├── .gitignore ├── CITATION.cff ├── LICENSE ├── README.md ├── doc ├── figures │ └── thesis_figures │ │ ├── 2_site_system │ │ ├── 2.10_heom_trace_distance_temperature.pdf │ │ ├── 2.10_heom_trace_distance_temperature.txt │ │ ├── 2.10_local_therm_trace_distance_temperature.pdf │ │ ├── 2.10_local_therm_trace_distance_temperature.txt │ │ ├── 2.2_closed_system_dynamics.pdf │ │ ├── 2.2_closed_system_dynamics.txt │ │ ├── 2.3_purity_all_models.pdf │ │ ├── 2.3_purity_all_models.txt │ │ ├── 2.4_iprs_all_models.pdf │ │ ├── 2.4_iprs_all_models.txt │ │ ├── 2.5_local_deph.pdf │ │ ├── 2.5_local_deph.txt │ │ ├── 2.5_local_deph_heom.pdf │ │ ├── 2.5_local_deph_heom.txt │ │ ├── 2.6_global_therm.pdf │ │ ├── 2.6_global_therm.txt │ │ ├── 2.6_global_therm_heom.pdf │ │ ├── 2.6_global_therm_heom.txt │ │ ├── 2.7_local_therm.pdf │ │ ├── 2.7_local_therm.txt │ │ ├── 2.7_local_therm_heom.pdf │ │ ├── 2.7_local_therm_heom.txt │ │ ├── 2.8_global_therm_trace_distance.pdf │ │ ├── 2.8_global_therm_trace_distance.txt │ │ ├── 2.8_heom_trace_distance.pdf │ │ ├── 2.8_heom_trace_distance.txt │ │ ├── 2.8_local_deph_trace_distance.pdf │ │ ├── 2.8_local_deph_trace_distance.txt │ │ ├── 2.8_local_therm_trace_distance.pdf │ │ ├── 2.8_local_therm_trace_distance.txt │ │ ├── 2.9_all_lindblad_trace_distances_fixed.pdf │ │ ├── 2.9_all_lindblad_trace_distances_fixed.txt │ │ ├── 2.9_loc_therm_heom_trace_distance_fitted.pdf │ │ ├── 2.9_loc_therm_heom_trace_distance_fitted.txt │ │ ├── 2.9_local_therm_heom_fitted.pdf │ │ ├── 2.9_local_therm_heom_fitted.txt │ │ ├── 2.9_local_therm_heom_fixed.pdf │ │ └── 2.9_local_therm_heom_fixed.txt │ │ ├── README.md │ │ ├── fmo_system │ │ ├── 2.11_all_model_comparison_300K.pdf │ │ ├── 2.11_all_model_comparison_300K.txt │ │ ├── 2.12_canon_equil_temperature.pdf │ │ ├── 2.12_iprs_all_lindblads.pdf │ │ ├── 2.12_iprs_all_lindblads.txt │ │ ├── 2.13_loc_therm_sys_only_sys_bath_77K.pdf │ │ ├── 2.13_loc_therm_sys_only_sys_bath_77K.txt │ │ ├── 2.14_local_therm_bath_relax_times_300K.pdf │ │ └── 2.14_local_therm_bath_relax_times_300K.txt │ │ └── future_work │ │ ├── 3.1_all_populations_comparison.pdf │ │ ├── 3.1_all_populations_comparison.txt │ │ ├── 3.1_site_1_population_comparison.pdf │ │ ├── 3.1_site_1_population_comparison.txt │ │ ├── 3.1_spectral_desnity_comparison.pdf │ │ └── 3.1_spectral_desnity_comparison.txt └── tutorials │ ├── 0_reproducing_figures.ipynb │ ├── 1_unit_system.ipynb │ ├── 2_system_parameters.ipynb │ └── 3_example_plots.ipynb ├── environment.yml ├── quantum_heom ├── __init__.py ├── bath.py ├── evolution.py ├── figures.py ├── hamiltonian.py ├── heom.py ├── lindbladian.py ├── metadata.py ├── quantum_system.py └── utilities.py ├── run_tests.sh ├── setup.py └── tests ├── test_bath.py ├── test_evolution.py ├── test_hamiltonian.py ├── test_heom.py ├── test_lindbladian.py ├── test_meta_data.py ├── test_quantum_system.py └── test_utilities.py /.gitignore: -------------------------------------------------------------------------------- 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