elkoa 1.2.0

plot and analyze Elk optics output data

Description

Elk Optics Analyzer (ElkOA) helps to analyze optics output data from The Elk Code.

Features

Elk Optics Analyzer…

• Comes with a GUI as well as a python CLI

• Supports Elk tasks 121, 187, 320 and 330

• Recognizes available tasks / (tensor) fields automatically

• Is easily extendable

Users can…

• Visualize real and imaginary parts of Elk optics output data in various ways

• Import additional data files, e.g. experimental measurements (CTRL+O)

• Select tensor elements to plot individually via dialog (CTRL+T)

• Use global tensor elements settings for all plots (CTRL+G)

• Batch-load parameter studies to visually analyze the impact of different parameter settings (CTRL+B)

Soon to come:

• Conversion of wavevector independent response functions into wavevector dependent ones via Universal Response Relations

• Conversion of dielectric tensors in ordinary and extra-ordinary refractive indices for arbitrary k-vectors

• Plotting of index ellipsoids

Requirements

• Python 3.x

• numpy

• matplotlib

• PyQt5

• pbr

You should use the packages provided by your linux distribution. On recent Debian systems for example, you can get all requirements by running

apt install python3-numpy python3-matplotlib python3-pyqt5 python3-pbr

Alternatively, you can get the latest PyPI versions of each package automatically by installing via pip (see below).

Installation

The easiest way to install ElkOA is via pip, either from PyPI directly

pip install elkoa

or, if you want the latest git version,

git clone https://github.com/PandaScience/ElkOpticsAnalyzer.git
cd ElkOpticsAnalyzer
pip install .

This will also install all required but absent python packages automatically from PyPI.

If you like to install ElkOA only for the current user, add the flag --user. If you want to take care of the required python packages yourself (i.e. by using the ones provided by your Linux distribution), add --no-deps. If you like to run a developer installation (no copying of files, instead use git repo files directly), add -e.

In any case, after installation you can run the ElkOA GUI from everywhere in a terminal using either elkoa or ElkOpticsAnalyzer.

Another way to install is by cloning the repo as above and instead of installing via pip, put something like

export PATH=$PATH:/path/to/ElkOpticsAnalyzer/elkoa/gui
export PYTHONPATH=$PYTHONPATH:/path/to/ElkOpticsAnalyzer/

to your .bashrc or .bash_profile. Then you can start the ElkOA GUI with ElkOpticsAnalyzer.py.

Python CLI

In an Elk output directory containing e.g. the files

elk.in INFO.OUT EPSILON_11.OUT EPSILON_12.OUT EPSILON_13.OUT EPSILON_21.OUT
EPSILON_22.OUT EPSILON_23.OUT EPSILON_31.OUT EPSILON_32.OUT EPSILON_33.OUT

you can run in a python3 interpreter:

# parsing Elk input file
from elkoa.utils import elk
elk_input = elk.ElkInput()
# reading tensorial Elk optics output
from elkoa.utils import io
eps = io.readTenElk("EPSILON_TDDFT")
# convert to optical conductivity
from elkoa.utils import convert
sig = convert.eps2sig(eps, limit="optical")
# write out converted tensor
io.write(sig, format="twocolumn")

Misc

• Auto-converting filenames to tex-labels

  • For this feature to work, filenames must follow the pattern root+_sub+.ext, which will show up as rootsub.

  • In case root contains a case-insensitive substring like eps, EPSILON, Sig, SIGma etc., corresponding greek letters will be used, i.e. eps_ex.dat ➙ εex.

• Additional data plots

  • Number is restricted to 6, but in return we use consistent coloring after consecutively adding more plots.

Usage Examples GUI