Add CalcMinimizeInput dataclass example to notebook

[jan-janssen]

Summary

• Extends notebooks/example.ipynb with a CalcMinimizeInput dataclass example
• The existing notebook already demonstrated CalcMDInput; this PR adds the corresponding CalcMinimizeInput usage for geometry optimisation via lammps_file_interface_function(calc_dataclass=...)

Test plan

• Open the notebook and run the new CalcMinimizeInput cell to confirm it executes without errors and prints a final energy

🤖 Generated with Claude Code

Summary by CodeRabbit

• Documentation
  • Added a new geometry optimization example section to the sample notebook. The tutorial demonstrates how to set up and execute optimization tasks using structured configuration methods, and shows how to extract and interpret computed results from the output. Users can now reference this example when implementing similar analyses.

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ℹ️ Review info

⚙️ Run configuration

Configuration used: defaults

Review profile: CHILL

Plan: Pro

Run ID: ef533b06-bd00-4a96-8d1d-a022b9fdbe96

📥 Commits

Reviewing files that changed from the base of the PR and between 0540b83 and 6259a11.

📒 Files selected for processing (1)

• notebooks/example.ipynb

📝 Walkthrough

Walkthrough

The PR adds a new example section to the Jupyter notebook demonstrating typed dataclass usage for geometry optimization. It includes markdown introducing CalcMinimizeInput and code showing construction of the dataclass, calling the interface function with the calc_dataclass parameter, and printing the final potential energy from the output.

Changes

Typed Dataclass Geometry Optimization Example

Layer / File(s)	Summary
CalcMinimizeInput example and usage demonstration notebooks/example.ipynb	Adds markdown introducing CalcMinimizeInput and code cell demonstrating dataclass construction, passing it to lammps_file_interface_function via calc_dataclass=, and extracting energy_pot from parsed results.

Estimated code review effort

🎯 2 (Simple) | ⏱️ ~10 minutes

Possibly related PRs

• pyiron/lammpsparser#330: Introduces the CalcMinimizeInput dataclass and calc_dataclass parameter support that this notebook example demonstrates.

Poem

🐰 A rabbit hops through notebooks bright,
With dataclass examples, clean and tight,
Minimizing geometries with typed grace,
Energy results in their proper place! ✨

🚥 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 directly and accurately summarizes the main change: adding a CalcMinimizeInput dataclass example to the notebook.
Docstring Coverage	✅ Passed	No functions found in the changed files to evaluate docstring coverage. Skipping docstring coverage check.
Linked Issues check	✅ Passed	Check skipped because no linked issues were found for this pull request.
Out of Scope Changes check	✅ Passed	Check skipped because no linked issues were found for this pull request.

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✨ Finishing Touches

🧪 Generate unit tests (beta)

• Create PR with unit tests
• Commit unit tests in branch dataclass_example

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[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 89.61%. Comparing base (33a2098) to head (6259a11).
⚠️ Report is 1 commits behind head on main.

Additional details and impacted files

@@           Coverage Diff           @@
##             main     #347   +/-   ##
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  Coverage   89.61%   89.61%           
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  Files          13       13           
  Lines        1204     1204           
=======================================
  Hits         1079     1079           
  Misses        125      125           

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Actionable comments posted: 1

🤖 Prompt for all review comments with AI agents

Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.

Inline comments:
In `@notebooks/example.ipynb`:
- Around line 503-507: The new notebook cell for the CalcMinimizeInput example
is unexecuted (execution_count: null) and has empty outputs; run the cell that
creates/uses CalcMinimizeInput in the notebook, capture and save the cell's
outputs (including the final energy value), ensure the cell's execution_count is
set and the outputs field contains the execution result, then save and commit
the updated notebook so the example output is persisted and verifiable.

🪄 Autofix (Beta)

Fix all unresolved CodeRabbit comments on this PR:

• Push a commit to this branch (recommended)
• Create a new PR with the fixes

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ℹ️ Review info

⚙️ Run configuration

Configuration used: defaults

Review profile: CHILL

Plan: Pro

Run ID: 228fcdcd-de3a-4e06-83ae-82e359160774

📥 Commits

Reviewing files that changed from the base of the PR and between 33a2098 and 0540b83.

📒 Files selected for processing (1)

• notebooks/example.ipynb

[coderabbitai]

⚠️ Potential issue | 🟡 Minor | ⚡ Quick win

Run and persist the new CalcMinimizeInput example cell output.

Line 503 is unexecuted (execution_count: null) and Line 506 has empty outputs, while this notebook otherwise stores executed examples. Please run this new cell and commit the output (final energy) to match the PR test plan and keep the notebook verifiable.

🤖 Prompt for AI Agents

Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.

In `@notebooks/example.ipynb` around lines 503 - 507, The new notebook cell for
the CalcMinimizeInput example is unexecuted (execution_count: null) and has
empty outputs; run the cell that creates/uses CalcMinimizeInput in the notebook,
capture and save the cell's outputs (including the final energy value), ensure
the cell's execution_count is set and the outputs field contains the execution
result, then save and commit the updated notebook so the example output is
persisted and verifiable.