FAQs#

My LAMMPS run dies immediately with a pair_style / pair_coeff error.

The most common cause is that the pair_coeff element list does not match the element list (or is in a different order). For multi-element systems calphy enforces strict ordering: element[i] is mapped to LAMMPS atom type i+1, and the elements at the end of pair_coeff must appear in the same order. Reorder both lists so they agree.

calphy_kernel complains that the simulation folder already exists.

calphy refuses to overwrite an existing run folder so that data is never silently lost. Either remove the offending mode-lattice-temp-pressure directory or set folder_prefix to a unique tag.

My liquid free-energy calculation reports MSD = 0 / spring constant warnings.

This happens when the structure has not actually melted during the equilibration cycle. Increase temperature_high (calphy will overheat to this value before quenching) and/or set melting_cycle: True.

My liquid free-energy calculation loses atoms during the integration (ERROR: Lost atoms).

This is most common for molecular liquids (e.g. water) where the single-component Uhlenbeck–Ford reference cannot represent two well-separated length scales. There are two distinct failure modes:

  • Detonation — the UFM energy spikes just before the crash. The single sigma is larger than a bonded distance, so bonded pairs sit inside the UFM repulsive core and are blown apart. Use the two-leg path with a per-element-pair sigma dict and a small cross-term (e.g. H_O: 0.9) so bonded pairs stay outside the core.

  • Drift — atoms wander off slowly with no energy spike. The UFM is purely repulsive, so once the real potential is switched off the reference must confine the atoms on its own; a too-small p (the confinement is p in units of kB·T) lets light atoms escape. Increase p (the default 50 is usually sufficient).

The two effects are independent: sigma controls detonation, p controls drift. See the uhlenbeck_ford_model block for the two-leg setup.

How do I run calphy with the GPU / KOKKOS package?

Use the md.cmdargs keyword to pass the standard LAMMPS accelerator command-line arguments:

md:
  cmdargs: "-k on g 1 -sf kk -pk kokkos newton on neigh half"