PyEELS is a python package intended for simulating Electron Energy Loss Spectroscopy from model band structures.
The use of the package can be seen as threefold:
- Constructing a real space model system
- Create/generate model band structures in reciprocal space
- Simulate EELS on the model band structure
The creation of model band structures is mainly based on PythTB, an additional model with parabolic bands is also provided.
The simulation of EELS is based on (https://www.duo.uio.no/handle/10852/63504) and implemented in an C extension thus can be multiprocessed for faster calculation.
HyperSpy has been chosen as a framework for an interactive visualization of EELS-spectra, in this process Jupyter Notebook is a natural platform for scripting purpose.
An example is presented below:
# Generate real space crystal model
from pyeels import Crystal
myCrystal = Crystal(lattice=np.eye(3))
myAtom = Atom(number=0,position=[0,0,0])
myAtom.add_orbital(Orbital(label="s", onsite=0))
myCrystal.add_atom(atom=myAtom)
# Create parabolic bands in reciprocal space
from pyeels import ParabolicBand
reci = ParabolicBand(myCrystal)
reci.set_grid(mesh=31) # Number of k-points in each dimension
# Parabolic valence band
reci.set_parabolic(effective_mass=[-0.5, -0.5, -0.5],
energy_offset=0,
k_center=[0,0,0],
wave=np.array([0,0.02])
)
# Parabolic conduction band
reci.set_parabolic(effective_mass=[ 0.5, 0.5, 0.5],
energy_offset=1,
k_center=[0,0,0],
wave=np.array([0,1])
)
# Calculate EELS on the parabolic bands
from pyeels import EELS
mySystem = EELS(myCrystal)
mySystem.temperature = 0 # Absolute zero
mySystem.fermienergy = 0.5 # Placing the fermi level at center of the band gap
mySystem.set_meta(
name="My test sample",
author=["Author1", "Author2"],
title="myCrystal",
notes="This model is just an example."
)
# The q-resolution of the scattering cross section
# no argument correspond to the density of the k-grid in Brillouin Zone
mySystem.set_diffraction_zone()
mySignal = mySystem.calculate_eels_multiproc(energyBins=np.linspace(0,4,200),
smearing=0.05
max_cpu=4
)
#HyperSpy visuailzation
mySignal.plot()
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