Plot Atom Property Workflow
Direct command workflow for spatial per-atom property plots.
This module implements CLI workflow orchestration for its command family, including argument parsing, request construction, execution dispatch, and result presentation handoff.
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: plot_atom_property
Arguments
No command-specific arguments found.
The figure below shows an example output plot when plotting the charges of atoms at a specific frame across their 3D coordinates.
Figure: Sample plot for charges of atoms at a specific frame across their 3D coordinates.
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 |
|---|---|---|---|---|
--engine |
No | Engine override. Example: --engine reaxff, which applies ReaxFF-specific loading rules. | reaxff, ams, lammps | |
--input |
No | . | Input file or directory for engine resolution. Example: --input runs/job1, which sets base context for file discovery. | |
--run-dir, --dir |
No | . | Run directory fallback for engine detection. Example: --run-dir runs/job1, which acts as backup lookup path. | |
--xmolout |
No | xmolout | Path to trajectory file. Example: --xmolout runs/job1/xmolout, which provides atom coordinates over frames. | |
--fort7 |
No | fort.7 | Path to fort.7 file. Example: --fort7 runs/job1/fort.7, which provides connectivity/bond-order data. | |
--summary |
No | Optional summary.txt path. Example: --summary runs/job1/summary.txt, which supplies auxiliary simulation metadata when available. | ||
--log |
No | Logging level. Example: --log verbose, which prints more runtime details. | verbose, quiet | |
--run-id |
No | Run identifier for run-scoped layout (e.g., run_91ac0e). | ||
--project-root |
No | Project root that contains inputs/, data/, analysis/, etc. | ||
--analysis-id |
No | Optional analysis artifact id; defaults to run id. | ||
--property |
No | Property to map: charge, q, partial_charge, sum_BOs, connectivity. Example: --property charge, which colors atoms by partial charge. | ||
--frames |
No | Frame selector syntax. Example: --frames 0:20:2, which selects frames 0,2,4,...,20. | ||
--every |
No | 1 | Use every Nth selected frame. Example: --every 5, which subsamples selected frames by a factor of five. | |
--atom-ids |
No | Restrict to selected 1-based atom ids. Example: --atom-ids 1 2 5, which keeps only those atoms. | ||
--atom-types |
No | Restrict to selected atom types/elements. Example: --atom-types O H, which keeps only oxygen and hydrogen. | ||
--save |
No | Directory used when saving frame plots. Example: --save plots3d, which writes one image per frame to that folder. | ||
--show |
No | Show the generated plot windows. Example: --show, which opens plots interactively. | ||
--export |
No | Export the assembled per-atom table to CSV. Example: --export atom_values.csv, which saves coordinates and mapped values. | ||
--vmin |
No | Color scale minimum. Example: --vmin -0.5, which clamps the lower color bound. | ||
--vmax |
No | Color scale maximum. Example: --vmax 0.5, which clamps the upper color bound. | ||
--cmap |
No | Matplotlib colormap. Example: --cmap coolwarm, which sets the visualization color palette. | ||
--type |
Yes | Plot type selector. Example: --type heatmap2d, which projects atom data and aggregates it on a 2D grid. | heatmap2d, scatter3d | |
--size |
No | 8.0 | Marker size for scatter3d. Example: --size 12, which renders larger point markers. | |
--alpha |
No | 0.9 | Marker transparency for scatter3d. Example: --alpha 0.6, which makes points more transparent. | |
--elev |
No | 22.0 | 3D view elevation for scatter3d. Example: --elev 30, which raises the camera tilt angle. | |
--azim |
No | 38.0 | 3D view azimuth for scatter3d. Example: --azim 120, which rotates camera around the scene. | |
--plane |
No | xy | Projection plane for heatmap2d. Example: --plane xz, which projects points onto XZ before binning. | xy, xz, yz |
--bins |
No | 40 | Grid bins for heatmap2d: "N" or "Nx,Ny". Example: --bins 80,60, which sets non-square grid resolution. | |
--agg |
No | mean | Aggregation for heatmap2d: mean|max|min|sum|count. Example: --agg max, which stores the maximum value in each bin. |