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Gen Plot Workflow

General-purpose plotting workflow for ReaxKit.

This workflow provides flexible plotting utilities for arbitrary tabular data (text, CSV, TSV, or whitespace-delimited files), without assuming any specific ReaxFF file format or column headers.

It supports multiple plot types, including: - single and multi-series line or scatter plots, - directed (arrowed) line plots, - dual y-axis plots, - tornado plots for sensitivity-style visualization, - 3D scatter plots with scalar coloring, - 2D aggregated heatmaps projected from 3D data.

Columns are selected using simple 1-based column tokens (e.g. c1, c2, c3), making the workflow suitable for rapid visualization of simulation outputs, summaries, and post-processed analysis tables.

Usage context

  • Command routing: Resolve CLI aliases and normalized command names.
  • Task execution: Build request objects and invoke registered tasks.
  • Output handling: Forward results to table, plot, export, or report flows.

Command: gen-plot

Arguments

No command-specific arguments found.

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.

Flag Required Default Help Choices
--type Yes Plot type selector. Example: --type single, which enables single-plot mode. single, directed, dual, tornado, scatter3d, heatmap2d
--file Yes Path to input txt/csv/tsv table. Example: --file table.csv, which loads plotting data from that file.
--save No Path to save plot (file or directory). Example: --save figures/msd.png, which writes the generated figure to that path.
--title No Optional custom plot title. Example: --title "MSD vs Time", which overrides the default auto title.
--plot No Generate and display/save the plot. Example: --plot, which opens the plot interactively when supported.
--xaxis No X column(s), format depends on --type. Example: --xaxis c1,c3, which selects x columns for single/dual/directed.
--yaxis No Y column(s), format depends on --type. Example: --yaxis c2,c4, which selects y columns for single/directed.
--xlabel No Optional x-axis label. Example: --xlabel Time, which customizes axis text.
--ylabel No Optional y-axis label. Example: --ylabel MSD, which customizes axis text.
--scatter No Use scatter instead of line (single mode). Example: --scatter, which switches marker-style rendering.
--y1 No Left y-axis column for dual mode. Example: --y1 c2, which maps c2 to left axis.
--y2 No Right y-axis column for dual mode. Example: --y2 c3, which maps c3 to right axis.
--ylabel1 No Optional left y-axis label. Example: --ylabel1 Temp, which labels left axis.
--ylabel2 No Optional right y-axis label. Example: --ylabel2 Pressure, which labels right axis.
--label No Label column for tornado mode. Example: --label c1, which provides tornado labels.
--min No Minimum-value column for tornado mode. Example: --min c2, which sets low bound column.
--max No Maximum-value column for tornado mode. Example: --max c3, which sets high bound column.
--median No Optional median column for tornado mode. Example: --median c4, which adds median markers.
--top No 0 Top-N for tornado mode. Example: --top 10, which keeps widest 10 bars.
--vline No Reference vertical line for tornado mode. Example: --vline 0.0, which draws baseline.
--x No X coordinate column for scatter3d/heatmap2d. Example: --x c1, which maps column 1 to x.
--y No Y coordinate column for scatter3d/heatmap2d. Example: --y c2, which maps column 2 to y.
--z No Z coordinate column for scatter3d/heatmap2d. Example: --z c3, which maps column 3 to z.
--value No Value column for scatter3d/heatmap2d color/aggregation. Example: --value c4, which supplies scalar values.
--plane No xy Projection plane for heatmap2d. Example: --plane xz, which projects onto XZ. xy, xz, yz
--bins No 50 Heatmap bins: int or nx,ny. Example: --bins 100,80, which sets asymmetric grid resolution.