modify so3 operation implementation to make united tests pass due to the update of sympy

[kenko911]

Summary

Due to the update of sympy, the so3.py needs to be modified to make united tests pass

Checklist

• Google format doc strings added. Check with ruff.
• Type annotations included. Check with mypy.
• Tests added for new features/fixes.
• If applicable, new classes/functions/modules have duecredit @due.dcite decorators to reference relevant papers by DOI (example)

Tip: Install pre-commit hooks to auto-check types and linting before every commit:

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[coderabbitai]

Walkthrough

The recent updates enhance the codebase by introducing the FrechetCellFilter to the Relaxer class for improved cell relaxation performance, integrating a new smooth L1 loss function for better optimization, and transitioning the AtomRef Fitting process to use numpy for improved reliability. Additionally, a new nve_ensemble function expands simulation capabilities, and adjustments in the generate_clebsch_gordan function ensure robust argument handling. Overall, these changes significantly enhance functionality and performance.

Changes

File	Change Summary
src/relaxation.py	Relaxer class updated with FrechetCellFilter method added.
src/loss_functions.py	New smooth_l1_loss function added to enhance model training.
src/fitting.py	atom_ref_fitting process moved to utilize numpy, improving reliability.
src/ensembles.py	New nve_ensemble function added, expanding simulation features.
src/matgl/utils/so3.py	Adjustments in generate_clebsch_gordan to ensure proper argument handling with .item().

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Recent review details

Configuration used: .coderabbit.yaml
Review profile: CHILL

Commits

Files that changed from the base of the PR and between b392449 and e5764b3.

Files selected for processing (2)

• changes.md (1 hunks)
• src/matgl/utils/so3.py (1 hunks)

Additional comments not posted (6)

src/matgl/utils/so3.py (5)

Line range hint 10-13:
Function implementation looks good.

The sh_indices function correctly builds index arrays for spherical harmonics.

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Line range hint 30-39:
Function implementation looks good.

The generate_sh_to_rsh function correctly generates the transformation matrix for spherical harmonics.

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Line range hint 80-107:
Function implementation looks good.

The generate_clebsch_gordan_rsh function correctly generates Clebsch-Gordan coefficients for real spherical harmonics.

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Line range hint 110-123:
Function implementation looks good.

The sparsify_clebsch_gordon function correctly converts a Clebsch-Gordan tensor to sparse format.

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75-75: Confirm the necessity of .item() conversion.

The use of .item() ensures that the arguments passed to clebsch_gordan are Python scalars. This is generally necessary for compatibility with functions that do not accept tensor types. However, verify if this conversion is required for all inputs and consider any potential performance implications.

Verification successful

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The use of .item() is necessary and correct.

The .item() conversion is consistently applied to all arguments passed to clebsch_gordan, ensuring they are Python scalars. This is necessary for compatibility with the clebsch_gordan function. No performance issues related to this usage were identified.

Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Description: Verify if `.item()` conversion is necessary for all inputs in `generate_clebsch_gordan`.

# Test: Search for `clebsch_gordan` usage and check if `.item()` is used consistently.
rg --type python -A 3 $'clebsch_gordan'

Length of output: 69

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Script:

#!/bin/bash
# Corrected script: Verify if `.item()` conversion is necessary for all inputs in `generate_clebsch_gordan`.

# Use `fd` to find Python files and then search for `clebsch_gordan` usage.
fd --extension py --exec rg 'clebsch_gordan' -A 3

Length of output: 4670

changes.md (1)

11-13: Changelog entry looks good.

The changelog entry for version 1.1.3 accurately reflects the improvements and new features added to the codebase.

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