feat: directional nlist

[wanghan-iapcm]

this pr implement the directional nlist, with which the central and neighboring atoms are treated as different atoms.

Summary by CodeRabbit

• New Features
  • Introduced a new function for building a directional neighbor list, enhancing detailed neighbor analysis.
• Bug Fixes
  • Improved handling of neighbor lists, ensuring proper management of virtual atoms and accurate sizing.
• Tests
  • Added new tests for the directional neighbor list functionality and modified existing tests to cover additional scenarios.

[coderabbitai]

Walkthrough

Walkthrough

The recent updates significantly enhance neighbor list generation in the codebase. The build_neighbor_list function has been improved to manage virtual atoms more effectively, utilizing a new helper function. Additionally, the introduction of the build_directional_neighbor_list function allows for detailed analysis of neighboring atoms within a specified cutoff distance. The testing suite has been expanded to validate these enhancements, ensuring robustness and flexibility in neighbor list handling.

Changes

Files	Change Summary
deepmd/pt/utils/nlist.py	Enhanced build_neighbor_list with _trim_mask_distinguish_nlist for better virtual atom management. Introduced build_directional_neighbor_list for detailed directional neighbor analysis.
source/tests/pt/model/test_nlist.py	Added test_build_directional_nlist to validate the new directional neighbor list functionality. Modified test_build_notype to evaluate behavior with larger selection sizes.

Sequence Diagram(s)

sequenceDiagram
    participant User
    participant NeighborList
    participant Helper

    User->>NeighborList: Call build_neighbor_list()
    NeighborList->>Helper: Call _trim_mask_distinguish_nlist()
    Helper-->>NeighborList: Return trimmed neighbor list
    NeighborList-->>User: Return neighbor list

    User->>NeighborList: Call build_directional_neighbor_list()
    NeighborList-->>User: Return directional neighbor list

Loading

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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 3c3226e and e255f24.

Files selected for processing (1)

• deepmd/pt/utils/nlist.py (3 hunks)

Additional comments not posted (2)

deepmd/pt/utils/nlist.py (2)

144-144: Remove unused variable assignment.

The variable nsel is assigned but never used. Consider removing this assignment to clean up the code.

---

170-172: Verify logic for distinguishing types.

Ensure that the function nlist_distinguish_types correctly handles the logic for distinguishing atom types as intended. This is crucial for maintaining the integrity of the neighbor list when distinguishing types.

Verification successful

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Function nlist_distinguish_types correctly handles atom type distinction.

The function processes the neighbor list using PyTorch to distinguish atom types as intended. It employs appropriate tensor operations to maintain the integrity of the list while distinguishing types. No issues found with the implementation.

• Location: deepmd/pt/utils/nlist.py lines 1-40

Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Description: Verify the logic for distinguishing atom types in `nlist_distinguish_types`.

# Test: Search for the function implementation and its usage. Expect: Correct handling of atom types.
ast-grep --lang python --pattern 'def nlist_distinguish_types($_, $_, $_):'

Length of output: 77

---

Script:

#!/bin/bash
# Broader search for functions related to distinguishing types in the codebase.
rg 'def ' --context 5 --glob '*.py' | grep 'distinguish'

Length of output: 7082

---

Script:

#!/bin/bash
# Extract and review the implementation of `nlist_distinguish_types` from `deepmd/pt/utils/nlist.py`.
ast-grep --lang python --pattern 'def nlist_distinguish_types($_, $_, $_):' --after 20 deepmd/pt/utils/nlist.py

Length of output: 113

---

Script:

#!/bin/bash
# Use ripgrep to search for the function definition and provide more context to ensure its implementation is captured.
rg 'def nlist_distinguish_types' -A 50 deepmd/pt/utils/nlist.py

Length of output: 1493

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[coderabbitai]

Actionable comments posted: 1

[codecov]

Codecov Report

Attention: Patch coverage is 96.15385% with 1 line in your changes missing coverage. Please review.

Project coverage is 82.95%. Comparing base (1a6834d) to head (e255f24).
Report is 157 commits behind head on devel.

Files with missing lines	Patch %	Lines
deepmd/pt/utils/nlist.py	96.15%	1 Missing ⚠️

Additional details and impacted files

@@           Coverage Diff           @@
##            devel    #4052   +/-   ##
=======================================
  Coverage   82.94%   82.95%           
=======================================
  Files         522      522           
  Lines       51021    51044   +23     
  Branches     3028     3028           
=======================================
+ Hits        42319    42342   +23     
+ Misses       7758     7756    -2     
- Partials      944      946    +2     

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

[wanghan-iapcm]

crashed env on my local computer, the UTs will be fixed later on

[njzjz]

What is the purpose of introducing a different neighbor list?

[wanghan-iapcm]

What is the purpose of introducing a different neighbor list?

For the development of charge density models.

[coderabbitai]

Actionable comments posted: 0

Outside diff range, codebase verification and nitpick comments (1)

deepmd/pt/utils/nlist.py (1)

183-228: Correct parameter names in the docstring.

The parameter names in the docstring do not match the function signature. Update them for clarity and accuracy.

-    coord_central : torch.Tensor
+    coord_cntl : torch.Tensor
-    atype_central : torch.Tensor
+    atype_cntl : torch.Tensor
-    coord_neighbor : torch.Tensor
+    coord_neig : torch.Tensor
-    atype_central : torch.Tensor
+    atype_neig : torch.Tensor

[coderabbitai]

Actionable comments posted: 0

Outside diff range, codebase verification and nitpick comments (1)

deepmd/pt/utils/nlist.py (1)

195-205: Correct parameter names in the docstring.

The parameter names in the docstring do not match the function signature. Ensure that the names are consistent to avoid confusion.

-    coord_central : torch.Tensor
+    coord_cntl : torch.Tensor
-    atype_central : torch.Tensor
+    atype_cntl : torch.Tensor
-    coord_neighbor : torch.Tensor
+    coord_neig : torch.Tensor
-    atype_central : torch.Tensor
+    atype_neig : torch.Tensor