calphy

Plugin calphy from marketplace calphy-skills in thermoatoms/calphy-skills. Commands read from the repo's manifest — 1 month ago.

Skills (10)

• 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 b

• 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 right

• 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 meltin

• 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", "legacy

• 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 th

• 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 l

• 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 progr

• 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,

Similar plugins