Extra information

Electronic structure

The electronic structure dictionary is designed to contain the data from sources other than the output. Most of its contents are from the fchk file, but also contains data from scratch files such as the hessian and the fock matrix. Other data will be included in this dictionary in the future.

The basic structure of the electronic structure dictionary is the following:

root
 ├── basis
 │   ├── name
 │   ├── primitive_type
 │   └── atoms(list)
 │         ├── shells (list)
 │         ├── symbol
 │         └── atomic_number
 ├── coefficients
 │   ├── alpha
 │   └── beta (optional)
 ├── mo_energies
 │   ├── alpha
 │   └── beta (optional)
 ├── number_of_electrons
 │   ├── alpha
 │   └── beta
 ├── nato_coefficients (optional)
 │   ├── alpha
 │   └── beta
 ├── nato_occupancies (optional)
 │   ├── alpha
 │   └── beta
 ├── structure
 └── overlap

Using the information of this dictionary a Fchk file can be generated. This may be used to visualize the molecular orbitals, electronic density and other properties using an (external) visualization program.

from pyqchem.file_io import build_fchk
with open('file.fchk', 'w') as f:
    f.write(build_fchk(electronic_structure))

While electronic structure is a simple dictionary, its elements are designed to be interoperable along the pyqchem code such as guess and basis. Some examples of this interoperability can be found in the examples folder.