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fix(tf): fix model out_bias deserialize #4350

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merged 3 commits into from
Nov 14, 2024

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@njzjz njzjz commented Nov 13, 2024

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Summary by CodeRabbit

  • New Features

    • Enhanced handling of model serialization and deserialization, particularly for bias parameters.
    • Updated output structure for the PT backend in the energy model tests.
  • Bug Fixes

    • Improved logic for managing unsupported model configurations, ensuring clearer error reporting.
  • Documentation

    • Updated method signatures to reflect changes in functionality for model handling and testing.

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coderabbitai bot commented Nov 13, 2024

📝 Walkthrough
📝 Walkthrough

Walkthrough

The pull request introduces changes to the Model and StandardModel classes in deepmd/tf/model/model.py, enhancing the serialization and deserialization processes, particularly for bias parameters. It updates the handling of bias_atom_e and unsupported keys, ensuring stricter checks and improved logic. Additionally, modifications are made in the TestEner class to adjust the instantiation of EnergyModelPT and the output structure for the PT backend. These changes collectively refine model parameter management and testing procedures.

Changes

File Change Summary
deepmd/tf/model/model.py - Added import for GLOBAL_NP_FLOAT_PRECISION.
- Updated deserialize method to adjust bias_atom_e and handle unsupported keys with NotImplementedError.
- Modified serialize method to reshape out_bias and reset bias_atom_e.
source/tests/consistent/model/test_ener.py - Updated pass_data_to_cls method to adjust out_bias for EnergyModelPT.
- Changed extract_ret method to return extended_force and extended_virial for the PT backend.

Possibly related PRs

Suggested reviewers

  • wanghan-iapcm

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📥 Commits

Reviewing files that changed from the base of the PR and between 4939e1e and f6538a7.

📒 Files selected for processing (1)
  • deepmd/tf/model/model.py (5 hunks)
🚧 Files skipped from review as they are similar to previous changes (1)
  • deepmd/tf/model/model.py

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Actionable comments posted: 0

🧹 Outside diff range and nitpick comments (1)
deepmd/tf/model/model.py (1)

891-892: Specify explicit data type for out_std to ensure consistency

Consider specifying the data type explicitly in the np.ones call for out_std to avoid potential issues with default data types across different NumPy versions or platforms. This enhances code portability and eliminates the need to suppress linter warnings.

Apply this diff to specify the data type and remove the linter suppression:

"out_bias": out_bias,
-    "out_std": np.ones([1, ntypes, dict_fit["dim_out"]]),  # pylint: disable=no-explicit-dtype
+    "out_std": np.ones([1, ntypes, dict_fit["dim_out"]], dtype=GLOBAL_NP_FLOAT_PRECISION)
📜 Review details

Configuration used: CodeRabbit UI
Review profile: CHILL

📥 Commits

Reviewing files that changed from the base of the PR and between 85e5e20 and 72957bb.

📒 Files selected for processing (2)
  • deepmd/tf/model/model.py (5 hunks)
  • source/tests/consistent/model/test_ener.py (1 hunks)
🔇 Additional comments (5)
source/tests/consistent/model/test_ener.py (1)

144-146: Verify test coverage for bias deserialization

The modification to increment out_bias by 1.0 appears to be testing the bias deserialization fix. However, we should ensure comprehensive test coverage.

Consider adding explicit assertions to verify:

  1. The bias value is correctly serialized
  2. The bias value is correctly deserialized
  3. The model produces expected outputs with modified bias

Example test structure:

def test_bias_serialization(self):
    # Arrange
    model = get_model_pt(data)
    original_bias = model.atomic_model.out_bias.copy()
    
    # Act
    model.atomic_model.out_bias += 1.0
    serialized = model.serialize()
    deserialized = get_model_pt(serialized)
    
    # Assert
    np.testing.assert_array_equal(
        deserialized.atomic_model.out_bias,
        original_bias + 1.0
    )
✅ Verification successful

Let me check the content of test_change_bias.py since it seems directly relevant to our verification.


Based on the review of both test files, I can now provide the final response:

Bias modification is well-tested across multiple test suites

The modification to increment out_bias by 1.0 in test_ener.py is part of a comprehensive test coverage for bias functionality, complemented by dedicated test cases in test_change_bias.py which includes:

  • Testing bias changes with data statistics
  • Testing bias changes with system files
  • Testing user-defined bias modifications
  • Proper serialization/deserialization verification

The current modification serves as an additional verification point in the cross-backend consistency tests.

🏁 Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Description: Check test coverage for bias-related functionality
# Look for other bias-related tests and verify coverage

# Search for bias-related test cases
echo "Searching for bias-related tests..."
rg -l 'out_bias|bias_atom' 'source/tests'

# Search for bias-related functionality in implementation
echo "Searching for bias implementation..."
rg -l 'out_bias|bias_atom' 'source' --glob '!tests/**'

Length of output: 3969


Script:

#!/bin/bash
# Check the content of test_change_bias.py
echo "Content of test_change_bias.py:"
cat source/tests/pt/test_change_bias.py

# Also check test_ener.py to understand the full context
echo -e "\nContent of test_ener.py:"
cat source/tests/consistent/model/test_ener.py

Length of output: 18917

deepmd/tf/model/model.py (4)

19-21: Importing GLOBAL_NP_FLOAT_PRECISION is appropriate

The import of GLOBAL_NP_FLOAT_PRECISION from deepmd.env is necessary for specifying the data type in subsequent NumPy array initializations.


812-822: Correct adjustment of bias_atom_e during deserialization

The code properly adjusts bias_atom_e by adding the reshaped out_bias during deserialization, ensuring the model variables are correctly updated without modifying the original data structures.


831-834: Explicitly handling unsupported keys enhances error reporting

By checking for non-empty atom_exclude_types and pair_exclude_types and raising NotImplementedError, the code now explicitly informs users when they attempt to use unsupported features, improving clarity and maintainability.


867-877: Proper handling of bias_atom_e and out_bias during serialization

The code correctly reshapes bias_atom_e to form out_bias, resets bias_atom_e to zeros with appropriate dimensions, and initializes out_bias when bias_atom_e is not present. This ensures consistency in the serialized model data.

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Actionable comments posted: 0

🧹 Outside diff range and nitpick comments (1)
source/tests/consistent/model/test_ener.py (1)

144-146: Consider adding a test for out_bias serialization/deserialization.

Since this change is related to fixing model out_bias deserialization, it would be beneficial to add explicit tests verifying that the out_bias values are correctly preserved after serialization and deserialization cycles.

Would you like me to help generate test cases for verifying out_bias serialization/deserialization?

📜 Review details

Configuration used: CodeRabbit UI
Review profile: CHILL

📥 Commits

Reviewing files that changed from the base of the PR and between 72957bb and 4939e1e.

📒 Files selected for processing (1)
  • source/tests/consistent/model/test_ener.py (1 hunks)
🔇 Additional comments (1)
source/tests/consistent/model/test_ener.py (1)

144-146: LGTM! Uniform initialization of out_bias implemented correctly.

The suggested initialization of out_bias using uniform_() has been implemented as discussed in the previous review.

@iProzd iProzd added this pull request to the merge queue Nov 14, 2024
Merged via the queue into deepmodeling:devel with commit d7cf48c Nov 14, 2024
51 checks passed
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3 participants