changed colab badges to png

dehe1011 · Dec 4, 2024 · 616f547 · 616f547
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diff --git a/docs/apidoc/plotting.rst b/docs/apidoc/plotting.rst
@@ -1,22 +1,22 @@
-Plotting
-========
+Visualization
+=============
 
-Plot DNA base frequency
+Plot DNA Base Frequency
 -----------------------
 
 .. automodule:: qDNA.visualization
    :members: plot_dna_base_frequency
    :show-inheritance: False
 
-Plot eigenspectrum
+Plot Eigenspectrum
 ------------------
 
 .. automodule:: qDNA.visualization
    :members: plot_eigv, plot_eigs
    :show-inheritance: False
    :noindex:
 
-Plot Fourier analysis
+Plot Fourier Analysis
 ---------------------
 
 .. automodule:: qDNA.visualization
@@ -25,7 +25,7 @@ Plot Fourier analysis
    :noindex:
 
 
-Plot poulations and coherences
+Plot Poulations and Coherences
 ------------------------------
 
 .. automodule:: qDNA.visualization

diff --git a/docs/apidoc/utils.rst b/docs/apidoc/utils.rst
@@ -1,22 +1,22 @@
 Utilities
 =========
 
-Unit conversion
+Unit Conversion
 ---------------
 
 .. automodule:: qDNA.utils
    :members: get_conversion, get_all_conversions, get_conversion_dict
    :show-inheritance: False
 
-Hamiltonian analysis
+Hamiltonian Analysis
 --------------------
 
 .. automodule:: qDNA.utils
    :members: calc_average_pop, calc_amplitudes, calc_frequencies, get_pop_fourier, calc_ipr_hamiltonian
    :show-inheritance: False
    :noindex:
 
-Density matrix analysis
+Density Matrix Analysis
 -----------------------
 
 .. automodule:: qDNA.utils

diff --git a/docs/guide/tutorials/1_Tight_Binding_Parameters.ipynb b/docs/guide/tutorials/1_Tight_Binding_Parameters.ipynb
@@ -15,7 +15,7 @@
       "source": [
         "Learn to use the Linear Combination of Atomic Orbitals (LCAO) approach with Slater\u2013Koster two-center interaction integrals and Harrison-type expressions. As an example we consider the geometries from PubChem, RCSB PDB and Biovia. \n",
         "\n",
-        "[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/dehe1011/QuantumDNA-notebooks/blob/main/tutorials/1_Tight_Binding_Parameters.ipynb)"
+        "[![Open In Colab](https://colab.research.google.com/assets/colab-badge.png)](https://colab.research.google.com/github/dehe1011/QuantumDNA-notebooks/blob/main/tutorials/1_Tight_Binding_Parameters.ipynb)"
       ]
     },
     {

diff --git a/docs/guide/tutorials/2_Tight_Binding_Method.ipynb b/docs/guide/tutorials/2_Tight_Binding_Method.ipynb
@@ -15,7 +15,7 @@
       "source": [
         "Explore predefined and custom tight-binding models. This tutorial demonstrates calculating time-averaged exciton populations in a Fishbone Ladder Model (FLM) and simulating charge transfer in the Fenna-Matthews-Olson (FMO) complex in green sulfur bacteria, showcasing how `qDNA` can define custom models.\n",
         "\n",
-        "[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/dehe1011/QuantumDNA-notebooks/blob/main/tutorials/1_TB_Models.ipynb)"
+        "[![Open In Colab](https://colab.research.google.com/assets/colab-badge.png)](https://colab.research.google.com/github/dehe1011/QuantumDNA-notebooks/blob/main/tutorials/1_TB_Models.ipynb)"
       ]
     },
     {

diff --git a/docs/guide/tutorials/3_Environment_Simulation.ipynb b/docs/guide/tutorials/3_Environment_Simulation.ipynb
@@ -22,7 +22,7 @@
         "  \n",
         "Through these examples, the notebook demonstrates advanced techniques for simulating and analyzing DNA-related quantum phenomena.\n",
         "\n",
-        "[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/dehe1011/QuantumDNA-notebooks/blob/main/tutorials/3_Environment_Simulation.ipynb)"
+        "[![Open In Colab](https://colab.research.google.com/assets/colab-badge.png)](https://colab.research.google.com/github/dehe1011/QuantumDNA-notebooks/blob/main/tutorials/3_Environment_Simulation.ipynb)"
       ]
     },
     {

diff --git a/docs/guide/tutorials/4_Visualization.ipynb b/docs/guide/tutorials/4_Visualization.ipynb
@@ -15,7 +15,7 @@
       "source": [
         "Learn how to use `qDNA`'s predefined plotting routines for visualizing results effectively. In this notebook you can explore the potential of data visualizations within the package.   \n",
         "\n",
-        "[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/dehe1011/QuantumDNA-notebooks/blob/main/tutorials/4_Visualization.ipynb)"
+        "[![Open In Colab](https://colab.research.google.com/assets/colab-badge.png)](https://colab.research.google.com/github/dehe1011/QuantumDNA-notebooks/blob/main/tutorials/4_Visualization.ipynb)"
       ]
     },
     {

diff --git a/docs/guide/tutorials/5_Evaluation.ipynb b/docs/guide/tutorials/5_Evaluation.ipynb
@@ -22,7 +22,7 @@
         "  \n",
         "As an example, the calculations are applied to all 64 possible DNA trimer/ triplet sequences.\n",
         "\n",
-        "[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/dehe1011/QuantumDNA-notebooks/blob/main/tutorials/5_Evaluation.ipynb)"
+        "[![Open In Colab](https://colab.research.google.com/assets/colab-badge.png)](https://colab.research.google.com/github/dehe1011/QuantumDNA-notebooks/blob/main/tutorials/5_Evaluation.ipynb)"
       ]
     },
     {

diff --git a/docs/guide/tutorials/6_Reproduce_Papers.ipynb b/docs/guide/tutorials/6_Reproduce_Papers.ipynb
@@ -13,7 +13,7 @@
       "id": "c00a0fae-51f2-4073-9559-f6db4712d0f9",
       "metadata": {},
       "source": [
-        "[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/dehe1011/QuantumDNA-notebooks/blob/main/tutorials/Reproduce.ipynb)"
+        "[![Open In Colab](https://colab.research.google.com/assets/colab-badge.png)](https://colab.research.google.com/github/dehe1011/QuantumDNA-notebooks/blob/main/tutorials/Reproduce.ipynb)"
       ]
     },
     {

diff --git a/docs/guide/tutorials/PRE_2024.ipynb b/docs/guide/tutorials/PRE_2024.ipynb
@@ -15,7 +15,7 @@
       "source": [
         "This notebook reproduces the figures contained in the article [D. Herb, M. Rossini, J. Ankerhold, PRE 109, 064413 (2024)](https://doi.org/10.1103/PhysRevE.109.064413).\n",
         "\n",
-        "[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/dehe1011/QuantumDNA-notebooks/blob/main/tutorials/PRE2024.ipynb)"
+        "[![Open In Colab](https://colab.research.google.com/assets/colab-badge.png)](https://colab.research.google.com/github/dehe1011/QuantumDNA-notebooks/blob/main/tutorials/PRE2024.ipynb)"
       ]
     },
     {

diff --git a/docs/installation.rst b/docs/installation.rst
@@ -197,4 +197,4 @@ To remove the package:
 If you cloned the GitHub repository, manually delete the `QuantumDNA` folder from your computer.
 
 
-🎉 **Congratulations!** You’ve successfully installed and set up `QuantumDNA`. Enjoy exploring the physics of DNA with this powerful tool.
+**Congratulations!** You've successfully installed and set up `QuantumDNA`. Enjoy exploring the physics of DNA with this powerful tool.
diff --git a/qDNA/data/logs/qDNA.log b/qDNA/data/logs/qDNA.log
@@ -2,3 +2,5 @@
 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
-Original file line number
+Diff line change
@@ Expand Up / @@ -22,7 +22,7 @@ @@
             "  \n",
             "Through these examples, the notebook demonstrates advanced techniques for simulating and analyzing DNA-related quantum phenomena.\n",
             "\n",
-            "[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/dehe1011/QuantumDNA-notebooks/blob/main/tutorials/3_Environment_Simulation.ipynb)"
+            "[![Open In Colab](https://colab.research.google.com/assets/colab-badge.png)](https://colab.research.google.com/github/dehe1011/QuantumDNA-notebooks/blob/main/tutorials/3_Environment_Simulation.ipynb)"
           ]
         },
         {
@@ Expand Down @@
Original file line number	Diff line number	Diff line change
Expand Up		@@ -197,4 +197,4 @@ To remove the package:
		If you cloned the GitHub repository, manually delete the `QuantumDNA` folder from your computer.


		🎉 Congratulations! You’ve successfully installed and set up `QuantumDNA`. Enjoy exploring the physics of DNA with this powerful tool.
		Congratulations! You've successfully installed and set up `QuantumDNA`. Enjoy exploring the physics of DNA with this powerful tool.