structure-models - SKILL.md Agent Skill

name: structure-models description: Advanced Structure Models (8 sub-skills: alloy-builder, defect-builder, heterostructure, moire-superlattice, nanowire-nanotube, quantum-dot, supercell-builder, surface-builder)

Advanced Structure Models

Overview

This skill group covers construction of advanced structural models for computational materials science. It corresponds to VASPKIT menu 08 (tasks 800--827) and provides equivalent functionality using Python tools (pymatgen, ASE, spglib), with output in CIF, POSCAR, and QE input formats.

Sub-Skills

Sub-Skill	Directory	Description
Supercell Builder	`supercell-builder/`	Build supercells (diagonal and non-diagonal), orthogonal supercells from non-orthogonal cells. (VASPKIT 800, 401)
Surface Builder	`surface-builder/`	Build surface slabs by Miller indices using pymatgen SlabGenerator. (VASPKIT 803)
Alloy Builder	`alloy-builder/`	Random substitutional alloys, SQS (Special Quasi-random Structure) generation. (VASPKIT 802)
Heterostructure	`heterostructure/`	Build heterostructures from two slabs, lattice matching. (VASPKIT 804)
Nanowire/Nanotube	`nanowire-nanotube/`	Build nanowires, nanotubes, quantum dots, nanoribbons. (VASPKIT 806--808)
Defect Builder	`defect-builder/`	Build point defects (vacancies, substitutions, interstitials) in supercells. (VASPKIT 821--822)

Method Decision Guide

Need a supercell?
  Simple NxNxN --> supercell-builder/ (make_supercell)
  Orthogonal from non-orthogonal --> supercell-builder/ (CubicSupercellTransformation)

Need a surface slab?
  --> surface-builder/ (SlabGenerator by Miller index)

Need an alloy model?
  Random alloy --> alloy-builder/ (random substitution)
  Ordered representative --> alloy-builder/ (SQS via icet or pymatgen)

Need a heterostructure (interface)?
  --> heterostructure/ (ZSLGenerator for lattice matching)

Need a nanostructure?
  Nanowire --> nanowire-nanotube/ (carve from bulk)
  Nanotube --> nanowire-nanotube/ (roll a sheet)
  Nanoribbon --> nanowire-nanotube/ (cut from 2D sheet)

Need a defect model?
  Vacancy, substitution, interstitial --> defect-builder/

Common Prerequisites

pymatgen: pre-installed (Structure, SlabGenerator, SubstitutionTransformation, etc.)
ASE: pre-installed (structure manipulation, visualization)
spglib: pre-installed (symmetry analysis)
numpy: pre-installed
Optional: pip install icet for SQS generation, pip install pymatgen-analysis-defects for advanced defect workflows