lazy commit

qDNA/data/logs/qDNA.log

@@ -1,22 +0,0 @@
-2024-12-03 18:01:43,681 - qDNA.tools.save_load - INFO - Data loaded from C:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA\qDNA\data\raw\config.json
-2024-12-03 18:01:43,681 - qDNA.tools.save_load - INFO - Data loaded from C:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA\qDNA\data\raw\tb_models.json
-2024-12-03 18:02:09,739 - qDNA.tools.save_load - INFO - Data loaded from C:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA\qDNA\data\raw\config.json
-2024-12-03 18:02:09,739 - qDNA.tools.save_load - INFO - Data loaded from C:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA\qDNA\data\raw\tb_models.json
-2024-12-04 10:46:07,160 - qDNA.tools.save_load - INFO - Data loaded from C:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA\qDNA\data\raw\config.json
-2024-12-04 10:46:07,160 - qDNA.tools.save_load - INFO - Data loaded from C:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA\qDNA\data\raw\tb_models.json
-2024-12-04 11:03:14,362 - qDNA.tools.save_load - INFO - Data loaded from C:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA\qDNA\data\raw\config.json
-2024-12-04 11:03:14,362 - qDNA.tools.save_load - INFO - Data loaded from C:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA\qDNA\data\raw\tb_models.json
-2024-12-04 11:10:22,405 - qDNA.tools.save_load - INFO - Data loaded from C:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA\qDNA\data\raw\config.json
-2024-12-04 11:10:22,405 - qDNA.tools.save_load - INFO - Data loaded from C:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA\qDNA\data\raw\tb_models.json
-2024-12-04 11:12:41,336 - qDNA.tools.save_load - INFO - Data loaded from C:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA\qDNA\data\raw\config.json
-2024-12-04 11:12:41,337 - qDNA.tools.save_load - INFO - Data loaded from C:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA\qDNA\data\raw\tb_models.json
-2024-12-04 11:15:02,788 - qDNA.tools.save_load - INFO - Data loaded from C:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA\qDNA\data\raw\config.json
-2024-12-04 11:15:02,788 - qDNA.tools.save_load - INFO - Data loaded from C:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA\qDNA\data\raw\tb_models.json
-2024-12-04 11:45:08,931 - qDNA.tools.save_load - INFO - Data loaded from C:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA\qDNA\data\raw\config.json
-2024-12-04 11:45:08,931 - qDNA.tools.save_load - INFO - Data loaded from C:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA\qDNA\data\raw\tb_models.json
-2024-12-04 11:45:21,520 - qDNA.tools.save_load - INFO - Data loaded from C:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA\qDNA\data\raw\config.json
-2024-12-04 11:45:21,520 - qDNA.tools.save_load - INFO - Data loaded from C:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA\qDNA\data\raw\tb_models.json
-2024-12-04 11:47:37,380 - qDNA.tools.save_load - INFO - Data loaded from C:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA\qDNA\data\raw\config.json
-2024-12-04 11:47:37,380 - qDNA.tools.save_load - INFO - Data loaded from C:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA\qDNA\data\raw\tb_models.json
-2024-12-04 11:47:49,433 - qDNA.tools.save_load - INFO - Data loaded from C:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA\qDNA\data\raw\config.json
-2024-12-04 11:47:49,433 - qDNA.tools.save_load - INFO - Data loaded from C:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA\qDNA\data\raw\tb_models.json

qDNA/data/raw/config.json

@@ -17,12 +17,13 @@
       "exciton"
     ],
     "SOURCES": [
+      "Endres2002",
+      "Bittner2007",
       "Hawke2010",
       "Simserides2014",
       "Mantela2021",
       "Simserides2024",
       "Herb2024",
-      "Bittner2007",
       "1BNA"
     ],
     "SPECTRAL_DENSITIES": [

qDNA/data/raw/tb_params/Endres2002_electron_WM copy.json

@@ -0,0 +1,19 @@
+{
+  "data": {
+    "E_A": -4.2,
+    "E_C": -4.6,
+    "E_G": -4.0,
+    "E_T": -4.6,
+    "t_AA": 0.1054,
+    "t_AG": 0.1124,
+    "t_GA": 0.0472,
+    "t_GG": 0.0525
+  },
+  "metadata": {
+    "notes": "Calculated with SIESTA and DZP basis set",
+    "particle": "hole",
+    "source": "Endres2002",
+    "tb_model_name": "WM",
+    "unit": "eV"
+  }
+}

qDNA/data/raw/tb_params/Endres2002_hole_WM.json

@@ -0,0 +1,19 @@
+{
+  "data": {
+    "E_A": -7.95,
+    "E_C": -8.3,
+    "E_G": -7.75,
+    "E_T": -8.3,
+    "t_AA": -0.0695,
+    "t_AG": -0.071,
+    "t_GA": -0.1871,
+    "t_GG": -0.1409
+  },
+  "metadata": {
+    "notes": "Calculated with SIESTA and DZP basis set",
+    "particle": "hole",
+    "source": "Endres2002",
+    "tb_model_name": "WM",
+    "unit": "eV"
+  }
+}

qDNA/dna_seq.py

@@ -68,6 +68,8 @@ class DNA_Seq:
 
     def __init__(self, upper_strand, tb_model_name, methylated=True, lower_strand=None):
         # Initialize the DNA sequence
+        if isinstance(upper_strand, str):
+            upper_strand = list(upper_strand)
         self.upper_strand = upper_strand
         self.lower_strand = lower_strand
         self.methylated = methylated

qDNA/gui/diss_frame.py

@@ -55,9 +55,10 @@ def __init__(self, master, configs, **kwargs):
         self.diss_relax_rate_label.grid(row=4, 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.insert(
+        #     0, str(self.diss_kwargs_default["relax_rate"])
+        # )
+        self.diss_relax_rate_entry.insert(0, 3.0)
         self.diss_relax_rate_entry.grid(row=4, column=1, padx=10, pady=10)
 
         # -----------------------------------

qDNA/gui/initial_frame.py

@@ -50,7 +50,7 @@ def __init__(self, master, **kwargs):
 
         self.tb_model_combo = ctk.CTkComboBox(self, values=master.configs["TB_MODELS"])
         self.tb_model_combo.grid(row=7, column=0, pady=10, padx=10)
-        self.tb_model_combo.set("WM")
+        self.tb_model_combo.set("ELM")
 
         self.grid_rowconfigure(8, weight=1)
 

qDNA/gui/plot_options_frame.py

@@ -14,7 +14,7 @@
 # --------------------------------------------------
 
 
-class LifetimeFrame(ctk.CTkFrame):
+class ExcitonFrame(ctk.CTkFrame):
     def __init__(self, master, **kwargs):
         """
         Notes:
@@ -59,23 +59,19 @@ def _calc_lifetime(self):
         if isinstance(lifetime, str):
             print("---------------------------")
             print(f"Exciton Lifetime: {lifetime}")
-            print("---------------------------")
         else:
             print("---------------------------")
             print(f"Exciton Lifetime: {lifetime} fs")
-            print("---------------------------")
 
     def _calc_dipole(self):
         dipole = calc_dipole(**self.kwargs)
         print("---------------------------")
         print(f"Charge Separation: {dipole} A")
-        print("---------------------------")
 
     def _calc_dipole_moment(self):
         dipole_moment = calc_dipole_moment(**self.kwargs)
         print("---------------------------")
         print(f"Dipole Moment: {dipole_moment} D")
-        print("---------------------------")
 
     def _calc_exciton_transfer(self):
         avg_pop_upper_strand, avg_pop_lower_strand = calc_exciton_transfer(
@@ -88,7 +84,6 @@ def _calc_exciton_transfer(self):
         print("---------------------------")
         print(f"Average Exciton Population (upper strand): {avg_pop_upper_strand}")
         print(f"Average Exciton Population (lower strand): {avg_pop_lower_strand}")
-        print("---------------------------")
 
 
 # --------------------------------------------------
@@ -113,9 +108,11 @@ def __init__(self, master, tb_basis, **kwargs):
         self.tb_site_label = ctk.CTkLabel(self, text="TB site:")
         self.tb_site_label.grid(row=1, column=0, padx=10, pady=10)
 
-        self.tb_site_combo = ctk.CTkComboBox(self, values=["All DNA Bases"] + tb_basis)
+        self.tb_site_combo = ctk.CTkComboBox(
+            self, values=["Heatmap", "All DNA Bases"] + tb_basis
+        )
         self.tb_site_combo.grid(row=1, column=1, padx=10, pady=10)
-        self.tb_site_combo.set("All DNA Bases")
+        self.tb_site_combo.set("Heatmap")
 
     def get_pop_kwargs(self):
         """Returns the values of widgets with get() method in dictionary format."""
@@ -236,7 +233,7 @@ def __init__(self, master, tb_basis, **kwargs):
         self.pop_frame = PopFrame(self.pop_tab, tb_basis, **kwargs)
         self.coh_frame = CohFrame(self.coh_tab, **kwargs)
         self.fourier_frame = FourierFrame(self.fourier_tab, tb_basis, **kwargs)
-        self.lifetime_frame = LifetimeFrame(self.lifetime_tab, **kwargs)
+        self.exciton_frame = ExcitonFrame(self.lifetime_tab, **kwargs)
 
 
 class PlotOptionsFrame(ctk.CTkFrame):
@@ -272,6 +269,6 @@ def change_state(self, state):
         change_state_all_widgets(self.plot_options_tab.pop_frame, state=state)
         change_state_all_widgets(self.plot_options_tab.coh_frame, state=state)
         change_state_all_widgets(self.plot_options_tab.fourier_frame, state=state)
-        change_state_all_widgets(self.plot_options_tab.lifetime_frame, state=state)
+        change_state_all_widgets(self.plot_options_tab.exciton_frame, state=state)
         self.submit_button.configure(state=state)
         self.back_button.configure(state=state)

qDNA/gui/plotting_window.py

@@ -4,7 +4,13 @@
 import matplotlib.pyplot as plt
 from matplotlib.backends.backend_tkagg import FigureCanvasTkAgg
 
-from ..visualization import plot_pop, plot_pops, plot_coh, plot_fourier
+from ..visualization import (
+    plot_pop,
+    plot_pops,
+    plot_coh,
+    plot_fourier,
+    plot_pops_heatmap,
+)
 from ..tools import save_figure
 
 # -----------------------------------------------------------------------------------------------------
@@ -73,7 +79,9 @@ def __init__(self, master, **kwargs):
 
         if self.plot_option == "Population":
             self.init_tb_site = self.plot_options_kwargs["init_tb_site"]
-            if self.init_tb_site == "All DNA Bases":
+            if self.init_tb_site == "Heatmap":
+                self.plot_pops_heatmap()
+            elif self.init_tb_site == "All DNA Bases":
                 self.plot_pops()
             else:
                 self.plot_pop()
@@ -103,16 +111,19 @@ def plot_pop(self):
     def plot_pops(self):
         self.fig, self.axes = plot_pops(self.me_solver)
 
+    def plot_pops_heatmap(self):
+        self.fig, self.ax = plot_pops_heatmap(self.me_solver)
+
     def plot_coh(self):
         self.fig, self.ax = plt.subplots()
-        plot_coh(self.ax, self.me_solver)
+        self.ax = plot_coh(self.ax, self.me_solver)
 
     def plot_fourier(self):
         self.fig, self.ax = plt.subplots()
         init_state = self.plot_options_kwargs["init_state"]
         end_state = self.plot_options_kwargs["end_state"]
         x_axis = self.plot_options_kwargs["x_axis"]
-        plot_fourier(self.ax, self.tb_ham, init_state, end_state, x_axis)
+        self.ax = plot_fourier(self.ax, self.tb_ham, init_state, end_state, x_axis)
 
     def save(self):
         self.filename = self.plotting_frame.filename_entry.get()

qDNA/gui/qdna_app.py

@@ -34,6 +34,8 @@ def __init__(self):
         # initialization of the ctk.CTk class
         super().__init__()
 
+        # self.tk.call('tk', 'scaling', 1.0)
+
         self.title("QuantumDNA")
         self.configs = CONFIG
         self.kwargs = dict()
@@ -213,15 +215,15 @@ def submit(self):
 
     def enable_initial_frame(self):
         self.initial_frame.change_state("normal")
-        self.options_frame.change_state("disabled")
-        self.plot_options_frame.change_state("disabled")
+        self.options_frame.change_state("normal")
+        self.plot_options_frame.change_state("normal")
 
     def enable_options_frame(self):
-        self.initial_frame.change_state("disabled")
+        self.initial_frame.change_state("normal")
         self.options_frame.change_state("normal")
-        self.plot_options_frame.change_state("disabled")
+        self.plot_options_frame.change_state("normal")
 
     def enable_plotting_frame(self):
-        self.initial_frame.change_state("disabled")
-        self.options_frame.change_state("disabled")
+        self.initial_frame.change_state("normal")
+        self.options_frame.change_state("normal")
         self.plot_options_frame.change_state("normal")

qDNA/qDNA-default.mplstyle

@@ -1,39 +1,73 @@
+# QuantumDNA Custom Matplotlib Stylefile
+# --------------------------------------
+
+# Improting qDNA saves this Matplotlib style file in the directory specified by
+# `import matplotlib as mpl; mpl.get_configdir()`
+# >>> 'C:\\Users\\<username>\\.matplotlib'
+# Once saved, it becomes globally accessible and can be applied using
+# `import matplotlib.pyplot as plt; plt.style.use('qDNA-default')`.
+
 
 # LaTeX rendering
+# ---------------
+# Note: Latex must be installed locally
+
 # text.usetex: True
 # text.latex.preamble: \usepackage{amsmath}\usepackage{siunitx}
 
+
 # Font settings
-font.family: serif
-# font.serif: Times New Roman  # Used in elsarticle (Elsevier)
-font.serif: Computer Modern Roman  # Used in revtex4-2 (APS)
+# -------------
+# View all available fonts by running
+# `import matplotlib.font_manager as fm; sorted([f.name for f in fm.fontManager.ttflist])`
+# Use serif font Latex, e.g. Times New Roman for elsarticle (Elsevier) and revtex4-2 (APS)
+# DejaVu fonts are matplotlib default and therefore always available
+
+# font.family: serif
+# font.serif: DejaVu Serif, Times New Roman, cmr10
+# mathtext.fontset: dejavuserif
+font.family: sans-serif
+font.sans-serif: DejaVu Sans, Calibri, Arial
+mathtext.fontset: dejavusans
 font.size: 15
 
+
 # Figure size
+# -----------
 # revtex4-2 (APS) one-column: [8.64468/2.54, 8.64468/2.54 * 3/4]
 # elsarticle (Elsevier) one-column: [8.85553/2.54, 8.85553/2.54 * 3/4]
 figure.figsize: 6.4, 4.8  # Default ratio 4:3
 
+
 # Axes, labels, and legend
+# ------------------------
 axes.titlesize: large  # Font size for title
 axes.labelsize: medium  # Font size for axis labels
 legend.fontsize: small  # Font size for legend
 xtick.labelsize: small  # Font size for x-tick labels
 ytick.labelsize: small  # Font size for y-tick labels
 
+
 # Lines and markers
+# -----------------
 lines.linewidth: 2.0  # Default line width
 lines.markersize: 8.0  # Default marker size
 
+
 # Grid and layout
+# ---------------
 axes.grid: True  # Always show grid
 grid.linestyle: --  # Grid line style
 # grid.color: lightgray
 grid.alpha: 0.7  # Grid transparency
 figure.autolayout: True  # Automatically apply tight_layout
 
-# Define the color cycle using the full seaborn deep palette
+
+# Colors
+# ------
+
+# Color cycle using the full seaborn deep palette
 axes.prop_cycle: cycler('color', ['4C72B0', '55A868', 'C44E52', '8172B2', 'CCB974', '64B5CD'])
 
-# Define the color cycle using the tab10 palette
+# Color cycle using the matplotlib default tab10 palette
 # axes.prop_cycle: cycler('color', ['#1f77b4', '#ff7f0e', '#2ca02c', '#d62728', '#9467bd', '#8c564b', '#e377c2', '#7f7f7f', '#bcbd22', '#17becf'])