vibrations

Command Line Tool for Vibrational Analysis

This command line tool calculates vibrational frequencies, force constants, reduced masses, normal modes and optional IR intensities from a structure file and a Hessian file.

For the vibrational analysis input file several keys are available.

Required keys

Key	Value
structure_file	The restart or single-frame XYZ structure file.
hessian_file	The plain square Hessian matrix file.
out_file	The tabular output file.

Optional keys

Key	Value
moldescriptor_file	The moldescriptor file used for IR intensities.
unit	Hessian unit. Options are kcal, hartree and ev. Default is kcal.
hessian_sign	Hessian sign convention. Options are auto, positive, negative, 1 and -1.
normal_modes_file	Optional matrix-format normal-mode output file.
modes_prefix	Optional prefix for one sinusoidal XYZ animation file per selected mode.
modes_file	Optional extended XYZ file with all selected mode vectors and metadata.
modes	Modes to write. Options are all, nonzero, positive, one integer, a list of integers or a range. Explicit mode numbers are one-based.
modes_frames	Number of frames per animated mode trajectory. Default is 30.
modes_amplitude	Maximum displacement in Angstrom for fixed-amplitude animations. Default is 0.25.
modes_temperature	Optional temperature in Kelvin for ASE-style energy-scaled animations.
modes_threshold	Wavenumber threshold in cm-1 for nonzero and positive selections. Default is 1.0e-8.

Summary

Classes:

VibrationsCLI

Command Line Tool for Vibrational Analysis

Functions:

main	Main function for the standalone vibrational analysis CLI.

Reference

class VibrationsCLI

Bases: CLIBase

Command Line Tool for Vibrational Analysis

classmethod add_arguments(

parser: _ArgumentParser,

) → None

Adds the arguments to the parser.

classmethod program_name() → str

Returns the name of the program.

classmethod run(args) → None

Runs the command line tool.

main()

Main function for the standalone vibrational analysis CLI.