Refactor code for improved readability and consistency across multiple scripts

- Updated spacing and formatting in `franck_condon_model_system.py` for better clarity.
- Enhanced function definition formatting in `gaussian_to_xyz.py` for improved readability.
- Standardized spacing and comments in `matmul_method_slowest_2_fastest.py` to enhance code structure.
- Added spacing in `monte_carlo_area_of_circle.py` for better visual separation of code blocks.
- Improved formatting and spacing in `pca_program.py` for consistency and readability.
- Refined spacing and comments in `pytorched_strassen_matmul.py` to enhance clarity and maintainability.
- Standardized formatting and improved readability in `qmsolvet_to_strip_solvent.py` for better code organization.

Author: Ajaykhanna

align_spectra_with_offset.py

@@ -1,77 +1,77 @@
 # The code creates a normalized plot using the matplotlib library in Python. It imports the necessary
 # libraries (matplotlib.pyplot, numpy, and sys) and defines a conversion factor from inverse
-# centimeters to electron volts. Plots the reference data, which is the first argument and 
-#, then plot the remaining spectra arguments 2 and onwards and align them with respect to the 
-# desired offset. Here, it aligns with the first index of the x-axis of the reference data. 
+# centimeters to electron volts. Plots the reference data, which is the first argument and
+# , then plot the remaining spectra arguments 2 and onwards and align them with respect to the
+# desired offset. Here, it aligns with the first index of the x-axis of the reference data.
 import matplotlib.pyplot as plt
 import numpy as np
 import sys
 
-# Conversion factor  
-invcm_to_eV = 1.0/8065.54429
+# Conversion factor
+invcm_to_eV = 1.0 / 8065.54429
 offset = int(0)
 
 # Set up plot
-fig, axs = plt.subplots(1, 2, figsize=(10,5))
+fig, axs = plt.subplots(1, 2, figsize=(10, 5))
 filename = str(sys.argv[1])
-ref_data = np.loadtxt(f'{filename}', skiprows=7, usecols=(0,1,2))
-ref_data[:,0] = ref_data[:,0] * invcm_to_eV
+ref_data = np.loadtxt(f"{filename}", skiprows=7, usecols=(0, 1, 2))
+ref_data[:, 0] = ref_data[:, 0] * invcm_to_eV
 
 # Plot reference
-axs[0].plot(ref_data[:,0], ref_data[:,1]/ref_data[:,1].max(), label='Explicit')
-axs[1].plot(ref_data[:,0], ref_data[:,2]/ref_data[:,2].max(), label='Explicit')
+axs[0].plot(ref_data[:, 0], ref_data[:, 1] / ref_data[:, 1].max(), label="Explicit")
+axs[1].plot(ref_data[:, 0], ref_data[:, 2] / ref_data[:, 2].max(), label="Explicit")
 
-# Process each file provided as command line argument 
+# Process each file provided as command line argument
 for i, filename in enumerate(sys.argv[2:]):
 
     # Load data
-    data = np.loadtxt(filename, skiprows=7, usecols=(0,1,2))
-    
+    data = np.loadtxt(filename, skiprows=7, usecols=(0, 1, 2))
+
     # Convert x-axis to eV
-    data[:,0] = data[:,0] * invcm_to_eV
-    
+    data[:, 0] = data[:, 0] * invcm_to_eV
+
     # Normalize y-axis
-    data[:,1] /= data[:,1].max() 
-    data[:,2] /= data[:,2].max()
+    data[:, 1] /= data[:, 1].max()
+    data[:, 2] /= data[:, 2].max()
 
-    label = f'File {i+1}'
+    label = f"File {i+1}"
 
     # Plot 0K data
     if i == 0:
-       # Reference plot  
-       axs[0].plot(data[:,0], data[:,1], label=label)
+        # Reference plot
+        axs[0].plot(data[:, 0], data[:, 1], label=label)
     else:
-       # Align to reference 
-       offset = data[offset,offset] - ref_data[offset,offset]
-       axs[0].plot(data[:,0] - offset, data[:,1]/ref_data[0,1], label=label)
+        # Align to reference
+        offset = data[offset, offset] - ref_data[offset, offset]
+        axs[0].plot(data[:, 0] - offset, data[:, 1] / ref_data[0, 1], label=label)
 
     # Plot 300K data
     if i == 0:
-       # Reference plot
-       axs[1].plot(data[:,0], data[:,2], label=label)  
+        # Reference plot
+        axs[1].plot(data[:, 0], data[:, 2], label=label)
     else:
-       # Align to reference
-       offset = data[0,0] - ref_data[0,0]
-       axs[1].plot(data[:,0] - offset, data[:,2]/ref_data[0,2], label=label)
-        
-# Add axes labels  
-axs[0].set_xlabel('Energy (eV)')
-axs[0].set_ylabel('Intensity')
-axs[1].set_xlabel('Energy (eV)')
-axs[1].set_ylabel('Intensity')
+        # Align to reference
+        offset = data[0, 0] - ref_data[0, 0]
+        axs[1].plot(data[:, 0] - offset, data[:, 2] / ref_data[0, 2], label=label)
+
+# Add axes labels
+axs[0].set_xlabel("Energy (eV)")
+axs[0].set_ylabel("Intensity")
+axs[1].set_xlabel("Energy (eV)")
+axs[1].set_ylabel("Intensity")
 
 # Add legend
 axs[0].legend()
-axs[1].legend() 
+axs[1].legend()
 
 # Set axes limits
-axs[0].set_ylim(0, 1.1) 
+axs[0].set_ylim(0, 1.1)
 axs[1].set_ylim(0, 1.1)
 
 # Set number of ticks
-axs[0].locator_params(axis='x', nbins=5)
-axs[1].locator_params(axis='x', nbins=5)
+axs[0].locator_params(axis="x", nbins=5)
+axs[1].locator_params(axis="x", nbins=5)
 
 # Save figure
 fig.tight_layout()
-fig.savefig('plot.png', dpi=300)
+fig.savefig("plot.png", dpi=300)