Nonadiabatic Nanoreactor Use Guide¶

Last updated: October 2025
Primary Branch: major (used by Pierilab in the Martinezlab repo)

This page is an evolving “Best Use Guide” for beginners — please update it whenever YAML formatting or workflow structures change.

Important External Info¶

GitHub: Nonadiabatic Nanoreactor – major branch
Paper: Chemical Science (2021)

The Science behind NANR¶

The NANR explores photochemical reactivity by combining metadynamics and seam constraints to locate conical intersections efficiently.

The Environment¶

❗ Make sure to conda activate nanr before running.

Recommended Directory Structure¶

<molecule>/
├── seam_sampling/
│   ├── molecule.xyz
│   ├── seam_sampling.yaml
│   ├── seam_traj.xyz
│   └── clustering/
│       ├── full_geom_seam.xyz
│       ├── clustering.yaml
│       ├── ciopt0/
│       │   ├── centroid0.xyz
│       │   ├── tc.in
│       │   ├── submit.sh
│       │   └── cone_sampling/
│       │       ├── ci0.xyz
│       │       ├── sampling.yaml
│       │       ├── ci0_radial_XXXX.xyz
│       │       └── O0/
│       │           ├── opt.in
│       │           ├── submit.sh
│       │           └── scr.start/optim.xyz
└── logs/, figures/, or results/ (optional)