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deepmodeling / deepmd-kit

A deep learning package for many-body potential energy representation and molecular dynamics
https://docs.deepmodeling.com/projects/deepmd/
GNU Lesser General Public License v3.0
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refactor: refactor update_sel and save min_nbor_dist #3829

Closed njzjz closed 4 months ago

njzjz commented 4 months ago

Fix https://github.com/deepmodeling/deepmd-kit/issues/3525. Fix https://github.com/deepmodeling/deepmd-kit/issues/3544.

Summary by CodeRabbit

coderabbitai[bot] commented 4 months ago
Walkthrough ## Walkthrough The changes across multiple files enhance the `update_sel` method by adding parameters for `train_data` and `type_map`, and updating its return type to include a tuple with updated local data and an optional float value. This modification aims to improve neighbor statistics calculations. Additionally, the `UpdateSel.hook` method was removed, affecting the control flow related to saving data to the model. ## Changes | Files | Change Summary | |-------|----------------| | `deepmd/dpmodel/descriptor/dpa1.py`, `deepmd/dpmodel/descriptor/dpa2.py`, `deepmd/dpmodel/descriptor/hybrid.py`, `deepmd/dpmodel/descriptor/make_base_descriptor.py`, `deepmd/dpmodel/descriptor/se_e2_a.py`, `deepmd/dpmodel/descriptor/se_r.py` | Updated `update_sel` method to accept `train_data`, `type_map`, and return a tuple with updated local data and optional float value. | | `deepmd/dpmodel/model/base_model.py`, `deepmd/dpmodel/model/dp_model.py`, `deepmd/dpmodel/model/spin_model.py` | Added `min_nbor_dist` attribute and related methods for model compression. Modified `update_sel` method signature. | | `deepmd/dpmodel/utils/update_sel.py`, `deepmd/pt/utils/update_sel.py` | Removed `hook` method from `UpdateSel` class. | | `deepmd/pt/entrypoints/main.py` | Modified `train` function to handle `min_nbor_dist` and updated model selection and training data processing logic. | | `deepmd/pt/model/descriptor/dpa1.py`, `deepmd/pt/model/descriptor/dpa2.py`, `deepmd/pt/model/descriptor/hybrid.py`, `deepmd/pt/model/descriptor/se_a.py`, `deepmd/pt/model/descriptor/se_r.py`, `deepmd/pt/model/descriptor/se_t.py` | Updated `update_sel` method to accept `train_data`, `type_map`, and return a tuple with updated local data and optional float value. | | `deepmd/pt/model/model/dp_model.py`, `deepmd/pt/model/model/dp_zbl_model.py`, `deepmd/pt/model/model/frozen.py`, `deepmd/pt/model/model/model.py`, `deepmd/pt/model/model/spin_model.py` | Modified `update_sel` method signature and added `min_nbor_dist` related methods. | | `deepmd/pt/utils/serialization.py` | Added serialization and deserialization support for `min_nbor_dist` variable. | | `deepmd/tf/descriptor/descriptor.py`, `deepmd/tf/descriptor/hybrid.py`, `deepmd/tf/descriptor/loc_frame.py`, `deepmd/tf/descriptor/se.py`, `deepmd/tf/descriptor/se_a_mask.py`, `deepmd/tf/descriptor/se_atten.py` | Updated `update_sel` method to accept `train_data`, `type_map`, and return a tuple with updated local data and optional float value. | | `deepmd/tf/entrypoints/compress.py` | Modified `compress` function to retrieve `train_data` and pass it to `update_sel.get_min_nbor_dist`. | ## Assessment against linked issues | Objective | Addressed | Explanation | |-----------|-----------|-------------| | Save to the model in `UpdateSel.hook` (#3525) | ❌ | The `hook` method was removed instead of implementing the save functionality. |
Recent review details **Configuration used: CodeRabbit UI** **Review profile: CHILL**
Commits Files that changed from the base of the PR and between 27ea21892bc1ab670a7ff227cef22a36b44bdea3 and ecb7b6671c33573480082aae5646e2f4bea0ba3a.
Files selected for processing (4) * deepmd/dpmodel/descriptor/se_t.py (2 hunks) * deepmd/pt/entrypoints/main.py (4 hunks) * deepmd/pt/model/descriptor/se_a.py (2 hunks) * deepmd/pt/model/descriptor/se_t.py (2 hunks)
Files skipped from review due to trivial changes (1) * deepmd/pt/model/descriptor/se_a.py
Files skipped from review as they are similar to previous changes (1) * deepmd/pt/entrypoints/main.py
Additional comments not posted (2)
deepmd/dpmodel/descriptor/se_t.py (1)
`354-382`: Refactor of `update_sel` method aligns with PR objectives. The method now correctly handles the `train_data` and `type_map` parameters to perform neighbor statistics and update selections. The return type has been adjusted to include both the updated local data and the minimum neighbor distance, which is a useful addition for further processing.
deepmd/pt/model/descriptor/se_t.py (1)
`330-358`: Refactor of `update_sel` method aligns with PR objectives. The method now correctly handles the `train_data` and `type_map` parameters to perform neighbor statistics and update selections. The return type has been adjusted to include both the updated local data and the minimum neighbor distance, which is a useful addition for further processing.
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codecov[bot] commented 4 months ago

Codecov Report

Attention: Patch coverage is 81.68317% with 37 lines in your changes missing coverage. Please review.

Project coverage is 82.62%. Comparing base (8de0aba) to head (ecb7b66). Report is 127 commits behind head on devel.

Files with missing lines Patch % Lines
deepmd/dpmodel/descriptor/dpa2.py 28.57% 5 Missing :warning:
deepmd/pt/entrypoints/main.py 58.33% 5 Missing :warning:
deepmd/pt/model/descriptor/dpa2.py 28.57% 5 Missing :warning:
deepmd/tf/model/pairtab.py 40.00% 3 Missing :warning:
deepmd/dpmodel/descriptor/se_r.py 50.00% 2 Missing :warning:
deepmd/dpmodel/descriptor/se_t.py 50.00% 2 Missing :warning:
deepmd/pt/model/descriptor/se_r.py 50.00% 2 Missing :warning:
deepmd/pt/model/descriptor/se_t.py 50.00% 2 Missing :warning:
deepmd/pt/model/model/dp_zbl_model.py 50.00% 2 Missing :warning:
deepmd/pt/utils/serialization.py 50.00% 2 Missing :warning:
... and 6 more
Additional details and impacted files ```diff @@ Coverage Diff @@ ## devel #3829 +/- ## ========================================== + Coverage 82.53% 82.62% +0.08% ========================================== Files 515 515 Lines 49492 49563 +71 Branches 2985 2987 +2 ========================================== + Hits 40849 40949 +100 + Misses 7732 7703 -29 Partials 911 911 ```

:umbrella: View full report in Codecov by Sentry.
:loudspeaker: Have feedback on the report? Share it here.

njzjz commented 4 months ago

The UT for the dp model is necessary. or shall we provide consistency test for the behavior of update_sel across backends?

Good idea. The e2e and unit tests are not in conflict.

njzjz commented 4 months ago

We haven't had fixtures for descriptors, though.

njzjz commented 4 months ago

@coderabbitai resolve