Convenient tools and useful home-brewed modifications for DFT software

A handy Python plotting script for Quantum Espresso (QE).

It reads the band-structure data file generated by QE and plots the data with matplotlib. Currently, it supports both electron and phonon bands.

Usage:

from qeplotter import plot 
point_names = ['$\Gamma$','X','U','L','$\Gamma$','K','X','W']
Q = [0,20,30,40,65,85,95,105]
ef = 7.4953
plot(infile="some_electron_bands.txt",Q=Q,point_names=point_names,efermi=ef)

Or

from qeplotter import plot 
point_names = ['$\Gamma$','X','U','L','$\Gamma$','K','X','W']
Q = [0,20,30,40,65,85,95,105]
plot(infile="some_phonon_bands.txt",Q=Q,phonon=True,point_names=point_names,phdos="phonon_dos.txt")

A handy Python script to plot electron band-structures from ABINIT. The input file has a post-fix like _DS_EIG and _DS1_EIG if you enable ABINIT to dump its eigen-energies.

An example can be:

import numpy as np
from abplotter import plot,ha2ev,plot_pdos
a = np.array([[.5,.5,.0],[.5,.0,.5],[.0,.5,.5]]) # lattice vectors
Q = np.cumsum([0,40,20,20,40,40,20,20]) # positions of the special points
point_names = ['$\Gamma$', 'X', 'U', 'L', '$\Gamma$', 'K', 'X', 'W']
ef = -3.94158

# #if you want only the band without/with total DOS, you can use the line below
# plot(a,"abinit.abo_DS2_EIG",Q,point_names,ef=ef,ymin=-4,ymax=7)# ,fildos="abinit.abo_DS3_DOS"

# #if you want PDOS in a big figure, use the next two lines
# atoms = ['Cs','Cs','Sn'] + 6*['Br']
# plot_pdos('abinit.abo_DS3_',atoms,xmin=-4,xmax=8,ymax=20)

# #if you want bands with PDOS, use the following lines
atoms = ['Cs','Cs','Sn'] + 6*['Br']
plot(a,"abinit.abo_DS2_EIG",Q,point_names,ymin=-4,ymax=7,ef=ef,
    pdos_pref='abinit.abo_DS3_',atoms=atoms,pdos_max=15)

The modifications in this part enable QE to seamlessly compute the partial/projected density of states for phonons. In the output file of a DOS calculation, one will find the total and the partial DOS (decomposed to each atom in the system).

I would suggest backup the original files before recompiling the software with this patch.

The following two files need to be replaced.

$YOUR_DIR_TO_QE/PHonon/PH/matdyn.f90

and

$YOUR_DIR_TO_QE/flib/dost.f90

After replacing these two files, you can cd $YOUR_DIR_TO_QE/PHonon/PH and make to update QE.

Yambo is an excited state code that finds the quasi-particle energy levels using GW methods. Its convergence testing is very tedious and complex. Therefore, an automation tool and a visualisation function is provided to ease the burden of researchers.

ppa_conv.py: one needs to set some parameters for the test, most of which have the same name as those in the yambo documentation.

plot_conv.py: plot function.

An example plot is shown below where the convergence of each parameters can be determined.

This home-brewed code is used to calculate the phonon decay rate at GAMMA point for crystals. Input cards are listed below:

! Input cards: namelist &input
! nat : number of basis in the unit cell. ***MUST BE SET***
! fldp : decay path file. Default "decaypath.txt". Format for this file is illustrated below:
!       nksp !  number of q-point in the decay path in 2pin/alat
!   j1 j2 nks_1
!   i1 i2 nks_2
!   ........
! fldos : DOS file generated by matdyn.x . Default "matdyn.dos".
! flphi : corresponding anharmonic coefficients for the path. Default "phi.raw". 
!           The array has this shape: phi(3,3,3,nat,nat,nat,nksp).
! j0 : the target mode whose decay rate is interested. ***MUST BE SET***
! flfreq : freq for the mesh. Default "freq.txt". QE band file.
!             It contains nks: number of q-point in the mesh. and nbnd
! fleig:    eig for the mesh. Default "zall.raw". z(3*nat,3*nat,nks).
! At the end of the input namelist, you append a mass array:
! ATOMIC MASS
! m1
! m2
! m3
! ....