs.yaml`, to see what the default
- ``POTCAR`` settings are. (Default: None)
+ recommended to look at output ``POTCAR``\s, or
+ ``shakenbreak/SnB_input_files/default_POTCARs.yaml``, to see what
+ the default ``POTCAR`` settings are. (Default: None)
write_files (:obj:`bool`):
Whether to write output files (Default: True)
output_path (:obj:`str`):
@@ -2496,7 +2496,7 @@ def write_vasp_files(
Whether to print distortion information (bond atoms and
distances). (Default: None -- medium level verbosity)
kwargs:
- Additional keyword arguments to pass to ``_create_vasp_input()`
+ Additional keyword arguments to pass to ``_create_vasp_input()``
(Mainly for testing purposes).
Returns:
@@ -2581,12 +2581,13 @@ def write_espresso_files(
(Defaults: None)
input_parameters (:obj:`dict`, optional):
Dictionary of user Quantum Espresso input parameters, to
- overwrite/update ``shakenbreak`` default ones (see
- ``shakenbreak/SnB_input_files/qe_input.yaml`).
+ overwrite/update ShakeNBreak defaults (see
+ ``shakenbreak/SnB_input_files/qe_input.yaml``).
(Default: None)
input_file (:obj:`str`, optional):
Path to Quantum Espresso input file, to overwrite/update
- ``shakenbreak`` default ones (see ``shakenbreak/SnB_input_files/qe_input.yaml`).
+ ShakeNBreak defaults (see
+ ``shakenbreak/SnB_input_files/qe_input.yaml``).
If both ``input_parameters`` and ``input_file`` are provided,
the input_parameters will be used.
(Default: None)
@@ -2711,7 +2712,7 @@ def write_cp2k_files(
Args:
input_file (:obj:`str`, optional):
Path to CP2K input file. If not set, default input file will be
- used (see ``shakenbreak/SnB_input_files/cp2k_input.inp`).
+ used (see ``shakenbreak/SnB_input_files/cp2k_input.inp``).
write_structures_only (:obj:`bool`, optional):
Whether to only write the structure files (in CIF format)
(without calculation inputs).
@@ -2773,8 +2774,8 @@ def write_castep_files(
Args:
input_file (:obj:`str`, optional):
- Path to CASTEP input (`.param`) file. If not set, default input
- file will be used (see ``shakenbreak/SnB_input_files/castep.param`).
+ Path to CASTEP input (``.param``) file. If not set, default input
+ file will be used (see ``shakenbreak/SnB_input_files/castep.param``).
write_structures_only (:obj:`bool`, optional):
Whether to only write the structure files (in CIF format)
(without calculation inputs).
@@ -2995,7 +2996,7 @@ def from_structures(
[(defect Structure, frac_coords/index), ...] to aid site-matching.
Defect charge states (from which bond distortions are determined) are
- set to the range: 0 - {Defect oxidation state}, with a ``padding`
+ set to the range: 0 - {Defect oxidation state}, with a ``padding``
(default = 1) on either side of this range.
bulk (:obj:`pymatgen.core.structure.Structure`):
Bulk supercell structure, matching defect supercells.
@@ -3018,7 +3019,7 @@ def from_structures(
(Default: None)
distortion_increment (:obj:`float`):
Bond distortion increment. Distortion factors will range from
- 0 to +/-0.6, in increments of ``distortion_increment`.
+ 0 to +/-0.6, in increments of ``distortion_increment``.
Recommended values: 0.1-0.3
(Default: 0.1)
bond_distortions (:obj:`list`):
diff --git a/shakenbreak/io.py b/shakenbreak/io.py
index b442f5a5..cbc6603f 100644
--- a/shakenbreak/io.py
+++ b/shakenbreak/io.py
@@ -199,7 +199,7 @@ def parse_fhi_aims_energy(defect_dir, dist, energy, aims_out):
if defect == os.path.basename(os.path.normpath(path)) and not [
dir for dir in path if (os.path.isdir(dir) and os.path.basename(os.path.normpath(dir)) == defect)
- ]: # if ``defect`` is in end of ``path`` and ``path`` doesn't have a subdirectory called ``defect`
+ ]: # if ``defect`` is in end of ``path`` and ``path`` doesn't have a subdirectory called ``defect``
# then remove defect from end of path
path = os.path.dirname(path)
@@ -555,7 +555,7 @@ def read_castep_structure(
filename: str,
) -> Union[Structure, str]:
"""
- Reads a structure from CASTEP output (`.castep`) file and returns it as a
+ Reads a structure from CASTEP output (``.castep``) file and returns it as a
pymatgen Structure.
Args:
diff --git a/shakenbreak/plotting.py b/shakenbreak/plotting.py
index 84a8d8f1..b55b70e8 100644
--- a/shakenbreak/plotting.py
+++ b/shakenbreak/plotting.py
@@ -99,7 +99,7 @@ def _verify_data_directories_exist(
output_path: str,
defect_species: str,
) -> None:
- """Check top-level directory (e.g. ``output_path`) and defect folders exist."""
+ """Check top-level directory (e.g. ``output_path``) and defect folders exist."""
# Check directories and input
if not os.path.isdir(output_path): # if output_path does not exist, raise error
raise FileNotFoundError(f"Path {output_path} does not exist! Skipping {defect_species}.")
@@ -155,7 +155,7 @@ def _cast_energies_to_floats(
Args:
energies_dict (:obj:`dict`):
Dictionary matching distortion to final energy (eV), as produced by
- ``_organize_data()`` or ``analysis.get_energies()`)..
+ ``_organize_data()`` or ``analysis.get_energies()``)..
defect_species (:obj:`str`):
Defect name including charge (e.g. 'vac_1_Cd_0')
@@ -222,7 +222,7 @@ def _purge_data_dicts(
disp_dict (dict):
dictionary with displacements (for each structure relative to
Unperturbed), in the output format of
- ``analysis.calculate_struct_comparison()`
+ ``analysis.calculate_struct_comparison()``
energies_dict (dict):
dictionary with final energies (for each structure relative to ¡
Unperturbed), in the output format of ``analysis.get_energies()`` or
@@ -252,18 +252,18 @@ def _remove_high_energy_points(
) -> tuple[dict, dict]:
"""
Remove points whose energy is higher than the reference (Unperturbed) by
- more than ``max_energy_above_unperturbed`.
+ more than ``max_energy_above_unperturbed``.
Args:
energies_dict (:obj:`dict`):
Dictionary matching distortion to final energy (eV), as produced by
- ``analysis._organize_data()`` or ``analysis.get_energies()`
+ ``analysis._organize_data()`` or ``analysis.get_energies()``
max_energy_above_unperturbed (:obj:`float`):
- Maximum energy (in chosen ``units`), relative to the unperturbed
+ Maximum energy (in chosen ``units``), relative to the unperturbed
structure, to show on plot
disp_dict (:obj:`dict`):
Dictionary matching distortion to sum of atomic displacements, as
- produced by ``analysis.calculate_struct_comparison()`
+ produced by ``analysis.calculate_struct_comparison()``
(Default: None)
Returns:
@@ -273,7 +273,7 @@ def _remove_high_energy_points(
# remove high energy points
if energies_dict["distortions"][key] - energies_dict["Unperturbed"] > max_energy_above_unperturbed:
energies_dict["distortions"].pop(key)
- if disp_dict and key in disp_dict: # only exists if user selected ``add_colorbar=True`
+ if disp_dict and key in disp_dict: # only exists if user selected ``add_colorbar=True``
disp_dict.pop(key)
return energies_dict, disp_dict
@@ -310,7 +310,7 @@ def _get_displacement_dict(
(Default: 'max_dist')
energies_dict (:obj:`dict`):
Dictionary matching distortion to final energy (eV), as produced by
- ``_organize_data()`` or ``analysis.get_energies()`)
+ ``_organize_data()`` or ``analysis.get_energies()``)
add_colorbar (:obj:`bool`):
Whether to add a colorbar indicating structural similarity between
each structure and the unperturbed one.
@@ -320,8 +320,8 @@ def _get_displacement_dict(
(Default: "vasp")
Returns:
- Tuple[bool, dict, dict]: tuple of ``add_colorbar`, ``energies_dict`` and
- ``disp_dict`
+ Tuple[bool, dict, dict]: tuple of ``add_colorbar``, ``energies_dict`` and
+ ``disp_dict``
"""
try:
defect_structs = analysis.get_structures(
@@ -834,7 +834,7 @@ def plot_all_defects(
matched sites ('max_dist', default).
(Default: "max_dist")
max_energy_above_unperturbed (:obj:`float`):
- Maximum energy (in chosen ``units`), relative to the unperturbed structure,
+ Maximum energy (in chosen ``units``), relative to the unperturbed structure,
to show on the plot.
(Default: 0.5 eV)
units (:obj:`str`):
@@ -1023,7 +1023,7 @@ def plot_defect(
Defect name including charge (e.g. 'vac_1_Cd_0')
energies_dict (:obj:`dict`):
Dictionary matching distortion to final energy (eV), as produced by
- ``_organize_data()`` or ``analysis.get_energies()`)
+ ``_organize_data()`` or ``analysis.get_energies()``)
output_path (:obj:`str`):
Path to top-level directory with your distorted defect calculations
(to calculate structure comparisons and save plots)
@@ -1047,7 +1047,7 @@ def plot_defect(
matched sites ('max_dist', default).
(Default: "max_dist")
max_energy_above_unperturbed (:obj:`float`):
- Maximum energy (in chosen ``units`), relative to the unperturbed
+ Maximum energy (in chosen ``units``), relative to the unperturbed
structure, to show on the plot.
(Default: 0.5 eV)
units (:obj:`str`):
@@ -1434,11 +1434,11 @@ def plot_colorbar(
Args:
energies_dict (:obj:`dict`):
Dictionary matching distortion to final energy (eV), as produced by
- ``analysis.get_energies()`` or ``analysis._organize_data()`.
+ ``analysis.get_energies()`` or ``analysis._organize_data()``.
disp_dict (:obj:`dict`):
Dictionary matching bond distortions to structure comparison metric
(metric = 'disp' or 'max_dist'), as produced by
- ``analysis.calculate_struct_comparison()`.
+ ``analysis.calculate_struct_comparison()``.
defect_species (:obj:`str`):
Specific defect name that will appear in plot labels (in LaTeX form)
and file names (e.g 'vac_1_Cd_0')
@@ -1465,7 +1465,7 @@ def plot_colorbar(
or the maximum distance between matched sites ('max_dist', default).
(Default: "max_dist")
max_energy_above_unperturbed (:obj:`float`):
- Maximum energy (in chosen ``units`), relative to the unperturbed
+ Maximum energy (in chosen ``units``), relative to the unperturbed
structure, to show on the plot.
(Default: 0.5 eV)
save_plot (:obj:`bool`):
@@ -1617,7 +1617,7 @@ def plot_datasets(
datasets (:obj:`list`):
List of {distortion: energy} dictionaries to plot (each dictionary
matching distortion to final energy (eV), as produced by
- ``analysis._organize_data()`` or ``analysis.get_energies()`)
+ ``analysis._organize_data()`` or ``analysis.get_energies()``)
dataset_labels (:obj:`list`):
Labels for each dataset plot legend. If None, defaults to
["Distortions"]*len(datasets).
@@ -1637,7 +1637,7 @@ def plot_datasets(
num_nearest_neighbours (:obj:`int`):
Number of distorted neighbour atoms (e.g. 2)
max_energy_above_unperturbed (:obj:`float`):
- Maximum energy (in chosen ``units`), relative to the unperturbed
+ Maximum energy (in chosen ``units``), relative to the unperturbed
structure, to show on the plot.
(Default: 0.5 eV)
style_file (PathLike):
diff --git a/tests/test_input.py b/tests/test_input.py
index f328c0de..6b608072 100644
--- a/tests/test_input.py
+++ b/tests/test_input.py
@@ -11,7 +11,6 @@
import numpy as np
from ase.build import bulk, make_supercell
-from ase.calculators.aims import Aims
from ase.io import read
from doped.generation import get_defect_name_from_entry
from doped.vasp import _test_potcar_functional_choice, DefectRelaxSet
@@ -2990,6 +2989,7 @@ def test_write_fhi_aims_files(self):
# # User defined parameters
# for i in self.cdte_defect_folders_old_names:
# if_present_rm(i) # remove test-generated defect folders
+ # from ase.calculators.aims import Aims
# ase_calculator = Aims(
# k_grid=(1, 1, 1),
# relax_geometry=("bfgs", 5e-4),