Standalone Tools

ARC ships several Jupyter notebooks under ipython/Tools. They are not embedded web apps in the documentation site; they are notebooks you open and run locally from the repository after activating arc_env.

Run them from the repository root:

conda activate arc_env
jupyter notebook ipython/Tools

The notebooks are useful for diagnostics, geometry inspection, conversion, and small calculations that reuse ARC internals without launching a full ARC project.

Available Notebooks

ARC ESS diagnostics.ipynb

Checks configured servers and reports which electronic structure software ARC can find. Use this after editing ~/.arc/settings.py and ~/.arc/submit.py.

GitHub: ARC ESS diagnostics notebook

conformers.ipynb

Runs ARC conformer-generation utilities for a molecule and lets you inspect candidate conformers before launching expensive ESS jobs.

GitHub: Conformers notebook

coordinates conversions.ipynb

Demonstrates conversions between XYZ strings, ARC XYZ dictionaries, Z-matrices, and related coordinate formats.

GitHub: Coordinate conversions notebook

Plot xyz.ipynb

Visualizes a 3D geometry from XYZ-style input.

GitHub: Plot XYZ notebook

Visualize 1D Torsion scan.ipynb

Plots a one-dimensional rotor scan from ARC scan data.

GitHub: Visualize 1D torsion scan notebook

Visualize 2D Torsion scan.ipynb

Plots a two-dimensional rotor scan from the YAML files ARC creates for scan surfaces. It can also show the conformer closest to selected dihedral values, and lets you change the colormap and resolution of the resulting image.

GitHub: Visualize 2D torsion scan notebook

External symmetry and optical isomers.ipynb

Calculates external symmetry and optical isomer counts from 3D coordinates.

GitHub: External symmetry notebook

Determine harmonic frequencies scaling factor.ipynb

Uses Truhlar’s method to determine a harmonic frequency scaling factor for a selected level of theory.

GitHub: Frequency scaling notebook

Perceive_xyz_(xyz_to_smiles).ipynb

Attempts to infer connectivity and return a SMILES representation from 3D coordinates.

GitHub: XYZ perception notebook

OneDMin script.ipynb

Helps choose r_min and r_max for OneDMin calculations by visualizing bath gas placement around the target species.

GitHub: OneDMin notebook

TS Guesses.ipynb

Demonstrates transition-state guess utilities and inspection workflows.

GitHub: TS guesses notebook

delete all arc jobs.ipynb

Deletes jobs on a selected server whose names start with a_.

Warning

This notebook can cause unintentional loss of data (running jobs). It might delete non-ARC-related jobs, and it will delete ARC jobs of all projects you are currently running on the selected server(s). Use it only when you understand exactly what it does and the selected server, user, and job-name filter.

GitHub: Delete jobs notebook

Demo notebooks are also available under ipython/Demo: