Main text figure data and scripts for "Simulating fluorescence spectroscopy of mesoscale molecular aggregates with dyadic adaptive hierarchy of pure states"
Creators: name: Gera, Tarun
name: Alexia Hartzell
name: Raccah, Doran
name: Eisfeld, Alexander
name: CHEN, LIPENG
name: Lynd, Jacob
Publisher: name: Zenodo
Year: 2025
Subjects: Open Quantum System
Spectroscopy
Fluorescence
Reduced-Scaling Calculations

description: This document contains the details needed to reproduce the figures reported in the paper

titled “Simulating fluorescence spectroscopy of mesoscale molecular aggregates

with dyadic adaptive hierarchy of pure states”, by Tarun Gera, Alexia Hartzell,

Lipeng Chen, Alex Eisfeld, and Doran I. G. B. Raccah.

 

Each directory is dedicated to a particular figure published in the paper and contains

analyzed data as well as python scripts to generate, analyze (analysis.py), and plot

(plotting.py) the data used in each figure.

 

Figure_3: 

 

- Fig_3.png: Figure 3 from main text.

- plotting.py: Script used to generate Figure 3.

- TOTAL:

- Fluor_4site_TOTAL.py: Script used to generate trajectories for the total

                        fluorescence time correlation function for 4-site chain.

- analysis.py: Script used to perform ensemble averaging, zero padding, and fast

               fourier transform to obtain the ensemble total fluorescence

               frequency correlation function and frequency axis for 4-site

               chain.

- Cw_TOTAL.npy: Calculated frequency domain correlation function for the total

                fluorescence of 4-site chain.

- w_axis_TOTAL.npy: Frequency axis for the total fluorescence of 4-site chain.

- K1BALL:

- Fluor_4site_K1BALL.py: Script used to generate trajectories for the decomposed

                         ket-1 bra-all (Where the first ket and all bra sites

                         are initially excited) fluorescence time correlation

                         function for 4-site chain.

- analysis.py: Script used to perform ensemble averaging, zero padding, and

               fast fourier transform to obtain the ensemble ket-1 bra-all

               fluorescence frequency correlation function and frequency axis

               for 4-site chain.

- Cw_K1BALL.npy: Calculated frequency domain correlation function for the ket-1

                 bra-all fluorescence of 4-site chain.

- w_axis_K1BALL.npy: Frequency axis for the ket-1 bra-all fluorescence of

                     4-site chain.

- K2BALL:

- Fluor_4site_K2BALL.py: Script used to generate trajectories for the decomposed

                         ket-2 bra-all fluorescence time correlation function

                         for 4-site chain.

- analysis.py: Script used to perform ensemble averaging, zero padding, and

               fast fourier transform to obtain the ensemble ket-2 bra-all

               fluorescence frequency correlation function and frequency axis

               for 4-site chain.

- Cw_K2BALL.npy: Calculated frequency domain correlation function for the ket-2

                 bra-all fluorescence of 4-site chain.

- w_axis_K2BALL.npy: Frequency axis for the ket-2 bra-all fluorescence of

                     4-site chain.

- K1B1:

- Fluor_4site_K1B1.py: Script used to generate trajectories for the decomposed

                       ket-1 bra-1 fluorescence time correlation function for

                       4-site chain.

- analysis.py: Script used to perform ensemble averaging, zero padding, and

               fast fourier transform to obtain the ensemble ket-1 bra-1

               fluorescence frequency correlation function and frequency axis

               for 4-site chain.

- Cw_K1B1.npy: Calculated frequency domain correlation function for the ket-1

               bra-1 fluorescence of 4-site chain.

- w_axis_K1B1.npy: Frequency axis for the ket-1 bra-1 fluorescence of 4-site

                   chain.

- K1B2:

- Fluor_4site_K1B2.py: Script used to generate trajectories for the decomposed

                       ket-1 bra-2 fluorescence time correlation function for

                       4-site chain.

- analysis.py: Script used to perform ensemble averaging, zero padding, and

               fast fourier transform to obtain the ensemble ket-1 bra-2

               fluorescence frequency correlation function and frequency axis

               for 4-site chain.

- Cw_K1B2.npy: Calculated frequency domain correlation function for the ket-1

               bra-2 fluorescence of 4-site chain.

- w_axis_K1B2.npy: Frequency axis for the ket-1 bra-2 fluorescence of 4-site

                   chain.

- K1B3:

- Fluor_4site_K1B3.py: Script used to generate trajectories for the decomposed

                       ket-1 bra-3 fluorescence time correlation function for

                       4-site chain.

- analysis.py: Script used to perform ensemble averaging, zero padding, and

               fast fourier transform to obtain the ensemble ket-1 bra-3

               fluorescence frequency correlation function and frequency axis

               for 4-site chain.

- Cw_K1B3.npy: Calculated frequency domain correlation function for the ket-1

               bra-3 fluorescence of 4-site chain.

- w_axis_K1B3.npy: Frequency axis for the ket-1 bra-3 fluorescence of 4-site

                   chain.

- K1B4:

- Fluor_4site_K1B4.py: Script used to generate trajectories for the decomposed

                       ket-1 bra-4 fluorescence time correlation function for

                       4-site chain.

- analysis.py: Script used to perform ensemble averaging, zero padding, and

               fast fourier transform to obtain the ensemble ket-1 bra-4

               fluorescence frequency correlation function and frequency axis

               for 4-site chain.

- Cw_K1B4.npy: Calculated frequency domain correlation function for the ket-1

               bra-4 fluorescence of 4-site chain.

- w_axis_K1B4.npy: Frequency axis for the ket-1 bra-4 fluorescence of 4-site

                   chain.

- K2B1:

- Fluor_4site_K2B1.py: Script used to generate trajectories for the decomposed

                       ket-2 bra-1 fluorescence time correlation function for

                       4-site chain.

- analysis.py: Script used to perform ensemble averaging, zero padding, and

               fast fourier transform to obtain the ensemble ket-2 bra-1

               fluorescence frequency correlation function and frequency axis

               for 4-site chain.

- Cw_K2B1.npy: Calculated frequency domain correlation function for the ket-2

               bra-1 fluorescence of 4-site chain.

- w_axis_K2B1.npy: Frequency axis for the ket-2 bra-1 fluorescence of 4-site

                   chain.

- K2B2:

- Fluor_4site_K2B2.py: Script used to generate trajectories for the decomposed

                       ket-2 bra-2 fluorescence time correlation function for

                       4-site chain.

- analysis.py: Script used to perform ensemble averaging, zero padding, and

               fast fourier transform to obtain the ensemble ket-2 bra-2

               fluorescence frequency correlation function and frequency axis

               for 4-site chain.

- Cw_K2B2.npy: Calculated frequency domain correlation function for the ket-2

               bra-2 fluorescence of 4-site chain.

- w_axis_K2B2.npy: Frequency axis for the ket-2 bra-2 fluorescence of 4-site

                   chain.

- K2B3:

- Fluor_4site_K2B3.py: Script used to generate trajectories for the decomposed

                       ket-2 bra-3 fluorescence time correlation function for

                       4-site chain.

- analysis.py: Script used to perform ensemble averaging, zero padding, and

               fast fourier transform to obtain the ensemble ket-2 bra-3

               fluorescence frequency correlation function and frequency axis

               for 4-site chain.

- Cw_K2B3.npy: Calculated frequency domain correlation function for the ket-2

               bra-3 fluorescence of 4-site chain.

- w_axis_K2B3.npy: Frequency axis for the ket-2 bra-3 fluorescence of 4-site

                   chain.

- K2B4:

- Fluor_4site_K2B4.py: Script used to generate trajectories for the decomposed

                       ket-2 bra-4 fluorescence time correlation function for

                       4-site chain.

- analysis.py: Script used to perform ensemble averaging, zero padding, and

               fast fourier transform to obtain the ensemble ket-2 bra-4

               fluorescence frequency correlation function and frequency axis

               for 4-site chain.

- Cw_K2B4.npy: Calculated frequency domain correlation function for the ket-2

               bra-4 fluorescence of 4-site chain.

- w_axis_K2B4.npy: Frequency axis for the ket-2 bra-4 fluorescence of 4-site

                   chain.

 

Figure_4:

 

- Fig_4.png: Figure 4 from main text.

- plotting.py: Script used to generate Figure 4.

- Flu_input_script_V_0_coh.py: Script used to generate trajectories for the

                               coherence contributions to the fluorescence time

                               correlation function for dimer with nearest-neighbor

                               coupling V=0.

- Flu_input_script_V_0_pop.py: Script used to generate trajectories for the

                               population contributions to the fluorescence time

                               correlation function for dimer with V=0.

- Flu_input_script_V_m100_coh.py: Script used to generate trajectories for the

                                  coherence contributions to the fluorescence time

                                  correlation function for dimer with V=-100.

- Flu_input_script_V_m100_pop.py: Script used to generate trajectories for the

                                  population contributions to the fluorescence time

                                  correlation function for dimer with V=-100.

- analysis.py: Script used to calculate amplitudes and phases of the time

               correlation functions for dimer data.

- data_coh_V0_phase.npz: Calculated phases for the coherence contributions of the

                         V=0 dimer.

- data_coh_V0_amp.npz: Calculated amplitudes for the coherence contributions of the

                       V=0 dimer.

- data_pop_V0_phase.npz: Calculated phases for the population contributions of the

                         V=0 dimer.

- data_pop_V0_amp.npz: Calculated amplitudes for the population contributions of the

                       V=0 dimer.

- data_coh_Vm100_phase.npz: Calculated phases for the coherence contributions of the

                            V=-100 dimer.

- data_coh_Vm100_amp.npz: Calculated amplitudes for the coherence contributions of

                          the V=-100 dimer.

- data_pop_Vm100_phase.npz: Calculated phases for the population contributions of

                            the V=-100 dimer.

- data_pop_Vm100_amp.npz: Calculated amplitudes for the population contributions of

                          the V=-100 dimer.

 

Figure_5:

 

- Fig_5.png: Figure 5 from the main text.

- plotting.py: Script used to generate Figure 5.

- Flu_input_script_pop.py: Script used to generate trajectories for the population

                           contributions to the fluorescence time correlation

                           function for 100-site chain.

- Flu_input_script_pop_pm1.py: Script used to generate trajectories for the

                               population ± 1 contributions to the fluorescence

                               time correlation function for 100-site chain.

- Flu_input_script_pop_pm4.py: Script used to generate trajectories for the

                               population ± 4 contributions to the fluorescence time

                               correlation function for 100-site chain.

- analysis.py: Script used to perform ensemble averaging, zero padding, and fast

               fourier transform to obtain the ensemble fluorescence frequency

               correlation functions and frequency axes for population,

               population ± 1, and population ± 4 contributions for 100-site chain.

- Norm_Cw_init_ket_bra_same.npy: Calculated normalized frequency domain correlation

                                 function and frequency axis for the population

                                 contributions of 100-site chain.

- Norm_Cw_init_ket_bra_same_pm1.npy: Calculated normalized frequency domain

                                     correlation function and frequency axis for the

                                     population ± 1 contributions of 100-site chain.

- Norm_Cw_init_ket_bra_same_pm4.npy: Calculated normalized frequency domain

                                     correlation function and frequency axis for the

                                     population ± 4 contributions of 100-site chain.

 

Figure_6:

 

- Fig_6.png: Figure 6 from the main text.

- plotting.py: Script used to generate Figure 6.

- Flu_input_script.py: Script used to run the fluorescence simulation and record

                       number of auxiliary wave functions, system states, and CPU

                       time for each N-pigment system.

- analysis.py: Script used to calculate mean and standard deviation of the number of

               auxiliary wave functions, system states, and CPU time for each

               N-pigment system in a DadHOPS calculation, as well as generating the

               number of auxiliary and system states for a HOPS calculation.

- nhier_hops.npy: Calculated number of auxiliary wave functions for each N-pigment

                  system in a HOPS calculation.

- nhier_mean_std.npy: Calculated mean and standard deviation of the number of

                      auxiliary wave functions for each N-pigment system in a

                      DadHOPS calculation.

- nstate_hops.npy: Calculated number of system states for each N-pigment system in a

                   HOPS calculation.

- nstate_mean_std.npy: Calculated mean and standard deviation of the number of

                       system states for each N-pigment system in a DadHOPS

                       calculation.

- time_mean_std.npy: Calculated mean and standard deviation of the CPU time for each

                     N-pigment system in a DadHOPS calculation.

 

Figure_7:

 

- Fig_7.png: Figure 7 from the main text.

- plotting.py: Script used to generate Figure 7.

- Abs_input_script.py: Script used to run the absorption simulation and record the

                       fluorescence time correlation function and the wave function

                       for each N-pigment system.

- Flu_input_script.py: Script used to run the fluorescence simulation and record the

                       fluorescence time correlation function and the wave function

                       for each N-pigment system.

- analysis.py: Script used to perform ensemble averaging, zero padding, and fast

               fourier transform to obtain the ensemble fluorescence frequency

               correlation function and frequency axis, generate a Gaussian peak fit

               for the fluorescence spectra, calculate Stokes shift,

               Spano's coherence measure (see main text eq. 58), and mean IPR.

- data_abs_peak_00_position.npy: Calculated peak position for the 0-0 peak of the

                                 absorption spectrum for each N-pigment system.

- data_flu_peak_00_position.npy: Calculated peak position for the 0-0 peak of the

                                 fluorescence spectrum for each N-pigment system.

- data_mean_IPR.npy: Calculated mean IPR for each N-pigment system.

- data_N_coh.npy: Calculated Spano's coherence measure for each N-pigment system.

- data_stoke_shift.npy: Calculated Stokes shift for each N-pigment system.

- Gauss_Fit_N_1_I_00.npy: Gaussian peak fit and frequency axis for the 0-0 peak of

                          the fluorescence spectrum of 1-pigment system.

- Gauss_Fit_N_1_I_01.npy: Gaussian peak fit and frequency axis for the 0-1 peak of

                          the fluorescence spectrum of 1-pigment system.

- Gauss_Fit_N_2_I_00.npy: Gaussian peak fit and frequency axis for the 0-0 peak of

                          the fluorescence spectrum of 2-pigment system.

- Gauss_Fit_N_2_I_01.npy: Gaussian peak fit and frequency axis for the 0-1 peak of

                          the fluorescence spectrum of 2-pigment system.

- Gauss_Fit_N_10_I_00.npy: Gaussian peak fit and frequency axis for the 0-0 peak of

                           the fluorescence spectrum of 10-pigment system.

- Gauss_Fit_N_10_I_01.npy: Gaussian peak fit and frequency axis for the 0-1 peak of

                           the fluorescence spectrum of 10-pigment system.

- Gauss_Fit_N_100_I_00.npy: Gaussian peak fit and frequency axis for the 0-0 peak of

                            the fluorescence spectrum of 100-pigment system.

- Gauss_Fit_N_100_I_01.npy: Gaussian peak fit and frequency axis for the 0-1 peak of

                            the fluorescence spectrum of 100-pigment system.

- Norm_Cw_Abs_N_1.npy: Calculated normalized frequency domain correlation function

                       and frequency axis for the absorption of 1-pigment system.

- Norm_Cw_Abs_N_2.npy: Calculated normalized frequency domain correlation function

                       and frequency axis for the absorption of 2-pigment system.

- Norm_Cw_Abs_N_10.npy: Calculated normalized frequency domain correlation function

                        and frequency axis for the absorption of 10-pigment system.

- Norm_Cw_Abs_N_100.npy: Calculated normalized frequency domain correlation function

                         and frequency axis for the absorption of 100-pigment

                         system.

- Norm_Cw_Flu_N_1.npy: Calculated normalized frequency domain correlation function

                       and frequency axis for the fluorescence of 1-pigment system.

- Norm_Cw_Flu_N_2.npy: Calculated normalized frequency domain correlation function

                       and frequency axis for the fluorescence of 2-pigment system.

- Norm_Cw_Flu_N_10.npy: Calculated normalized frequency domain correlation function

                        and frequency axis for the fluorescence of 10-pigment

                        system.

- Norm_Cw_Flu_N_100.npy: Calculated normalized frequency domain correlation function

                         and frequency axis for the fluorescence of 100-pigment

                         system.

 

Figure_AppC:

 

- Fig_AppC.png: Figure 8 from Appendix C in the main text.

- plotting.py: Script used to generate Figure 8.

- Flu_input_script_pop.py: Script used to generate trajectories for the population

                           contributions to the fluorescence time correlation

                           function for 100-site chain.

- Flu_input_script_pop_pm1.py: Script used to generate trajectories for the

                               population ± 1 contributions to the fluorescence time

                               correlation function for 100-site chain.

- Flu_input_script_pop_pm4.py: Script used to generate trajectories for the

                               population ± 4 contributions to the fluorescence time

                               correlation function for 100-site chain.

- analysis.py: Script used to perform ensemble averaging, zero padding, and fast

               fourier transform to obtain the ensemble absolute fluorescence

               frequency correlation functions and frequency axes for population,

               population ± 1, and population ± 4 contributions for 100-site chain,

               as well as the difference spectra between population/population ± 1

               and population ± 1/population ± 4.

- Abs_Cw_diff_pm4_pm1.npy: Calculated difference spectrum and frequency axis for the

                           absolute frequency domain correlation functions for the

                           population ± 4 and population ± 1 contributions of

                           100-site chain.

- Abs_Cw_diff_same_pm1.npy: Calculated difference spectrum and frequency axis for

                            the absolute frequency domain correlation functions for

                            the population and population ± 1 contributions of

                            100-site chain.

- Abs_Cw_init_ket_bra_same.npy: Calculated absolute frequency domain correlation

                                function and frequency axis for the population

                                contributions of 100-site chain.

- Abs_Cw_init_ket_bra_same_pm1.npy: Calculated absolute frequency domain correlation

                                    function and frequency axis for the

                                    population ± 1 contributions of 100-site chain.

- Abs_Cw_init_ket_bra_same_pm4.npy: Calculated absolute frequency domain correlation

                                    function and frequency axis for the

                                    population ± 4 contributions of 100-site chain.

 

mesohops_lib: Implementation of mesohops used in the main text.