vacf_input_file_reader

A module containing a class to read input files to setup the VACF class.

Summary

Classes:

VACFInputFileReader

A class to read input files to setup the

Reference

class VACFInputFileReader(filename: str)[source]

Bases: PQAnalysisInputFileReader

A class to read input files to setup the VACF class.

For the VACF analysis input file several keys are available of which some are required and some are optional. For more details on the grammar and syntax of the input file see Input File.

Required keys
Key	Value
traj_files	The velocity trajectory files to read. This can be a single file or a list of files.
target_selection	The selection string to select the atoms for which the VACF is calculated. For more details see `Selection`.
out_file	The output file to write the VACF data to. It must not exist yet.
time_step	The time step between two frames in ps. It is used to build the time axis of the VACF and the frequency axis of the spectrum.

Optional keys
Key	Value
window	The correlation window size in frames. Default is 1000. It has to be an integer multiple of the gap.
gap	The gap between two time origins in frames. Default is 1.
method	The VACF estimator, either “direct” (legacy-exact sliding origins, default) or “fft” (denser-origin Wiener-Khinchin estimator, ignores the gap).
charge_file	A static charge file for the charge-flux mode. The file consists of a header line with the number of atoms, a comment line and one “name charge” line per atom.
charge_files	Charge trajectory files (.chrg) for the charge-flux mode with time-dependent charges, read in lockstep with the velocity trajectory. Cannot be combined with charge_file.
spectrum_file	The output file for the cosine-transform spectrum of the VACF. If not given, no spectrum is calculated.
ftsize	The Fourier transform point size of the spectrum. The VACF is zero-padded (or truncated) to this size. Default is 2000.
window_function	The apodization window function of the spectrum, one of “none”, “exponential”, “hann” and “blackman”. Default is “none”.
window_param	The decay coefficient of the exponential window. Default is 4.0.
window_start	The time in ps at which the apodization window starts to decay. Default is 0.0.
window_stop	The time in ps at which the apodization window becomes zero. Default is 1000.0.
windowed_out_file	The output file for the windowed VACF. Can only be used together with spectrum_file.
log_file	The log file to write the log information to.
use_full_atom_info	Whether to use full atom information for the selections.

Note

The VACF output file follows the legacy FreqCalc format: one row per lag with the columns lag time in ps and normalized VACF. The spectrum output file follows the legacy ft.f format: one row per frequency index with the columns wavenumber in cm^-1 and amplitude.

Parameters:: filename (str) – the filename of the input file

read()[source]

Reads the input file and parses it. It also sets the raw_input_file and the dictionary. It checks if all required keys are set and if all keys are known.

Raises:

InputFileError – if not all required keys are set in the input file
InputFileWarning – if unknown keys are set in the input file
InputFileError – if both a static charge file and charge trajectory files are given
InputFileError – if a windowed output file is requested without a spectrum file
InputFileError – if the window function is unknown

property charge_file: str | None

The static charge file for the charge-flux mode.

Type:: str | None

charge_file_key = 'charge_file'

property charge_files: list[str] | None

The charge trajectory files for the charge-flux mode.

Type:: List[str] | None

charge_files_key = 'charge_files'

property ftsize: PositiveInt | None

The Fourier transform point size.

Type:: PositiveInt | None

ftsize_key = 'ftsize'

property gap: PositiveInt | None

The gap between two time origins in frames.

Type:: PositiveInt | None

gap_key = 'gap'

logger = <CustomLogger PQAnalysis.VACFInputFileReader (INFO)>

property method: str | None

The VACF estimator method (direct or fft).

Type:: str | None

method_key = 'method'

optional_keys = ['traj_files', 'target_selection', 'out_file', 'time_step', 'window', 'gap', 'method', 'charge_file', 'charge_files', 'spectrum_file', 'ftsize', 'window_function', 'window_param', 'window_start', 'window_stop', 'windowed_out_file', 'log_file', 'use_full_atom_info']

The optional keys of the input file

Type:: List[str]

required_keys = ['traj_files', 'target_selection', 'out_file', 'time_step']

The required keys of the input file

Type:: List[str]

property spectrum_file: str | None

The output file for the VACF spectrum.

Type:: str | None

spectrum_file_key = 'spectrum_file'

property time_step: PositiveReal | None

The time step between two frames in ps.

Type:: PositiveReal | None

time_step_key = 'time_step'

property window: PositiveInt | None

The correlation window size in frames.

Type:: PositiveInt | None

property window_function: str | None

The apodization window function of the spectrum.

Type:: str | None

window_function_key = 'window_function'

window_key = 'window'

property window_param: PositiveReal | None

The exponential window decay coefficient.

Type:: PositiveReal | None

window_param_key = 'window_param'

property window_start: PositiveReal | None

The window start time in ps.

Type:: PositiveReal | None

window_start_key = 'window_start'

property window_stop: PositiveReal | None

The window stop time in ps.

Type:: PositiveReal | None

window_stop_key = 'window_stop'

property windowed_out_file: str | None

The output file for the windowed correlation function.

Type:: str | None

windowed_out_file_key = 'windowed_out_file'