Build gamma from PariserParr module

[RichRick1]

Description

The idea is not to overload connectivity parameter in the __init__ method of HamPPP, but instead invoke PPP module to build $\gamma$ matrix directly, and then pass it to the HamPPP . This is very easy for user, and I feel like this is the way we will use it.

We already have a functionality to do this, since we initially separated Rauk in a stand-alone module for this reason. However, there are few changes in API that can make this much more user friendly and structured code-wise.

ToDo:

• We need to rename function generate_connectivity_matrix from the api.py file into parse_connectivity . It’s also a good idea to move it into the utils file, since it doesn’t relate to hamiltonians anymore.

    def parse_connectivity(system):
  	  r"""
  	
  	    Parse the connectivity of the system given as list of tuples.
  	    
  	    Parameters
  	    ----------
  	    system: list
  			   list of tuples that specifies sites and bonds between them
              For example, for a linear chain of 4 sites, the connectivity
              can be specified as [(C1, C2, 1), (C2, C3, 1), (C3, C4, 1)]
  	
  	    Returns
  	    -------
  	    tuple: (list np.ndarray)
  		        First element is a list of atoms in the order they apperar in the attice, second element is matrix that corresponds to the either distance matrix, or adjacency matrix. 
  	    """

• The function above should be reused in both hamiltonins.py file and PariserParr.py module. Specifically, function calculate_gamma in PariserParr.py file should either get system as list of tuples, and then call parse_connectivity inside of it or directly gets distance matrix.

• Move these lines into the PariserParr.py file

• Don't use the connectivity name here, instead use the adjacency parameter, that is either provided by user, or build during the initialization from connectivity. Note: connectivity is a list of tuples.

Once this is done, we can easily build $\gamma$ matrix using the PariserParr module such as:

system = [(C1, C2, 2.3), (C2, C3, 1.1), (C3,  C4, 1.5)]
gamma_1 = moha.rauk.PariserParr.calculate_gamma(system)

gamma_2 = moha.rauk.PariserParr.calculate_gamma(atom_lst = [C, C, C, C], R_xy = np.array([[0, 2.3, 0, 0],
                                                                                                                                                                    [2.3, 0, 1.1, 0],
                                                                                                                                                                    [0, 0, 1.5, 0]])
gamma_3 = moha.rauk.PariserParr.calculate_gamma(U_xy, R_xy)

[RichRick1]

This has been done