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Agent Instructions

This repo contains exploratory Python/Cython analysis code for LAMMPS H5MD trajectory files.

Main entry points:

  • src/h5md_analysis/trajectory.py reads H5MD files and runs one-time or two-time calculations.
  • src/h5md_analysis/analysis_tool.py backs the h5md-analysis console command.
  • src/h5md_analysis/calculations/ contains observable functions such as MSD, ISF, RDF, contact maps, and gyration metrics.
  • src/h5md_analysis/_core/*.pyx contains Cython kernels built through setup.py.

Coding Style

This repo is for exploratory data analysis and research code, not production software.

Default style

Write code for clarity, directness, and easy debugging.

Prefer:

  • simple, linear code
  • explicit intermediate variables
  • transparent assumptions
  • fail-fast behavior
  • minimal necessary checks

Avoid unless explicitly requested:

  • defensive programming
  • broad try/except
  • classes or heavy abstraction
  • generic utility layers
  • handling many hypothetical edge cases
  • silent fixes, fallbacks, or auto-cleaning

Error philosophy

Do not hide errors.

If assumptions are violated, let the code fail clearly at the relevant step. Use only a few targeted checks for important assumptions, such as required columns, merge keys, or missing IDs.

Scope

Solve the specific task described. Do not generalize the code into a reusable framework unless asked.

Project maintenance

  • Inspect the existing analysis modules before adding a new calculation.
  • Prefer a small callable that matches the existing cal_onetime or cal_twotime patterns over adding new orchestration code.
  • Keep H5MD dataset assumptions explicit, especially paths under particles/all/....
  • Avoid new dependencies unless explicitly requested.
  • Keep generated trajectories, large analysis outputs, .pyc, and __pycache__ out of commits.
  • If changing a Cython kernel or setup.py, rebuild the extension and run a small import or smoke check for the affected module.

Output preference

Write code like a careful researcher working in a notebook, not like a backend engineer building a service. Keep it short, inspectable, and easy to modify.

Markdown math convention

For Markdown documents, use single dollar signs for inline math, such as $R(s)$, and double dollar signs for block equations. Do not use \(...\) for inline math or \[...\] for block equations in new or edited Markdown prose.