From 7bc2f8b860de83df7e6f7b98c6d45bc53e54fe2d Mon Sep 17 00:00:00 2001
From: Dennis Herb <dennis.herb@uni-ulm.de>
Date: Mon, 11 Nov 2024 15:02:10 +0100
Subject: [PATCH] preparing for new release

---
 MANIFEST.in                                   |   3 +-
 README.md                                     |   2 +-
 pyproject.toml                                |   1 +
 qDNA/__init__.py                              |   2 +-
 qDNA/data/logs/qDNA.log                       | 221 ++++++++++++++++++
 qDNA/data/raw/config.json                     |  15 +-
 qDNA/data/raw/tb_models.json                  |  92 ++++----
 .../Simserides2024_electron_ELM.json          |   4 +-
 .../Simserides2024_electron_FELM.json         |   4 +-
 .../tb_params/Simserides2024_hole_ELM.json    |   4 +-
 .../tb_params/Simserides2024_hole_FELM.json   |   4 +-
 qDNA/defaults.yaml                            |   2 +-
 qDNA/dna_seq.py                               |  10 +-
 qDNA/plotting/__init__.py                     |   8 +-
 qDNA/plotting/plot_dna_base_frequency.py      |   2 +-
 qDNA/tools/save_load.py                       | 126 ++++++++--
 requirements/requirements.txt                 |   2 +-
 17 files changed, 404 insertions(+), 98 deletions(-)

diff --git a/MANIFEST.in b/MANIFEST.in
index ae50cbc..c28c30a 100644
--- a/MANIFEST.in
+++ b/MANIFEST.in
@@ -16,6 +16,7 @@ include qDNA/defaults.yaml
 
 # Include specific data files
 include qDNA/data/data_paper/*.json
-include qDNA/data/figures_paper/*.pdf *.png
+include qDNA/data/figures_paper/*.pdf
+include qDNA/data/figures_paper/*.png
 include qDNA/data/raw/tb_params/*.json
 include qDNA/data/raw/*.json
diff --git a/README.md b/README.md
index d40ed6e..25cd041 100644
--- a/README.md
+++ b/README.md
@@ -12,7 +12,7 @@
         <img src="https://readthedocs.org/projects/quantumdna/badge/?version=latest"
             alt="Documentation Status"></a>
     <a href="https://github.com/dehe1011/QuantumDNA/releases">
-        <img src="https://img.shields.io/badge/version-0.1.7-blue"
+        <img src="https://img.shields.io/badge/version-0.1.10-blue"
             alt="Release"></a>
     <a href='https://coveralls.io/github/dehe1011/QuantumDNA?branch=main'>
         <img src='https://coveralls.io/repos/github/dehe1011/QuantumDNA/badge.svg?branch=main'
diff --git a/pyproject.toml b/pyproject.toml
index a5da5c4..3d58d2b 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -27,6 +27,7 @@ dependencies = [
     "tqdm==4.66.4",
     "customtkinter==5.2.2",
     "scipy==1.11.4",
+    "openpyxl==3.1.5",
 ]
 
 [project.urls]
diff --git a/qDNA/__init__.py b/qDNA/__init__.py
index c309d90..e4934c8 100644
--- a/qDNA/__init__.py
+++ b/qDNA/__init__.py
@@ -1,4 +1,4 @@
-__version__ = "0.1.7"
+__version__ = "0.1.10"
 
 import pathlib
 import os
diff --git a/qDNA/data/logs/qDNA.log b/qDNA/data/logs/qDNA.log
index e69de29..b94ce66 100644
--- a/qDNA/data/logs/qDNA.log
+++ b/qDNA/data/logs/qDNA.log
@@ -0,0 +1,221 @@
+2024-10-28 11:51:09,324 - qDNA.tools.save_load - INFO - Data loaded from C:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA\qDNA\data\raw\config.json
+2024-10-28 11:51:09,324 - 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
+2024-10-28 11:51:17,406 - qDNA.tools.save_load - INFO - Data loaded from C:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA\qDNA\data\raw\config.json
+2024-10-28 11:51:17,406 - 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
+2024-10-28 11:53:36,101 - qDNA.tools.save_load - INFO - Data loaded from C:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA\qDNA\data\raw\config.json
+2024-10-28 11:53:36,101 - qDNA.tools.save_load - WARNING - File C:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA\qDNA\data\raw\config.json already exists.
+2024-10-28 11:53:36,101 - qDNA.tools.save_load - INFO - Value author2024 added to key SOURCES in config.json
+2024-10-28 11:55:33,278 - qDNA.tools.save_load - INFO - Data loaded from C:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA\qDNA\data\raw\config.json
+2024-10-28 11:55:33,279 - qDNA.tools.save_load - WARNING - File C:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA\qDNA\data\raw\config.json already exists.
+2024-10-28 11:55:33,279 - qDNA.tools.save_load - INFO - Value author2024 added to key SOURCES in config.json
+2024-10-28 11:56:39,205 - qDNA.tools.save_load - INFO - Data loaded from C:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA\qDNA\data\raw\config.json
+2024-10-28 11:56:39,205 - qDNA.tools.save_load - WARNING - File C:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA\qDNA\data\raw\config.json already exists.
+2024-10-28 11:56:39,205 - qDNA.tools.save_load - INFO - Value author2024 added to key SOURCES in config.json
+2024-10-28 11:57:59,054 - qDNA.tools.save_load - INFO - Data loaded from C:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA\qDNA\data\raw\config.json
+2024-10-28 11:57:59,054 - qDNA.tools.save_load - WARNING - File C:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA\qDNA\data\raw\config.json already exists.
+2024-10-28 11:57:59,054 - qDNA.tools.save_load - INFO - Value author2024 added to key SOURCES in config.json
+2024-10-28 11:58:34,639 - qDNA.tools.save_load - INFO - Data loaded from C:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA\qDNA\data\raw\config.json
+2024-10-28 11:58:34,639 - qDNA.tools.save_load - INFO - Data saved as C:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA\qDNA\data\raw\config.json
+2024-10-28 11:58:34,639 - qDNA.tools.save_load - INFO - Value author2024 added to key SOURCES in config.json
+2024-10-28 12:02:42,299 - qDNA.tools.save_load - INFO - Data loaded from C:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA\qDNA\data\raw\config.json
+2024-10-28 12:02:42,300 - qDNA.tools.save_load - INFO - Data saved as C:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA\qDNA\data\raw\config.json
+2024-10-28 12:02:42,300 - qDNA.tools.save_load - INFO - Value ['Hawke2010', 'Simserides2014', 'Mantela2021', 'Simserides2024'] added to key SOURCES in config.json
+2024-10-28 12:03:06,298 - qDNA.tools.save_load - INFO - Data loaded from C:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA\qDNA\data\raw\config.json
+2024-10-28 12:03:06,298 - qDNA.tools.save_load - INFO - Data saved as C:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA\qDNA\data\raw\config.json
+2024-10-28 12:03:06,298 - qDNA.tools.save_load - INFO - Value None added to key SOURCES in config.json
+2024-10-28 12:03:22,290 - qDNA.tools.save_load - INFO - Data loaded from C:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA\qDNA\data\raw\config.json
+2024-10-28 12:03:22,290 - qDNA.tools.save_load - INFO - Data saved as C:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA\qDNA\data\raw\config.json
+2024-10-28 12:03:22,290 - qDNA.tools.save_load - INFO - Value ['Hawke2010', 'Simserides2014', 'Mantela2021', 'Simserides2024', 'my_source'] added to key SOURCES in config.json
+2024-10-28 12:05:11,099 - 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
+2024-10-28 12:05:11,099 - qDNA.tools.save_load - INFO - Data saved as C:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA\qDNA\data\raw\tb_models.json
+2024-10-28 12:05:11,099 - qDNA.tools.save_load - INFO - Value {'A': 1, 'B': 2, 'C': 3} added to key new in tb_models.json
+2024-10-28 12:06:24,624 - qDNA.tools.save_load - INFO - Data loaded from C:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA\qDNA\data\raw\config.json
+2024-10-28 12:06:24,624 - 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
+2024-10-28 12:08:50,841 - qDNA.tools.save_load - INFO - Data loaded from c:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA-notebooks\data\data_paper\dipole_7bp_J0.json
+2024-10-28 12:08:50,866 - qDNA.tools.save_load - INFO - Data loaded from c:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA-notebooks\data\data_paper\lifetime_7bp_J0.json
+2024-10-28 12:08:55,258 - qDNA.tools.save_load - INFO - Data loaded from c:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA-notebooks\data\data_paper\lifetime_7bp_J0.json
+2024-10-28 12:08:58,505 - qDNA.tools.save_load - INFO - Data loaded from c:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA-notebooks\data\data_paper\dipole_7bp_J0.json
+2024-10-28 12:08:59,558 - qDNA.tools.save_load - INFO - Data loaded from c:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA-notebooks\data\data_paper\lifetime_7bp_J0.json
+2024-10-28 12:10:03,223 - qDNA.tools.save_load - INFO - Data loaded from C:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA\qDNA\data\raw\config.json
+2024-10-28 12:10:03,223 - 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
+2024-10-28 12:10:10,006 - qDNA.tools.save_load - INFO - Data loaded from c:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA-notebooks\data\data_paper\dipole_7bp_J0.json
+2024-10-28 12:10:10,016 - qDNA.tools.save_load - INFO - Data loaded from c:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA-notebooks\data\data_paper\lifetime_7bp_J0.json
+2024-10-28 12:10:14,233 - qDNA.tools.save_load - INFO - Data loaded from c:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA-notebooks\data\data_paper\lifetime_7bp_J0.json
+2024-10-28 12:10:16,711 - qDNA.tools.save_load - INFO - Data loaded from c:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA-notebooks\data\data_paper\lifetime_7bp_J0.json
+2024-10-28 12:12:43,340 - qDNA.tools.save_load - INFO - Data loaded from C:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA\qDNA\data\raw\config.json
+2024-10-28 12:12:43,340 - 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
+2024-10-28 12:12:46,664 - qDNA.tools.save_load - INFO - Data loaded from c:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA-notebooks\data\data_paper\dipole_7bp_J0.json
+2024-10-28 12:12:46,670 - qDNA.tools.save_load - INFO - Data loaded from c:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA-notebooks\data\data_paper\lifetime_7bp_J0.json
+2024-10-28 12:12:48,776 - qDNA.tools.save_load - INFO - Data loaded from c:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA-notebooks\data\data_paper\lifetime_7bp_J0.json
+2024-10-28 12:12:51,880 - qDNA.tools.save_load - INFO - Data loaded from c:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA-notebooks\data\data_paper\dipole_7bp_J0.json
+2024-10-28 12:12:51,887 - qDNA.tools.save_load - INFO - Data loaded from c:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA-notebooks\data\data_paper\lifetime_7bp_J0.json
+2024-10-28 12:12:56,727 - qDNA.tools.save_load - INFO - Data loaded from c:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA-notebooks\data\data_paper\lifetime_7bp_J0.json
+2024-10-28 12:13:50,727 - qDNA.tools.save_load - INFO - Data loaded from c:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA-notebooks\data\data_paper\lifetime_7bp_J0.json
+2024-10-28 12:14:28,109 - qDNA.tools.save_load - INFO - Data loaded from c:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA-notebooks\data\data_paper\dipole_7bp_J0.json
+2024-10-28 12:14:28,127 - qDNA.tools.save_load - INFO - Data loaded from c:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA-notebooks\data\data_paper\lifetime_7bp_J0.json
+2024-10-28 12:14:28,591 - qDNA.tools.save_load - INFO - Data loaded from c:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA-notebooks\data\data_paper\lifetime_7bp_J0.json
+2024-10-28 12:14:28,974 - qDNA.tools.save_load - INFO - Data loaded from c:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA-notebooks\data\data_paper\dipole_7bp_J0.json
+2024-10-28 12:14:29,511 - qDNA.tools.save_load - INFO - Data loaded from c:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA-notebooks\data\data_paper\lifetime_7bp_J0.json
+2024-10-28 12:14:41,174 - qDNA.tools.save_load - INFO - Data loaded from C:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA\qDNA\data\raw\config.json
+2024-10-28 12:14:41,174 - 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
+2024-10-28 12:14:42,158 - qDNA.tools.save_load - INFO - Data loaded from c:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA-notebooks\data\data_paper\dipole_7bp_J0.json
+2024-10-28 12:14:42,176 - qDNA.tools.save_load - INFO - Data loaded from c:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA-notebooks\data\data_paper\lifetime_7bp_J0.json
+2024-10-28 12:14:42,762 - qDNA.tools.save_load - INFO - Data loaded from c:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA-notebooks\data\data_paper\lifetime_7bp_J0.json
+2024-10-28 12:14:43,177 - qDNA.tools.save_load - INFO - Data loaded from c:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA-notebooks\data\data_paper\dipole_7bp_J0.json
+2024-10-28 12:14:43,876 - qDNA.tools.save_load - INFO - Data loaded from c:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA-notebooks\data\data_paper\lifetime_7bp_J0.json
+2024-10-28 12:14:48,509 - qDNA.tools.save_load - INFO - Data loaded from C:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA\qDNA\data\raw\tb_params\Simserides2014_electron_WM.json
+2024-10-28 12:14:48,513 - qDNA.tools.save_load - INFO - Data loaded from C:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA\qDNA\data\raw\tb_params\Simserides2014_hole_WM.json
+2024-10-28 12:14:50,863 - qDNA.tools.save_load - INFO - Data loaded from C:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA\qDNA\data\raw\tb_params\Simserides2014_electron_WM.json
+2024-10-28 12:14:50,863 - qDNA.tools.save_load - INFO - Data loaded from C:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA\qDNA\data\raw\tb_params\Simserides2014_hole_WM.json
+2024-10-28 12:15:17,207 - qDNA.tools.save_load - INFO - Data loaded from c:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA-notebooks\data\data_paper\lifetime_7bp_J0.json
+2024-10-28 12:15:17,228 - qDNA.tools.save_load - INFO - Data loaded from c:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA-notebooks\data\data_paper\lifetime_7bp_J0.5.json
+2024-10-28 12:15:17,258 - qDNA.tools.save_load - INFO - Data loaded from c:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA-notebooks\data\data_paper\lifetime_7bp_J1.json
+2024-10-28 12:15:19,722 - qDNA.tools.save_load - INFO - Data loaded from c:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA-notebooks\data\data_paper\lifetime_7bp_J0.json
+2024-10-28 12:15:19,732 - qDNA.tools.save_load - INFO - Data loaded from c:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA-notebooks\data\data_paper\lifetime_7bp_J0.json
+2024-10-28 12:15:19,739 - qDNA.tools.save_load - INFO - Data loaded from c:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA-notebooks\data\data_paper\lifetime_7bp_J0.5.json
+2024-10-28 12:15:20,706 - qDNA.tools.save_load - INFO - Data loaded from c:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA-notebooks\data\data_paper\lifetime_7bp_J0.json
+2024-10-28 12:15:20,708 - qDNA.tools.save_load - INFO - Data loaded from c:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA-notebooks\data\data_paper\lifetime_7bp_J0.json
+2024-10-28 12:15:20,708 - qDNA.tools.save_load - INFO - Data loaded from c:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA-notebooks\data\data_paper\lifetime_7bp_J1.json
+2024-10-28 12:15:21,641 - qDNA.tools.save_load - INFO - Data loaded from c:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA-notebooks\data\data_paper\lifetime_7bp_J0.json
+2024-10-28 12:15:21,657 - qDNA.tools.save_load - INFO - Data loaded from c:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA-notebooks\data\data_paper\lifetime_7bp_J0.5.json
+2024-10-28 12:15:22,559 - qDNA.tools.save_load - INFO - Data loaded from c:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA-notebooks\data\data_paper\lifetime_7bp_J0.json
+2024-10-28 12:15:22,575 - qDNA.tools.save_load - INFO - Data loaded from c:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA-notebooks\data\data_paper\lifetime_7bp_J1.json
+2024-10-28 12:15:23,777 - qDNA.tools.save_load - INFO - Data loaded from c:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA-notebooks\data\data_paper\lifetime_7bp_J0.5.json
+2024-10-28 12:15:24,062 - qDNA.tools.save_load - INFO - Data loaded from c:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA-notebooks\data\data_paper\lifetime_7bp_J1.json
+2024-10-28 12:15:26,191 - qDNA.tools.save_load - INFO - Data loaded from c:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA-notebooks\data\data_paper\dipole_7bp_J0.json
+2024-10-28 12:15:26,198 - qDNA.tools.save_load - INFO - Data loaded from c:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA-notebooks\data\data_paper\lifetime_7bp_J0.json
+2024-10-28 12:15:26,224 - qDNA.tools.save_load - INFO - Data loaded from c:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA-notebooks\data\data_paper\dipole_7bp_J0.5.json
+2024-10-28 12:15:26,224 - qDNA.tools.save_load - INFO - Data loaded from c:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA-notebooks\data\data_paper\lifetime_7bp_J0.5.json
+2024-10-28 12:15:26,258 - qDNA.tools.save_load - INFO - Data loaded from c:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA-notebooks\data\data_paper\dipole_7bp_J1.json
+2024-10-28 12:15:26,274 - qDNA.tools.save_load - INFO - Data loaded from c:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA-notebooks\data\data_paper\lifetime_7bp_J1.json
+2024-10-28 12:15:27,146 - qDNA.tools.save_load - INFO - Data loaded from c:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA-notebooks\data\data_paper\dipole_7bp_J0.json
+2024-10-28 12:15:27,146 - qDNA.tools.save_load - INFO - Data loaded from c:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA-notebooks\data\data_paper\lifetime_7bp_J0.json
+2024-10-28 12:15:27,162 - qDNA.tools.save_load - INFO - Data loaded from c:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA-notebooks\data\data_paper\dipole_7bp_J0.5.json
+2024-10-28 12:15:27,168 - qDNA.tools.save_load - INFO - Data loaded from c:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA-notebooks\data\data_paper\lifetime_7bp_J0.5.json
+2024-10-28 12:15:27,176 - qDNA.tools.save_load - INFO - Data loaded from c:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA-notebooks\data\data_paper\dipole_7bp_J1.json
+2024-10-28 12:15:27,182 - qDNA.tools.save_load - INFO - Data loaded from c:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA-notebooks\data\data_paper\lifetime_7bp_J1.json
+2024-10-28 12:15:27,426 - qDNA.tools.save_load - INFO - Data loaded from C:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA\qDNA\data\raw\tb_params\Simserides2014_electron_WM.json
+2024-10-28 12:15:27,426 - qDNA.tools.save_load - INFO - Data loaded from C:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA\qDNA\data\raw\tb_params\Simserides2014_hole_WM.json
+2024-10-28 12:15:27,760 - qDNA.tools.save_load - INFO - Data loaded from C:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA\qDNA\data\raw\tb_params\Simserides2014_electron_WM.json
+2024-10-28 12:15:27,760 - qDNA.tools.save_load - INFO - Data loaded from C:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA\qDNA\data\raw\tb_params\Simserides2014_hole_WM.json
+2024-10-28 12:15:28,151 - qDNA.tools.save_load - INFO - Data loaded from c:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA-notebooks\data\data_paper\dipole_7bp_J0.json
+2024-10-28 12:15:28,161 - qDNA.tools.save_load - INFO - Data loaded from c:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA-notebooks\data\data_paper\dipole_7bp_J0.json
+2024-10-28 12:15:28,169 - qDNA.tools.save_load - INFO - Data loaded from c:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA-notebooks\data\data_paper\dipole_7bp_J0.5.json
+2024-10-28 12:15:29,239 - qDNA.tools.save_load - INFO - Data loaded from c:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA-notebooks\data\data_paper\dipole_7bp_J0.json
+2024-10-28 12:15:29,245 - qDNA.tools.save_load - INFO - Data loaded from c:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA-notebooks\data\data_paper\dipole_7bp_J0.json
+2024-10-28 12:15:29,245 - qDNA.tools.save_load - INFO - Data loaded from c:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA-notebooks\data\data_paper\dipole_7bp_J1.json
+2024-10-28 12:15:30,316 - qDNA.tools.save_load - INFO - Data loaded from c:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA-notebooks\data\data_paper\dipole_7bp_J0.json
+2024-10-28 12:15:30,325 - qDNA.tools.save_load - INFO - Data loaded from c:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA-notebooks\data\data_paper\dipole_7bp_J0.5.json
+2024-10-28 12:15:31,377 - qDNA.tools.save_load - INFO - Data loaded from c:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA-notebooks\data\data_paper\dipole_7bp_J0.json
+2024-10-28 12:15:31,385 - qDNA.tools.save_load - INFO - Data loaded from c:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA-notebooks\data\data_paper\dipole_7bp_J1.json
+2024-10-28 12:15:32,704 - qDNA.tools.save_load - INFO - Data loaded from c:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA-notebooks\data\data_paper\lifetime_4bp_relax0.02.json
+2024-10-28 12:15:32,709 - qDNA.tools.save_load - WARNING - File c:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA-notebooks\data\data_paper\lifetime_7bp_relax0.01.json does not exist.
+2024-10-28 12:16:02,037 - qDNA.tools.save_load - INFO - Data loaded from c:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA-notebooks\data\data_paper\lifetime_4bp_relax0.02.json
+2024-10-28 12:16:02,037 - qDNA.tools.save_load - WARNING - File c:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA-notebooks\data\data_paper\lifetime_7bp_relax0.01.json does not exist.
+2024-10-28 12:16:57,286 - qDNA.tools.save_load - INFO - Data loaded from c:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA-notebooks\data\data_paper\lifetime_4bp_relax0.02.json
+2024-10-28 12:16:57,287 - qDNA.tools.save_load - INFO - Data loaded from c:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA-notebooks\data\data_paper\lifetime_4bp_relax0.01.json
+2024-10-28 12:16:57,294 - qDNA.tools.save_load - INFO - Data loaded from c:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA-notebooks\data\data_paper\lifetime_4bp_relax0.02.json
+2024-10-28 12:16:57,294 - qDNA.tools.save_load - INFO - Data loaded from c:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA-notebooks\data\data_paper\lifetime_4bp_relax0.02.json
+2024-10-28 12:16:57,294 - qDNA.tools.save_load - INFO - Data loaded from c:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA-notebooks\data\data_paper\lifetime_4bp_relax0.05.json
+2024-10-28 12:16:57,308 - qDNA.tools.save_load - INFO - Data loaded from c:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA-notebooks\data\data_paper\lifetime_4bp_relax0.02.json
+2024-10-28 12:16:57,308 - qDNA.tools.save_load - INFO - Data loaded from c:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA-notebooks\data\data_paper\lifetime_4bp_relax0.02.json
+2024-10-28 12:16:57,309 - qDNA.tools.save_load - INFO - Data loaded from c:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA-notebooks\data\data_paper\lifetime_4bp_relax0.01.json
+2024-10-28 12:16:57,309 - qDNA.tools.save_load - INFO - Data loaded from c:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA-notebooks\data\data_paper\lifetime_4bp_relax0.02.json
+2024-10-28 12:16:57,310 - qDNA.tools.save_load - INFO - Data loaded from c:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA-notebooks\data\data_paper\lifetime_4bp_relax0.02.json
+2024-10-28 12:16:57,310 - qDNA.tools.save_load - INFO - Data loaded from c:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA-notebooks\data\data_paper\lifetime_4bp_relax0.05.json
+2024-10-28 19:53:54,376 - qDNA.tools.save_load - INFO - Data loaded from C:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA\qDNA\data\raw\comp_time.json
+2024-10-28 19:53:57,039 - qDNA.tools.save_load - INFO - Data loaded from C:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA\qDNA\data\raw\config.json
+2024-10-28 19:53:57,039 - qDNA.tools.save_load - INFO - Data loaded from C:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA\qDNA\data\raw\config.json
+2024-10-28 19:53:57,041 - 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
+2024-10-28 19:53:57,041 - 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
+2024-10-28 19:54:00,023 - qDNA.tools.save_load - INFO - Data loaded from C:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA\qDNA\data\raw\tb_params\Simserides2024_electron_ELM.json
+2024-10-28 19:54:00,023 - qDNA.tools.save_load - INFO - Data loaded from C:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA\qDNA\data\raw\tb_params\Simserides2024_electron_ELM.json
+2024-10-28 19:54:00,023 - qDNA.tools.save_load - INFO - Data loaded from C:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA\qDNA\data\raw\tb_params\Simserides2024_hole_ELM.json
+2024-10-28 19:54:00,023 - qDNA.tools.save_load - INFO - Data loaded from C:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA\qDNA\data\raw\tb_params\Simserides2024_hole_ELM.json
+2024-10-28 19:54:02,622 - qDNA.tools.save_load - INFO - Data saved as C:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA\qDNA\data\gui\lifetime_delete.json
+2024-10-28 19:54:02,623 - qDNA.tools.save_load - INFO - Data loaded from C:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA\qDNA\data\gui\lifetime_delete.json
+2024-10-28 19:54:02,792 - qDNA.tools.save_load - INFO - Data loaded from C:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA\qDNA\data\raw\config.json
+2024-10-28 19:54:02,792 - qDNA.tools.save_load - INFO - Data loaded from C:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA\qDNA\data\raw\config.json
+2024-10-28 19:54:02,792 - 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
+2024-10-28 19:54:02,792 - 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
+2024-10-28 19:54:03,737 - qDNA.tools.save_load - INFO - Data loaded from C:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA\qDNA\data\raw\tb_params\Simserides2024_electron_ELM.json
+2024-10-28 19:54:03,737 - qDNA.tools.save_load - INFO - Data loaded from C:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA\qDNA\data\raw\tb_params\Simserides2024_hole_ELM.json
+2024-10-28 19:54:03,753 - qDNA.tools.save_load - INFO - Data loaded from C:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA\qDNA\data\raw\tb_params\Simserides2024_electron_ELM.json
+2024-10-28 19:54:03,753 - qDNA.tools.save_load - INFO - Data loaded from C:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA\qDNA\data\raw\tb_params\Simserides2024_hole_ELM.json
+2024-10-28 19:54:03,753 - qDNA.tools.save_load - INFO - Data loaded from C:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA\qDNA\data\raw\tb_params\Simserides2024_electron_ELM.json
+2024-10-28 19:54:03,753 - qDNA.tools.save_load - INFO - Data loaded from C:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA\qDNA\data\raw\tb_params\Simserides2024_hole_ELM.json
+2024-10-28 19:54:03,761 - qDNA.tools.save_load - INFO - Data loaded from C:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA\qDNA\data\raw\tb_params\Simserides2024_electron_ELM.json
+2024-10-28 19:54:03,761 - qDNA.tools.save_load - INFO - Data loaded from C:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA\qDNA\data\raw\tb_params\Simserides2024_hole_ELM.json
+2024-10-28 19:54:05,124 - qDNA.tools.save_load - INFO - Data saved as C:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA\qDNA\data\gui\dipole_delete.json
+2024-10-28 19:54:05,125 - qDNA.tools.save_load - INFO - Data loaded from C:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA\qDNA\data\gui\dipole_delete.json
+2024-10-28 19:54:05,129 - qDNA.tools.save_load - WARNING - File C:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA\qDNA\data\gui\dipole_delete.json already exists.
+2024-10-28 19:54:05,129 - qDNA.tools.save_load - INFO - Data loaded from C:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA\qDNA\data\gui\lifetime_delete.json
+2024-10-28 19:54:05,293 - qDNA.tools.save_load - INFO - Data loaded from C:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA\qDNA\data\raw\config.json
+2024-10-28 19:54:05,293 - qDNA.tools.save_load - INFO - Data loaded from C:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA\qDNA\data\raw\config.json
+2024-10-28 19:54:05,293 - 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
+2024-10-28 19:54:05,293 - 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
+2024-10-28 19:54:06,242 - qDNA.tools.save_load - INFO - Data loaded from C:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA\qDNA\data\raw\tb_params\Simserides2024_electron_ELM.json
+2024-10-28 19:54:06,242 - qDNA.tools.save_load - INFO - Data loaded from C:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA\qDNA\data\raw\tb_params\Simserides2024_electron_ELM.json
+2024-10-28 19:54:06,242 - qDNA.tools.save_load - INFO - Data loaded from C:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA\qDNA\data\raw\tb_params\Simserides2024_hole_ELM.json
+2024-10-28 19:54:06,242 - qDNA.tools.save_load - INFO - Data loaded from C:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA\qDNA\data\raw\tb_params\Simserides2024_hole_ELM.json
+2024-10-28 19:54:06,264 - qDNA.tools.save_load - INFO - Data loaded from C:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA\qDNA\data\raw\tb_params\Simserides2024_electron_ELM.json
+2024-10-28 19:54:06,264 - qDNA.tools.save_load - INFO - Data loaded from C:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA\qDNA\data\raw\tb_params\Simserides2024_electron_ELM.json
+2024-10-28 19:54:06,264 - qDNA.tools.save_load - INFO - Data loaded from C:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA\qDNA\data\raw\tb_params\Simserides2024_hole_ELM.json
+2024-10-28 19:54:06,264 - qDNA.tools.save_load - INFO - Data loaded from C:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA\qDNA\data\raw\tb_params\Simserides2024_hole_ELM.json
+2024-10-28 19:54:07,645 - qDNA.tools.save_load - INFO - Data saved as C:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA\qDNA\data\gui\exciton_transfer_delete.json
+2024-10-28 20:16:28,592 - qDNA.tools.save_load - INFO - Data loaded from C:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA\qDNA\data\raw\config.json
+2024-10-28 20:16:28,592 - 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
+2024-10-29 11:43:00,818 - qDNA.tools.save_load - INFO - Data loaded from C:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA\qDNA\data\raw\tb_params\Hawke2010_electron_WM.json
+2024-10-29 11:43:00,833 - qDNA.tools.save_load - INFO - Data loaded from C:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA\qDNA\data\raw\tb_params\Hawke2010_hole_WM.json
+2024-10-29 12:12:28,887 - qDNA.tools.save_load - INFO - Data loaded from C:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA\qDNA\data\raw\comp_time.json
+2024-10-29 12:12:30,283 - qDNA.tools.save_load - INFO - Data loaded from C:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA\qDNA\data\raw\config.json
+2024-10-29 12:12:30,283 - qDNA.tools.save_load - INFO - Data loaded from C:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA\qDNA\data\raw\config.json
+2024-10-29 12:12:30,283 - 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
+2024-10-29 12:12:30,283 - 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
+2024-10-29 12:12:31,301 - qDNA.tools.save_load - INFO - Data loaded from C:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA\qDNA\data\raw\tb_params\Simserides2024_electron_ELM.json
+2024-10-29 12:12:31,301 - qDNA.tools.save_load - INFO - Data loaded from C:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA\qDNA\data\raw\tb_params\Simserides2024_electron_ELM.json
+2024-10-29 12:12:31,301 - qDNA.tools.save_load - INFO - Data loaded from C:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA\qDNA\data\raw\tb_params\Simserides2024_hole_ELM.json
+2024-10-29 12:12:31,301 - qDNA.tools.save_load - INFO - Data loaded from C:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA\qDNA\data\raw\tb_params\Simserides2024_hole_ELM.json
+2024-10-29 12:12:33,303 - qDNA.tools.save_load - INFO - Data saved as C:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA\qDNA\data\gui\lifetime_delete.json
+2024-10-29 12:12:33,304 - qDNA.tools.save_load - INFO - Data loaded from C:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA\qDNA\data\gui\lifetime_delete.json
+2024-10-29 12:12:33,471 - qDNA.tools.save_load - INFO - Data loaded from C:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA\qDNA\data\raw\config.json
+2024-10-29 12:12:33,471 - qDNA.tools.save_load - INFO - Data loaded from C:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA\qDNA\data\raw\config.json
+2024-10-29 12:12:33,471 - 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
+2024-10-29 12:12:33,471 - 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
+2024-10-29 12:12:34,419 - qDNA.tools.save_load - INFO - Data loaded from C:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA\qDNA\data\raw\tb_params\Simserides2024_electron_ELM.json
+2024-10-29 12:12:34,419 - qDNA.tools.save_load - INFO - Data loaded from C:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA\qDNA\data\raw\tb_params\Simserides2024_electron_ELM.json
+2024-10-29 12:12:34,419 - qDNA.tools.save_load - INFO - Data loaded from C:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA\qDNA\data\raw\tb_params\Simserides2024_hole_ELM.json
+2024-10-29 12:12:34,419 - qDNA.tools.save_load - INFO - Data loaded from C:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA\qDNA\data\raw\tb_params\Simserides2024_hole_ELM.json
+2024-10-29 12:12:34,436 - qDNA.tools.save_load - INFO - Data loaded from C:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA\qDNA\data\raw\tb_params\Simserides2024_electron_ELM.json
+2024-10-29 12:12:34,436 - qDNA.tools.save_load - INFO - Data loaded from C:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA\qDNA\data\raw\tb_params\Simserides2024_electron_ELM.json
+2024-10-29 12:12:34,436 - qDNA.tools.save_load - INFO - Data loaded from C:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA\qDNA\data\raw\tb_params\Simserides2024_hole_ELM.json
+2024-10-29 12:12:34,436 - qDNA.tools.save_load - INFO - Data loaded from C:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA\qDNA\data\raw\tb_params\Simserides2024_hole_ELM.json
+2024-10-29 12:12:35,473 - qDNA.tools.save_load - INFO - Data saved as C:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA\qDNA\data\gui\dipole_delete.json
+2024-10-29 12:12:35,486 - qDNA.tools.save_load - INFO - Data loaded from C:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA\qDNA\data\gui\dipole_delete.json
+2024-10-29 12:12:35,490 - qDNA.tools.save_load - WARNING - File C:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA\qDNA\data\gui\dipole_delete.json already exists.
+2024-10-29 12:12:35,490 - qDNA.tools.save_load - INFO - Data loaded from C:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA\qDNA\data\gui\lifetime_delete.json
+2024-10-29 12:12:35,653 - qDNA.tools.save_load - INFO - Data loaded from C:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA\qDNA\data\raw\config.json
+2024-10-29 12:12:35,653 - qDNA.tools.save_load - INFO - Data loaded from C:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA\qDNA\data\raw\config.json
+2024-10-29 12:12:35,653 - 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
+2024-10-29 12:12:35,653 - 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
+2024-10-29 12:12:36,599 - qDNA.tools.save_load - INFO - Data loaded from C:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA\qDNA\data\raw\tb_params\Simserides2024_electron_ELM.json
+2024-10-29 12:12:36,599 - qDNA.tools.save_load - INFO - Data loaded from C:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA\qDNA\data\raw\tb_params\Simserides2024_hole_ELM.json
+2024-10-29 12:12:36,599 - qDNA.tools.save_load - INFO - Data loaded from C:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA\qDNA\data\raw\tb_params\Simserides2024_electron_ELM.json
+2024-10-29 12:12:36,599 - qDNA.tools.save_load - INFO - Data loaded from C:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA\qDNA\data\raw\tb_params\Simserides2024_hole_ELM.json
+2024-10-29 12:12:36,621 - qDNA.tools.save_load - INFO - Data loaded from C:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA\qDNA\data\raw\tb_params\Simserides2024_electron_ELM.json
+2024-10-29 12:12:36,621 - qDNA.tools.save_load - INFO - Data loaded from C:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA\qDNA\data\raw\tb_params\Simserides2024_hole_ELM.json
+2024-10-29 12:12:36,621 - qDNA.tools.save_load - INFO - Data loaded from C:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA\qDNA\data\raw\tb_params\Simserides2024_electron_ELM.json
+2024-10-29 12:12:36,621 - qDNA.tools.save_load - INFO - Data loaded from C:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA\qDNA\data\raw\tb_params\Simserides2024_hole_ELM.json
+2024-10-29 12:12:37,693 - qDNA.tools.save_load - INFO - Data saved as C:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA\qDNA\data\gui\exciton_transfer_delete.json
+2024-11-05 11:47:57,511 - qDNA.tools.save_load - INFO - Data loaded from C:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA\qDNA\data\raw\tb_params\Hawke2010_electron_ELM.json
+2024-11-05 11:47:57,520 - qDNA.tools.save_load - INFO - Data loaded from C:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA\qDNA\data\raw\tb_params\Hawke2010_hole_ELM.json
+2024-11-05 11:48:10,855 - qDNA.tools.save_load - INFO - Data loaded from C:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA\qDNA\data\raw\tb_params\Simserides2024_electron_ELM.json
+2024-11-05 11:48:10,865 - qDNA.tools.save_load - INFO - Data loaded from C:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA\qDNA\data\raw\tb_params\Simserides2024_hole_ELM.json
+2024-11-05 11:48:44,136 - qDNA.tools.save_load - INFO - Data loaded from C:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA\qDNA\data\raw\tb_params\Simserides2024_electron_ELM.json
+2024-11-05 11:48:44,136 - qDNA.tools.save_load - INFO - Data loaded from C:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA\qDNA\data\raw\tb_params\Simserides2024_hole_ELM.json
+2024-11-05 11:50:29,323 - qDNA.tools.save_load - INFO - Data loaded from C:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA\qDNA\data\raw\config.json
+2024-11-05 11:50:29,323 - 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
+2024-11-05 11:50:32,085 - qDNA.tools.save_load - INFO - Data loaded from C:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA\qDNA\data\raw\tb_params\Simserides2024_electron_ELM.json
+2024-11-05 11:50:32,085 - qDNA.tools.save_load - INFO - Data loaded from C:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA\qDNA\data\raw\tb_params\Simserides2024_hole_ELM.json
+2024-11-05 11:50:45,922 - qDNA.tools.save_load - INFO - Data loaded from C:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA\qDNA\data\raw\tb_params\Simserides2024_electron_ELM.json
+2024-11-05 11:50:45,922 - qDNA.tools.save_load - INFO - Data loaded from C:\Users\Dennis Herb\OneDrive\2_Uni\Doktor\python_projects\QuantumDNA\qDNA\data\raw\tb_params\Simserides2024_hole_ELM.json
diff --git a/qDNA/data/raw/config.json b/qDNA/data/raw/config.json
index 226b39d..899327f 100644
--- a/qDNA/data/raw/config.json
+++ b/qDNA/data/raw/config.json
@@ -1,14 +1 @@
-{
-"data": {
-    "DNA_BASES": ["A", "T", "G", "C", "c"],
-    "TB_MODELS": ["WM", "LM", "ELM", "FWM", "FLM", "FELM", "FC"],
-    "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"]
-    },
-"metadata": {
-    }
-}
+{"data": {"DNA_BASES": ["A", "T", "G", "C", "F"], "TB_MODELS": ["WM", "LM", "ELM", "FWM", "FLM", "FELM", "FC"], "SOURCES": ["Hawke2010", "Simserides2014", "Mantela2021", "Simserides2024", "MMYY"], "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"]}, "metadata": {}}
diff --git a/qDNA/data/raw/tb_models.json b/qDNA/data/raw/tb_models.json
index f5aa432..846894c 100644
--- a/qDNA/data/raw/tb_models.json
+++ b/qDNA/data/raw/tb_models.json
@@ -1,48 +1,48 @@
 {
-"data": {
-    "WM": {
-        "backbone": false,
-        "double_stranded": false,
-        "num_strands": 1,
-        "diagonal_hopping": false
-    },
-    "LM": {
-        "backbone": false,
-        "double_stranded": true,
-        "num_strands": 2,
-        "diagonal_hopping": false
-    },
-    "ELM": {
-        "backbone": false,
-        "double_stranded": true,
-        "num_strands": 2,
-        "diagonal_hopping": true
-    },
-    "FWM": {
-        "backbone": true,
-        "double_stranded": false,
-        "num_strands": 3,
-        "diagonal_hopping": false
-    },
-    "FLM": {
-        "backbone": true,
-        "double_stranded": true,
-        "num_strands": 4,
-        "diagonal_hopping": false
-    },
-    "FELM": {
-        "backbone": true,
-        "double_stranded": true,
-        "num_strands": 4,
-        "diagonal_hopping": true
-    },
-    "FC": {
-        "backbone": true,
-        "double_stranded": true,
-        "num_strands": 4,
-        "diagonal_hopping": true
+    "data": {
+        "WM": {
+            "backbone": false,
+            "double_stranded": false,
+            "num_strands": 1,
+            "diagonal_hopping": false
+        },
+        "LM": {
+            "backbone": false,
+            "double_stranded": true,
+            "num_strands": 2,
+            "diagonal_hopping": false
+        },
+        "ELM": {
+            "backbone": false,
+            "double_stranded": true,
+            "num_strands": 2,
+            "diagonal_hopping": true
+        },
+        "FWM": {
+            "backbone": true,
+            "double_stranded": false,
+            "num_strands": 3,
+            "diagonal_hopping": false
+        },
+        "FLM": {
+            "backbone": true,
+            "double_stranded": true,
+            "num_strands": 4,
+            "diagonal_hopping": false
+        },
+        "FELM": {
+            "backbone": true,
+            "double_stranded": true,
+            "num_strands": 4,
+            "diagonal_hopping": true
+        },
+        "FC": {
+            "backbone": true,
+            "double_stranded": true,
+            "num_strands": 4,
+            "diagonal_hopping": true
+        }
+        },
+    "metadata": {
+        }
     }
-    },
-"metadata": {
-    }
-}
diff --git a/qDNA/data/raw/tb_params/Simserides2024_electron_ELM.json b/qDNA/data/raw/tb_params/Simserides2024_electron_ELM.json
index d6336dd..6f952ab 100644
--- a/qDNA/data/raw/tb_params/Simserides2024_electron_ELM.json
+++ b/qDNA/data/raw/tb_params/Simserides2024_electron_ELM.json
@@ -1,8 +1,8 @@
 {
 "data": {
-"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
+"E_A": -0.130, "E_T": -0.350, "E_G": -0.520, "E_C": -0.290, "E_F": -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_FF": 0.056, "t_CF": 0.067, "t_FC": 0.091, "t_FG": 0.031, "t_GF": 0.002, "h_GC": 0.073, "h_GF": 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-_FF": 0.097, "r-_CF": 0.094, "r-_FC": 0.094, "r-_FG": 0.084, "r-_GF": 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+_FF": 0.192, "r+_CF": 0.186, "r+_FC": 0.186, "r+_FG": 0.030, "r+_GF": 0.030
 },
 "metadata": {
-"source": "Simserides2024", "particle": "electron", "tb_model_name": "ELM", "unit": "eV", "notes": "includes 5'-methylated cytosine denoted as 'c' "
+"source": "Simserides2024", "particle": "electron", "tb_model_name": "ELM", "unit": "eV", "notes": "includes 5'-methylated cytosine denoted as 'F' "
 }
 }
diff --git a/qDNA/data/raw/tb_params/Simserides2024_electron_FELM.json b/qDNA/data/raw/tb_params/Simserides2024_electron_FELM.json
index 446126f..d9d4f10 100644
--- a/qDNA/data/raw/tb_params/Simserides2024_electron_FELM.json
+++ b/qDNA/data/raw/tb_params/Simserides2024_electron_FELM.json
@@ -1,8 +1,8 @@
 {
 "data": {
-"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
+"E_A": -0.130, "E_T": -0.350, "E_G": -0.520, "E_C": -0.290, "E_F": -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_FF": 0.056, "t_CF": 0.067, "t_FC": 0.091, "t_FG": 0.031, "t_GF": 0.002, "t_BB": 0.700, "h_GC": 0.073, "h_GF": 0.069, "h_AT": 0.002, "h_FB": 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-_FF": 0.097, "r-_CF": 0.094, "r-_FC": 0.094, "r-_FG": 0.084, "r-_GF": 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+_FF": 0.192, "r+_CF": 0.186, "r+_FC": 0.186, "r+_FG": 0.030, "r+_GF": 0.030
 },
 "metadata": {
-"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' "
+"source": "Simserides2024", "particle": "electron", "tb_model_name": "FELM", "unit": "eV", "notes": "includes 5'-methylated cytosine denoted as 'F' and sugar-phosphate backbone denoted as 'B' "
 }
 }
diff --git a/qDNA/data/raw/tb_params/Simserides2024_hole_ELM.json b/qDNA/data/raw/tb_params/Simserides2024_hole_ELM.json
index 370216f..66b6236 100644
--- a/qDNA/data/raw/tb_params/Simserides2024_hole_ELM.json
+++ b/qDNA/data/raw/tb_params/Simserides2024_hole_ELM.json
@@ -1,8 +1,8 @@
 {
 "data": {
-"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
+"E_A": -7.610, "E_T": -8.240, "E_G": -7.130, "E_C": -7.900, "E_F": -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_FF": 0.105, "t_CF": 0.098, "t_FC": 0.067, "t_FG": 0.029, "t_GF": 0.208, "h_GC": 0.026, "h_GF": 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-_FF": 0.004, "r-_CF": 0.004, "r-_FC": 0.004, "r-_FG": 0.027, "r-_GF": 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+_FF": 0.000, "r+_CF": 0.000, "r+_FC": 0.000, "r+_FG": 0.002, "r+_GF": 0.002
 },
 "metadata": {
-"source": "Simserides2024", "particle": "hole", "tb_model_name": "ELM", "unit": "eV", "notes": "includes 5'-methylated cytosine denoted as 'c' "
+"source": "Simserides2024", "particle": "hole", "tb_model_name": "ELM", "unit": "eV", "notes": "includes 5'-methylated cytosine denoted as 'F' "
 }
 }
diff --git a/qDNA/data/raw/tb_params/Simserides2024_hole_FELM.json b/qDNA/data/raw/tb_params/Simserides2024_hole_FELM.json
index 8ba9dd8..b1cf517 100644
--- a/qDNA/data/raw/tb_params/Simserides2024_hole_FELM.json
+++ b/qDNA/data/raw/tb_params/Simserides2024_hole_FELM.json
@@ -1,8 +1,8 @@
 {
 "data": {
-"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
+"E_A": -7.610, "E_T": -8.240, "E_G": -7.130, "E_C": -7.900, "E_F": -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_FF": 0.105, "t_CF": 0.098, "t_FC": 0.067, "t_FG": 0.029, "t_GF": 0.208, "t_BB": 0.026, "h_GC": 0.026, "h_GF": 0.028, "h_AT": 0.034, "h_FB": 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-_FF": 0.004, "r-_CF": 0.004, "r-_FC": 0.004, "r-_FG": 0.027, "r-_GF": 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+_FF": 0.000, "r+_CF": 0.000, "r+_FC": 0.000, "r+_FG": 0.002, "r+_GF": 0.002
 },
 "metadata": {
-"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' "
+"source": "Simserides2024", "particle": "hole", "tb_model_name": "ELM", "unit": "eV", "notes": "includes 5'-methylated cytosine denoted as 'F' and the sugar-phosphate backbone denoted as 'B' "
 }
 }
diff --git a/qDNA/defaults.yaml b/qDNA/defaults.yaml
index 215ea61..dcdda80 100644
--- a/qDNA/defaults.yaml
+++ b/qDNA/defaults.yaml
@@ -16,7 +16,7 @@ diss_kwargs_default:
     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}
+    relax_rates: {'A': 0, 'T': 0, 'G': 0, 'C': 0, 'F':0, 'B': 0}
     loc_therm: False
     glob_therm: False
     deph_rate: 7. # in rad/ps
diff --git a/qDNA/dna_seq.py b/qDNA/dna_seq.py
index 6949f05..bfe3829 100644
--- a/qDNA/dna_seq.py
+++ b/qDNA/dna_seq.py
@@ -88,7 +88,7 @@ def __init__(self, upper_strand, tb_model_name, methylated=True, lower_strand=No
             "T": "A",
             "G": "C",
             "C": "G",
-            "c": "G",
+            "F": "G",
         }
         # Generate the DNA sequence
         self.dna_seq = self._create_dna_seq()
@@ -162,17 +162,17 @@ def _create_dna_seq(self):
     def _add_methylation(self):
         """
         Adds methylation to the lower DNA strand according to the fragile X syndrome.
-        This method searches for occurrences of the sequence "cG" in the upper DNA strand.
+        This method searches for occurrences of the sequence "FG" in the upper DNA strand.
         For each occurrence, it modifies the corresponding position in the lower DNA strand
-        by changing the character following the match to "c".
+        by changing the character following the match to "F".
         """
         # Find all occurrences of "cG" in the upper DNA strand
-        matches = [match.start() for match in re.finditer("cG", self.upper_strand)]
+        matches = [match.start() for match in re.finditer("FG", self.upper_strand)]
 
         # Modify the lower DNA strand based on the matches
         lower_strand_list = list(self.lower_strand)
         for match in matches:
-            lower_strand_list[match + 1] = "c"
+            lower_strand_list[match + 1] = "F"
         self.lower_strand = "".join(lower_strand_list)
 
 
diff --git a/qDNA/plotting/__init__.py b/qDNA/plotting/__init__.py
index 1a5700c..74d2a42 100644
--- a/qDNA/plotting/__init__.py
+++ b/qDNA/plotting/__init__.py
@@ -7,11 +7,11 @@
 
 plt.rcParams.update(
     {
-        "text.usetex": True,
-        "font.family": "serif",
-        "font.serif": ["Times"],  # used in elsarticle (Elsevier)
+        # "text.usetex": True,
+        # "font.family": "serif",
+        # "font.serif": ["Times"],  # used in elsarticle (Elsevier)
         # "font.serif": ["Computer Modern Roman"], # used in revtex4-2 (APS)
-        "text.latex.preamble": r"\usepackage{amsmath}\usepackage{siunitx}",
+        # "text.latex.preamble": r"\usepackage{amsmath}\usepackage{siunitx}",
         "legend.fontsize": 20,
         "xtick.labelsize": 20,
         "ytick.labelsize": 20,
diff --git a/qDNA/plotting/plot_dna_base_frequency.py b/qDNA/plotting/plot_dna_base_frequency.py
index 51f1286..4be0d47 100644
--- a/qDNA/plotting/plot_dna_base_frequency.py
+++ b/qDNA/plotting/plot_dna_base_frequency.py
@@ -51,7 +51,7 @@ def plot_dna_base_frequency(lifetime_dict, cutoff_num=10):
 
     # calculation
     lifetimes = np.array(list(lifetime_dict.values())[cutoff_num:])  # in fs
-    lifetime *= 1e-3  # Convert fs to ps
+    lifetimes *= 1e-3  # Convert fs to ps
 
     base_freq_dict = {}
     for base in ["A", "T", "G", "C"]:
diff --git a/qDNA/tools/save_load.py b/qDNA/tools/save_load.py
index ae3720a..8ded84d 100644
--- a/qDNA/tools/save_load.py
+++ b/qDNA/tools/save_load.py
@@ -12,7 +12,9 @@
 
 from .. import ROOT_DIR, DATA_DIR
 
-# ------------------------------------------------
+# -------------------------------------------------------------------
+
+# ----------------------------- Logging -----------------------------
 
 
 def setup_logging():
@@ -37,24 +39,85 @@ def setup_logging():
 setup_logging()
 logger = logging.getLogger(__name__)
 
+# ----------------------------- YAML -----------------------------
+
 
 def load_yaml(filepath):
     """
-    Load a YAML file and return its contents.
+    Load data from a YAML file.
 
     Parameters
     ----------
     filepath : str
         The path to the YAML file to be loaded.
-
     Returns
     -------
     dict
-        The contents of the YAML file as a dictionary.
+        The data loaded from the YAML file. If an error occurs during loading,
+        an empty dictionary is returned.
+
+    Raises
+    ------
+    yaml.YAMLError
+        If there is an error while parsing the YAML file.
+    """
+
+    with open(filepath, "r") as file:
+        try:
+            data = yaml.safe_load(file)
+            return data
+        except yaml.YAMLError as exc:
+            print(f"Error loading YAML file: {exc}")
+            return {}
+
+
+def save_yaml(filepath, data):
+    """
+    Save data to a YAML file.
+
+    Parameters
+    ----------
+    file_path : str
+        The path to the file where the data should be saved.
+    data : dict
+        The data to be saved in YAML format.
+
+    Raises
+    ------
+    yaml.YAMLError
+        If there is an error during the YAML serialization process.
+    """
+
+    with open(filepath, "w") as file:
+        try:
+            yaml.safe_dump(data, file, default_flow_style=False)
+        except yaml.YAMLError as exc:
+            print(f"Error saving YAML file: {exc}")
+
+
+def modify_yaml(filepath, key, value):
+    """
+    Modify a specific key-value pair in a YAML file.
+
+    Parameters
+    ----------
+    file_path : str
+        The path to the YAML file to be modified.
+    key : str
+        The key whose value needs to be modified.
+    value : any
+        The new value to be assigned to the specified key.
+
+    Raises
+    ------
+    yaml.YAMLError
+        If there is an error while parsing or saving the YAML file.
     """
 
-    with open(filepath, "r") as yaml_file:
-        return yaml.safe_load(yaml_file)
+    data = load_yaml(filepath)
+    if data is not None:
+        data[key] = value
+        save_yaml(filepath, data)
 
 
 def get_defaults():
@@ -72,10 +135,37 @@ def get_defaults():
 # Load the default values
 DEFAULTS = get_defaults()
 
+# ----------------------------- JSON -----------------------------
+
+
+def modify_json(filename, directory, key, value):
+    """
+    Modify a JSON file by adding a value to a specified key.
+
+    Parameters
+    ----------
+    filename : str
+        The name of the JSON file to modify.
+    directory : str
+        The directory where the JSON file is located.
+    key : str
+        The key in the JSON file whose value will be modified.
+    value : int or float
+        The value to add to the specified key's current value.
+    """
+
+    data, metadata = load_json(filename, directory, load_metadata=True)
+
+    if data is not None:
+        data[key] = value
+        save_json(data, metadata, filename, directory, override=True)
+        logger.info(f"Value {value} added to key {key} in {filename}.json")
+
 
-def save_json(data, metadata, filename, directory):
+def save_json(data, metadata, filename, directory, override=False):
     """
     Save data and metadata to a JSON file.
+
     Parameters
     ----------
     data : dict
@@ -86,9 +176,7 @@ def save_json(data, metadata, filename, directory):
         The name of the file (without extension) to save the data to.
     directory : str
         The directory where the file should be saved.
-    Returns
-    -------
-    None
+
     Notes
     -----
     If a file with the same name already exists in the specified directory,
@@ -99,11 +187,12 @@ def save_json(data, metadata, filename, directory):
     filepath = os.path.join(directory, filename + ".json")
 
     # check if the file already exists
-    if os.path.exists(filepath):
-        logger.warning(f"File {filepath} already exists.")
-        if DEFAULTS["verbose"]:
-            print(f"File {filepath} already exists")
-        return
+    if not override:
+        if os.path.exists(filepath):
+            logger.warning(f"File {filepath} already exists.")
+            if DEFAULTS["verbose"]:
+                print(f"File {filepath} already exists")
+            return
 
     # save the data and metadata to a JSON file
     combined_data = dict(data=data, metadata=metadata)
@@ -119,6 +208,7 @@ def save_json(data, metadata, filename, directory):
 def load_json(filename, directory, load_metadata=False):
     """
     Load data from a JSON file.
+
     Parameters
     ----------
     filename : str
@@ -127,15 +217,18 @@ def load_json(filename, directory, load_metadata=False):
         The directory where the JSON file is located.
     load_metadata : bool, optional
         If True, also load metadata from the JSON file. Default is False.
+
     Returns
     -------
     dict or tuple
         If `load_metadata` is False, returns a dictionary containing the data.
         If `load_metadata` is True, returns a tuple containing the data and metadata.
+
     Raises
     ------
     FileNotFoundError
         If the specified JSON file does not exist.
+
     Notes
     -----
     Logs a warning if the file does not exist and an info message when the data is successfully loaded.
@@ -167,6 +260,7 @@ def load_json(filename, directory, load_metadata=False):
 def save_figure(fig, filename, directory, extension="svg"):
     """
     Save a figure to a specified directory with a given filename and extension.
+
     Parameters
     ----------
     fig : matplotlib.figure.Figure
@@ -177,12 +271,14 @@ def save_figure(fig, filename, directory, extension="svg"):
         The directory where the figure will be saved.
     extension : str, optional
         The file extension for the saved figure (default is "svg").
+
     Notes
     -----
     If a file with the same name already exists in the specified directory,
     a random index will be appended to the filename to avoid overwriting.
     The function logs the saving process and prints messages if the verbose
     configuration is enabled.
+
     Raises
     ------
     OSError
diff --git a/requirements/requirements.txt b/requirements/requirements.txt
index 9bb80fa..01dfb9f 100644
--- a/requirements/requirements.txt
+++ b/requirements/requirements.txt
@@ -5,4 +5,4 @@ seaborn==0.12.2
 tqdm==4.66.4
 customtkinter==5.2.2
 scipy==1.11.4
-openpyxl==3.0.9
+openpyxl==3.1.5