bug: fix numerical diff in DPA1 dotr between DP/PT

[iProzd]

Summary by CodeRabbit

• Bug Fixes
  • Improved stability in calculations by handling potential division by zero errors.

[coderabbitai]

Walkthrough

Walkthrough

The update involves a modification in the call method within the dpa1.py file, specifically enhancing the stability of a division operation. This is achieved by incorporating the np.maximum function to prevent division by zero or extremely small numbers during the normalization process of a matrix.

Changes

File Path	Change Summary
.../descriptor/dpa1.py	Added np.maximum in the calculation of input_r to ensure stability in division by avoiding small denominators.

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Recent Review Details

Configuration used: CodeRabbit UI
Review profile: CHILL

Commits

Files that changed from the base of the PR and between 49f17cc and 3a34c56.

Files selected for processing (1)

• deepmd/dpmodel/descriptor/dpa1.py (1 hunks)

Additional comments not posted (1)

deepmd/dpmodel/descriptor/dpa1.py (1)

508-512: The modification to input_r calculation enhances numerical stability by preventing division by near-zero values.

Verification successful

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The changes to the input_r calculation in the DescrptDPA1 class have been successfully verified. The new method using np.maximum is correctly implemented in dpa1.py, and the old division method has been completely replaced across the codebase. The module is actively used in several test files, ensuring that the changes are integrated and tested.

• source/tests/pt/model/test_dpa1.py
• source/tests/consistent/descriptor/test_dpa1.py
• source/tests/common/dpmodel/test_descriptor_hybrid.py

Scripts Executed

The following scripts were executed for the analysis:

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Script:

#!/bin/bash
# Test: Search to find files that import dpa1 module. Expect: Matches.
rg -C3 --type python $'from deepmd.dpmodel.descriptor.dpa1'
# Test: Search old division method to find omissions. Expect: No matches.
ast-grep --lang python --pattern $'dmatrix.reshape(-1, nnei, 4)[:, :, 1:4] / np.linalg.norm(dmatrix.reshape(-1, nnei, 4)[:, :, 1:4], axis=-1, keepdims=True)'
# Test: Search new division method to validate usage. Expect: Matches.
ast-grep --lang python --pattern $'dmatrix.reshape(-1, nnei, 4)[:, :, 1:4] / np.maximum(np.linalg.norm(dmatrix.reshape(-1, nnei, 4)[:, :, 1:4], axis=-1, keepdims=True), 1e-12)'

Length of output: 892

---

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Script:

#!/bin/bash
# Correct file type error and search for files that import the dpa1 module. Expect: Matches.
rg -C3 --type py 'from deepmd.dpmodel.descriptor.dpa1'
# Re-run the search for the old division method to ensure it has been completely replaced. Expect: No matches.
ast-grep --lang python --pattern $'dmatrix.reshape(-1, nnei, 4)[:, :, 1:4] / np.linalg.norm(dmatrix.reshape(-1, nnei, 4)[:, :, 1:4], axis=-1, keepdims=True)'

Length of output: 1629

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[njzjz]

I confirm it works!

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 82.15%. Comparing base (49f17cc) to head (3a34c56).

Additional details and impacted files

@@           Coverage Diff           @@
##            devel    #3725   +/-   ##
=======================================
  Coverage   82.15%   82.15%           
=======================================
  Files         511      511           
  Lines       47364    47364           
  Branches     2953     2955    +2     
=======================================
  Hits        38910    38910           
  Misses       7561     7561           
  Partials      893      893           

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