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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
1.41k stars 487 forks source link

fix: correct `exclude_types` in descriptors #3841

Closed iProzd closed 1 month ago

iProzd commented 1 month ago
  1. make exclude_types consistent with mask in nlist for all descriptors. (bugs fixed in dpa1 and dpa2)
  2. add universal tests for descriptor. (now only test_exclude_types)
  3. TestCaseSingleFrameWithNlist in source/tests/pt/model/test_env_mat.py will be removed in a seperate PR.

Summary by CodeRabbit

coderabbitai[bot] commented 1 month ago
Walkthrough ## Walkthrough Recent updates to the `deepmd` project include modifications to several descriptor classes to handle `exclude_mask` and `nlist` reshaping, and the inclusion of an optional `ntypes` parameter for compatibility. Additionally, test cases and utilities have been added to ensure the robustness of these changes. The CI workflow for CUDA has also been streamlined by switching from an external CMake action to a direct pip installation. ## Changes | File(s) | Change Summary | |---------|----------------| | `deepmd/dpmodel/descriptor/dpa1.py` | Modified `call()` function to reshape `exclude_mask` and `nlist`, and update `nlist` calculation using `exclude_mask`. | | `deepmd/dpmodel/descriptor/repformers.py` | Updated `call` function logic to use `np.where` for conditionally replacing values in `nlist` with `-1`. | | `deepmd/dpmodel/descriptor/se_e2_a.py`, `deepmd/dpmodel/descriptor/se_r.py`, `deepmd/dpmodel/descriptor/se_t.py` | Added an optional `ntypes` parameter to the `DescrptSeA`, `DescrptSeR`, and `DescrptSeT` classes for compatibility. | | `deepmd/pt/model/descriptor/se_atten.py` | Modified `forward` method to adjust `sw` behavior based on `nlist_mask` and `exclude_mask`. | | `deepmd/tf/descriptor/se_atten.py` | Updated `_pass_filter` function to include new calculations for `nei_exclude_mask` and `negative_mask`. | | `source/tests/universal/common/cases/cases.py` | Added test case classes for various simulation scenarios. | | `source/tests/universal/common/cases/descriptor/utils.py` | Introduced `DescriptorTestCase` class with methods for setting up test data and conducting tests on forward propagation and excluding types. | | `.github/workflows/test_cuda.yml` | Replaced `lukka/get-cmake` action with `pip install cmake` command in the CI workflow. |
Recent review details **Configuration used: CodeRabbit UI** **Review profile: CHILL**
Commits Files that changed from the base of the PR and between c7aaef504c4bad06b94329dbb53c3971e760c365 and 0e11a4921a59b2d4974b570409c8ae71f6abb90c.
Files selected for processing (1) * .github/workflows/test_cuda.yml (1 hunks)
Files skipped from review as they are similar to previous changes (1) * .github/workflows/test_cuda.yml
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codecov[bot] commented 1 month ago

Codecov Report

All modified and coverable lines are covered by tests :white_check_mark:

Project coverage is 80.86%. Comparing base (f23c77e) to head (0e11a49).

Additional details and impacted files ```diff @@ Coverage Diff @@ ## devel #3841 +/- ## ========================================== - Coverage 82.63% 80.86% -1.78% ========================================== Files 515 515 Lines 49533 49542 +9 Branches 2985 2985 ========================================== - Hits 40932 40060 -872 - Misses 7690 8576 +886 + Partials 911 906 -5 ```

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