---
title: "calphy"
description: "Agent skills for installing, running, analysing, and troubleshooting calphy free-energy calculations with LAMMPS."
canonical: https://agentpluginsdirectory.com/plugins/calphy
last-updated: 2026-09-11
---

# calphy
Agent skills for installing, running, analysing, and troubleshooting calphy free-energy calculations with LAMMPS.
- Slug: calphy
- Publisher: Sarath Menon
- Repository: https://github.com/thermoatoms/calphy-skills
- Manifest: plugin.json
- Version: 0.2.0
- License: MIT
- Category (editorial): other
- Skills: 10 (calphy-alchemy, calphy-analyse-results, calphy-choose-mode, calphy-free-energy, calphy-input-file, calphy-install, calphy-melting-temperature, calphy-run, calphy-temperature-sweep, calphy-troubleshoot)
- MCP servers: 0
- Stars: 0
- Repository created: 2026-09-10
- Repository last pushed: 2026-09-10
- Publisher type: Organization
- Listing: https://agentpluginsdirectory.com/plugins/calphy
- Schema: https://agent-plugins.org/schemas/1.0.0/plugin.schema.json

## What calphy does, in the publisher's words

Agent skills for calphy, the free-energy calculation code built on LAMMPS. Each skill is a SKILL.md folder in the Agent Skills format and works with OpenAI Codex and Claude Code. The skills help an AI agent install calphy, write a valid input, pick the right calculation, run it on a laptop or cluster, read the results, and judge whether they can be trusted.

Written against calphy 2.1.2. The keyword table and error messages were taken from the calphy source and the test inputs were run against a real LAMMPS binary.

From the project README, punctuation lightly normalized. Full text: https://raw.githubusercontent.com/thermoatoms/calphy-skills/HEAD/README.md

## Skills

- calphy-alchemy: Run calphy alchemical transformations: `mode: alchemy` to get the free-energy difference between two interatomic potentials for the same structure (upsampling a cheap potential to an expensive one, comparing potentials), and `mode: composition_scaling` to get the free-energy change with composition…
- calphy-analyse-results: Read and interpret calphy output: report.yaml fields, temperature_sweep.dat and pressure_sweep.dat, forward/backward switching files, logs, and the `calphy.postprocessing` helpers (`read_report`, `gather_results`, `find_transition_temperature`), including how to combine runs, propagate errors, and…
- calphy-choose-mode: Decide which calphy calculation mode and settings answer a thermodynamics question (free energy at a state point, free energy vs temperature or pressure, melting point, solid-solid transition, phase diagram, potential comparison, composition dependence, specific heat) and whether calphy is the righ…
- calphy-free-energy: Run a calphy `mode: fe` (or `fe-qtb`) calculation to get the absolute Helmholtz or Gibbs free energy of a solid or liquid at one temperature and pressure, and judge whether the number can be trusted. Use for single-point free energies, Einstein-crystal or Uhlenbeck-Ford reference runs, liquid melti…
- calphy-input-file: Write or fix a calphy `input.yaml` that passes calphy 2.x validation. Use when creating an input file for any calphy calculation, converting a v1 (top-level keys) file to the v2 `calculations:` list, or resolving a pydantic validation error such as "unknown key", "Element ordering mismatch", "legac…
- calphy-install: Install calphy and a LAMMPS binary that has the packages calphy needs, then verify the setup with a preflight check. Use when setting up calphy for the first time, when `lmp` cannot be found, when a run fails with a missing LAMMPS package or a pair_style/fix "unrecognized" error, or when enabling t…
- calphy-melting-temperature: Compute a melting point with calphy, either automatically with `mode: melting_temperature` or manually from solid and liquid `ts` sweeps whose free-energy curves cross, and decide whether the resulting Tm is trustworthy. Use for melting temperatures of single-component or alloy potentials, melting…
- calphy-run: Launch, monitor, and rerun calphy calculations: `calphy_kernel` for one calculation in the foreground, `calphy` to submit every entry through the local, SLURM, or SGE scheduler, hand-written batch scripts, MPI core counts, the pylammpsmpi library backend, the in-process Python API, and reading prog…
- calphy-temperature-sweep: Run calphy reversible scaling (`mode: ts`), direct temperature scaling (`mode: tscale`), or pressure scaling (`mode: pscale`) to get the free energy of one phase as a continuous function of temperature or pressure, and check the sweep for hidden phase transitions. Use for F(T) or G(P) curves, solid…
- calphy-troubleshoot: Diagnose a failed, hanging, or suspicious calphy run from its error text, calphy.log, LAMMPS segment logs, and report.yaml. Covers pair_style/pair_coeff and potential-path errors, MEAM and ML potentials, Kokkos and hybrid/scaled, pressure not converging, lost atoms, melted solids and frozen liquids…

Descriptions come from the frontmatter of each SKILL.md, punctuation lightly normalized.