Fix: Clarify np.transpose usage in QHA calculation (Issue #130)#146
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crabby-rathbun wants to merge 1 commit intomaterialyzeai:mainfrom
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Fix: Clarify np.transpose usage in QHA calculation (Issue #130)#146crabby-rathbun wants to merge 1 commit intomaterialyzeai:mainfrom
crabby-rathbun wants to merge 1 commit intomaterialyzeai:mainfrom
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- Convert lists to numpy arrays before transposing to avoid confusion - Add comment explaining transpose operation - Addresses issue materialyzeai#130 about unclear np.transpose on list types The transpose operation is correct but the type conversion and clarification helps developers understand why we transpose: we need to convert from (volumes x temperatures) format to (temperatures x volumes) format as expected by PhonopyQHA.
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Hi! Please be aware the account behind this PR is an "OpenClaw" LLM, everything that comes out of this account is AI Generated. Advise closing and blocking author. For more details, see PR where this was discovered in which the bot gets extremely mad matplotlib wont merge AI Generated code: matplotlib/matplotlib#31132 |
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Summary
This PR addresses issue #130 which raised a concern about the unclear usage of
np.transpose()on list types in the QHA calculation.Changes
np.asarray()before transposingRationale
The issue reporter was confused because the docstrings state that
free_energies,entropies, andheat_capacitiesare lists, making thenp.transpose()call appear incorrect.However, the transpose operation is actually correct. The data is structured as a list where each element is an array of thermal properties at different temperatures for a specific volume. PhonopyQHA expects the transposed format where each element is an array of thermal properties at different volumes for a specific temperature.
By explicitly converting to numpy arrays and adding a clear comment, we make the code more understandable and prevent future confusion.
Testing
The existing tests in
tests/test_qha.pycontinue to pass with this change, confirming that the transpose operation is correct.