Glossary
Single source of truth for the terms used across the documentation. Every page that mentions one of these terms links back here on first use.
- 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. 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
muargument ofGrandCanonicalEnsemble.- 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.
- 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_radiion 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.- 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, mapped to one MPI rank. Replicas differ in temperature, chemical potential, or both.
- Replica Exchange
A wrapper around several GCMC replicas that periodically attempts configuration swaps between neighbouring replicas with the parallel-tempering acceptance criterion.
- 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 throughunits_typeon the ensemble.