Note

This is documentation related to the PyOrbb Python library. For documentation related to the PyOrbb application, please click here.

Basic Usage

The main method to interact with orbital data in PyOrbb is with the Orbitals class. This class allows you to load the data and also access it later on. Simply supply the adf.rkf file from your ADF calculation to the class to load the data.

>>> orbs = pyorbb.Orbitals('adf.rkf')

The data is then divided into the MOs and FMOs objects inside the Orbitals object. The MOs and FMOs objects provide tools to select specific MO and FMO objects to analyse further.

Selecting Orbitals

To get an MO of the complex we can use the indexing notation of Python.

>>> homo = orbs.mos['2E1:2']
>>> homo
2E1:2

or using its relative name

>>> homo = orbs.mos['HOMO']
>>> homo
2E1:2

To select an FMO object we must also specify the fragment.

>>> nh3_fmo = orbs.fmos['NH3(LUMO)']
>>> nh3_fmo
NH3(4A1)

We can also select multiple objects at once using the filter() methods of MOs and FMOs. For example, to select all MO objects belonging to the A2 irreducible representation.

>>> a2_mos = orbs.mos.filter(symmetry='A2')
>>> a2_mos
[1A2, 2A2, 3A2, 4A2, 5A2, 6A2, 7A2, 8A2]

Or to select all FMO objects of the NH3 fragment.

>>> nh3_fmos = orbs.fmos.filter(fragment='NH3')
>>> nh3_fmos
[NH3(1A1), NH3(2A1), NH3(3A1), NH3(4A1), NH3(5A1), ...

Obtaining Data

The selected MO and FMO objects contain data pertaining to the orbitals themselves (e.g. orbital energies) but also to data relevant to the interaction of two orbitals (e.g. overlaps). PyOrbb offers tools to easily obtain the required data.

To get the energy (in \(\text{eV}\)) of an MO or FMO we can access the energy attribute.

>>> homo.energy
-6.392959708485001
>>> nh3_fmo.energy
-0.6265287931324357

Other properties can be accessed in the same way. See the MO and FMO documentation to see an overview of all properties available.

To obtain data related to the interaction between orbitals we need two objects. For example, to obtain the overlap between two FMO orbitals.

>>> nh3_homo = orbs.fmos['NH3(HOMO)']
>>> bh3_lumo = orbs.fmos['BH3(LUMO)']
>>> nh3_homo.overlap(bh3_lumo)
-0.34332312250605734

Or to obtain the coefficient of an FMO into an MO.

>>> fmo = orbs.fmos['NH3(4A1)']
>>> mo = orbs.mos['5A1']
>>> fmo.coefficient(mo)
0.02125011726149327

Examples

For more advanced examples please see the Example PyOrbb Analysis Scripts section of this site.