sumo-dosplot

sumo-dosplot is a program for generating publication-ready density of states diagrams and extracting the density of states from VASP calculations. A large number of features are provided, including the ability to break the density of states down into the contributions from specific elements, orbitals, and atoms.

Usage

The full range of options supported by sumo-dosplot are detailed in the Command-Line Interface section, and be can be accessed using the command:

sumo-dosplot -h

To plot a density of states, simply run the following command in a folder containing a vasprun.xml or vasprun.xml.gz file:

sumo-dosplot

The plot will be written to a file named dos.pdf, with the raw density of states data written to a series files. These will be named total_dos.dat, with additional files named El_dos.dat where el is an element name, for each element in the structure.

For example, if we run the command in the sumo/tests/data/Cs2SnI6/dos directory, the density of states will look like:

_images/dos_basic.png

Basic Options

The program automatically looks for files in the current directory, to specify alternative files, the --filename option can be used.

The number of columns in the legend is controlled using the --columns option.

The height, and width of the graphic, along with the x-axis limits, can be controlled via the --width, --height, --xmax, and --xmin options. For example, the plot above could be made more appealing using the following command:

sumo-dosplot --width 6 --height 6 --xmin -4 --xmax 6 --columns 1
_images/dos_square.png

Additional gaussian broadening can be applied using the --gaussian option. The setting expects a floating point number as the argument and controls the standard deviation of the broadening applied.

Subplots

sumo-dosplot supports plotting the total and elemental density of states on separate panels, or subplots, using the --subplot option. For example, if we run the following command in the sumo/tests/data/OsO2 folder, the output will look like:

sumo-dosplot --subplot
_images/dos_subplot.png

Legend Labels

You may have noticed that not all elements and their orbitals are displayed in the legend. This is because sumo-dosplot only labels states that have a significant contribution in the plotting area. By default, a significant contribution is defined as greater than 3 % of the max total density of states. The number of labels present in the legend can be controlled via the --legend-cutoff option, which controls the cutoff in %, at which a label is given to an orbital.

For example, if we wish to give all orbitals a label, simply set the cutoff to 0 For example:

sumo-dosplot --legend-cutoff 0

Will give a density of states that looks like:

_images/dos_all_labels.png

Selective Plotting of Specific Orbitals and Atoms

By default sumo-dosplot includes all elements, orbitals, and atoms when plotting the density of states. However, sometimes it may be desirable to plot the density of states of only of a specific orbital, or even specific atoms.

Selecting Elements

The --elements option controls which elemental orbitals are included in the plot. The syntax for specifying which elemental orbitals to include is as follows:

  • Elements are identified using their symbol from the POSCAR

  • Multiple elements are separated via commas.

  • Specific orbitals can be chosen by adding the orbital after the element using a period as a separator.

  • If no orbitals are specified but the atomic symbol is included, then all orbitals of that element will be plotted.

For example, to plot the Os s and d and all O orbitals, the command would be:

sumo-dosplot --elements Os.s.d,O

Selecting Atoms

The --atoms option controls which atoms are included in the plot. The syntax for specifying which atoms to include is as follows:

  • Elements are identified using their symbol from the POSCAR

  • Multiple elements are separated via commas.

  • Specific atoms can be chosen by adding the atomic index after the element using a period as a separator.

  • Atomic indexes begin at 1 for each species in the structure.

  • If no atoms are specified but the atomic symbol is included, then all atoms of that element will be plotted.

For example, to plot the second Os atom and the first two O atoms, the command would be:

sumo-dosplot --atoms Os.2,O.1.2

lm-Decomposed Orbitals

By default all lm-decomposed orbitals (e.g. px, py, and pz) are summed into a single orbital contribution (e.g. p). The --orbitals option can be used to plot the individual lm-decomposed contributions. Please note that the structure should be correctly oriented in cartesian space if the orbitals are to have any physical meaning. If you are unsure what this means, then you probably shouldn’t use this option.

The syntax for specifying which orbitals to split into their lm contributions is as follows:

  • Elements are identified using their symbol from the POSCAR

  • Multiple elements are separated via commas.

  • Specific orbitals can be chosen by adding the orbital after the element using a period as a separator.

  • If no orbitals are specified but the atomic symbol is included, then all orbitals of that element will be split.

For example, to split the Os d orbitals, the command would be:

sumo-dosplot --orbitals Os.d

All the above options can be used simultaneously. For example, plot the lm-decomposed d orbitals for the first Os atom, the following command would be used:

sumo-dosplot --orbitals Os.d --elements Os.d --atoms Os.1 --no-total

The resulting plot looks like:

_images/dos_specific.png

Custom Line Colours

Sumo uses a config file for choosing the colours of elements and orbitals in density of states plots. The default colours can be found in sumo/conf/orbital_colours.conf. The format of this file is simple:

[N]
s = r
p = #D93B2B

The element is specified in square brackets, with the orbitals and their colours listed beneath. The supported colour identifiers include hex codes, rgb values or any other format supported by matplotlib.

To use your own custom colours, simply create your own config file in the current directory (e.g. my_colours.conf) and use the --config option to read in your settings. For example:

sumo-dosplot --config my_colours.conf

Questaal

A typical workflow for plotting the DOS in Questaal is to first converge a density with LMF, then run a non-self-consistent step to output DOS files with a command such as:

lmf ctrl.ext --dos:npts=2001:window=-1,1 --pdos --quit=rho

Setting –pdos defaults to mode 2, decomposing the DOS contributions by l, m and each structure site. However, that decomposed data is written in a binary format to moms.ext while dos.ext contains a total-DOS. This will be overwritten in the next step, so for usage with Sumo please rename this file to “tdos.ext”:

mv dos.ext tdos.ext

Part of Questaal, the lmdos program converts from moms.ext to a plottable PDOS. It needs to run with the same –dos and –pdos flags as the previous step, i.e. in this case:

lmdos --dos:npts=2001:window=-1,1 --pdos ext

This generates a new dos.ext containing pdos data and replacing the existing file if present.

To plot with Sumo, provide either file. If a single-channel file is provided, Sumo will plot a TDOS, e.g.:

sumo-dosplot --code questaal -f tdos.ext

If a multichannel PDOS file is provided, this will be interpreted as if decomposed by site, l, and m. The site.ext file is read in, and if present a file named tdos.ext will also be used to add the total DOS.:

sumo-dosplot --code questaal -f dos.ext

The –elements and –orbitals options may be used to specify which channels are grouped and/or shown. Note that empty sites may be included in the output if they have a non-negligible contribution to the DOS. The –elements switch may be useful for hiding these if desired.

Castep

When plotting from CASTEP, give the seedname.bands path as –filename. If a .pdos_bin file is in the same directory, orbital-project DOS plots are possible; this requires the .cell file to also be available. Otherwise, a total DOS will be obtained by summing over the eigenvalue data in the .bands file.

Command-Line Interface

dosplot is a script to produce publication-ready density of states diagrams

usage: sumo-dosplot [-h] [-f F] [-c C] [-p P] [-d D] [-e E] [-o O] [-a A]
                    [--spin SPIN] [-s] [-g G] [--columns N]
                    [--legend-cutoff C] [--no-legend] [--legend-frame]
                    [--no-shift] [--total-only] [--no-total] [--height HEIGHT]
                    [--width WIDTH] [--xmin XMIN] [--xmax XMAX]
                    [--config CONFIG] [--style STYLE [STYLE ...]]
                    [--no-base-style] [--xlabel XLABEL] [--ylabel YLABEL]
                    [--yscale YSCALE] [--format FORMAT] [--dpi DPI]
                    [--font FONT]

Named Arguments

-f, --filename

vasprun.xml file to plot

-c, --code

Input file format: “vasp” (vasprun.xml) or “questaal” (opt.ext)

Default: “vasp”

-p, --prefix

prefix for the files generated

-d, --directory

output directory for files

-e, --elements

elemental orbitals to plot (e.g. “C.s.p,O”)

-o, --orbitals

orbitals to split into lm-decomposed contributions (e.g. “Ru.d”)

-a, --atoms

atoms to include (e.g. “O.1.2.3,Ru.1.2.3”)

--spin

select one spin channel only for a spin-polarised calculation (options: up, 1; down, -1)

-s, --subplot

plot each element on separate subplots

Default: False

-g, --gaussian

standard deviation of gaussian broadening

--columns

number of columns in the legend

Default: 2

--legend-cutoff

cut-off in % of total DOS that determines if a line is given a label (default: 3)

Default: 3

--no-legend

hide the plot legend

Default: True

--legend-frame

display a box around the legend

Default: False

--no-shift

don’t shift the VBM/Fermi level to 0 eV

Default: True

--total-only

only plot the total density of states

Default: False

--no-total

don’t plot the total density of states

Default: True

--height

height of the graph

--width

width of the graph

--xmin

minimum energy on the x-axis

Default: -6.0

--xmax

maximum energy on the x-axis

Default: 6.0

--config

colour configuration file

--style

matplotlib style specifications

--no-base-style

prevent use of sumo base style

Default: False

--xlabel

x-axis (i.e. energy) label/units

Default: “Energy (eV)”

--ylabel

y-axis (i.e. DOS) label/units

Default: “Arb. units”

--yscale

scaling factor for the y-axis

Default: 1

--format

image file format (options: pdf, svg, jpg, png)

Default: “pdf”

--dpi

pixel density for image file

Default: 400

--font

font to use

Author: Alex Ganose Version: 1.0 Last updated: April 9, 2018