CLI Tools Reference

The main driver ensemble_analyzer accepts various command-line arguments to configure the runtime environment, physical constants, and post-processing options.

Input & Flow Control

  • -e, --ensemble (path) The input XYZ file containing the initial conformational ensemble.

  • -p, --protocol (path) Path to the protocol.json file. If omitted, the internal default protocol is used.

  • --restart Resumes the calculation from the last completed protocol step using the generated checkpoint.json.

  • -o, --output (str) Name of the main log file (default: output.out).

Physics & Thermodynamics

  • -T, --temperature (float) Temperature in Kelvin used for Boltzmann weighting and thermochemical analysis (default: 298.15 K).

  • -P, --pressure (float) Pressure in kPa (default: 101.325).

  • --linear Flag to indicate that the molecules should be treated as linear rigid rotors (affects entropy calculations).

  • -cut-off, --cut-off (float) The frequency cut-off value (\(\omega_0\)) for the Grimme qRRHO approximation (default: 100.0 cm⁻¹).

  • -no-H, --exclude-H If set, excludes Hydrogen atoms from RMSD and PCA distance matrix calculations.

  • -cpu (int) Number of CPU cores to allocate for each QM calculation step (default: 1).

  • -calc, --calculator (str) Selects the external QM engine driver. Options: "orca" (default), "gaussian".

Spectral Analysis (Graphing)

  • --fwhm-vibro / --fwhm-electro Define the Full Width at Half Maximum (FWHM) for convolution.

    • Can be a single float (fixed value).

    • Can be a range [min, max] for auto-optimization against a reference spectrum.

  • --shift-vibro / --shift-electro Define the spectral shift parameter.

    • Vibronic (IR/VCD): Multiplicative scaling factor.

    • Electronic (UV/ECD): Additive shift [eV].

  • --invert Inverts the y-axis for chiral spectra (VCD/ECD).

  • --definition (int) Resolution of the spectral grid, defined as \(10^N\) points (default: 4, i.e., 10,000 points).

Utilities

  • -h, --help Shows the main help message.

  • -h-p, --help-protocol Prints a JSON template for the protocol file.

  • -h-t, --help-threshold Prints a JSON template for the threshold file.

  • --disable-color Disables ANSI colored output in the terminal logs.