Update README.md

[AsymmetryChou]

This pull request updates references to the DPNEGF method in the README.md to reflect its recent publication in a peer-reviewed journal, replacing previous mentions of the preprint. The changes ensure users are directed to cite the correct, updated source.

Documentation updates:

• Updated the main reference for DPNEGF in the "For more details, see our papers" section to cite the published npj Computational Materials article instead of the earlier arXiv preprint.
• Revised the "How to cite" section to require citation of the published DPNEGF paper, updating both the method name and the bibliographic details accordingly.

Summary by CodeRabbit

• Documentation
  • Updated research paper citations and references to reflect the latest published versions.

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[coderabbitai]

Walkthrough

The README.md file is updated to replace references to DeePTB-NEGF with DPNEGF and to update journal citations from arXiv preprints to published papers in Nature npj Computational Materials and Nature Communications with corrected metadata.

Changes

Cohort / File(s)	Summary
Citation and Reference Updates README.md	Replaces DeePTB-NEGF with DPNEGF throughout; updates DPNEGF citation from arXiv to npj Comput Mater 11, 375 (2025); updates DeePTB-SK citation to Nat Commun 15, 6772 (2024) with revised author list and title text; removes arXiv URLs in favor of journal references.

Estimated code review effort

🎯 2 (Simple) | ⏱️ ~8 minutes

• Straightforward citation and reference updates following a consistent pattern across one file
• No code logic or control flow changes; purely documentation metadata updates
• Quick verification of accuracy for citation formats and journal details recommended

Possibly related PRs

• DeePTB-Lab/dpnegf#34: Makes identical documentation and citation updates, replacing DeePTB-NEGF references with DPNEGF and modernizing journal citations.

Poem

🐰 A nose twitch for citations reborn,
From preprints to journals all worn,
DPNEGF takes the stage,
Published papers engage,
References polished this morn! 📚✨

Pre-merge checks and finishing touches

❌ Failed checks (1 inconclusive)

Check name	Status	Explanation	Resolution
Title check	❓ Inconclusive	The title 'Update README.md' is vague and generic, using non-descriptive language that fails to convey the specific nature of the changes (updating DPNEGF references from arXiv to published journal citations).	Consider a more specific title such as 'Update README.md to cite published DPNEGF paper in npj Computational Materials' to clearly indicate the main purpose of the documentation update.

✅ Passed checks (2 passed)

Check name	Status	Explanation
Description Check	✅ Passed	Check skipped - CodeRabbit’s high-level summary is enabled.
Docstring Coverage	✅ Passed	No functions found in the changed files to evaluate docstring coverage. Skipping docstring coverage check.

✨ Finishing touches

🧪 Generate unit tests (beta)

• Create PR with unit tests
• Post copyable unit tests in a comment

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📜 Recent review details

Configuration used: defaults

Review profile: CHILL

Plan: Pro

📥 Commits

Reviewing files that changed from the base of the PR and between 20083c2 and c93458e.

📒 Files selected for processing (1)

• README.md

⏰ Context from checks skipped due to timeout of 90000ms. You can increase the timeout in your CodeRabbit configuration to a maximum of 15 minutes (900000ms). (1)

• GitHub Check: run-tests

🔇 Additional comments (3)

README.md (3)

43-43: Clear and appropriate citation guidance.

The updated section heading "For DPNEGF" is clear and the requirement to cite it is explicit and appropriate. The guidance is consistent with academic best practices.

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50-52: Citation metadata is accurate.

All citation details verified:

• Journal reference: Nature Communications volume 15, Article number: 6772 (2024)
• DOI: 10.1038/s41467-024-51006-4
• Authors: Q. Gu, Z. Zhouyin, S. K. Pandey, P. Zhang, L. Zhang, and W. E
• Title: "Deep learning tight-binding approach for large-scale electronic simulations at finite temperatures with ab initio accuracy"

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9-9: DPNEGF citation is accurate and properly formatted.

The citation "npj Comput Mater 11, 375 (2025)" correctly references the published paper, and the Nature URL resolves correctly to the article. No revisions needed.

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