vibrational_input_file_reader

Input-file reader for vibrational analysis.

Summary

Classes:

VibrationalAnalysisInputFileReader

A class to read input files for vibrational analysis.

Reference

class VibrationalAnalysisInputFileReader(filename: str)

Bases: PQAnalysisInputFileReader

A class to read input files for vibrational analysis.

For the vibrational analysis input file several keys are available.

The following keys are required:

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. See vibrational-analysis output for its columns and the optional mode-file layouts.

The following keys are optional:

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.

Parameters:

filename (str) – The input file.

read() → None

Read and validate the input file.

property hessian_file: str

The Hessian file.

Type:

str

hessian_file_key = 'hessian_file'

property hessian_sign: str

The Hessian sign convention.

The key accepts the names auto, positive and negative as well as the numbers 1 and -1. A number is returned as its string form, so that the value can be validated and passed on like any other name.

Type:

str

hessian_sign_key = 'hessian_sign'

logger = <CustomLogger PQAnalysis.VibrationalAnalysisInputFileReader (INFO)>

property modes: str | list[int]

The normal modes selected for visualization.

Type:

str | list[int]

property modes_amplitude: float

The maximum displacement in animated mode trajectories.

Type:

float

modes_amplitude_key = 'modes_amplitude'

property modes_file: str | None

The extended XYZ mode file.

Type:

str | None

modes_file_key = 'modes_file'

property modes_frames: int

The number of frames per animated mode trajectory.

Type:

int

modes_frames_key = 'modes_frames'

modes_key = 'modes'

property modes_prefix: str | None

The XYZ mode file prefix.

Type:

str | None

modes_prefix_key = 'modes_prefix'

property modes_temperature: float | None

The ASE-style temperature used to scale modes.

Type:

float | None

modes_temperature_key = 'modes_temperature'

property modes_threshold: float

Wavenumber threshold for named mode selections.

Type:

float

modes_threshold_key = 'modes_threshold'

property normal_modes_file: str | None

The normal-mode matrix output file.

Type:

str | None

normal_modes_file_key = 'normal_modes_file'

optional_keys = ['structure_file', 'hessian_file', 'out_file', 'moldescriptor_file', 'unit', 'hessian_sign', 'normal_modes_file', 'modes_prefix', 'modes_file', 'modes', 'modes_frames', 'modes_amplitude', 'modes_temperature', 'modes_threshold']

required_keys = ['structure_file', 'hessian_file', 'out_file']

property structure_file: str

The structure file.

Type:

str

structure_file_key = 'structure_file'

property unit: str

The Hessian unit.

Type:

str

unit_key = 'unit'