Bug fixes for ML workflow, step3, CP2K methods and data reading for BLLZ

[MohammadShakiba]

Fixed and added the following:

• Data reading in step4.get_Hvib_scipy for BLLZ for compchemcybertraining tutorials
• Fixed single-particle excited states energy saving in step 3
• Fixed the number of unoccupied orbitals variable in step 3
• Modified job distribution in step 2 with numpy version
• Simplified ML workflow by adding and removing new parameters compatible with the tutorials
• Modified the reading of the CP2K TD-DFT data with lowest and highest orbital variables
• Added coordinate extraction from ADF input files (recently used in EFG project)
• Fixed labeling of pDOS plotting