Large-scale examples¶

The repository includes small-scale variants of each example (reduced system sizes) for quick testing. For production-scale validation and regression testing, large-scale variants are available. Their inputs are sourced from the bakery project.

Layout¶

Each example directory has a large/ subdirectory:

Example	Small-scale (root)	Large-scale (`large/`)
Dodecane	`examples/dodecane/`	`examples/dodecane/large/`
PE	`examples/pe/`	`examples/pe/large/`
PE4	`examples/pe4/`	`examples/pe4/large/`
PE-10	`examples/pe_10/`	`examples/pe_10/large/`
PE-AA	`examples/pe_aa/`	`examples/pe_aa/large/`
Melamine	`examples/melamine/`	`examples/melamine/large/`

The large/ directory holds (or documents how to obtain) bakery-scale inputs and generated LAMMPS files.

Source of large-scale inputs¶

Large-scale coordinates, topologies, and tabulated potentials come from bakery:

Bakery repository: bakery-cg2at/bakery
Paths: bakery/examples/<name>/ (and bakery/tests/<name>/ where needed)
Typical sizes: e.g. 75 chains for PE systems, ~500 molecules for melamine

Each examples/<name>/large/README.md describes which files to copy and how to refresh them from bakery.

How to run large-scale examples¶

Obtain inputs Copy the required files from bakery into examples/<name>/large/ as described in that directory’s README.
Generate LAMMPS input and data From the repository root:
```
cd python && uv run backmap-prep ../examples/<name>/large/settings.yaml
```
Output (.data and in.<name>) is written according to the paths in settings.yaml (often into the same large/ directory).
Run LAMMPS (optional) From the directory that contains the generated files:
```
lmp -in in.<name>
```

Large-scale runs can be slow; use short test runs or reduced output frequency if you only need to verify the pipeline.

Optional validation script¶

A script is provided to verify that backmap-prep runs successfully on at least one large-scale example (file generation only; it does not run LAMMPS). From the repository root:

./scripts/validate-large-scale-prep.sh dodecane

You can pass any example name (dodecane, pe, pe4, pe_10, pe_aa, melamine) to validate that example's large-scale settings. This is suitable for CI or manual checks.