Publication data for "Environmentally driven symmetry-breaking quenches dual fluorescence in proflavine" by Kye E. Hunter, Yuezhi Mao, Alex W. Chin, and Tim J. Zuehlsdoff. This repository contains all raw data for results presented in both the main text and the SI (Results), as well as input files necessary to reproduce all calculations performed in this work, from EOM-CCSD calculations (EOM_CCSD_input_data), to molecular dynamics simulations (MD_input_data), the TDDFT calulations of vertical energies (TDDFT_input_data) and the quantum dynamics (chain_coefficients and quantum_dynamics_input_data). Additionally, the repository contains a number of python scripts to process some of the data generated by certain calculations.
├── EOM_CCSD_input_data # input files for Q-Chem for running EOM-CCSD calculations
├── MD_input_data # input files and force field files for MD calculations. All QM/MM calculations are performed with Amber/Terachem, vacuum
| | # calculations are performed with TeraChem.
│ ├── acetonitrile
│ ├── acetonitrile_mm
│ ├── acetonitrile_qmmm
│ ├── methanol
│ ├── methanol_mm
│ ├── methanol_qmmm
│ └── vacuum
├── Results # Raw data for all results presented in the SI and the main manuscript
│ ├── Acetonitrile
│ │ ├── QM_correction
│ │ ├── TDDFT
│ │ └── shifted
│ ├── MeOH
│ │ ├── EOM-CCSD
│ │ ├── QM_correction
│ │ ├── TDDFT
│ │ ├── shifted
│ │ └── stim_emission
│ ├── MeOH_stripped
│ │ └── QM_correction
│ ├── Vacuum
│ │ ├── EOM_CCSD
│ │ ├── TDDFT
│ │ ├── gap_scan
│ │ │ ├── 0.16
│ │ │ ├── 0.18
│ │ │ ├── 0.20
│ │ │ ├── 0.21
│ │ │ ├── 0.22
│ │ │ ├── 0.23
│ │ │ ├── 0.24
│ │ │ └── 0.26
│ │ ├── model_SDs
│ │ │ ├── 0.0005
│ │ │ ├── 0.0025
│ │ │ ├── 0.0075
│ │ │ ├── Debye
│ │ │ └── Debye_gaussian
│ │ ├── shifted
│ │ │ ├── fully_correlated
│ │ │ └── uncorrelated
│ │ └── stim_emission
│ └── vacuum_large_gap
├── TDDFT_input_data # example input files for TeraChem used to compute vertical excitation energies.
│ ├── methanol
│ └── vacuum
├── chain_coefficients # chain coefficients for all stystems studied in this work. They are needed for the MPSDynamics.jl code
│ ├── chain_coefficients
│ │ ├── chain_coeffs_MeOH.hdf5
│ │ ├── chain_coeffs_MeOH_stripped.hdf5
│ │ ├── chain_coeffs_acetonitrile.hdf5
│ │ ├── chain_coeffs_vacuum.hdf5
│ │ ├── chain_coeffs_vacuum_model_coupling_debye.hdf5
│ │ ├── chain_coeffs_vacuum_model_coupling_debye_and_gaussian.hdf5
│ │ ├── chain_coeffs_vacuum_model_coupling_lorentzian_0.0005.hdf5
│ │ ├── chain_coeffs_vacuum_model_coupling_lorentzian_0.0025.hdf5
│ │ └── chain_coeffs_vacuum_model_coupling_lorentzian_0.0075.hdf5
│ ├── python_scripts # python scripts to process raw diabatic data obtained from MD trajectories into chain coefficieents
│ │ ├── compute_diabatic_sds.py # Script computing diabatic spectral densities from the raw diabatic data
│ │ └── spectral_dens_to_chain # script mapping the spectral densities to chains using orthogonal polynomials.
│ ├── raw_diabatic_data # raw input data from which the spectral densities are constructed
│ │ ├── full_energy_coupling_dipole_proflavine_camb3lyp_RPA_MeOH_diabatic_coupling.dat
│ │ ├── full_energy_coupling_dipole_proflavine_camb3lyp_RPA_MeOH_stripped_diabatic_coupling.dat
│ │ ├── full_energy_coupling_dipole_proflavine_camb3lyp_RPA_acetonitrile_diabatic_coupling.dat
│ │ └── full_energy_coupling_dipole_proflavine_camb3lyp_RPA_vacuum_diabatic_coupling.dat
│ └── spectral_densities
│ ├── acetonitrile
│ ├── methanol
│ ├── methanol_stripped
│ ├── vacuum
│ └── vacuum_model_sds
└── quantum_dynamics_input_data # input data for the quantum dynamics calculation
├── example_fluorescence_input
├── hamiltonian_parameters.txt
└── process_output # example python script to compute the linear optical spectrum from a dipole dipole correlation function