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Get Potential Energy Workflow

Dedicated workflow for potential-energy time series.

Command: get_potential_energy

Get potential energy as a time series.

Examples

  reaxkit get_potential_energy --summary summary.txt --plot single
  reaxkit get_potential_energy --summary summary.txt --per-atom --plot single --save pot_en_per_atom.png

Arguments

Scientific choices

Flag Required Default Help Choices
--frames No Frame selector, for example --frames 0:20:2 or --frames 0,5,10.
--every No 1 Keep every Nth selected frame.
--frame-source No Trajectory file whose headers define frame iterations when no control file exists. By default, the configured or sibling xmolout is used.
--frame-count No Total trajectory frame count used to infer frame spacing only when neither a control file nor a trajectory frame source exists.
--per-atom No False Divide potential energy by the number of atoms in each frame. The atom counts are read from xmolout and may vary across frames.

Input and file selection

Flag Required Default Help Choices
--engine No reaxff, ams, lammps
--input No . Input file or directory used for engine detection.
--run-dir No . Run directory used as a fallback for input discovery.
--xmolout No xmolout Trajectory input path.
--summary No Optional summary.txt input path.
--control No control Control file used for frame (iout2) and time conversion. The default also searches beside the selected input files.

Outputs and plots

Flag Required Default Help Choices
--plot No Plot all series together (single), in one multi-panel figure (subplot), or as one figure file per series (separate). single, subplot, separate
--show No False
--save No
--export No
--grid No Subplot grid such as 2x2.
--xaxis No iter iter, frame, time
--detail-format No Optional detail format (default: Parquet; legacy: CSV). parquet, csv

Execution

Flag Required Default Help Choices
--execution No auto Execution backend; unsupported backends fall back to serial with a logged reason. auto, serial, threads, processes
--workers No 0 Frame workers: auto or N (default: auto).
--chunk-size No 0 Maximum in-flight frames: auto or N.

Storage and cache

Flag Required Default Help Choices
--run-id No Run identifier for run-scoped layout. Example: --run-id run_91ac0e, which reuses that run identifier.
--project-root No reaxkit_workspace Project root that contains inputs/, data/, analysis/, etc. Example: --project-root ./workspace, which stores run artifacts there.
--analysis-id No Optional analysis artifact id; defaults to run id. Example: --analysis-id comparison-a, which names the analysis artifact explicitly.
--input-cache, --no-input-cache No True Reuse parsed input frames across commands (default: enabled; use --no-input-cache to force source reads for reproducibility checks or benchmarks). Example: --no-input-cache, which reloads frames from their source files.
--frame-cache-max-gb No 10.0 Maximum workspace frame-cache size in GiB (default: 10; use 0 for unlimited). Example: --frame-cache-max-gb 20, which caps cached frames at 20 GiB.
--output-profile No standard Select the shared artifact policy. Standard writes declared default outputs; minimal keeps core tables; full and legacy include optional details. Default: standard. Example: --output-profile full, which includes declared optional detail tables. minimal, standard, full, legacy

Diagnostics and compatibility

Flag Required Default Help Choices
-h, --help No show this help message and exit
--help-all, --all-flags No Show every option, grouped by purpose.
--log No verbose, quiet

Common Runtime and Presentation Arguments

These are shared workflow-level CLI flags added before command-specific options, covering runtime context (engine/input/storage) and output presentation/export behavior.

Each command table above includes its shared and inherited options.