nanobuilder 0.1.0

Standalone crystal-to-cluster builder

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nanobuilder

In this repository are stored the Jupyter Notebooks used to build bare nanoparticle and polarised nanoparticle(including virtual sites) of platonic shapes.

NanoBuilder

NanoBuilder is a standalone crystal-to-cluster package for the QPIAI Matter Group. It borrows architectural ideas from ASE, but it does not import or depend on ASE.

Full usage and project-layout documentation:

• doc/USER_GUIDE.md

Quick setup options:

• local virtual environment with make venv install-dev
• smoke checks with make smoke
• Docker-based run with docker build -t nanobuilder:local . && docker run --rm nanobuilder:local
• CI workflow in .github/workflows/ci.yml

Current features

• Read CIF files with multiple data blocks, loops, cartesian or fractional atom sites, and symmetry-operation expansion.
• Build bulk crystal prototypes from formulas such as Au, Cu, or simple alloys with automatic lattice inference for supported materials.
• Create finite particles from repeated crystals using shape cuts and Wulff-like facet rules.
• Generate advanced motifs such as icosahedra, decahedra, and octahedra.
• Build simple slabs for common surfaces such as FCC(100), FCC(111), BCC(100), and BCC(110).
• Create simple linear polymers and attach them to clusters.
• Export generated structures to XYZ.

Package layout

• nanobuilder/core: atom, lattice, structure, and geometry primitives
• nanobuilder/io: CIF parsing and composition parsing
• nanobuilder/build: bulk and surface constructors
• nanobuilder/builders: generic shape and Wulff-style builders
• nanobuilder/lattice: prototype crystal definitions
• nanobuilder/cluster: advanced nanoparticle motifs
• nanobuilder/spacegroup: lightweight symmetry expansion tools
• nanobuilder/materials: reference lattice data and inference
• nanobuilder/polymers: polymer generation and attachment
• nanobuilder/export: structure writers
• tests: smoke and feature tests
• tools: helper scripts
• examples: runnable examples
• doc: project documentation
• requirements: dependency groups for base, development, and docs

Quick examples

Build a bulk reference from composition:

from nanobuilder.build import bulk

au = bulk("Au")

Build a cluster from CIF input:

from nanobuilder.io import read_cif
from nanobuilder.builders import ClusterBuilder, SphereShape

structure = read_cif("input.cif")
cluster = ClusterBuilder(structure).build(SphereShape(radius=12.0), repetitions=(8, 8, 8))

Build an advanced motif:

from nanobuilder.cluster import IcosahedronBuilder

particle = IcosahedronBuilder("Au", shells=4).build()

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