octopuspy 1.0.1

Python package for manipulating Octopus output files

octopuspy

octopuspy is a Python package that allows for the manipulation and processing of files generated by the Octopus DFT scientific program. This package was created with the intent of using with the effmass package.

Installation

octopuspy can be installed from PyPI:

pip install octopuspy

Or download the source code and install:

git clone https://github.com/afatt/octopuspy.git
cd octopuspy
python3 setup.py install

How To Use

Required Octopus files: bandstructure, info, results.out(typically out.log), eigenvalues, and total-dos-efermi.dat

API

bandstructure file includes: number of kpoints, number of bands, energies:

band_data = Bandstructure(filepath='./GaAs_HSE06', name='GaAs_HSE06_04092021')

info file includes: direct lattice vector, reciprocal lattice vector, and number of ions:

info_data = Info(filepath='./GaAs_HSE06')

results.out file includes: kpoint weights. results.out is obtained by redirecting the stdout to a new file named results.out when running Octopus.Octopus > results.out. More explanation found on the Octopus wiki here

results_out = Results(filepath='./GaAs_HSE06', band_data.num_kpoints)

Scripts

The octopuspy package includes the script octo2vasp.py for converting the bandstructure, info, results.out, eigenvalues files into VASP PROCAR and OUTCAR files.⚠️ The PROCAR and OUTCAR files generated are not true VASP files, they contain only the minimum data required to use in the effmass package.

Copy your Octopus files: bandstructure, info, results.out, and eigenvalues into a new folder anywhere inside the octopuspy package and run:

cd scripts
python3 octo2vasp.py --name name_of_semiconductor

The octo2vasp.py script will write the PROCAR, OUTCAR, and a bandstructure_plot.png to the gen_vasp folder inside the octopuspy package.

Recommended Octopus Settings

Garbage in equals garbage out and testing this package produced a lot of garbage. Included with this package are Octopus settings that helped to achieve results matching the literature anotated_example_inp. The inp file is also included with each set of /test_data for reference. More information about input settings can be found on the Octopus wiki here

Testing

Unittests are included with this package and can be run using:

python3 -m unittest discover