fix: correct exclude_types in descriptors

[iProzd]

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

• New Features

  • Added new test case classes for simulation testing and common test cases on atomic models.

• Bug Fixes

  • Adjusted exclusion mask calculations and applications affecting neighbor lists and switch behavior in various descriptors.

• Chores

  • Updated GitHub Actions workflow to install CMake directly via pip, removing dependency on an external action.

[coderabbitai]

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.

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Recent review details

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Commits

Files that changed from the base of the PR and between c7aaef5 and 0e11a49.

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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[coderabbitai]

Actionable comments posted: 5

Outside diff range and nitpick comments (1)

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

Line range hint 813-827: Refactor the reshaping and masking logic for clarity.

The reshaping and masking operations in the call method are crucial for performance but currently are a bit convoluted. Consider refactoring this part to improve readability and possibly performance. Here's a suggested refactor:

def reshape_and_apply_masks(self, nf, nloc, nnei, nlist, exclude_mask, sw):
    # Reshape operations
    flat_dim = nf * nloc
    exclude_mask = exclude_mask.reshape(flat_dim, nnei)
    nlist = nlist.reshape(flat_dim, nnei)
    sw = sw.reshape(flat_dim, nnei, 1)

    # Apply masks
    nlist_mask = nlist != -1
    nlist_mask = nlist_mask * exclude_mask.astype(bool)
    sw = np.where(nlist_mask[:, :, None], sw, 0.0)
    nlist_masked = np.where(nlist_mask, nlist, 0)

    return nlist_masked, sw

This method encapsulates the reshaping and masking logic into a single method, improving the modularity and testability of the code.

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

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

Additional details and impacted files

@@            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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