qDNA 0.1.0__py3-none-any.whl

configs/config.yaml

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+# This file contains all the default values used for the simulations
+project_name: "QuantumDNA"
+
+verbose: False
+DNA_BASES: ["A", "T", "G", "C", "c"]
+
+SOURCES: ['Hawke2010', 'Simserides2014', 'Mantela2021', 'Simserides2024']
+DESCRIPTIONS: ["1P", "2P"]
+PARTICLES: ["electron", "hole", "exciton"]
+UNITS: ['meV', 'eV', '100meV', 'rad/ps', 'rad/fs', '1/cm', 'K', 'J', '1/fs', '1/ps']
+T_UNITS: ['fs', 'ps']
+SPECTRAL_DENSITIES: ['debye', 'ohmic']
+TB_MODELS: ['WM', 'LM', 'ELM', 'FWM', 'FLM', 'FELM', 'FC']
+
+ham_kwargs_default:
+    source: 'Hawke2010'
+    description: '2P'
+    particles: ['electron','hole','exciton']
+    unit: 'rad/ps' 
+    interaction_param: 0. # in rad/ps
+    relaxation: True
+    nn_cutoff: True
+
+diss_kwargs_default:
+    loc_deph_rate: 0. # rad/fs
+    glob_deph_rate: 0. # rad/fs
+    uniform_relaxation: True
+    relax_rate: 0. # rad/fs
+    relax_rates: {'A': 0, 'T': 0, 'G': 0, 'C': 0, 'B': 0}
+    loc_therm: False
+    glob_therm: False
+    deph_rate: 7. # in rad/ps
+    cutoff_freq: 20. # in rad/ps
+    reorg_energy: 1. # in rad/ps
+    temperature: 300. # in K
+    spectral_density: 'debye'
+    exponent: 1.
+
+me_kwargs_default: 
+    t_steps: 500.
+    t_end: 3. # ps
+    t_unit: 'ps'
+    init_e_state: '(0, 0)'
+    init_h_state: '(0, 0)'
+    solver_method: 'adams'

data/raw/tb_params/Hawke2010_electron_ELM.json

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+[{"E_A": -44, "E_T": -49, "E_G": -45, "E_C": -43, "t_AA": 0.16, "t_AT": 0.07, "t_AG": 0.01, "t_AC": -0.03, "t_TA": -0.07, "t_TT": -0.3, "t_TG": -0.17, "t_TC": 0.22, "t_GA": 0.3, "t_GT": -0.32, "t_GG": 0.2, "t_GC": 0.43, "t_CA": -0.12, "t_CT": 0.63, "t_CG": 0.15, "t_CC": -0.47, "h_AT": -0.09, "h_GC": 0.16, "h_TA": -0.09, "h_CG": 0.16, "r+_AA": 0.06, "r+_AT": 0.02, "r+_AG": 0.03, "r+_AC": -0.02, "r+_TA": 0.02, "r+_TT": 0.02, "r+_TG": 0.03, "r+_TC": -0.02, "r+_GA": 0.03, "r+_GT": 0.03, "r+_GG": -0.02, "r+_GC": -0.03, "r+_CA": -0.02, "r+_CT": -0.02, "r+_CG": -0.03, "r+_CC": 0.02, "r-_AA": 0.29, "r-_AT": 0.03, "r-_AG": -0.06, "r-_AC": -0.03, "r-_TA": 0.03, "r-_TT": 0.002, "r-_TG": 0.02, "r-_TC": -0.002, "r-_GA": -0.06, "r-_GT": 0.02, "r-_GG": -0.05, "r-_GC": -0.04, "r-_CA": -0.03, "r-_CT": -0.002, "r-_CG": -0.04, "r-_CC": 0.003}, {"source": "Hawke2010", "particle": "electron", "tb_model_name": "ELM", "unit": "100meV", "notes": "energy unit: 100 meV"}]

data/raw/tb_params/Hawke2010_electron_LM.json

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+[{"E_A": -44, "E_T": -49, "E_G": -45, "E_C": -43, "t_AA": 0.16, "t_AT": 0.07, "t_AG": 0.01, "t_AC": -0.03, "t_TA": -0.07, "t_TT": -0.3, "t_TG": -0.17, "t_TC": 0.22, "t_GA": 0.3, "t_GT": -0.32, "t_GG": 0.2, "t_GC": 0.43, "t_CA": -0.12, "t_CT": 0.63, "t_CG": 0.15, "t_CC": -0.47, "h_AT": -0.09, "h_GC": 0.16, "h_TA": -0.09, "h_CG": 0.16}, {"source": "Hawke2010", "particle": "electron", "tb_model_name": "LM", "unit": "100meV", "notes": "energy unit: 100 meV"}]

data/raw/tb_params/Hawke2010_electron_WM.json

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+[{"E_A": -49, "E_T": -49, "E_G": -45, "E_C": -45, "t_AA": -0.29, "t_AT": 0.005, "t_AG": 0.03, "t_AC": 0.32, "t_TA": 0.02, "t_TT": -0.29, "t_TG": 0.17, "t_TC": -0.01, "t_GA": -0.01, "t_GT": 0.32, "t_GG": 0.2, "t_GC": -0.1, "t_CA": 0.17, "t_CT": 0.03, "t_CG": -0.08, "t_CC": 0.2}, {"source": "Hawke2010", "particle": "electron", "tb_model_name": "WM", "unit": "100meV", "notes": "energy unit: 100 meV"}]

data/raw/tb_params/Hawke2010_hole_ELM.json

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+[{"E_A": -83, "E_T": -90, "E_G": -80, "E_C": -88, "t_AA": -0.08, "t_AT": 0.68, "t_AG": -0.05, "t_AC": 0.68, "t_TA": 0.26, "t_TT": -1.17, "t_TG": 0.28, "t_TC": -0.86, "t_GA": -0.79, "t_GT": 0.73, "t_GG": -0.62, "t_GC": 0.8, "t_CA": 0.05, "t_CT": -1.07, "t_CG": -0.01, "t_CC": -0.66, "h_AT": -0.12, "h_GC": -0.12, "h_TA": -0.12, "h_CG": -0.12, "r+_AA": 0.02, "r+_AT": 0.09, "r+_AG": 0.04, "r+_AC": 0.05, "r+_TA": 0.09, "r+_TT": 0.04, "r+_TG": 0.05, "r+_TC": 0.02, "r+_GA": 0.04, "r+_GT": 0.05, "r+_GG": 0.03, "r+_GC": 0.04, "r+_CA": 0.05, "r+_CT": 0.02, "r+_CG": 0.04, "r+_CC": 0.01, "r-_AA": 0.48, "r-_AT": -0.03, "r-_AG": -0.03, "r-_AC": -0.05, "r-_TA": -0.03, "r-_TT": 0.005, "r-_TG": 0.05, "r-_TC": 0.005, "r-_GA": -0.03, "r-_GT": 0.05, "r-_GG": -0.44, "r-_GC": 0.04, "r-_CA": 0.05, "r-_CT": 0.005, "r-_CG": 0.04, "r-_CC": 0.01}, {"source": "Hawke2010", "particle": "hole", "tb_model_name": "ELM", "unit": "100meV", "notes": "energy unit: 100 meV"}]

data/raw/tb_params/Hawke2010_hole_FWM.json

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+[{"E_A": -83, "E_T": -83, "E_G": -80, "E_C": -80, "t_AA": -0.08, "t_AT": 0.2, "t_AG": -0.05, "t_AC": 0.02, "t_TA": 0.47, "t_TT": -0.08, "t_TG": -0.04, "t_TC": -0.79, "t_GA": -0.79, "t_GT": 0.02, "t_GG": -0.62, "t_GC": 0.01, "t_CA": -0.04, "t_CT": -0.05, "t_CG": -0.44, "t_CC": -0.62, "t_BB": 0.1, "h_AB": 0.1, "h_TB": 0.1, "h_GB": 0.1, "h_CB": 0.1, "h_BA": 0.1, "h_BT": 0.1, "h_BG": 0.1, "h_BC": 0.1}, {"source": "Hawke2010", "particle": "hole", "tb_model_name": "WM", "unit": "100meV", "notes": "energy unit: 100 meV"}]

data/raw/tb_params/Hawke2010_hole_LM.json

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+[{"E_A": -83, "E_T": -90, "E_G": -80, "E_C": -88, "t_AA": -0.08, "t_AT": 0.68, "t_AG": -0.05, "t_AC": 0.68, "t_TA": 0.26, "t_TT": -1.17, "t_TG": 0.28, "t_TC": -0.86, "t_GA": -0.79, "t_GT": 0.73, "t_GG": -0.62, "t_GC": 0.8, "t_CA": 0.05, "t_CT": -1.07, "t_CG": -0.01, "t_CC": -0.66, "h_AT": -0.12, "h_GC": -0.12, "h_TA": -0.12, "h_CG": -0.12}, {"source": "Hawke2010", "particle": "hole", "tb_model_name": "LM", "unit": "100meV", "notes": "energy unit: 100 meV"}]

data/raw/tb_params/Hawke2010_hole_WM.json

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+[{"E_A": -83, "E_T": -83, "E_G": -80, "E_C": -80, "t_AA": -0.08, "t_AT": 0.2, "t_AG": -0.05, "t_AC": 0.02, "t_TA": 0.47, "t_TT": -0.08, "t_TG": -0.04, "t_TC": -0.79, "t_GA": -0.79, "t_GT": 0.02, "t_GG": -0.62, "t_GC": 0.01, "t_CA": -0.04, "t_CT": -0.05, "t_CG": -0.44, "t_CC": -0.62}, {"source": "Hawke2010", "particle": "hole", "tb_model_name": "WM", "unit": "100meV", "notes": "energy unit: 100 meV"}]

data/raw/tb_params/Mantela2021_electron_WM.json

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+[{"E_A": -43.1, "E_T": -43.1, "E_G": -41.4, "E_C": -41.4, "t_AA": 0.22, "t_AT": 0.01, "t_AG": 0.11, "t_AC": 0.01, "t_TA": 0.02, "t_TT": 0.22, "t_TG": 0.09, "t_TC": 0.06, "t_GA": 0.06, "t_GT": 0.01, "t_GG": 0.02, "t_GC": 0.19, "t_CA": 0.09, "t_CT": 0.11, "t_CG": 0.09, "t_CC": 0.02}, {"source": "Mantela2021", "particle": "electron", "tb_model_name": "WM", "unit": "100meV", "notes": "energy unit: 100 meV"}]

data/raw/tb_params/Mantela2021_hole_WM.json

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+[{"E_A": -84.9, "E_T": -84.9, "E_G": -83, "E_C": -83, "t_AA": 0.38, "t_AT": 0.5, "t_AG": 0.37, "t_AC": 0.16, "t_TA": 0.37, "t_TT": 0.38, "t_TG": 0.28, "t_TC": 1.42, "t_GA": 1.42, "t_GT": 0.16, "t_GG": 1.16, "t_GC": 0.1, "t_CA": 0.28, "t_CT": 0.37, "t_CG": 0.75, "t_CC": 116}, {"source": "Mantela2021", "particle": "hole", "tb_model_name": "WM", "unit": "100meV", "notes": "energy unit: 100 meV"}]

data/raw/tb_params/Simserides2014_electron_WM.json

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+[{"E_A": -49, "E_T": -49, "E_G": -45, "E_C": -45, "t_AA": -0.29, "t_AT": 0.005, "t_AG": 0.03, "t_AC": 0.32, "t_TA": 0.02, "t_TT": -0.29, "t_TG": 0.17, "t_TC": -0.01, "t_GA": -0.01, "t_GT": 0.32, "t_GG": 0.2, "t_GC": -0.1, "t_CA": 0.17, "t_CT": 0.03, "t_CG": -0.08, "t_CC": 0.2}, {"source": "Simserides2014", "particle": "electron", "tb_model_name": "WM", "unit": "100meV", "notes": "energy unit: 100 meV"}]

data/raw/tb_params/Simserides2014_hole_WM.json

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+[{"E_A": -83, "E_T": -83, "E_G": -80, "E_C": -80, "t_AA": -0.2, "t_AT": 0.35, "t_AG": -0.3, "t_AC": 0.1, "t_TA": 0.5, "t_TT": -0.2, "t_TG": -0.1, "t_TC": -1.1, "t_GA": -1.1, "t_GT": 0.1, "t_GG": -1.0, "t_GC": 0.1, "t_CA": -0.1, "t_CT": -0.3, "t_CG": -0.5, "t_CC": -1.0}, {"source": "Simserides2014", "particle": "hole", "tb_model_name": "WM", "unit": "100meV", "notes": "energy unit: 100 meV"}]

data/raw/tb_params/Simserides2024_electron_ELM.json

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+[{"E_A": -0.130, "E_T": -0.350, "E_G": -0.520, "E_C": -0.290, "E_c": -0.290, "t_GG": 0.206, "t_CC": 0.099, "t_AA": 0.074, "t_TT": 0.035, "t_GC": 0.007, "t_CG": 0.031, "t_AT": 0.071, "t_TA": 0.011, "t_CT": 0.071, "t_AG": 0.017, "t_TC": 0.077, "t_GA": 0.008, "t_CA": 0.020, "t_TG": 0.004, "t_AC": 0.021, "t_GT": 0.022, "t_cc": 0.056, "t_Cc": 0.067, "t_cC": 0.091, "t_cG": 0.031, "t_Gc": 0.002, "h_GC": 0.073, "h_Gc": 0.069, "h_AT": 0.002, "r-_GG": 0.021, "r-_CC": 0.090, "r-_AA": 0.081, "r-_TT": 0.009, "r-_GC": 0.097, "r-_CG": 0.097, "r-_AT": 0.005, "r-_TA": 0.005, "r-_CT": 0.010, "r-_AG": 0.051, "r-_TC": 0.010, "r-_GA": 0.051, "r-_CA": 0.023, "r-_TG": 0.017, "r-_AC": 0.023, "r-_GT": 0.017, "r-_cc": 0.097, "r-_Cc": 0.094, "r-_cC": 0.094, "r-_cG": 0.084, "r-_Gc": 0.084, "r+_GG": 0.212, "r+_CC": 0.181, "r+_AA": 0.037, "r+_TT": 0.009, "r+_GC": 0.019, "r+_CG": 0.019, "r+_AT": 0.008, "r+_TA": 0.008, "r+_CT": 0.023, "r+_AG": 0.043, "r+_TC": 0.023, "r+_GA": 0.043, "r+_CA": 0.041, "r+_TG": 0.031, "r+_AC": 0.041, "r+_GT": 0.031, "r+_cc": 0.192, "r+_Cc": 0.186, "r+_cC": 0.186, "r+_cG": 0.030, "r+_Gc": 0.030}, {"source": "Simserides2024", "particle": "electron", "tb_model_name": "ELM", "unit": "eV", "notes": "includes 5'-methylated cytosine denoted as 'c' "}]

data/raw/tb_params/Simserides2024_electron_FELM.json

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+[{"E_A": -0.130, "E_T": -0.350, "E_G": -0.520, "E_C": -0.290, "E_c": -0.290, "E_B": -5.000, "t_GG": 0.206, "t_CC": 0.099, "t_AA": 0.074, "t_TT": 0.035, "t_GC": 0.007, "t_CG": 0.031, "t_AT": 0.071, "t_TA": 0.011, "t_CT": 0.071, "t_AG": 0.017, "t_TC": 0.077, "t_GA": 0.008, "t_CA": 0.020, "t_TG": 0.004, "t_AC": 0.021, "t_GT": 0.022, "t_cc": 0.056, "t_Cc": 0.067, "t_cC": 0.091, "t_cG": 0.031, "t_Gc": 0.002, "t_BB": 0.700, "h_GC": 0.073, "h_Gc": 0.069, "h_AT": 0.002, "h_cB": 0.066, "h_GB": 0.092, "h_CB": 0.047, "h_AB": 0.260, "h_TB": 0.079, "r-_GG": 0.021, "r-_CC": 0.090, "r-_AA": 0.081, "r-_TT": 0.009, "r-_GC": 0.097, "r-_CG": 0.097, "r-_AT": 0.005, "r-_TA": 0.005, "r-_CT": 0.010, "r-_AG": 0.051, "r-_TC": 0.010, "r-_GA": 0.051, "r-_CA": 0.023, "r-_TG": 0.017, "r-_AC": 0.023, "r-_GT": 0.017, "r-_cc": 0.097, "r-_Cc": 0.094, "r-_cC": 0.094, "r-_cG": 0.084, "r-_Gc": 0.084, "r+_GG": 0.212, "r+_CC": 0.181, "r+_AA": 0.037, "r+_TT": 0.009, "r+_GC": 0.019, "r+_CG": 0.019, "r+_AT": 0.008, "r+_TA": 0.008, "r+_CT": 0.023, "r+_AG": 0.043, "r+_TC": 0.023, "r+_GA": 0.043, "r+_CA": 0.041, "r+_TG": 0.031, "r+_AC": 0.041, "r+_GT": 0.031, "r+_cc": 0.192, "r+_Cc": 0.186, "r+_cC": 0.186, "r+_cG": 0.030, "r+_Gc": 0.030}, {"source": "Simserides2024", "particle": "electron", "tb_model_name": "FELM", "unit": "eV", "notes": "includes 5'-methylated cytosine denoted as 'c' and sugar-phosphate backbone denoted as 'B' "}]

data/raw/tb_params/Simserides2024_hole_ELM.json

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+[{"E_A": -7.610, "E_T": -8.240, "E_G": -7.130, "E_C": -7.900, "E_c": -7.630, "t_GG": 0.126, "t_CC": 0.064, "t_AA": 0.028, "t_TT": 0.120, "t_GC": 0.151, "t_CG": 0.025, "t_AT": 0.073, "t_TA": 0.081, "t_CT": 0.048, "t_AG": 0.059, "t_TC": 0.092, "t_GA": 0.131, "t_CA": 0.030, "t_TG": 0.079, "t_AC": 0.074, "t_GT": 0.132, "t_cc": 0.105, "t_Cc": 0.098, "t_cC": 0.067, "t_cG": 0.029, "t_Gc": 0.208, "h_GC": 0.026, "h_Gc": 0.028, "h_AT": 0.034, "r-_GG": 0.030, "r-_CC": 0.004, "r-_AA": 0.082, "r-_TT": 0.002, "r-_GC": 0.027, "r-_CG": 0.027, "r-_AT": 0.008, "r-_TA": 0.008, "r-_CT": 0.002, "r-_AG": 0.014, "r-_TC": 0.002, "r-_GA": 0.014, "r-_CA": 0.018, "r-_TG": 0.018, "r-_AC": 0.018, "r-_GT": 0.018, "r-_cc": 0.004, "r-_Cc": 0.004, "r-_cC": 0.004, "r-_cG": 0.027, "r-_Gc": 0.027, "r+_GG": 0.028, "r+_CC": 0.000, "r+_AA": 0.043, "r+_TT": 0.002, "r+_GC": 0.001, "r+_CG": 0.001, "r+_AT": 0.013, "r+_TA": 0.013, "r+_CT": 0.000, "r+_AG": 0.018, "r+_TC": 0.000, "r+_GA": 0.018, "r+_CA": 0.000, "r+_TG": 0.007, "r+_AC": 0.000, "r+_GT": 0.007, "r+_cc": 0.000, "r+_Cc": 0.000, "r+_cC": 0.000, "r+_cG": 0.002, "r+_Gc": 0.002}, {"source": "Simserides2024", "particle": "hole", "tb_model_name": "ELM", "unit": "eV", "notes": "includes 5'-methylated cytosine denoted as 'c' "}]

data/raw/tb_params/Simserides2024_hole_FELM.json

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+[{"E_A": -7.610, "E_T": -8.240, "E_G": -7.130, "E_C": -7.900, "E_c": -7.630, "E_B": -9.400, "t_GG": 0.126, "t_CC": 0.064, "t_AA": 0.028, "t_TT": 0.120, "t_GC": 0.151, "t_CG": 0.025, "t_AT": 0.073, "t_TA": 0.081, "t_CT": 0.048, "t_AG": 0.059, "t_TC": 0.092, "t_GA": 0.131, "t_CA": 0.030, "t_TG": 0.079, "t_AC": 0.074, "t_GT": 0.132, "t_cc": 0.105, "t_Cc": 0.098, "t_cC": 0.067, "t_cG": 0.029, "t_Gc": 0.208, "t_BB": 0.026, "h_GC": 0.026, "h_Gc": 0.028, "h_AT": 0.034, "h_cB": 0.178, "h_GB": 0.016, "h_CB": 0.173, "h_AB": 0.024, "h_TB": 0.179, "r-_GG": 0.030, "r-_CC": 0.004, "r-_AA": 0.082, "r-_TT": 0.002, "r-_GC": 0.027, "r-_CG": 0.027, "r-_AT": 0.008, "r-_TA": 0.008, "r-_CT": 0.002, "r-_AG": 0.014, "r-_TC": 0.002, "r-_GA": 0.014, "r-_CA": 0.018, "r-_TG": 0.018, "r-_AC": 0.018, "r-_GT": 0.018, "r-_cc": 0.004, "r-_Cc": 0.004, "r-_cC": 0.004, "r-_cG": 0.027, "r-_Gc": 0.027, "r+_GG": 0.028, "r+_CC": 0.000, "r+_AA": 0.043, "r+_TT": 0.002, "r+_GC": 0.001, "r+_CG": 0.001, "r+_AT": 0.013, "r+_TA": 0.013, "r+_CT": 0.000, "r+_AG": 0.018, "r+_TC": 0.000, "r+_GA": 0.018, "r+_CA": 0.000, "r+_TG": 0.007, "r+_AC": 0.000, "r+_GT": 0.007, "r+_cc": 0.000, "r+_Cc": 0.000, "r+_cC": 0.000, "r+_cG": 0.002, "r+_Gc": 0.002}, {"source": "Simserides2024", "particle": "hole", "tb_model_name": "ELM", "unit": "eV", "notes": "includes 5'-methylated cytosine denoted as 'c' and the sugar-phosphate backbone denoted as 'B' "}]

gui/__init__.py

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+from .user_interface_utils import *
+
+from .initial_frame import InitialFrame
+from .config_frame import ConfigFrame
+from .custom_window import CustomWindow
+
+from .ham_frame import HamFrame
+from .diss_frame import DissFrame
+from .dynamics_frame import DynamicsFrame
+from .options_frame import OptionsFrame
+
+from .plot_options_frame import PlotOptionsFrame
+from .plotting_window import *
+from .scrollable_console_frame import ScrollableConsoleFrame
+
+from .qdna_app import *

gui/config_frame.py

@@ -0,0 +1,29 @@
+import customtkinter as ctk
+
+class ConfigFrame(ctk.CTkFrame):
+    def __init__(self, master, **kwargs):
+        """
+        Notes: 
+            This frame is located in the main/ menu window. This means that the main window is its master. 
+            The frame uses the commands open_custom_window() and open_github() from the master 
+            
+        Widgets with get() method:
+            appearance_mode_combo
+        """
+        
+        # initialization of the ctk.CTkFrame class
+        super().__init__(master)
+        
+        # widgets
+        self.open_github_button = ctk.CTkButton(self, text="GitHub", command=master.open_github)
+        self.open_github_button.grid(row=8, column=0, pady=10, padx=10)
+    
+        self.open_custom_window_button = ctk.CTkButton(self, text="Customize", command=master.open_custom_window)
+        self.open_custom_window_button.grid(row=9, column=0, pady=10, padx=10)
+    
+        self.appearance_mode_label = ctk.CTkLabel(self, text="Appearance Mode:", anchor="w")
+        self.appearance_mode_label.grid(row=10, column=0, pady=10, padx=10)
+        
+        self.appearance_mode_combo = ctk.CTkComboBox(self, values=["Light", "Dark", "System"], command=ctk.set_appearance_mode)
+        self.appearance_mode_combo.grid(row=11, column=0, pady=10, padx=10)
+        self.appearance_mode_combo.set('System')

gui/custom_window.py

@@ -0,0 +1,102 @@
+import customtkinter as ctk
+import webbrowser
+
+from qDNA import wrap_save_tb_params
+
+class CustomFrame(ctk.CTkFrame):
+    def __init__(self, master, configs):
+        """
+        Notes: 
+            This frame is located in the custom window. This means that the custom window is its master. 
+            The frame uses the commands save() and cancel() from the master 
+        
+        Widgets with get() method:
+            tb_params_entry, source_entry, particle_combobox, tb_model_combobox, unit_combobox, methylation_checkbox
+        """
+        
+        # initialization of the ctk.CTkFrame class
+        super().__init__(master)
+        self.configs = configs
+        
+        # widgets
+        self.tb_params_label = ctk.CTkLabel(self, text="TB parameters:")
+        self.tb_params_label.grid(row=0, column=0, columnspan=2, pady=10, padx=10)
+    
+        self.tb_params_entry = ctk.CTkEntry(self)
+        self.tb_params_entry.grid(row=1, column=0, columnspan=2, padx=10, pady=10)
+
+        self.source_label = ctk.CTkLabel(self, text="Source:")
+        self.source_label.grid(row=2, column=0, columnspan=2, padx=10, pady=10)
+    
+        self.source_entry = ctk.CTkEntry(self)
+        self.source_entry.grid(row=3, column=0, columnspan=2, padx=10, pady=10)
+        
+        self.particle_label = ctk.CTkLabel(self, text="Particle:")
+        self.particle_label.grid(row=4, column=0, columnspan=2, padx=10, pady=10)
+
+        self.particle_combobox = ctk.CTkComboBox(self, values=self.configs['PARTICLES'] )
+        self.particle_combobox.grid(row=5, column=0, columnspan=2, padx=10, pady=10)
+
+        self.tb_model_label = ctk.CTkLabel(self, text="TB Model:")
+        self.tb_model_label.grid(row=6, column=0, columnspan=2, padx=10, pady=10)
+
+        self.tb_model_combobox = ctk.CTkComboBox(self, values=self.configs['TB_MODELS'] )
+        self.tb_model_combobox.grid(row=7, column=0, columnspan=2, padx=10, pady=10)
+
+        self.unit_label = ctk.CTkLabel(self, text="Unit:")
+        self.unit_label.grid(row=8, column=0, columnspan=2, padx=10, pady=10)
+
+        self.unit_combobox = ctk.CTkComboBox(self, values=self.configs['UNITS'] )
+        self.unit_combobox.grid(row=9, column=0, columnspan=2, padx=10, pady=10)
+
+        check_var = ctk.BooleanVar(value=True)
+        self.methylation_checkbox = ctk.CTkCheckBox(self, text="Methylation", variable=check_var, onvalue=True, offvalue=False)
+        self.methylation_checkbox.grid(row=10, column=0, columnspan=2, padx=10, pady=10)
+       
+        self.save_button = ctk.CTkButton(self, text="Save", command=master.save)
+        self.save_button.grid(row=11, column=0, padx=10, pady=10)
+        
+        self.cancel_button = ctk.CTkButton(self, text="Cancel", command=master.cancel)
+        self.cancel_button.grid(row=11, column=1, padx=10, pady=10)
+
+class CustomWindow(ctk.CTkToplevel):
+    def __init__(self, master, configs): 
+        """
+        Notes: 
+            This window is a toplevel window of the main window. This means that the main window is its master. 
+            The frame uses the commands save() and cancel() from the master 
+        """
+        
+        # initialization of the ctk.CTkToplevel class
+        super().__init__(master)
+        self.title("Customize")
+        
+        # add a instance of CustomFrame to the window
+        self.custom_frame = CustomFrame(self, configs)
+        self.custom_frame.grid(row=0, column=0, columnspan=2, padx=10, pady=10, sticky="nsew")
+        
+    def get_custom_frame_params(self):
+        """
+        Makes all parameters of custom_frame available in this window.
+        """
+        self.tb_param_dict = self.custom_frame.tb_params_entry.get()
+        self.source = self.custom_frame.source_entry.get()
+        self.particle = self.custom_frame.particle_combobox.get()
+        self.tb_model_name = self.custom_frame.tb_model_combobox.get()
+        self.unit = self.custom_frame.unit_combobox.get()
+        self.methylated = self.custom_frame.methylation_checkbox.get()
+        
+    def save(self):
+        """
+        Saves the tight-binding parameters and closes the window.
+        """
+        self.get_custom_frame_params()
+        notes = f"methlation {self.methylated}"
+        wrap_save_tb_params(self.tb_param_dict, self.source, self.particle, self.tb_model_name, self.unit, notes=notes)
+        self.destroy()
+    
+    def cancel(self):
+        """
+        Closes the window.
+        """
+        self.destroy()

gui/diss_frame.py

@@ -0,0 +1,134 @@
+import customtkinter as ctk
+
+from tools import get_config
+
+class DissFrame(ctk.CTkFrame):
+    def __init__(self, master, configs, **kwargs):
+        """
+        Notes: 
+            This frame is located in the options tab. This means that the options tab is its master. 
+        """
+        
+        # initialization of the ctk.CTkFrame class
+        super().__init__(master)
+        self.pack(fill="both", expand=True)
+        self.configs = configs
+        self.diss_kwargs_default = self.configs['diss_kwargs_default']
+        
+        # widgets
+        self.diss_loc_deph_rate_label = ctk.CTkLabel(self, text="Local Dephasing Rate:")
+        self.diss_loc_deph_rate_label.grid(row=0, column=0, padx=10, pady=10)
+        
+        self.diss_loc_deph_rate_entry = ctk.CTkEntry(self)
+        self.diss_loc_deph_rate_entry.insert(0, str(self.diss_kwargs_default['loc_deph_rate']))
+        self.diss_loc_deph_rate_entry.grid(row=0, column=1, padx=10, pady=10)
+    
+        self.diss_glob_deph_rate_label = ctk.CTkLabel(self, text="Global Dephasing Rate:")
+        self.diss_glob_deph_rate_label.grid(row=1, column=0, padx=10, pady=10)
+        
+        self.diss_glob_deph_rate_entry = ctk.CTkEntry(self)
+        self.diss_glob_deph_rate_entry.insert(0, str(self.diss_kwargs_default['glob_deph_rate']))
+        self.diss_glob_deph_rate_entry.grid(row=1, column=1, padx=10, pady=10)
+
+        # -------------------------------
+        
+        self.diss_uniform_relaxation_var = ctk.BooleanVar(value=self.diss_kwargs_default['uniform_relaxation'])
+        self.diss_uniform_relaxation_check = ctk.CTkCheckBox(self, text="Uniform Relaxation", variable=self.diss_uniform_relaxation_var, 
+                                                             command=self.set_uniform_relax)
+        self.diss_uniform_relaxation_check.grid(row=2, column=0, columnspan=2, padx=10, pady=10)
+    
+        self.diss_relax_rate_label = ctk.CTkLabel(self, text="Relaxation Rate \n (uniform):")
+        self.diss_relax_rate_label.grid(row=3, column=0, padx=10, pady=10)
+        
+        self.diss_relax_rate_entry = ctk.CTkEntry(self)
+        self.diss_relax_rate_entry.insert(0, str(self.diss_kwargs_default['relax_rate']))
+        self.diss_relax_rate_entry.grid(row=3, column=1, padx=10, pady=10)
+    
+        self.diss_relax_rates_label = ctk.CTkLabel(self, text="Relaxation Rates \n (non-uniform):")
+        self.diss_relax_rates_label.grid(row=4, column=0, padx=10, pady=10)
+        
+        self.diss_relax_rates_entry = ctk.CTkEntry(self, state='disabled')
+        self.diss_relax_rates_entry.insert(0, str(self.diss_kwargs_default['relax_rates']) )
+        self.diss_relax_rates_entry.grid(row=4, column=1, padx=10, pady=10)
+        
+        # -----------------------------------
+    
+        self.diss_loc_therm_var = ctk.BooleanVar(value=self.diss_kwargs_default['loc_therm'])
+        self.diss_loc_therm_check = ctk.CTkCheckBox(self, text="Local Thermalization", variable=self.diss_loc_therm_var)
+        self.diss_loc_therm_check.grid(row=5, column=0, padx=10, pady=10)
+    
+        self.diss_glob_therm_var = ctk.BooleanVar(value=self.diss_kwargs_default['glob_therm'])
+        self.diss_glob_therm_check = ctk.CTkCheckBox(self, text="Global Thermalization", variable=self.diss_glob_therm_var)
+        self.diss_glob_therm_check.grid(row=6, column=0, padx=10, pady=10)
+    
+        self.diss_deph_rate_label = ctk.CTkLabel(self, text="Dephasing Rate:")
+        self.diss_deph_rate_label.grid(row=7, column=0, padx=10, pady=10)
+        
+        self.diss_deph_rate_entry = ctk.CTkEntry(self)
+        self.diss_deph_rate_entry.insert(0, str(self.diss_kwargs_default['deph_rate']))
+        self.diss_deph_rate_entry.grid(row=7, column=1, padx=10, pady=10)
+    
+        self.diss_cutoff_freq_label = ctk.CTkLabel(self, text="Cutoff Frequency:")
+        self.diss_cutoff_freq_label.grid(row=8, column=0, padx=10, pady=10)
+        
+        self.diss_cutoff_freq_entry = ctk.CTkEntry(self)
+        self.diss_cutoff_freq_entry.insert(0, str(self.diss_kwargs_default['cutoff_freq']))
+        self.diss_cutoff_freq_entry.grid(row=8, column=1, padx=10, pady=10)
+    
+        self.diss_reorg_energy_label = ctk.CTkLabel(self, text="Reorganization Energy:")
+        self.diss_reorg_energy_label.grid(row=9, column=0, padx=10, pady=10)
+        
+        self.diss_reorg_energy_entry = ctk.CTkEntry(self)
+        self.diss_reorg_energy_entry.insert(0, str(self.diss_kwargs_default['reorg_energy']))
+        self.diss_reorg_energy_entry.grid(row=9, column=1, padx=10, pady=10)
+    
+        self.diss_temperature_label = ctk.CTkLabel(self, text="Temperature (K):")
+        self.diss_temperature_label.grid(row=10, column=0, padx=10, pady=10)
+        
+        self.diss_temperature_entry = ctk.CTkEntry(self)
+        self.diss_temperature_entry.insert(0, str(self.diss_kwargs_default['temperature']))
+        self.diss_temperature_entry.grid(row=10, column=1, padx=10, pady=10)
+    
+        self.diss_spectral_density_label = ctk.CTkLabel(self, text="Spectral Density:")
+        self.diss_spectral_density_label.grid(row=11, column=0, padx=10, pady=10)
+        
+        self.diss_spectral_density_combo = ctk.CTkComboBox(self, values=self.configs['SPECTRAL_DENSITIES'] )
+        self.diss_spectral_density_combo.set(self.diss_kwargs_default['spectral_density'])
+        self.diss_spectral_density_combo.grid(row=11, column=1, padx=10, pady=10)
+    
+        self.diss_exponent_label = ctk.CTkLabel(self, text="Exponent:")
+        self.diss_exponent_label.grid(row=12, column=0, padx=10, pady=10)
+        
+        self.diss_exponent_entry = ctk.CTkEntry(self)
+        self.diss_exponent_entry.insert(0, str(self.diss_kwargs_default['exponent']))
+        self.diss_exponent_entry.grid(row=12, column=1, padx=10, pady=10)
+
+    def set_uniform_relax(self): 
+        if self.diss_uniform_relaxation_var.get():
+            self.diss_relax_rate_entry.configure(state='normal')
+            self.diss_relax_rates_entry.configure(state='disabled')
+        else: 
+            self.diss_relax_rate_entry.configure(state='disabled')
+            self.diss_relax_rates_entry.configure(state='normal')
+
+    def get_diss_kwargs(self):
+        """
+        Returns the values of widgets with get() method in dictionary format. 
+        """
+        
+        diss_kwargs = {
+            "loc_deph_rate": float(self.diss_loc_deph_rate_entry.get()),
+            "glob_deph_rate": float(self.diss_glob_deph_rate_entry.get()),
+            "uniform_relaxation": self.diss_uniform_relaxation_var.get(),
+            "relax_rate": float(self.diss_relax_rate_entry.get()),
+            "relax_rates": dict(self.diss_relax_rates_entry.get()),
+            "loc_therm": self.diss_loc_therm_var.get(),
+            "glob_therm": self.diss_glob_therm_var.get(),
+            "deph_rate": float(self.diss_deph_rate_entry.get()),
+            "cutoff_freq": float(self.diss_cutoff_freq_entry.get()),
+            "reorg_energy": float(self.diss_reorg_energy_entry.get()),
+            "temperature": float(self.diss_temperature_entry.get()),
+            "spectral_density": self.diss_spectral_density_combo.get(),
+            "exponent": float(self.diss_exponent_entry.get()),
+        }
+        return diss_kwargs

gui/dynamics_frame.py

@@ -0,0 +1,66 @@
+import customtkinter as ctk
+
+from tools import get_config
+
+class DynamicsFrame(ctk.CTkFrame):
+    def __init__(self, master, configs, **kwargs):
+        """
+        Notes: 
+            This frame is located in the options tab. This means that the options tab is its master. 
+        """
+        
+        # initialization of the ctk.CTkFrame class
+        super().__init__(master)
+        self.pack(fill="both", expand=True)
+        self.configs = configs
+        self.me_kwargs_default = self.configs['me_kwargs_default']
+
+        # widgets
+        self.me_t_steps_label = ctk.CTkLabel(self, text="Time Steps:")
+        self.me_t_steps_label.grid(row=0, column=0, padx=10, pady=10)
+        
+        self.me_t_steps_entry = ctk.CTkEntry(self)
+        self.me_t_steps_entry.insert(0, str(self.me_kwargs_default['t_steps']))
+        self.me_t_steps_entry.grid(row=0, column=1, padx=10, pady=10)
+    
+        self.me_t_end_label = ctk.CTkLabel(self, text="Time End:")
+        self.me_t_end_label.grid(row=1, column=0, padx=10, pady=10)
+        
+        self.me_t_end_entry = ctk.CTkEntry(self)
+        self.me_t_end_entry.insert(0, str(self.me_kwargs_default['t_end']))
+        self.me_t_end_entry.grid(row=1, column=1, padx=10, pady=10)
+    
+        self.me_t_unit_label = ctk.CTkLabel(self, text="Time Unit:")
+        self.me_t_unit_label.grid(row=2, column=0, padx=10, pady=10)
+        
+        self.me_t_unit_combo = ctk.CTkComboBox(self, values=self.configs['T_UNITS'] )
+        self.me_t_unit_combo.set(self.me_kwargs_default['t_unit'])
+        self.me_t_unit_combo.grid(row=2, column=1, padx=10, pady=10)
+    
+        self.me_init_e_state_label = ctk.CTkLabel(self, text="Initial Electron State:")
+        self.me_init_e_state_label.grid(row=3, column=0, padx=10, pady=10)
+        
+        self.me_init_e_state_combo = ctk.CTkComboBox(self, values=self.me_kwargs_default['init_e_state'])
+        self.me_init_e_state_combo.grid(row=3, column=1, padx=10, pady=10)
+        self.me_init_e_state_combo.set(self.me_kwargs_default['init_e_state'])
+    
+        self.me_init_h_state_label = ctk.CTkLabel(self, text="Initial Hole State:")
+        self.me_init_h_state_label.grid(row=4, column=0, padx=10, pady=10)
+        
+        self.me_init_h_state_combo = ctk.CTkComboBox(self, values=self.me_kwargs_default['init_h_state'])
+        self.me_init_h_state_combo.grid(row=4, column=1, padx=10, pady=10)
+        self.me_init_h_state_combo.set(self.me_kwargs_default['init_h_state'])
+
+    def get_me_kwargs(self):
+        """
+        Returns the values of widgets with get() method in dictionary format. 
+        """
+            
+        me_kwargs = {
+            "t_steps": float(self.me_t_steps_entry.get()),
+            "t_end": float(self.me_t_end_entry.get()),
+            "t_unit": self.me_t_unit_combo.get(),
+            "init_e_state": self.me_init_e_state_combo.get(),
+            "init_h_state": self.me_init_h_state_combo.get(),
+        }
+        return me_kwargs

gui/ham_frame.py

@@ -0,0 +1,79 @@
+import customtkinter as ctk
+
+from qDNA import wrap_save_tb_params
+from tools import get_config
+
+class HamFrame(ctk.CTkFrame):
+    def __init__(self, master, configs, **kwargs):
+        """
+        Notes: 
+            This frame is located in the options tab. This means that the options tab is its master. 
+        """
+        
+        # initialization of the ctk.CTkFrame class
+        super().__init__(master)
+        self.pack(fill="both", expand=True)
+        self.configs = configs
+        self.ham_kwargs_default = self.configs['ham_kwargs_default']
+
+        # widgets
+        self.ham_source_label = ctk.CTkLabel(self, text="Source:")
+        self.ham_source_label.grid(row=0, column=0, padx=10, pady=10)
+        
+        self.ham_source_combo = ctk.CTkComboBox(self, values=self.configs['SOURCES'] )
+        self.ham_source_combo.set(self.ham_kwargs_default['source'])
+        self.ham_source_combo.grid(row=0, column=1, padx=10, pady=10)
+    
+        self.ham_description_label = ctk.CTkLabel(self, text="Description:")
+        self.ham_description_label.grid(row=1, column=0, padx=10, pady=10)
+        
+        self.ham_description_combo = ctk.CTkComboBox(self, values=self.configs['DESCRIPTIONS'] )
+        self.ham_description_combo.set(self.ham_kwargs_default['description'])
+        self.ham_description_combo.grid(row=1, column=1, padx=10, pady=10)
+    
+        self.ham_particles_label = ctk.CTkLabel(self, text="Particles:")
+        self.ham_particles_label.grid(row=2, column=0, padx=10, pady=10)
+        
+        self.particles = self.configs['PARTICLES']
+        self.selected_particles = {particle: ctk.BooleanVar(value=True) for particle in self.particles}
+        for idx, particle in enumerate(self.particles):
+            checkbox = ctk.CTkCheckBox(self, text=particle, variable=self.selected_particles[particle])
+            checkbox.grid(row=3+idx, column=0, padx=20, pady=5, columnspan=2)
+    
+        self.ham_unit_label = ctk.CTkLabel(self, text="Unit:")
+        self.ham_unit_label.grid(row=6, column=0, padx=10, pady=10)
+        
+        self.ham_unit_combo = ctk.CTkComboBox(self, values=self.configs['UNITS'] )
+        self.ham_unit_combo.set(self.ham_kwargs_default['unit'])
+        self.ham_unit_combo.grid(row=6, column=1, padx=10, pady=10)
+    
+        self.ham_interaction_param_label = ctk.CTkLabel(self, text="Interaction Param:")
+        self.ham_interaction_param_label.grid(row=7, column=0, padx=10, pady=10)
+        
+        self.ham_interaction_param_entry = ctk.CTkEntry(self)
+        self.ham_interaction_param_entry.insert(0, str(self.ham_kwargs_default['interaction_param']))
+        self.ham_interaction_param_entry.grid(row=7, column=1, padx=10, pady=10)
+    
+        self.ham_relaxation_var = ctk.BooleanVar(value=self.ham_kwargs_default['relaxation'])
+        self.ham_relaxation_check = ctk.CTkCheckBox(self, text="Relaxation", variable=self.ham_relaxation_var)
+        self.ham_relaxation_check.grid(row=12, column=0, padx=10, pady=10, columnspan=2)
+    
+        self.ham_nn_cutoff_var = ctk.BooleanVar(value=self.ham_kwargs_default['nn_cutoff'])
+        self.ham_nn_cutoff_check = ctk.CTkCheckBox(self, text="NN Cutoff", variable=self.ham_nn_cutoff_var)
+        self.ham_nn_cutoff_check.grid(row=13, column=0, padx=10, pady=10, columnspan=2)
+
+    def get_ham_kwargs(self):
+        """
+        Returns the values of widgets with get() method in dictionary format. 
+        """
+        
+        ham_kwargs = {
+            "source": self.ham_source_combo.get(),
+            "description": self.ham_description_combo.get(),
+            "particles": [particle for particle, var in self.selected_particles.items() if var.get()],
+            "unit": self.ham_unit_combo.get(),
+            "interaction_param": float(self.ham_interaction_param_entry.get()),
+            "relaxation": self.ham_relaxation_var.get(),
+            "nn_cutoff": self.ham_nn_cutoff_var.get(),
+        }
+        return ham_kwargs

gui/initial_frame.py

@@ -0,0 +1,44 @@
+import customtkinter as ctk
+
+class InitialFrame(ctk.CTkFrame):
+    def __init__(self, master, **kwargs):
+        """
+        Notes: 
+            This frame is located in the main/ menu window. This means that the main window is its master. 
+            The frame uses the commands press_first_confirm() from the master.
+            
+        Widgets with get() method:
+            upper_strand_entry, tb_model_combo
+        """
+        
+        # initialization of the ctk.CTkFrame class
+        super().__init__(master)
+
+        # widgets
+        self.logo_label = ctk.CTkLabel(self, text="QuantumDNA", font=ctk.CTkFont(size=20, weight="bold"))
+        self.logo_label.grid(row=0, column=0, pady=10, padx=10)
+
+        self.upper_strand_label = ctk.CTkLabel(self, text="DNA Sequence \n (upper strand):")
+        self.upper_strand_label.grid(row=1, column=0, pady=10, padx=10)
+        
+        self.upper_strand_entry = ctk.CTkEntry(self)
+        self.upper_strand_entry.grid(row=2, column=0, pady=10, padx=10)
+        self.upper_strand_entry.insert(0, 'GCG')
+        
+        self.tb_model_label = ctk.CTkLabel(self, text="TB Model:")
+        self.tb_model_label.grid(row=3, column=0, pady=10, padx=10)
+        
+        self.tb_model_combo = ctk.CTkComboBox(self, values=master.configs['TB_MODELS'])
+        self.tb_model_combo.grid(row=4, column=0, pady=10, padx=10)
+        self.tb_model_combo.set('WM')
+
+        self.first_confirm_button = ctk.CTkButton(self, text="Confirm", command=master.press_first_confirm)
+        self.first_confirm_button.grid(row=5, column=0, pady=10, padx=10)
+    
+    def change_state(self, state):
+        """
+        Changes the state of certain widgets (between 'normal' and 'disabled').
+        """
+        self.upper_strand_entry.configure(state=state)
+        self.tb_model_combo.configure(state=state)
+        self.first_confirm_button.configure(state=state)