Blame for README.md

---
license: apache-2.0
pretty_name: "A model builds a model: architected graphene trajectories and figures"
tags:
  - materials-science
  - atomistic-simulation
  - molecular-mechanics
  - graphene
  - fracture
  - interatomic-potential
  - autonomous-science
size_categories:
  - n<1K
---

# Models building models for discovery of graphene metamaterial design principles in the context of failure

Companion data for the GitHub repository **lamm-mit/graphene-agent** and the manuscript *Models building models for discovery of graphene
metamaterial design principles in the context of failure*. The repository holds the code, the experiment database (all 132 records
with structures and stress–strain curves), the report, the figures and the app; this dataset holds the files that are
too large for a code repository.


![image](https://cdn-uploads.huggingface.co/production/uploads/623ce1c6b66fedf374859fe7/zi9QI6ZwmZ4TnmEbgWUpN.png)

## Contents

| folder | files | size | description |
|---|---|---|---|
| `trajectories/` | 132 `.npz` | 309 MB | one file per simulation, named by run id (`run_YYYYMMDD_HHMMSS_xxxxxx.npz`), matching `experiments/database/runs/<run_id>/record.json` in the repository |
| `large_svg_figures/` | 47 `.svg` | 396 MB | the SVG versions of the atom-resolved fracture panels (each > 3 MB); paths mirror the repository (`carbon_discovery/figures/progression/…`, `paper_analysis/figures/…`) |
| `movies/` | 10 + 10 `.mp4`, 10 `.png` | see `movies/README.md` | synchronised multi-panel fracture movies of the key trajectories (2560×1440 masters, `*_1080p.mp4` for supplementary information) with poster frames and captions; no text other than the chart axes |
| `movies/social/` | 28 + 28 `.mp4`, 28 `.png` | see `movies/social/README.md` | clean single-structure movies (14 designs × 2 fields: energy change per atom, maximum principal stress per atom), square 1440×1440 and 1080×1080, dark background, no text |
| `SHA256SUMS.txt` | | | checksums of every file |

All simulations are athermal quasi-static uniaxial tensile tests of periodic graphene-derived sheets with the screened
second-generation REBO potential (Brenner 2002; Pastewka 2008, 2013), run with the PyTorch implementation validated in
the repository. Units: eV, Å; 2D stress in eV/Ų (multiply by 16.0218 for N/m).


![image](https://cdn-uploads.huggingface.co/production/uploads/623ce1c6b66fedf374859fe7/aCi3Hb3ZPst_8s9_Sh8Q3.png)

## Movies

The multi-panel movies show several designs advancing at the same engineering strain, coloured by the energy change per atom, above the stress–strain curves with moving markers. The single-structure movies in `movies/social/` show one design filling the frame on a dark background, coloured by the energy change per atom (`_energy`) or by the per-atom maximum principal 2D stress (`_stress`), with freshly broken bonds flashing white. In both series the frames between the stored quasi-static states are interpolated (positions, cell, field; bonds recomputed) and are not simulated states, and the strain rate is slowed 3× around first damage, peak load and major propagation. Captions and the design/run id of every panel are in the `captions.json` and `README.md` files next to the movies; the generator is `paper_analysis/make_movies.py` in the repository.


![image](https://cdn-uploads.huggingface.co/production/uploads/623ce1c6b66fedf374859fe7/QWQpfCIPykuvP5jCvTbVs.png)


## Trajectory format

Each `.npz` contains, per stored frame of the loading sequence: `positions` (frames × atoms × 3, Å), `cells` (frames × 3 × 3), `peratom_energy` (eV), `peratom_virial` (eV, three diagonal components), `coordination`, `eps_x`, `eps_y` (engineering strains), `sigma_xx`, `sigma_yy`, `sigma_xy` (2D stress, eV/Ų), `energy` (eV), `n_bonds`, `n_broken_cum` (bonds counted as broken beyond 2.0 Å), and `bonds_<k>` (bond pairs of frame k). The reader used by all analysis
scripts is `carbon_discovery/analysis/fracture_viz.load_traj` in the repository.

## Use with the repository

```bash
git clone https://github.com/lamm-mit/graphene-agent
cd graphene-agent && pip install huggingface_hub
python scripts/fetch_data_from_huggingface.py --what all
```

## License and citation

Please cite the manuscript above and the potential (Brenner et al., J. Phys.: Condens. Matter 14, 783 (2002);
Pastewka et al., Phys. Rev. B 78, 161402(R) (2008); 87, 205410 (2013)). The simulations were carried out by an AI agent
(Claude Fable 5.1 in Claude Code) as described in the manuscript.