Allow writing multi-model structure files with different atoms in each model

[padix-key]

Fixes #131 .

[codspeed-hq]

Merging this PR will improve performance by 15.7%

⚡ 2 improved benchmarks
✅ 101 untouched benchmarks
⏩ 4 skipped benchmarks¹

Performance Changes

	Benchmark	BASE	HEAD	Efficiency
⚡	benchmark_set_structure	10.8 ms	9.3 ms	+16.21%
⚡	benchmark_set_structure_with_bonds	11.1 ms	9.6 ms	+15.19%

Tip

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_{Comparing padix-key:issue-131 (efb271e) with main (9e9f6a1)}

Footnotes

1. 4 benchmarks were skipped, so the baseline results were used instead. If they were deleted from the codebase, click here and archive them to remove them from the performance reports. ↩