Plotting Fleur DOS/bandstructures

This section discusses how to obtain plots of data in the banddos.hdf for density of states and bandstructure calculations.

The process here is divided in two parts. First we extract and transform the data in a way to make it easy to plot via the HDF5Reader. For a detailed explanation of the capabilities of this tool refer to General HDF5 file reader. Here we show the basic usage:

#Example: Bandstructure calculation

from masci_tools.io.parsers.hdf5 import HDF5Reader
from masci_tools.io.parsers.hdf5.recipes import FleurBands

with HDF5Reader('/path/to/banddos.hdf') as h5reader:
   data, attributes = h5reader.read(recipe=FleurBands)

In the following bandstructure and DOS plots are explained. Each section leads with the names of the recipes from the recipes module that can be used with the explained visualization function.

All Fleur specific plotting routines are found in fleur have implementations for both the matplotlib and bokeh plotting libraries and can be customized heavily. For an explanation on customizing plots refer to General Plotting routines.

Bandstructures

Compatible Recipes: FleurBands

The bandstructure visualization plot_fleur_bands() can be used to plot

1. Non-spinpolarized/spinpolarized bandstructures

2. Bandstructures with emphasized weights on all eigenvalues (Also non-spinpolarized and spinpolarized)

Standard bandstructure

To plot a simple bandstructure without any weighting we just have to pass the data, that the HDF5Reader provided to the plot_fleur_bands()

The two exmaples below show the resulting plots for a non-psinpolarized system (bulk Si) and a spin-polarized system (Fe fcc). For both systems the necessary code is exactly the same and is shown above the plots. The shown plots are the ones for the matplotlib plotting backend:

from masci_tools.io.parsers.hdf5 import HDF5Reader
from masci_tools.io.parsers.hdf5.recipes import FleurBands
from masci_tools.vis.fleur import plot_fleur_bands

#Read in data
with HDF5Reader('/path/to/banddos.hdf') as h5reader:
   data, attributes = h5reader.read(recipe=FleurBands)

#Plot the data
#Notice that you get the axis object of this plot is returned
#if you want to make any special additions
ax = plot_fleur_bands(data, attributes)

Non spinpolarized bandstructure

Spinpolarized bandstructure

Bandstructure with weights

To plot a simple bandstructure with weighting we do the same procedure as above, but we pass in the entry we want to use for weights. These correspond to the entries in the banddos.hdf file (for example the weight for the s-orbital on the first atom type is called MT:1s)

The weights will be used to change the size and color (according to a colormap) to indicate regions of high weight.

The two exmaples below show the resulting plots for a non-psinpolarized system (bulk Si) weighted for the s-orbital on the first atom and a spin-polarized system (Fe fcc) with weights for the d-orbital on the first atom type. For both systems the necessary code is exactly the same and is shown above the plots. The shown plots are the ones for the matplotlib plotting backend:

from masci_tools.io.parsers.hdf5 import HDF5Reader
from masci_tools.io.parsers.hdf5.recipes import FleurBands
from masci_tools.vis.fleur import plot_fleur_bands

#Read in data
with HDF5Reader('/path/to/banddos.hdf') as h5reader:
   data, attributes = h5reader.read(recipe=FleurBands)

#Plot the data
#Notice that you get the axis object of this plot is returned
#if you want to make any special additions
ax = plot_fleur_bands(data, attributes, weight='MT:1s')

Non spinpolarized bandstructure (weights for s-orbital)

Spinpolarized bandstructure (weights for d-orbital)

Density of States

Compatible Recipes: FleurDOS, FleurJDOS, FleurORBCOMP, FleurMCD

The dos visualization plot_fleur_dos() can be used to plot non spinpolarized and spinpolarized DOS, with selection of which components to plot.

Standard density of states plot

from masci_tools.io.parsers.hdf5 import HDF5Reader
from masci_tools.io.parsers.hdf5.recipes import FleurDOS
from masci_tools.vis.fleur import plot_fleur_dos

#Read in data
with HDF5Reader('/path/to/banddos.hdf') as h5reader:
   data, attributes = h5reader.read(recipe=FleurDOS)

#Plot the data
#Notice that you get the axis object of this plot is returned
#if you want to make any special additions
ax = plot_fleur_dos(data, attributes)

Non spinpolarized DOS

Spinpolarized DOS

Plotting options for DOS plots

The plot_fleur_dos() function has a couple of options to modify, what is being displayed from the banddos.hdf file. Below we show a few examples of ways to use these options, together with examples of resulting plots.

DOS with atom components scaled with equivalent atoms

When you look at the example plot for the non spin-polarized DOS, you might notice that the interstitial component and the atom projected components do not add up to the total density of states. This system has two symmetry equivalent Si atoms. By default the atom projected density of states corresponds to only one of these atoms.

If you wish to show the atom projected components of the DOS scaled with the number of symmetry equivalent atoms you can provide the option multiply_by_equiv_atoms=True option to the plotting function.

ax = plot_fleur_dos(data, attributes, multiply_by_equiv_atoms=True)

Selecting specific DOS components

The DOS is made up of a lot of contributions that can be displayed separately.

Here we list the options that are available and show exmaple plots for only selecting the atom projected compinents of the density of states

• plot_keys

  Can be used to provide a explicit list of keys you want to display (Same format as in the banddos.hdf)

• show_total

  Control, whether to show the total density of states (default True)

• show_interstitial

  Control, whether to show the interstitial contribution of the density of states (default True)

• show_atoms

  Control, which total atom projected DOS to show. Can be either the string all (All components are shown), the value None (no components are shown) or a list of the integer indices of the atom types that should be displayed (default all)

• show_lresolved

  Control, on which atoms to show the orbital projected DOS. Can be either the string all (All components are shown), the value None (no components are shown) or a list of the integer indices of the atom types for which to display the orbital components (default None)

Below an example of only displaying the atom projected DOS together with their orbital contributions is shown.

ax = plot_fleur_dos(data, attributes,
                    show_total=False,
                    show_interstitial=False,
                    show_lresolved='all')