Feature: substitute "wll" with svd method inferring nzeta #99
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📝 Walkthrough📝 WalkthroughWalkthroughThe changes in this pull request enhance the spillage optimization algorithm by modifying the Changes
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Actionable comments posted: 6
🧹 Outside diff range and nitpick comments (3)
SIAB/spillage/lcao_wfc_analysis.py (2)
155-163: Improve code readability with additional comments and variable explanations.The nested loops and indexing in
_wfc_reinterpand_svdlzare complex. Adding comments to explain the purpose of variables likemu,stride, and the reshaping logic can enhance maintainability and help future developers understand the code.Also applies to: 247-265
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157-157: Ambiguous variable name:
l(E741)
170-172: Simplify scaling factor application in SVD computation.Currently, the scaling factor
prefis calculated based onl_isotropand applied after computing the singular values. Consider integrating this scaling directly into the SVD computation or documenting the reasoning behindpreffor clarity.SIAB/spillage/api.py (1)
1086-1097: Consider adding tests for invalidpopparameter values.To enhance test coverage, add test cases that verify the function's behavior when an invalid
popvalue is provided. This ensures that error handling works as intended.You can add a test like this:
def test_nzeta_infer_invalid_pop(self): with self.assertRaises(ValueError): nzeta = _nzeta_infer(fpath, nbnd, 'invalid_method')
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📒 Files selected for processing (2)
- SIAB/spillage/api.py (7 hunks)
- SIAB/spillage/lcao_wfc_analysis.py (5 hunks)
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🪛 Ruff
SIAB/spillage/lcao_wfc_analysis.py
84-84: Ambiguous variable name:
l(E741)
88-88: Ambiguous variable name:
l(E741)
153-153: Ambiguous variable name:
l(E741)
157-157: Ambiguous variable name:
l(E741)
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l(E741)
294-294: Ambiguous variable name:
l(E741)
314-314: Loop control variable
ntnot used within loop bodyRename unused
ntto_nt(B007)
318-318: Loop control variable
ntnot used within loop bodyRename unused
ntto_nt(B007)
318-318: Loop control variable
nznot used within loop body(B007)
320-320: Ambiguous variable name:
l(E741)
345-345: Loop control variable
ntnot used within loop bodyRename unused
ntto_nt(B007)
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ntnot used within loop bodyRename unused
ntto_nt(B007)
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🔇 Additional comments (7)
SIAB/spillage/api.py (7)
651-651: Ensure consistency of thepopparameter usage in_nzeta_infer.In line 651, the
_nzeta_inferfunction is called with'wll'as thepopparameter, while its default value is'svd'. Please verify that this intentional usage aligns with the desired behavior across the codebase.
656-656: Function_nzeta_infercorrectly updated withpopparameter.The function now accepts an additional
popparameter with a default value'svd', enhancing its flexibility for different population analysis methods.
668-670: Docstring appropriately updated for the newpopparameter.The added documentation clearly describes the purpose of the
popparameter, the accepted values'svd'or'wll', and its default setting.
680-681: Necessary imports added for population analysis methods.The functions
_wlland_svdlzare correctly imported fromSIAB.spillage.lcao_wfc_analysisto support the new functionality.
682-687: Kernel functions defined for dynamic population analysis method selection.The
_wll_kerneland_svd_kernelfunctions are properly defined, and theinfer_kerneldictionary allows for dynamic method selection based on thepopparameter.
719-719: Function_nzeta_inferreturnsnzetacorrectly.The function concludes by returning the calculated
nzetaarray as expected.
1016-1032: Test cases updated to cover both'wll'and'svd'methods.Including tests for both population analysis methods ensures that the new functionality is properly validated and existing functionality remains unaffected.
…gular Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com>
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Actionable comments posted: 1
🧹 Outside diff range and nitpick comments (4)
SIAB/spillage/lcao_wfc_analysis.py (4)
50-95: LGTM! New function_wfc_reinterplooks good.The implementation of
_wfc_reinterpis well-structured and efficiently written. It provides a clear docstring explaining its purpose and parameters. The function correctly reinterprets wavefunction coefficients based on the specified view.Consider using
isinstance(nbands, str)instead ofnbands == 'all'for more robust type checking:-nbands = nbands_max if nbands == 'all' else nbands +nbands = nbands_max if isinstance(nbands, str) and nbands.lower() == 'all' else nbandsThis change would handle cases where
nbandsmight be a different string value or a non-string type more gracefully.🧰 Tools
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84-84: Ambiguous variable name:
l(E741)
88-88: Ambiguous variable name:
l(E741)
97-179: LGTM! Updates to_svdlzfunction enhance its functionality.The changes to
_svdlzfunction, including the addition of thereinterp_viewparameter and the use of Cholesky decomposition for orthogonalization, improve its functionality and performance. The integration with the new_wfc_reinterpfunction is well-implemented.For consistency with the
_wfc_reinterpfunction, consider updating the assertion forreinterp_view:-assert reinterp_view in ['decompose', 'reduce'] +assert reinterp_view in ['decompose', 'reduce'], f"Invalid reinterp_view '{reinterp_view}'. Expected 'decompose' or 'reduce'."This change would provide a more informative error message if an invalid value is passed.
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154-154: Ambiguous variable name:
l(E741)
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170-170: Ambiguous variable name:
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216-298: LGTM! Comprehensive test method for_wfc_reinterp.The
test_wfc_reinterpmethod provides thorough testing for the new_wfc_reinterpfunction. It covers both 'decompose' and 'reduce' views and checks the output shape and content in detail.Consider splitting this test method into two separate methods, one for each view ('decompose' and 'reduce'). This would improve test isolation and make it easier to identify which specific functionality fails if an issue arises:
def test_wfc_reinterp_decompose(self): # Test for 'decompose' view ... def test_wfc_reinterp_reduce(self): # Test for 'reduce' view ...This change would make the tests more modular and easier to maintain.
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263-263: Ambiguous variable name:
l(E741)
295-295: Ambiguous variable name:
l(E741)
315-315: Consider renaming unused loop variables.There are several instances where loop variables are unused within the loop body. While this doesn't affect functionality, renaming these variables to underscore can improve code clarity.
Consider applying the following changes:
-for i, (nt, nz) in enumerate(zip(dat['natom'], dat['nzeta'])): +for i, (_, nz) in enumerate(zip(dat['natom'], dat['nzeta'])): self.assertEqual(len(sigma[i]), len(nz)) -for i, (nt, nz) in enumerate(zip(dat['natom'], dat['nzeta'])): +for i, (_, _) in enumerate(zip(dat['natom'], dat['nzeta'])): print(f"Atom type {i+1}")This change applies to lines 315, 319, 346, and 350. It clearly indicates that these variables are intentionally unused in the loop body.
Also applies to: 319-319, 346-346, 350-350
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315-315: Loop control variable
ntnot used within loop bodyRename unused
ntto_nt(B007)
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📒 Files selected for processing (1)
- SIAB/spillage/lcao_wfc_analysis.py (5 hunks)
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📓 Learnings (1)
SIAB/spillage/lcao_wfc_analysis.py (5)
Learnt from: kirk0830 PR: kirk0830/ABACUS-ORBGEN#99 File: SIAB/spillage/lcao_wfc_analysis.py:317-317 Timestamp: 2024-10-10T01:46:08.751Z Learning: Using `return` in test methods to suppress output may skip important assertions. Instead, suppress output by temporarily redirecting `stdout` within the test method.Learnt from: kirk0830 PR: kirk0830/ABACUS-ORBGEN#99 File: SIAB/spillage/lcao_wfc_analysis.py:76-76 Timestamp: 2024-10-10T01:50:47.453Z Learning: In `SIAB/spillage/lcao_wfc_analysis.py`, the function `_wfc_reinterp` is kept for unit testing purposes, allowing testing of parts of `_svdlz` individually.Learnt from: kirk0830 PR: kirk0830/ABACUS-ORBGEN#99 File: SIAB/spillage/lcao_wfc_analysis.py:76-76 Timestamp: 2024-10-10T01:40:51.700Z Learning: In `SIAB/spillage/lcao_wfc_analysis.py`, the function `_wfc_reinterp` is no longer used, as its functionality has been moved into the `_svdlz` function.Learnt from: kirk0830 PR: kirk0830/ABACUS-ORBGEN#96 File: SIAB/spillage/api.py:783-783 Timestamp: 2024-09-29T07:56:50.811Z Learning: When `l` is used as a variable for angular momentum, do not flag it as ambiguous.Learnt from: kirk0830 PR: kirk0830/ABACUS-ORBGEN#96 File: SIAB/spillage/api.py:783-783 Timestamp: 2024-10-09T11:06:34.325Z Learning: When `l` is used as a variable for angular momentum, do not flag it as ambiguous.
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SIAB/spillage/lcao_wfc_analysis.py
84-84: Ambiguous variable name:
l(E741)
88-88: Ambiguous variable name:
l(E741)
154-154: Ambiguous variable name:
l(E741)
158-158: Ambiguous variable name:
l(E741)
170-170: Ambiguous variable name:
l(E741)
179-179: Ambiguous variable name:
l(E741)
263-263: Ambiguous variable name:
l(E741)
295-295: Ambiguous variable name:
l(E741)
315-315: Loop control variable
ntnot used within loop bodyRename unused
ntto_nt(B007)
319-319: Loop control variable
ntnot used within loop bodyRename unused
ntto_nt(B007)
319-319: Loop control variable
nznot used within loop body(B007)
321-321: Ambiguous variable name:
l(E741)
346-346: Loop control variable
ntnot used within loop bodyRename unused
ntto_nt(B007)
350-350: Loop control variable
ntnot used within loop bodyRename unused
ntto_nt(B007)
350-350: Loop control variable
nznot used within loop body(B007)
352-352: Ambiguous variable name:
l(E741)
🔇 Additional comments (1)
SIAB/spillage/lcao_wfc_analysis.py (1)
Line range hint
1-363: Overall, the changes in this file are well-implemented and improve functionality.The addition of the
_wfc_reinterpfunction and the updates to_svdlzenhance the capabilities of the module. The new test methodtest_wfc_reinterpprovides good coverage for the new functionality.Some minor improvements have been suggested:
- More robust type checking in
_wfc_reinterp.- Consistent error messaging in
_svdlz.- Splitting the
test_wfc_reinterpmethod for better test isolation.- Improving output suppression in test methods.
- Renaming unused loop variables.
These suggestions aim to further improve code clarity and maintainability.
The changes are approved with the suggested minor improvements. Great work on enhancing the functionality of this module!
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263-263: Ambiguous variable name:
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295-295: Ambiguous variable name:
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ntnot used within loop bodyRename unused
ntto_nt(B007)
319-319: Loop control variable
ntnot used within loop bodyRename unused
ntto_nt(B007)
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321-321: Ambiguous variable name:
l(E741)
346-346: Loop control variable
ntnot used within loop bodyRename unused
ntto_nt(B007)
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ntnot used within loop bodyRename unused
ntto_nt(B007)
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kirk0830
changed the title
Summary by CodeRabbit
New Features
Bug Fixes
Tests