.. _07_fod_extra:

.. include:: ../../examples/07_fod_extra/README.rst

----

.. code-block:: python

   from eminus import Atoms, read, SCF
   from eminus.dft import get_psi
   from eminus.extras import get_fods, remove_core_fods
   from eminus.localizer import get_FLO
   

Start by with a DFT calculation for methane

.. code-block:: python

   atom, pos = read("CH4.xyz")
   atoms = Atoms(atom, pos, ecut=10, center=True)
   scf = SCF(atoms)
   scf.run()
   

Calculate all FODs

.. code-block:: python

   fods_all = get_fods(atoms)
   print(f"\nAll FODs:\n{fods_all}")
   

Remove core FODs, since the calculation uses a GTH pseudopotential

.. code-block:: python

   fods = remove_core_fods(atoms, fods_all)
   print(f"\nCore FODs:\n{fods}")
   

The quality from the FOD guess can vary, but you can use these as a decent guess

.. code-block:: python

   # import numpy as np
   # fods = [np.array([[10.71617803, 10.75510917, 10.73689087],
   #                   [10.82635834,  9.25127336,  9.25068483],
   #                   [ 9.24857483, 10.79169744,  9.24052496],
   #                   [ 9.25441172,  9.25005662, 10.82402898]]),
   #         np.array([])]
   

Write the FODs to an XYZ file to view them

.. code-block:: python

   atoms.write("CH4_fods.xyz", fods)
   

Generate the Kohn-Sham orbitals

.. code-block:: python

   psi = get_psi(scf, scf.W)
   

Calculate the FLOs

.. code-block:: python

   FLO = get_FLO(atoms, psi, fods)
   

Write all FLOs to CUBE files

.. code-block:: python

   print("\nWrite cube files:")
   for i in range(atoms.occ.Nstate):
       print(f"{i + 1} of {atoms.occ.Nstate}")
       atoms.write(f"CH4_FLO_{i + 1}.cube", FLO[0][0, :, i])
   

All of the functionality above can be achieved with the following workflow function

.. code-block:: python

   # from eminus.orbitals import FLO
   # FLO = FLO(scf, write_cubes=True)

Download :download:`07_fod_extra.py <../../examples/07_fod_extra/07_fod_extra.py>` :download:`CH4.xyz <../../examples/07_fod_extra/CH4.xyz>`