md-analysis-planner

HeshamFS

更新于 Yesterday

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关于

This Claude Skill helps developers plan molecular dynamics post-processing by recommending appropriate analyses like RDF, MSD, and stress-strain calculations. It guides trajectory format choices and prerequisites before writing analysis scripts. Use it to ensure reliable results from materials simulations.

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Claude Code

技能文档

MD Analysis Planner

Goal

Choose the right MD trajectory analyses and prerequisites before writing post-processing code.

Requirements

Python 3.10+
No external dependencies
Works on Linux, macOS, and Windows

Inputs to Gather

Input	Description	Example
System	Material or molecular system	`oxide glass`, `liquid water`
Goals	Analysis goals	`rdf,diffusion,coordination`
Trajectory format	Dump, DCD, XYZ, H5MD, etc.	`LAMMPS dump`
Velocities	Whether velocities are stored	`true`
Stress	Whether stress/virial is stored	`true`
Unwrap needed	Whether atoms cross PBC	`true`
Timestep	fs per saved frame	`10`

Decision Guidance

Use RDF and coordination for local structure.
Use MSD for diffusion, but unwrap trajectories and verify diffusive regime.
Use VACF/VDOS only when velocities or reliable finite-difference velocities exist.
Use stress-strain only if stress/virial and deformation history are available.
Always perform equilibration checks before fitting transport or thermodynamic properties.

Script Outputs

scripts/md_analysis_planner.py emits:

analysis_plan
required_data
equilibration_checks
pbc_handling
warnings

Workflow

python3 skills/simulation-workflow/md-analysis-planner/scripts/md_analysis_planner.py \
  --system "oxide glass" \
  --goals rdf,coordination,bond-angle \
  --trajectory-format dump \
  --unwrap-needed \
  --timestep-fs 10 \
  --json

Error Handling

If velocities, stress, or timestep information is missing, downgrade dependent analyses and report warnings.

Limitations

This skill plans analysis and prerequisites; it does not parse large trajectories directly.

Security

Inputs are scalar CLI values and booleans only.
The script does not read trajectory files or execute external analysis programs.
The skill uses Bash only to run the bundled script.

References

See references/md_analysis_checks.md for analysis prerequisites and failure modes.

Version History

1.0.0: Initial MD analysis planning skill.

GitHub 仓库

HeshamFS/materials-simulation-skills

路径: skills/simulation-workflow/md-analysis-planner

agent-skillsagentscli-toolscomputational-sciencellmmaterials-science