rgpycrumbs.eon.plt_kmc

Visualize an eOn aKMC trajectory: N2 ejection vs simulation time.

Added in version 1.8.0.

Reads an eOn aKMC output directory (dynamics.txt + per-state states/<id>/reactant.con) and plots, against cumulative KMC simulation time:

1. the cumulative number of N2 molecules ejected from the Si core, and

2. the system energy and visited-state index.

An N2 is detected as a bonded N-N pair whose midpoint lies further than a threshold (default 4 Angstrom) from the Si-core center of mass. The reader is robust to partial aKMC directories (missing states are skipped).

Attributes

warn_on_direct_script_import
log
_COLUMN_ALIASES
_DEFAULT_ORDER

Classes

DynamicsStep	One accepted aKMC transition from dynamics.txt.
KmcTimeline	Cumulative N2 ejection and energy vs time across visited states.

Functions

parse_dynamics(→ list[DynamicsStep])	Parse an eOn aKMC dynamics.txt into ordered DynamicsStep.
visited_state_sequence(→ list[int])	Ordered list of visited state ids: initial reactant then each product.
count_ejected_n2(→ int)	Count N2 molecules ejected from the Si core in an ASE Atoms.
collect_kmc_n2_timeline(→ KmcTimeline)	Build the N2-ejection timeline for an eOn aKMC directory.
plot_kmc_timeline(timeline, out_path[, log_time])	Render the two-panel N2-ejection + energy figure to out_path.
main(akmc_dir, out_path, core_threshold, nn_cutoff, ...)	Plot N2 ejection vs KMC time for an eOn aKMC directory.

Module Contents

rgpycrumbs.eon.plt_kmc.warn_on_direct_script_import = None

rgpycrumbs.eon.plt_kmc.log

class rgpycrumbs.eon.plt_kmc.DynamicsStep

One accepted aKMC transition from dynamics.txt.

Added in version 1.8.0.

step: int

reactant_id: int

process_id: int

product_id: int

step_time: float

total_time: float

barrier: float

rate: float

energy: float

rgpycrumbs.eon.plt_kmc._COLUMN_ALIASES

rgpycrumbs.eon.plt_kmc._DEFAULT_ORDER = ['step', 'reactant_id', 'process_id', 'product_id', 'step_time', 'total_time', 'barrier',...

rgpycrumbs.eon.plt_kmc.parse_dynamics(dynamics_file) → list[DynamicsStep]

Parse an eOn aKMC dynamics.txt into ordered DynamicsStep.

Uses the header row to map columns when present; otherwise assumes the canonical eOn column order. Separator and comment lines are skipped.

Added in version 1.8.0.

rgpycrumbs.eon.plt_kmc.visited_state_sequence(steps: list[DynamicsStep]) → list[int]

Ordered list of visited state ids: initial reactant then each product.

Added in version 1.8.0.

rgpycrumbs.eon.plt_kmc.count_ejected_n2(atoms, core_threshold: float = 4.0, nn_cutoff: float = 1.6) → int

Count N2 molecules ejected from the Si core in an ASE Atoms.

An N2 is a bonded N-N pair (separation < nn_cutoff) whose midpoint lies further than core_threshold from the Si-atom center of mass. N atoms are greedily paired nearest-first. Falls back to the all-atom COM as the core reference when no Si atoms are present.

Added in version 1.8.0.

class rgpycrumbs.eon.plt_kmc.KmcTimeline

Cumulative N2 ejection and energy vs time across visited states.

Added in version 1.8.0.

times: list[float]

cumulative_n2: list[int]

energies: list[float]

state_ids: list[int]

rgpycrumbs.eon.plt_kmc.collect_kmc_n2_timeline(akmc_dir, core_threshold: float = 4.0, nn_cutoff: float = 1.6) → KmcTimeline

Build the N2-ejection timeline for an eOn aKMC directory.

Robust to partial directories: states missing reactant.con reuse the previous count. Requires readcon and ase.

Added in version 1.8.0.

rgpycrumbs.eon.plt_kmc.plot_kmc_timeline(timeline: KmcTimeline, out_path, log_time: bool = True)

Render the two-panel N2-ejection + energy figure to out_path.

Added in version 1.8.0.

rgpycrumbs.eon.plt_kmc.main(akmc_dir: pathlib.Path, out_path: pathlib.Path | None, core_threshold: float, nn_cutoff: float, log_time: bool)

Plot N2 ejection vs KMC time for an eOn aKMC directory.