rust-knot-cli

name	rust-knot-cli
description	Run and troubleshoot rust_knot for XYZ files with the global entrypoint (~/.local/bin/rust_knot and /home/yongjian/.local/share/rust_knot/table_knot_Alexander_polynomial.txt). Use for command construction, flag handling, and output interpretation.

Rust Knot CLI

Entrypoint

• BIN=~/.local/bin/rust_knot
• TABLE=/home/yongjian/.local/share/rust_knot/table_knot_Alexander_polynomial.txt

Default to this entrypoint unless user asks to override.

Quick Use

$BIN input.xyz --table "$TABLE"
$BIN trajectory.xyz --table "$TABLE" --ring --threads 8 --batch 128 --output result.txt
$BIN input.xyz 3_1 --table "$TABLE"

Rules

• First positional arg is xyz_file.
• Next non-flag positional token is target_type.
• Use --threads;
• --ring flag for ring closure, default is open chain analysis with convex hull closure.
• Unknown flags only warn and can shift parsing.
• Default output file is knot_index.txt.

Debug

• Commands: references/commands.md
• Troubleshooting: references/troubleshooting.md
• Smoke script: scripts/smoke_cli.sh