Pymatgen attribute error: specie

pymatgen
1

While running CGCNN over a cif file pymatgen throws the following attribute error.

Traceback (most recent call last):
  File "C:\Users\fes33\Documents\GIK - R&D\Personal - Papers and Reports\17 - MOF Database and Review\Personal - DB Codes\cgcnn\main.py", line 514, in <module>
    main()
  File "C:\Users\fes33\Documents\GIK - R&D\Personal - Papers and Reports\17 - MOF Database and Review\Personal - DB Codes\cgcnn\main.py", line 119, in main
    sample_data_list = [dataset[i] for i in range(len(dataset))]
  File "C:\Users\fes33\Documents\GIK - R&D\Personal - Papers and Reports\17 - MOF Database and Review\Personal - DB Codes\cgcnn\main.py", line 119, in <listcomp>
    sample_data_list = [dataset[i] for i in range(len(dataset))]
  File "C:\Users\fes33\Documents\GIK - R&D\Personal - Papers and Reports\17 - MOF Database and Review\Personal - DB Codes\cgcnn\cgcnn\data.py", line 330, in __getitem__
    print("Specie: ", crystal[i].specie.name)
  File "C:\Users\fes33\anaconda3\envs\cgcnn\lib\site-packages\pymatgen\core\sites.py", line 79, in __getattr__
    raise AttributeError(a)
AttributeError: specie. Did you mean: 'species'?

This is the code (from CGCNN) which I’ve modified slightly to print the specie causing the error:

    cif_id, target = self.id_prop_data[idx]
    crystal = Structure.from_file(os.path.join(self.root_dir,
                                               cif_id+'.cif'))
    
    temp = []
    for i in range(len(crystal)):
        print("Specie: ", crystal[i].specie.name)
        temp.append(self.ari.get_atom_fea(crystal[i].specie.number))
        
        #atom_fea = np.vstack([self.ari.get_atom_fea(crystal[i].specie.number)
        #                  for i in range(len(crystal))])
    atom_fea = np.vstack(temp)

The output shows that it works fine for several sites (i.e. I get list of element symbols) before one hydrogen throws this error. Can anyone explain why this happens?

2

Specie only works for ordered sites:

def specie(self) -> Element | Species | DummySpecies:
        """
        The Species/Element at the site. Only works for ordered sites. Otherwise
        an AttributeError is raised. Use this property sparingly.  Robust
        design should make use of the property species instead. Note that the
        singular of species is also species. So the choice of this variable
        name is governed by programmatic concerns as opposed to grammar.
        Raises:
            AttributeError if Site is not ordered.
        """
1 Like
3

Thank you. Apparently I was reading the documentation for class Specie

1 Like
4

Were you able to fix this issue, or modify the code to work with unordered sites? As I’m having the same issue at the moment, any advice would be greatly appreciated.