feat: add support for non-orthogonal cells in amber/md format

[Copilot]

The amber/md format previously only supported orthogonal unit cells (90° angles), raising a RuntimeError("Unsupported cells") for any simulation with non-orthogonal cells. This limitation prevented users from processing AMBER trajectories with triclinic, monoclinic, or hexagonal crystal systems.

Changes

• Added cell_lengths_angles_to_cell() function that converts cell lengths and angles to 3×3 cell vector matrices using standard crystallographic conventions
• Removed orthogonal-only restriction in read_amber_traj() by replacing the angle check with general cell conversion
• Maintains full backward compatibility - orthogonal cells produce identical results to the previous implementation

Supported Crystal Systems

The implementation now handles all crystal systems:

• Cubic/Orthorhombic: α = β = γ = 90°
• Monoclinic: α = γ = 90°, β ≠ 90°
• Hexagonal: α = β = 90°, γ = 120°
• Triclinic: α, β, γ ≠ 90°

Example Usage

import dpdata # Previously would raise RuntimeError for non-orthogonal cells system = dpdata.LabeledSystem("simulation", fmt="amber/md") # Now works with any cell angles, including: # - Protein crystals with monoclinic cells # - Hexagonal ice simulations  # - Triclinic organic crystals

Testing

Added comprehensive test coverage including:

• Unit tests for all crystal system types
• Edge case validation (extreme angles, multiple frames)
• Integration tests verifying RuntimeError elimination
• Backward compatibility verification

All existing amber/md tests continue to pass, ensuring no breaking changes.

Fixes #869.

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[njzjz]

pre-commit.ci autofix

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 85.53%. Comparing base (beee99a) to head (14d6447).

Additional details and impacted files

@@ Coverage Diff @@ ## devel #870 +/- ## ========================================== + Coverage 85.48% 85.53% +0.04%  ========================================== Files 82 82 Lines 7607 7625 +18 ========================================== + Hits 6503 6522 +19  + Misses 1104 1103 -1 

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[codspeed-hq]

CodSpeed WallTime Performance Report

Merging #870 will not alter performance

_{Comparing copilot/fix-869 (14d6447) with devel (beee99a)}

Summary

✅ 2 untouched benchmarks

[njzjz]

pre-commit.ci autofix

[njzjz]

The current state looks good to me - cell_lengths_angles_to_cell replaces the original code, and this method has a unit test that almost covers all cases. @wanghan-iapcm please double-check since this PR is LLM-generated.