Wannier & vASP Postprocessing module

Overview

WASPP module

Wannier90 & vASP Postprocessing module with functionalities I needed during my PhD.

Being updated Version: 0.5

Main functions:

Wannier90 - VASP interface preparation and evaluation.

  1. plot_pdos

For plotting pDOS select LORBIT = 11 in INCAR file

Main function for plotting the partial density of states, for desired atoms and orbitals at all the different Wyckoff positions. Usage is straightforward:

  • file = "vasprun.xml" of your VASP run.
  • _atoms = Atoms whose pDOS you wanna plot as a list of strings e.g. ["P","I","O","Rn","Al"].
  • _orbitals = Orbitals whose pDOS you wanna know from _atoms as a list of strings. They can be "big" orbitals (s,p,d,f) or "small" (px,py,pz,dxy,...), e.g ["s","px","d"].
  • e_window = Range of energies of interest.

If _atoms and _orbitals are None, the function will plot every atom and big orbital at every different Wyckoff position. For a better visualization each kind of big orbital is displayed with a different linestyle.

For example (Ta6Se24I2):

wap.plot_dos("vasprun.xml",e_window = (-7.5,4))

Returns:

TaSeI pDOS

The first tag in the legend is the atom, the second is the Wyckoff position and the third the orbital.

  1. band_counter

Counts the numebr of bands in a energy window in the whole FBZ. It gives a good clue of how to choose the energy window. Usage is as following:

wap.band_counter(file = "vasprun.xml", emin = 0.0, emax = 0.0)
  • file = "vasprun.xml" of your VASP run.
  • emin and emax are the lower and upper part of the energy window given in reference to Fermi energy.

For example:

wap.band_counter(file = "vasprun.xml", emin = -7.0, emax = 4.0)

Returns:

Efermi = 3.01610496.
Total bands = 544.
The number of bands between -7.00 eV (-3.98 eV) and 4.00 eV (7.02 eV) is 368.

Which is, the Fermi energy in eV, the total number of bands of the vasp run and the number of bands in the energy window (with real energies in parenthesis for wannier90.win)

  1. plot_wannierbands

Function for plotting wannier bands from .dat and .gnu files.

Usage:

wap.plot_wannierbands(file_dat = "wannier90_band.dat", gnu = "wannier90_band.gnu",efermi = 0.0, e_window = None, fig_size = (15,8),savename = "wannierbands.png")
  • file_dat: *_band.dat output file from a wannier90.x run.
  • file_dat: *_band.gnu output file from a wannier90.x run.
  • efermi: Fermi energy.
  • e_window = Energy window for the plot

It generates a "wannierbands.png" file.

4 . plot_vaspbands

Function for plotting VASP bands from a non self-consistent calculation in a KPATH. Usage:

wap.plot_vaspbands(outcar = "OUTCAR", kpoints = "KPOINTS")

  • outcar: OUTCAR file from VASP run.
  • kpoints: KPOINTS file from nsc VASP run (linemode expected).
  1. plot_comparison

Function for comparing VASP and Wannier90 bandstructures combining the previous functions and tags. Usage:

wap.plot_comparison(outcar = "OUTCAR", kpoints = "KPOINTS",file_dat = "wannier90_band.dat", gnu = "wannier90_band.gnu",efermi = 0.0, fig_size = (12,8), e_window = (-4,4),savename = "comparison.png"):
  • outcar: OUTCAR file from VASP run.
  • kpoints: KPOINTS file from nsc VASP run (linemode expected).
  • file_dat: *_band.dat output file from a wannier90.x run.
  • file_dat: *_band.gnu output file from a wannier90.x run.
  • efermi: Fermi energy.
  • e_window = Energy window for the plot

Example: RhSi

wap.plot_comparison(outcar = "OUTCAR", kpoints = "KPOINTS",file_dat = "wannier90_band.dat", gnu = "plottt/wannier90_band.gnu",efermi = 0.0, fig_size = (12,8), e_window = (-4,4),savename = "comparison.png") 

RhSi VASP vs Wannier90

  1. wann_kpoints

Function for generating kpath string for seedname.win using a KPOINT file from a nsc VASP calculation. Usage is as follows:

wann_kpoints(file = "KPOINTS")

Where KPOINTS is like:

Cubic
20   ! 20 grids
Line-mode
reciprocal
   0.000   0.000   0.000   ! GAMMA
   0.000   0.500   0.000   ! X
   0.000   0.500   0.000   ! X
   0.500   0.500   0.000   ! M
   0.500   0.500   0.000   ! M
   0.000   0.000   0.000   ! GAMMA
   0.000   0.000   0.000   ! GAMMA
   0.500   0.500   0.500   ! R
   0.500   0.500   0.500   ! R
   0.000   0.500   0.000   ! X
   0.500   0.500   0.000   ! M
   0.500   0.500   0.500   ! R

And it generates a WKPTS.txt file as:

G 0.000 0.000 0.000 X 0.000 0.500 0.000 
X 0.000 0.500 0.000 M 0.500 0.500 0.000 
M 0.500 0.500 0.000 G 0.000 0.000 0.000 
G 0.000 0.000 0.000 R 0.500 0.500 0.500 
R 0.500 0.500 0.500 X 0.000 0.500 0.000 
M 0.500 0.500 0.000 R 0.500 0.500 0.500 
  1. plot_custom_vaspbands

Similar to plot_vaspbands but more customizable. Usage is as follows:

wap.plot_custom_vaspbands(outcar = "OUTCAR",kpoints = "KPOINTS",
                          figsize = (10,7.5),ewindow = (-3,3),
                          dpi = 500,linewidth = 0.5,
                          kp_i=None,kp_f=None,
                          title=None,fname=None)

Where:

  • kp_i & kp_f is the number of the fist and last KPOINT in the path that you want to plot. E.g. in the KPOINTS file from above example kp_i = 2 would correspond to M.
  • title and fname are the title to be printed in the figure and the path to the figure when saved.

MBJ and PBE potentials bandstructure comparison.

compare_MBJ

Function for comparing PBE nscc and MBJ scc functional bandstructures using pymatgen treatment of vasprun.

wap.compare_MBJ(vasprun_pbe = "vasprun1.xml",
            vasprun_mbj = "vasprun2.xml",
            kpoint_file = "KPOINTS",
            e_window = (-4,4),
            fig_title = None,
            fig_name = "comparison.png")

Usage:

  • vasprun_pbe: vasprun file for PBE nsc run.
  • vasprun_mbj: vasprun file for MBJ scc run.
  • kpoint_file: kpoint file for nsc (linemode expected).

For example:

wap.compare(vasprun_pbe = "vasprun81_rel.xml",
            vasprun_mbj = "vasprun81.xml",
            kpoint_file = "KPOINTS",
            e_window = (-2,2),
            fig_title = "SG81",
            fig_name = "comparison81.png")

Returns:

VASP PBE vs MBJ potetntial

More functionalities are present in the code and many more are coming, stay tuned & take a look at WASPP05.py. (^³^)~♪

Package Requeriments:

  • numpy
  • matplotlib
  • scipy
  • itertools
  • re
  • pymatgen
Owner
Irián Sánchez Ramírez
PhD student @ DIPC
Irián Sánchez Ramírez
Ssma is a tool that helps you collect your badges in a satr platform

satr-statistics-maker ssma is a tool that helps you collect your badges in a satr platform 🎖️ Requirements python = 3.7 Installation first clone the

TheAwiteb 3 Jan 04, 2022
Bionic is Python Framework for crafting beautiful, fast user experiences for web and is free and open source.

Bionic is Python Framework for crafting beautiful, fast user experiences for web and is free and open source. Getting Started This is an example of ho

14 Apr 10, 2022
Standard mutable string (character array) implementation for Python.

chararray A standard mutable character array implementation for Python.

Tushar Sadhwani 3 Dec 18, 2021
Cup Noodle Vending Maching Ordering Queue

Noodle-API Cup Noodle Vending Machine Ordering Queue Install dependencies in virtual environment python3 -m venv

Jonas Kazlauskas 1 Dec 09, 2021
OpenTable Reservation Maker For Python

OpenTable-Reservation-Maker The code that corresponds with this blog post on writing a script to make reservations for me on opentable Getting started

JonLuca De Caro 36 Nov 10, 2022
A python script that changes your desktop background based on current weather and time of the day.

Desktop background wallpaper, based on current weather and time A python script that changes your computer's desktop background based on current weath

Maj Gaberšček 1 Nov 16, 2021
Never see escaped bytes in output.

Uniout It makes Python print the object representation in readable chars instead of the escaped string. Example from pprint import pprint lang

Mosky Liu 156 Oct 21, 2022
Covid-19-Trends - A project that me and my friends created as the CSC110 Final Project at UofT

Covid-19-Trends Introduction The COVID-19 pandemic has caused severe financial s

1 Jan 07, 2022
Svg-turtle - Use the Python turtle to write SVG files

SaVaGe Turtle Use the Python turtle to write SVG files If you're using the Pytho

Don Kirkby 7 Dec 21, 2022
A streamlit app for exploring image search results from HuggingPics

title emoji colorFrom colorTo sdk app_file pinned huggingpics-explorer 🤗 blue red streamlit app.py false huggingpics-explorer A streamlit app for exp

Nathan Raw 4 Sep 10, 2022
Assignment for python course, BUPT 2021.

pyFuujinrokuDestiny Assignment for python course, BUPT 2021. Notice username and password must be ASCII encoding. If username exists in database, syst

Ellias Kiri Stuart 3 Jun 18, 2021
UUID_ApiGenerator - This an API that will return a key-value pair of randomly generated UUID

This an API that will return a key-value pair of randomly generated UUID. Key will be a timestamp and value will be UUID. While the

1 Jan 28, 2022
This is a repository built by the community for the community.

Nutshell Machine Learning Machines can see, hear and learn. Welcome to the future 🌍 The repository was built with a tree-like structure in mind, it c

Edem Gold 82 Nov 18, 2022
Distribute PySPI jobs across a PBS cluster

Distribute PySPI jobs across a PBS cluster This repository contains scripts for distributing PySPI jobs across a PBS-type cluster. Each job will conta

Oliver Cliff 1 Feb 10, 2022
A small program to vote for Councilors at 42 Heilbronn.

This Docker container is build to run on server an provide an easy to use interface for every student to vote for their councillors. To run docker on

Kevin Hirsig 2 Jan 17, 2022
A python script to run any executable and pass test cases to it's stdin and compare stdout with correct output.

quera_testcase_checker A python script to run any executable and pass test cases to it's stdin and compare stdout with correct output. proper way to u

k3y1 1 Nov 15, 2021
Python client library for the Databento API

Databento Python Library The Databento Python client library provides access to the Databento API for both live and historical data, from applications

Databento, Inc. 35 Dec 24, 2022
A turtlebot auto controller allows robot to autonomously explore environment.

A turtlebot auto controller allows robot to autonomously explore environment.

Yuliang Zhong 1 Nov 10, 2021
A project to find out all the words in a crossword.

A project to find out all the words in a crossword.

Kalpesh Dhoundiyal 1 Feb 06, 2022
Script to work around some quirks of the blender obj importer

ObjFix 1.0 (WIP) Script to work around some quirks of the blender obj importer Installation Download this repo In Blender, press "Edit" on the top-bar

Red_3D 4 Nov 20, 2021