Glossary

The terms used across the documentation. The same vocabulary, with the names to avoid, is kept for contributors in CONTEXT.md at the repository root.

Activity: The reservoir activity of a chemical species, \(z = e^{\beta \mu}\), with \(\beta = 1/(k_B T)\) and \(\mu\) the species’ chemical potential. Appears in the GCMC insertion and deletion acceptance criteria.
Cell: An object that defines the spatial region in which trial moves are proposed and returns the accessible free volume to the ensemble (the sampling volume of CONTEXT.md; not the lattice atoms.cell). See Cells for the available geometries.
Chemical potential: The thermodynamic driving force the reservoir applies to a species. In mcpy it is supplied per species through the mu argument of GrandCanonicalEnsemble. For a molecular species it is the full molecular chemical potential.
de Broglie wavelength: The thermal de Broglie wavelength \(\Lambda = h / \sqrt{2\pi m\, k_B T}\). Enters GCMC acceptance through the per-species \(\Lambda^3\) factor.
Ensemble: The object that owns the Monte Carlo loop: it stores the atoms and calculator, evaluates acceptance, and writes outputs. See Ensembles.
Exchangeable region: The part of a cell from which atoms and molecules may be deleted and in which they are counted. It equals the insertion region for every cell except CustomCell, whose exchangeable region has no upper z bound, so species that desorb above the window stay deletable.
Exclusion radius: The element-wise radius used by a cell to decide whether a random sample point is occupied by an existing atom. Set through species_radii on each cell; calibrated as described in Calibrating species_radii.
Free volume: The accessible volume \(V_{\mathrm{free}}\) returned by a cell, estimated by Monte Carlo sampling with exclusion radii. Replaces the geometric \(V\) of the textbook GCMC acceptance criteria.
GCMC: Grand Canonical Monte Carlo. Samples the \((\mu, V, T)\) ensemble: temperature and chemical potentials are fixed, the number of selected species fluctuates.
Hybrid GCMC: The variant of GCMC introduced by Senftle et al. in which each trial move is followed by a short local relaxation before acceptance is evaluated. This is the default workflow in mcpy.
Move: A proposed change to the configuration: insertion, deletion, displacement, permutation, shake, or Brownian. Moves are mixed by a MoveSelector. See Moves.
molecule_id: The per-atom integer array that records molecule membership: members of one molecule share a value, free atoms carry -1. It survives rollback and is written to the trajectory.
Molecular species: An exchangeable species that is a rigid molecule, registered with the molecules argument of the ensemble under a name that is also its key in mu. See Simulating molecular adsorbates.
MoveSelector: The weighted sampler that draws a move from a list of registered moves on every MC step and tracks per-move acceptance counters.
Relaxation: Short local geometry optimisation (LBFGS by default) applied to a trial configuration before its energy is used in the acceptance criterion. Mandatory for the hybrid GCMC workflow.
Replica: One independent GCMC trajectory in a Replica-Exchange run - one MPI rank each in ReplicaExchange, or one slot of a single process in BatchedReplicaExchange. Replicas differ in temperature or chemical potential.
Replica Exchange: A wrapper around several GCMC replicas that periodically attempts configuration swaps between neighbouring replicas. The ladder runs along temperature or chemical potential, so the name “parallel tempering” fits only the temperature ladder.
Trajectory: The extended-XYZ file written by the ensemble. Each frame stores atomic positions, the simulation cell, and the current energy on its comment line.
Units type: 'metal' (eV/Å/amu/K) or 'LJ' - selects the set of thermodynamic constants used to compute \(\beta\) and the de Broglie wavelengths. Configured through units_type on the ensemble.