fracture-mechanics

name	fracture-mechanics
description	Run parameterized 2D lattice fracture simulations from the Fracture and Mechanics notebook as offline artifacts. Use when asked to simulate a pre-cracked triangular lattice, Mode I tension, Mode II shear, Morse/Lennard-Jones/MLIP pair potentials, temperature effects, strain-rate effects, crack propagation, stress-strain curves, or fracture movies. Produces an animated movie, stress-strain plot, final lattice image, CSV data, JSON run metrics, and README by running a bundled Python script.
license	3-clause BSD license
metadata	{"version":"1.1","skill-author":"Markus J. Buehler, Massachusetts Institute of Technology (MIT), Laboratory for Atomistic and Molecular Mechanics (LAMM)"}

Fracture Mechanics

Run a 2D triangular-lattice fracture simulation with a sharp edge pre-crack, moving grip boundaries, and a vectorized bond network with permanent stretch-based bond breaking. Always use the bundled script; do not rewrite the simulation from scratch.

Required Workflow

1. Create or use an output directory, usually skill_output_<timestamp>_fracture-mechanics.
2. Run scripts/run_fracture_sim.py with either the defaults or the user's selected parameters. Use --steps 10000 for final fracture-producing runs unless the user explicitly asks for a quick smoke test.
3. Use the default high-quality movie settings, --frames 48 --dpi 120 --movie-fps 16, unless a server-side timeout requires the fallback --frames 16 --dpi 90. The renderer uses fixed slab bounds, fixed stress-strain axes, and a fixed color scale across frames to prevent movie flicker.
4. Run the simulation as its own shell command. Do not chain find or cat summary.json after the long simulation command in the same shell call.
5. Verify the artifacts with find in a separate shell call after the simulation succeeds.
6. Final answer must list exact artifact paths and mention the peak stress/strain from summary.json.

Default command:

python3 skills/fracture-mechanics/scripts/run_fracture_sim.py \
  --out skill_output_<timestamp>_fracture-mechanics \
  --title "2D Lattice Fracture" \
  --potential morse \
  --mode I \
  --orientation 90 \
  --nx 96 \
  --ny 36 \
  --max-atoms 5000 \
  --crack-length 0.30 \
  --temperature 0.004 \
  --strain-rate 0.003 \
  --damping 0.30 \
  --dt 0.005 \
  --steps 10000 \
  --frames 48 \
  --dpi 120 \
  --movie-fps 16 \
  --bond-cutoff 1.35 \
  --break-stretch 1.75 \
  --color-by stress

Verify:

find skill_output_<timestamp>_fracture-mechanics -maxdepth 2 -type f -print

User Parameters

Use these options when the user asks for specific settings:

• --potential: morse, lj, or mlip.
• --mode: I for tension/opening, II for shear.
• --nx, --ny: lattice dimensions. Defaults are 96 x 36. Larger systems are clamped by --max-atoms.
• --max-atoms: safety clamp for local runs. Default 5000, maximum 40000.
• --orientation: 0 or 90; 90 is default.
• --crack-length: edge crack length as a fraction of specimen width, 0.0-0.80.
• --temperature: initial kinetic temperature scale.
• --strain-rate: grip loading rate.
• --damping: viscous damping. Use 0 for near-NVE after loading; use 0.1-0.5 for stable visual demos.
• --dt: timestep.
• --steps: number of velocity-Verlet steps. Use 10000 for final fracture-producing runs.
• --frames: number of movie frames. Default 48 for a smoother GIF; use 16 only as a timeout fallback.
• --seed: deterministic random seed.
• --a0: auto or an explicit lattice spacing.
• --morse-a: Morse stiffness/brittleness. Lower values are tougher; higher values are more brittle.
• --morse-De, --morse-re: Morse energy and equilibrium distance.
• --lj-eps, --lj-sigma: Lennard-Jones parameters.
• --mlip-weights: optional JSON file with w, b_in, c, and b_out for a neural pair potential.
• --bond-cutoff: initial bonded-neighbor cutoff in units of a0; default 1.35.
• --break-stretch: permanently break bonds stretched past this multiple of a0; default 1.75. Use lower values for more brittle movies and higher values for tougher response.
• --color-by: , , , , or .

Local Shell Timeout Policy

The local mistral.rs shell executor may stop a single shell call after about 30 seconds. The CLI --response-timeout controls the HTTP response wait, not the per-shell-call runtime. Avoid sending a long simulation plus verification commands in one shell call, because the timeout can prevent find and summary.json inspection from running.

Local-safe final artifact profile:

nx <= 96
ny <= 36
max-atoms <= 5000
steps = 10000
frames = 48
dpi = 120

Timeout fallback profile:

nx <= 96
ny <= 36
max-atoms <= 5000
steps = 10000
frames = 16
dpi = 90

If the user requests a larger exact run, such as steps 30000, nx 128, ny 48, or max-atoms 50000, first decide whether exact parameters are required:

• If exact parameters are required, do not claim the agent shell completed the run. Explain that the exact run exceeds the per-shell-call limit and provide the direct command for the user to run in a normal terminal.
• If the user mainly wants artifacts, run the timeout fallback profile while preserving the requested physics choices where possible: potential, mode, orientation, crack length, temperature, strain rate, damping, dt, bond-cutoff, break-stretch, color-by, and potential parameters. State explicitly which size/rendering/step parameters were reduced.

If a command times out, do not end with failure if a fallback artifact can still be produced. Rerun with the timeout fallback profile, verify files with find, read summary.json, and report the fallback results clearly.

Recommended Recipes

Brittle Mode I Fracture

python3 skills/fracture-mechanics/scripts/run_fracture_sim.py \
  --out skill_output_<timestamp>_fracture-mechanics \
  --title "Brittle Mode I Fracture" \
  --potential morse \
  --mode I \
  --orientation 90 \
  --morse-a 7.0 \
  --temperature 0.002 \
  --strain-rate 0.0035 \
  --crack-length 0.34 \
  --steps 10000 \
  --frames 48 \
  --dpi 120 \
  --movie-fps 16 \
  --break-stretch 1.65 \
  --color-by stress

Tougher Morse Lattice

python3 skills/fracture-mechanics/scripts/run_fracture_sim.py \
  --out skill_output_<timestamp>_fracture-mechanics \
  --title "Tougher Morse Lattice" \
  --potential morse \
  --mode I \
  --orientation 90 \
  --morse-a 3.5 \
  --temperature 0.006 \
  --strain-rate 0.0025 \
  --crack-length 0.25 \
  --steps 10000 \
  --frames 48 \
  --dpi 120 \
  --movie-fps 16 \
  --break-stretch 2.05 \
  --color-by coordination

Mode II Shear

python3 skills/fracture-mechanics/scripts/run_fracture_sim.py \
  --out skill_output_<timestamp>_fracture-mechanics \
  --title "Mode II Shear Crack" \
  --potential morse \
  --mode II \
  --orientation 90 \
  --morse-a 5.0 \
  --temperature 0.004 \
  --strain-rate 0.003 \
  --crack-length 0.30 \
  --steps 10000 \
  --frames 48 \
  --dpi 120 \
  --movie-fps 16 \
  --break-stretch 1.80 \
  --color-by speed

Lennard-Jones Comparison

python3 skills/fracture-mechanics/scripts/run_fracture_sim.py \
  --out skill_output_<timestamp>_fracture-mechanics \
  --title "Lennard-Jones Fracture Response" \
  --potential lj \
  --mode I \
  --orientation 90 \
  --lj-eps 1.0 \
  --lj-sigma 0.90 \
  --temperature 0.004 \
  --strain-rate 0.003 \
  --steps 10000 \
  --frames 48 \
  --dpi 120 \
  --movie-fps 16 \
  --break-stretch 1.85 \
  --color-by pe

Outputs

The script writes:

• fracture_movie.gif: animated fracture movie when Pillow GIF writing is available.
• fracture_movie.html: HTML fallback playback of rendered frames.
• frames/frame_*.png: individual movie frames.
• stress_strain.png: stress-strain plot.
• final_lattice.png: final atomistic lattice state.
• stress_strain.csv: step, strain, stress data.
• summary.json: peak stress, peak strain, final stress, final strain, atom count, and artifact names.
• parameters.json: exact input parameters and resolved lattice spacing.
• README.md: explanation and run summary.

If fracture_movie.gif is missing, report fracture_movie.html and the frames/ directory as the movie output. Do not claim success unless find lists the movie or fallback, stress-strain plot, CSV, JSON run metrics, and README.

Notes

This is a simple fracture model for qualitative mechanism exploration and artifact generation, not a calibrated predictor of a specific material. Runs with fewer than 10000 steps are useful only for code smoke tests; do not present them as final fracture results because the crack may not propagate visibly. If the shell tool times out after partial frames, rerun the same physics with --frames 16 --dpi 90; do not reduce --steps below 10000 for the final run.