Add calc_displacements_ellipsoid function #86

teruya7 · 2024-08-20T14:07:27Z

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coderabbitai

Actionable comments posted: 0

Outside diff range, codebase verification and nitpick comments (6)

docs/Future_ToDo.md (1)
89-89: Grammar Suggestion: Use "as" instead of "like"

Consider changing "like shown" to "as shown" for grammatical correctness.
- Eigenvalue corrections for the eigenvalue plots, like shown in 10.1103/PhysRevB.109.054106?
+ Eigenvalue corrections for the eigenvalue plots, as shown in 10.1103/PhysRevB.109.054106?
Tools

LanguageTool

[grammar] ~89-~89: Did you mean “as”?
Context: ...e corrections for the eigenvalue plots, like shown in 10.1103/PhysRevB.109.054106? ...

(LIKE_SHOWN_TO_AS_SHOWN)
docs/Dev_ToDo.md (1)
91-91: Add missing article "the".

Consider adding "the" before "LaTeX table generator website" for grammatical correctness.
- Note in chempots tutorial that LaTeX table generator website can also be used
+ Note in the chempots tutorial that the LaTeX table generator website can also be used
Tools

LanguageTool

[uncategorized] ~91-~91: You might be missing the article “the” here.
Context: ... above - Note in chempots tutorial that LaTeX table generator website can also be use...

(AI_EN_LECTOR_MISSING_DETERMINER_THE)
doped/utils/displacements.py (4)
558-576: Comprehensive Implementation of calc_displacements_ellipsoid.

The function is well-documented and includes robust error handling. It leverages pandas and plotly effectively for data manipulation and visualization.

Consider addressing the following static analysis hints for improved code quality:

Remove the blank line after the function docstring.

Remove trailing whitespace on line 577.

Remove whitespace from the blank line on line 582.
-    """
+    """Calculate displacements around a defect site and fit an ellipsoid to these displacements.
-    
+
-    
+
Tools

Ruff

564-576: No blank lines allowed after function docstring (found 1)

Remove blank line(s) after function docstring

(D202)

583-600: Refine Docstring Formatting for _get_minimum_volume_ellipsoid.

The function logic is correct, but consider addressing the following static analysis hints to improve code quality:

Remove surrounding whitespace from the docstring.

Ensure the first line ends with a period.
-        """ Find the minimum volume ellipsoid which holds all the points
+        """Find the minimum volume ellipsoid which holds all the points.
Tools

Ruff

584-600: No whitespaces allowed surrounding docstring text

Trim surrounding whitespace

(D210)

584-600: First line should end with a period, question mark, or exclamation point

Add closing punctuation

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585-585: Blank line contains whitespace

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591-591: Blank line contains whitespace

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596-596: Blank line contains whitespace

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599-599: Blank line contains whitespace

Remove whitespace from blank line

(W293)

641-693: Improve String Formatting and Line Length in _plot_ellipsoid.

Consider the following improvements:

Use double quotes for consistency.

Address line length issues.
-                mode='markers',
-                line=dict(color='black', width=2)
+                mode="markers",
+                line={"color": "black", "width": 2}
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655-655: Line too long (118 > 107)

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662-662: Single quotes found but double quotes preferred

Replace single quotes with double quotes

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663-663: Unnecessary dict call (rewrite as a literal)

Rewrite as a literal

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663-663: Single quotes found but double quotes preferred

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665-665: Blank line contains whitespace

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(W293)

666-668: Unnecessary dict call (rewrite as a literal)

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(C408)

667-667: Single quotes found but double quotes preferred

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(Q000)

669-669: Single quotes found but double quotes preferred

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669-669: Trailing whitespace

Remove trailing whitespace

(W291)

690-690: Single quotes found but double quotes preferred

Replace single quotes with double quotes

(Q000)

691-691: Unnecessary dict call (rewrite as a literal)

Rewrite as a literal

(C408)

691-691: Single quotes found but double quotes preferred

Replace single quotes with double quotes

(Q000)

693-693: Blank line contains whitespace

Remove whitespace from blank line

(W293)

712-779: Enhance String Formatting and Dictionary Usage in _plot_anisotropy.

Consider the following improvements:

Use double quotes for consistency.

Remove unnecessary dict calls.
-    fig.add_trace(go.Box(
-        y=disp_df['Displacement norm'],
-        boxpoints='all'
+    fig.add_trace(go.Box(y=disp_df["Displacement norm"], boxpoints="all")
-                mode="markers", 
-                marker=dict(
-                    size=10,
-                    opacity=0.5,
-                    color=anisotropy_info_df["the_longest_radius"],  # Set color according to column "a"
-                    colorscale='rainbow',
-                    colorbar=dict(
-                        title=f'The longest radius of ellipsoid',
-                        titleside='right'
+                mode="markers",
+                marker={
+                    "size": 10,
+                    "opacity": 0.5,
+                    "color": anisotropy_info_df["the_longest_radius"],  # Set color according to column "a"
+                    "colorscale": "rainbow",
+                    "colorbar": {
+                        "title": "The longest radius of ellipsoid",
+                        "titleside": "right"
Tools

Ruff

713-713: Trailing whitespace

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714-714: f-string without any placeholders

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714-714: Trailing whitespace

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715-715: f-string without any placeholders

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715-715: Single quotes found but double quotes preferred

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720-720: Single quotes found but double quotes preferred

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721-721: Single quotes found but double quotes preferred

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727-727: Single quotes found but double quotes preferred

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728-728: Single quotes found but double quotes preferred

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728-728: Single quotes found but double quotes preferred

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728-728: Line too long (119 > 107)

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732-732: Trailing whitespace

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737-737: Line too long (131 > 107)

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738-738: Line too long (179 > 107)

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739-739: Blank line contains whitespace

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741-741: Trailing whitespace

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742-742: Trailing whitespace

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743-743: Trailing whitespace

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744-753: Unnecessary dict call (rewrite as a literal)

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748-748: Single quotes found but double quotes preferred

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(Q000)

749-752: Unnecessary dict call (rewrite as a literal)

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750-750: f-string without any placeholders

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(F541)

750-750: Single quotes found but double quotes preferred

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(Q000)

751-751: Single quotes found but double quotes preferred

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(Q000)

755-755: Single quotes found but double quotes preferred

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758-758: Blank line contains whitespace

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(W293)

761-761: Trailing whitespace

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762-762: Trailing whitespace

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(W291)

763-763: Single quotes found but double quotes preferred

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(Q000)

763-763: Trailing whitespace

Remove trailing whitespace

(W291)

764-764: Unnecessary dict call (rewrite as a literal)

Rewrite as a literal

(C408)

764-764: Single quotes found but double quotes preferred

Replace single quotes with double quotes

(Q000)

764-764: Single quotes found but double quotes preferred

Replace single quotes with double quotes

(Q000)

765-765: Single quotes found but double quotes preferred

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(Q000)

770-770: Single quotes found but double quotes preferred

Replace single quotes with double quotes

(Q000)

770-770: Line too long (222 > 107)

(E501)

770-770: Unnecessary dict call (rewrite as a literal)

Rewrite as a literal

(C408)

770-770: Unnecessary dict call (rewrite as a literal)

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(C408)

770-770: Single quotes found but double quotes preferred

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(Q000)

771-771: Single quotes found but double quotes preferred

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(Q000)

771-771: Line too long (237 > 107)

(E501)

771-771: Unnecessary dict call (rewrite as a literal)

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(C408)

771-771: Unnecessary dict call (rewrite as a literal)

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(C408)

771-771: Single quotes found but double quotes preferred

Replace single quotes with double quotes

(Q000)

777-777: Single quotes found but double quotes preferred

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(Q000)

Review details

Configuration used: CodeRabbit UI
Review profile: CHILL

Commits

Files that changed from the base of the PR and between a696129 and 74a523d.

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Files selected for processing (27)

CHANGELOG.rst (1 hunks)
README.md (2 hunks)
docs/Dev_ToDo.md (3 hunks)
docs/Future_ToDo.md (1 hunks)
docs/Installation.rst (1 hunks)
docs/Tips.rst (2 hunks)
docs/Troubleshooting.rst (2 hunks)
docs/docs_requirements.txt (2 hunks)
docs/index.rst (3 hunks)
doped/VASP_sets/DefectSet.yaml (1 hunks)
doped/init.py (1 hunks)
doped/analysis.py (27 hunks)
doped/core.py (18 hunks)
doped/corrections.py (13 hunks)
doped/generation.py (12 hunks)
doped/thermodynamics.py (30 hunks)
doped/utils/displacements.py (3 hunks)
doped/utils/eigenvalues.py (10 hunks)
doped/utils/parsing.py (9 hunks)
doped/utils/plotting.py (1 hunks)
doped/utils/supercells.py (6 hunks)
doped/utils/symmetry.py (7 hunks)
doped/vasp.py (22 hunks)
examples/generation_tutorial.ipynb (1 hunks)
examples/parsing_tutorial.ipynb (4 hunks)
examples/thermodynamics_tutorial.ipynb (5 hunks)
pyproject.toml (2 hunks)

Files skipped from review due to trivial changes (4)

CHANGELOG.rst
docs/Installation.rst
doped/VASP_sets/DefectSet.yaml
doped/utils/plotting.py

Additional context used

LanguageTool

docs/Future_ToDo.md

[grammar] ~89-~89: Did you mean “as”?
Context: ...e corrections for the eigenvalue plots, like shown in 10.1103/PhysRevB.109.054106? ...

(LIKE_SHOWN_TO_AS_SHOWN)

docs/Dev_ToDo.md

[uncategorized] ~91-~91: You might be missing the article “the” here.
Context: ... above - Note in chempots tutorial that LaTeX table generator website can also be use...

(AI_EN_LECTOR_MISSING_DETERMINER_THE)

Ruff

doped/utils/displacements.py

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Additional comments not posted (76)

docs/docs_requirements.txt (1)

1-5: LGTM! Dependency version updates are appropriate.

The addition of minimum version constraints and a new dependency ensures compatibility and functionality improvements.

pyproject.toml (3)

24-24: Dependency Update: pymatgen

The pymatgen dependency has been updated to version 2024.5.31. Ensure that all parts of the codebase using pymatgen are compatible with this version, especially considering the breaking changes related to VaspInputSet.

44-44: Dependency Update: pytest

The pytest version constraint has been relaxed to >=8.3. Verify that all test cases are compatible with this version, especially if there were any specific issues with memory usage in CI environments.

46-46: New Dependency: mp-api

The mp-api package has been added to the test dependencies. Ensure that the tests requiring this package are correctly configured and that its inclusion doesn't introduce any conflicts.

docs/Troubleshooting.rst (1)

79-79: Simplified Troubleshooting for spglib

The instructions for resolving spglib errors have been simplified to suggest updating to spglib>=2.5. This change makes the process more straightforward for users.

README.md (2)

57-60: Streamlined Installation Instructions

The installation instructions have been simplified by removing specific spglib installation commands. This change reduces complexity for users.

61-64: Updated Citations

New citations have been added to the "Studies using doped" section. These additions enhance the documentation's relevance and provide users with more resources.

docs/index.rst (2)

92-93: New Citation Added

A new citation for Quadir et al. has been added. This enhances the comprehensiveness of the literature review.

95-98: Citation Updates

Existing citations have been updated with hyperlinks and standardized formats, improving accessibility and accuracy.

docs/Dev_ToDo.md (1)

Line range hint 3-91: LGTM!

The task updates and additions improve clarity and focus on development priorities.

Tools

LanguageTool

[grammar] ~17-~17: If ‘want’ is used as a verb, it usually requires the infinitive.
Context: ...a of the AiiDA-defects preprint, want plotting tools like this - Kumagai GKFO and CC d...

(AFFORD_VBG)

[typographical] ~20-~20: Except for inverted sentences, ‘Can we’ requires a question mark at the end of the sentence.
Context: ...defect-structures) – seems quite useful tbf ## Housekeeping - Tutorials general st...

(MD_PRP_QUESTION_MARK)

Markdownlint

20-20: null
Bare URL used

(MD034, no-bare-urls)

doped/corrections.py (7)

50-50: Import PathLike improves type handling.

The addition of PathLike from pymatgen.util.typing enhances flexibility for file path inputs.

102-103: Refactor improves flexibility with PathLike.

Renaming the function to _check_if_pathlike_and_get_pmg_obj and using PathLike instead of str allows for more flexible path handling.

120-126: Update to PathLike enhances input flexibility.

Changing parameters to accept PathLike objects improves the function's flexibility and integration with different file systems.

201-202: Consistent use of _check_if_pathlike_and_get_pmg_obj.

The consistent use of the updated function ensures robust handling of path-like objects across the codebase.

317-322: PathLike support extends to Kumagai correction.

The changes to get_kumagai_correction to accept PathLike objects improve the function's usability with different path representations.

Line range hint 503-513: Improved error handling with warnings.warn.

Replacing ValueError with warnings.warn provides more informative feedback without halting execution, enhancing user experience.

539-542: Warning for lattice mismatch is user-friendly.

Using warnings.warn for lattice mismatches provides a non-blocking way to alert users about potential issues with the correction's reliability.

doped/utils/eigenvalues.py (4)

22-22: Import PathLike enhances type handling.

The addition of PathLike from pymatgen.util.typing improves flexibility for file path inputs.

188-193: PathLike support in _parse_procar improves flexibility.

Updating the function to accept PathLike objects allows for more flexible handling of file paths.

215-216: Enhanced flexibility for get_band_edge_info.

Changing parameters to accept PathLike objects improves the function's usability with different path representations.

386-389: PathLike support extends to get_eigenvalue_analysis.

The changes to accept PathLike objects improve the function's flexibility and integration with different file systems.

doped/utils/supercells.py (3)

Line range hint 184-220: New rms parameter adds flexibility to cell_metric.

The addition of the rms parameter allows users to choose between RMS and MSD calculations, enhancing flexibility and performance.

301-303: Performance optimization in _P_matrix_sorting_func.

Setting rms=False in cell_metric calls optimizes performance by avoiding unnecessary RMS calculations.

789-791: Improved efficiency in find_optimal_cell_shape.

The use of rms=False in cell_metric calls enhances performance by skipping RMS calculations when not needed.

docs/Tips.rst (1)

468-482: Shift to compressed JSON files improves storage efficiency.

Updating file extensions to .json.gz reduces file sizes and enhances storage efficiency. Ensure users are aware of the new format.

doped/utils/displacements.py (2)

37-55: Improved Type Annotations and Documentation.

The addition of type annotations and enhanced docstrings improves code clarity and maintainability. The function's logic appears sound.

269-297: Enhanced Type Safety and Clarity.

The update to type annotations and the change of style_file to PathLike improve code clarity and type safety. The logic of the function remains consistent with its intended purpose.

doped/utils/parsing.py (5)

Line range hint 101-123: Type Annotation Update for get_vasprun.

The change to PathLike for vasprun_path enhances type safety and clarity. The function logic remains consistent with its purpose.

Line range hint 125-137: Type Annotation Update for get_locpot.

The update to PathLike for locpot_path improves type safety and clarity. The function logic is correct and remains unchanged.

Line range hint 140-152: Type Annotation Update for get_outcar.

The update to PathLike for outcar_path enhances type safety and clarity. The function logic remains consistent with its intended purpose.

Line range hint 155-195: Type Annotation Update for get_procar.

The update to PathLike for procar_path improves type safety and clarity. The function logic is correct and remains unchanged.

Line range hint 197-214: Type Annotation Updates for _get_output_files_and_check_if_multiple.

The updates to PathLike for output_file and path enhance type safety and clarity. The function logic remains consistent with its intended purpose.

doped/utils/symmetry.py (1)

554-589: Enhanced Flexibility and Documentation for get_primitive_structure.

The updated function signature to accept either a SpacegroupAnalyzer or a Structure object increases flexibility. The expanded docstring improves clarity and usability.

doped/core.py (9)

175-189: LGTM: Updated to_json method in DefectEntry.

The change to use PathLike for the filename parameter enhances flexibility in handling file paths. The docstring is updated accordingly.

194-201: LGTM: Updated from_json method in DefectEntry.

The use of PathLike for the filename parameter is a good improvement for handling file paths. The docstring is updated to reflect this change.

291-298: LGTM: Updated get_freysoldt_correction method in DefectEntry.

The use of PathLike for file path parameters ensures consistent and flexible file handling. The docstring updates are accurate.

421-427: LGTM: Updated get_kumagai_correction method in DefectEntry.

The transition to PathLike for file path parameters enhances flexibility. The docstring is updated to reflect these changes.

557-560: LGTM: Updated _load_and_parse_eigenvalue_data method in DefectEntry.

The use of PathLike for file path parameters is consistent with the overall improvements in file handling. The docstring changes are appropriate.

701-705: LGTM: Updated get_eigenvalue_analysis method in DefectEntry.

The transition to PathLike for file path parameters is a beneficial update. The docstring is updated to reflect these changes.

Line range hint 1291-1312: LGTM: Updated plot_site_displacements method in DefectEntry.

The use of PathLike for the mpl_style_file parameter enhances flexibility. The docstring changes are accurate.

1944-1958: LGTM: Updated to_json method in Defect.

The use of PathLike for the filename parameter enhances flexibility in handling file paths. The docstring is updated accordingly.

1965-1970: LGTM: Updated from_json method in Defect.

The change to use PathLike for the filename parameter is consistent with improved file handling practices. The docstring reflects this update.

doped/generation.py (8)

149-153: LGTM: Updated closest_site_info function with type hints.

The addition of type hints enhances readability and maintainability. The function logic is unchanged.

235-240: LGTM: Updated get_defect_name_from_defect function with type hints.

The addition of type hints enhances readability and maintainability. The function logic is consistent.

411-415: LGTM: Updated name_defect_entries function with type hints.

The addition of type hints enhances readability and maintainability. The function logic is unchanged.

2001-2019: LGTM: Updated to_json method in DefectsGenerator.

The use of PathLike for the filename parameter enhances flexibility in handling file paths. The docstring is updated accordingly.

2024-2031: LGTM: Updated from_json method in DefectsGenerator.

The change to use PathLike for the filename parameter is consistent with improved file handling practices. The docstring reflects this update.

2183-2183: LGTM: Updated _first_and_second_element function with type hint.

The addition of a type hint enhances readability. The function logic is unchanged.

2200-2202: LGTM: Updated _sort_defect_entries function with type hints.

The addition of type hints enhances readability and maintainability. The function logic is consistent.

Line range hint 2284-2294: LGTM: Updated _sort_defects function with type hints.

The addition of type hints enhances readability and maintainability. The function logic is unchanged.

doped/vasp.py (9)

Line range hint 485-499: Good use of PathLike for output_path.

Changing output_path to PathLike enhances flexibility in handling file paths across different operating systems.

1252-1254: Good use of PathLike for path parameters.

Updating defect_dir and subfolder to PathLike enhances the flexibility and compatibility of file path handling.

Line range hint 275-275: Efficient use of compressed JSON files.

Switching to .json.gz for JSON files improves storage efficiency and is a good practice for handling potentially large datasets.

1279-1280: Good use of PathLike for path parameters.

Using PathLike for defect_dir and subfolder enhances the flexibility and compatibility of file path handling.

1368-1369: Good use of PathLike for path parameters.

Updating defect_dir and subfolder to PathLike enhances the flexibility and compatibility of file path handling.

1469-1470: Good use of PathLike for path parameters.

Using PathLike for defect_dir and subfolder enhances the flexibility and compatibility of file path handling.

1577-1578: Good use of PathLike for path parameters.

Updating defect_dir and subfolder to PathLike enhances the flexibility and compatibility of file path handling.

1684-1684: Good use of PathLike for path parameters.

Using PathLike for defect_dir enhances the flexibility and compatibility of file path handling.

2167-2167: Good use of PathLike for path parameters.

Updating output_path to PathLike enhances the flexibility and compatibility of file path handling.
doped/analysis.py (7)
167-171: Type annotations enhance clarity and safety.

The addition of type annotations improves the function's usability by clearly defining expected input types.

348-349: Type annotations improve function clarity.

The addition of type annotations for bulk_structure and defect_structure enhances the function's clarity and type safety.

2244-2250: Type annotations improve function robustness.

The use of PathLike and Optional types enhances the function's clarity and robustness, ensuring correct type usage.

1381-1383: PathLike and Optional types enhance function robustness.

The use of PathLike for path parameters and Optional for optional parameters improves the function's robustness and reduces potential errors.

371-378: PathLike and Optional types improve robustness.

The use of PathLike for path parameters and Optional for optional parameters enhances the function's robustness and reduces potential runtime errors.

Ensure all calls to defect_entry_from_paths match the updated signature.

Verification successful

Function Calls Match Updated Signature

The calls to defect_entry_from_paths in the codebase align with the updated function signature, ensuring compatibility and robustness.

Instances in tests/test_plotting.py and tests/test_corrections.py show correct usage of the updated parameters.
Scripts executed

The following scripts were executed for the analysis:

Script:
#!/bin/bash
# Description: Verify all function calls to `defect_entry_from_paths` match the new signature.

# Test: Search for the function usage. Expect: Only occurrences of the new signature.
rg --type python -A 5 $'defect_entry_from_paths'
Length of output: 78

Script:
#!/bin/bash
# Description: Verify all function calls to `defect_entry_from_paths` match the new signature.

# Test: Search for the function usage. Expect: Only occurrences of the new signature.
rg 'defect_entry_from_paths' -A 5
Length of output: 22974
1486-1495: PathLike and Optional types improve function robustness.

The use of PathLike for path parameters and Optional for optional parameters enhances the function's robustness and reduces potential errors.

Ensure all calls to DefectParser.from_paths match the updated signature.

464-472: PathLike and Optional types enhance constructor robustness.

The use of PathLike for path parameters and Optional for optional parameters in the constructor improves the class's robustness and reduces potential errors.

Ensure all instantiations of DefectsParser match the updated constructor signature.
doped/thermodynamics.py (10)
679-691: JSON deserialization looks good! Verify PathLike handling.

The method correctly loads an object from a JSON file. Ensure that PathLike type handling is consistent across the codebase.

You may want to verify that PathLike is used consistently in other methods that handle file paths.

3227-3241: FermiDos creation looks good! Verify input type handling.

The method correctly creates a FermiDos object from a PathLike or Vasprun. Ensure type handling and conversion logic are consistent across the codebase.

You may want to verify that input type handling is consistent in other methods that create or manipulate FermiDos objects.

Line range hint 2458-2568: Plotting logic looks good! Verify PathLike handling and plotting robustness.

The method correctly generates a plot of defect formation energies. Ensure PathLike handling is consistent and the plotting logic is robust.

You may want to verify that PathLike is used consistently and that the plotting logic handles all expected scenarios.

194-226: LGTM! Verify the usage of raw_energy_from_chempots.

The function correctly calculates raw energy and includes necessary input validation. Ensure that all calls to this function handle exceptions appropriately.

You may want to verify that this function is used correctly throughout the codebase.

656-674: JSON serialization looks good! Verify PathLike handling.

The method correctly saves the object as a JSON file. Ensure that PathLike type handling is consistent across the codebase.

You may want to verify that PathLike is used consistently in other methods that handle file paths.

Verification successful

Let's correct the file type in the search command and try again.

Consistent PathLike Usage Across Codebase

The usage of PathLike is consistent across various modules in the codebase. It is used appropriately in function signatures and type annotations for handling file paths. Here are some key observations:

PathLike is imported from pymatgen.util.typing and used across multiple files such as doped/corrections.py, doped/generation.py, doped/vasp.py, and others.

It is consistently used in method parameters and type annotations for file paths, ensuring uniformity in how file paths are handled.

No issues were found with the usage of PathLike. The implementation appears to be consistent and correct.
Scripts executed

The following scripts were executed for the analysis:

Script:
#!/bin/bash
# Description: Verify `PathLike` handling in methods dealing with file paths.

# Test: Search for `PathLike` usage. Expect: Consistent type handling across the codebase.
rg --type python -A 5 $'PathLike'
Length of output: 63

Script:
#!/bin/bash
# Description: Verify `PathLike` handling in methods dealing with file paths.

# Test: Search for `PathLike` usage. Expect: Consistent type handling across the codebase.
rg --type py -A 5 $'PathLike'
Length of output: 62662
Line range hint 1471-1547: Equilibrium Fermi level calculation looks good! Verify calculation logic.

The method correctly calculates the equilibrium Fermi level. Ensure the calculation logic handles all edge cases effectively.

You may want to verify that the calculation logic is robust and handles all expected scenarios.

Line range hint 433-577: Initialization looks good! Verify check_compatibility usage.

The constructor initializes attributes correctly, including the new check_compatibility property. Ensure this property is used consistently across the class.

You may want to verify that check_compatibility is used appropriately throughout the class methods.

Verification successful

Let's correct the previous script and search for the usage of check_compatibility in Python files.

Consistent Usage of check_compatibility Confirmed

The check_compatibility attribute is used consistently across the DefectThermodynamics class to conditionally perform compatibility checks on bulk entries and chemical potentials. This ensures that compatibility checks are only executed when the attribute is set to True.

The attribute is initialized and used to control the execution of methods like _check_bulk_compatibility and _check_bulk_chempots_compatibility.
Scripts executed

The following scripts were executed for the analysis:

Script:
#!/bin/bash
# Description: Verify the usage of `check_compatibility` in `DefectThermodynamics`.

# Test: Search for the usage of `check_compatibility`. Expect: Consistent usage across the class.
rg --type python -A 5 $'self.check_compatibility'
Length of output: 79

Script:
#!/bin/bash
# Description: Verify the usage of `check_compatibility` in `DefectThermodynamics`.

# Test: Search for the usage of `check_compatibility`. Expect: Consistent usage across the class.
rg 'self\.check_compatibility' --glob '*.py' -A 5
Length of output: 2265
1007-1054: Compatibility check logic looks good! Verify robustness.

The method correctly checks the compatibility of chemical potentials with the bulk supercell. Ensure the logic is robust and handles edge cases effectively.

You may want to verify that the compatibility check logic is robust and handles all expected scenarios.

Line range hint 587-612: Sorting and parsing logic looks good! Verify logic consistency.

The method correctly sorts defect entries and parses transition levels. Ensure the sorting and parsing logic is consistent with the rest of the class.

You may want to verify that the sorting and parsing logic aligns with the intended behavior.

Verification successful

Sorting and Parsing Logic Verified:

The sorting and parsing logic in _sort_parse_and_check_entries aligns with the intended behavior. The _rename_key_and_dicts function ensures unique key names, while _sort_defect_entries provides deterministic sorting, both crucial for the method's functionality. No issues found with the current implementation.

_rename_key_and_dicts ensures unique dictionary keys.

_sort_defect_entries sorts entries deterministically.
Scripts executed

The following scripts were executed for the analysis:

Script:
#!/bin/bash
# Description: Verify the sorting and parsing logic in `_sort_parse_and_check_entries`.

# Test: Check for consistency in sorting and parsing logic. Expect: Logic aligns with class behavior.
rg --type python -A 5 $'_sort_parse_and_check_entries'
Length of output: 84

Script:
#!/bin/bash
# Description: Verify the sorting and parsing logic in `_sort_parse_and_check_entries`.

# Test: Check for consistency in sorting and parsing logic. Expect: Logic aligns with class behavior.
rg --type py -A 5 $'_sort_parse_and_check_entries'
Length of output: 1502

Script:
#!/bin/bash
# Description: Search for the definitions of `_rename_key_and_dicts` and `_sort_defect_entries` to verify their logic.

# Test: Ensure the sorting and renaming logic aligns with the intended behavior.
rg --type py 'def _rename_key_and_dicts'
rg --type py 'def _sort_defect_entries'
Length of output: 181

Script:
#!/bin/bash
# Description: Extract the implementation of `_rename_key_and_dicts` from `doped/utils/plotting.py`.

# Extract the function implementation.
rg --type py -A 10 'def _rename_key_and_dicts' doped/utils/plotting.py
Length of output: 468

Script:
#!/bin/bash
# Description: Extract the implementation of `_sort_defect_entries` from `doped/generation.py`.

# Extract the function implementation.
rg --type py -A 10 'def _sort_defect_entries' doped/generation.py
Length of output: 637
Line range hint 1627-1769: Quenched Fermi level calculation looks good! Verify annealing logic.

The method correctly calculates the quenched Fermi level and concentrations. Ensure the annealing and quenching logic handles all edge cases effectively.

You may want to verify that the annealing and quenching logic is robust and handles all expected scenarios.

Verification successful

Quenched Fermi level calculation logic verified!

The get_quenched_fermi_level_and_concentrations function's implementation and documentation confirm that it correctly handles the annealing and quenching processes. The logic for fixing total concentrations at the annealing temperature and recalculating them at the quenched temperature is appropriately described and implemented.

File: doped/thermodynamics.py

Function: get_quenched_fermi_level_and_concentrations
Scripts executed

The following scripts were executed for the analysis:

Script:
#!/bin/bash
# Description: Verify the robustness of `get_quenched_fermi_level_and_concentrations`.

# Test: Check for edge cases in annealing and quenching logic. Expect: Robust handling of all scenarios.
rg --type python -A 5 $'get_quenched_fermi_level_and_concentrations'
Length of output: 98

Script:
#!/bin/bash
# Description: Search for the `get_quenched_fermi_level_and_concentrations` function definition and its context.

# Corrected command to search for the function definition in Python files.
rg 'def get_quenched_fermi_level_and_concentrations' -A 50
Length of output: 4183

kavanase · 2024-08-20T16:27:11Z

@teruya7 I have moved this PR to #87 so that it's in a doped branch (displacements2) meaning we can all contribute 😃

coderabbitai · 2024-08-20T16:27:31Z

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teruya7 added 2 commits August 12, 2024 14:13

added print function

55974b7

added calc_displacements_ellipsoid function

74a523d

coderabbitai bot reviewed Aug 20, 2024

View reviewed changes

kavanase changed the base branch from main to develop August 20, 2024 15:55

SMTG-Bham deleted a comment from coderabbitai bot Aug 20, 2024

kavanase closed this Aug 20, 2024

kavanase added the enhancement New feature or request label Aug 20, 2024

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Add calc_displacements_ellipsoid function #86

Add calc_displacements_ellipsoid function #86

teruya7 commented Aug 20, 2024

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Add calc_displacements_ellipsoid function #86

Add calc_displacements_ellipsoid function #86

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kavanase commented Aug 20, 2024

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