mat-disorder

Generate ordered crystal candidates from disordered CIF/POSCAR inputs using Ewald-energy sampling.

144|21|Updated Jan 8, 2026
One-click install
npx skills add https://github.com/learningmatter-mit/AtomisticSkills --skill mat-disorder
Or copy as Structured Prompt for Agent
Please help me install this Agent Skill.
Skill: mat-disorder
Source: https://github.com/learningmatter-mit/AtomisticSkills/tree/main/.agents/skills/mat-disorder
Command: npx skills add https://github.com/learningmatter-mit/AtomisticSkills --skill mat-disorder

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires pymatgen, ase, numpy, sklearn, scipy, pytorch, smol, pymatgen-ase-adaptor, and includes scripts (resource) components.

What problem does it solve?

Disordered or partially occupied crystal structures are hard to convert into clean, ordered atomic configurations suitable for downstream energy, phase-stability, or model-training calculations.

Core Features & Use Cases

  • Generates ordered candidates from partial occupancies: Produces stoichiometry-consistent ordered structures starting from CIF/POSCAR-like inputs with fractional site occupancies.
  • Ranks candidates using Ewald-energy sampling: Uses an Ewald-based solver (fast ALGO_FAST) to prioritize configurations with lower electrostatic repulsion while still sampling beyond only the absolute minimum.
  • Provides structures ready for relaxation and CE/MLIP workflows: Outputs ordered ASE structures that can be used as starting points for ground-state property calculations, phase stability analysis, or cluster-expansion/MLIP training pipelines.

Quick Start

Ask the agent to generate 50 ordered candidates from disordered.cif by running the ordering script with a target of 50 atoms per structure.

Frequently Asked Questions about mat-disorder

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I generate ordered crystal structures from disordered CIF files with partial occupancies?

To generate ordered crystal structures from disordered CIF files with partial occupancies, use an Ewald-energy based ordering transformation with ALGO_FAST. This samples stoichiometry-consistent orderings and ranks candidates by electrostatic repulsion to output clean configurations.

Can I use pymatgen to convert fractional occupancy sites for cluster expansion training?

Yes, you can use pymatgen to convert fractional occupancy sites for cluster expansion training. The process generates ordered candidates from disordered inputs and outputs ASE structures suitable for CE and MLIP training pipeline preparation.

What is the best way to sample ordered candidates from partially occupied structures for phase stability studies?

The best way to sample ordered candidates from partially occupied structures for phase stability studies is using an Ewald-energy based solver. It prioritizes lower electrostatic repulsion configurations via ALGO_FAST while sampling beyond the absolute minimum to provide diverse candidates.

Does this ordering workflow require a specific target atom count for supercell expansion?

Yes, this ordering workflow requires a specific target atom count for supercell expansion. The transformation tunes supercell expansion to reach a target number of atoms per structure, ensuring the generated ordered configurations match your desired calculation scale.

Why does my disordered crystal structure need stoichiometry-consistent ordering before ground-state property calculations?

Disordered crystal structures need stoichiometry-consistent ordering before ground-state property calculations because partial occupancies create fractional sites unsuitable for direct energy computation. Generating ordered candidates preserves the original stoichiometry while providing clean atomic configurations for accurate relaxation.

What input format preserves occupancy information for generating ordered atomic configurations?

CIF or POSCAR-like input files preserve occupancy information for generating ordered atomic configurations. These formats maintain fractional site occupancy data required by the Ewald-energy ordering transformation to sample and rank stoichiometry-consistent ordered structures.