.. _06_advanced_functionalities:

.. include:: ../../examples/06_advanced_functionalities/README.rst

----

.. code-block:: python

   import numpy as np
   
   import eminus
   from eminus import Atoms, SCF
   from eminus.dft import get_psi
   from eminus.localizer import wannier_cost
   from eminus.tools import center_of_mass, check_orthonorm, get_dipole, get_ip
   from eminus.units import ebohr2d, ha2kcalmol
   

Start with a simple DFT calculation for neon

If one needs cell parameters from the :code:`Atoms` object one can use the :code:`atoms.build` function to generate them

eminus also supports GGA functionals like the Chachiyo GGA

A different cg-form can be used if the system is hard to converge

.. code-block:: python

   atoms = Atoms("Ne", [0, 0, 0], ecut=10, center=True)
   scf = SCF(atoms, xc="chachiyo")
   scf.run(cgform=3)
   

Calculate the dipole moment

Make sure that the cell is big enough, and that the density does not extend over the borders

Centering the system is recommended to achieve this

.. code-block:: python

   dip = get_dipole(scf)
   print(f"\nDipole moments = {dip} a0")
   print(f"Total dipole moment = {ebohr2d(np.linalg.norm(dip))} D")
   

Calculate ionization potentials

.. code-block:: python

   ip = get_ip(scf)
   print(f"\nIonization potential = {ha2kcalmol(ip)} kcal/mol\n")
   

Transform the orbitals to real-space to get the Kohn-Sham orbitals

Make sure to use orthogonal wave functions to generate them

.. code-block:: python

   psi = atoms.I(get_psi(scf, scf.W))
   

Some functions are controlled with a global logging level that can be changed with

.. code-block:: python

   eminus.config.verbose = 3
   

Check orthonormality of Kohn-Sham orbitals

.. code-block:: python

   print("Orthonormality of Kohn-Sham orbitals:")
   check_orthonorm(atoms, psi)
   

Calculate the orbital variance and spread of the orbitals

.. code-block:: python

   cost = wannier_cost(atoms, psi)
   print(f"\nOrbital variances = {cost} a0^2")
   print(f"Total spread = {np.sum(np.sqrt(cost))} a0")
   

Calculate the center of mass of the density

.. code-block:: python

   com = center_of_mass(atoms.r, scf.n)
   print(f"\nDensity center of mass = {com} a0")
   print(f"Neon position = {atoms.pos[0]} a0")
   

Write all orbitals 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"Ne_{i + 1}.cube", psi[0][0, :, i])
   

Another useful setting is the number of threads

.. code-block:: python

   print(f"\nThreads: {eminus.config.threads}\n")
   

You can also set them and check the configuration afterwards

.. code-block:: python

   eminus.config.threads = 2
   eminus.config.info()
   

eminus uses the NumPy and SciPy packages

These packages will listen to the OMP_NUM_THREADS and/or MKL_NUM_THREADS flags

Setting these flags will control how many threads eminus uses.

Download :download:`06_advanced_functionalities.py <../../examples/06_advanced_functionalities/06_advanced_functionalities.py>`