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
General-purpose plotting command for tabular data files. Select plot behavior with --type and provide the related flags for that type.
Examples
1. Single plot:
reaxkit gen-plot --type single --file msd.csv --xaxis c1 --yaxis c2 --plot
2. Directed plot:
reaxkit gen-plot --type directed --file table.csv --xaxis c1 --yaxis c2 --save directed.png
3. Heatmap2d plot:
reaxkit gen-plot --type heatmap2d --file table.csv --x c1 --y c2 --z c3 --value c4 --plane xz --bins 100,80 --save heat_xz.png
Arguments
Scientific choices
| Flag | Required | Default | Help | Choices |
|---|---|---|---|---|
--type |
Yes | Plot type selector. Example: --type single, which enables single-plot mode. | single, directed, dual, tornado, scatter3d, heatmap2d | |
--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. | ||
--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. | |
--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. |
Input and file selection
| Flag | Required | Default | Help | Choices |
|---|---|---|---|---|
--file |
Yes | Path to input txt/csv/tsv table. Example: --file table.csv, which loads plotting data from that file. |
Outputs and plots
| Flag | Required | Default | Help | Choices |
|---|---|---|---|---|
--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 | False | 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 | False | Use scatter instead of line (single mode). Example: --scatter, which switches marker-style rendering. | |
--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. | ||
--vline |
No | Reference vertical line for tornado mode. Example: --vline 0.0, which draws baseline. | ||
--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 |
|---|---|---|---|---|
--output-profile |
No | standard | Artifact profile (default: standard). | standard, minimal, 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. |
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.