Liouville Pathway Analysis

Liouville pathway analysis module

This module defines classes and function to help in Liouvile pathway analysis

Classes

LiouvillePathwayAnalyzer

Functions

max_amplitude(pathways)

class quantarhei.spectroscopy.pathwayanalyzer.LiouvillePathwayAnalyzer(pathways=None)

Class providing methods for Liouville pathway analysis

Parameters:pathways (list) – List of pathways to analyze

set_pathways(pathways=None)

Set the pathways for the analysis

get_pathways()

Returns current list of pathways

max_amplitude()

Returns a tuple containing the value of the amplitude of the pathway from current list of pathways with the maximum amplitude and its index in the list

select_amplitide_GT(val, replace=True, verbose=False)

In the current list of pathways this method selects those that have absolute value of amplitude larger that a given value

Methods

get_number_of_pathways()	Returns the number of available pathways
get_pathways()	Returns Liouville pathways
max_amplitude()	Return the maximum of pathway prefactors
max_pref(pathways)	Return the maximum of pathway prefactors
order_by_pref(pthways)	Orders the list of pathways by pathway prefactors
select_amplitude_GT(val[, replace, verbose])	Select all pathways with abs value of prefactors greater than a value
select_frequency_window(window[, replace, …])	Selects pathways with omega_1 and omega_3 in a certain range
select_omega2(interval[, replace, verbose])	Selects pathways with omega_2 in a certain interval
select_pref_GT(val[, pathways, replace, verbose])	Select all pathways with prefactors greater than a value
set_pathways(pathways)	Sets pathways to be analyzed

convert_energy_2_current_u
convert_energy_2_internal_u
convert_length_2_current_u
convert_length_2_internal_u
order_by_amplitude
select_sign
select_type
unit_repr
unit_repr_latex

get_number_of_pathways()

Returns the number of available pathways

get_pathways()

Returns Liouville pathways

max_amplitude()

Return the maximum of pathway prefactors

Parameters:pathways (list) – List of Liouville pathways Returns:

• pmax (float) – Maximum prefactor of the pathways
• rec (int) – position of the pathway with the maximum prefactor

max_pref(pathways)

Return the maximum of pathway prefactors

Parameters:pathways (list) – List of Liouville pathways Returns:

• pmax (float) – Maximum prefactor of the pathways
• rec (int) – position of the pathway with the maximum prefactor

order_by_pref(pthways)

Orders the list of pathways by pathway prefactors

select_amplitude_GT(val, replace=True, verbose=False)

Select all pathways with abs value of prefactors greater than a value

select_frequency_window(window, replace=True, verbose=False)

Selects pathways with omega_1 and omega_3 in a certain range

select_omega2(interval, replace=True, verbose=False)

Selects pathways with omega_2 in a certain interval

select_pref_GT(val, pathways=None, replace=True, verbose=False)

Select all pathways with prefactors greater than a value

set_pathways(pathways)

Sets pathways to be analyzed

quantarhei.spectroscopy.pathwayanalyzer.get_TwoDSpectrumContainer_from_saved_pathways(t1axis, t3axis, name='pathways', ext='qrp', directory='.', tag_type=<class 'numpy.float64'>)

Returns a container with 2D spectra calculated from saved pathways

quantarhei.spectroscopy.pathwayanalyzer.get_TwoDSpectrum_from_pathways(pathways, t1axis, t3axis)

Returns a 2D spectrum calculated based on submitted Liouville pathways

quantarhei.spectroscopy.pathwayanalyzer.get_TwoDSpectrum_from_saved_pathways(t2, t1axis, t3axis, name='pathways', ext='qrp', directory='.', tag_type=<class 'numpy.float64'>)

Returns a 2D spectrum calculated based on the saved Liouville pathways

quantarhei.spectroscopy.pathwayanalyzer.get_evolution_from_saved_pathways(states, name='pathways', ext='qrp', directory='.', tag_type=<class 'numpy.float64'>, repl=0.0)

Reconstructs the evolution of the pathway contribution in t2 time

quantarhei.spectroscopy.pathwayanalyzer.get_prefactors_from_saved_pathways(states, name='pathways', ext='qrp', directory='.', tag_type=<class 'numpy.float64'>, repl=0.0)

Reconstructs the evolution of the pathway contribution in t2 time

quantarhei.spectroscopy.pathwayanalyzer.load_pathways_by_t2(t2, name='pathways', ext='qrp', directory='.', tag_type=<class 'numpy.float64'>)

Load pathways by t2 time

quantarhei.spectroscopy.pathwayanalyzer.look_for_pathways(name='pathways', ext='qrp', check=False, directory='.')

Load pathways by t2

quantarhei.spectroscopy.pathwayanalyzer.max_amplitude(pathways)

Return the maximum of pathway prefactors

Parameters:pathways (list) – List of Liouville pathways Returns:

• pmax (float) – Maximum prefactor of the pathways
• rec (int) – position of the pathway with the maximum prefactor

quantarhei.spectroscopy.pathwayanalyzer.order_by_amplitude(pthways)

Orders the list of pathways by pathway prefactors

quantarhei.spectroscopy.pathwayanalyzer.select_amplitude_GT(val, pathways, verbose=False)

Select all pathways with abs value of prefactors greater than a value

Parameters:

• val (float) – Value to compare with the pathway prefactor
• pathways (list of pathways) – List of the Liouville pathways to analyze
• verbose (bool) – If set True, number of selected pathways is reported

Returns:

selected – List of selected pathways

Return type:

list

quantarhei.spectroscopy.pathwayanalyzer.select_by_states(pathways, states)

Returns one pathway which goes through a given pattern of states

Returns unique pathway which goes through a given pattern of states or does not return anything

The following diagram

|12 12|

—>|———–|

|

|48 12| 2.0

—>|———–|

|

|21 12| 0.0

>>|***********|<<

|

|6 6| 0.0

—>|———–|

|

|0 6| -2.0 |-----------|<--- | | |0 0|

turns into the following tuple

((0,0), (0,6), (6,6), (21, 12), (48, 12), (12,12))

Parameters:

• pathways (list, tuple) – List of tuple of states to analyze
• states (list, tuple) – List of dyads which describe the states involved in a given Liouville pathway. States are listed from left to right, from bottom to the top

quantarhei.spectroscopy.pathwayanalyzer.select_frequency_window(window, pathways, verbose=False)

Selects pathways with omega_1 and omega_3 in a certain range

quantarhei.spectroscopy.pathwayanalyzer.select_omega2(interval, pathways, secular=True, tolerance=0.0018836515673088532, verbose=False)

Selects pathways with omega_2 in a certain interval

quantarhei.spectroscopy.pathwayanalyzer.select_sign(pathways, sign)

Selects all pathways depending on the overall sign

quantarhei.spectroscopy.pathwayanalyzer.select_type(pathways, stype)

Selects all pathways of a given type

Parameters:

• pathways (list) – List of pathways to be analyzed
• stype (str) – Type of the pathways to be selected. Possible values are “REPH”, “NONR”.