vacf

Command Line Tool for VACF Analysis

This command line tool can be used to calculate the normalized velocity auto-correlation function (VACF) of given velocity trajectory file(s) using multiple time origins on a sliding window. In the charge-flux mode the velocities are weighted with static or time-dependent atomic partial charges. Optionally, the legacy cosine-transform spectrum of the VACF is calculated. This is an input file based tool, so that the input file can be used to specify the parameters of the VACF calculation. For more information on the general the VACF analysis and its input file options please visit PQAnalysis.analysis.vacf.vacf.VACF and PQAnalysis.analysis.vacf.vacf_input_file_reader

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.

Summary

Classes:

VACFCLI

Command Line Tool for VACF Analysis

Functions:

main

The main function of the VACF analysis command line tool, which is basically just a wrapper for the vacf function.

Reference

class VACFCLI[source]

Bases: CLIBase

Command Line Tool for VACF Analysis

classmethod add_arguments( parser: _ArgumentParser, ) → None[source]

Adds the arguments to the parser.

Parameters:: parser (_ArgumentParser) – The parser to which the arguments should be added.

classmethod program_name() → str[source]

Returns the name of the program.

Returns:: The name of the program.
Return type:: str

classmethod run(args)[source]

Runs the command line tool.

Parameters:: args (argparse.Namespace) – The arguments parsed by the parser.

main()[source]: The main function of the VACF analysis command line tool, which is basically just a wrapper for the vacf function. For more information on the vacf function please visit PQAnalysis.analysis.vacf.api.vacf().