md-analysis-planner

name	md-analysis-planner
description	Plan molecular dynamics post-processing for materials simulations, including RDF, MSD and diffusion, VACF/VDOS, coordination numbers, bond-angle distributions, stress-strain curves, equilibration detection, PBC unwrapping, and trajectory format choices. Use before writing MD analysis scripts or trusting trajectory-derived results.
allowed-tools	Read, Bash, Write, Grep, Glob
metadata	{"author":"HeshamFS","version":"1.2.2","security_tier":"high","security_reviewed":true,"tested_with":["claude-code"],"last_evaluated":"2026-06-23","eval_cases":3,"last_reviewed":"2026-06-24","standards":["Yeh & Hummer (2004), 1/L finite-size diffusion correction (xi ~= 2.837, cubic box)","Einstein relation for self-diffusion, D = lim MSD/(2*d*t)","Allen & Tildesley, Computer Simulation of Liquids (RDF, coordination, VACF/VDOS, block averaging)","Flyvbjerg & Petersen (1989), block-averaging error estimation"]}

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.

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. The script exits with code 2 and a message on stderr for invalid input (empty system, no goals, non-positive or non-finite timestep, or inputs exceeding the size caps below).

Limitations

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

Verification checklist

Do not trust trajectory-derived results until each applicable item below is recorded against the planner's own output:

• Ran scripts/md_analysis_planner.py and confirmed no analysis_plan entry is blocked or needs time axis; record any needs review goal and how its custom analysis was resolved.
• Confirmed every item in the planner's required_data list is actually present in the trajectory (e.g. velocities for VACF/VDOS, stress or virial + strain history for stress-strain) before running the corresponding analysis.
• For diffusion/MSD: recorded the log-log MSD-vs-time slope and confirmed it is ~1 (diffusive regime) over the fit window, excluding ballistic/sub-diffusive transients, before quoting D = lim MSD/(2dt).
• For diffusion/MSD: applied the Yeh-Hummer 1/L finite-size correction and recorded the box length L and shear viscosity eta used (D_0 = D_PBC + k_BTxi/(6pieta*L), xi~=2.837 cubic box).
• For any displacement-based analysis when pbc_handling.unwrap_needed is true: confirmed positions were unwrapped using cell + image flags before computing displacements (not raw wrapped coordinates).
• Worked through the planner's equilibration_checks: discarded the startup transient, confirmed temperature/pressure plateaus, and compared first-half vs second-half property estimates before any transport/thermodynamic fit.
• Reported an uncertainty from block averaging (or independent trajectories) for every quoted transport/thermodynamic property, not a single-window point value.

Common pitfalls & rationalizations

Tempting shortcut	Why it's wrong / what to do
"MSD vs time looks straight, so it's diffusive — just fit a line."	A straight-looking MSD can still include ballistic/sub-diffusive transients. Confirm the log-log slope is ~1 over the fit window first, then fit D = lim MSD/(2dt).
"D from the simulation is the diffusion coefficient."	PBC self-diffusion is system-size dependent. Apply the Yeh-Hummer 1/L correction with the actual box length L and viscosity eta; report D_0, not D_PBC.
"Positions are in the dump, so MSD is fine."	Wrapped coordinates make atoms jump across the box and corrupt displacements. When unwrap_needed is true, unwrap using cell + image flags before any displacement analysis.
"No velocities stored, but I can get VACF/VDOS from positions."	The planner marks VACF/VDOS blocked without velocities for a reason. A finite-difference velocity estimate must be explicitly justified (frame spacing, aliasing); otherwise the result is unreliable.
"The run finished, so I can fit transport properties on the whole trajectory."	Run completion is not equilibration. Discard the startup transient and verify temperature/pressure plateaus (the equilibration_checks) before fitting.
"One window gave a clean number, no need for error bars."	A single window hides correlation-driven variance. Use block averaging or independent trajectories so every transport/thermodynamic value carries an uncertainty.

Security

Input Validation

Inputs are scalar CLI values and booleans only. plan_md_analysis validates and bounds every field before use; any violation raises ValueError, which main catches to print a message on stderr and exit with code 2:

• system must be non-empty (after stripping) and at most 256 characters.
• At most 64 goals are allowed; each goal at most 256 characters.
• trajectory_format at most 256 characters.
• timestep_fs, if given, must be a positive, finite number (math.isfinite and > 0).

Goals are not allowlisted: an unrecognized goal is not rejected but is reported with status needs review and an "unknown goal" warning. The --has-velocities, --has-stress, and --unwrap-needed flags are plain booleans and need no validation.

File Access

The script reads and writes no files; all I/O is stdin/args -> stdout (plain text or JSON), with warnings additionally mirrored to stderr. It takes no path arguments and opens no trajectory or output files, so there is no filesystem sandboxing concern. There are no per-file size limits because no files are read; input size is instead capped by the field/goal limits above.

Tool Restrictions

Frontmatter allowed-tools is Read, Bash, Write, Grep, Glob:

• Bash is used only to run the bundled scripts/md_analysis_planner.py.
• Read, Write, Grep, and Glob are used only to inspect, edit, and search this skill's own files (the script, references, and SKILL.md) when authoring analysis plans; they are not used to touch trajectory data.

Safety Measures

• No use of eval, exec, os.system, or dynamic imports.
• The script spawns no subprocesses and executes no external analysis programs; it only parses arguments with argparse and computes a plan in-process.
• Output is structured JSON produced via json.dumps (or deterministic plain text), never interpolated shell.
• Denial-of-service caps (MAX_GOALS = 64, MAX_SYSTEM_LEN = 256, MAX_FIELD_LEN = 256) bound the work so a planning helper never materializes pathological input.

References

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

Version History

• 1.2.0: Add deterministic script_checks to all three eval cases that pin the exact planner output (statuses, sorted required_data, PBC note, and the specific diffusive-regime / Yeh-Hummer / blocked-not-demoted warnings) so the evals discriminate the skill from a from-memory baseline.
• 1.1.0: Fix status demotion (blocked never downgraded to needs time axis), surface warnings/required-data/PBC in non-JSON mode, add diffusive-regime and Yeh-Hummer finite-size guidance, and enforce documented input caps.
• 1.0.0: Initial MD analysis planning skill.