fix: build pymatgen Molecule species from atom_types order (#994)

[CedricConday]

Fixes #994.

Summary

PyMatgenMoleculeFormat.to_system() built the species list by expanding grouped atom_names/atom_numbs (e.g. H, H, O), but passed coords in their atom_types order (e.g. H, O, H). When atoms are not grouped by type, the resulting pymatgen.core.Molecule assigns species to the wrong coordinates.

Change

Build species per-atom from atom_types, matching the coordinate order — the same construction the sibling Structure exporter already uses in this file:

species = [data["atom_names"][tt] for tt in data["atom_types"]]

This is the fix suggested in the issue.

Testing

• Added a regression test (test_ungrouped_atom_types_species_match_coords) using the reporter's reproducer: species now follow the coordinate order (H, O, H) and each site sits on its original coordinate. It fails on master and passes with this change.
• All 50 pymatgen-related tests pass; ruff check and ruff format --check clean.

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Disclosure: authored with AI assistance (Claude Code); reviewed by me and I'll shepherd it through review.

Summary by CodeRabbit

• Bug Fixes

  • Fixed molecule conversion so atom species now follow the actual per-atom type order.
  • Ensured converted molecule coordinates continue to match the source structure for each frame.

• Tests

  • Added a regression test covering ungrouped atom types to verify species ordering and coordinate mapping during molecule conversion.

[codspeed-hq]

Merging this PR will not alter performance

⚠️ Unknown Walltime execution environment detected

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For the most accurate results, we recommend using CodSpeed Macro Runners: bare-metal machines fine-tuned for performance measurement consistency.

✅ 2 untouched benchmarks

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_{Comparing CedricConday:fix/pymatgen-molecule-species-order-994 (7e073a4) with master (7092ff0)}

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 86.87%. Comparing base (7092ff0) to head (7e073a4).

Additional details and impacted files

@@            Coverage Diff             @@
##           master    #1010      +/-   ##
==========================================
- Coverage   86.87%   86.87%   -0.01%     
==========================================
  Files          89       89              
  Lines        8266     8264       -2     
==========================================
- Hits         7181     7179       -2     
  Misses       1085     1085              

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[coderabbitai]

No actionable comments were generated in the recent review. 🎉

ℹ️ Recent review info

⚙️ Run configuration

Configuration used: Organization UI

Review profile: CHILL

Plan: Pro

Run ID: 6bf3e812-43aa-43b3-bc9c-c319f044d29a

📥 Commits

Reviewing files that changed from the base of the PR and between 7092ff0 and 7e073a4.

📒 Files selected for processing (2)

• dpdata/plugins/pymatgen.py
• tests/test_pymatgen_molecule.py

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📝 Walkthrough

Walkthrough

This PR fixes a bug in PyMatgenMoleculeFormat.to_system where the species list was built from grouped atom_names/atom_numbs counts instead of per-atom atom_types, causing species-coordinate misalignment for ungrouped atom types. A regression test is added.

Changes

Species ordering fix

Layer / File(s)	Summary
Fix species-coordinate mismatch dpdata/plugins/pymatgen.py	Species list is now built by mapping each atom_types index to its corresponding atom_names entry, ensuring species order matches the coordinate order instead of grouping by type counts.
Regression test for species ordering tests/test_pymatgen_molecule.py	Adds a test constructing a dpdata.System with ungrouped atom types, converting to pymatgen/molecule, and asserting species order and coordinates match the input.

Estimated code review effort: 1 (Trivial) | ~5 minutes

Sequence Diagram(s)

Not applicable; the change is a localized bug fix without multi-component interaction flow.

Suggested labels: bug, tests

Suggested reviewers: none identified from the provided context

Poem:
A rabbit hopped through atoms small,
Found species scrambled, out of thrall.
With atom_types now leading the way,
Each H and O finds its rightful place to stay.
Coordinates matched, no more mix-up call! 🐇✨

🚥 Pre-merge checks | ✅ 5

✅ Passed checks (5 passed)

Check name	Status	Explanation
Description Check	✅ Passed	Check skipped - CodeRabbit’s high-level summary is enabled.
Title check	✅ Passed	The title clearly states the pymatgen Molecule species-order fix and references the issue.
Linked Issues check	✅ Passed	The PR builds species from atom_types order and adds a regression test for the H,O,H case described in #994.
Out of Scope Changes check	✅ Passed	Changes are limited to the pymatgen molecule fix and its regression test, matching the stated objective.
Docstring Coverage	✅ Passed	No functions found in the changed files to evaluate docstring coverage. Skipping docstring coverage check.

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