How isif-3/frenkel-ladd-method works
This repository packages a documented Frenkel–Ladd workflow for LAMMPS ACE free-energy calculations: prepare and equilibrate each phase, define Einstein reference positions, run forward/backward switching, integrate the switching work and add reference corrections, then compare phase free energies. The README supports the calculation sequence and the sampled scripts support switching analysis, run inspection, and phase-difference summaries. The input template, skill, and example directories document or demonstrate usage; unsampled internals are represented only where the README establishes their role.
Main entry points: analyze_fl_switching.py Switching integration · 04_workflow.md Workflow guidance · in.lammps LAMMPS input template · 03_lammps_fix_ti_spring.md TI spring switching
Components 19
Calculation workflow
- Workflow guidance
docs/04_workflow.md - LAMMPS input template
templates/in.lammps - Relax and equilibrate
docs/04_workflow.md - Einstein reference positions
docs/04_workflow.md - TI spring switching
docs/03_lammps_fix_ti_spring.md
Analysis tools
- Run inspection
scripts/check_fl_run.py - Switching integration
scripts/analyze_fl_switching.py - Phase comparison
scripts/summarize_phase_differences.py
Guidance and examples
- Theory and formulas
docs/02_formulas.md - Validation guidance
docs/05_validation_checklist.md - Amorphous cautions
docs/06_amorphous_caveats.md - Codex workflow skill
skills/frenkel-ladd-lammps/SKILL.md - Workflow examples
examples
Other components
- Researcher
- Structure and ACE inputs
- LAMMPS
- Switching data
- Phase free energies
- Signed differences
Connections 20
- Researcher → Structure and ACE inputs: provides
- Researcher → Workflow guidance: follows
- Workflow guidance → LAMMPS input template: uses
- Structure and ACE inputs → Relax and equilibrate: supplies inputs
- LAMMPS input template → LAMMPS: configures
- Relax and equilibrate → LAMMPS: runs in
- LAMMPS → Einstein reference positions: minimizes
- Einstein reference positions → TI spring switching: defines reference
- TI spring switching → LAMMPS: runs in
- LAMMPS → Switching data: writes
- Switching data → Run inspection: inspected by
- Switching data → Switching integration: read by
- Switching integration → Phase free energies: calculates
- Theory and formulas → Switching integration: describes formulas
- Phase free energies → Phase comparison: read from CSV
- Phase comparison → Signed differences: reports
- Validation guidance → Researcher: guides checks
- Amorphous cautions → Researcher: warns about
- Codex workflow skill → Researcher: guides use
- Workflow examples → Researcher: demonstrates