https://github.com/bjmorgan/nbo2f_analysis

https://github.com/bjmorgan/nbo2f_analysis

Last synced: about 1 month ago
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• Host: GitHub
• URL: https://github.com/bjmorgan/nbo2f_analysis
• Owner: bjmorgan
• Created: 2026-05-22T10:00:21.000Z (2 months ago)
• Default Branch: main
• Last Pushed: 2026-06-09T20:54:40.000Z (about 1 month ago)
• Last Synced: 2026-06-09T22:20:47.924Z (about 1 month ago)
• Language: Python
• Size: 180 KB
• Stars: 0
• Watchers: 0
• Forks: 0
• Open Issues: 2
• Metadata Files:
  • Readme: README.md
  • Changelog: CHANGELOG.md

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README

          
# nbo2f_analysis

NbO2F-specific infrastructure library for the chirality-emergence

paper. Provides:

- `ce_tools` — atoms builders, F-mask manipulation, orbit-rep loading,

  ground-state construction.

- `chain_geometry` — anion-chain decomposition and chain-aware MC moves

  for the ReO3 topology.

- `cell_symmetry` — whole-cell `<100>` reflection move (`CellReflect`)

  for bridging the enantiomeric chiral basins.

- `rewl` — Replica-Exchange Wang-Landau driver for finite-size scaling

  studies.

- Bundled production CE and 12 N=3 orbit representatives under

  `nbo2f_analysis/data/`.

## Install

From inside a clone of this repo:

    pip install -e .

From anywhere (e.g. ARCHER2):

    pip install git+https://github.com/bjmorgan/nbo2f_analysis.git

Four dependencies are fetched directly from their git remotes rather

than from PyPI: the `icet` fork, `mchammer-pt`, `mchammer-moves`, and

`chainorder`.

**If you have any of those four installed editably from a local

checkout, install this package with `--no-deps`** to avoid pip

replacing those editable installs with fresh wheels:

    pip install -e . --no-deps

Verify the editable installs are intact afterwards with

`pip list | grep -iE "icet|mchammer|chainorder"`.

## REWL driver

    rewl run         [--seed N] [--out-dir DIR] [--force] 

    rewl resume      [--extra-cycles N] [--out-dir DIR] 

    rewl postprocess [--out-dir DIR] 

The driver writes the checkpoint (`rewl_state.h5`), three run-summary

CSVs (`convergence.csv`, `exchange_rates.csv`,

`per_move_rejection_rates.csv`), and a 4-panel WL-health diagnostic

figure (`rewl_diagnostics.png`). Stitching and canonical reweighting

are separate post-processing steps provided by `mchammer-pt`:

    mchammer-pt-stitch rewl_state.h5 -o stitched_dos.csv

    mchammer-pt-reweight stitched_dos.csv --T-min 200 --T-max 800 --T-step 2.0 -o canonical_reweighted.csv

See `nbo2f_analysis/rewl/configs/template.yaml` for the full config

schema.