QD3SET-1: A Database with Quantum Dissipative Dynamics Data sets

This package is provided to make easy the extraction of data from our QD3SET-1 databasse. Our QD3SET-1 database contains 8 datasets with trajectories propagated for reduced density matrix of spin-boson model and FMO complex. Two methods were used: Local-thermalizing Lindblad Equation of Motion (LTLME) and Hierarachical Equations of Motion (HEOM). For more details, please read our article " Arif Ullah, Luis E. Herrera Rodriguez, Pavlo O. Dral, and Alexei A. Kananenka, QD3SET-1: A Database with Quantum Dissipative Dynamics Data sets https://doi.org/10.48550/arXiv.2301.12096

For hands-on paractice:

In example.ipynb, we demonstrate how to use this package for extraction of data

Basic Instructions

To use the package, we need to import qddset class from dataset.py module

from dataset import qddset

Parameters to pass are

extr_choice: dtpe =  str 
methodType: dtype = str  
FMOtype:  dtype = str  
dataPath:  dtype =  str  
Nsites: dtype =  int  

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Details

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extr_choice (extraction choice):

We can pass multiple extraction choices. For instance, To extract data from trajectories with initial excitation on site-1, pass extr_choice = 'site-1'. For data-extraction from trajectories with initial excitation on site-6, pass extr_choice = 'site-6' and similarly for site-8 data pass 'site-8'. To extract data from all trajectories, just pass extr_choice = 'all'. The default choice is 'cal_details' which only shows calculation details. For spin-boson model, extr_choices are 'all', 'sym', 'asym', and 'cal_details'.

systemType (system type):

Pass 'SB' for spin-boson and 'FMO' for FMO complex

methodType (method type):

Pass 'HEOM' or 'LTLME' for the extraction of the corresponding data. If the trajectories are generated with LTLME method, we need to pass LTLME and if with HEOM method, we need to pass HEOM. Otherwise, it will give incorrect data.

FMOtype (Type of FMO):

In our database, we have generated LTLME data with two different Hamiltonians for both 7-site and 8-site FMO. Here we represent them as I and II. check output.details for more

dataPath (path to data directory):

Nsites (number of sites in FMO case):

it can be 7, 8, or 24 (for trimer)

Defining input parameters

param = {'extr_choice': 'site-1', 
        'systemType': 'FMO', 
        'methodType': 'HEOM',
        'FMOtype' : 'II',
        'dataPath': 'HEOM_data',
        'Nsites': 8, 
        }

Pass the param

dataset = qddset(**param) #  initializing parameters \
output = dataset.extract() # extracting the data

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Output details

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If the extr_choice : cal_details, then we only get calculation details and Hamiltonian print(output.details and output.H)

If extr_choice is some other choice, then we get the following data:

output.details for calculation details

output.H for Hamiltonian

output.N_trajs to see the number of trajectories

outout.initial_site to see the site with initial excitation (only in FMO complex)

output.gamma to see the values of gamma (cutoff frequencies of bath in units of cm-1 for FMO complex and in atomic units for SB model)

output.lamb to see the values of lambda (system bath coupling strengths in units of cm-1 for FMO complex and in atomic units for SB model)

output.temp to see the values of temperature in units of K (in the case of FMO)

output.beta to see the values of inverse temperature in units of (a.u.) (in the case of spin-boson model)

output.epsilon to see the values of energy difference in the case of spin-boson model (in atomic units)

output.Delta to see the values of coupling strength between the two states in spin-boson model (in atomic units)

data = list(output.data.values()) makes the trajectories accessible. With data[i], we access the ith trajectory

To print the output

print(output.details, output.H, output.N_trajs, output.gamma, output.lamb, output.temp, output.beta, output.epsilon, output.Delta)

data = list(output.data.values())

print(data[0]) print the reduced density matrix from the first trajectory, and for other trajectories, just use data[1], data[2] and so on.