Main text figure data and scripts for "Formally exact fluorescence spectroscopy simulations for mesoscale molecular aggregates with N⁰ scaling".

This document contains the details needed to reproduce the figures reported in the paper titled “Formally exact fluorescence spectroscopy simulations for mesoscale molecular aggregates with N⁰ scaling”, 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 cont