spinit 0.0.3

Physically informed spin initialisation for carbon-rich atomistic structures.

Physically informed spin initialisation for atomistic structures

spinit seeds initial magnetic moments to ase.Atoms using local chemistry, topology, and geometry criteria to provide physically motivated spin initialisation. This is useful for e.g. spin-polarised DFT of large structures where spins cannot (reasonably) be manually assigned.

It is designed for carbon-rich systems, including graphenic, nanoporous, and amorphous carbon, as well as mixed chemistries containing heteroatoms such as H, O, and N.

Scientific Scope

spinit is a heuristic spin seed generator.

• It does not prove magnetic ground states.
• It provides physically motivated initial spin patterns to improve exploration of plausible spin solutions.
• It combines undercoordination, local geometry/strain, ring topology, and explicit motif detection.
• Motif labels are heuristic local-environment descriptors (*_like) and do not by themselves assign formal bond order, oxidation state, or molecular charge.

Features

• PBC-aware bond graph construction (ASE + MIC vectors).
• Ring/topology analysis from local graph cycles.
• Hybridization-like local classification (sp, sp2, sp3, distorted variants).
• Motif-aware handling of O/N/H/C-centered local environments.
• Connectivity-aware classification of network-bound vs molecular fragments.
• Transparent additive scoring with configurable thresholds and weights.
• Multiple assignment strategies:
  • fm
  • afm_clusters
  • random_candidates

Installation

git clone https://github.com/joehart2001/spinit.git
cd spinit
pip install -e .

Optional reporting extras:

pip install -e .[reporting]

Quickstart

from ase.io import read
from spinit.api import assign_initial_magnetic_moments

atoms = read("structure.xyz")

magmoms, feature_dict, graph, ring_info = assign_initial_magnetic_moments(
    atoms,
    strategy="afm_clusters",
    cutoff=1.85,
    maxlength=12,
    k_hops=5,
    seed=0,
)

atoms.set_initial_magnetic_moments(magmoms)

Package Layout

• spinit.api: high-level end-to-end API.
• spinit.config: defaults and config merge helpers.
• spinit.graph: graph/ring/geometry/topology utilities.
• spinit.chemistry: hybridization, motif detection, and per-atom feature construction.
• spinit.seeding: magnetic scoring and moment assignment strategies.
• spinit.output: reporting/summary utilities.

Citation

If you use spinit in scientific work, please cite:

@software{spinit,
  author  = {Hart, Joseph},
  title   = {spinit: Physically informed spin initialisation for atomistic structures},
  year    = {2026},
  version = {0.1.0},
  url     = {https://github.com/joehart2001/spinit}
}

Full machine-readable metadata is available in CITATION.cff.