Getting it into your agent
One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.
npx skills add HeshamFS/materials-simulation-skills --skill md-analysis-plannergit clone --depth 1 https://github.com/HeshamFS/materials-simulation-skillsWrote this? Show the measurements
A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.
[](https://agentmods.dev/skills/heshamfs/materials-simulation-skills/md-analysis-planner)<a href="https://agentmods.dev/skills/heshamfs/materials-simulation-skills/md-analysis-planner"><img src="https://agentmods.dev/badge/skills/heshamfs/materials-simulation-skills/md-analysis-planner.svg" alt="Measured on agentmods" height="20"></a>What it costs to keep this loaded
Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.
| Model | Per session | Once invoked |
|---|---|---|
| Fable 5.1 | $0.00066 | $0.02360 |
| Opus 5 | $0.00033 | $0.01180 |
| Sonnet 5 | $0.00013 | $0.00472 |
| Haiku 4.5 | $0.00007 | $0.00236 |
Grade A, and why
md-analysis-planner scanned grade A with 1 finding against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 9d ago.
A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.
Runs shell commandslowCapability
Expected in a hook, worth knowing in a rule or an instructions file.
- No use of `eval`, `exec`, `os.system`, or dynamic imports. How it starts
The opening of the file, as written. The whole thing — 192 lines — stays where its author put it; the contents beside it link to each section on GitHub.
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 these fields (JSON under results):
| Field | Description |
|---|---|
analysis_plan |
One entry per goal: goal, method, and status |
required_data |
Sorted, de-duplicated data needed across all goals |
equilibration_checks |
Standard pre-fit equilibration checklist |
pbc_handling |
unwrap_needed, minimum_action, format_note |
warnings |
Safety-critical caveats and blockers |
Status values
status is one of, from most to least severe: blocked > needs time axis >
needs review > ready. A more-severe status is never demoted by a less-severe
one. For example, a VACF/VDOS goal with no stored velocities reports blocked
even when the timestep is also missing (both warnings are still emitted).
Default (non-JSON) output
Without --json the script prints the plan lines, a Required data: list, a
one-line PBC: note, and a Warnings: section (also mirrored to stderr) so the
safety-critical caveats are visible even when stdout is piped.
What ships with it
4 files beside SKILL.md in the same directory: the scripts, references and assets a skill reads on demand. Not counted in the per-session cost; read them before you install if any of them is executable.
What this file has done since we first saw it
Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.
- 9d ago First seen · 192 lines · 66 tokens per session scan A 987728e61d76
md-analysis-planner is a skill published in the GitHub repository HeshamFS/materials-simulation-skills (66 stars, last pushed 2mo ago), licensed Apache-2.0. It adds 66 tokens to every session and 2,360 once invoked, about $0.0003 per session on Opus 5. A static security scan graded it A with 1 finding (runs shell commands). No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-30.
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