phase-transition - SKILL.md Agent Skill

name: phase-transition description: Phase Transitions (6 sub-skills: amorphous-structure, melting-point-coexistence, metadynamics, mpmorph-melting, order-parameter, phase-diagram)

Phase Transitions

Melting point determination, amorphous structure generation, free energy surface exploration via metadynamics, and solid-solid phase transition analysis using molecular dynamics and energy-based methods.

Sub-Skills

Sub-Skill	Directory	Description
MPMorph Melting	`mpmorph-melting/`	Melting point determination via heating curves, Lindemann criterion, two-phase coexistence, and liquid structure analysis (ASE+MACE or LAMMPS)
Amorphous Structure	`amorphous-structure/`	Amorphous/glassy structure generation via melt-quench MD; structural analysis (RDF, coordination, bond angles, structure factor); glass transition temperature
Melting Point Coexistence	`melting-point-coexistence/`	Melting point via solid-liquid coexistence method (two-phase simulation); more accurate than heating curves; MACE or LAMMPS
Metadynamics	`metadynamics/`	Free energy surface exploration via well-tempered metadynamics; bias potential on collective variables (distance, coordination number, volume, Steinhardt Q6); ASE+MACE or LAMMPS+PLUMED; FES reconstruction and convergence analysis

Method Decision Guide

What phase transition property do you need?

Melting point / melting temperature?
  --> mpmorph-melting/  (heating curve or Lindemann criterion)
  --> melting-point-coexistence/  (solid-liquid coexistence, more accurate)

Liquid structure (RDF, diffusion, viscosity)?
  --> mpmorph-melting/  (high-temperature MD above Tm)

Amorphous / glassy structure generation?
  --> amorphous-structure/  (melt-quench protocol)

Glass transition temperature (Tg)?
  --> amorphous-structure/  (volume vs T during quench)

Structural analysis of disordered phase (RDF, coordination, bond angles)?
  --> amorphous-structure/  (post-processing tools)

Free energy surface / barrier for rare events (phase transition, diffusion, reaction)?
  --> metadynamics/  (well-tempered metadynamics with ASE+MACE or LAMMPS+PLUMED)

Free energy landscape along structural order parameters (Q4, Q6)?
  --> metadynamics/  (Steinhardt CV with PLUMED)

Quick screening vs. publication accuracy?
  Quick --> ASE + MACE (both sub-skills support this)
  Publication --> LAMMPS with validated potential (mpmorph-melting/) or larger MACE supercells