sumo-dosplot is a program for generating publication-ready density of states diagrams and extractingthe density of states from VASP calculations. A large number of features are provided, includingthe ability to break the density of states down into the contributions from specific elements,orbitals, and atoms.
Table of Contents
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:
If you want a bleeding edge nightly build or need tests or source files, you can download them from the Download page. For building SUMO from source see building SUMO under Windows. Automounter 1 5 7. Linux# If you run debian or ubuntu, SUMO is part of the regular distribution and can be installed like this: sudo apt-get install sumo sumo-tools sumo-doc. Source file: sumo-gui.1.en.gz (from sumo 1.4.0+dfsg1-1): Source last updated: 2020-01-16T21:12:23Z Converted to HTML: 2020-06-11T15:38:39Z.
To plot a density of states, simply run the following command in a folder containing a vasprun.xml orvasprun.xml.gz file:
The plot will be written to a file named dos.pdf, with the raw density of states data written to a seriesfiles. These will be named total_dos.dat, with additional files named El_dos.dat where el is anelement 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 willlook like:
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 bemade more appealing using the following command:
Additional gaussian broadening can be applied using the --gaussian option. The setting expects a floatingpoint number as the argument and controls the standard deviation of the broadening applied.
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 thesumo/tests/data/OsO2 folder, the output will look like:
You may have noticed that not all elements and their orbitals are displayed in the legend. This is becausesumo-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. Thenumber of labels present in the legend can be controlled via the --legend-cutoff option, which controlsthe 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 0For example:
Will give a density of states that looks like:
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 willbe plotted.
For example, to plot the Os s and d and all O orbitals, the command would be:
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 willbe plotted.
For example, to plot the second Os atom and the first two O atoms, the command would be:
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 haveany 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 willbe split.
For example, to split the Os d orbitals, the command would be:
All the above options can be used simultaneously. For example, plot the lm-decomposed d orbitals forthe first Os atom, the following command would be used:
The resulting plot looks like: Things 3 11 2 – elegant personal task management.
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:
The element is specified in square brackets, with the orbitals and their colours listed beneath. The supportedcolour 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:
A typical workflow for plotting the DOS in Questaal is to firstconverge a density with LMF, then run a non-self-consistent step tooutput DOS files with a command such as:
Setting –pdos defaults to mode 2, decomposing the DOS contributionsby l, m and each structure site. However, that decomposed data iswritten in a binary format to moms.ext while dos.ext contains atotal-DOS. This will be overwritten in the next step, so for usage with Sumo please rename this file to “tdos.ext”:
Part of Questaal, the lmdos program converts from moms.ext to aplottable PDOS. It needs to run with the same –dos and –pdosflags as the previous step, i.e. in this case:
This generates a new dos.ext containing pdos data and replacing theexisting file if present.
To plot with Sumo, provide either file. If a single-channel file isprovided, Sumo will plot a TDOS, e.g.:
If a multichannel PDOS file is provided, this will be interpreted asif decomposed by site, l, and m. The site.ext file is read in, andif present a file named tdos.ext will also be used to add the totalDOS.:
The –elements and –orbitals options may be used to specify whichchannels are grouped and/or shown. Note that empty sites may beincluded in the output if they have a non-negligible contribution tothe DOS. The –elements switch may be useful for hiding these ifdesired.
dosplot is a script to produce publication-ready density ofstates diagrams
vasprun.xml file to plot Adobe premiere pro cs4 32 bit free with crack.
Input file format: “vasp” (vasprun.xml) or “questaal” (opt.ext)
Default: “vasp”
prefix for the files generated
output directory for files
elemental orbitals to plot (e.g. “C.s.p,O”)
orbitals to split into lm-decomposed contributions (e.g. “Ru.d”)
atoms to include (e.g. “O.1.2.3,Ru.1.2.3”)
select one spin channel only for a spin-polarised calculation (options: up, 1; down, -1)
plot each element on separate subplots
Default: False
standard deviation of gaussian broadening
number of columns in the legend
Affinity designer 1 5 3 – vector graphic design software. Default: 2
cut-off in % of total DOS that determines if a line is given a label (default: 3)
Default: 3
hide the plot legend
Default: True
display a box around the legend
Default: False
don’t shift the VBM/Fermi level to 0 eV
Default: True
only plot the total density of states
Default: False
don’t plot the total density of states
Default: True
height of the graph
width of the graph
minimum energy on the x-axis
Default: -6.0
maximum energy on the x-axis
Decor graphics 3 3 1 – templates lab. Default: 6.0
colour configuration file
matplotlib style specifications
prevent use of sumo base style
Default: False
x-axis (i.e. energy) label/units
Default: “Energy (eV)”
y-axis (i.e. DOS) label/units
Default: “Arb. units”
scaling factor for the y-axis
Default: 1
image file format (options: pdf, svg, jpg, png)
Default: “pdf”
pixel density for image file
Default: 400 Bartender 3 tnt.
font to use
Author: Alex GanoseVersion: 1.0Last updated: April 9, 2018
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