feat: add support for multiple LAMMPS atom styles with automatic detection

[Copilot]

This PR adds comprehensive support for different LAMMPS atom styles beyond the previously supported "atomic" style. The implementation now supports 8 common LAMMPS atom styles with automatic detection and charge extraction while maintaining full backward compatibility.

Supported Atom Styles

• atomic: atom-ID atom-type x y z (default fallback)
• full: atom-ID molecule-ID atom-type q x y z (includes charges and molecule IDs)
• charge: atom-ID atom-type q x y z (includes charges)
• bond: atom-ID molecule-ID atom-type x y z (includes molecule IDs)
• angle: atom-ID molecule-ID atom-type x y z
• molecular: atom-ID molecule-ID atom-type x y z
• dipole: atom-ID atom-type q x y z mux muy muz (includes charges)
• sphere: atom-ID atom-type diameter density x y z

Key Features

• Automatic atom style detection: Parses LAMMPS data file headers and comments (e.g., Atoms # full) with intelligent fallback based on column analysis
• Automatic charge extraction and registration: For atom styles that include charges (full, charge, dipole), charges are automatically extracted, stored, and properly registered as a DataType
• Smart defaults: atom_style="auto" is now the default, eliminating the need for manual specification in most cases
• Backward compatibility: Existing code continues to work without any changes
• Robust error handling: Clear error messages for unsupported atom styles with graceful fallbacks

Usage

# Automatic detection (new default behavior)
system = dpdata.System("data.lmp", type_map=["O", "H"])  # Detects style automatically

# Full style with charges and molecule IDs
system = dpdata.System("data.lmp", type_map=["O", "H"])  # Auto-detects "full" style
print(system["charges"])  # Access extracted charges

# Explicit styles still supported for edge cases
system = dpdata.System("data.lmp", type_map=["O", "H"], atom_style="charge")

Implementation Details

The solution adds intelligent atom style detection that:

1. Parses header comments after "Atoms" sections for explicit style declarations
2. Uses heuristic analysis of column count and content patterns as fallback
3. Maintains the existing configurable atom style parameter for explicit control
4. Automatically registers charge DataType when charge data is present

All parsing functions (get_atype, get_posi, get_charges) were updated to handle different column arrangements with full type hints. Comprehensive tests cover both comment-based and heuristic detection scenarios.

Fixes #853.

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[codecov]

Codecov Report

❌ Patch coverage is 89.28571% with 9 lines in your changes missing coverage. Please review.
✅ Project coverage is 85.47%. Comparing base (beee99a) to head (77d0560).
⚠️ Report is 28 commits behind head on devel.

Files with missing lines	Patch %	Lines
dpdata/lammps/lmp.py	88.31%	9 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##            devel     #867      +/-   ##
==========================================
- Coverage   85.48%   85.47%   -0.02%     
==========================================
  Files          82       82              
  Lines        7607     7675      +68     
==========================================
+ Hits         6503     6560      +57     
- Misses       1104     1115      +11     

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[codspeed-hq]

CodSpeed WallTime Performance Report

Merging #867 will not alter performance

_{Comparing copilot/fix-853 (1e6356f) with devel (beee99a)}

Summary

✅ 2 untouched benchmarks

[njzjz]

pre-commit.ci autofix

[njzjz]

pre-commit.ci autofix

[njzjz]

@copilot please add type hints to all methods you added. Thanks!

[Copilot]

@copilot please add type hints to all methods you added. Thanks!

Added comprehensive type hints to all new methods including the core parsing functions in dpdata/lammps/lmp.py, the charge registration function in dpdata/plugins/lammps.py, and all test helper methods in tests/test_lammps_atom_styles.py. All functions now have proper parameter and return type annotations following the project's type hinting conventions. Commit: 54d9709

[njzjz]

pre-commit.ci autofix

[njzjz]

LGTM (the CI status is not related) - @wanghan-iapcm, please double-check the PR.

[njzjz]

@copilot Use conventional commit format for the PR title.

[Copilot]

@copilot Use conventional commit format for the PR title.

I cannot directly change the PR title as I don't have permissions to update PR metadata. However, the conventional commit format for this PR title should be:

feat: add support for multiple LAMMPS atom styles with automatic detection

You can update the PR title manually to follow this conventional commit format.